Starting phenix.real_space_refine on Mon Jul 6 04:45:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9hge_52134/07_2026/9hge_52134.cif Found real_map, /net/cci-nas-00/data/ceres_data/9hge_52134/07_2026/9hge_52134.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9hge_52134/07_2026/9hge_52134.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9hge_52134/07_2026/9hge_52134.map" model { file = "/net/cci-nas-00/data/ceres_data/9hge_52134/07_2026/9hge_52134.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9hge_52134/07_2026/9hge_52134.cif" } resolution = 4.5 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 240 5.16 5 C 20360 2.51 5 N 5480 2.21 5 O 6240 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 40 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32320 Number of models: 1 Model: "" Number of chains: 40 Chain: "A" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "B" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "C" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "D" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "E" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "F" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "G" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "H" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "I" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "J" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "K" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "L" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "M" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "N" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "O" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "P" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "Q" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "R" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "S" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "T" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "U" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "V" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "W" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "X" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "Y" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "Z" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "a" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "b" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "c" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "d" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "e" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "f" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "g" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "h" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "i" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "j" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "k" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "l" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "m" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Chain: "n" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 808 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Time building chain proxies: 6.33, per 1000 atoms: 0.20 Number of scatterers: 32320 At special positions: 0 Unit cell: (176.169, 176.169, 296.971, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 240 16.00 O 6240 8.00 N 5480 7.00 C 20360 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.45 Conformation dependent library (CDL) restraints added in 1.2 seconds 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7840 Finding SS restraints... Secondary structure from input PDB file: 120 helices and 80 sheets defined 22.1% alpha, 34.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 42 through 55 removed outlier: 3.524A pdb=" N LEU A 47 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 82 through 87 Processing helix chain 'A' and resid 88 through 90 No H-bonds generated for 'chain 'A' and resid 88 through 90' Processing helix chain 'B' and resid 42 through 55 removed outlier: 3.521A pdb=" N LEU B 47 " --> pdb=" O PRO B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 87 Processing helix chain 'B' and resid 88 through 90 No H-bonds generated for 'chain 'B' and resid 88 through 90' Processing helix chain 'C' and resid 42 through 55 removed outlier: 3.523A pdb=" N LEU C 47 " --> pdb=" O PRO C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 87 Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing helix chain 'D' and resid 42 through 55 removed outlier: 3.525A pdb=" N LEU D 47 " --> pdb=" O PRO D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 82 through 87 Processing helix chain 'D' and resid 88 through 90 No H-bonds generated for 'chain 'D' and resid 88 through 90' Processing helix chain 'E' and resid 42 through 55 removed outlier: 3.529A pdb=" N LEU E 47 " --> pdb=" O PRO E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 87 Processing helix chain 'E' and resid 88 through 90 No H-bonds generated for 'chain 'E' and resid 88 through 90' Processing helix chain 'F' and resid 42 through 55 removed outlier: 3.528A pdb=" N LEU F 47 " --> pdb=" O PRO F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 87 Processing helix chain 'F' and resid 88 through 90 No H-bonds generated for 'chain 'F' and resid 88 through 90' Processing helix chain 'G' and resid 42 through 55 removed outlier: 3.527A pdb=" N LEU G 47 " --> pdb=" O PRO G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 87 Processing helix chain 'G' and resid 88 through 90 No H-bonds generated for 'chain 'G' and resid 88 through 90' Processing helix chain 'H' and resid 42 through 55 removed outlier: 3.523A pdb=" N LEU H 47 " --> pdb=" O PRO H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 82 through 87 Processing helix chain 'H' and resid 88 through 90 No H-bonds generated for 'chain 'H' and resid 88 through 90' Processing helix chain 'I' and resid 42 through 55 removed outlier: 3.522A pdb=" N LEU I 47 " --> pdb=" O PRO I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 82 through 87 Processing helix chain 'I' and resid 88 through 90 No H-bonds generated for 'chain 'I' and resid 88 through 90' Processing helix chain 'J' and resid 42 through 55 removed outlier: 3.523A pdb=" N LEU J 47 " --> pdb=" O PRO J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 82 through 87 Processing helix chain 'J' and resid 88 through 90 No H-bonds generated for 'chain 'J' and resid 88 through 90' Processing helix chain 'K' and resid 42 through 55 removed outlier: 3.526A pdb=" N LEU K 47 " --> pdb=" O PRO K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 87 Processing helix chain 'K' and resid 88 through 90 No H-bonds generated for 'chain 'K' and resid 88 through 90' Processing helix chain 'L' and resid 42 through 55 removed outlier: 3.528A pdb=" N LEU L 47 " --> pdb=" O PRO L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 87 Processing helix chain 'L' and resid 88 through 90 No H-bonds generated for 'chain 'L' and resid 88 through 90' Processing helix chain 'M' and resid 42 through 55 removed outlier: 3.529A pdb=" N LEU M 47 " --> pdb=" O PRO M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 87 Processing helix chain 'M' and resid 88 through 90 No H-bonds generated for 'chain 'M' and resid 88 through 90' Processing helix chain 'N' and resid 42 through 55 removed outlier: 3.526A pdb=" N LEU N 47 " --> pdb=" O PRO N 43 " (cutoff:3.500A) Processing helix chain 'N' and resid 82 through 87 Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'O' and resid 42 through 55 removed outlier: 3.524A pdb=" N LEU O 47 " --> pdb=" O PRO O 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 87 Processing helix chain 'O' and resid 88 through 90 No H-bonds generated for 'chain 'O' and resid 88 through 90' Processing helix chain 'P' and resid 42 through 55 removed outlier: 3.522A pdb=" N LEU P 47 " --> pdb=" O PRO P 43 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 87 Processing helix chain 'P' and resid 88 through 90 No H-bonds generated for 'chain 'P' and resid 88 through 90' Processing helix chain 'Q' and resid 42 through 55 removed outlier: 3.523A pdb=" N LEU Q 47 " --> pdb=" O PRO Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 82 through 87 Processing helix chain 'Q' and resid 88 through 90 No H-bonds generated for 'chain 'Q' and resid 88 through 90' Processing helix chain 'R' and resid 42 through 55 removed outlier: 3.526A pdb=" N LEU R 47 " --> pdb=" O PRO R 43 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 87 Processing helix chain 'R' and resid 88 through 90 No H-bonds generated for 'chain 'R' and resid 88 through 90' Processing helix chain 'S' and resid 42 through 55 removed outlier: 3.528A pdb=" N LEU S 47 " --> pdb=" O PRO S 43 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 87 Processing helix chain 'S' and resid 88 through 90 No H-bonds generated for 'chain 'S' and resid 88 through 90' Processing helix chain 'T' and resid 42 through 55 removed outlier: 3.528A pdb=" N LEU T 47 " --> pdb=" O PRO T 43 " (cutoff:3.500A) Processing helix chain 'T' and resid 82 through 87 Processing helix chain 'T' and resid 88 through 90 No H-bonds generated for 'chain 'T' and resid 88 through 90' Processing helix chain 'U' and resid 42 through 55 removed outlier: 3.530A pdb=" N LEU U 47 " --> pdb=" O PRO U 43 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE U 55 " --> pdb=" O VAL U 51 " (cutoff:3.500A) Processing helix chain 'U' and resid 82 through 87 Processing helix chain 'U' and resid 88 through 90 No H-bonds generated for 'chain 'U' and resid 88 through 90' Processing helix chain 'V' and resid 42 through 55 removed outlier: 3.527A pdb=" N LEU V 47 " --> pdb=" O PRO V 43 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE V 55 " --> pdb=" O VAL V 51 " (cutoff:3.500A) Processing helix chain 'V' and resid 82 through 87 Processing helix chain 'V' and resid 88 through 90 No H-bonds generated for 'chain 'V' and resid 88 through 90' Processing helix chain 'W' and resid 42 through 55 removed outlier: 3.524A pdb=" N LEU W 47 " --> pdb=" O PRO W 43 " (cutoff:3.500A) Processing helix chain 'W' and resid 82 through 87 Processing helix chain 'W' and resid 88 through 90 No H-bonds generated for 'chain 'W' and resid 88 through 90' Processing helix chain 'X' and resid 42 through 55 removed outlier: 3.524A pdb=" N LEU X 47 " --> pdb=" O PRO X 43 " (cutoff:3.500A) Processing helix chain 'X' and resid 82 through 87 Processing helix chain 'X' and resid 88 through 90 No H-bonds generated for 'chain 'X' and resid 88 through 90' Processing helix chain 'Y' and resid 42 through 55 removed outlier: 3.525A pdb=" N LEU Y 47 " --> pdb=" O PRO Y 43 " (cutoff:3.500A) Processing helix chain 'Y' and resid 82 through 87 Processing helix chain 'Y' and resid 88 through 90 No H-bonds generated for 'chain 'Y' and resid 88 through 90' Processing helix chain 'Z' and resid 42 through 55 removed outlier: 3.529A pdb=" N LEU Z 47 " --> pdb=" O PRO Z 43 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE Z 55 " --> pdb=" O VAL Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 82 through 87 Processing helix chain 'Z' and resid 88 through 90 No H-bonds generated for 'chain 'Z' and resid 88 through 90' Processing helix chain 'a' and resid 42 through 55 removed outlier: 3.531A pdb=" N LEU a 47 " --> pdb=" O PRO a 43 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE a 55 " --> pdb=" O VAL a 51 " (cutoff:3.500A) Processing helix chain 'a' and resid 82 through 87 Processing helix chain 'a' and resid 88 through 90 No H-bonds generated for 'chain 'a' and resid 88 through 90' Processing helix chain 'b' and resid 42 through 55 removed outlier: 3.530A pdb=" N LEU b 47 " --> pdb=" O PRO b 43 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N PHE b 55 " --> pdb=" O VAL b 51 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 87 Processing helix chain 'b' and resid 88 through 90 No H-bonds generated for 'chain 'b' and resid 88 through 90' Processing helix chain 'c' and resid 42 through 55 removed outlier: 3.526A pdb=" N LEU c 47 " --> pdb=" O PRO c 43 " (cutoff:3.500A) Processing helix chain 'c' and resid 82 through 87 Processing helix chain 'c' and resid 88 through 90 No H-bonds generated for 'chain 'c' and resid 88 through 90' Processing helix chain 'd' and resid 42 through 55 removed outlier: 3.524A pdb=" N LEU d 47 " --> pdb=" O PRO d 43 " (cutoff:3.500A) Processing helix chain 'd' and resid 82 through 87 Processing helix chain 'd' and resid 88 through 90 No H-bonds generated for 'chain 'd' and resid 88 through 90' Processing helix chain 'e' and resid 42 through 55 removed outlier: 3.524A pdb=" N LEU e 47 " --> pdb=" O PRO e 43 " (cutoff:3.500A) Processing helix chain 'e' and resid 82 through 87 Processing helix chain 'e' and resid 88 through 90 No H-bonds generated for 'chain 'e' and resid 88 through 90' Processing helix chain 'f' and resid 42 through 55 removed outlier: 3.526A pdb=" N LEU f 47 " --> pdb=" O PRO f 43 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 87 Processing helix chain 'f' and resid 88 through 90 No H-bonds generated for 'chain 'f' and resid 88 through 90' Processing helix chain 'g' and resid 42 through 55 removed outlier: 3.529A pdb=" N LEU g 47 " --> pdb=" O PRO g 43 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE g 55 " --> pdb=" O VAL g 51 " (cutoff:3.500A) Processing helix chain 'g' and resid 82 through 87 Processing helix chain 'g' and resid 88 through 90 No H-bonds generated for 'chain 'g' and resid 88 through 90' Processing helix chain 'h' and resid 42 through 55 removed outlier: 3.530A pdb=" N LEU h 47 " --> pdb=" O PRO h 43 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE h 55 " --> pdb=" O VAL h 51 " (cutoff:3.500A) Processing helix chain 'h' and resid 82 through 87 Processing helix chain 'h' and resid 88 through 90 No H-bonds generated for 'chain 'h' and resid 88 through 90' Processing helix chain 'i' and resid 42 through 55 removed outlier: 3.529A pdb=" N LEU i 47 " --> pdb=" O PRO i 43 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N PHE i 55 " --> pdb=" O VAL i 51 " (cutoff:3.500A) Processing helix chain 'i' and resid 82 through 87 Processing helix chain 'i' and resid 88 through 90 No H-bonds generated for 'chain 'i' and resid 88 through 90' Processing helix chain 'j' and resid 42 through 55 removed outlier: 3.526A pdb=" N LEU j 47 " --> pdb=" O PRO j 43 " (cutoff:3.500A) Processing helix chain 'j' and resid 82 through 87 Processing helix chain 'j' and resid 88 through 90 No H-bonds generated for 'chain 'j' and resid 88 through 90' Processing helix chain 'k' and resid 42 through 55 removed outlier: 3.524A pdb=" N LEU k 47 " --> pdb=" O PRO k 43 " (cutoff:3.500A) Processing helix chain 'k' and resid 82 through 87 Processing helix chain 'k' and resid 88 through 90 No H-bonds generated for 'chain 'k' and resid 88 through 90' Processing helix chain 'l' and resid 42 through 55 removed outlier: 3.524A pdb=" N LEU l 47 " --> pdb=" O PRO l 43 " (cutoff:3.500A) Processing helix chain 'l' and resid 82 through 87 Processing helix chain 'l' and resid 88 through 90 No H-bonds generated for 'chain 'l' and resid 88 through 90' Processing helix chain 'm' and resid 42 through 55 removed outlier: 3.526A pdb=" N LEU m 47 " --> pdb=" O PRO m 43 " (cutoff:3.500A) Processing helix chain 'm' and resid 82 through 87 Processing helix chain 'm' and resid 88 through 90 No H-bonds generated for 'chain 'm' and resid 88 through 90' Processing helix chain 'n' and resid 42 through 55 removed outlier: 3.528A pdb=" N LEU n 47 " --> pdb=" O PRO n 43 " (cutoff:3.500A) Processing helix chain 'n' and resid 82 through 87 Processing helix chain 'n' and resid 88 through 90 No H-bonds generated for 'chain 'n' and resid 88 through 90' Processing sheet with id=AA1, first strand: chain 'A' and resid 17 through 20 removed outlier: 6.731A pdb=" N LEU A 10 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE A 20 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA A 8 " --> pdb=" O ILE A 20 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 20 removed outlier: 6.731A pdb=" N LEU A 10 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE A 20 " --> pdb=" O ALA A 8 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ALA A 8 " --> pdb=" O ILE A 20 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR A 5 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ILE A 97 " --> pdb=" O THR A 5 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LYS A 7 " --> pdb=" O ILE A 97 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE A 99 " --> pdb=" O LYS A 7 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR A 9 " --> pdb=" O ILE A 99 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU A 101 " --> pdb=" O TYR A 9 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N LEU A 11 " --> pdb=" O GLU A 101 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ARG A 96 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG A 68 " --> pdb=" O ARG A 96 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 17 through 20 removed outlier: 6.731A pdb=" N LEU B 10 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE B 20 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA B 8 " --> pdb=" O ILE B 20 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 17 through 20 removed outlier: 6.731A pdb=" N LEU B 10 " --> pdb=" O ARG B 18 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE B 20 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA B 8 " --> pdb=" O ILE B 20 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR B 5 " --> pdb=" O PHE B 95 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ILE B 97 " --> pdb=" O THR B 5 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LYS B 7 " --> pdb=" O ILE B 97 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE B 99 " --> pdb=" O LYS B 7 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N TYR B 9 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N GLU B 101 " --> pdb=" O TYR B 9 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N LEU B 11 " --> pdb=" O GLU B 101 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ARG B 96 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ARG B 68 " --> pdb=" O ARG B 96 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 17 through 20 removed outlier: 6.736A pdb=" N LEU C 10 " --> pdb=" O ARG C 18 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE C 20 " --> pdb=" O ALA C 8 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA C 8 " --> pdb=" O ILE C 20 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 17 through 20 removed outlier: 6.736A pdb=" N LEU C 10 " --> pdb=" O ARG C 18 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE C 20 " --> pdb=" O ALA C 8 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA C 8 " --> pdb=" O ILE C 20 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR C 5 " --> pdb=" O PHE C 95 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE C 97 " --> pdb=" O THR C 5 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LYS C 7 " --> pdb=" O ILE C 97 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE C 99 " --> pdb=" O LYS C 7 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR C 9 " --> pdb=" O ILE C 99 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N GLU C 101 " --> pdb=" O TYR C 9 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N LEU C 11 " --> pdb=" O GLU C 101 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ARG C 96 " --> pdb=" O ARG C 68 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ARG C 68 " --> pdb=" O ARG C 96 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 17 through 20 removed outlier: 6.742A pdb=" N LEU D 10 " --> pdb=" O ARG D 18 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE D 20 " --> pdb=" O ALA D 8 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA D 8 " --> pdb=" O ILE D 20 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 17 through 20 removed outlier: 6.742A pdb=" N LEU D 10 " --> pdb=" O ARG D 18 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE D 20 " --> pdb=" O ALA D 8 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA D 8 " --> pdb=" O ILE D 20 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR D 5 " --> pdb=" O PHE D 95 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILE D 97 " --> pdb=" O THR D 5 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LYS D 7 " --> pdb=" O ILE D 97 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE D 99 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR D 9 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU D 101 " --> pdb=" O TYR D 9 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N LEU D 11 " --> pdb=" O GLU D 101 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ARG D 96 " --> pdb=" O ARG D 68 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ARG D 68 " --> pdb=" O ARG D 96 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 17 through 20 removed outlier: 6.744A pdb=" N LEU E 10 " --> pdb=" O ARG E 18 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE E 20 " --> pdb=" O ALA E 8 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA E 8 " --> pdb=" O ILE E 20 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 17 through 20 removed outlier: 6.744A pdb=" N LEU E 10 " --> pdb=" O ARG E 18 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE E 20 " --> pdb=" O ALA E 8 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA E 8 " --> pdb=" O ILE E 20 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR E 5 " --> pdb=" O PHE E 95 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE E 97 " --> pdb=" O THR E 5 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS E 7 " --> pdb=" O ILE E 97 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE E 99 " --> pdb=" O LYS E 7 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR E 9 " --> pdb=" O ILE E 99 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU E 101 " --> pdb=" O TYR E 9 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N LEU E 11 " --> pdb=" O GLU E 101 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N ARG E 96 " --> pdb=" O ARG E 68 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ARG E 68 " --> pdb=" O ARG E 96 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 17 through 20 removed outlier: 6.741A pdb=" N LEU F 10 " --> pdb=" O ARG F 18 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE F 20 " --> pdb=" O ALA F 8 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA F 8 " --> pdb=" O ILE F 20 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 17 through 20 removed outlier: 6.741A pdb=" N LEU F 10 " --> pdb=" O ARG F 18 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N ILE F 20 " --> pdb=" O ALA F 8 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA F 8 " --> pdb=" O ILE F 20 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR F 5 " --> pdb=" O PHE F 95 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE F 97 " --> pdb=" O THR F 5 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LYS F 7 " --> pdb=" O ILE F 97 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE F 99 " --> pdb=" O LYS F 7 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR F 9 " --> pdb=" O ILE F 99 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU F 101 " --> pdb=" O TYR F 9 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N LEU F 11 " --> pdb=" O GLU F 101 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N ARG F 96 " --> pdb=" O ARG F 68 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ARG F 68 " --> pdb=" O ARG F 96 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 17 through 20 removed outlier: 6.735A pdb=" N LEU G 10 " --> pdb=" O ARG G 18 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE G 20 " --> pdb=" O ALA G 8 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA G 8 " --> pdb=" O ILE G 20 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 17 through 20 removed outlier: 6.735A pdb=" N LEU G 10 " --> pdb=" O ARG G 18 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE G 20 " --> pdb=" O ALA G 8 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA G 8 " --> pdb=" O ILE G 20 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR G 5 " --> pdb=" O PHE G 95 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE G 97 " --> pdb=" O THR G 5 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LYS G 7 " --> pdb=" O ILE G 97 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE G 99 " --> pdb=" O LYS G 7 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR G 9 " --> pdb=" O ILE G 99 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N GLU G 101 " --> pdb=" O TYR G 9 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N LEU G 11 " --> pdb=" O GLU G 101 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ARG G 96 " --> pdb=" O ARG G 68 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG G 68 " --> pdb=" O ARG G 96 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 17 through 20 removed outlier: 6.730A pdb=" N LEU H 10 " --> pdb=" O ARG H 18 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE H 20 " --> pdb=" O ALA H 8 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA H 8 " --> pdb=" O ILE H 20 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 17 through 20 removed outlier: 6.730A pdb=" N LEU H 10 " --> pdb=" O ARG H 18 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE H 20 " --> pdb=" O ALA H 8 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA H 8 " --> pdb=" O ILE H 20 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR H 5 " --> pdb=" O PHE H 95 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE H 97 " --> pdb=" O THR H 5 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LYS H 7 " --> pdb=" O ILE H 97 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE H 99 " --> pdb=" O LYS H 7 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR H 9 " --> pdb=" O ILE H 99 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N GLU H 101 " --> pdb=" O TYR H 9 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N LEU H 11 " --> pdb=" O GLU H 101 " (cutoff:3.500A) removed outlier: 8.020A pdb=" N ARG H 96 " --> pdb=" O ARG H 68 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG H 68 " --> pdb=" O ARG H 96 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 17 through 20 removed outlier: 6.731A pdb=" N LEU I 10 " --> pdb=" O ARG I 18 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE I 20 " --> pdb=" O ALA I 8 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA I 8 " --> pdb=" O ILE I 20 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 17 through 20 removed outlier: 6.731A pdb=" N LEU I 10 " --> pdb=" O ARG I 18 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ILE I 20 " --> pdb=" O ALA I 8 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ALA I 8 " --> pdb=" O ILE I 20 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR I 5 " --> pdb=" O PHE I 95 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ILE I 97 " --> pdb=" O THR I 5 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LYS I 7 " --> pdb=" O ILE I 97 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE I 99 " --> pdb=" O LYS I 7 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR I 9 " --> pdb=" O ILE I 99 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N GLU I 101 " --> pdb=" O TYR I 9 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N LEU I 11 " --> pdb=" O GLU I 101 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N ARG I 96 " --> pdb=" O ARG I 68 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ARG I 68 " --> pdb=" O ARG I 96 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 17 through 20 removed outlier: 6.737A pdb=" N LEU J 10 " --> pdb=" O ARG J 18 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE J 20 " --> pdb=" O ALA J 8 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA J 8 " --> pdb=" O ILE J 20 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 17 through 20 removed outlier: 6.737A pdb=" N LEU J 10 " --> pdb=" O ARG J 18 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE J 20 " --> pdb=" O ALA J 8 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ALA J 8 " --> pdb=" O ILE J 20 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR J 5 " --> pdb=" O PHE J 95 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE J 97 " --> pdb=" O THR J 5 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LYS J 7 " --> pdb=" O ILE J 97 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE J 99 " --> pdb=" O LYS J 7 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR J 9 " --> pdb=" O ILE J 99 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N GLU J 101 " --> pdb=" O TYR J 9 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N LEU J 11 " --> pdb=" O GLU J 101 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ARG J 96 " --> pdb=" O ARG J 68 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ARG J 68 " --> pdb=" O ARG J 96 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 17 through 20 removed outlier: 6.742A pdb=" N LEU K 10 " --> pdb=" O ARG K 18 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE K 20 " --> pdb=" O ALA K 8 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA K 8 " --> pdb=" O ILE K 20 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 17 through 20 removed outlier: 6.742A pdb=" N LEU K 10 " --> pdb=" O ARG K 18 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE K 20 " --> pdb=" O ALA K 8 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA K 8 " --> pdb=" O ILE K 20 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR K 5 " --> pdb=" O PHE K 95 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE K 97 " --> pdb=" O THR K 5 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS K 7 " --> pdb=" O ILE K 97 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE K 99 " --> pdb=" O LYS K 7 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR K 9 " --> pdb=" O ILE K 99 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N GLU K 101 " --> pdb=" O TYR K 9 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N LEU K 11 " --> pdb=" O GLU K 101 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ARG K 96 " --> pdb=" O ARG K 68 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ARG K 68 " --> pdb=" O ARG K 96 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 17 through 20 removed outlier: 6.744A pdb=" N LEU L 10 " --> pdb=" O ARG L 18 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE L 20 " --> pdb=" O ALA L 8 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA L 8 " --> pdb=" O ILE L 20 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 17 through 20 removed outlier: 6.744A pdb=" N LEU L 10 " --> pdb=" O ARG L 18 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE L 20 " --> pdb=" O ALA L 8 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ALA L 8 " --> pdb=" O ILE L 20 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR L 5 " --> pdb=" O PHE L 95 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE L 97 " --> pdb=" O THR L 5 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS L 7 " --> pdb=" O ILE L 97 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE L 99 " --> pdb=" O LYS L 7 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR L 9 " --> pdb=" O ILE L 99 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU L 101 " --> pdb=" O TYR L 9 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N LEU L 11 " --> pdb=" O GLU L 101 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ARG L 96 " --> pdb=" O ARG L 68 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ARG L 68 " --> pdb=" O ARG L 96 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 17 through 20 removed outlier: 6.740A pdb=" N LEU M 10 " --> pdb=" O ARG M 18 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE M 20 " --> pdb=" O ALA M 8 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA M 8 " --> pdb=" O ILE M 20 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 17 through 20 removed outlier: 6.740A pdb=" N LEU M 10 " --> pdb=" O ARG M 18 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE M 20 " --> pdb=" O ALA M 8 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA M 8 " --> pdb=" O ILE M 20 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N THR M 5 " --> pdb=" O PHE M 95 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE M 97 " --> pdb=" O THR M 5 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS M 7 " --> pdb=" O ILE M 97 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE M 99 " --> pdb=" O LYS M 7 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR M 9 " --> pdb=" O ILE M 99 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU M 101 " --> pdb=" O TYR M 9 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N LEU M 11 " --> pdb=" O GLU M 101 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ARG M 96 " --> pdb=" O ARG M 68 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ARG M 68 " --> pdb=" O ARG M 96 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 17 through 20 removed outlier: 6.733A pdb=" N LEU N 10 " --> pdb=" O ARG N 18 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE N 20 " --> pdb=" O ALA N 8 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA N 8 " --> pdb=" O ILE N 20 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 17 through 20 removed outlier: 6.733A pdb=" N LEU N 10 " --> pdb=" O ARG N 18 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ILE N 20 " --> pdb=" O ALA N 8 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA N 8 " --> pdb=" O ILE N 20 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR N 5 " --> pdb=" O PHE N 95 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE N 97 " --> pdb=" O THR N 5 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LYS N 7 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE N 99 " --> pdb=" O LYS N 7 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR N 9 " --> pdb=" O ILE N 99 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU N 101 " --> pdb=" O TYR N 9 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N LEU N 11 " --> pdb=" O GLU N 101 " (cutoff:3.500A) removed outlier: 8.021A pdb=" N ARG N 96 " --> pdb=" O ARG N 68 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG N 68 " --> pdb=" O ARG N 96 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 17 through 20 removed outlier: 6.731A pdb=" N LEU O 10 " --> pdb=" O ARG O 18 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE O 20 " --> pdb=" O ALA O 8 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA O 8 " --> pdb=" O ILE O 20 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 17 through 20 removed outlier: 6.731A pdb=" N LEU O 10 " --> pdb=" O ARG O 18 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ILE O 20 " --> pdb=" O ALA O 8 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ALA O 8 " --> pdb=" O ILE O 20 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N THR O 5 " --> pdb=" O PHE O 95 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE O 97 " --> pdb=" O THR O 5 " (cutoff:3.500A) removed outlier: 6.115A pdb=" N LYS O 7 " --> pdb=" O ILE O 97 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE O 99 " --> pdb=" O LYS O 7 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N TYR O 9 " --> pdb=" O ILE O 99 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU O 101 " --> pdb=" O TYR O 9 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N LEU O 11 " --> pdb=" O GLU O 101 " (cutoff:3.500A) removed outlier: 8.019A pdb=" N ARG O 96 " --> pdb=" O ARG O 68 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ARG O 68 " --> pdb=" O ARG O 96 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 17 through 20 removed outlier: 6.731A pdb=" N LEU P 10 " --> pdb=" O ARG P 18 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE P 20 " --> pdb=" O ALA P 8 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA P 8 " --> pdb=" O ILE P 20 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 17 through 20 removed outlier: 6.731A pdb=" N LEU P 10 " --> pdb=" O ARG P 18 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE P 20 " --> pdb=" O ALA P 8 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ALA P 8 " --> pdb=" O ILE P 20 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N THR P 5 " --> pdb=" O PHE P 95 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N ILE P 97 " --> pdb=" O THR P 5 " (cutoff:3.500A) removed outlier: 6.116A pdb=" N LYS P 7 " --> pdb=" O ILE P 97 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE P 99 " --> pdb=" O LYS P 7 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR P 9 " --> pdb=" O ILE P 99 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU P 101 " --> pdb=" O TYR P 9 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N LEU P 11 " --> pdb=" O GLU P 101 " (cutoff:3.500A) removed outlier: 8.013A pdb=" N ARG P 96 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 4.839A pdb=" N ARG P 68 " --> pdb=" O ARG P 96 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 17 through 20 removed outlier: 6.737A pdb=" N LEU Q 10 " --> pdb=" O ARG Q 18 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE Q 20 " --> pdb=" O ALA Q 8 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA Q 8 " --> pdb=" O ILE Q 20 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 17 through 20 removed outlier: 6.737A pdb=" N LEU Q 10 " --> pdb=" O ARG Q 18 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ILE Q 20 " --> pdb=" O ALA Q 8 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N ALA Q 8 " --> pdb=" O ILE Q 20 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR Q 5 " --> pdb=" O PHE Q 95 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE Q 97 " --> pdb=" O THR Q 5 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LYS Q 7 " --> pdb=" O ILE Q 97 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ILE Q 99 " --> pdb=" O LYS Q 7 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR Q 9 " --> pdb=" O ILE Q 99 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU Q 101 " --> pdb=" O TYR Q 9 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N LEU Q 11 " --> pdb=" O GLU Q 101 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N ARG Q 96 " --> pdb=" O ARG Q 68 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ARG Q 68 " --> pdb=" O ARG Q 96 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 17 through 20 removed outlier: 6.743A pdb=" N LEU R 10 " --> pdb=" O ARG R 18 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE R 20 " --> pdb=" O ALA R 8 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA R 8 " --> pdb=" O ILE R 20 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 17 through 20 removed outlier: 6.743A pdb=" N LEU R 10 " --> pdb=" O ARG R 18 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE R 20 " --> pdb=" O ALA R 8 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA R 8 " --> pdb=" O ILE R 20 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR R 5 " --> pdb=" O PHE R 95 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE R 97 " --> pdb=" O THR R 5 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS R 7 " --> pdb=" O ILE R 97 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE R 99 " --> pdb=" O LYS R 7 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR R 9 " --> pdb=" O ILE R 99 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N GLU R 101 " --> pdb=" O TYR R 9 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N LEU R 11 " --> pdb=" O GLU R 101 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ARG R 96 " --> pdb=" O ARG R 68 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ARG R 68 " --> pdb=" O ARG R 96 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'S' and resid 17 through 20 removed outlier: 6.743A pdb=" N LEU S 10 " --> pdb=" O ARG S 18 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE S 20 " --> pdb=" O ALA S 8 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA S 8 " --> pdb=" O ILE S 20 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 17 through 20 removed outlier: 6.743A pdb=" N LEU S 10 " --> pdb=" O ARG S 18 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE S 20 " --> pdb=" O ALA S 8 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA S 8 " --> pdb=" O ILE S 20 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR S 5 " --> pdb=" O PHE S 95 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE S 97 " --> pdb=" O THR S 5 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS S 7 " --> pdb=" O ILE S 97 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE S 99 " --> pdb=" O LYS S 7 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR S 9 " --> pdb=" O ILE S 99 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU S 101 " --> pdb=" O TYR S 9 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N LEU S 11 " --> pdb=" O GLU S 101 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ARG S 96 " --> pdb=" O ARG S 68 " (cutoff:3.500A) removed outlier: 4.837A pdb=" N ARG S 68 " --> pdb=" O ARG S 96 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'T' and resid 17 through 20 removed outlier: 6.740A pdb=" N LEU T 10 " --> pdb=" O ARG T 18 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE T 20 " --> pdb=" O ALA T 8 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA T 8 " --> pdb=" O ILE T 20 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'T' and resid 17 through 20 removed outlier: 6.740A pdb=" N LEU T 10 " --> pdb=" O ARG T 18 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N ILE T 20 " --> pdb=" O ALA T 8 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA T 8 " --> pdb=" O ILE T 20 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR T 5 " --> pdb=" O PHE T 95 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N ILE T 97 " --> pdb=" O THR T 5 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LYS T 7 " --> pdb=" O ILE T 97 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE T 99 " --> pdb=" O LYS T 7 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR T 9 " --> pdb=" O ILE T 99 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N GLU T 101 " --> pdb=" O TYR T 9 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N LEU T 11 " --> pdb=" O GLU T 101 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N ARG T 96 " --> pdb=" O ARG T 68 " (cutoff:3.500A) removed outlier: 4.840A pdb=" N ARG T 68 " --> pdb=" O ARG T 96 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'U' and resid 17 through 20 removed outlier: 6.754A pdb=" N LEU U 10 " --> pdb=" O ARG U 18 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE U 20 " --> pdb=" O ALA U 8 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA U 8 " --> pdb=" O ILE U 20 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'U' and resid 17 through 20 removed outlier: 6.754A pdb=" N LEU U 10 " --> pdb=" O ARG U 18 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE U 20 " --> pdb=" O ALA U 8 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA U 8 " --> pdb=" O ILE U 20 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR U 5 " --> pdb=" O PHE U 95 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE U 97 " --> pdb=" O THR U 5 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LYS U 7 " --> pdb=" O ILE U 97 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE U 99 " --> pdb=" O LYS U 7 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR U 9 " --> pdb=" O ILE U 99 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU U 101 " --> pdb=" O TYR U 9 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N LEU U 11 " --> pdb=" O GLU U 101 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ARG U 96 " --> pdb=" O ARG U 68 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ARG U 68 " --> pdb=" O ARG U 96 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 17 through 20 removed outlier: 6.752A pdb=" N LEU V 10 " --> pdb=" O ARG V 18 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE V 20 " --> pdb=" O ALA V 8 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA V 8 " --> pdb=" O ILE V 20 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'V' and resid 17 through 20 removed outlier: 6.752A pdb=" N LEU V 10 " --> pdb=" O ARG V 18 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE V 20 " --> pdb=" O ALA V 8 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA V 8 " --> pdb=" O ILE V 20 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR V 5 " --> pdb=" O PHE V 95 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE V 97 " --> pdb=" O THR V 5 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LYS V 7 " --> pdb=" O ILE V 97 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE V 99 " --> pdb=" O LYS V 7 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR V 9 " --> pdb=" O ILE V 99 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU V 101 " --> pdb=" O TYR V 9 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N LEU V 11 " --> pdb=" O GLU V 101 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N ARG V 96 " --> pdb=" O ARG V 68 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ARG V 68 " --> pdb=" O ARG V 96 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'W' and resid 17 through 20 removed outlier: 6.747A pdb=" N LEU W 10 " --> pdb=" O ARG W 18 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE W 20 " --> pdb=" O ALA W 8 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA W 8 " --> pdb=" O ILE W 20 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'W' and resid 17 through 20 removed outlier: 6.747A pdb=" N LEU W 10 " --> pdb=" O ARG W 18 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE W 20 " --> pdb=" O ALA W 8 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N ALA W 8 " --> pdb=" O ILE W 20 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR W 5 " --> pdb=" O PHE W 95 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILE W 97 " --> pdb=" O THR W 5 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LYS W 7 " --> pdb=" O ILE W 97 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE W 99 " --> pdb=" O LYS W 7 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR W 9 " --> pdb=" O ILE W 99 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU W 101 " --> pdb=" O TYR W 9 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N LEU W 11 " --> pdb=" O GLU W 101 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ARG W 96 " --> pdb=" O ARG W 68 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG W 68 " --> pdb=" O ARG W 96 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'X' and resid 17 through 20 removed outlier: 6.742A pdb=" N LEU X 10 " --> pdb=" O ARG X 18 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE X 20 " --> pdb=" O ALA X 8 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA X 8 " --> pdb=" O ILE X 20 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'X' and resid 17 through 20 removed outlier: 6.742A pdb=" N LEU X 10 " --> pdb=" O ARG X 18 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE X 20 " --> pdb=" O ALA X 8 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ALA X 8 " --> pdb=" O ILE X 20 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR X 5 " --> pdb=" O PHE X 95 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE X 97 " --> pdb=" O THR X 5 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LYS X 7 " --> pdb=" O ILE X 97 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE X 99 " --> pdb=" O LYS X 7 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR X 9 " --> pdb=" O ILE X 99 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU X 101 " --> pdb=" O TYR X 9 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N LEU X 11 " --> pdb=" O GLU X 101 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N ARG X 96 " --> pdb=" O ARG X 68 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ARG X 68 " --> pdb=" O ARG X 96 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Y' and resid 17 through 20 removed outlier: 6.741A pdb=" N LEU Y 10 " --> pdb=" O ARG Y 18 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE Y 20 " --> pdb=" O ALA Y 8 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA Y 8 " --> pdb=" O ILE Y 20 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Y' and resid 17 through 20 removed outlier: 6.741A pdb=" N LEU Y 10 " --> pdb=" O ARG Y 18 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE Y 20 " --> pdb=" O ALA Y 8 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA Y 8 " --> pdb=" O ILE Y 20 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR Y 5 " --> pdb=" O PHE Y 95 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE Y 97 " --> pdb=" O THR Y 5 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LYS Y 7 " --> pdb=" O ILE Y 97 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE Y 99 " --> pdb=" O LYS Y 7 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR Y 9 " --> pdb=" O ILE Y 99 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU Y 101 " --> pdb=" O TYR Y 9 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N LEU Y 11 " --> pdb=" O GLU Y 101 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ARG Y 96 " --> pdb=" O ARG Y 68 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ARG Y 68 " --> pdb=" O ARG Y 96 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Z' and resid 17 through 20 removed outlier: 6.747A pdb=" N LEU Z 10 " --> pdb=" O ARG Z 18 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE Z 20 " --> pdb=" O ALA Z 8 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA Z 8 " --> pdb=" O ILE Z 20 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Z' and resid 17 through 20 removed outlier: 6.747A pdb=" N LEU Z 10 " --> pdb=" O ARG Z 18 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE Z 20 " --> pdb=" O ALA Z 8 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA Z 8 " --> pdb=" O ILE Z 20 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR Z 5 " --> pdb=" O PHE Z 95 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE Z 97 " --> pdb=" O THR Z 5 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LYS Z 7 " --> pdb=" O ILE Z 97 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE Z 99 " --> pdb=" O LYS Z 7 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR Z 9 " --> pdb=" O ILE Z 99 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N GLU Z 101 " --> pdb=" O TYR Z 9 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N LEU Z 11 " --> pdb=" O GLU Z 101 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ARG Z 96 " --> pdb=" O ARG Z 68 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ARG Z 68 " --> pdb=" O ARG Z 96 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'a' and resid 17 through 20 removed outlier: 6.753A pdb=" N LEU a 10 " --> pdb=" O ARG a 18 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE a 20 " --> pdb=" O ALA a 8 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA a 8 " --> pdb=" O ILE a 20 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 17 through 20 removed outlier: 6.753A pdb=" N LEU a 10 " --> pdb=" O ARG a 18 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N ILE a 20 " --> pdb=" O ALA a 8 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N ALA a 8 " --> pdb=" O ILE a 20 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR a 5 " --> pdb=" O PHE a 95 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE a 97 " --> pdb=" O THR a 5 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LYS a 7 " --> pdb=" O ILE a 97 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE a 99 " --> pdb=" O LYS a 7 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR a 9 " --> pdb=" O ILE a 99 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU a 101 " --> pdb=" O TYR a 9 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N LEU a 11 " --> pdb=" O GLU a 101 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ARG a 96 " --> pdb=" O ARG a 68 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ARG a 68 " --> pdb=" O ARG a 96 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'b' and resid 17 through 20 removed outlier: 6.755A pdb=" N LEU b 10 " --> pdb=" O ARG b 18 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE b 20 " --> pdb=" O ALA b 8 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA b 8 " --> pdb=" O ILE b 20 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'b' and resid 17 through 20 removed outlier: 6.755A pdb=" N LEU b 10 " --> pdb=" O ARG b 18 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE b 20 " --> pdb=" O ALA b 8 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA b 8 " --> pdb=" O ILE b 20 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR b 5 " --> pdb=" O PHE b 95 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N ILE b 97 " --> pdb=" O THR b 5 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LYS b 7 " --> pdb=" O ILE b 97 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE b 99 " --> pdb=" O LYS b 7 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR b 9 " --> pdb=" O ILE b 99 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU b 101 " --> pdb=" O TYR b 9 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N LEU b 11 " --> pdb=" O GLU b 101 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ARG b 96 " --> pdb=" O ARG b 68 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ARG b 68 " --> pdb=" O ARG b 96 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'c' and resid 17 through 20 removed outlier: 6.752A pdb=" N LEU c 10 " --> pdb=" O ARG c 18 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE c 20 " --> pdb=" O ALA c 8 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA c 8 " --> pdb=" O ILE c 20 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'c' and resid 17 through 20 removed outlier: 6.752A pdb=" N LEU c 10 " --> pdb=" O ARG c 18 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N ILE c 20 " --> pdb=" O ALA c 8 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA c 8 " --> pdb=" O ILE c 20 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR c 5 " --> pdb=" O PHE c 95 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE c 97 " --> pdb=" O THR c 5 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LYS c 7 " --> pdb=" O ILE c 97 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE c 99 " --> pdb=" O LYS c 7 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR c 9 " --> pdb=" O ILE c 99 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU c 101 " --> pdb=" O TYR c 9 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N LEU c 11 " --> pdb=" O GLU c 101 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ARG c 96 " --> pdb=" O ARG c 68 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ARG c 68 " --> pdb=" O ARG c 96 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'd' and resid 17 through 20 removed outlier: 6.746A pdb=" N LEU d 10 " --> pdb=" O ARG d 18 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE d 20 " --> pdb=" O ALA d 8 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA d 8 " --> pdb=" O ILE d 20 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'd' and resid 17 through 20 removed outlier: 6.746A pdb=" N LEU d 10 " --> pdb=" O ARG d 18 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE d 20 " --> pdb=" O ALA d 8 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA d 8 " --> pdb=" O ILE d 20 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR d 5 " --> pdb=" O PHE d 95 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILE d 97 " --> pdb=" O THR d 5 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N LYS d 7 " --> pdb=" O ILE d 97 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE d 99 " --> pdb=" O LYS d 7 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR d 9 " --> pdb=" O ILE d 99 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N GLU d 101 " --> pdb=" O TYR d 9 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N LEU d 11 " --> pdb=" O GLU d 101 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ARG d 96 " --> pdb=" O ARG d 68 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ARG d 68 " --> pdb=" O ARG d 96 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'e' and resid 17 through 20 removed outlier: 6.742A pdb=" N LEU e 10 " --> pdb=" O ARG e 18 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE e 20 " --> pdb=" O ALA e 8 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA e 8 " --> pdb=" O ILE e 20 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'e' and resid 17 through 20 removed outlier: 6.742A pdb=" N LEU e 10 " --> pdb=" O ARG e 18 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N ILE e 20 " --> pdb=" O ALA e 8 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA e 8 " --> pdb=" O ILE e 20 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N THR e 5 " --> pdb=" O PHE e 95 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ILE e 97 " --> pdb=" O THR e 5 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N LYS e 7 " --> pdb=" O ILE e 97 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE e 99 " --> pdb=" O LYS e 7 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR e 9 " --> pdb=" O ILE e 99 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N GLU e 101 " --> pdb=" O TYR e 9 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N LEU e 11 " --> pdb=" O GLU e 101 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ARG e 96 " --> pdb=" O ARG e 68 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N ARG e 68 " --> pdb=" O ARG e 96 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'f' and resid 17 through 20 removed outlier: 6.743A pdb=" N LEU f 10 " --> pdb=" O ARG f 18 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE f 20 " --> pdb=" O ALA f 8 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA f 8 " --> pdb=" O ILE f 20 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'f' and resid 17 through 20 removed outlier: 6.743A pdb=" N LEU f 10 " --> pdb=" O ARG f 18 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ILE f 20 " --> pdb=" O ALA f 8 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA f 8 " --> pdb=" O ILE f 20 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR f 5 " --> pdb=" O PHE f 95 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE f 97 " --> pdb=" O THR f 5 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LYS f 7 " --> pdb=" O ILE f 97 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE f 99 " --> pdb=" O LYS f 7 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR f 9 " --> pdb=" O ILE f 99 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU f 101 " --> pdb=" O TYR f 9 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N LEU f 11 " --> pdb=" O GLU f 101 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ARG f 96 " --> pdb=" O ARG f 68 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N ARG f 68 " --> pdb=" O ARG f 96 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'g' and resid 17 through 20 removed outlier: 6.748A pdb=" N LEU g 10 " --> pdb=" O ARG g 18 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE g 20 " --> pdb=" O ALA g 8 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA g 8 " --> pdb=" O ILE g 20 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'g' and resid 17 through 20 removed outlier: 6.748A pdb=" N LEU g 10 " --> pdb=" O ARG g 18 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N ILE g 20 " --> pdb=" O ALA g 8 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA g 8 " --> pdb=" O ILE g 20 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR g 5 " --> pdb=" O PHE g 95 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE g 97 " --> pdb=" O THR g 5 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LYS g 7 " --> pdb=" O ILE g 97 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE g 99 " --> pdb=" O LYS g 7 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR g 9 " --> pdb=" O ILE g 99 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N GLU g 101 " --> pdb=" O TYR g 9 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N LEU g 11 " --> pdb=" O GLU g 101 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ARG g 96 " --> pdb=" O ARG g 68 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG g 68 " --> pdb=" O ARG g 96 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'h' and resid 17 through 20 removed outlier: 6.752A pdb=" N LEU h 10 " --> pdb=" O ARG h 18 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE h 20 " --> pdb=" O ALA h 8 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA h 8 " --> pdb=" O ILE h 20 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'h' and resid 17 through 20 removed outlier: 6.752A pdb=" N LEU h 10 " --> pdb=" O ARG h 18 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE h 20 " --> pdb=" O ALA h 8 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA h 8 " --> pdb=" O ILE h 20 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N THR h 5 " --> pdb=" O PHE h 95 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ILE h 97 " --> pdb=" O THR h 5 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LYS h 7 " --> pdb=" O ILE h 97 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N ILE h 99 " --> pdb=" O LYS h 7 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR h 9 " --> pdb=" O ILE h 99 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N GLU h 101 " --> pdb=" O TYR h 9 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N LEU h 11 " --> pdb=" O GLU h 101 " (cutoff:3.500A) removed outlier: 8.001A pdb=" N ARG h 96 " --> pdb=" O ARG h 68 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N ARG h 68 " --> pdb=" O ARG h 96 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'i' and resid 17 through 20 removed outlier: 6.755A pdb=" N LEU i 10 " --> pdb=" O ARG i 18 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE i 20 " --> pdb=" O ALA i 8 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA i 8 " --> pdb=" O ILE i 20 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'i' and resid 17 through 20 removed outlier: 6.755A pdb=" N LEU i 10 " --> pdb=" O ARG i 18 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ILE i 20 " --> pdb=" O ALA i 8 " (cutoff:3.500A) removed outlier: 6.694A pdb=" N ALA i 8 " --> pdb=" O ILE i 20 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N THR i 5 " --> pdb=" O PHE i 95 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE i 97 " --> pdb=" O THR i 5 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N LYS i 7 " --> pdb=" O ILE i 97 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE i 99 " --> pdb=" O LYS i 7 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N TYR i 9 " --> pdb=" O ILE i 99 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N GLU i 101 " --> pdb=" O TYR i 9 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N LEU i 11 " --> pdb=" O GLU i 101 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N ARG i 96 " --> pdb=" O ARG i 68 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N ARG i 68 " --> pdb=" O ARG i 96 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'j' and resid 17 through 20 removed outlier: 6.751A pdb=" N LEU j 10 " --> pdb=" O ARG j 18 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE j 20 " --> pdb=" O ALA j 8 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA j 8 " --> pdb=" O ILE j 20 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'j' and resid 17 through 20 removed outlier: 6.751A pdb=" N LEU j 10 " --> pdb=" O ARG j 18 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ILE j 20 " --> pdb=" O ALA j 8 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N ALA j 8 " --> pdb=" O ILE j 20 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR j 5 " --> pdb=" O PHE j 95 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N ILE j 97 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LYS j 7 " --> pdb=" O ILE j 97 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE j 99 " --> pdb=" O LYS j 7 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR j 9 " --> pdb=" O ILE j 99 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU j 101 " --> pdb=" O TYR j 9 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N LEU j 11 " --> pdb=" O GLU j 101 " (cutoff:3.500A) removed outlier: 7.992A pdb=" N ARG j 96 " --> pdb=" O ARG j 68 " (cutoff:3.500A) removed outlier: 4.826A pdb=" N ARG j 68 " --> pdb=" O ARG j 96 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'k' and resid 17 through 20 removed outlier: 6.745A pdb=" N LEU k 10 " --> pdb=" O ARG k 18 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE k 20 " --> pdb=" O ALA k 8 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA k 8 " --> pdb=" O ILE k 20 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'k' and resid 17 through 20 removed outlier: 6.745A pdb=" N LEU k 10 " --> pdb=" O ARG k 18 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE k 20 " --> pdb=" O ALA k 8 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ALA k 8 " --> pdb=" O ILE k 20 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR k 5 " --> pdb=" O PHE k 95 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILE k 97 " --> pdb=" O THR k 5 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LYS k 7 " --> pdb=" O ILE k 97 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE k 99 " --> pdb=" O LYS k 7 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR k 9 " --> pdb=" O ILE k 99 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU k 101 " --> pdb=" O TYR k 9 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N LEU k 11 " --> pdb=" O GLU k 101 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N ARG k 96 " --> pdb=" O ARG k 68 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ARG k 68 " --> pdb=" O ARG k 96 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'l' and resid 17 through 20 removed outlier: 6.741A pdb=" N LEU l 10 " --> pdb=" O ARG l 18 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE l 20 " --> pdb=" O ALA l 8 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA l 8 " --> pdb=" O ILE l 20 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'l' and resid 17 through 20 removed outlier: 6.741A pdb=" N LEU l 10 " --> pdb=" O ARG l 18 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE l 20 " --> pdb=" O ALA l 8 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ALA l 8 " --> pdb=" O ILE l 20 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N THR l 5 " --> pdb=" O PHE l 95 " (cutoff:3.500A) removed outlier: 7.381A pdb=" N ILE l 97 " --> pdb=" O THR l 5 " (cutoff:3.500A) removed outlier: 6.114A pdb=" N LYS l 7 " --> pdb=" O ILE l 97 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N ILE l 99 " --> pdb=" O LYS l 7 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR l 9 " --> pdb=" O ILE l 99 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU l 101 " --> pdb=" O TYR l 9 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N LEU l 11 " --> pdb=" O GLU l 101 " (cutoff:3.500A) removed outlier: 8.002A pdb=" N ARG l 96 " --> pdb=" O ARG l 68 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ARG l 68 " --> pdb=" O ARG l 96 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'm' and resid 17 through 20 removed outlier: 6.743A pdb=" N LEU m 10 " --> pdb=" O ARG m 18 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE m 20 " --> pdb=" O ALA m 8 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA m 8 " --> pdb=" O ILE m 20 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'm' and resid 17 through 20 removed outlier: 6.743A pdb=" N LEU m 10 " --> pdb=" O ARG m 18 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ILE m 20 " --> pdb=" O ALA m 8 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ALA m 8 " --> pdb=" O ILE m 20 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR m 5 " --> pdb=" O PHE m 95 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE m 97 " --> pdb=" O THR m 5 " (cutoff:3.500A) removed outlier: 6.112A pdb=" N LYS m 7 " --> pdb=" O ILE m 97 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE m 99 " --> pdb=" O LYS m 7 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR m 9 " --> pdb=" O ILE m 99 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU m 101 " --> pdb=" O TYR m 9 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N LEU m 11 " --> pdb=" O GLU m 101 " (cutoff:3.500A) removed outlier: 8.007A pdb=" N ARG m 96 " --> pdb=" O ARG m 68 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N ARG m 68 " --> pdb=" O ARG m 96 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'n' and resid 17 through 20 removed outlier: 6.748A pdb=" N LEU n 10 " --> pdb=" O ARG n 18 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE n 20 " --> pdb=" O ALA n 8 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA n 8 " --> pdb=" O ILE n 20 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'n' and resid 17 through 20 removed outlier: 6.748A pdb=" N LEU n 10 " --> pdb=" O ARG n 18 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N ILE n 20 " --> pdb=" O ALA n 8 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA n 8 " --> pdb=" O ILE n 20 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N THR n 5 " --> pdb=" O PHE n 95 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ILE n 97 " --> pdb=" O THR n 5 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LYS n 7 " --> pdb=" O ILE n 97 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE n 99 " --> pdb=" O LYS n 7 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N TYR n 9 " --> pdb=" O ILE n 99 " (cutoff:3.500A) removed outlier: 8.365A pdb=" N GLU n 101 " --> pdb=" O TYR n 9 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N LEU n 11 " --> pdb=" O GLU n 101 " (cutoff:3.500A) removed outlier: 8.006A pdb=" N ARG n 96 " --> pdb=" O ARG n 68 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ARG n 68 " --> pdb=" O ARG n 96 " (cutoff:3.500A) 912 hydrogen bonds defined for protein. 2496 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: 5.34 Time building geometry restraints manager: 3.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 10833 1.34 - 1.46: 7065 1.46 - 1.58: 14742 1.58 - 1.70: 0 1.70 - 1.81: 320 Bond restraints: 32960 Sorted by residual: bond pdb=" C SER F 28 " pdb=" N PRO F 29 " ideal model delta sigma weight residual 1.332 1.384 -0.052 1.34e-02 5.57e+03 1.50e+01 bond pdb=" C SER a 28 " pdb=" N PRO a 29 " ideal model delta sigma weight residual 1.332 1.384 -0.052 1.34e-02 5.57e+03 1.49e+01 bond pdb=" C SER M 28 " pdb=" N PRO M 29 " ideal model delta sigma weight residual 1.332 1.384 -0.052 1.34e-02 5.57e+03 1.48e+01 bond pdb=" C SER U 28 " pdb=" N PRO U 29 " ideal model delta sigma weight residual 1.332 1.383 -0.052 1.34e-02 5.57e+03 1.48e+01 bond pdb=" C SER T 28 " pdb=" N PRO T 29 " ideal model delta sigma weight residual 1.332 1.383 -0.051 1.34e-02 5.57e+03 1.48e+01 ... (remaining 32955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 41938 2.17 - 4.35: 2153 4.35 - 6.52: 149 6.52 - 8.70: 40 8.70 - 10.87: 80 Bond angle restraints: 44360 Sorted by residual: angle pdb=" C PRO d 31 " pdb=" N GLU d 32 " pdb=" CA GLU d 32 " ideal model delta sigma weight residual 121.31 126.58 -5.27 1.49e+00 4.50e-01 1.25e+01 angle pdb=" C PRO C 31 " pdb=" N GLU C 32 " pdb=" CA GLU C 32 " ideal model delta sigma weight residual 121.31 126.55 -5.24 1.49e+00 4.50e-01 1.24e+01 angle pdb=" C PRO P 31 " pdb=" N GLU P 32 " pdb=" CA GLU P 32 " ideal model delta sigma weight residual 121.31 126.54 -5.23 1.49e+00 4.50e-01 1.23e+01 angle pdb=" C PRO B 31 " pdb=" N GLU B 32 " pdb=" CA GLU B 32 " ideal model delta sigma weight residual 121.31 126.52 -5.21 1.49e+00 4.50e-01 1.22e+01 angle pdb=" C PRO k 31 " pdb=" N GLU k 32 " pdb=" CA GLU k 32 " ideal model delta sigma weight residual 121.31 126.50 -5.19 1.49e+00 4.50e-01 1.22e+01 ... (remaining 44355 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.60: 17335 8.60 - 17.19: 1945 17.19 - 25.79: 440 25.79 - 34.38: 440 34.38 - 42.98: 200 Dihedral angle restraints: 20360 sinusoidal: 8240 harmonic: 12120 Sorted by residual: dihedral pdb=" CA GLY E 40 " pdb=" C GLY E 40 " pdb=" N PRO E 41 " pdb=" CA PRO E 41 " ideal model delta harmonic sigma weight residual 180.00 155.44 24.56 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA GLY i 40 " pdb=" C GLY i 40 " pdb=" N PRO i 41 " pdb=" CA PRO i 41 " ideal model delta harmonic sigma weight residual 180.00 155.45 24.55 0 5.00e+00 4.00e-02 2.41e+01 dihedral pdb=" CA GLY a 40 " pdb=" C GLY a 40 " pdb=" N PRO a 41 " pdb=" CA PRO a 41 " ideal model delta harmonic sigma weight residual 180.00 155.46 24.54 0 5.00e+00 4.00e-02 2.41e+01 ... (remaining 20357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 2436 0.032 - 0.063: 1412 0.063 - 0.095: 500 0.095 - 0.127: 264 0.127 - 0.158: 68 Chirality restraints: 4680 Sorted by residual: chirality pdb=" CA ILE e 20 " pdb=" N ILE e 20 " pdb=" C ILE e 20 " pdb=" CB ILE e 20 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.27e-01 chirality pdb=" CA ILE R 20 " pdb=" N ILE R 20 " pdb=" C ILE R 20 " pdb=" CB ILE R 20 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.26e-01 chirality pdb=" CA ILE c 20 " pdb=" N ILE c 20 " pdb=" C ILE c 20 " pdb=" CB ILE c 20 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.24e-01 ... (remaining 4677 not shown) Planarity restraints: 5920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 40 " 0.051 5.00e-02 4.00e+02 7.76e-02 9.64e+00 pdb=" N PRO F 41 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO F 41 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO F 41 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY h 40 " -0.051 5.00e-02 4.00e+02 7.76e-02 9.64e+00 pdb=" N PRO h 41 " 0.134 5.00e-02 4.00e+02 pdb=" CA PRO h 41 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO h 41 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY N 40 " 0.051 5.00e-02 4.00e+02 7.76e-02 9.64e+00 pdb=" N PRO N 41 " -0.134 5.00e-02 4.00e+02 pdb=" CA PRO N 41 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO N 41 " 0.043 5.00e-02 4.00e+02 ... (remaining 5917 not shown) Histogram of nonbonded interaction distances: 1.25 - 1.98: 20 1.98 - 2.71: 1680 2.71 - 3.44: 41109 3.44 - 4.17: 71933 4.17 - 4.90: 127015 Nonbonded interactions: 241757 Sorted by model distance: nonbonded pdb=" OD1 ASP Q 92 " pdb=" OD1 ASP k 92 " model vdw 1.251 3.040 nonbonded pdb=" OD1 ASP K 92 " pdb=" OD1 ASP e 92 " model vdw 1.251 3.040 nonbonded pdb=" OD1 ASP C 92 " pdb=" OD1 ASP W 92 " model vdw 1.252 3.040 nonbonded pdb=" OD1 ASP P 92 " pdb=" OD1 ASP j 92 " model vdw 1.252 3.040 nonbonded pdb=" OD1 ASP R 92 " pdb=" OD1 ASP l 92 " model vdw 1.252 3.040 ... (remaining 241752 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: 0.14 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' } Set up NCS constraints Number of NCS constrained groups: 1 pdb_interpretation.ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' } Set refine NCS operators NCS operators will be refined. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.560 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: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 25.400 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.010 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5255 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 : 0.007 0.052 32960 Z= 0.321 Angle : 1.099 10.870 44360 Z= 0.603 Chirality : 0.048 0.158 4680 Planarity : 0.009 0.078 5920 Dihedral : 10.464 42.977 12520 Min Nonbonded Distance : 1.251 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.42 % Favored : 83.58 % Rotamer: Outliers : 0.00 % Allowed : 4.82 % Favored : 95.18 % 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: -5.42 (0.10), residues: 4080 helix: -4.84 (0.04), residues: 960 sheet: -3.35 (0.12), residues: 1160 loop : -2.95 (0.12), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 21 TYR 0.014 0.003 TYR b 67 PHE 0.032 0.005 PHE K 95 HIS 0.003 0.002 HIS L 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00674 / 0.32 (32960) covalent geometry : angle 1.09882 / 0.60 (44360) hydrogen bonds : bond 0.28675 / 18.91 ( 872) hydrogen bonds : angle 11.50554 / 7.81 ( 2496) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.034 Fit side-chains REVERT: A 87 MET cc_start: 0.3848 (ttm) cc_final: 0.2584 (mmm) outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0864 time to fit residues: 1.5772 Evaluate side-chains 3 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 8.9990 chunk 20 optimal weight: 10.0000 chunk 132 optimal weight: 0.5980 chunk 261 optimal weight: 0.0470 chunk 248 optimal weight: 0.0670 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 20.0000 overall best weight: 1.1018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3904 r_free = 0.3904 target = 0.083620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.061546 restraints weight = 3761.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.064753 restraints weight = 2366.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.067256 restraints weight = 1690.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.068959 restraints weight = 1320.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.070206 restraints weight = 1113.809| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6072 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 32960 Z= 0.137 Angle : 0.728 7.816 44360 Z= 0.378 Chirality : 0.047 0.178 4680 Planarity : 0.007 0.065 5920 Dihedral : 6.092 21.492 4600 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.73 % Favored : 86.27 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.31 (0.11), residues: 4080 helix: -2.95 (0.12), residues: 960 sheet: -2.70 (0.13), residues: 1240 loop : -2.81 (0.13), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG V 18 TYR 0.012 0.002 TYR l 9 PHE 0.010 0.002 PHE B 95 HIS 0.004 0.003 HIS L 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.14 (32960) covalent geometry : angle 0.72819 / 0.38 (44360) hydrogen bonds : bond 0.03392 / 2.23 ( 872) hydrogen bonds : angle 6.39599 / 4.36 ( 2496) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 10 time to evaluate : 0.035 Fit side-chains REVERT: f 58 LEU cc_start: 0.6085 (pp) cc_final: 0.5878 (mp) REVERT: f 73 ASP cc_start: 0.7768 (t0) cc_final: 0.7173 (p0) REVERT: f 85 MET cc_start: 0.8994 (mmp) cc_final: 0.8033 (ttt) REVERT: f 87 MET cc_start: 0.4553 (ttm) cc_final: 0.4093 (mtm) outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 0.0216 time to fit residues: 0.2849 Evaluate side-chains 5 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 189 optimal weight: 1.9990 chunk 326 optimal weight: 8.9990 chunk 270 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 192 optimal weight: 6.9990 chunk 209 optimal weight: 0.0570 chunk 4 optimal weight: 0.0470 chunk 213 optimal weight: 5.9990 chunk 372 optimal weight: 3.9990 chunk 164 optimal weight: 0.0270 chunk 225 optimal weight: 1.9990 overall best weight: 0.8258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.083977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.061114 restraints weight = 4109.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.065295 restraints weight = 2318.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.067826 restraints weight = 1650.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.069442 restraints weight = 1337.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.069764 restraints weight = 1162.300| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6203 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 32960 Z= 0.104 Angle : 0.627 7.385 44360 Z= 0.324 Chirality : 0.042 0.117 4680 Planarity : 0.006 0.058 5920 Dihedral : 5.480 20.174 4600 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 5.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.75 % Favored : 87.25 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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: -3.37 (0.13), residues: 4080 helix: -1.57 (0.17), residues: 960 sheet: -2.05 (0.15), residues: 1240 loop : -2.67 (0.13), residues: 1880 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG a 50 TYR 0.007 0.001 TYR c 9 PHE 0.015 0.002 PHE W 95 HIS 0.001 0.001 HIS R 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.10 (32960) covalent geometry : angle 0.62725 / 0.32 (44360) hydrogen bonds : bond 0.02283 / 1.50 ( 872) hydrogen bonds : angle 5.04473 / 3.43 ( 2496) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.036 Fit side-chains REVERT: b 73 ASP cc_start: 0.7500 (t0) cc_final: 0.7038 (p0) REVERT: b 85 MET cc_start: 0.8784 (mmp) cc_final: 0.8101 (ttt) outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0315 time to fit residues: 0.3713 Evaluate side-chains 7 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 7 time to evaluate : 0.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 142 optimal weight: 0.4980 chunk 167 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 203 optimal weight: 8.9990 chunk 242 optimal weight: 0.6980 chunk 267 optimal weight: 9.9990 chunk 69 optimal weight: 0.0070 chunk 21 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 289 optimal weight: 4.9990 chunk 177 optimal weight: 9.9990 overall best weight: 1.6402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... b 66 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.073357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.054859 restraints weight = 4514.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.057424 restraints weight = 2861.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.059274 restraints weight = 2125.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.060426 restraints weight = 1727.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.061261 restraints weight = 1493.512| |-----------------------------------------------------------------------------| r_work (final): 0.3424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6411 moved from start: 0.5903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 32960 Z= 0.102 Angle : 0.611 7.676 44360 Z= 0.307 Chirality : 0.042 0.127 4680 Planarity : 0.006 0.054 5920 Dihedral : 5.056 19.376 4600 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.71 % Favored : 85.29 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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: -2.72 (0.13), residues: 4080 helix: -0.29 (0.18), residues: 840 sheet: -1.72 (0.15), residues: 1280 loop : -2.54 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG O 22 TYR 0.006 0.002 TYR B 67 PHE 0.011 0.002 PHE T 95 HIS 0.001 0.001 HIS h 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.10 (32960) covalent geometry : angle 0.61108 / 0.31 (44360) hydrogen bonds : bond 0.02195 / 1.43 ( 872) hydrogen bonds : angle 4.42387 / 3.00 ( 2496) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 9 time to evaluate : 0.041 Fit side-chains REVERT: e 73 ASP cc_start: 0.7421 (t0) cc_final: 0.7054 (p0) REVERT: e 85 MET cc_start: 0.8881 (mmp) cc_final: 0.8272 (ttt) outliers start: 0 outliers final: 0 residues processed: 9 average time/residue: 0.0307 time to fit residues: 0.3693 Evaluate side-chains 5 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 96 optimal weight: 6.9990 chunk 370 optimal weight: 10.0000 chunk 167 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 265 optimal weight: 5.9990 chunk 277 optimal weight: 3.9990 chunk 364 optimal weight: 9.9990 chunk 304 optimal weight: 10.0000 chunk 298 optimal weight: 9.9990 chunk 222 optimal weight: 0.0770 chunk 77 optimal weight: 4.9990 overall best weight: 3.6146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.069888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.052594 restraints weight = 5126.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.055177 restraints weight = 3002.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.056906 restraints weight = 2213.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.058009 restraints weight = 1804.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.058787 restraints weight = 1579.833| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6752 moved from start: 0.7321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 32960 Z= 0.147 Angle : 0.636 4.746 44360 Z= 0.324 Chirality : 0.042 0.115 4680 Planarity : 0.007 0.064 5920 Dihedral : 5.332 18.929 4600 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.69 % Favored : 84.31 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.52 (0.13), residues: 4080 helix: 0.59 (0.18), residues: 800 sheet: -1.85 (0.14), residues: 1440 loop : -2.52 (0.14), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 22 TYR 0.006 0.002 TYR H 9 PHE 0.013 0.002 PHE V 55 HIS 0.004 0.002 HIS O 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 (32960) covalent geometry : angle 0.63616 / 0.32 (44360) hydrogen bonds : bond 0.02409 / 1.57 ( 872) hydrogen bonds : angle 5.31267 / 3.59 ( 2496) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.036 Fit side-chains REVERT: d 73 ASP cc_start: 0.7498 (t0) cc_final: 0.6925 (p0) REVERT: d 85 MET cc_start: 0.8892 (mmp) cc_final: 0.8506 (ttt) REVERT: d 87 MET cc_start: 0.5000 (ppp) cc_final: 0.2606 (mtm) outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0316 time to fit residues: 0.3348 Evaluate side-chains 4 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 88 optimal weight: 8.9990 chunk 313 optimal weight: 8.9990 chunk 226 optimal weight: 9.9990 chunk 161 optimal weight: 9.9990 chunk 296 optimal weight: 10.0000 chunk 167 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 chunk 290 optimal weight: 9.9990 chunk 393 optimal weight: 10.0000 chunk 321 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 overall best weight: 9.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.063101 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.045124 restraints weight = 6035.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.047413 restraints weight = 3828.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.048942 restraints weight = 2912.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.049800 restraints weight = 2456.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.049842 restraints weight = 2218.018| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7185 moved from start: 1.0140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 32960 Z= 0.325 Angle : 0.969 8.056 44360 Z= 0.493 Chirality : 0.051 0.120 4680 Planarity : 0.008 0.052 5920 Dihedral : 7.010 22.650 4600 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 22.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.61 % Favored : 80.39 % Rotamer: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.91 (0.12), residues: 4080 helix: -1.74 (0.15), residues: 840 sheet: -2.31 (0.13), residues: 1440 loop : -3.18 (0.12), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG W 50 TYR 0.015 0.004 TYR T 98 PHE 0.027 0.004 PHE a 55 HIS 0.007 0.005 HIS M 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00727 / 0.32 (32960) covalent geometry : angle 0.96853 / 0.49 (44360) hydrogen bonds : bond 0.04566 / 2.96 ( 872) hydrogen bonds : angle 8.31436 / 5.62 ( 2496) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.033 Fit side-chains REVERT: b 71 ASP cc_start: 0.8911 (p0) cc_final: 0.8503 (p0) REVERT: b 73 ASP cc_start: 0.7505 (t0) cc_final: 0.6641 (p0) REVERT: b 85 MET cc_start: 0.8857 (mmp) cc_final: 0.8191 (ttt) REVERT: b 87 MET cc_start: 0.8015 (ppp) cc_final: 0.6495 (mtp) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0315 time to fit residues: 0.1895 Evaluate side-chains 4 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 248 optimal weight: 7.9990 chunk 78 optimal weight: 0.0670 chunk 204 optimal weight: 9.9990 chunk 345 optimal weight: 6.9990 chunk 220 optimal weight: 8.9990 chunk 202 optimal weight: 0.6980 chunk 365 optimal weight: 4.9990 chunk 392 optimal weight: 0.0010 chunk 300 optimal weight: 9.9990 chunk 369 optimal weight: 4.9990 chunk 307 optimal weight: 9.9990 overall best weight: 2.1528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.067303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.048476 restraints weight = 5347.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.050668 restraints weight = 3229.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.052982 restraints weight = 2411.712| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.053907 restraints weight = 1955.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.054824 restraints weight = 1741.170| |-----------------------------------------------------------------------------| r_work (final): 0.3277 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 1.0054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 32960 Z= 0.115 Angle : 0.603 6.292 44360 Z= 0.303 Chirality : 0.044 0.132 4680 Planarity : 0.006 0.049 5920 Dihedral : 5.469 17.063 4600 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.45 (0.12), residues: 4080 helix: -0.70 (0.18), residues: 720 sheet: -2.18 (0.14), residues: 1440 loop : -2.98 (0.11), residues: 1920 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG O 46 TYR 0.004 0.001 TYR f 89 PHE 0.011 0.002 PHE H 95 HIS 0.004 0.002 HIS P 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.11 (32960) covalent geometry : angle 0.60346 / 0.30 (44360) hydrogen bonds : bond 0.02369 / 1.54 ( 872) hydrogen bonds : angle 5.68802 / 3.86 ( 2496) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 8 time to evaluate : 0.034 Fit side-chains revert: symmetry clash REVERT: b 71 ASP cc_start: 0.8917 (p0) cc_final: 0.8451 (p0) REVERT: b 73 ASP cc_start: 0.7132 (t0) cc_final: 0.6611 (p0) REVERT: b 85 MET cc_start: 0.8755 (mmp) cc_final: 0.8147 (ttt) REVERT: b 87 MET cc_start: 0.7686 (ppp) cc_final: 0.6484 (mtp) outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.0613 time to fit residues: 0.5704 Evaluate side-chains 6 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 6 time to evaluate : 0.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 48 optimal weight: 9.9990 chunk 71 optimal weight: 20.0000 chunk 214 optimal weight: 7.9990 chunk 383 optimal weight: 20.0000 chunk 96 optimal weight: 9.9990 chunk 367 optimal weight: 1.9990 chunk 66 optimal weight: 9.9990 chunk 91 optimal weight: 9.9990 chunk 352 optimal weight: 5.9990 chunk 136 optimal weight: 9.9990 chunk 141 optimal weight: 7.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.059564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.043450 restraints weight = 5659.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.045233 restraints weight = 3297.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.046620 restraints weight = 2487.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.047223 restraints weight = 2080.572| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.047771 restraints weight = 1892.815| |-----------------------------------------------------------------------------| r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7084 moved from start: 1.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 32960 Z= 0.232 Angle : 0.760 5.756 44360 Z= 0.383 Chirality : 0.048 0.150 4680 Planarity : 0.006 0.045 5920 Dihedral : 6.066 20.673 4600 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.65 % Favored : 82.35 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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: -3.70 (0.12), residues: 4080 helix: -0.71 (0.18), residues: 800 sheet: -2.33 (0.13), residues: 1440 loop : -3.34 (0.11), residues: 1840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 46 TYR 0.008 0.002 TYR B 67 PHE 0.013 0.002 PHE c 55 HIS 0.003 0.002 HIS O 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00521 / 0.23 (32960) covalent geometry : angle 0.75991 / 0.38 (44360) hydrogen bonds : bond 0.03165 / 2.05 ( 872) hydrogen bonds : angle 7.66986 / 5.19 ( 2496) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 5 time to evaluate : 0.033 Fit side-chains REVERT: a 71 ASP cc_start: 0.9005 (p0) cc_final: 0.8672 (p0) REVERT: a 73 ASP cc_start: 0.7066 (t0) cc_final: 0.6368 (p0) REVERT: a 85 MET cc_start: 0.9268 (mmp) cc_final: 0.8213 (ttt) REVERT: a 87 MET cc_start: 0.7502 (ppp) cc_final: 0.6049 (mtt) outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 0.0279 time to fit residues: 0.2078 Evaluate side-chains 4 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 88 optimal weight: 10.0000 chunk 183 optimal weight: 7.9990 chunk 315 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 355 optimal weight: 8.9990 chunk 135 optimal weight: 6.9990 chunk 251 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 228 optimal weight: 0.0870 chunk 80 optimal weight: 10.0000 chunk 124 optimal weight: 10.0000 overall best weight: 5.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.058799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.043216 restraints weight = 5637.388| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.045120 restraints weight = 3498.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3136 r_free = 0.3136 target = 0.046402 restraints weight = 2628.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.047083 restraints weight = 2200.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.047293 restraints weight = 1982.265| |-----------------------------------------------------------------------------| r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 1.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 32960 Z= 0.173 Angle : 0.675 7.940 44360 Z= 0.329 Chirality : 0.046 0.126 4680 Planarity : 0.006 0.039 5920 Dihedral : 5.618 17.241 4600 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.76 % Favored : 88.24 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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: -3.32 (0.12), residues: 4080 helix: -0.70 (0.16), residues: 800 sheet: -1.88 (0.15), residues: 1200 loop : -3.08 (0.11), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG j 46 TYR 0.006 0.002 TYR n 98 PHE 0.015 0.002 PHE h 55 HIS 0.004 0.002 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00386 / 0.17 (32960) covalent geometry : angle 0.67460 / 0.33 (44360) hydrogen bonds : bond 0.02957 / 1.92 ( 872) hydrogen bonds : angle 7.59561 / 5.15 ( 2496) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.036 Fit side-chains revert: symmetry clash REVERT: a 85 MET cc_start: 0.8972 (mmp) cc_final: 0.8305 (ttt) REVERT: a 87 MET cc_start: 0.7564 (ppp) cc_final: 0.6253 (mtt) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0316 time to fit residues: 0.1942 Evaluate side-chains 3 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 3 time to evaluate : 0.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 269 optimal weight: 0.8980 chunk 90 optimal weight: 9.9990 chunk 82 optimal weight: 7.9990 chunk 220 optimal weight: 10.0000 chunk 383 optimal weight: 20.0000 chunk 365 optimal weight: 0.0170 chunk 360 optimal weight: 10.0000 chunk 394 optimal weight: 9.9990 chunk 374 optimal weight: 7.9990 chunk 101 optimal weight: 10.0000 chunk 153 optimal weight: 20.0000 overall best weight: 5.3824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** a 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.056648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.042690 restraints weight = 5736.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.044574 restraints weight = 3509.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.045549 restraints weight = 2629.605| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.046468 restraints weight = 2232.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.046974 restraints weight = 1967.759| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 1.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 32960 Z= 0.194 Angle : 0.701 6.078 44360 Z= 0.350 Chirality : 0.046 0.139 4680 Planarity : 0.006 0.042 5920 Dihedral : 5.683 19.266 4600 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.69 % Favored : 84.31 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.51 (0.12), residues: 4080 helix: -1.28 (0.15), residues: 800 sheet: -1.79 (0.16), residues: 1200 loop : -3.15 (0.11), residues: 2080 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG i 46 TYR 0.006 0.002 TYR U 9 PHE 0.013 0.003 PHE L 55 HIS 0.004 0.002 HIS i 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00443 / 0.19 (32960) covalent geometry : angle 0.70114 / 0.35 (44360) hydrogen bonds : bond 0.03018 / 1.96 ( 872) hydrogen bonds : angle 8.21705 / 5.58 ( 2496) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8160 Ramachandran restraints generated. 4080 Oldfield, 0 Emsley, 4080 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 4 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 4 time to evaluate : 0.034 Fit side-chains REVERT: Z 85 MET cc_start: 0.9059 (mmp) cc_final: 0.8526 (ttt) REVERT: Z 87 MET cc_start: 0.7113 (ppp) cc_final: 0.5716 (mtp) outliers start: 0 outliers final: 0 residues processed: 4 average time/residue: 0.0328 time to fit residues: 0.1972 Evaluate side-chains 2 residues out of total 83 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 2 time to evaluate : 0.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 400 random chunks: chunk 232 optimal weight: 5.9990 chunk 107 optimal weight: 6.9990 chunk 135 optimal weight: 0.1980 chunk 391 optimal weight: 10.0000 chunk 214 optimal weight: 7.9990 chunk 333 optimal weight: 30.0000 chunk 223 optimal weight: 20.0000 chunk 251 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 175 optimal weight: 0.5980 chunk 320 optimal weight: 10.0000 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Update NCS operators ******************** ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.058898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.044700 restraints weight = 5506.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.046614 restraints weight = 3328.374| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3210 r_free = 0.3210 target = 0.047853 restraints weight = 2465.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3228 r_free = 0.3228 target = 0.048704 restraints weight = 2031.840| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.049190 restraints weight = 1783.245| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6918 moved from start: 1.2888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 32960 Z= 0.107 Angle : 0.587 5.582 44360 Z= 0.288 Chirality : 0.045 0.127 4680 Planarity : 0.006 0.044 5920 Dihedral : 4.907 14.859 4600 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % 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: -2.91 (0.13), residues: 4080 helix: -0.92 (0.16), residues: 720 sheet: -1.42 (0.16), residues: 1200 loop : -2.64 (0.12), residues: 2160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG K 46 TYR 0.004 0.001 TYR l 9 PHE 0.011 0.002 PHE i 95 HIS 0.002 0.001 HIS U 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.11 (32960) covalent geometry : angle 0.58745 / 0.29 (44360) hydrogen bonds : bond 0.02435 / 1.58 ( 872) hydrogen bonds : angle 6.95394 / 4.73 ( 2496) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1991.08 seconds wall clock time: 36 minutes 14.59 seconds (2174.59 seconds total)