Starting phenix.real_space_refine on Thu Feb 5 17:50:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ic7_52833/02_2026/9ic7_52833.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ic7_52833/02_2026/9ic7_52833.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ic7_52833/02_2026/9ic7_52833.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ic7_52833/02_2026/9ic7_52833.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ic7_52833/02_2026/9ic7_52833.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ic7_52833/02_2026/9ic7_52833.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 28 5.16 5 C 6048 2.51 5 N 1680 2.21 5 O 1932 1.98 5 H 9422 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 19110 Number of models: 1 Model: "" Number of chains: 1 Chain: "n" Number of atoms: 1365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1365 Classifications: {'peptide': 99} Link IDs: {'TRANS': 98} Restraints were copied for chains: a, b, c, d, e, f, g, h, i, j, k, l, m Time building chain proxies: 1.37, per 1000 atoms: 0.07 Number of scatterers: 19110 At special positions: 0 Unit cell: (97.266, 137.982, 55.796, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 28 16.00 O 1932 8.00 N 1680 7.00 C 6048 6.00 H 9422 1.00 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: 1.70 Conformation dependent library (CDL) restraints added in 590.9 milliseconds 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2380 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 68.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'n' and resid 3 through 10 removed outlier: 6.486A pdb=" N VAL n 3 " --> pdb=" O PHE m 4 " (cutoff:3.500A) removed outlier: 8.347A pdb=" N LYS m 6 " --> pdb=" O VAL n 3 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N MET n 5 " --> pdb=" O LYS m 6 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N LEU m 8 " --> pdb=" O MET n 5 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N GLY n 7 " --> pdb=" O LEU m 8 " (cutoff:3.500A) removed outlier: 9.484A pdb=" N LYS m 10 " --> pdb=" O GLY n 7 " (cutoff:3.500A) removed outlier: 5.902A pdb=" N SER n 9 " --> pdb=" O LYS m 10 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY m 7 " --> pdb=" O LYS l 6 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU l 8 " --> pdb=" O GLY m 7 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER m 9 " --> pdb=" O LEU l 8 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY l 7 " --> pdb=" O LYS k 6 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU k 8 " --> pdb=" O GLY l 7 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER l 9 " --> pdb=" O LEU k 8 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY k 7 " --> pdb=" O LYS j 6 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU j 8 " --> pdb=" O GLY k 7 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER k 9 " --> pdb=" O LEU j 8 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY j 7 " --> pdb=" O LYS i 6 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU i 8 " --> pdb=" O GLY j 7 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER j 9 " --> pdb=" O LEU i 8 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY i 7 " --> pdb=" O LYS h 6 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU h 8 " --> pdb=" O GLY i 7 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER i 9 " --> pdb=" O LEU h 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'n' and resid 13 through 24 removed outlier: 6.975A pdb=" N THR n 22 " --> pdb=" O LYS m 21 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LYS m 23 " --> pdb=" O THR n 22 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N GLN n 24 " --> pdb=" O LYS m 23 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU l 13 " --> pdb=" O GLY m 14 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N VAL m 16 " --> pdb=" O GLU l 13 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL l 15 " --> pdb=" O VAL m 16 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ALA m 18 " --> pdb=" O VAL l 15 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA l 17 " --> pdb=" O ALA m 18 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N GLU m 20 " --> pdb=" O ALA l 17 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA l 19 " --> pdb=" O GLU m 20 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR m 22 " --> pdb=" O ALA l 19 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LYS l 21 " --> pdb=" O THR m 22 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N GLN m 24 " --> pdb=" O LYS l 21 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N LYS l 23 " --> pdb=" O GLN m 24 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU k 13 " --> pdb=" O GLY l 14 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N VAL l 16 " --> pdb=" O GLU k 13 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL k 15 " --> pdb=" O VAL l 16 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ALA l 18 " --> pdb=" O VAL k 15 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA k 17 " --> pdb=" O ALA l 18 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N GLU l 20 " --> pdb=" O ALA k 17 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA k 19 " --> pdb=" O GLU l 20 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR l 22 " --> pdb=" O ALA k 19 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LYS k 21 " --> pdb=" O THR l 22 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N GLN l 24 " --> pdb=" O LYS k 21 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N LYS k 23 " --> pdb=" O GLN l 24 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU j 13 " --> pdb=" O GLY k 14 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N VAL k 16 " --> pdb=" O GLU j 13 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL j 15 " --> pdb=" O VAL k 16 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ALA k 18 " --> pdb=" O VAL j 15 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA j 17 " --> pdb=" O ALA k 18 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N GLU k 20 " --> pdb=" O ALA j 17 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA j 19 " --> pdb=" O GLU k 20 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR k 22 " --> pdb=" O ALA j 19 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LYS j 21 " --> pdb=" O THR k 22 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N GLN k 24 " --> pdb=" O LYS j 21 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N LYS j 23 " --> pdb=" O GLN k 24 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU i 13 " --> pdb=" O GLY j 14 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N VAL j 16 " --> pdb=" O GLU i 13 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL i 15 " --> pdb=" O VAL j 16 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ALA j 18 " --> pdb=" O VAL i 15 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA i 17 " --> pdb=" O ALA j 18 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N GLU j 20 " --> pdb=" O ALA i 17 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA i 19 " --> pdb=" O GLU j 20 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR j 22 " --> pdb=" O ALA i 19 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LYS i 21 " --> pdb=" O THR j 22 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N GLN j 24 " --> pdb=" O LYS i 21 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N LYS i 23 " --> pdb=" O GLN j 24 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU h 13 " --> pdb=" O GLY i 14 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N VAL i 16 " --> pdb=" O GLU h 13 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL h 15 " --> pdb=" O VAL i 16 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ALA i 18 " --> pdb=" O VAL h 15 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA h 17 " --> pdb=" O ALA i 18 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N GLU i 20 " --> pdb=" O ALA h 17 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA h 19 " --> pdb=" O GLU i 20 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR i 22 " --> pdb=" O ALA h 19 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LYS h 21 " --> pdb=" O THR i 22 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N GLN i 24 " --> pdb=" O LYS h 21 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N LYS h 23 " --> pdb=" O GLN i 24 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'n' and resid 27 through 40 removed outlier: 7.072A pdb=" N GLU m 28 " --> pdb=" O ALA n 27 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ALA n 29 " --> pdb=" O GLU m 28 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ALA m 30 " --> pdb=" O ALA n 29 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N GLY n 31 " --> pdb=" O ALA m 30 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N VAL n 37 " --> pdb=" O GLY m 36 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU m 38 " --> pdb=" O VAL n 37 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N TYR n 39 " --> pdb=" O LEU m 38 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL m 40 " --> pdb=" O TYR n 39 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N GLU l 28 " --> pdb=" O ALA m 29 " (cutoff:3.500A) removed outlier: 10.726A pdb=" N GLY m 31 " --> pdb=" O GLU l 28 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA l 30 " --> pdb=" O GLY m 31 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N THR m 33 " --> pdb=" O ALA l 30 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS l 32 " --> pdb=" O THR m 33 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLU m 35 " --> pdb=" O LYS l 32 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS l 34 " --> pdb=" O GLU m 35 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL m 37 " --> pdb=" O LYS l 34 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N GLY l 36 " --> pdb=" O VAL m 37 " (cutoff:3.500A) removed outlier: 10.492A pdb=" N TYR m 39 " --> pdb=" O GLY l 36 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N LEU l 38 " --> pdb=" O TYR m 39 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N GLU k 28 " --> pdb=" O ALA l 29 " (cutoff:3.500A) removed outlier: 10.726A pdb=" N GLY l 31 " --> pdb=" O GLU k 28 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA k 30 " --> pdb=" O GLY l 31 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N THR l 33 " --> pdb=" O ALA k 30 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS k 32 " --> pdb=" O THR l 33 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N GLU l 35 " --> pdb=" O LYS k 32 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS k 34 " --> pdb=" O GLU l 35 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL l 37 " --> pdb=" O LYS k 34 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N GLY k 36 " --> pdb=" O VAL l 37 " (cutoff:3.500A) removed outlier: 10.492A pdb=" N TYR l 39 " --> pdb=" O GLY k 36 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N LEU k 38 " --> pdb=" O TYR l 39 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N GLU j 28 " --> pdb=" O ALA k 29 " (cutoff:3.500A) removed outlier: 10.726A pdb=" N GLY k 31 " --> pdb=" O GLU j 28 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA j 30 " --> pdb=" O GLY k 31 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N THR k 33 " --> pdb=" O ALA j 30 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS j 32 " --> pdb=" O THR k 33 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLU k 35 " --> pdb=" O LYS j 32 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS j 34 " --> pdb=" O GLU k 35 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL k 37 " --> pdb=" O LYS j 34 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N GLY j 36 " --> pdb=" O VAL k 37 " (cutoff:3.500A) removed outlier: 10.492A pdb=" N TYR k 39 " --> pdb=" O GLY j 36 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N LEU j 38 " --> pdb=" O TYR k 39 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N GLU i 28 " --> pdb=" O ALA j 29 " (cutoff:3.500A) removed outlier: 10.725A pdb=" N GLY j 31 " --> pdb=" O GLU i 28 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA i 30 " --> pdb=" O GLY j 31 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N THR j 33 " --> pdb=" O ALA i 30 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS i 32 " --> pdb=" O THR j 33 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLU j 35 " --> pdb=" O LYS i 32 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS i 34 " --> pdb=" O GLU j 35 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL j 37 " --> pdb=" O LYS i 34 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N GLY i 36 " --> pdb=" O VAL j 37 " (cutoff:3.500A) removed outlier: 10.492A pdb=" N TYR j 39 " --> pdb=" O GLY i 36 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N LEU i 38 " --> pdb=" O TYR j 39 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N GLU h 28 " --> pdb=" O ALA i 29 " (cutoff:3.500A) removed outlier: 10.725A pdb=" N GLY i 31 " --> pdb=" O GLU h 28 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA h 30 " --> pdb=" O GLY i 31 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N THR i 33 " --> pdb=" O ALA h 30 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS h 32 " --> pdb=" O THR i 33 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLU i 35 " --> pdb=" O LYS h 32 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS h 34 " --> pdb=" O GLU i 35 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL i 37 " --> pdb=" O LYS h 34 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N GLY h 36 " --> pdb=" O VAL i 37 " (cutoff:3.500A) removed outlier: 10.492A pdb=" N TYR i 39 " --> pdb=" O GLY h 36 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N LEU h 38 " --> pdb=" O TYR i 39 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'n' and resid 45 through 58 removed outlier: 6.889A pdb=" N VAL m 48 " --> pdb=" O GLY n 47 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N VAL n 49 " --> pdb=" O VAL m 48 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N HIS m 50 " --> pdb=" O VAL n 49 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LYS m 58 " --> pdb=" O GLU n 57 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLU l 46 " --> pdb=" O GLY m 47 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N VAL m 49 " --> pdb=" O GLU l 46 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N VAL l 48 " --> pdb=" O VAL m 49 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N GLY m 51 " --> pdb=" O VAL l 48 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS l 50 " --> pdb=" O GLY m 51 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ALA m 53 " --> pdb=" O HIS l 50 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL l 52 " --> pdb=" O ALA m 53 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL m 55 " --> pdb=" O VAL l 52 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N THR l 54 " --> pdb=" O VAL m 55 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLU m 57 " --> pdb=" O THR l 54 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N ALA l 56 " --> pdb=" O GLU m 57 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLU k 46 " --> pdb=" O GLY l 47 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N VAL l 49 " --> pdb=" O GLU k 46 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N VAL k 48 " --> pdb=" O VAL l 49 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N GLY l 51 " --> pdb=" O VAL k 48 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS k 50 " --> pdb=" O GLY l 51 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ALA l 53 " --> pdb=" O HIS k 50 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL k 52 " --> pdb=" O ALA l 53 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL l 55 " --> pdb=" O VAL k 52 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N THR k 54 " --> pdb=" O VAL l 55 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLU l 57 " --> pdb=" O THR k 54 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N ALA k 56 " --> pdb=" O GLU l 57 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLU j 46 " --> pdb=" O GLY k 47 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N VAL k 49 " --> pdb=" O GLU j 46 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N VAL j 48 " --> pdb=" O VAL k 49 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N GLY k 51 " --> pdb=" O VAL j 48 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N HIS j 50 " --> pdb=" O GLY k 51 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N ALA k 53 " --> pdb=" O HIS j 50 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL j 52 " --> pdb=" O ALA k 53 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL k 55 " --> pdb=" O VAL j 52 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N THR j 54 " --> pdb=" O VAL k 55 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLU k 57 " --> pdb=" O THR j 54 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N ALA j 56 " --> pdb=" O GLU k 57 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLU i 46 " --> pdb=" O GLY j 47 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N VAL j 49 " --> pdb=" O GLU i 46 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N VAL i 48 " --> pdb=" O VAL j 49 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N GLY j 51 " --> pdb=" O VAL i 48 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS i 50 " --> pdb=" O GLY j 51 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ALA j 53 " --> pdb=" O HIS i 50 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL i 52 " --> pdb=" O ALA j 53 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL j 55 " --> pdb=" O VAL i 52 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N THR i 54 " --> pdb=" O VAL j 55 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLU j 57 " --> pdb=" O THR i 54 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N ALA i 56 " --> pdb=" O GLU j 57 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLU h 46 " --> pdb=" O GLY i 47 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N VAL i 49 " --> pdb=" O GLU h 46 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N VAL h 48 " --> pdb=" O VAL i 49 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N GLY i 51 " --> pdb=" O VAL h 48 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS h 50 " --> pdb=" O GLY i 51 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ALA i 53 " --> pdb=" O HIS h 50 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL h 52 " --> pdb=" O ALA i 53 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL i 55 " --> pdb=" O VAL h 52 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N THR h 54 " --> pdb=" O VAL i 55 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLU i 57 " --> pdb=" O THR h 54 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N ALA h 56 " --> pdb=" O GLU i 57 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'n' and resid 65 through 79 removed outlier: 6.681A pdb=" N ASN n 65 " --> pdb=" O VAL m 66 " (cutoff:3.500A) removed outlier: 8.509A pdb=" N GLY m 68 " --> pdb=" O ASN n 65 " (cutoff:3.500A) removed outlier: 9.103A pdb=" N GLY n 67 " --> pdb=" O GLY m 68 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N VAL m 70 " --> pdb=" O GLY n 67 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N ALA n 69 " --> pdb=" O VAL m 70 " (cutoff:3.500A) removed outlier: 10.427A pdb=" N THR m 72 " --> pdb=" O ALA n 69 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N VAL n 71 " --> pdb=" O THR m 72 " (cutoff:3.500A) removed outlier: 9.450A pdb=" N VAL m 74 " --> pdb=" O VAL n 71 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLY n 73 " --> pdb=" O VAL m 74 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ALA m 76 " --> pdb=" O GLY n 73 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N THR n 75 " --> pdb=" O ALA m 76 " (cutoff:3.500A) removed outlier: 8.696A pdb=" N ALA m 78 " --> pdb=" O THR n 75 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL n 77 " --> pdb=" O ALA m 78 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA m 69 " --> pdb=" O GLY l 68 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL l 70 " --> pdb=" O ALA m 69 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL m 71 " --> pdb=" O VAL l 70 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR l 72 " --> pdb=" O VAL m 71 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY m 73 " --> pdb=" O THR l 72 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA l 69 " --> pdb=" O GLY k 68 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL k 70 " --> pdb=" O ALA l 69 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL l 71 " --> pdb=" O VAL k 70 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR k 72 " --> pdb=" O VAL l 71 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY l 73 " --> pdb=" O THR k 72 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA k 69 " --> pdb=" O GLY j 68 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL j 70 " --> pdb=" O ALA k 69 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL k 71 " --> pdb=" O VAL j 70 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR j 72 " --> pdb=" O VAL k 71 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY k 73 " --> pdb=" O THR j 72 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA j 69 " --> pdb=" O GLY i 68 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL i 70 " --> pdb=" O ALA j 69 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL j 71 " --> pdb=" O VAL i 70 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR i 72 " --> pdb=" O VAL j 71 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY j 73 " --> pdb=" O THR i 72 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA i 69 " --> pdb=" O GLY h 68 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL h 70 " --> pdb=" O ALA i 69 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL i 71 " --> pdb=" O VAL h 70 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR h 72 " --> pdb=" O VAL i 71 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY i 73 " --> pdb=" O THR h 72 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'n' and resid 88 through 98 removed outlier: 7.122A pdb=" N ALA n 89 " --> pdb=" O ILE m 88 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ALA m 90 " --> pdb=" O ALA n 89 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N ALA n 91 " --> pdb=" O ALA m 90 " (cutoff:3.500A) removed outlier: 7.120A pdb=" N THR m 92 " --> pdb=" O ALA n 91 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N GLY n 93 " --> pdb=" O THR m 92 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ASP m 98 " --> pdb=" O LYS n 97 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N ILE l 88 " --> pdb=" O ALA m 89 " (cutoff:3.500A) removed outlier: 10.386A pdb=" N ALA m 91 " --> pdb=" O ILE l 88 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N ALA l 90 " --> pdb=" O ALA m 91 " (cutoff:3.500A) removed outlier: 10.466A pdb=" N GLY m 93 " --> pdb=" O ALA l 90 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR l 92 " --> pdb=" O GLY m 93 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N VAL m 95 " --> pdb=" O THR l 92 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE l 94 " --> pdb=" O VAL m 95 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LYS m 97 " --> pdb=" O PHE l 94 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LYS l 96 " --> pdb=" O LYS m 97 " (cutoff:3.500A) removed outlier: 9.329A pdb=" N ILE k 88 " --> pdb=" O ALA l 89 " (cutoff:3.500A) removed outlier: 10.386A pdb=" N ALA l 91 " --> pdb=" O ILE k 88 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N ALA k 90 " --> pdb=" O ALA l 91 " (cutoff:3.500A) removed outlier: 10.466A pdb=" N GLY l 93 " --> pdb=" O ALA k 90 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR k 92 " --> pdb=" O GLY l 93 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N VAL l 95 " --> pdb=" O THR k 92 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE k 94 " --> pdb=" O VAL l 95 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LYS l 97 " --> pdb=" O PHE k 94 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LYS k 96 " --> pdb=" O LYS l 97 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N ILE j 88 " --> pdb=" O ALA k 89 " (cutoff:3.500A) removed outlier: 10.386A pdb=" N ALA k 91 " --> pdb=" O ILE j 88 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N ALA j 90 " --> pdb=" O ALA k 91 " (cutoff:3.500A) removed outlier: 10.466A pdb=" N GLY k 93 " --> pdb=" O ALA j 90 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR j 92 " --> pdb=" O GLY k 93 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N VAL k 95 " --> pdb=" O THR j 92 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE j 94 " --> pdb=" O VAL k 95 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LYS k 97 " --> pdb=" O PHE j 94 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LYS j 96 " --> pdb=" O LYS k 97 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N ILE i 88 " --> pdb=" O ALA j 89 " (cutoff:3.500A) removed outlier: 10.386A pdb=" N ALA j 91 " --> pdb=" O ILE i 88 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N ALA i 90 " --> pdb=" O ALA j 91 " (cutoff:3.500A) removed outlier: 10.466A pdb=" N GLY j 93 " --> pdb=" O ALA i 90 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR i 92 " --> pdb=" O GLY j 93 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N VAL j 95 " --> pdb=" O THR i 92 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE i 94 " --> pdb=" O VAL j 95 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LYS j 97 " --> pdb=" O PHE i 94 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LYS i 96 " --> pdb=" O LYS j 97 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N ILE h 88 " --> pdb=" O ALA i 89 " (cutoff:3.500A) removed outlier: 10.386A pdb=" N ALA i 91 " --> pdb=" O ILE h 88 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N ALA h 90 " --> pdb=" O ALA i 91 " (cutoff:3.500A) removed outlier: 10.466A pdb=" N GLY i 93 " --> pdb=" O ALA h 90 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR h 92 " --> pdb=" O GLY i 93 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N VAL i 95 " --> pdb=" O THR h 92 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE h 94 " --> pdb=" O VAL i 95 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LYS i 97 " --> pdb=" O PHE h 94 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LYS h 96 " --> pdb=" O LYS i 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'a' and resid 3 through 10 removed outlier: 6.837A pdb=" N GLY b 7 " --> pdb=" O LYS a 6 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU a 8 " --> pdb=" O GLY b 7 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER b 9 " --> pdb=" O LEU a 8 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY c 7 " --> pdb=" O LYS b 6 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU b 8 " --> pdb=" O GLY c 7 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER c 9 " --> pdb=" O LEU b 8 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY d 7 " --> pdb=" O LYS c 6 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU c 8 " --> pdb=" O GLY d 7 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER d 9 " --> pdb=" O LEU c 8 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY e 7 " --> pdb=" O LYS d 6 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU d 8 " --> pdb=" O GLY e 7 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER e 9 " --> pdb=" O LEU d 8 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY f 7 " --> pdb=" O LYS e 6 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU e 8 " --> pdb=" O GLY f 7 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER f 9 " --> pdb=" O LEU e 8 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N GLY g 7 " --> pdb=" O LYS f 6 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N LEU f 8 " --> pdb=" O GLY g 7 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N SER g 9 " --> pdb=" O LEU f 8 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'a' and resid 13 through 24 removed outlier: 6.634A pdb=" N GLU a 13 " --> pdb=" O GLY b 14 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N VAL b 16 " --> pdb=" O GLU a 13 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL a 15 " --> pdb=" O VAL b 16 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ALA b 18 " --> pdb=" O VAL a 15 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA a 17 " --> pdb=" O ALA b 18 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N GLU b 20 " --> pdb=" O ALA a 17 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA a 19 " --> pdb=" O GLU b 20 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR b 22 " --> pdb=" O ALA a 19 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LYS a 21 " --> pdb=" O THR b 22 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N GLN b 24 " --> pdb=" O LYS a 21 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N LYS a 23 " --> pdb=" O GLN b 24 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU b 13 " --> pdb=" O GLY c 14 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N VAL c 16 " --> pdb=" O GLU b 13 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL b 15 " --> pdb=" O VAL c 16 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ALA c 18 " --> pdb=" O VAL b 15 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA b 17 " --> pdb=" O ALA c 18 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N GLU c 20 " --> pdb=" O ALA b 17 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA b 19 " --> pdb=" O GLU c 20 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N THR c 22 " --> pdb=" O ALA b 19 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LYS b 21 " --> pdb=" O THR c 22 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N GLN c 24 " --> pdb=" O LYS b 21 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N LYS b 23 " --> pdb=" O GLN c 24 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU c 13 " --> pdb=" O GLY d 14 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N VAL d 16 " --> pdb=" O GLU c 13 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL c 15 " --> pdb=" O VAL d 16 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ALA d 18 " --> pdb=" O VAL c 15 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA c 17 " --> pdb=" O ALA d 18 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N GLU d 20 " --> pdb=" O ALA c 17 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA c 19 " --> pdb=" O GLU d 20 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR d 22 " --> pdb=" O ALA c 19 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LYS c 21 " --> pdb=" O THR d 22 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N GLN d 24 " --> pdb=" O LYS c 21 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N LYS c 23 " --> pdb=" O GLN d 24 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU d 13 " --> pdb=" O GLY e 14 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N VAL e 16 " --> pdb=" O GLU d 13 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL d 15 " --> pdb=" O VAL e 16 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ALA e 18 " --> pdb=" O VAL d 15 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA d 17 " --> pdb=" O ALA e 18 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N GLU e 20 " --> pdb=" O ALA d 17 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA d 19 " --> pdb=" O GLU e 20 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR e 22 " --> pdb=" O ALA d 19 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LYS d 21 " --> pdb=" O THR e 22 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N GLN e 24 " --> pdb=" O LYS d 21 " (cutoff:3.500A) removed outlier: 9.283A pdb=" N LYS d 23 " --> pdb=" O GLN e 24 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLU e 13 " --> pdb=" O GLY f 14 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N VAL f 16 " --> pdb=" O GLU e 13 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL e 15 " --> pdb=" O VAL f 16 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N ALA f 18 " --> pdb=" O VAL e 15 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA e 17 " --> pdb=" O ALA f 18 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N GLU f 20 " --> pdb=" O ALA e 17 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ALA e 19 " --> pdb=" O GLU f 20 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR f 22 " --> pdb=" O ALA e 19 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LYS e 21 " --> pdb=" O THR f 22 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N GLN f 24 " --> pdb=" O LYS e 21 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N LYS e 23 " --> pdb=" O GLN f 24 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU f 13 " --> pdb=" O GLY g 14 " (cutoff:3.500A) removed outlier: 8.320A pdb=" N VAL g 16 " --> pdb=" O GLU f 13 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N VAL f 15 " --> pdb=" O VAL g 16 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N ALA g 18 " --> pdb=" O VAL f 15 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ALA f 17 " --> pdb=" O ALA g 18 " (cutoff:3.500A) removed outlier: 8.493A pdb=" N GLU g 20 " --> pdb=" O ALA f 17 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ALA f 19 " --> pdb=" O GLU g 20 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N THR g 22 " --> pdb=" O ALA f 19 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N LYS f 21 " --> pdb=" O THR g 22 " (cutoff:3.500A) removed outlier: 9.835A pdb=" N GLN g 24 " --> pdb=" O LYS f 21 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N LYS f 23 " --> pdb=" O GLN g 24 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'a' and resid 27 through 40 removed outlier: 8.971A pdb=" N GLU a 28 " --> pdb=" O ALA b 29 " (cutoff:3.500A) removed outlier: 10.725A pdb=" N GLY b 31 " --> pdb=" O GLU a 28 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA a 30 " --> pdb=" O GLY b 31 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N THR b 33 " --> pdb=" O ALA a 30 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS a 32 " --> pdb=" O THR b 33 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLU b 35 " --> pdb=" O LYS a 32 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS a 34 " --> pdb=" O GLU b 35 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL b 37 " --> pdb=" O LYS a 34 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N GLY a 36 " --> pdb=" O VAL b 37 " (cutoff:3.500A) removed outlier: 10.492A pdb=" N TYR b 39 " --> pdb=" O GLY a 36 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N LEU a 38 " --> pdb=" O TYR b 39 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N GLU b 28 " --> pdb=" O ALA c 29 " (cutoff:3.500A) removed outlier: 10.725A pdb=" N GLY c 31 " --> pdb=" O GLU b 28 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA b 30 " --> pdb=" O GLY c 31 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N THR c 33 " --> pdb=" O ALA b 30 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS b 32 " --> pdb=" O THR c 33 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLU c 35 " --> pdb=" O LYS b 32 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS b 34 " --> pdb=" O GLU c 35 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL c 37 " --> pdb=" O LYS b 34 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N GLY b 36 " --> pdb=" O VAL c 37 " (cutoff:3.500A) removed outlier: 10.492A pdb=" N TYR c 39 " --> pdb=" O GLY b 36 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N LEU b 38 " --> pdb=" O TYR c 39 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N GLU c 28 " --> pdb=" O ALA d 29 " (cutoff:3.500A) removed outlier: 10.726A pdb=" N GLY d 31 " --> pdb=" O GLU c 28 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA c 30 " --> pdb=" O GLY d 31 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N THR d 33 " --> pdb=" O ALA c 30 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N LYS c 32 " --> pdb=" O THR d 33 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLU d 35 " --> pdb=" O LYS c 32 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS c 34 " --> pdb=" O GLU d 35 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL d 37 " --> pdb=" O LYS c 34 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N GLY c 36 " --> pdb=" O VAL d 37 " (cutoff:3.500A) removed outlier: 10.492A pdb=" N TYR d 39 " --> pdb=" O GLY c 36 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N LEU c 38 " --> pdb=" O TYR d 39 " (cutoff:3.500A) removed outlier: 8.972A pdb=" N GLU d 28 " --> pdb=" O ALA e 29 " (cutoff:3.500A) removed outlier: 10.726A pdb=" N GLY e 31 " --> pdb=" O GLU d 28 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA d 30 " --> pdb=" O GLY e 31 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N THR e 33 " --> pdb=" O ALA d 30 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS d 32 " --> pdb=" O THR e 33 " (cutoff:3.500A) removed outlier: 8.264A pdb=" N GLU e 35 " --> pdb=" O LYS d 32 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS d 34 " --> pdb=" O GLU e 35 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL e 37 " --> pdb=" O LYS d 34 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N GLY d 36 " --> pdb=" O VAL e 37 " (cutoff:3.500A) removed outlier: 10.492A pdb=" N TYR e 39 " --> pdb=" O GLY d 36 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N LEU d 38 " --> pdb=" O TYR e 39 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N GLU e 28 " --> pdb=" O ALA f 29 " (cutoff:3.500A) removed outlier: 10.726A pdb=" N GLY f 31 " --> pdb=" O GLU e 28 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N ALA e 30 " --> pdb=" O GLY f 31 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N THR f 33 " --> pdb=" O ALA e 30 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS e 32 " --> pdb=" O THR f 33 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLU f 35 " --> pdb=" O LYS e 32 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS e 34 " --> pdb=" O GLU f 35 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL f 37 " --> pdb=" O LYS e 34 " (cutoff:3.500A) removed outlier: 7.869A pdb=" N GLY e 36 " --> pdb=" O VAL f 37 " (cutoff:3.500A) removed outlier: 10.492A pdb=" N TYR f 39 " --> pdb=" O GLY e 36 " (cutoff:3.500A) removed outlier: 9.192A pdb=" N LEU e 38 " --> pdb=" O TYR f 39 " (cutoff:3.500A) removed outlier: 8.971A pdb=" N GLU f 28 " --> pdb=" O ALA g 29 " (cutoff:3.500A) removed outlier: 10.726A pdb=" N GLY g 31 " --> pdb=" O GLU f 28 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ALA f 30 " --> pdb=" O GLY g 31 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N THR g 33 " --> pdb=" O ALA f 30 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LYS f 32 " --> pdb=" O THR g 33 " (cutoff:3.500A) removed outlier: 8.263A pdb=" N GLU g 35 " --> pdb=" O LYS f 32 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N LYS f 34 " --> pdb=" O GLU g 35 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N VAL g 37 " --> pdb=" O LYS f 34 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N GLY f 36 " --> pdb=" O VAL g 37 " (cutoff:3.500A) removed outlier: 10.493A pdb=" N TYR g 39 " --> pdb=" O GLY f 36 " (cutoff:3.500A) removed outlier: 9.193A pdb=" N LEU f 38 " --> pdb=" O TYR g 39 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'a' and resid 45 through 58 removed outlier: 8.611A pdb=" N GLU a 46 " --> pdb=" O GLY b 47 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N VAL b 49 " --> pdb=" O GLU a 46 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N VAL a 48 " --> pdb=" O VAL b 49 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N GLY b 51 " --> pdb=" O VAL a 48 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS a 50 " --> pdb=" O GLY b 51 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ALA b 53 " --> pdb=" O HIS a 50 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL a 52 " --> pdb=" O ALA b 53 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL b 55 " --> pdb=" O VAL a 52 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N THR a 54 " --> pdb=" O VAL b 55 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLU b 57 " --> pdb=" O THR a 54 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N ALA a 56 " --> pdb=" O GLU b 57 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLU b 46 " --> pdb=" O GLY c 47 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N VAL c 49 " --> pdb=" O GLU b 46 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N VAL b 48 " --> pdb=" O VAL c 49 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N GLY c 51 " --> pdb=" O VAL b 48 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS b 50 " --> pdb=" O GLY c 51 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ALA c 53 " --> pdb=" O HIS b 50 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL b 52 " --> pdb=" O ALA c 53 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL c 55 " --> pdb=" O VAL b 52 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N THR b 54 " --> pdb=" O VAL c 55 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLU c 57 " --> pdb=" O THR b 54 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N ALA b 56 " --> pdb=" O GLU c 57 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLU c 46 " --> pdb=" O GLY d 47 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N VAL d 49 " --> pdb=" O GLU c 46 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N VAL c 48 " --> pdb=" O VAL d 49 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N GLY d 51 " --> pdb=" O VAL c 48 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N HIS c 50 " --> pdb=" O GLY d 51 " (cutoff:3.500A) removed outlier: 8.336A pdb=" N ALA d 53 " --> pdb=" O HIS c 50 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL c 52 " --> pdb=" O ALA d 53 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL d 55 " --> pdb=" O VAL c 52 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N THR c 54 " --> pdb=" O VAL d 55 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLU d 57 " --> pdb=" O THR c 54 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N ALA c 56 " --> pdb=" O GLU d 57 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLU d 46 " --> pdb=" O GLY e 47 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N VAL e 49 " --> pdb=" O GLU d 46 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N VAL d 48 " --> pdb=" O VAL e 49 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N GLY e 51 " --> pdb=" O VAL d 48 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS d 50 " --> pdb=" O GLY e 51 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ALA e 53 " --> pdb=" O HIS d 50 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL d 52 " --> pdb=" O ALA e 53 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL e 55 " --> pdb=" O VAL d 52 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N THR d 54 " --> pdb=" O VAL e 55 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLU e 57 " --> pdb=" O THR d 54 " (cutoff:3.500A) removed outlier: 8.868A pdb=" N ALA d 56 " --> pdb=" O GLU e 57 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLU e 46 " --> pdb=" O GLY f 47 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N VAL f 49 " --> pdb=" O GLU e 46 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N VAL e 48 " --> pdb=" O VAL f 49 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N GLY f 51 " --> pdb=" O VAL e 48 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS e 50 " --> pdb=" O GLY f 51 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ALA f 53 " --> pdb=" O HIS e 50 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL e 52 " --> pdb=" O ALA f 53 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL f 55 " --> pdb=" O VAL e 52 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N THR e 54 " --> pdb=" O VAL f 55 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLU f 57 " --> pdb=" O THR e 54 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N ALA e 56 " --> pdb=" O GLU f 57 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N GLU f 46 " --> pdb=" O GLY g 47 " (cutoff:3.500A) removed outlier: 8.201A pdb=" N VAL g 49 " --> pdb=" O GLU f 46 " (cutoff:3.500A) removed outlier: 9.226A pdb=" N VAL f 48 " --> pdb=" O VAL g 49 " (cutoff:3.500A) removed outlier: 10.151A pdb=" N GLY g 51 " --> pdb=" O VAL f 48 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N HIS f 50 " --> pdb=" O GLY g 51 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N ALA g 53 " --> pdb=" O HIS f 50 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL f 52 " --> pdb=" O ALA g 53 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL g 55 " --> pdb=" O VAL f 52 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N THR f 54 " --> pdb=" O VAL g 55 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLU g 57 " --> pdb=" O THR f 54 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N ALA f 56 " --> pdb=" O GLU g 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'a' and resid 65 through 79 removed outlier: 7.003A pdb=" N ALA b 69 " --> pdb=" O GLY a 68 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL a 70 " --> pdb=" O ALA b 69 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL b 71 " --> pdb=" O VAL a 70 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR a 72 " --> pdb=" O VAL b 71 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY b 73 " --> pdb=" O THR a 72 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA c 69 " --> pdb=" O GLY b 68 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL b 70 " --> pdb=" O ALA c 69 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL c 71 " --> pdb=" O VAL b 70 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR b 72 " --> pdb=" O VAL c 71 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY c 73 " --> pdb=" O THR b 72 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA d 69 " --> pdb=" O GLY c 68 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL c 70 " --> pdb=" O ALA d 69 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL d 71 " --> pdb=" O VAL c 70 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR c 72 " --> pdb=" O VAL d 71 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY d 73 " --> pdb=" O THR c 72 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA e 69 " --> pdb=" O GLY d 68 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL d 70 " --> pdb=" O ALA e 69 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL e 71 " --> pdb=" O VAL d 70 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR d 72 " --> pdb=" O VAL e 71 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY e 73 " --> pdb=" O THR d 72 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA f 69 " --> pdb=" O GLY e 68 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL e 70 " --> pdb=" O ALA f 69 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL f 71 " --> pdb=" O VAL e 70 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR e 72 " --> pdb=" O VAL f 71 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY f 73 " --> pdb=" O THR e 72 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ALA g 69 " --> pdb=" O GLY f 68 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N VAL f 70 " --> pdb=" O ALA g 69 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL g 71 " --> pdb=" O VAL f 70 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N THR f 72 " --> pdb=" O VAL g 71 " (cutoff:3.500A) removed outlier: 6.906A pdb=" N GLY g 73 " --> pdb=" O THR f 72 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'a' and resid 88 through 98 removed outlier: 9.330A pdb=" N ILE a 88 " --> pdb=" O ALA b 89 " (cutoff:3.500A) removed outlier: 10.386A pdb=" N ALA b 91 " --> pdb=" O ILE a 88 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N ALA a 90 " --> pdb=" O ALA b 91 " (cutoff:3.500A) removed outlier: 10.466A pdb=" N GLY b 93 " --> pdb=" O ALA a 90 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR a 92 " --> pdb=" O GLY b 93 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N VAL b 95 " --> pdb=" O THR a 92 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE a 94 " --> pdb=" O VAL b 95 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LYS b 97 " --> pdb=" O PHE a 94 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LYS a 96 " --> pdb=" O LYS b 97 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N ILE b 88 " --> pdb=" O ALA c 89 " (cutoff:3.500A) removed outlier: 10.386A pdb=" N ALA c 91 " --> pdb=" O ILE b 88 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N ALA b 90 " --> pdb=" O ALA c 91 " (cutoff:3.500A) removed outlier: 10.466A pdb=" N GLY c 93 " --> pdb=" O ALA b 90 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR b 92 " --> pdb=" O GLY c 93 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N VAL c 95 " --> pdb=" O THR b 92 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE b 94 " --> pdb=" O VAL c 95 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LYS c 97 " --> pdb=" O PHE b 94 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N LYS b 96 " --> pdb=" O LYS c 97 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N ILE c 88 " --> pdb=" O ALA d 89 " (cutoff:3.500A) removed outlier: 10.386A pdb=" N ALA d 91 " --> pdb=" O ILE c 88 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N ALA c 90 " --> pdb=" O ALA d 91 " (cutoff:3.500A) removed outlier: 10.466A pdb=" N GLY d 93 " --> pdb=" O ALA c 90 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N THR c 92 " --> pdb=" O GLY d 93 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N VAL d 95 " --> pdb=" O THR c 92 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE c 94 " --> pdb=" O VAL d 95 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LYS d 97 " --> pdb=" O PHE c 94 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LYS c 96 " --> pdb=" O LYS d 97 " (cutoff:3.500A) removed outlier: 9.329A pdb=" N ILE d 88 " --> pdb=" O ALA e 89 " (cutoff:3.500A) removed outlier: 10.386A pdb=" N ALA e 91 " --> pdb=" O ILE d 88 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N ALA d 90 " --> pdb=" O ALA e 91 " (cutoff:3.500A) removed outlier: 10.466A pdb=" N GLY e 93 " --> pdb=" O ALA d 90 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR d 92 " --> pdb=" O GLY e 93 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N VAL e 95 " --> pdb=" O THR d 92 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE d 94 " --> pdb=" O VAL e 95 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LYS e 97 " --> pdb=" O PHE d 94 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LYS d 96 " --> pdb=" O LYS e 97 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N ILE e 88 " --> pdb=" O ALA f 89 " (cutoff:3.500A) removed outlier: 10.386A pdb=" N ALA f 91 " --> pdb=" O ILE e 88 " (cutoff:3.500A) removed outlier: 9.129A pdb=" N ALA e 90 " --> pdb=" O ALA f 91 " (cutoff:3.500A) removed outlier: 10.466A pdb=" N GLY f 93 " --> pdb=" O ALA e 90 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR e 92 " --> pdb=" O GLY f 93 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N VAL f 95 " --> pdb=" O THR e 92 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE e 94 " --> pdb=" O VAL f 95 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LYS f 97 " --> pdb=" O PHE e 94 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LYS e 96 " --> pdb=" O LYS f 97 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N ILE f 88 " --> pdb=" O ALA g 89 " (cutoff:3.500A) removed outlier: 10.386A pdb=" N ALA g 91 " --> pdb=" O ILE f 88 " (cutoff:3.500A) removed outlier: 9.128A pdb=" N ALA f 90 " --> pdb=" O ALA g 91 " (cutoff:3.500A) removed outlier: 10.466A pdb=" N GLY g 93 " --> pdb=" O ALA f 90 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N THR f 92 " --> pdb=" O GLY g 93 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N VAL g 95 " --> pdb=" O THR f 92 " (cutoff:3.500A) removed outlier: 6.501A pdb=" N PHE f 94 " --> pdb=" O VAL g 95 " (cutoff:3.500A) removed outlier: 7.825A pdb=" N LYS g 97 " --> pdb=" O PHE f 94 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LYS f 96 " --> pdb=" O LYS g 97 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 169 hydrogen bonds defined for protein. 507 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: 4.32 Time building geometry restraints manager: 2.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9422 1.03 - 1.22: 0 1.22 - 1.42: 3556 1.42 - 1.61: 6118 1.61 - 1.80: 56 Bond restraints: 19152 Sorted by residual: bond pdb=" CA GLY m 51 " pdb=" C GLY m 51 " ideal model delta sigma weight residual 1.516 1.508 0.008 8.10e-03 1.52e+04 9.10e-01 bond pdb=" CA GLY f 51 " pdb=" C GLY f 51 " ideal model delta sigma weight residual 1.516 1.508 0.008 8.10e-03 1.52e+04 9.10e-01 bond pdb=" CA GLY a 51 " pdb=" C GLY a 51 " ideal model delta sigma weight residual 1.516 1.508 0.007 8.10e-03 1.52e+04 8.35e-01 bond pdb=" CA GLY h 51 " pdb=" C GLY h 51 " ideal model delta sigma weight residual 1.516 1.508 0.007 8.10e-03 1.52e+04 8.35e-01 bond pdb=" CA GLY n 51 " pdb=" C GLY n 51 " ideal model delta sigma weight residual 1.516 1.508 0.007 8.10e-03 1.52e+04 8.12e-01 ... (remaining 19147 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.55: 28278 0.55 - 1.10: 5112 1.10 - 1.65: 848 1.65 - 2.19: 226 2.19 - 2.74: 74 Bond angle restraints: 34538 Sorted by residual: angle pdb=" C HIS k 50 " pdb=" N GLY k 51 " pdb=" CA GLY k 51 " ideal model delta sigma weight residual 122.33 120.82 1.51 7.30e-01 1.88e+00 4.27e+00 angle pdb=" C HIS d 50 " pdb=" N GLY d 51 " pdb=" CA GLY d 51 " ideal model delta sigma weight residual 122.33 120.82 1.51 7.30e-01 1.88e+00 4.27e+00 angle pdb=" C HIS g 50 " pdb=" N GLY g 51 " pdb=" CA GLY g 51 " ideal model delta sigma weight residual 122.33 120.82 1.51 7.30e-01 1.88e+00 4.26e+00 angle pdb=" C HIS n 50 " pdb=" N GLY n 51 " pdb=" CA GLY n 51 " ideal model delta sigma weight residual 122.33 120.82 1.51 7.30e-01 1.88e+00 4.26e+00 angle pdb=" C HIS i 50 " pdb=" N GLY i 51 " pdb=" CA GLY i 51 " ideal model delta sigma weight residual 122.33 120.82 1.51 7.30e-01 1.88e+00 4.26e+00 ... (remaining 34533 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.73: 7702 17.73 - 35.46: 600 35.46 - 53.20: 364 53.20 - 70.93: 210 70.93 - 88.66: 56 Dihedral angle restraints: 8932 sinusoidal: 4942 harmonic: 3990 Sorted by residual: dihedral pdb=" CB GLU b 57 " pdb=" CG GLU b 57 " pdb=" CD GLU b 57 " pdb=" OE1 GLU b 57 " ideal model delta sinusoidal sigma weight residual 0.00 -88.66 88.66 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU j 57 " pdb=" CG GLU j 57 " pdb=" CD GLU j 57 " pdb=" OE1 GLU j 57 " ideal model delta sinusoidal sigma weight residual 0.00 -88.65 88.65 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU f 57 " pdb=" CG GLU f 57 " pdb=" CD GLU f 57 " pdb=" OE1 GLU f 57 " ideal model delta sinusoidal sigma weight residual 0.00 -88.65 88.65 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 8929 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.023: 692 0.023 - 0.046: 474 0.046 - 0.069: 156 0.069 - 0.092: 36 0.092 - 0.115: 266 Chirality restraints: 1624 Sorted by residual: chirality pdb=" CA VAL j 71 " pdb=" N VAL j 71 " pdb=" C VAL j 71 " pdb=" CB VAL j 71 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.30e-01 chirality pdb=" CA VAL c 71 " pdb=" N VAL c 71 " pdb=" C VAL c 71 " pdb=" CB VAL c 71 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.30e-01 chirality pdb=" CA VAL k 71 " pdb=" N VAL k 71 " pdb=" C VAL k 71 " pdb=" CB VAL k 71 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.11 2.00e-01 2.50e+01 3.30e-01 ... (remaining 1621 not shown) Planarity restraints: 2940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS n 60 " -0.002 2.00e-02 2.50e+03 3.77e-03 1.42e-01 pdb=" C LYS n 60 " 0.007 2.00e-02 2.50e+03 pdb=" O LYS n 60 " -0.002 2.00e-02 2.50e+03 pdb=" N GLU n 61 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS g 60 " 0.002 2.00e-02 2.50e+03 3.66e-03 1.34e-01 pdb=" C LYS g 60 " -0.006 2.00e-02 2.50e+03 pdb=" O LYS g 60 " 0.002 2.00e-02 2.50e+03 pdb=" N GLU g 61 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS c 60 " 0.002 2.00e-02 2.50e+03 3.64e-03 1.33e-01 pdb=" C LYS c 60 " -0.006 2.00e-02 2.50e+03 pdb=" O LYS c 60 " 0.002 2.00e-02 2.50e+03 pdb=" N GLU c 61 " 0.002 2.00e-02 2.50e+03 ... (remaining 2937 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 1245 2.22 - 2.81: 41249 2.81 - 3.41: 44527 3.41 - 4.00: 68118 4.00 - 4.60: 103019 Nonbonded interactions: 258158 Sorted by model distance: nonbonded pdb=" OE1 GLU d 61 " pdb=" H GLU e 61 " model vdw 1.623 2.450 nonbonded pdb=" OE1 GLU k 61 " pdb=" H GLU l 61 " model vdw 1.623 2.450 nonbonded pdb=" OE1 GLU j 61 " pdb=" H GLU k 61 " model vdw 1.623 2.450 nonbonded pdb=" OE1 GLU c 61 " pdb=" H GLU d 61 " model vdw 1.623 2.450 nonbonded pdb=" OE1 GLU b 61 " pdb=" H GLU c 61 " model vdw 1.623 2.450 ... (remaining 258153 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: 0.04 Found NCS groups: ncs_group { reference = chain 'n' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' } 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: 5.020 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: 0.130 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 15.840 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 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:7.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 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 : 0.003 0.013 9730 Z= 0.148 Angle : 0.505 2.742 13048 Z= 0.315 Chirality : 0.052 0.115 1624 Planarity : 0.001 0.004 1638 Dihedral : 20.077 88.660 3472 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 4.35 % Allowed : 17.39 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.46 (0.19), residues: 1358 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.86 (0.14), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR e 39 PHE 0.003 0.001 PHE k 4 HIS 0.000 0.000 HIS k 50 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 9730) covalent geometry : angle 0.50497 (13048) hydrogen bonds : bond 0.25661 ( 169) hydrogen bonds : angle 9.34453 ( 507) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 260 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: n 80 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.7777 (mtmm) REVERT: a 50 HIS cc_start: 0.6658 (OUTLIER) cc_final: 0.4960 (p90) REVERT: a 54 THR cc_start: 0.6807 (m) cc_final: 0.6381 (p) REVERT: a 57 GLU cc_start: 0.7987 (tt0) cc_final: 0.7772 (pm20) REVERT: a 60 LYS cc_start: 0.5587 (tttp) cc_final: 0.4814 (mppt) REVERT: b 50 HIS cc_start: 0.6905 (OUTLIER) cc_final: 0.6319 (t-90) REVERT: b 54 THR cc_start: 0.7009 (m) cc_final: 0.6530 (p) REVERT: b 60 LYS cc_start: 0.5372 (tttp) cc_final: 0.5121 (tppt) REVERT: c 50 HIS cc_start: 0.7194 (OUTLIER) cc_final: 0.6896 (t-170) REVERT: c 54 THR cc_start: 0.6878 (m) cc_final: 0.6423 (p) REVERT: d 54 THR cc_start: 0.7082 (m) cc_final: 0.6586 (p) REVERT: d 99 GLN cc_start: 0.6730 (mm-40) cc_final: 0.6454 (mm110) REVERT: e 54 THR cc_start: 0.7017 (m) cc_final: 0.6505 (p) REVERT: e 58 LYS cc_start: 0.8283 (ttmm) cc_final: 0.7979 (tttt) REVERT: f 54 THR cc_start: 0.7052 (m) cc_final: 0.6669 (p) REVERT: f 80 LYS cc_start: 0.8033 (OUTLIER) cc_final: 0.7742 (mttt) REVERT: g 80 LYS cc_start: 0.7993 (OUTLIER) cc_final: 0.7771 (mtmm) REVERT: h 50 HIS cc_start: 0.6669 (OUTLIER) cc_final: 0.4970 (p90) REVERT: h 54 THR cc_start: 0.6805 (m) cc_final: 0.6378 (p) REVERT: h 57 GLU cc_start: 0.7985 (tt0) cc_final: 0.7771 (pm20) REVERT: h 60 LYS cc_start: 0.5600 (tttp) cc_final: 0.4821 (mppt) REVERT: i 50 HIS cc_start: 0.6899 (OUTLIER) cc_final: 0.6321 (t-90) REVERT: i 54 THR cc_start: 0.7020 (m) cc_final: 0.6542 (p) REVERT: i 60 LYS cc_start: 0.5364 (tttp) cc_final: 0.5118 (tppt) REVERT: j 50 HIS cc_start: 0.7182 (OUTLIER) cc_final: 0.6884 (t-170) REVERT: j 54 THR cc_start: 0.6861 (m) cc_final: 0.6416 (p) REVERT: k 54 THR cc_start: 0.7096 (m) cc_final: 0.6599 (p) REVERT: k 99 GLN cc_start: 0.6736 (mm-40) cc_final: 0.6464 (mm110) REVERT: l 54 THR cc_start: 0.6993 (m) cc_final: 0.6491 (p) REVERT: l 58 LYS cc_start: 0.8262 (ttmm) cc_final: 0.7953 (tttt) REVERT: m 54 THR cc_start: 0.7056 (m) cc_final: 0.6668 (p) REVERT: m 80 LYS cc_start: 0.8047 (OUTLIER) cc_final: 0.7738 (mttt) REVERT: m 99 GLN cc_start: 0.6445 (mm-40) cc_final: 0.6217 (mm110) outliers start: 42 outliers final: 8 residues processed: 298 average time/residue: 1.1511 time to fit residues: 366.3245 Evaluate side-chains 217 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 0.526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 50 HIS Chi-restraints excluded: chain n residue 80 LYS Chi-restraints excluded: chain a residue 50 HIS Chi-restraints excluded: chain b residue 50 HIS Chi-restraints excluded: chain c residue 50 HIS Chi-restraints excluded: chain d residue 50 HIS Chi-restraints excluded: chain e residue 50 HIS Chi-restraints excluded: chain f residue 50 HIS Chi-restraints excluded: chain f residue 80 LYS Chi-restraints excluded: chain g residue 50 HIS Chi-restraints excluded: chain g residue 80 LYS Chi-restraints excluded: chain h residue 50 HIS Chi-restraints excluded: chain i residue 50 HIS Chi-restraints excluded: chain j residue 50 HIS Chi-restraints excluded: chain k residue 50 HIS Chi-restraints excluded: chain l residue 50 HIS Chi-restraints excluded: chain m residue 50 HIS Chi-restraints excluded: chain m residue 80 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 6.9990 chunk 123 optimal weight: 6.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 7.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: c 65 ASN d 99 GLN f 65 ASN g 65 ASN j 65 ASN k 99 GLN m 65 ASN ** m 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.145365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.123227 restraints weight = 34050.283| |-----------------------------------------------------------------------------| r_work (start): 0.3699 rms_B_bonded: 2.51 r_work: 0.3592 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3473 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3473 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 9730 Z= 0.274 Angle : 0.670 6.027 13048 Z= 0.399 Chirality : 0.058 0.155 1624 Planarity : 0.003 0.012 1638 Dihedral : 9.238 53.943 1430 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.94 % Favored : 90.06 % Rotamer: Outliers : 6.00 % Allowed : 21.53 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.66 (0.18), residues: 1358 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.02 (0.14), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR d 39 PHE 0.014 0.002 PHE m 4 HIS 0.002 0.001 HIS k 50 Details of bonding type rmsd covalent geometry : bond 0.00645 ( 9730) covalent geometry : angle 0.66979 (13048) hydrogen bonds : bond 0.09469 ( 169) hydrogen bonds : angle 6.97625 ( 507) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 218 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: n 28 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7514 (pp20) REVERT: n 54 THR cc_start: 0.7248 (OUTLIER) cc_final: 0.7023 (p) REVERT: n 72 THR cc_start: 0.8442 (OUTLIER) cc_final: 0.8238 (m) REVERT: a 50 HIS cc_start: 0.6524 (OUTLIER) cc_final: 0.4286 (p90) REVERT: a 54 THR cc_start: 0.6972 (m) cc_final: 0.6436 (p) REVERT: a 57 GLU cc_start: 0.8641 (tt0) cc_final: 0.7579 (pm20) REVERT: a 60 LYS cc_start: 0.6014 (tttp) cc_final: 0.5215 (pmtt) REVERT: b 54 THR cc_start: 0.7268 (m) cc_final: 0.6830 (p) REVERT: b 60 LYS cc_start: 0.5877 (tttp) cc_final: 0.5561 (tppt) REVERT: b 99 GLN cc_start: 0.6551 (OUTLIER) cc_final: 0.6235 (mm-40) REVERT: c 6 LYS cc_start: 0.9055 (mtpp) cc_final: 0.8837 (mttm) REVERT: c 28 GLU cc_start: 0.8067 (OUTLIER) cc_final: 0.7519 (pp20) REVERT: c 54 THR cc_start: 0.7208 (m) cc_final: 0.6789 (p) REVERT: c 58 LYS cc_start: 0.8093 (ttmm) cc_final: 0.7801 (tttt) REVERT: d 28 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7466 (pp20) REVERT: d 54 THR cc_start: 0.7468 (m) cc_final: 0.7092 (p) REVERT: d 99 GLN cc_start: 0.6523 (mm110) cc_final: 0.6098 (mm110) REVERT: e 28 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.7433 (pp20) REVERT: e 54 THR cc_start: 0.7351 (m) cc_final: 0.6931 (p) REVERT: f 28 GLU cc_start: 0.7900 (OUTLIER) cc_final: 0.7344 (pp20) REVERT: f 54 THR cc_start: 0.7340 (m) cc_final: 0.7026 (p) REVERT: g 28 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7564 (pp20) REVERT: h 50 HIS cc_start: 0.6565 (OUTLIER) cc_final: 0.4306 (p90) REVERT: h 54 THR cc_start: 0.6989 (m) cc_final: 0.6461 (p) REVERT: h 57 GLU cc_start: 0.8623 (tt0) cc_final: 0.7569 (pm20) REVERT: h 60 LYS cc_start: 0.6037 (tttp) cc_final: 0.5226 (pmtt) REVERT: i 28 GLU cc_start: 0.7804 (OUTLIER) cc_final: 0.7287 (pp20) REVERT: i 54 THR cc_start: 0.7288 (m) cc_final: 0.6841 (p) REVERT: i 60 LYS cc_start: 0.5911 (tttp) cc_final: 0.5596 (tppt) REVERT: i 99 GLN cc_start: 0.6512 (OUTLIER) cc_final: 0.6254 (mm-40) REVERT: j 6 LYS cc_start: 0.9047 (mtpp) cc_final: 0.8836 (mttm) REVERT: j 28 GLU cc_start: 0.7979 (OUTLIER) cc_final: 0.7431 (pp20) REVERT: j 54 THR cc_start: 0.7230 (m) cc_final: 0.6821 (p) REVERT: j 58 LYS cc_start: 0.8080 (ttmm) cc_final: 0.7784 (tttt) REVERT: k 28 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7483 (pp20) REVERT: k 54 THR cc_start: 0.7493 (m) cc_final: 0.7115 (p) REVERT: k 99 GLN cc_start: 0.6463 (mm110) cc_final: 0.6045 (mm110) REVERT: l 28 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7470 (pp20) REVERT: l 54 THR cc_start: 0.7367 (m) cc_final: 0.6934 (p) REVERT: l 72 THR cc_start: 0.8373 (OUTLIER) cc_final: 0.8173 (p) REVERT: m 28 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7311 (pp20) REVERT: m 54 THR cc_start: 0.7369 (m) cc_final: 0.7087 (p) outliers start: 58 outliers final: 9 residues processed: 246 average time/residue: 1.2460 time to fit residues: 327.1941 Evaluate side-chains 236 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 209 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 28 GLU Chi-restraints excluded: chain n residue 33 THR Chi-restraints excluded: chain n residue 54 THR Chi-restraints excluded: chain n residue 58 LYS Chi-restraints excluded: chain n residue 72 THR Chi-restraints excluded: chain a residue 50 HIS Chi-restraints excluded: chain b residue 50 HIS Chi-restraints excluded: chain b residue 99 GLN Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain d residue 28 GLU Chi-restraints excluded: chain d residue 50 HIS Chi-restraints excluded: chain e residue 28 GLU Chi-restraints excluded: chain f residue 28 GLU Chi-restraints excluded: chain g residue 28 GLU Chi-restraints excluded: chain g residue 33 THR Chi-restraints excluded: chain g residue 58 LYS Chi-restraints excluded: chain h residue 50 HIS Chi-restraints excluded: chain i residue 28 GLU Chi-restraints excluded: chain i residue 50 HIS Chi-restraints excluded: chain i residue 99 GLN Chi-restraints excluded: chain j residue 28 GLU Chi-restraints excluded: chain k residue 28 GLU Chi-restraints excluded: chain k residue 50 HIS Chi-restraints excluded: chain l residue 28 GLU Chi-restraints excluded: chain l residue 72 THR Chi-restraints excluded: chain m residue 28 GLU Chi-restraints excluded: chain m residue 50 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 22 optimal weight: 4.9990 chunk 113 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 72 optimal weight: 0.8980 chunk 94 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.150348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.127930 restraints weight = 33302.079| |-----------------------------------------------------------------------------| r_work (start): 0.3760 rms_B_bonded: 2.49 r_work: 0.3654 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3536 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 9730 Z= 0.115 Angle : 0.516 5.752 13048 Z= 0.306 Chirality : 0.055 0.154 1624 Planarity : 0.001 0.006 1638 Dihedral : 7.058 51.629 1400 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.36 % Favored : 92.64 % Rotamer: Outliers : 1.55 % Allowed : 28.99 % Favored : 69.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.61 (0.18), residues: 1358 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.98 (0.14), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR d 39 PHE 0.009 0.001 PHE f 4 HIS 0.002 0.001 HIS i 50 Details of bonding type rmsd covalent geometry : bond 0.00243 ( 9730) covalent geometry : angle 0.51573 (13048) hydrogen bonds : bond 0.07060 ( 169) hydrogen bonds : angle 6.62242 ( 507) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 215 time to evaluate : 0.506 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: n 54 THR cc_start: 0.7146 (m) cc_final: 0.6937 (p) REVERT: a 50 HIS cc_start: 0.6591 (OUTLIER) cc_final: 0.4350 (p90) REVERT: a 54 THR cc_start: 0.7006 (m) cc_final: 0.6548 (p) REVERT: a 57 GLU cc_start: 0.8614 (tt0) cc_final: 0.7468 (pm20) REVERT: a 60 LYS cc_start: 0.6141 (tttp) cc_final: 0.5303 (pmtt) REVERT: b 54 THR cc_start: 0.7208 (m) cc_final: 0.6912 (p) REVERT: b 99 GLN cc_start: 0.6582 (OUTLIER) cc_final: 0.6246 (mm-40) REVERT: c 6 LYS cc_start: 0.9044 (mtpp) cc_final: 0.8790 (mttp) REVERT: c 54 THR cc_start: 0.7201 (m) cc_final: 0.6858 (p) REVERT: c 58 LYS cc_start: 0.8036 (ttmm) cc_final: 0.7757 (tttt) REVERT: d 50 HIS cc_start: 0.7386 (OUTLIER) cc_final: 0.7133 (t-170) REVERT: d 54 THR cc_start: 0.7328 (m) cc_final: 0.6964 (p) REVERT: d 99 GLN cc_start: 0.6605 (mm110) cc_final: 0.6303 (mm-40) REVERT: e 54 THR cc_start: 0.7273 (m) cc_final: 0.6916 (p) REVERT: f 54 THR cc_start: 0.7237 (m) cc_final: 0.6941 (p) REVERT: h 50 HIS cc_start: 0.6592 (OUTLIER) cc_final: 0.4332 (p90) REVERT: h 54 THR cc_start: 0.7033 (m) cc_final: 0.6568 (p) REVERT: h 57 GLU cc_start: 0.8593 (tt0) cc_final: 0.7463 (pm20) REVERT: h 60 LYS cc_start: 0.6144 (tttp) cc_final: 0.5292 (pmtt) REVERT: i 28 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7420 (pp20) REVERT: i 54 THR cc_start: 0.7201 (m) cc_final: 0.6920 (p) REVERT: i 99 GLN cc_start: 0.6646 (OUTLIER) cc_final: 0.6306 (mm-40) REVERT: j 6 LYS cc_start: 0.9035 (mtpp) cc_final: 0.8787 (mttp) REVERT: j 54 THR cc_start: 0.7236 (m) cc_final: 0.6891 (p) REVERT: j 58 LYS cc_start: 0.8046 (ttmm) cc_final: 0.7757 (tttt) REVERT: k 50 HIS cc_start: 0.7352 (OUTLIER) cc_final: 0.7103 (t-170) REVERT: k 54 THR cc_start: 0.7367 (m) cc_final: 0.6999 (p) REVERT: k 99 GLN cc_start: 0.6577 (mm110) cc_final: 0.6272 (mm-40) REVERT: l 54 THR cc_start: 0.7323 (m) cc_final: 0.6905 (p) REVERT: m 50 HIS cc_start: 0.7406 (OUTLIER) cc_final: 0.7193 (t-170) REVERT: m 54 THR cc_start: 0.7267 (m) cc_final: 0.7006 (p) outliers start: 15 outliers final: 2 residues processed: 219 average time/residue: 1.2189 time to fit residues: 284.8217 Evaluate side-chains 222 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 212 time to evaluate : 0.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 58 LYS Chi-restraints excluded: chain a residue 50 HIS Chi-restraints excluded: chain b residue 99 GLN Chi-restraints excluded: chain d residue 50 HIS Chi-restraints excluded: chain h residue 50 HIS Chi-restraints excluded: chain i residue 28 GLU Chi-restraints excluded: chain i residue 99 GLN Chi-restraints excluded: chain k residue 50 HIS Chi-restraints excluded: chain k residue 61 GLU Chi-restraints excluded: chain m residue 50 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 117 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 102 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 79 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 76 optimal weight: 5.9990 chunk 112 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.144233 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.122003 restraints weight = 33787.254| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.50 r_work: 0.3570 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3451 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3451 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.3373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 9730 Z= 0.254 Angle : 0.653 6.206 13048 Z= 0.390 Chirality : 0.057 0.147 1624 Planarity : 0.003 0.008 1638 Dihedral : 7.117 51.557 1396 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.35 % Favored : 90.65 % Rotamer: Outliers : 5.49 % Allowed : 26.19 % Favored : 68.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.17), residues: 1358 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.13), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR d 39 PHE 0.015 0.002 PHE f 4 HIS 0.002 0.000 HIS k 50 Details of bonding type rmsd covalent geometry : bond 0.00602 ( 9730) covalent geometry : angle 0.65263 (13048) hydrogen bonds : bond 0.08993 ( 169) hydrogen bonds : angle 6.91573 ( 507) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 216 time to evaluate : 0.521 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: n 28 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7576 (pp20) REVERT: n 60 LYS cc_start: 0.6332 (tppt) cc_final: 0.5481 (tppt) REVERT: a 50 HIS cc_start: 0.6609 (OUTLIER) cc_final: 0.4150 (p90) REVERT: a 54 THR cc_start: 0.7016 (m) cc_final: 0.6654 (p) REVERT: a 57 GLU cc_start: 0.8611 (tt0) cc_final: 0.7409 (pm20) REVERT: a 60 LYS cc_start: 0.6189 (tttp) cc_final: 0.5281 (pmtt) REVERT: a 99 GLN cc_start: 0.6812 (mt0) cc_final: 0.6402 (mt0) REVERT: b 50 HIS cc_start: 0.6974 (OUTLIER) cc_final: 0.6419 (t-170) REVERT: b 54 THR cc_start: 0.7262 (m) cc_final: 0.6969 (p) REVERT: b 99 GLN cc_start: 0.6626 (OUTLIER) cc_final: 0.6161 (mm-40) REVERT: c 6 LYS cc_start: 0.9036 (mtpp) cc_final: 0.8820 (mttm) REVERT: c 28 GLU cc_start: 0.8043 (OUTLIER) cc_final: 0.7553 (pp20) REVERT: c 50 HIS cc_start: 0.7188 (OUTLIER) cc_final: 0.6878 (t-170) REVERT: c 54 THR cc_start: 0.7337 (m) cc_final: 0.6960 (p) REVERT: c 99 GLN cc_start: 0.6304 (OUTLIER) cc_final: 0.5888 (mt0) REVERT: d 28 GLU cc_start: 0.7922 (OUTLIER) cc_final: 0.7500 (pp20) REVERT: d 50 HIS cc_start: 0.7323 (OUTLIER) cc_final: 0.7105 (t-170) REVERT: d 54 THR cc_start: 0.7440 (m) cc_final: 0.7135 (p) REVERT: d 99 GLN cc_start: 0.6451 (mm110) cc_final: 0.6002 (mt0) REVERT: e 28 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7447 (pp20) REVERT: e 54 THR cc_start: 0.7446 (m) cc_final: 0.7141 (p) REVERT: e 99 GLN cc_start: 0.6537 (mm110) cc_final: 0.6098 (mt0) REVERT: f 28 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7411 (pp20) REVERT: f 54 THR cc_start: 0.7359 (m) cc_final: 0.7143 (p) REVERT: f 99 GLN cc_start: 0.6615 (mm110) cc_final: 0.6276 (mt0) REVERT: g 28 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7583 (pp20) REVERT: g 60 LYS cc_start: 0.6345 (tppt) cc_final: 0.5525 (tppt) REVERT: g 99 GLN cc_start: 0.7200 (mm110) cc_final: 0.6921 (mt0) REVERT: h 50 HIS cc_start: 0.6601 (OUTLIER) cc_final: 0.4172 (p90) REVERT: h 54 THR cc_start: 0.7047 (m) cc_final: 0.6683 (p) REVERT: h 57 GLU cc_start: 0.8630 (tt0) cc_final: 0.7432 (pm20) REVERT: h 60 LYS cc_start: 0.6188 (tttp) cc_final: 0.5280 (pmtt) REVERT: h 99 GLN cc_start: 0.6780 (mt0) cc_final: 0.6369 (mt0) REVERT: i 28 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7252 (pp20) REVERT: i 50 HIS cc_start: 0.6952 (OUTLIER) cc_final: 0.6433 (t-170) REVERT: i 54 THR cc_start: 0.7292 (m) cc_final: 0.6951 (p) REVERT: i 99 GLN cc_start: 0.6636 (OUTLIER) cc_final: 0.6181 (mm-40) REVERT: j 6 LYS cc_start: 0.9047 (mtpp) cc_final: 0.8837 (mttm) REVERT: j 28 GLU cc_start: 0.7952 (OUTLIER) cc_final: 0.7450 (pp20) REVERT: j 50 HIS cc_start: 0.7239 (OUTLIER) cc_final: 0.6986 (t-170) REVERT: j 54 THR cc_start: 0.7365 (m) cc_final: 0.6987 (p) REVERT: j 99 GLN cc_start: 0.6271 (OUTLIER) cc_final: 0.5856 (mt0) REVERT: k 28 GLU cc_start: 0.7929 (OUTLIER) cc_final: 0.7516 (pp20) REVERT: k 50 HIS cc_start: 0.7427 (OUTLIER) cc_final: 0.7198 (t-170) REVERT: k 54 THR cc_start: 0.7449 (m) cc_final: 0.7137 (p) REVERT: k 99 GLN cc_start: 0.6500 (mm110) cc_final: 0.6048 (mt0) REVERT: l 28 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7518 (pp20) REVERT: l 54 THR cc_start: 0.7408 (m) cc_final: 0.7073 (p) REVERT: l 99 GLN cc_start: 0.6661 (mm110) cc_final: 0.6247 (mt0) REVERT: m 28 GLU cc_start: 0.7958 (OUTLIER) cc_final: 0.7452 (pp20) REVERT: m 54 THR cc_start: 0.7382 (m) cc_final: 0.7149 (p) REVERT: m 99 GLN cc_start: 0.6791 (mm110) cc_final: 0.6580 (mt0) outliers start: 53 outliers final: 8 residues processed: 244 average time/residue: 1.1501 time to fit residues: 300.4364 Evaluate side-chains 240 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 209 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 28 GLU Chi-restraints excluded: chain n residue 33 THR Chi-restraints excluded: chain n residue 58 LYS Chi-restraints excluded: chain a residue 50 HIS Chi-restraints excluded: chain b residue 50 HIS Chi-restraints excluded: chain b residue 99 GLN Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain c residue 50 HIS Chi-restraints excluded: chain c residue 99 GLN Chi-restraints excluded: chain d residue 28 GLU Chi-restraints excluded: chain d residue 50 HIS Chi-restraints excluded: chain e residue 28 GLU Chi-restraints excluded: chain f residue 28 GLU Chi-restraints excluded: chain f residue 50 HIS Chi-restraints excluded: chain g residue 28 GLU Chi-restraints excluded: chain g residue 33 THR Chi-restraints excluded: chain g residue 58 LYS Chi-restraints excluded: chain h residue 50 HIS Chi-restraints excluded: chain i residue 28 GLU Chi-restraints excluded: chain i residue 50 HIS Chi-restraints excluded: chain i residue 99 GLN Chi-restraints excluded: chain j residue 28 GLU Chi-restraints excluded: chain j residue 50 HIS Chi-restraints excluded: chain j residue 99 GLN Chi-restraints excluded: chain k residue 28 GLU Chi-restraints excluded: chain k residue 50 HIS Chi-restraints excluded: chain k residue 61 GLU Chi-restraints excluded: chain l residue 28 GLU Chi-restraints excluded: chain l residue 33 THR Chi-restraints excluded: chain l residue 50 HIS Chi-restraints excluded: chain m residue 28 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 46 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 114 optimal weight: 6.9990 chunk 69 optimal weight: 6.9990 chunk 14 optimal weight: 0.4980 overall best weight: 2.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.144994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.122548 restraints weight = 33681.733| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.50 r_work: 0.3586 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3468 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3468 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.3550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 9730 Z= 0.208 Angle : 0.608 6.102 13048 Z= 0.365 Chirality : 0.057 0.166 1624 Planarity : 0.002 0.007 1638 Dihedral : 6.759 48.945 1394 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.46 % Favored : 89.54 % Rotamer: Outliers : 4.55 % Allowed : 27.64 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.17), residues: 1358 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.13), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR d 39 PHE 0.013 0.002 PHE f 4 HIS 0.003 0.001 HIS d 50 Details of bonding type rmsd covalent geometry : bond 0.00480 ( 9730) covalent geometry : angle 0.60767 (13048) hydrogen bonds : bond 0.08184 ( 169) hydrogen bonds : angle 6.74607 ( 507) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 208 time to evaluate : 0.489 Fit side-chains REVERT: n 28 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7575 (pp20) REVERT: n 60 LYS cc_start: 0.6364 (tppt) cc_final: 0.5530 (tppt) REVERT: a 46 GLU cc_start: 0.6958 (OUTLIER) cc_final: 0.6606 (mp0) REVERT: a 50 HIS cc_start: 0.6633 (OUTLIER) cc_final: 0.4139 (p90) REVERT: a 54 THR cc_start: 0.7059 (m) cc_final: 0.6602 (p) REVERT: a 57 GLU cc_start: 0.8518 (tt0) cc_final: 0.7399 (pm20) REVERT: a 60 LYS cc_start: 0.6283 (tttp) cc_final: 0.5340 (pmtt) REVERT: a 99 GLN cc_start: 0.6706 (mt0) cc_final: 0.6479 (mt0) REVERT: b 50 HIS cc_start: 0.6993 (OUTLIER) cc_final: 0.6313 (t-170) REVERT: b 54 THR cc_start: 0.7124 (m) cc_final: 0.6722 (p) REVERT: b 99 GLN cc_start: 0.6596 (OUTLIER) cc_final: 0.6080 (mm-40) REVERT: c 6 LYS cc_start: 0.9054 (mtpp) cc_final: 0.8825 (mttm) REVERT: c 28 GLU cc_start: 0.8035 (OUTLIER) cc_final: 0.7581 (pp20) REVERT: c 50 HIS cc_start: 0.7134 (OUTLIER) cc_final: 0.6781 (t-170) REVERT: c 54 THR cc_start: 0.7432 (m) cc_final: 0.7050 (p) REVERT: c 99 GLN cc_start: 0.6396 (OUTLIER) cc_final: 0.6025 (mt0) REVERT: d 28 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7493 (pp20) REVERT: d 54 THR cc_start: 0.7400 (m) cc_final: 0.7082 (p) REVERT: d 99 GLN cc_start: 0.6494 (mm110) cc_final: 0.6077 (mt0) REVERT: e 28 GLU cc_start: 0.7887 (OUTLIER) cc_final: 0.7459 (pp20) REVERT: e 54 THR cc_start: 0.7434 (m) cc_final: 0.7147 (p) REVERT: e 99 GLN cc_start: 0.6528 (mm110) cc_final: 0.6101 (mt0) REVERT: f 28 GLU cc_start: 0.7936 (OUTLIER) cc_final: 0.7472 (pp20) REVERT: f 54 THR cc_start: 0.7296 (m) cc_final: 0.7060 (p) REVERT: f 98 ASP cc_start: 0.8820 (m-30) cc_final: 0.8603 (m-30) REVERT: f 99 GLN cc_start: 0.6752 (mm110) cc_final: 0.6400 (mt0) REVERT: g 28 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7607 (pp20) REVERT: g 60 LYS cc_start: 0.6375 (tppt) cc_final: 0.5516 (tppt) REVERT: g 99 GLN cc_start: 0.7226 (mm110) cc_final: 0.6988 (mt0) REVERT: h 46 GLU cc_start: 0.6960 (OUTLIER) cc_final: 0.6614 (mp0) REVERT: h 50 HIS cc_start: 0.6576 (OUTLIER) cc_final: 0.4131 (p90) REVERT: h 54 THR cc_start: 0.7132 (m) cc_final: 0.6674 (p) REVERT: h 57 GLU cc_start: 0.8529 (tt0) cc_final: 0.7391 (pm20) REVERT: h 60 LYS cc_start: 0.6279 (tttp) cc_final: 0.5331 (pmtt) REVERT: h 99 GLN cc_start: 0.6724 (mt0) cc_final: 0.6478 (mt0) REVERT: i 28 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7331 (pp20) REVERT: i 50 HIS cc_start: 0.7020 (OUTLIER) cc_final: 0.6297 (t-170) REVERT: i 54 THR cc_start: 0.7165 (m) cc_final: 0.6765 (p) REVERT: i 99 GLN cc_start: 0.6578 (OUTLIER) cc_final: 0.6061 (mm-40) REVERT: j 6 LYS cc_start: 0.9064 (mtpp) cc_final: 0.8835 (mttm) REVERT: j 28 GLU cc_start: 0.7943 (OUTLIER) cc_final: 0.7487 (pp20) REVERT: j 50 HIS cc_start: 0.7234 (OUTLIER) cc_final: 0.6767 (t-170) REVERT: j 54 THR cc_start: 0.7418 (m) cc_final: 0.7067 (p) REVERT: j 99 GLN cc_start: 0.6332 (OUTLIER) cc_final: 0.5961 (mt0) REVERT: k 28 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7514 (pp20) REVERT: k 54 THR cc_start: 0.7406 (m) cc_final: 0.7087 (p) REVERT: k 60 LYS cc_start: 0.6649 (tppt) cc_final: 0.6132 (tptp) REVERT: k 99 GLN cc_start: 0.6431 (mm110) cc_final: 0.6020 (mt0) REVERT: l 28 GLU cc_start: 0.7925 (OUTLIER) cc_final: 0.7506 (pp20) REVERT: l 54 THR cc_start: 0.7428 (m) cc_final: 0.7119 (p) REVERT: l 99 GLN cc_start: 0.6605 (mm110) cc_final: 0.6192 (mt0) REVERT: m 28 GLU cc_start: 0.7939 (OUTLIER) cc_final: 0.7496 (pp20) REVERT: m 54 THR cc_start: 0.7427 (m) cc_final: 0.7172 (p) REVERT: m 98 ASP cc_start: 0.8723 (m-30) cc_final: 0.8362 (m-30) REVERT: m 99 GLN cc_start: 0.6718 (mm110) cc_final: 0.6479 (mt0) outliers start: 44 outliers final: 7 residues processed: 229 average time/residue: 1.1273 time to fit residues: 276.5330 Evaluate side-chains 236 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 206 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 28 GLU Chi-restraints excluded: chain n residue 33 THR Chi-restraints excluded: chain n residue 58 LYS Chi-restraints excluded: chain a residue 46 GLU Chi-restraints excluded: chain a residue 50 HIS Chi-restraints excluded: chain b residue 50 HIS Chi-restraints excluded: chain b residue 99 GLN Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain c residue 46 GLU Chi-restraints excluded: chain c residue 50 HIS Chi-restraints excluded: chain c residue 99 GLN Chi-restraints excluded: chain d residue 28 GLU Chi-restraints excluded: chain e residue 28 GLU Chi-restraints excluded: chain e residue 33 THR Chi-restraints excluded: chain f residue 28 GLU Chi-restraints excluded: chain g residue 28 GLU Chi-restraints excluded: chain g residue 33 THR Chi-restraints excluded: chain g residue 58 LYS Chi-restraints excluded: chain h residue 46 GLU Chi-restraints excluded: chain h residue 50 HIS Chi-restraints excluded: chain i residue 28 GLU Chi-restraints excluded: chain i residue 50 HIS Chi-restraints excluded: chain i residue 99 GLN Chi-restraints excluded: chain j residue 28 GLU Chi-restraints excluded: chain j residue 50 HIS Chi-restraints excluded: chain j residue 99 GLN Chi-restraints excluded: chain k residue 28 GLU Chi-restraints excluded: chain l residue 28 GLU Chi-restraints excluded: chain m residue 28 GLU Chi-restraints excluded: chain m residue 50 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 84 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 110 optimal weight: 3.9990 chunk 10 optimal weight: 0.3980 chunk 77 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 123 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 103 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 overall best weight: 1.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4030 r_free = 0.4030 target = 0.146650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3755 r_free = 0.3755 target = 0.124228 restraints weight = 33459.036| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.50 r_work: 0.3611 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.3664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9730 Z= 0.153 Angle : 0.549 5.941 13048 Z= 0.329 Chirality : 0.056 0.162 1624 Planarity : 0.002 0.006 1638 Dihedral : 6.137 48.517 1390 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 3.62 % Allowed : 29.61 % Favored : 66.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.17), residues: 1358 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.13), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR d 39 PHE 0.012 0.002 PHE f 4 HIS 0.001 0.000 HIS l 50 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9730) covalent geometry : angle 0.54854 (13048) hydrogen bonds : bond 0.07345 ( 169) hydrogen bonds : angle 6.59380 ( 507) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 208 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: n 28 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7578 (pp20) REVERT: a 50 HIS cc_start: 0.6483 (OUTLIER) cc_final: 0.4038 (p90) REVERT: a 54 THR cc_start: 0.7048 (m) cc_final: 0.6631 (p) REVERT: a 57 GLU cc_start: 0.8521 (tt0) cc_final: 0.7370 (pm20) REVERT: a 60 LYS cc_start: 0.6364 (tttp) cc_final: 0.5388 (pmtt) REVERT: a 99 GLN cc_start: 0.6684 (mt0) cc_final: 0.6428 (mt0) REVERT: b 50 HIS cc_start: 0.6986 (OUTLIER) cc_final: 0.6300 (t-170) REVERT: b 54 THR cc_start: 0.7166 (m) cc_final: 0.6851 (p) REVERT: b 99 GLN cc_start: 0.6553 (OUTLIER) cc_final: 0.6055 (mm-40) REVERT: c 6 LYS cc_start: 0.9040 (mtpp) cc_final: 0.8796 (mttp) REVERT: c 28 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7627 (pp20) REVERT: c 54 THR cc_start: 0.7335 (m) cc_final: 0.7010 (p) REVERT: c 99 GLN cc_start: 0.6404 (OUTLIER) cc_final: 0.6030 (mm-40) REVERT: d 28 GLU cc_start: 0.7906 (OUTLIER) cc_final: 0.7544 (pp20) REVERT: d 50 HIS cc_start: 0.7351 (OUTLIER) cc_final: 0.7062 (t-170) REVERT: d 54 THR cc_start: 0.7384 (m) cc_final: 0.7119 (p) REVERT: d 60 LYS cc_start: 0.6664 (tppt) cc_final: 0.6150 (tptp) REVERT: d 99 GLN cc_start: 0.6464 (mm110) cc_final: 0.6075 (mt0) REVERT: e 28 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7478 (pp20) REVERT: e 54 THR cc_start: 0.7401 (m) cc_final: 0.7153 (p) REVERT: e 99 GLN cc_start: 0.6522 (mm110) cc_final: 0.6110 (mt0) REVERT: f 28 GLU cc_start: 0.7951 (OUTLIER) cc_final: 0.7514 (pp20) REVERT: f 54 THR cc_start: 0.7252 (m) cc_final: 0.7037 (p) REVERT: f 98 ASP cc_start: 0.8803 (m-30) cc_final: 0.8580 (m-30) REVERT: f 99 GLN cc_start: 0.6784 (mm110) cc_final: 0.6420 (mt0) REVERT: g 28 GLU cc_start: 0.7940 (OUTLIER) cc_final: 0.7625 (pp20) REVERT: g 60 LYS cc_start: 0.6357 (tppt) cc_final: 0.5506 (tppt) REVERT: g 99 GLN cc_start: 0.7278 (mm110) cc_final: 0.7021 (mt0) REVERT: h 50 HIS cc_start: 0.6469 (OUTLIER) cc_final: 0.4038 (p90) REVERT: h 54 THR cc_start: 0.7077 (m) cc_final: 0.6668 (p) REVERT: h 57 GLU cc_start: 0.8526 (tt0) cc_final: 0.7348 (pm20) REVERT: h 60 LYS cc_start: 0.6360 (tttp) cc_final: 0.5386 (pmtt) REVERT: h 99 GLN cc_start: 0.6666 (mt0) cc_final: 0.6401 (mt0) REVERT: i 28 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7401 (pp20) REVERT: i 50 HIS cc_start: 0.6938 (OUTLIER) cc_final: 0.6376 (t-170) REVERT: i 54 THR cc_start: 0.7142 (m) cc_final: 0.6826 (p) REVERT: i 99 GLN cc_start: 0.6534 (OUTLIER) cc_final: 0.6043 (mm-40) REVERT: j 6 LYS cc_start: 0.9042 (mtpp) cc_final: 0.8799 (mttp) REVERT: j 28 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7496 (pp20) REVERT: j 50 HIS cc_start: 0.7058 (OUTLIER) cc_final: 0.6631 (t-170) REVERT: j 54 THR cc_start: 0.7362 (m) cc_final: 0.7036 (p) REVERT: j 99 GLN cc_start: 0.6312 (OUTLIER) cc_final: 0.5936 (mm-40) REVERT: k 28 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7545 (pp20) REVERT: k 50 HIS cc_start: 0.7337 (OUTLIER) cc_final: 0.6977 (t-170) REVERT: k 54 THR cc_start: 0.7381 (m) cc_final: 0.7112 (p) REVERT: k 60 LYS cc_start: 0.6564 (tppt) cc_final: 0.6034 (tptp) REVERT: k 99 GLN cc_start: 0.6370 (mm110) cc_final: 0.5984 (mt0) REVERT: l 28 GLU cc_start: 0.7897 (OUTLIER) cc_final: 0.7517 (pp20) REVERT: l 54 THR cc_start: 0.7368 (m) cc_final: 0.7088 (p) REVERT: l 99 GLN cc_start: 0.6557 (mm110) cc_final: 0.6140 (mt0) REVERT: m 28 GLU cc_start: 0.7966 (OUTLIER) cc_final: 0.7536 (pp20) REVERT: m 54 THR cc_start: 0.7420 (m) cc_final: 0.7182 (p) outliers start: 35 outliers final: 4 residues processed: 220 average time/residue: 1.1787 time to fit residues: 276.9617 Evaluate side-chains 234 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 208 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 28 GLU Chi-restraints excluded: chain n residue 58 LYS Chi-restraints excluded: chain a residue 50 HIS Chi-restraints excluded: chain b residue 50 HIS Chi-restraints excluded: chain b residue 99 GLN Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain c residue 99 GLN Chi-restraints excluded: chain d residue 28 GLU Chi-restraints excluded: chain d residue 49 VAL Chi-restraints excluded: chain d residue 50 HIS Chi-restraints excluded: chain e residue 28 GLU Chi-restraints excluded: chain f residue 28 GLU Chi-restraints excluded: chain g residue 28 GLU Chi-restraints excluded: chain g residue 58 LYS Chi-restraints excluded: chain h residue 50 HIS Chi-restraints excluded: chain i residue 28 GLU Chi-restraints excluded: chain i residue 50 HIS Chi-restraints excluded: chain i residue 99 GLN Chi-restraints excluded: chain j residue 28 GLU Chi-restraints excluded: chain j residue 50 HIS Chi-restraints excluded: chain j residue 99 GLN Chi-restraints excluded: chain k residue 28 GLU Chi-restraints excluded: chain k residue 50 HIS Chi-restraints excluded: chain l residue 28 GLU Chi-restraints excluded: chain m residue 28 GLU Chi-restraints excluded: chain m residue 50 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 31 optimal weight: 3.9990 chunk 60 optimal weight: 6.9990 chunk 5 optimal weight: 0.0000 chunk 97 optimal weight: 0.4980 chunk 74 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 62 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 108 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 overall best weight: 1.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4042 r_free = 0.4042 target = 0.147717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.125278 restraints weight = 33495.073| |-----------------------------------------------------------------------------| r_work (start): 0.3731 rms_B_bonded: 2.50 r_work: 0.3625 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3506 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8620 moved from start: 0.3692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9730 Z= 0.128 Angle : 0.524 5.832 13048 Z= 0.313 Chirality : 0.055 0.169 1624 Planarity : 0.001 0.007 1638 Dihedral : 5.961 47.270 1390 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 3.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.24 % Favored : 89.76 % Rotamer: Outliers : 2.38 % Allowed : 31.68 % Favored : 65.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.87 (0.17), residues: 1358 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.13), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR k 39 PHE 0.012 0.002 PHE f 4 HIS 0.001 0.000 HIS a 50 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 9730) covalent geometry : angle 0.52362 (13048) hydrogen bonds : bond 0.06873 ( 169) hydrogen bonds : angle 6.47635 ( 507) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 211 time to evaluate : 0.502 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: n 28 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7570 (pp20) REVERT: a 50 HIS cc_start: 0.6502 (OUTLIER) cc_final: 0.4044 (p90) REVERT: a 54 THR cc_start: 0.7027 (m) cc_final: 0.6645 (p) REVERT: a 57 GLU cc_start: 0.8525 (tt0) cc_final: 0.7361 (pm20) REVERT: a 60 LYS cc_start: 0.6362 (tttp) cc_final: 0.5377 (pmtt) REVERT: a 99 GLN cc_start: 0.6731 (mt0) cc_final: 0.6505 (mt0) REVERT: b 50 HIS cc_start: 0.6965 (OUTLIER) cc_final: 0.6280 (t-170) REVERT: b 54 THR cc_start: 0.7165 (m) cc_final: 0.6924 (p) REVERT: b 99 GLN cc_start: 0.6573 (OUTLIER) cc_final: 0.6235 (mm-40) REVERT: c 6 LYS cc_start: 0.9038 (mtpp) cc_final: 0.8795 (mttp) REVERT: c 28 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7681 (pp20) REVERT: c 50 HIS cc_start: 0.7161 (OUTLIER) cc_final: 0.6724 (t-170) REVERT: c 54 THR cc_start: 0.7319 (m) cc_final: 0.7015 (p) REVERT: c 99 GLN cc_start: 0.6389 (mm-40) cc_final: 0.6064 (mt0) REVERT: d 54 THR cc_start: 0.7377 (m) cc_final: 0.7130 (p) REVERT: d 60 LYS cc_start: 0.6592 (tppt) cc_final: 0.6084 (tptp) REVERT: d 99 GLN cc_start: 0.6451 (mm110) cc_final: 0.6077 (mt0) REVERT: e 54 THR cc_start: 0.7333 (m) cc_final: 0.7120 (p) REVERT: e 99 GLN cc_start: 0.6486 (mm110) cc_final: 0.6066 (mt0) REVERT: f 98 ASP cc_start: 0.8788 (m-30) cc_final: 0.8547 (m-30) REVERT: f 99 GLN cc_start: 0.6789 (mm110) cc_final: 0.6448 (mt0) REVERT: g 28 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.7601 (pp20) REVERT: g 60 LYS cc_start: 0.6344 (tppt) cc_final: 0.5509 (tppt) REVERT: g 99 GLN cc_start: 0.7317 (mm110) cc_final: 0.7022 (mt0) REVERT: h 50 HIS cc_start: 0.6498 (OUTLIER) cc_final: 0.4048 (p90) REVERT: h 54 THR cc_start: 0.7062 (m) cc_final: 0.6709 (p) REVERT: h 57 GLU cc_start: 0.8514 (tt0) cc_final: 0.7338 (pm20) REVERT: h 60 LYS cc_start: 0.6355 (tttp) cc_final: 0.5372 (pmtt) REVERT: h 99 GLN cc_start: 0.6685 (mt0) cc_final: 0.6442 (mt0) REVERT: i 50 HIS cc_start: 0.6976 (OUTLIER) cc_final: 0.6305 (t-170) REVERT: i 54 THR cc_start: 0.7185 (m) cc_final: 0.6936 (p) REVERT: i 99 GLN cc_start: 0.6603 (OUTLIER) cc_final: 0.6268 (mm-40) REVERT: j 6 LYS cc_start: 0.9047 (mtpp) cc_final: 0.8804 (mttp) REVERT: j 54 THR cc_start: 0.7335 (m) cc_final: 0.7031 (p) REVERT: j 99 GLN cc_start: 0.6287 (mm-40) cc_final: 0.6034 (mt0) REVERT: k 54 THR cc_start: 0.7385 (m) cc_final: 0.7129 (p) REVERT: l 54 THR cc_start: 0.7371 (m) cc_final: 0.7119 (p) REVERT: l 99 GLN cc_start: 0.6471 (mm110) cc_final: 0.6032 (mm-40) REVERT: m 54 THR cc_start: 0.7409 (m) cc_final: 0.7191 (p) outliers start: 23 outliers final: 4 residues processed: 223 average time/residue: 1.1728 time to fit residues: 278.7584 Evaluate side-chains 222 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 208 time to evaluate : 0.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 28 GLU Chi-restraints excluded: chain n residue 58 LYS Chi-restraints excluded: chain a residue 50 HIS Chi-restraints excluded: chain b residue 50 HIS Chi-restraints excluded: chain b residue 99 GLN Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain c residue 50 HIS Chi-restraints excluded: chain g residue 28 GLU Chi-restraints excluded: chain g residue 58 LYS Chi-restraints excluded: chain h residue 50 HIS Chi-restraints excluded: chain i residue 50 HIS Chi-restraints excluded: chain i residue 99 GLN Chi-restraints excluded: chain k residue 49 VAL Chi-restraints excluded: chain m residue 50 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 2 optimal weight: 3.9990 chunk 97 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 101 optimal weight: 2.9990 chunk 103 optimal weight: 5.9990 chunk 114 optimal weight: 7.9990 chunk 13 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 chunk 96 optimal weight: 3.9990 chunk 89 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.144801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.122629 restraints weight = 33638.499| |-----------------------------------------------------------------------------| r_work (start): 0.3696 rms_B_bonded: 2.50 r_work: 0.3591 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9730 Z= 0.197 Angle : 0.596 6.034 13048 Z= 0.357 Chirality : 0.056 0.177 1624 Planarity : 0.002 0.007 1638 Dihedral : 6.185 47.464 1390 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 3.00 % Allowed : 31.37 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.97 (0.17), residues: 1358 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.13), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR d 39 PHE 0.014 0.002 PHE f 4 HIS 0.002 0.001 HIS k 50 Details of bonding type rmsd covalent geometry : bond 0.00455 ( 9730) covalent geometry : angle 0.59596 (13048) hydrogen bonds : bond 0.08044 ( 169) hydrogen bonds : angle 6.68754 ( 507) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 210 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: n 28 GLU cc_start: 0.7916 (OUTLIER) cc_final: 0.7574 (pp20) REVERT: a 50 HIS cc_start: 0.6545 (OUTLIER) cc_final: 0.4046 (p90) REVERT: a 54 THR cc_start: 0.7019 (m) cc_final: 0.6662 (p) REVERT: a 57 GLU cc_start: 0.8530 (tt0) cc_final: 0.7426 (pm20) REVERT: a 60 LYS cc_start: 0.6493 (tttp) cc_final: 0.5478 (pmtt) REVERT: a 99 GLN cc_start: 0.6640 (mt0) cc_final: 0.6384 (mt0) REVERT: b 50 HIS cc_start: 0.7058 (OUTLIER) cc_final: 0.6386 (t-170) REVERT: b 54 THR cc_start: 0.7229 (m) cc_final: 0.7012 (p) REVERT: b 99 GLN cc_start: 0.6595 (OUTLIER) cc_final: 0.6267 (mm-40) REVERT: c 6 LYS cc_start: 0.9043 (mtpp) cc_final: 0.8830 (mttm) REVERT: c 28 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7590 (pp20) REVERT: c 54 THR cc_start: 0.7386 (m) cc_final: 0.7071 (p) REVERT: c 99 GLN cc_start: 0.6404 (OUTLIER) cc_final: 0.6042 (mt0) REVERT: d 28 GLU cc_start: 0.7904 (OUTLIER) cc_final: 0.7538 (pp20) REVERT: d 54 THR cc_start: 0.7491 (m) cc_final: 0.7240 (p) REVERT: d 60 LYS cc_start: 0.6721 (tppt) cc_final: 0.6210 (tptp) REVERT: d 99 GLN cc_start: 0.6535 (mm110) cc_final: 0.6237 (mt0) REVERT: e 28 GLU cc_start: 0.7854 (OUTLIER) cc_final: 0.7450 (pp20) REVERT: e 99 GLN cc_start: 0.6503 (mm110) cc_final: 0.6151 (mt0) REVERT: f 28 GLU cc_start: 0.7944 (OUTLIER) cc_final: 0.7488 (pp20) REVERT: f 98 ASP cc_start: 0.8809 (m-30) cc_final: 0.8595 (m-30) REVERT: f 99 GLN cc_start: 0.6864 (mm110) cc_final: 0.6549 (mt0) REVERT: g 28 GLU cc_start: 0.7977 (OUTLIER) cc_final: 0.7638 (pp20) REVERT: g 60 LYS cc_start: 0.6432 (tppt) cc_final: 0.5593 (tppt) REVERT: g 99 GLN cc_start: 0.7317 (mm110) cc_final: 0.7028 (mt0) REVERT: h 50 HIS cc_start: 0.6526 (OUTLIER) cc_final: 0.4048 (p90) REVERT: h 54 THR cc_start: 0.7044 (m) cc_final: 0.6691 (p) REVERT: h 57 GLU cc_start: 0.8538 (tt0) cc_final: 0.7429 (pm20) REVERT: h 60 LYS cc_start: 0.6497 (tttp) cc_final: 0.5481 (pmtt) REVERT: h 99 GLN cc_start: 0.6602 (mt0) cc_final: 0.6354 (mt0) REVERT: i 28 GLU cc_start: 0.7852 (OUTLIER) cc_final: 0.7448 (pp20) REVERT: i 50 HIS cc_start: 0.7018 (OUTLIER) cc_final: 0.6448 (t-170) REVERT: i 54 THR cc_start: 0.7263 (m) cc_final: 0.7031 (p) REVERT: i 99 GLN cc_start: 0.6637 (OUTLIER) cc_final: 0.6301 (mm-40) REVERT: j 6 LYS cc_start: 0.9064 (mtpp) cc_final: 0.8851 (mttm) REVERT: j 28 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7502 (pp20) REVERT: j 50 HIS cc_start: 0.7106 (OUTLIER) cc_final: 0.6806 (t-170) REVERT: j 54 THR cc_start: 0.7408 (m) cc_final: 0.7100 (p) REVERT: j 99 GLN cc_start: 0.6318 (OUTLIER) cc_final: 0.6045 (mt0) REVERT: k 28 GLU cc_start: 0.7933 (OUTLIER) cc_final: 0.7577 (pp20) REVERT: k 54 THR cc_start: 0.7455 (m) cc_final: 0.7213 (p) REVERT: l 28 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7525 (pp20) REVERT: l 54 THR cc_start: 0.7412 (m) cc_final: 0.7171 (p) REVERT: l 99 GLN cc_start: 0.6571 (mm110) cc_final: 0.6103 (mm-40) REVERT: m 28 GLU cc_start: 0.7962 (OUTLIER) cc_final: 0.7525 (pp20) REVERT: m 54 THR cc_start: 0.7460 (m) cc_final: 0.7250 (p) outliers start: 29 outliers final: 6 residues processed: 222 average time/residue: 1.2026 time to fit residues: 284.3911 Evaluate side-chains 226 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 200 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 28 GLU Chi-restraints excluded: chain n residue 33 THR Chi-restraints excluded: chain n residue 58 LYS Chi-restraints excluded: chain a residue 50 HIS Chi-restraints excluded: chain b residue 50 HIS Chi-restraints excluded: chain b residue 99 GLN Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain c residue 99 GLN Chi-restraints excluded: chain d residue 28 GLU Chi-restraints excluded: chain d residue 61 GLU Chi-restraints excluded: chain e residue 28 GLU Chi-restraints excluded: chain f residue 28 GLU Chi-restraints excluded: chain g residue 28 GLU Chi-restraints excluded: chain g residue 58 LYS Chi-restraints excluded: chain h residue 50 HIS Chi-restraints excluded: chain i residue 28 GLU Chi-restraints excluded: chain i residue 50 HIS Chi-restraints excluded: chain i residue 99 GLN Chi-restraints excluded: chain j residue 28 GLU Chi-restraints excluded: chain j residue 50 HIS Chi-restraints excluded: chain j residue 99 GLN Chi-restraints excluded: chain k residue 28 GLU Chi-restraints excluded: chain k residue 49 VAL Chi-restraints excluded: chain l residue 28 GLU Chi-restraints excluded: chain m residue 28 GLU Chi-restraints excluded: chain m residue 50 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 57 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 113 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 101 optimal weight: 3.9990 chunk 71 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 102 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.144383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.122234 restraints weight = 33354.786| |-----------------------------------------------------------------------------| r_work (start): 0.3690 rms_B_bonded: 2.48 r_work: 0.3585 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3465 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 9730 Z= 0.203 Angle : 0.604 6.098 13048 Z= 0.361 Chirality : 0.057 0.181 1624 Planarity : 0.002 0.007 1638 Dihedral : 6.242 47.407 1390 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.68 % Favored : 89.32 % Rotamer: Outliers : 3.11 % Allowed : 32.09 % Favored : 64.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.17), residues: 1358 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.13), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR d 39 PHE 0.014 0.002 PHE f 4 HIS 0.002 0.001 HIS k 50 Details of bonding type rmsd covalent geometry : bond 0.00472 ( 9730) covalent geometry : angle 0.60386 (13048) hydrogen bonds : bond 0.08012 ( 169) hydrogen bonds : angle 6.64688 ( 507) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 200 time to evaluate : 0.550 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: n 28 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7589 (pp20) REVERT: a 50 HIS cc_start: 0.6546 (OUTLIER) cc_final: 0.4077 (p90) REVERT: a 54 THR cc_start: 0.7047 (m) cc_final: 0.6650 (p) REVERT: a 57 GLU cc_start: 0.8515 (tt0) cc_final: 0.7371 (pm20) REVERT: a 60 LYS cc_start: 0.6531 (tttp) cc_final: 0.5543 (pmtt) REVERT: a 99 GLN cc_start: 0.6655 (mt0) cc_final: 0.6372 (mt0) REVERT: b 54 THR cc_start: 0.7235 (m) cc_final: 0.7034 (p) REVERT: b 99 GLN cc_start: 0.6561 (OUTLIER) cc_final: 0.6233 (mm-40) REVERT: c 6 LYS cc_start: 0.9024 (mtpp) cc_final: 0.8804 (mttm) REVERT: c 28 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7578 (pp20) REVERT: c 50 HIS cc_start: 0.7243 (OUTLIER) cc_final: 0.6842 (t-170) REVERT: c 54 THR cc_start: 0.7373 (m) cc_final: 0.7068 (p) REVERT: c 99 GLN cc_start: 0.6367 (OUTLIER) cc_final: 0.6001 (mt0) REVERT: d 28 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7552 (pp20) REVERT: d 54 THR cc_start: 0.7493 (m) cc_final: 0.7239 (p) REVERT: d 60 LYS cc_start: 0.6746 (tppt) cc_final: 0.6163 (tptp) REVERT: d 99 GLN cc_start: 0.6534 (mm110) cc_final: 0.6230 (mt0) REVERT: e 28 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.7471 (pp20) REVERT: e 99 GLN cc_start: 0.6508 (mm110) cc_final: 0.6045 (mt0) REVERT: f 28 GLU cc_start: 0.7947 (OUTLIER) cc_final: 0.7490 (pp20) REVERT: f 99 GLN cc_start: 0.6829 (mm110) cc_final: 0.6419 (mt0) REVERT: g 28 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7605 (pp20) REVERT: g 54 THR cc_start: 0.7021 (m) cc_final: 0.6783 (p) REVERT: g 99 GLN cc_start: 0.7312 (mm110) cc_final: 0.7046 (mt0) REVERT: h 50 HIS cc_start: 0.6505 (OUTLIER) cc_final: 0.4012 (p90) REVERT: h 54 THR cc_start: 0.7020 (m) cc_final: 0.6660 (p) REVERT: h 57 GLU cc_start: 0.8518 (tt0) cc_final: 0.7367 (pm20) REVERT: h 60 LYS cc_start: 0.6529 (tttp) cc_final: 0.5539 (pmtt) REVERT: h 99 GLN cc_start: 0.6636 (mt0) cc_final: 0.6356 (mt0) REVERT: i 28 GLU cc_start: 0.7868 (OUTLIER) cc_final: 0.7468 (pp20) REVERT: i 50 HIS cc_start: 0.7044 (OUTLIER) cc_final: 0.6353 (t-170) REVERT: i 99 GLN cc_start: 0.6617 (OUTLIER) cc_final: 0.6289 (mm-40) REVERT: j 6 LYS cc_start: 0.9065 (mtpp) cc_final: 0.8846 (mttm) REVERT: j 28 GLU cc_start: 0.7915 (OUTLIER) cc_final: 0.7503 (pp20) REVERT: j 50 HIS cc_start: 0.7117 (OUTLIER) cc_final: 0.6708 (t-170) REVERT: j 54 THR cc_start: 0.7366 (m) cc_final: 0.7061 (p) REVERT: j 99 GLN cc_start: 0.6252 (OUTLIER) cc_final: 0.5769 (mt0) REVERT: k 28 GLU cc_start: 0.7919 (OUTLIER) cc_final: 0.7567 (pp20) REVERT: k 54 THR cc_start: 0.7424 (m) cc_final: 0.7168 (p) REVERT: k 99 GLN cc_start: 0.6294 (mm110) cc_final: 0.5829 (mt0) REVERT: l 28 GLU cc_start: 0.7923 (OUTLIER) cc_final: 0.7530 (pp20) REVERT: l 54 THR cc_start: 0.7370 (m) cc_final: 0.7135 (p) REVERT: l 99 GLN cc_start: 0.6619 (mm110) cc_final: 0.6217 (mt0) REVERT: m 28 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7553 (pp20) REVERT: m 54 THR cc_start: 0.7469 (m) cc_final: 0.7252 (p) REVERT: m 98 ASP cc_start: 0.8628 (m-30) cc_final: 0.8303 (m-30) outliers start: 30 outliers final: 6 residues processed: 212 average time/residue: 1.2703 time to fit residues: 287.0388 Evaluate side-chains 222 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 196 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 28 GLU Chi-restraints excluded: chain n residue 33 THR Chi-restraints excluded: chain n residue 58 LYS Chi-restraints excluded: chain a residue 50 HIS Chi-restraints excluded: chain b residue 99 GLN Chi-restraints excluded: chain c residue 28 GLU Chi-restraints excluded: chain c residue 50 HIS Chi-restraints excluded: chain c residue 99 GLN Chi-restraints excluded: chain d residue 28 GLU Chi-restraints excluded: chain d residue 61 GLU Chi-restraints excluded: chain e residue 28 GLU Chi-restraints excluded: chain f residue 28 GLU Chi-restraints excluded: chain g residue 28 GLU Chi-restraints excluded: chain g residue 58 LYS Chi-restraints excluded: chain h residue 50 HIS Chi-restraints excluded: chain i residue 28 GLU Chi-restraints excluded: chain i residue 50 HIS Chi-restraints excluded: chain i residue 99 GLN Chi-restraints excluded: chain j residue 28 GLU Chi-restraints excluded: chain j residue 50 HIS Chi-restraints excluded: chain j residue 99 GLN Chi-restraints excluded: chain k residue 28 GLU Chi-restraints excluded: chain k residue 49 VAL Chi-restraints excluded: chain l residue 28 GLU Chi-restraints excluded: chain m residue 28 GLU Chi-restraints excluded: chain m residue 50 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 54 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 66 optimal weight: 0.1980 chunk 36 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.150321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.127767 restraints weight = 33150.737| |-----------------------------------------------------------------------------| r_work (start): 0.3758 rms_B_bonded: 2.51 r_work: 0.3653 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3532 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.3966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 9730 Z= 0.095 Angle : 0.498 5.693 13048 Z= 0.295 Chirality : 0.054 0.162 1624 Planarity : 0.001 0.005 1638 Dihedral : 5.769 46.668 1390 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 1.14 % Allowed : 34.78 % Favored : 64.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.78 (0.17), residues: 1358 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.11 (0.13), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR c 39 PHE 0.010 0.001 PHE f 4 HIS 0.002 0.000 HIS h 50 Details of bonding type rmsd covalent geometry : bond 0.00203 ( 9730) covalent geometry : angle 0.49816 (13048) hydrogen bonds : bond 0.05940 ( 169) hydrogen bonds : angle 6.25629 ( 507) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2716 Ramachandran restraints generated. 1358 Oldfield, 0 Emsley, 1358 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 206 time to evaluate : 0.548 Fit side-chains revert: symmetry clash REVERT: a 50 HIS cc_start: 0.6368 (OUTLIER) cc_final: 0.4099 (p90) REVERT: a 54 THR cc_start: 0.6866 (m) cc_final: 0.6551 (p) REVERT: a 57 GLU cc_start: 0.8527 (tt0) cc_final: 0.7394 (pm20) REVERT: a 60 LYS cc_start: 0.6584 (tttp) cc_final: 0.5554 (pmtt) REVERT: a 99 GLN cc_start: 0.6707 (mt0) cc_final: 0.6455 (mt0) REVERT: b 54 THR cc_start: 0.7076 (m) cc_final: 0.6755 (p) REVERT: b 99 GLN cc_start: 0.6580 (OUTLIER) cc_final: 0.6268 (mm-40) REVERT: c 6 LYS cc_start: 0.9021 (mtpp) cc_final: 0.8785 (mttp) REVERT: c 54 THR cc_start: 0.7165 (m) cc_final: 0.6823 (p) REVERT: c 99 GLN cc_start: 0.6330 (OUTLIER) cc_final: 0.5965 (mt0) REVERT: d 54 THR cc_start: 0.7385 (m) cc_final: 0.7083 (p) REVERT: d 60 LYS cc_start: 0.6643 (tppt) cc_final: 0.6050 (tptp) REVERT: d 99 GLN cc_start: 0.6556 (mm110) cc_final: 0.6288 (mt0) REVERT: e 99 GLN cc_start: 0.6424 (mm110) cc_final: 0.6084 (mt0) REVERT: f 99 GLN cc_start: 0.6678 (mm110) cc_final: 0.6371 (mt0) REVERT: g 54 THR cc_start: 0.6763 (m) cc_final: 0.6537 (p) REVERT: g 58 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7962 (ttpt) REVERT: g 99 GLN cc_start: 0.7320 (mm110) cc_final: 0.7085 (mt0) REVERT: h 50 HIS cc_start: 0.6478 (OUTLIER) cc_final: 0.4077 (p90) REVERT: h 54 THR cc_start: 0.6926 (m) cc_final: 0.6622 (p) REVERT: h 57 GLU cc_start: 0.8502 (tt0) cc_final: 0.7358 (pm20) REVERT: h 60 LYS cc_start: 0.6564 (tttp) cc_final: 0.5537 (pmtt) REVERT: h 99 GLN cc_start: 0.6691 (mt0) cc_final: 0.6430 (mt0) REVERT: i 99 GLN cc_start: 0.6590 (OUTLIER) cc_final: 0.6277 (mm-40) REVERT: j 6 LYS cc_start: 0.9045 (mtpp) cc_final: 0.8805 (mttp) REVERT: j 54 THR cc_start: 0.7181 (m) cc_final: 0.6822 (p) REVERT: j 61 GLU cc_start: 0.7851 (mt-10) cc_final: 0.7407 (mm-30) REVERT: j 99 GLN cc_start: 0.6204 (mm-40) cc_final: 0.5935 (mt0) REVERT: k 54 THR cc_start: 0.7266 (m) cc_final: 0.6964 (p) REVERT: l 54 THR cc_start: 0.7211 (m) cc_final: 0.6984 (p) REVERT: l 99 GLN cc_start: 0.6640 (mm110) cc_final: 0.6207 (mm-40) REVERT: m 54 THR cc_start: 0.7342 (m) cc_final: 0.7138 (p) outliers start: 11 outliers final: 2 residues processed: 210 average time/residue: 1.2681 time to fit residues: 283.8685 Evaluate side-chains 207 residues out of total 966 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 199 time to evaluate : 0.529 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain n residue 58 LYS Chi-restraints excluded: chain a residue 50 HIS Chi-restraints excluded: chain b residue 99 GLN Chi-restraints excluded: chain c residue 99 GLN Chi-restraints excluded: chain g residue 58 LYS Chi-restraints excluded: chain h residue 50 HIS Chi-restraints excluded: chain i residue 99 GLN Chi-restraints excluded: chain k residue 49 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 126 random chunks: chunk 92 optimal weight: 3.9990 chunk 105 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 68 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 50 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 114 optimal weight: 0.8980 chunk 108 optimal weight: 0.0980 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4034 r_free = 0.4034 target = 0.145990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.123744 restraints weight = 33390.499| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 2.49 r_work: 0.3612 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.4022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9730 Z= 0.163 Angle : 0.558 5.928 13048 Z= 0.334 Chirality : 0.055 0.168 1624 Planarity : 0.002 0.006 1638 Dihedral : 5.977 47.493 1390 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.53 % Favored : 89.47 % Rotamer: Outliers : 1.14 % Allowed : 34.58 % Favored : 64.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.86 (0.17), residues: 1358 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.13), residues: 1358 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR k 39 PHE 0.012 0.002 PHE f 4 HIS 0.001 0.000 HIS h 50 Details of bonding type rmsd covalent geometry : bond 0.00374 ( 9730) covalent geometry : angle 0.55838 (13048) hydrogen bonds : bond 0.07448 ( 169) hydrogen bonds : angle 6.58359 ( 507) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6833.67 seconds wall clock time: 116 minutes 20.90 seconds (6980.90 seconds total)