Starting phenix.real_space_refine on Mon Jun 9 16:33:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cd9_45464/06_2025/9cd9_45464.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cd9_45464/06_2025/9cd9_45464.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9cd9_45464/06_2025/9cd9_45464.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cd9_45464/06_2025/9cd9_45464.map" model { file = "/net/cci-nas-00/data/ceres_data/9cd9_45464/06_2025/9cd9_45464.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cd9_45464/06_2025/9cd9_45464.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 6853 2.51 5 N 1914 2.21 5 O 2222 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 10989 Number of models: 1 Model: "" Number of chains: 2 Chain: "E" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 549 Classifications: {'peptide': 81} Link IDs: {'TRANS': 80} Chain: "F" Number of atoms: 450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 450 Classifications: {'peptide': 65} Link IDs: {'TRANS': 64} Restraints were copied for chains: H, J, L, N, P, R, T, V, X, Z, G, I, K, M, O, Q, S, U, W, Y Time building chain proxies: 3.59, per 1000 atoms: 0.33 Number of scatterers: 10989 At special positions: 0 Unit cell: (113.424, 92.574, 70.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 2222 8.00 N 1914 7.00 C 6853 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.83 Conformation dependent library (CDL) restraints added in 1.6 seconds 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2706 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 50.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.56 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'I' and resid 16 through 20 removed outlier: 6.486A pdb=" N VAL E 16 " --> pdb=" O ALA G 17 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N ALA G 19 " --> pdb=" O VAL E 16 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ALA E 18 " --> pdb=" O ALA G 19 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N VAL G 16 " --> pdb=" O ALA S 17 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N ALA S 19 " --> pdb=" O VAL G 16 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ALA G 18 " --> pdb=" O ALA S 19 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL U 16 " --> pdb=" O ALA W 17 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N ALA W 19 " --> pdb=" O VAL U 16 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N ALA U 18 " --> pdb=" O ALA W 19 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 25 through 30 removed outlier: 6.520A pdb=" N VAL E 26 " --> pdb=" O ALA G 27 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ALA G 29 " --> pdb=" O VAL E 26 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU E 28 " --> pdb=" O ALA G 29 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL G 26 " --> pdb=" O ALA S 27 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N ALA S 29 " --> pdb=" O VAL G 26 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N GLU G 28 " --> pdb=" O ALA S 29 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL U 26 " --> pdb=" O ALA W 27 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N ALA W 29 " --> pdb=" O VAL U 26 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N GLU U 28 " --> pdb=" O ALA W 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 38 through 40 removed outlier: 6.265A pdb=" N LEU E 38 " --> pdb=" O TYR G 39 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU G 38 " --> pdb=" O TYR S 39 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N LEU U 38 " --> pdb=" O TYR W 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 43 through 50 removed outlier: 8.794A pdb=" N LYS E 43 " --> pdb=" O THR I 44 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N GLU I 46 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N LYS E 45 " --> pdb=" O GLU I 46 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N VAL I 48 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY E 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N HIS I 50 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL E 49 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N THR E 44 " --> pdb=" O LYS G 43 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N LYS G 45 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLU E 46 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLY G 47 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N THR G 44 " --> pdb=" O LYS S 43 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS S 45 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N GLU G 46 " --> pdb=" O LYS S 45 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY S 47 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N LYS Q 43 " --> pdb=" O THR S 44 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N GLU S 46 " --> pdb=" O LYS Q 43 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N LYS Q 45 " --> pdb=" O GLU S 46 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N VAL S 48 " --> pdb=" O LYS Q 45 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY Q 47 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N HIS S 50 " --> pdb=" O GLY Q 47 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL Q 49 " --> pdb=" O HIS S 50 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N LYS O 43 " --> pdb=" O THR Q 44 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N GLU Q 46 " --> pdb=" O LYS O 43 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N LYS O 45 " --> pdb=" O GLU Q 46 " (cutoff:3.500A) removed outlier: 8.819A pdb=" N VAL Q 48 " --> pdb=" O LYS O 45 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY O 47 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N HIS Q 50 " --> pdb=" O GLY O 47 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL O 49 " --> pdb=" O HIS Q 50 " (cutoff:3.500A) removed outlier: 8.809A pdb=" N LYS M 43 " --> pdb=" O THR O 44 " (cutoff:3.500A) removed outlier: 10.240A pdb=" N GLU O 46 " --> pdb=" O LYS M 43 " (cutoff:3.500A) removed outlier: 9.121A pdb=" N LYS M 45 " --> pdb=" O GLU O 46 " (cutoff:3.500A) removed outlier: 8.833A pdb=" N VAL O 48 " --> pdb=" O LYS M 45 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N GLY M 47 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N HIS O 50 " --> pdb=" O GLY M 47 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N VAL M 49 " --> pdb=" O HIS O 50 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N LYS K 43 " --> pdb=" O THR M 44 " (cutoff:3.500A) removed outlier: 10.220A pdb=" N GLU M 46 " --> pdb=" O LYS K 43 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N LYS K 45 " --> pdb=" O GLU M 46 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N VAL M 48 " --> pdb=" O LYS K 45 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY K 47 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N HIS M 50 " --> pdb=" O GLY K 47 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N VAL K 49 " --> pdb=" O HIS M 50 " (cutoff:3.500A) removed outlier: 8.810A pdb=" N LYS Y 43 " --> pdb=" O THR K 44 " (cutoff:3.500A) removed outlier: 10.241A pdb=" N GLU K 46 " --> pdb=" O LYS Y 43 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N LYS Y 45 " --> pdb=" O GLU K 46 " (cutoff:3.500A) removed outlier: 8.834A pdb=" N VAL K 48 " --> pdb=" O LYS Y 45 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N GLY Y 47 " --> pdb=" O VAL K 48 " (cutoff:3.500A) removed outlier: 8.175A pdb=" N HIS K 50 " --> pdb=" O GLY Y 47 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL Y 49 " --> pdb=" O HIS K 50 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N LYS U 43 " --> pdb=" O THR Y 44 " (cutoff:3.500A) removed outlier: 10.221A pdb=" N GLU Y 46 " --> pdb=" O LYS U 43 " (cutoff:3.500A) removed outlier: 9.108A pdb=" N LYS U 45 " --> pdb=" O GLU Y 46 " (cutoff:3.500A) removed outlier: 8.818A pdb=" N VAL Y 48 " --> pdb=" O LYS U 45 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY U 47 " --> pdb=" O VAL Y 48 " (cutoff:3.500A) removed outlier: 8.168A pdb=" N HIS Y 50 " --> pdb=" O GLY U 47 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N VAL U 49 " --> pdb=" O HIS Y 50 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N THR U 44 " --> pdb=" O LYS W 43 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LYS W 45 " --> pdb=" O THR U 44 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLU U 46 " --> pdb=" O LYS W 45 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N GLY W 47 " --> pdb=" O GLU U 46 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'I' and resid 55 through 66 removed outlier: 8.967A pdb=" N VAL E 55 " --> pdb=" O ALA I 56 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N LYS I 58 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU E 57 " --> pdb=" O LYS I 58 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N LYS I 60 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR E 59 " --> pdb=" O LYS I 60 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLN I 62 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLU E 61 " --> pdb=" O GLN I 62 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N THR I 64 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL E 63 " --> pdb=" O THR I 64 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL I 66 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN E 65 " --> pdb=" O VAL I 66 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL G 55 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N ALA E 56 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N GLU G 57 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N VAL S 55 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA G 56 " --> pdb=" O VAL S 55 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLU S 57 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N VAL Q 55 " --> pdb=" O ALA S 56 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N LYS S 58 " --> pdb=" O VAL Q 55 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU Q 57 " --> pdb=" O LYS S 58 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N LYS S 60 " --> pdb=" O GLU Q 57 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N THR Q 59 " --> pdb=" O LYS S 60 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N GLN S 62 " --> pdb=" O THR Q 59 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU Q 61 " --> pdb=" O GLN S 62 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N THR S 64 " --> pdb=" O GLU Q 61 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL Q 63 " --> pdb=" O THR S 64 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL S 66 " --> pdb=" O VAL Q 63 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN Q 65 " --> pdb=" O VAL S 66 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N VAL O 55 " --> pdb=" O ALA Q 56 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N LYS Q 58 " --> pdb=" O VAL O 55 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU O 57 " --> pdb=" O LYS Q 58 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N LYS Q 60 " --> pdb=" O GLU O 57 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR O 59 " --> pdb=" O LYS Q 60 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLN Q 62 " --> pdb=" O THR O 59 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLU O 61 " --> pdb=" O GLN Q 62 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N THR Q 64 " --> pdb=" O GLU O 61 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N VAL O 63 " --> pdb=" O THR Q 64 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL Q 66 " --> pdb=" O VAL O 63 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN O 65 " --> pdb=" O VAL Q 66 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N VAL M 55 " --> pdb=" O ALA O 56 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N LYS O 58 " --> pdb=" O VAL M 55 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU M 57 " --> pdb=" O LYS O 58 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N LYS O 60 " --> pdb=" O GLU M 57 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR M 59 " --> pdb=" O LYS O 60 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N GLN O 62 " --> pdb=" O THR M 59 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N GLU M 61 " --> pdb=" O GLN O 62 " (cutoff:3.500A) removed outlier: 7.909A pdb=" N THR O 64 " --> pdb=" O GLU M 61 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N VAL M 63 " --> pdb=" O THR O 64 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N VAL O 66 " --> pdb=" O VAL M 63 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN M 65 " --> pdb=" O VAL O 66 " (cutoff:3.500A) removed outlier: 8.969A pdb=" N VAL K 55 " --> pdb=" O ALA M 56 " (cutoff:3.500A) removed outlier: 9.963A pdb=" N LYS M 58 " --> pdb=" O VAL K 55 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N GLU K 57 " --> pdb=" O LYS M 58 " (cutoff:3.500A) removed outlier: 8.439A pdb=" N LYS M 60 " --> pdb=" O GLU K 57 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N THR K 59 " --> pdb=" O LYS M 60 " (cutoff:3.500A) removed outlier: 8.224A pdb=" N GLN M 62 " --> pdb=" O THR K 59 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLU K 61 " --> pdb=" O GLN M 62 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N THR M 64 " --> pdb=" O GLU K 61 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL K 63 " --> pdb=" O THR M 64 " (cutoff:3.500A) removed outlier: 7.842A pdb=" N VAL M 66 " --> pdb=" O VAL K 63 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N ASN K 65 " --> pdb=" O VAL M 66 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N VAL Y 55 " --> pdb=" O ALA K 56 " (cutoff:3.500A) removed outlier: 9.970A pdb=" N LYS K 58 " --> pdb=" O VAL Y 55 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N GLU Y 57 " --> pdb=" O LYS K 58 " (cutoff:3.500A) removed outlier: 8.417A pdb=" N LYS K 60 " --> pdb=" O GLU Y 57 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N THR Y 59 " --> pdb=" O LYS K 60 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N GLN K 62 " --> pdb=" O THR Y 59 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N GLU Y 61 " --> pdb=" O GLN K 62 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N THR K 64 " --> pdb=" O GLU Y 61 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL Y 63 " --> pdb=" O THR K 64 " (cutoff:3.500A) removed outlier: 7.817A pdb=" N VAL K 66 " --> pdb=" O VAL Y 63 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ASN Y 65 " --> pdb=" O VAL K 66 " (cutoff:3.500A) removed outlier: 8.968A pdb=" N VAL U 55 " --> pdb=" O ALA Y 56 " (cutoff:3.500A) removed outlier: 9.964A pdb=" N LYS Y 58 " --> pdb=" O VAL U 55 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N GLU U 57 " --> pdb=" O LYS Y 58 " (cutoff:3.500A) removed outlier: 8.440A pdb=" N LYS Y 60 " --> pdb=" O GLU U 57 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N THR U 59 " --> pdb=" O LYS Y 60 " (cutoff:3.500A) removed outlier: 8.223A pdb=" N GLN Y 62 " --> pdb=" O THR U 59 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLU U 61 " --> pdb=" O GLN Y 62 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N THR Y 64 " --> pdb=" O GLU U 61 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N VAL U 63 " --> pdb=" O THR Y 64 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N VAL Y 66 " --> pdb=" O VAL U 63 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ASN U 65 " --> pdb=" O VAL Y 66 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL W 55 " --> pdb=" O THR U 54 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ALA U 56 " --> pdb=" O VAL W 55 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU W 57 " --> pdb=" O ALA U 56 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'I' and resid 69 through 71 removed outlier: 6.416A pdb=" N VAL E 70 " --> pdb=" O VAL I 71 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL Q 70 " --> pdb=" O VAL S 71 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL O 70 " --> pdb=" O VAL Q 71 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL M 70 " --> pdb=" O VAL O 71 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL K 70 " --> pdb=" O VAL M 71 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL Y 70 " --> pdb=" O VAL K 71 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL U 70 " --> pdb=" O VAL Y 71 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 75 through 80 removed outlier: 6.677A pdb=" N THR G 75 " --> pdb=" O ALA S 76 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N ALA S 78 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N VAL G 77 " --> pdb=" O ALA S 78 " (cutoff:3.500A) removed outlier: 7.732A pdb=" N LYS S 80 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N GLN G 79 " --> pdb=" O LYS S 80 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA Q 76 " --> pdb=" O VAL S 77 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLN S 79 " --> pdb=" O ALA Q 76 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA Q 78 " --> pdb=" O GLN S 79 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA M 76 " --> pdb=" O VAL O 77 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLN O 79 " --> pdb=" O ALA M 76 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N ALA M 78 " --> pdb=" O GLN O 79 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA Y 76 " --> pdb=" O VAL K 77 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N GLN K 79 " --> pdb=" O ALA Y 76 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ALA Y 78 " --> pdb=" O GLN K 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 89 through 93 removed outlier: 6.387A pdb=" N ALA E 89 " --> pdb=" O ALA G 90 " (cutoff:3.500A) removed outlier: 8.051A pdb=" N THR G 92 " --> pdb=" O ALA E 89 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA E 91 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA G 89 " --> pdb=" O ALA S 90 " (cutoff:3.500A) removed outlier: 8.059A pdb=" N THR S 92 " --> pdb=" O ALA G 89 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ALA G 91 " --> pdb=" O THR S 92 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ALA U 89 " --> pdb=" O ALA W 90 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N THR W 92 " --> pdb=" O ALA U 89 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA U 91 " --> pdb=" O THR W 92 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'J' and resid 38 through 40 removed outlier: 6.381A pdb=" N TYR F 39 " --> pdb=" O VAL J 40 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N TYR R 39 " --> pdb=" O VAL T 40 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N TYR P 39 " --> pdb=" O VAL R 40 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR N 39 " --> pdb=" O VAL P 40 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TYR L 39 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N TYR Z 39 " --> pdb=" O VAL L 40 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N TYR V 39 " --> pdb=" O VAL Z 40 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 45 through 57 removed outlier: 9.031A pdb=" N LYS F 45 " --> pdb=" O GLU J 46 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N VAL J 48 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLY F 47 " --> pdb=" O VAL J 48 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N HIS J 50 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL F 49 " --> pdb=" O HIS J 50 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL J 52 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N GLY F 51 " --> pdb=" O VAL J 52 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N THR J 54 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ALA F 53 " --> pdb=" O THR J 54 " (cutoff:3.500A) removed outlier: 10.436A pdb=" N ALA J 56 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N VAL F 55 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLU F 46 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY H 47 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL F 52 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ALA H 53 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N THR F 54 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL H 55 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N ALA F 56 " --> pdb=" O VAL H 55 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU H 57 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU H 46 " --> pdb=" O LYS T 45 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N GLY T 47 " --> pdb=" O GLU H 46 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL H 52 " --> pdb=" O GLY T 51 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N ALA T 53 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N THR H 54 " --> pdb=" O ALA T 53 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N VAL T 55 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N ALA H 56 " --> pdb=" O VAL T 55 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N GLU T 57 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 9.018A pdb=" N LYS R 45 " --> pdb=" O GLU T 46 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N VAL T 48 " --> pdb=" O LYS R 45 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLY R 47 " --> pdb=" O VAL T 48 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N HIS T 50 " --> pdb=" O GLY R 47 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL R 49 " --> pdb=" O HIS T 50 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL T 52 " --> pdb=" O VAL R 49 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLY R 51 " --> pdb=" O VAL T 52 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N THR T 54 " --> pdb=" O GLY R 51 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ALA R 53 " --> pdb=" O THR T 54 " (cutoff:3.500A) removed outlier: 10.425A pdb=" N ALA T 56 " --> pdb=" O ALA R 53 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N VAL R 55 " --> pdb=" O ALA T 56 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N LYS P 45 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 8.721A pdb=" N VAL R 48 " --> pdb=" O LYS P 45 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY P 47 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N HIS R 50 " --> pdb=" O GLY P 47 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N VAL P 49 " --> pdb=" O HIS R 50 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N VAL R 52 " --> pdb=" O VAL P 49 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N GLY P 51 " --> pdb=" O VAL R 52 " (cutoff:3.500A) removed outlier: 9.734A pdb=" N THR R 54 " --> pdb=" O GLY P 51 " (cutoff:3.500A) removed outlier: 8.930A pdb=" N ALA P 53 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 10.436A pdb=" N ALA R 56 " --> pdb=" O ALA P 53 " (cutoff:3.500A) removed outlier: 8.999A pdb=" N VAL P 55 " --> pdb=" O ALA R 56 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N LYS N 45 " --> pdb=" O GLU P 46 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N VAL P 48 " --> pdb=" O LYS N 45 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLY N 47 " --> pdb=" O VAL P 48 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N HIS P 50 " --> pdb=" O GLY N 47 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL N 49 " --> pdb=" O HIS P 50 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL P 52 " --> pdb=" O VAL N 49 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLY N 51 " --> pdb=" O VAL P 52 " (cutoff:3.500A) removed outlier: 9.721A pdb=" N THR P 54 " --> pdb=" O GLY N 51 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ALA N 53 " --> pdb=" O THR P 54 " (cutoff:3.500A) removed outlier: 10.427A pdb=" N ALA P 56 " --> pdb=" O ALA N 53 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N VAL N 55 " --> pdb=" O ALA P 56 " (cutoff:3.500A) removed outlier: 9.030A pdb=" N LYS L 45 " --> pdb=" O GLU N 46 " (cutoff:3.500A) removed outlier: 8.719A pdb=" N VAL N 48 " --> pdb=" O LYS L 45 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLY L 47 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N HIS N 50 " --> pdb=" O GLY L 47 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL L 49 " --> pdb=" O HIS N 50 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL N 52 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N GLY L 51 " --> pdb=" O VAL N 52 " (cutoff:3.500A) removed outlier: 9.732A pdb=" N THR N 54 " --> pdb=" O GLY L 51 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ALA L 53 " --> pdb=" O THR N 54 " (cutoff:3.500A) removed outlier: 10.436A pdb=" N ALA N 56 " --> pdb=" O ALA L 53 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N VAL L 55 " --> pdb=" O ALA N 56 " (cutoff:3.500A) removed outlier: 9.019A pdb=" N LYS Z 45 " --> pdb=" O GLU L 46 " (cutoff:3.500A) removed outlier: 8.710A pdb=" N VAL L 48 " --> pdb=" O LYS Z 45 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N GLY Z 47 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 8.131A pdb=" N HIS L 50 " --> pdb=" O GLY Z 47 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N VAL Z 49 " --> pdb=" O HIS L 50 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N VAL L 52 " --> pdb=" O VAL Z 49 " (cutoff:3.500A) removed outlier: 7.838A pdb=" N GLY Z 51 " --> pdb=" O VAL L 52 " (cutoff:3.500A) removed outlier: 9.720A pdb=" N THR L 54 " --> pdb=" O GLY Z 51 " (cutoff:3.500A) removed outlier: 8.918A pdb=" N ALA Z 53 " --> pdb=" O THR L 54 " (cutoff:3.500A) removed outlier: 10.426A pdb=" N ALA L 56 " --> pdb=" O ALA Z 53 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N VAL Z 55 " --> pdb=" O ALA L 56 " (cutoff:3.500A) removed outlier: 9.031A pdb=" N LYS V 45 " --> pdb=" O GLU Z 46 " (cutoff:3.500A) removed outlier: 8.720A pdb=" N VAL Z 48 " --> pdb=" O LYS V 45 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLY V 47 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N HIS Z 50 " --> pdb=" O GLY V 47 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N VAL V 49 " --> pdb=" O HIS Z 50 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N VAL Z 52 " --> pdb=" O VAL V 49 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N GLY V 51 " --> pdb=" O VAL Z 52 " (cutoff:3.500A) removed outlier: 9.733A pdb=" N THR Z 54 " --> pdb=" O GLY V 51 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ALA V 53 " --> pdb=" O THR Z 54 " (cutoff:3.500A) removed outlier: 10.435A pdb=" N ALA Z 56 " --> pdb=" O ALA V 53 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N VAL V 55 " --> pdb=" O ALA Z 56 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N GLU V 46 " --> pdb=" O LYS X 45 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLY X 47 " --> pdb=" O GLU V 46 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL V 52 " --> pdb=" O GLY X 51 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA X 53 " --> pdb=" O VAL V 52 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N THR V 54 " --> pdb=" O ALA X 53 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N VAL X 55 " --> pdb=" O THR V 54 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N ALA V 56 " --> pdb=" O VAL X 55 " (cutoff:3.500A) removed outlier: 6.871A pdb=" N GLU X 57 " --> pdb=" O ALA V 56 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 62 through 66 removed outlier: 6.360A pdb=" N GLN F 62 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 7.921A pdb=" N ASN H 65 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N THR F 64 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N GLN H 62 " --> pdb=" O VAL T 63 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N ASN T 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR H 64 " --> pdb=" O ASN T 65 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N GLN V 62 " --> pdb=" O VAL X 63 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N ASN X 65 " --> pdb=" O GLN V 62 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N THR V 64 " --> pdb=" O ASN X 65 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 69 through 71 removed outlier: 6.542A pdb=" N VAL F 70 " --> pdb=" O VAL J 71 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N ALA F 69 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N ALA H 69 " --> pdb=" O VAL T 70 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL L 70 " --> pdb=" O VAL N 71 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA V 69 " --> pdb=" O VAL X 70 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 75 through 83 removed outlier: 6.860A pdb=" N THR J 81 " --> pdb=" O LYS F 80 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N VAL F 82 " --> pdb=" O THR J 81 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLU J 83 " --> pdb=" O VAL F 82 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N THR F 75 " --> pdb=" O ALA H 76 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ALA H 78 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL F 77 " --> pdb=" O ALA H 78 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N LYS H 80 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N GLN F 79 " --> pdb=" O LYS H 80 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL H 82 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 8.998A pdb=" N THR F 81 " --> pdb=" O VAL H 82 " (cutoff:3.500A) removed outlier: 6.359A pdb=" N THR H 75 " --> pdb=" O ALA T 76 " (cutoff:3.500A) removed outlier: 7.731A pdb=" N ALA T 78 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N VAL H 77 " --> pdb=" O ALA T 78 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N LYS T 80 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 9.172A pdb=" N GLN H 79 " --> pdb=" O LYS T 80 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N VAL T 82 " --> pdb=" O GLN H 79 " (cutoff:3.500A) removed outlier: 9.003A pdb=" N THR H 81 " --> pdb=" O VAL T 82 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR T 81 " --> pdb=" O LYS R 80 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL R 82 " --> pdb=" O THR T 81 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU T 83 " --> pdb=" O VAL R 82 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR R 81 " --> pdb=" O LYS P 80 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL P 82 " --> pdb=" O THR R 81 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLU R 83 " --> pdb=" O VAL P 82 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR P 81 " --> pdb=" O LYS N 80 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL N 82 " --> pdb=" O THR P 81 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU P 83 " --> pdb=" O VAL N 82 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N THR N 81 " --> pdb=" O LYS L 80 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N VAL L 82 " --> pdb=" O THR N 81 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLU N 83 " --> pdb=" O VAL L 82 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR L 81 " --> pdb=" O LYS Z 80 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL Z 82 " --> pdb=" O THR L 81 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N GLU L 83 " --> pdb=" O VAL Z 82 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR Z 81 " --> pdb=" O LYS V 80 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL V 82 " --> pdb=" O THR Z 81 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N GLU Z 83 " --> pdb=" O VAL V 82 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N THR V 75 " --> pdb=" O ALA X 76 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N ALA X 78 " --> pdb=" O THR V 75 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N VAL V 77 " --> pdb=" O ALA X 78 " (cutoff:3.500A) removed outlier: 8.323A pdb=" N LYS X 80 " --> pdb=" O VAL V 77 " (cutoff:3.500A) removed outlier: 9.173A pdb=" N GLN V 79 " --> pdb=" O LYS X 80 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N VAL X 82 " --> pdb=" O GLN V 79 " (cutoff:3.500A) removed outlier: 8.997A pdb=" N THR V 81 " --> pdb=" O VAL X 82 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 91 through 96 removed outlier: 6.889A pdb=" N THR F 92 " --> pdb=" O ALA J 91 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY J 93 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 9.131A pdb=" N ALA F 91 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 8.682A pdb=" N PHE H 94 " --> pdb=" O ALA F 91 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY F 93 " --> pdb=" O PHE H 94 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LYS H 96 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL F 95 " --> pdb=" O LYS H 96 " (cutoff:3.500A) removed outlier: 9.153A pdb=" N ALA H 91 " --> pdb=" O THR T 92 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N PHE T 94 " --> pdb=" O ALA H 91 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N GLY H 93 " --> pdb=" O PHE T 94 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N LYS T 96 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N VAL H 95 " --> pdb=" O LYS T 96 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR R 92 " --> pdb=" O ALA T 91 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLY T 93 " --> pdb=" O THR R 92 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N THR P 92 " --> pdb=" O ALA R 91 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY R 93 " --> pdb=" O THR P 92 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N THR N 92 " --> pdb=" O ALA P 91 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY P 93 " --> pdb=" O THR N 92 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR L 92 " --> pdb=" O ALA N 91 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLY N 93 " --> pdb=" O THR L 92 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR Z 92 " --> pdb=" O ALA L 91 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N GLY L 93 " --> pdb=" O THR Z 92 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N THR V 92 " --> pdb=" O ALA Z 91 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N GLY Z 93 " --> pdb=" O THR V 92 " (cutoff:3.500A) removed outlier: 9.132A pdb=" N ALA V 91 " --> pdb=" O THR X 92 " (cutoff:3.500A) removed outlier: 8.683A pdb=" N PHE X 94 " --> pdb=" O ALA V 91 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY V 93 " --> pdb=" O PHE X 94 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N LYS X 96 " --> pdb=" O GLY V 93 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL V 95 " --> pdb=" O LYS X 96 " (cutoff:3.500A) 289 hydrogen bonds defined for protein. 867 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: 3.61 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 1958 1.28 - 1.35: 1716 1.35 - 1.41: 388 1.41 - 1.48: 1823 1.48 - 1.55: 5148 Bond restraints: 11033 Sorted by residual: bond pdb=" C GLY W 36 " pdb=" O GLY W 36 " ideal model delta sigma weight residual 1.238 1.230 0.008 8.90e-03 1.26e+04 8.26e-01 bond pdb=" C GLY E 36 " pdb=" O GLY E 36 " ideal model delta sigma weight residual 1.238 1.230 0.008 8.90e-03 1.26e+04 7.89e-01 bond pdb=" CA GLN V 99 " pdb=" CB GLN V 99 " ideal model delta sigma weight residual 1.528 1.505 0.023 2.61e-02 1.47e+03 7.78e-01 bond pdb=" CA LYS U 34 " pdb=" C LYS U 34 " ideal model delta sigma weight residual 1.526 1.516 0.010 1.08e-02 8.57e+03 7.78e-01 bond pdb=" CA LYS E 34 " pdb=" C LYS E 34 " ideal model delta sigma weight residual 1.526 1.516 0.009 1.08e-02 8.57e+03 7.73e-01 ... (remaining 11028 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.61: 12264 0.61 - 1.23: 2097 1.23 - 1.84: 362 1.84 - 2.45: 125 2.45 - 3.06: 57 Bond angle restraints: 14905 Sorted by residual: angle pdb=" N THR V 64 " pdb=" CA THR V 64 " pdb=" C THR V 64 " ideal model delta sigma weight residual 108.90 105.87 3.03 1.63e+00 3.76e-01 3.45e+00 angle pdb=" N THR T 64 " pdb=" CA THR T 64 " pdb=" C THR T 64 " ideal model delta sigma weight residual 108.90 105.87 3.03 1.63e+00 3.76e-01 3.45e+00 angle pdb=" N THR R 64 " pdb=" CA THR R 64 " pdb=" C THR R 64 " ideal model delta sigma weight residual 108.90 105.88 3.02 1.63e+00 3.76e-01 3.44e+00 angle pdb=" N THR Z 64 " pdb=" CA THR Z 64 " pdb=" C THR Z 64 " ideal model delta sigma weight residual 108.90 105.89 3.01 1.63e+00 3.76e-01 3.42e+00 angle pdb=" N THR X 64 " pdb=" CA THR X 64 " pdb=" C THR X 64 " ideal model delta sigma weight residual 108.90 105.89 3.01 1.63e+00 3.76e-01 3.41e+00 ... (remaining 14900 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.45: 5484 13.45 - 26.90: 610 26.90 - 40.35: 264 40.35 - 53.80: 55 53.80 - 67.25: 44 Dihedral angle restraints: 6457 sinusoidal: 2145 harmonic: 4312 Sorted by residual: dihedral pdb=" CB LYS E 23 " pdb=" CG LYS E 23 " pdb=" CD LYS E 23 " pdb=" CE LYS E 23 " ideal model delta sinusoidal sigma weight residual 180.00 121.05 58.95 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB LYS I 23 " pdb=" CG LYS I 23 " pdb=" CD LYS I 23 " pdb=" CE LYS I 23 " ideal model delta sinusoidal sigma weight residual 180.00 121.08 58.92 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB LYS Q 23 " pdb=" CG LYS Q 23 " pdb=" CD LYS Q 23 " pdb=" CE LYS Q 23 " ideal model delta sinusoidal sigma weight residual 180.00 121.10 58.90 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 6454 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 735 0.026 - 0.051: 625 0.051 - 0.076: 257 0.076 - 0.102: 176 0.102 - 0.127: 143 Chirality restraints: 1936 Sorted by residual: chirality pdb=" CA VAL J 70 " pdb=" N VAL J 70 " pdb=" C VAL J 70 " pdb=" CB VAL J 70 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.05e-01 chirality pdb=" CA VAL R 70 " pdb=" N VAL R 70 " pdb=" C VAL R 70 " pdb=" CB VAL R 70 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.97e-01 chirality pdb=" CA VAL Z 70 " pdb=" N VAL Z 70 " pdb=" C VAL Z 70 " pdb=" CB VAL Z 70 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 1933 not shown) Planarity restraints: 1870 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR P 64 " 0.005 2.00e-02 2.50e+03 1.05e-02 1.11e+00 pdb=" C THR P 64 " -0.018 2.00e-02 2.50e+03 pdb=" O THR P 64 " 0.007 2.00e-02 2.50e+03 pdb=" N ASN P 65 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR N 64 " 0.005 2.00e-02 2.50e+03 1.05e-02 1.10e+00 pdb=" C THR N 64 " -0.018 2.00e-02 2.50e+03 pdb=" O THR N 64 " 0.007 2.00e-02 2.50e+03 pdb=" N ASN N 65 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR X 64 " 0.005 2.00e-02 2.50e+03 1.05e-02 1.10e+00 pdb=" C THR X 64 " -0.018 2.00e-02 2.50e+03 pdb=" O THR X 64 " 0.007 2.00e-02 2.50e+03 pdb=" N ASN X 65 " 0.006 2.00e-02 2.50e+03 ... (remaining 1867 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.82: 3000 2.82 - 3.34: 8788 3.34 - 3.86: 18741 3.86 - 4.38: 21256 4.38 - 4.90: 43605 Nonbonded interactions: 95390 Sorted by model distance: nonbonded pdb=" NZ LYS F 60 " pdb=" OE1 GLU G 28 " model vdw 2.295 3.120 nonbonded pdb=" NZ LYS V 60 " pdb=" OE1 GLU W 28 " model vdw 2.295 3.120 nonbonded pdb=" OE1 GLU M 28 " pdb=" NZ LYS P 60 " model vdw 2.296 3.120 nonbonded pdb=" OE1 GLU Y 28 " pdb=" NZ LYS L 60 " model vdw 2.296 3.120 nonbonded pdb=" OE1 GLU Q 28 " pdb=" NZ LYS T 60 " model vdw 2.297 3.120 ... (remaining 95385 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: 0.13 Found NCS groups: ncs_group { reference = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' } 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: 32.090 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: 0.010 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 26.170 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.050 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 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 : 0.006 0.028 11033 Z= 0.267 Angle : 0.531 3.064 14905 Z= 0.312 Chirality : 0.052 0.127 1936 Planarity : 0.002 0.011 1870 Dihedral : 15.886 67.254 3751 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 9.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 1.10 % Allowed : 18.09 % Favored : 80.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.18), residues: 1562 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS Y 50 PHE 0.012 0.003 PHE T 94 TYR 0.009 0.002 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.13300 ( 289) hydrogen bonds : angle 7.55278 ( 867) covalent geometry : bond 0.00605 (11033) covalent geometry : angle 0.53098 (14905) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 245 time to evaluate : 1.089 Fit side-chains revert: symmetry clash REVERT: F 96 LYS cc_start: 0.8253 (tttt) cc_final: 0.8034 (tttp) REVERT: G 32 LYS cc_start: 0.8452 (ttmt) cc_final: 0.8227 (mtpp) REVERT: G 35 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7519 (mm-30) REVERT: G 43 LYS cc_start: 0.8500 (mttt) cc_final: 0.8118 (mtpt) REVERT: U 21 LYS cc_start: 0.8304 (mttp) cc_final: 0.8075 (mttm) REVERT: U 43 LYS cc_start: 0.8482 (mttt) cc_final: 0.8212 (mtpt) REVERT: U 83 GLU cc_start: 0.7386 (tt0) cc_final: 0.6902 (tt0) REVERT: U 87 SER cc_start: 0.8885 (p) cc_final: 0.8537 (m) REVERT: V 97 LYS cc_start: 0.8401 (mtmt) cc_final: 0.8200 (mttt) REVERT: W 23 LYS cc_start: 0.7896 (mttt) cc_final: 0.7602 (mtpp) REVERT: W 43 LYS cc_start: 0.8420 (mttt) cc_final: 0.8196 (mtpt) REVERT: W 83 GLU cc_start: 0.7794 (tt0) cc_final: 0.7497 (tt0) REVERT: Y 23 LYS cc_start: 0.7955 (mttt) cc_final: 0.7589 (mtpp) REVERT: N 43 LYS cc_start: 0.9099 (mttp) cc_final: 0.8863 (mttp) REVERT: O 43 LYS cc_start: 0.8592 (mttt) cc_final: 0.8296 (mttm) REVERT: Q 57 GLU cc_start: 0.8095 (tt0) cc_final: 0.7871 (tt0) REVERT: S 35 GLU cc_start: 0.7848 (mm-30) cc_final: 0.7339 (mm-30) outliers start: 12 outliers final: 3 residues processed: 256 average time/residue: 0.2723 time to fit residues: 93.1747 Evaluate side-chains 216 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 213 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain Z residue 37 VAL Chi-restraints excluded: chain P residue 37 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 130 optimal weight: 8.9990 chunk 116 optimal weight: 0.8980 chunk 64 optimal weight: 4.9990 chunk 39 optimal weight: 6.9990 chunk 78 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 120 optimal weight: 1.9990 chunk 46 optimal weight: 8.9990 chunk 73 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 139 optimal weight: 4.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 50 HIS V 50 HIS W 50 HIS X 50 HIS Y 50 HIS Y 79 GLN Z 50 HIS ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 79 GLN N 50 HIS ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.092107 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.074519 restraints weight = 14592.193| |-----------------------------------------------------------------------------| r_work (start): 0.3113 rms_B_bonded: 2.39 r_work: 0.2982 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 4.32 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8671 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 11033 Z= 0.211 Angle : 0.483 4.509 14905 Z= 0.278 Chirality : 0.052 0.177 1936 Planarity : 0.002 0.020 1870 Dihedral : 4.895 20.723 1609 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.57 % Allowed : 15.06 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.18), residues: 1562 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS P 50 PHE 0.010 0.002 PHE H 94 TYR 0.013 0.002 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.03538 ( 289) hydrogen bonds : angle 5.06631 ( 867) covalent geometry : bond 0.00491 (11033) covalent geometry : angle 0.48282 (14905) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 1.083 Fit side-chains REVERT: E 35 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7579 (mm-30) REVERT: E 38 LEU cc_start: 0.8927 (mp) cc_final: 0.8699 (mt) REVERT: E 43 LYS cc_start: 0.8154 (mttt) cc_final: 0.7546 (mtpt) REVERT: F 83 GLU cc_start: 0.7975 (pt0) cc_final: 0.7660 (tt0) REVERT: G 23 LYS cc_start: 0.7663 (mtpp) cc_final: 0.7308 (ttpt) REVERT: G 32 LYS cc_start: 0.8151 (ttmt) cc_final: 0.7920 (mtpp) REVERT: G 35 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7266 (mm-30) REVERT: G 94 PHE cc_start: 0.6688 (m-10) cc_final: 0.6405 (m-10) REVERT: H 83 GLU cc_start: 0.8233 (pt0) cc_final: 0.7961 (pt0) REVERT: J 97 LYS cc_start: 0.8439 (mtmt) cc_final: 0.8079 (mttm) REVERT: U 43 LYS cc_start: 0.8229 (mttt) cc_final: 0.7794 (mtpt) REVERT: U 61 GLU cc_start: 0.7932 (mt-10) cc_final: 0.7726 (mt-10) REVERT: V 58 LYS cc_start: 0.8941 (mttt) cc_final: 0.8734 (mttp) REVERT: W 23 LYS cc_start: 0.7942 (mttt) cc_final: 0.7553 (mtmt) REVERT: W 83 GLU cc_start: 0.8215 (tt0) cc_final: 0.7953 (mt-10) REVERT: Y 23 LYS cc_start: 0.7867 (mttt) cc_final: 0.7322 (mtpp) REVERT: M 23 LYS cc_start: 0.7938 (mtpp) cc_final: 0.7283 (mptt) REVERT: M 57 GLU cc_start: 0.8173 (tt0) cc_final: 0.7923 (tt0) REVERT: O 43 LYS cc_start: 0.8431 (mttt) cc_final: 0.7975 (mttm) REVERT: Q 57 GLU cc_start: 0.8186 (tt0) cc_final: 0.7900 (tt0) REVERT: S 23 LYS cc_start: 0.7631 (mttm) cc_final: 0.7107 (mtpt) REVERT: S 32 LYS cc_start: 0.8177 (ttmt) cc_final: 0.7756 (mtpp) REVERT: S 35 GLU cc_start: 0.8023 (mm-30) cc_final: 0.7265 (mm-30) REVERT: S 43 LYS cc_start: 0.8603 (mttt) cc_final: 0.7998 (mtpt) REVERT: T 58 LYS cc_start: 0.8676 (mttt) cc_final: 0.8433 (mttt) outliers start: 28 outliers final: 19 residues processed: 225 average time/residue: 0.3251 time to fit residues: 97.3962 Evaluate side-chains 217 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 198 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain S residue 75 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 36 optimal weight: 8.9990 chunk 20 optimal weight: 4.9990 chunk 107 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 109 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 142 optimal weight: 0.6980 chunk 111 optimal weight: 3.9990 chunk 85 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 126 optimal weight: 10.0000 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 HIS ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 GLN L 62 GLN ** M 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 50 HIS N 62 GLN ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 HIS P 50 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.090905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.072456 restraints weight = 14753.279| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 2.49 r_work: 0.2932 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2789 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 11033 Z= 0.222 Angle : 0.480 4.838 14905 Z= 0.275 Chirality : 0.052 0.161 1936 Planarity : 0.002 0.014 1870 Dihedral : 4.933 17.768 1606 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.20 % Allowed : 16.90 % Favored : 80.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.18), residues: 1562 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS V 50 PHE 0.008 0.002 PHE H 94 TYR 0.013 0.002 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.03019 ( 289) hydrogen bonds : angle 4.74615 ( 867) covalent geometry : bond 0.00522 (11033) covalent geometry : angle 0.47963 (14905) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 1.061 Fit side-chains REVERT: E 35 GLU cc_start: 0.8474 (mm-30) cc_final: 0.7688 (mm-30) REVERT: E 43 LYS cc_start: 0.8189 (mttt) cc_final: 0.7569 (mtpt) REVERT: G 32 LYS cc_start: 0.8162 (ttmt) cc_final: 0.7947 (mtpp) REVERT: G 35 GLU cc_start: 0.8141 (mm-30) cc_final: 0.7383 (mm-30) REVERT: J 97 LYS cc_start: 0.8403 (mtmt) cc_final: 0.7999 (mttm) REVERT: U 43 LYS cc_start: 0.8155 (mttt) cc_final: 0.7715 (mtpt) REVERT: U 61 GLU cc_start: 0.7990 (mt-10) cc_final: 0.7788 (mt-10) REVERT: V 58 LYS cc_start: 0.8921 (mttt) cc_final: 0.8669 (mttp) REVERT: W 23 LYS cc_start: 0.8105 (mttt) cc_final: 0.7668 (mtpt) REVERT: W 83 GLU cc_start: 0.8423 (tt0) cc_final: 0.7965 (mt-10) REVERT: Y 23 LYS cc_start: 0.7939 (mttt) cc_final: 0.7349 (mtpp) REVERT: M 23 LYS cc_start: 0.7920 (mtpp) cc_final: 0.7264 (mptt) REVERT: M 57 GLU cc_start: 0.8163 (tt0) cc_final: 0.7929 (tt0) REVERT: O 43 LYS cc_start: 0.8427 (mttt) cc_final: 0.7947 (mttm) REVERT: Q 57 GLU cc_start: 0.8155 (tt0) cc_final: 0.7836 (tt0) REVERT: R 83 GLU cc_start: 0.7708 (pt0) cc_final: 0.7495 (pt0) REVERT: S 35 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7452 (mm-30) REVERT: S 43 LYS cc_start: 0.8565 (mttt) cc_final: 0.7975 (mtpt) REVERT: T 97 LYS cc_start: 0.8131 (mtmt) cc_final: 0.7920 (mttt) outliers start: 24 outliers final: 21 residues processed: 219 average time/residue: 0.2784 time to fit residues: 82.5178 Evaluate side-chains 215 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 194 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain S residue 75 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 16 optimal weight: 3.9990 chunk 88 optimal weight: 7.9990 chunk 143 optimal weight: 0.9980 chunk 14 optimal weight: 10.0000 chunk 113 optimal weight: 7.9990 chunk 5 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 79 optimal weight: 4.9990 chunk 54 optimal weight: 0.2980 chunk 96 optimal weight: 6.9990 chunk 140 optimal weight: 0.9980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 50 HIS ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 65 ASN V 50 HIS ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 GLN N 50 HIS ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 HIS P 50 HIS S 50 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.091637 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.073077 restraints weight = 14499.365| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 2.48 r_work: 0.2955 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2812 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 11033 Z= 0.177 Angle : 0.439 3.810 14905 Z= 0.253 Chirality : 0.051 0.142 1936 Planarity : 0.002 0.013 1870 Dihedral : 4.779 16.696 1606 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.66 % Allowed : 17.81 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.03 (0.18), residues: 1562 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.30 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS V 50 PHE 0.008 0.001 PHE H 94 TYR 0.013 0.002 TYR I 39 Details of bonding type rmsd hydrogen bonds : bond 0.02448 ( 289) hydrogen bonds : angle 4.54243 ( 867) covalent geometry : bond 0.00412 (11033) covalent geometry : angle 0.43860 (14905) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 204 time to evaluate : 1.327 Fit side-chains REVERT: E 35 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7967 (mm-30) REVERT: E 43 LYS cc_start: 0.8239 (mttt) cc_final: 0.7631 (mtpt) REVERT: G 32 LYS cc_start: 0.8180 (ttmt) cc_final: 0.7956 (mtpp) REVERT: G 35 GLU cc_start: 0.8163 (mm-30) cc_final: 0.7511 (mm-30) REVERT: J 72 THR cc_start: 0.9107 (p) cc_final: 0.8641 (m) REVERT: J 97 LYS cc_start: 0.8423 (mtmt) cc_final: 0.8028 (mttm) REVERT: U 43 LYS cc_start: 0.8161 (mttt) cc_final: 0.7733 (mtpt) REVERT: V 58 LYS cc_start: 0.8954 (mttt) cc_final: 0.8699 (mttt) REVERT: W 23 LYS cc_start: 0.8124 (mttt) cc_final: 0.7665 (mtmt) REVERT: W 83 GLU cc_start: 0.8398 (tt0) cc_final: 0.7961 (mt-10) REVERT: Y 23 LYS cc_start: 0.8043 (mttt) cc_final: 0.7448 (mtpp) REVERT: L 65 ASN cc_start: 0.9198 (t0) cc_final: 0.8858 (t0) REVERT: M 23 LYS cc_start: 0.7940 (mtpp) cc_final: 0.7322 (mptt) REVERT: O 43 LYS cc_start: 0.8457 (mttt) cc_final: 0.7973 (mttm) REVERT: Q 38 LEU cc_start: 0.8974 (mp) cc_final: 0.8753 (mt) REVERT: Q 57 GLU cc_start: 0.8155 (tt0) cc_final: 0.7851 (tt0) REVERT: S 35 GLU cc_start: 0.8116 (mm-30) cc_final: 0.7403 (mm-30) REVERT: S 43 LYS cc_start: 0.8575 (mttt) cc_final: 0.7994 (mtpt) REVERT: T 97 LYS cc_start: 0.8084 (mtmt) cc_final: 0.7838 (mttt) outliers start: 29 outliers final: 22 residues processed: 220 average time/residue: 0.3143 time to fit residues: 94.8370 Evaluate side-chains 222 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain Y residue 33 THR Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain S residue 75 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 103 optimal weight: 7.9990 chunk 101 optimal weight: 2.9990 chunk 122 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 5 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 131 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 89 optimal weight: 1.9990 chunk 124 optimal weight: 7.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 HIS ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 50 HIS ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 HIS P 62 GLN Q 50 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.090746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.072163 restraints weight = 14496.402| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 2.43 r_work: 0.2928 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 11033 Z= 0.282 Angle : 0.513 5.258 14905 Z= 0.294 Chirality : 0.052 0.129 1936 Planarity : 0.002 0.011 1870 Dihedral : 5.099 17.207 1606 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 3.21 % Allowed : 19.01 % Favored : 77.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.12 (0.18), residues: 1562 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.37 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS F 50 PHE 0.010 0.002 PHE H 94 TYR 0.017 0.003 TYR I 39 Details of bonding type rmsd hydrogen bonds : bond 0.02892 ( 289) hydrogen bonds : angle 4.72875 ( 867) covalent geometry : bond 0.00661 (11033) covalent geometry : angle 0.51323 (14905) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 203 time to evaluate : 1.270 Fit side-chains REVERT: E 35 GLU cc_start: 0.8419 (mm-30) cc_final: 0.7920 (mm-30) REVERT: E 43 LYS cc_start: 0.8356 (mttt) cc_final: 0.7770 (mtpt) REVERT: G 35 GLU cc_start: 0.8143 (mm-30) cc_final: 0.7468 (mm-30) REVERT: I 58 LYS cc_start: 0.8274 (mtpt) cc_final: 0.7666 (mttt) REVERT: J 72 THR cc_start: 0.9149 (p) cc_final: 0.8611 (m) REVERT: J 97 LYS cc_start: 0.8408 (mtmt) cc_final: 0.8009 (mttm) REVERT: U 43 LYS cc_start: 0.8173 (mttt) cc_final: 0.7748 (mtpt) REVERT: V 58 LYS cc_start: 0.8963 (mttt) cc_final: 0.8668 (mttt) REVERT: W 23 LYS cc_start: 0.8124 (mttt) cc_final: 0.7666 (mtmt) REVERT: W 43 LYS cc_start: 0.8410 (mttt) cc_final: 0.7973 (mtpt) REVERT: W 83 GLU cc_start: 0.8483 (tt0) cc_final: 0.8106 (mt-10) REVERT: Y 23 LYS cc_start: 0.8103 (mttt) cc_final: 0.7487 (mtpp) REVERT: Y 57 GLU cc_start: 0.8696 (tt0) cc_final: 0.8414 (tt0) REVERT: Y 58 LYS cc_start: 0.7728 (mtpt) cc_final: 0.7277 (mttt) REVERT: M 23 LYS cc_start: 0.8005 (mtpp) cc_final: 0.7369 (mptt) REVERT: O 43 LYS cc_start: 0.8479 (mttt) cc_final: 0.8014 (mttm) REVERT: Q 57 GLU cc_start: 0.8086 (tt0) cc_final: 0.7692 (tt0) REVERT: S 35 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7407 (mm-30) REVERT: S 43 LYS cc_start: 0.8661 (mttt) cc_final: 0.8079 (mtpt) REVERT: S 57 GLU cc_start: 0.8209 (tt0) cc_final: 0.7924 (tt0) REVERT: T 97 LYS cc_start: 0.8123 (mtmt) cc_final: 0.7765 (mttt) outliers start: 35 outliers final: 25 residues processed: 224 average time/residue: 0.3199 time to fit residues: 98.0101 Evaluate side-chains 223 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 198 time to evaluate : 1.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain S residue 87 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 40 optimal weight: 5.9990 chunk 99 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 88 optimal weight: 5.9990 chunk 98 optimal weight: 0.9980 chunk 71 optimal weight: 4.9990 chunk 93 optimal weight: 3.9990 chunk 151 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 24 optimal weight: 3.9990 chunk 42 optimal weight: 7.9990 overall best weight: 2.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 HIS ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 50 HIS ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 HIS S 50 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.089703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.071110 restraints weight = 14715.632| |-----------------------------------------------------------------------------| r_work (start): 0.3069 rms_B_bonded: 2.45 r_work: 0.2923 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2773 rms_B_bonded: 4.39 restraints_weight: 0.2500 r_work (final): 0.2773 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.038 11033 Z= 0.301 Angle : 0.535 6.266 14905 Z= 0.304 Chirality : 0.052 0.129 1936 Planarity : 0.002 0.015 1870 Dihedral : 5.213 18.247 1606 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.49 % Allowed : 18.92 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.16 (0.18), residues: 1562 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS F 50 PHE 0.010 0.002 PHE H 94 TYR 0.018 0.003 TYR I 39 Details of bonding type rmsd hydrogen bonds : bond 0.02915 ( 289) hydrogen bonds : angle 4.76313 ( 867) covalent geometry : bond 0.00704 (11033) covalent geometry : angle 0.53469 (14905) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 201 time to evaluate : 1.130 Fit side-chains REVERT: E 35 GLU cc_start: 0.8437 (mm-30) cc_final: 0.7936 (mm-30) REVERT: E 43 LYS cc_start: 0.8363 (mttt) cc_final: 0.7765 (mtpt) REVERT: G 35 GLU cc_start: 0.8204 (mm-30) cc_final: 0.7531 (mm-30) REVERT: I 58 LYS cc_start: 0.8322 (mtpt) cc_final: 0.7650 (mttp) REVERT: J 72 THR cc_start: 0.9121 (p) cc_final: 0.8576 (m) REVERT: J 96 LYS cc_start: 0.9013 (tttt) cc_final: 0.8690 (tttm) REVERT: J 97 LYS cc_start: 0.8416 (mtmt) cc_final: 0.7988 (mttm) REVERT: U 43 LYS cc_start: 0.8179 (mttt) cc_final: 0.7751 (mtpt) REVERT: V 58 LYS cc_start: 0.8981 (mttt) cc_final: 0.8707 (mttp) REVERT: W 23 LYS cc_start: 0.8114 (mttt) cc_final: 0.7663 (mtmt) REVERT: W 43 LYS cc_start: 0.8410 (mttt) cc_final: 0.7970 (mtpt) REVERT: W 57 GLU cc_start: 0.8247 (mm-30) cc_final: 0.7357 (pm20) REVERT: W 83 GLU cc_start: 0.8463 (tt0) cc_final: 0.8076 (mt-10) REVERT: Y 23 LYS cc_start: 0.8132 (mttt) cc_final: 0.7522 (mtpp) REVERT: Y 57 GLU cc_start: 0.8703 (tt0) cc_final: 0.8430 (tt0) REVERT: Y 58 LYS cc_start: 0.7857 (mtpt) cc_final: 0.7353 (mttt) REVERT: L 64 THR cc_start: 0.9037 (OUTLIER) cc_final: 0.8772 (p) REVERT: M 23 LYS cc_start: 0.8046 (mtpp) cc_final: 0.7416 (mptt) REVERT: O 43 LYS cc_start: 0.8517 (mttt) cc_final: 0.8052 (mttm) REVERT: Q 57 GLU cc_start: 0.8095 (tt0) cc_final: 0.7720 (tt0) REVERT: S 35 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7393 (mm-30) REVERT: S 43 LYS cc_start: 0.8654 (mttt) cc_final: 0.8075 (mtpt) REVERT: S 57 GLU cc_start: 0.8213 (tt0) cc_final: 0.7995 (tt0) outliers start: 38 outliers final: 28 residues processed: 222 average time/residue: 0.2759 time to fit residues: 82.6339 Evaluate side-chains 229 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 200 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 50 HIS Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain L residue 64 THR Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain S residue 87 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 108 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 26 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 18 optimal weight: 8.9990 chunk 94 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 123 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 136 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS ** H 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 50 HIS ** Z 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 50 HIS ** N 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 50 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.091505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.072950 restraints weight = 14493.481| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.44 r_work: 0.2953 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 11033 Z= 0.181 Angle : 0.447 5.897 14905 Z= 0.257 Chirality : 0.051 0.124 1936 Planarity : 0.002 0.014 1870 Dihedral : 4.906 17.114 1606 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.66 % Favored : 98.34 % Rotamer: Outliers : 3.58 % Allowed : 19.10 % Favored : 77.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.09 (0.19), residues: 1562 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.35 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS F 50 PHE 0.008 0.001 PHE H 94 TYR 0.014 0.002 TYR I 39 Details of bonding type rmsd hydrogen bonds : bond 0.02317 ( 289) hydrogen bonds : angle 4.55033 ( 867) covalent geometry : bond 0.00419 (11033) covalent geometry : angle 0.44749 (14905) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 207 time to evaluate : 1.273 Fit side-chains revert: symmetry clash REVERT: E 35 GLU cc_start: 0.8443 (mm-30) cc_final: 0.7921 (mm-30) REVERT: E 43 LYS cc_start: 0.8276 (mttt) cc_final: 0.7677 (mtpt) REVERT: G 35 GLU cc_start: 0.8178 (mm-30) cc_final: 0.7516 (mm-30) REVERT: I 58 LYS cc_start: 0.8298 (mtpt) cc_final: 0.7686 (mttt) REVERT: J 72 THR cc_start: 0.9151 (p) cc_final: 0.8616 (m) REVERT: J 97 LYS cc_start: 0.8412 (mtmt) cc_final: 0.8028 (mttm) REVERT: J 99 GLN cc_start: 0.7312 (mt0) cc_final: 0.7094 (mm-40) REVERT: U 43 LYS cc_start: 0.8173 (mttt) cc_final: 0.7756 (mtpt) REVERT: V 58 LYS cc_start: 0.8959 (mttt) cc_final: 0.8708 (mttt) REVERT: W 23 LYS cc_start: 0.8088 (mttt) cc_final: 0.7658 (mtmt) REVERT: W 43 LYS cc_start: 0.8416 (mttt) cc_final: 0.7989 (mtpt) REVERT: W 83 GLU cc_start: 0.8458 (tt0) cc_final: 0.8068 (mt-10) REVERT: Y 23 LYS cc_start: 0.8120 (mttt) cc_final: 0.7497 (mtpp) REVERT: Y 57 GLU cc_start: 0.8673 (tt0) cc_final: 0.8424 (tt0) REVERT: Y 58 LYS cc_start: 0.7861 (mtpt) cc_final: 0.7374 (mttt) REVERT: M 23 LYS cc_start: 0.7980 (mtpp) cc_final: 0.7348 (mptt) REVERT: O 43 LYS cc_start: 0.8506 (mttt) cc_final: 0.8050 (mttm) REVERT: P 83 GLU cc_start: 0.7696 (pt0) cc_final: 0.7452 (pt0) REVERT: Q 57 GLU cc_start: 0.8150 (tt0) cc_final: 0.7747 (tt0) REVERT: S 35 GLU cc_start: 0.8095 (mm-30) cc_final: 0.7391 (mm-30) REVERT: S 43 LYS cc_start: 0.8609 (mttt) cc_final: 0.7942 (mtpt) REVERT: S 57 GLU cc_start: 0.8162 (tt0) cc_final: 0.7928 (tt0) REVERT: T 99 GLN cc_start: 0.7631 (mt0) cc_final: 0.6992 (mm-40) outliers start: 39 outliers final: 28 residues processed: 230 average time/residue: 0.3165 time to fit residues: 99.0644 Evaluate side-chains 227 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 199 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 50 HIS Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain M residue 38 LEU Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain M residue 83 GLU Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain S residue 87 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 139 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 149 optimal weight: 4.9990 chunk 42 optimal weight: 8.9990 chunk 105 optimal weight: 7.9990 chunk 69 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 127 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS H 65 ASN J 65 ASN V 50 HIS Z 65 ASN K 79 GLN L 65 ASN N 50 HIS N 65 ASN P 50 HIS S 50 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.088339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.069465 restraints weight = 14617.073| |-----------------------------------------------------------------------------| r_work (start): 0.3026 rms_B_bonded: 2.44 r_work: 0.2882 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2735 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2735 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.067 11033 Z= 0.490 Angle : 0.677 7.881 14905 Z= 0.383 Chirality : 0.057 0.163 1936 Planarity : 0.003 0.014 1870 Dihedral : 5.629 21.259 1606 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.76 % Allowed : 18.64 % Favored : 77.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.18), residues: 1562 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.53 (0.14), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS F 50 PHE 0.013 0.003 PHE G 94 TYR 0.024 0.003 TYR I 39 Details of bonding type rmsd hydrogen bonds : bond 0.03517 ( 289) hydrogen bonds : angle 4.88056 ( 867) covalent geometry : bond 0.01148 (11033) covalent geometry : angle 0.67691 (14905) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 210 time to evaluate : 0.927 Fit side-chains REVERT: E 35 GLU cc_start: 0.8475 (mm-30) cc_final: 0.7652 (mm-30) REVERT: E 43 LYS cc_start: 0.8425 (mttt) cc_final: 0.7827 (mtpt) REVERT: G 35 GLU cc_start: 0.8225 (mm-30) cc_final: 0.7542 (mm-30) REVERT: I 58 LYS cc_start: 0.8305 (mtpt) cc_final: 0.7640 (mttp) REVERT: J 96 LYS cc_start: 0.9037 (tttt) cc_final: 0.8703 (tttm) REVERT: J 97 LYS cc_start: 0.8415 (mtmt) cc_final: 0.8023 (mttm) REVERT: U 43 LYS cc_start: 0.8213 (mttt) cc_final: 0.7771 (mtpt) REVERT: W 23 LYS cc_start: 0.8127 (mttt) cc_final: 0.7802 (mtpt) REVERT: W 43 LYS cc_start: 0.8425 (mttt) cc_final: 0.7984 (mtpt) REVERT: W 57 GLU cc_start: 0.8284 (OUTLIER) cc_final: 0.7504 (pm20) REVERT: W 83 GLU cc_start: 0.8548 (tt0) cc_final: 0.8327 (mt-10) REVERT: Y 57 GLU cc_start: 0.8799 (tt0) cc_final: 0.8533 (tt0) REVERT: Y 58 LYS cc_start: 0.7974 (mtpt) cc_final: 0.7486 (mttt) REVERT: M 23 LYS cc_start: 0.8135 (mtpp) cc_final: 0.7427 (mptt) REVERT: O 43 LYS cc_start: 0.8594 (mttt) cc_final: 0.8136 (mttm) REVERT: Q 57 GLU cc_start: 0.8255 (tt0) cc_final: 0.7854 (tt0) REVERT: S 35 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7494 (mm-30) REVERT: S 43 LYS cc_start: 0.8705 (mttt) cc_final: 0.8111 (mtpt) REVERT: S 57 GLU cc_start: 0.8191 (tt0) cc_final: 0.7985 (tt0) outliers start: 41 outliers final: 29 residues processed: 234 average time/residue: 0.2762 time to fit residues: 87.3805 Evaluate side-chains 238 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 208 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 37 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 50 HIS Chi-restraints excluded: chain J residue 59 THR Chi-restraints excluded: chain J residue 64 THR Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain V residue 72 THR Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 57 GLU Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain K residue 75 THR Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain M residue 75 THR Chi-restraints excluded: chain N residue 81 THR Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain O residue 75 THR Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain R residue 44 THR Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain R residue 81 THR Chi-restraints excluded: chain S residue 87 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 45 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 58 optimal weight: 0.8980 chunk 28 optimal weight: 5.9990 chunk 53 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 71 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 132 optimal weight: 0.7980 chunk 152 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 HIS ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS V 50 HIS W 50 HIS Z 62 GLN N 50 HIS P 50 HIS R 50 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.093684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.074995 restraints weight = 14245.922| |-----------------------------------------------------------------------------| r_work (start): 0.3128 rms_B_bonded: 2.43 r_work: 0.2986 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 4.38 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.2988 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 11033 Z= 0.101 Angle : 0.424 7.384 14905 Z= 0.240 Chirality : 0.051 0.160 1936 Planarity : 0.001 0.013 1870 Dihedral : 4.812 17.134 1606 Min Nonbonded Distance : 2.620 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.20 % Allowed : 20.11 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.19), residues: 1562 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS N 50 PHE 0.006 0.001 PHE H 94 TYR 0.011 0.001 TYR I 39 Details of bonding type rmsd hydrogen bonds : bond 0.01839 ( 289) hydrogen bonds : angle 4.41413 ( 867) covalent geometry : bond 0.00232 (11033) covalent geometry : angle 0.42353 (14905) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 204 time to evaluate : 1.735 Fit side-chains revert: symmetry clash REVERT: E 35 GLU cc_start: 0.8500 (mm-30) cc_final: 0.7966 (mm-30) REVERT: E 43 LYS cc_start: 0.8255 (mttt) cc_final: 0.7632 (mtpt) REVERT: G 35 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7563 (mm-30) REVERT: I 58 LYS cc_start: 0.8249 (mtpt) cc_final: 0.7629 (mttp) REVERT: J 72 THR cc_start: 0.9127 (p) cc_final: 0.8849 (m) REVERT: J 97 LYS cc_start: 0.8474 (mtmt) cc_final: 0.8105 (mttm) REVERT: J 99 GLN cc_start: 0.7340 (mt0) cc_final: 0.7139 (mm-40) REVERT: U 43 LYS cc_start: 0.8247 (mttt) cc_final: 0.7818 (mtpt) REVERT: W 23 LYS cc_start: 0.8004 (mttt) cc_final: 0.7561 (mtmt) REVERT: W 83 GLU cc_start: 0.8484 (tt0) cc_final: 0.8253 (mt-10) REVERT: X 96 LYS cc_start: 0.8168 (tttt) cc_final: 0.7683 (tttm) REVERT: Y 23 LYS cc_start: 0.8266 (mttp) cc_final: 0.7692 (mtpp) REVERT: Y 57 GLU cc_start: 0.8652 (tt0) cc_final: 0.8422 (tt0) REVERT: Y 58 LYS cc_start: 0.7927 (mtpt) cc_final: 0.7459 (mttt) REVERT: M 23 LYS cc_start: 0.8041 (mtpp) cc_final: 0.7378 (mptt) REVERT: O 43 LYS cc_start: 0.8525 (mttt) cc_final: 0.8058 (mttm) REVERT: P 83 GLU cc_start: 0.7750 (pt0) cc_final: 0.7535 (pt0) REVERT: Q 57 GLU cc_start: 0.8187 (tt0) cc_final: 0.7867 (tt0) REVERT: S 35 GLU cc_start: 0.8122 (mm-30) cc_final: 0.7435 (mm-30) REVERT: S 43 LYS cc_start: 0.8622 (mttt) cc_final: 0.7945 (mtpt) REVERT: S 57 GLU cc_start: 0.8086 (tt0) cc_final: 0.7866 (tt0) REVERT: T 99 GLN cc_start: 0.7733 (mt0) cc_final: 0.7138 (mm-40) outliers start: 24 outliers final: 14 residues processed: 215 average time/residue: 0.3358 time to fit residues: 97.6364 Evaluate side-chains 210 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 196 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain M residue 83 GLU Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain S residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 14 optimal weight: 7.9990 chunk 79 optimal weight: 0.0030 chunk 10 optimal weight: 0.8980 chunk 127 optimal weight: 9.9990 chunk 110 optimal weight: 7.9990 chunk 58 optimal weight: 0.8980 chunk 49 optimal weight: 9.9990 chunk 22 optimal weight: 0.0050 chunk 153 optimal weight: 3.9990 chunk 123 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 overall best weight: 1.1606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 HIS ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS V 50 HIS W 50 HIS K 50 HIS N 50 HIS P 50 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.092659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.074012 restraints weight = 14154.816| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.42 r_work: 0.2975 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.2827 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11033 Z= 0.135 Angle : 0.443 8.536 14905 Z= 0.247 Chirality : 0.051 0.167 1936 Planarity : 0.001 0.010 1870 Dihedral : 4.732 15.600 1606 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % Rotamer: Outliers : 2.02 % Allowed : 20.29 % Favored : 77.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.04 (0.19), residues: 1562 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.31 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS F 50 PHE 0.007 0.001 PHE H 94 TYR 0.016 0.002 TYR E 39 Details of bonding type rmsd hydrogen bonds : bond 0.01980 ( 289) hydrogen bonds : angle 4.39799 ( 867) covalent geometry : bond 0.00314 (11033) covalent geometry : angle 0.44292 (14905) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3124 Ramachandran restraints generated. 1562 Oldfield, 0 Emsley, 1562 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 191 time to evaluate : 1.217 Fit side-chains revert: symmetry clash REVERT: E 35 GLU cc_start: 0.8488 (mm-30) cc_final: 0.7945 (mm-30) REVERT: E 43 LYS cc_start: 0.8287 (mttt) cc_final: 0.7654 (mtpt) REVERT: G 35 GLU cc_start: 0.8206 (mm-30) cc_final: 0.7564 (mm-30) REVERT: I 58 LYS cc_start: 0.8264 (mtpt) cc_final: 0.7688 (mttt) REVERT: J 72 THR cc_start: 0.9110 (p) cc_final: 0.8843 (m) REVERT: J 97 LYS cc_start: 0.8485 (mtmt) cc_final: 0.8107 (mttm) REVERT: J 99 GLN cc_start: 0.7321 (mt0) cc_final: 0.7111 (mm-40) REVERT: U 43 LYS cc_start: 0.8257 (mttt) cc_final: 0.7829 (mtpt) REVERT: W 23 LYS cc_start: 0.8016 (mttt) cc_final: 0.7563 (mtmt) REVERT: W 83 GLU cc_start: 0.8452 (tt0) cc_final: 0.8223 (mt-10) REVERT: Y 23 LYS cc_start: 0.8307 (mttp) cc_final: 0.7716 (mtpp) REVERT: Y 57 GLU cc_start: 0.8623 (tt0) cc_final: 0.8363 (tt0) REVERT: M 23 LYS cc_start: 0.8036 (mtpp) cc_final: 0.7377 (mptt) REVERT: O 43 LYS cc_start: 0.8559 (mttt) cc_final: 0.8116 (mttm) REVERT: P 83 GLU cc_start: 0.7718 (pt0) cc_final: 0.7492 (pt0) REVERT: Q 57 GLU cc_start: 0.8242 (tt0) cc_final: 0.7922 (tt0) REVERT: S 35 GLU cc_start: 0.8107 (mm-30) cc_final: 0.7415 (mm-30) REVERT: S 43 LYS cc_start: 0.8637 (mttt) cc_final: 0.7992 (mtpt) REVERT: S 57 GLU cc_start: 0.8119 (tt0) cc_final: 0.7878 (tt0) REVERT: T 99 GLN cc_start: 0.7763 (mt0) cc_final: 0.7105 (mm-40) outliers start: 22 outliers final: 16 residues processed: 201 average time/residue: 0.2707 time to fit residues: 73.7587 Evaluate side-chains 205 residues out of total 1089 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 189 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 87 SER Chi-restraints excluded: chain U residue 75 THR Chi-restraints excluded: chain U residue 81 THR Chi-restraints excluded: chain W residue 33 THR Chi-restraints excluded: chain W residue 75 THR Chi-restraints excluded: chain Y residue 75 THR Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain K residue 50 HIS Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain M residue 83 GLU Chi-restraints excluded: chain O residue 38 LEU Chi-restraints excluded: chain O residue 57 GLU Chi-restraints excluded: chain Q residue 33 THR Chi-restraints excluded: chain Q residue 75 THR Chi-restraints excluded: chain R residue 64 THR Chi-restraints excluded: chain S residue 87 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 154 random chunks: chunk 18 optimal weight: 10.0000 chunk 103 optimal weight: 0.0570 chunk 58 optimal weight: 0.0070 chunk 146 optimal weight: 1.9990 chunk 91 optimal weight: 8.9990 chunk 26 optimal weight: 5.9990 chunk 114 optimal weight: 6.9990 chunk 87 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 56 optimal weight: 8.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.6918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 50 HIS ** G 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 HIS V 50 HIS W 50 HIS K 50 HIS N 50 HIS P 50 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.093815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.075197 restraints weight = 14128.861| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.43 r_work: 0.3016 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 11033 Z= 0.095 Angle : 0.410 7.833 14905 Z= 0.231 Chirality : 0.051 0.130 1936 Planarity : 0.001 0.009 1870 Dihedral : 4.535 14.667 1606 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.11 % Allowed : 20.39 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.19), residues: 1562 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.15), residues: 1562 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS F 50 PHE 0.006 0.001 PHE H 94 TYR 0.013 0.002 TYR I 39 Details of bonding type rmsd hydrogen bonds : bond 0.01642 ( 289) hydrogen bonds : angle 4.22533 ( 867) covalent geometry : bond 0.00218 (11033) covalent geometry : angle 0.40957 (14905) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6355.21 seconds wall clock time: 114 minutes 16.48 seconds (6856.48 seconds total)