Starting phenix.real_space_refine on Mon Aug 10 06:20:10 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/10xw_75516/08_2026/10xw_75516.cif Found real_map, /net/cci-nas-00/data/ceres_data/10xw_75516/08_2026/10xw_75516.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/10xw_75516/08_2026/10xw_75516.map" default_real_map = "/net/cci-nas-00/data/ceres_data/10xw_75516/08_2026/10xw_75516.map" model { file = "/net/cci-nas-00/data/ceres_data/10xw_75516/08_2026/10xw_75516.cif" } default_model = "/net/cci-nas-00/data/ceres_data/10xw_75516/08_2026/10xw_75516.cif" } resolution = 3.5 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= 0.002 sd= 0.068 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 120 5.16 5 C 26976 2.51 5 N 7104 2.21 5 O 8448 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42648 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 240, 1777 Classifications: {'peptide': 240} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 5} Link IDs: {'PTRANS': 12, 'TRANS': 227} Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ASP:plan': 4} Unresolved non-hydrogen planarities: 13 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X Time building chain proxies: 3.95, per 1000 atoms: 0.09 Number of scatterers: 42648 At special positions: 0 Unit cell: (139.365, 139.365, 185.535, 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 120 16.00 O 8448 8.00 N 7104 7.00 C 26976 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.36 Conformation dependent library (CDL) restraints added in 1.8 seconds 11424 Ramachandran restraints generated. 5712 Oldfield, 0 Emsley, 5712 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10608 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 120 sheets defined 13.3% alpha, 52.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 63 through 67 Processing helix chain 'A' and resid 165 through 177 removed outlier: 4.453A pdb=" N ILE A 169 " --> pdb=" O PRO A 165 " (cutoff:3.500A) Processing helix chain 'A' and resid 188 through 193 removed outlier: 3.898A pdb=" N GLY A 192 " --> pdb=" O ALA A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 240 removed outlier: 3.579A pdb=" N LEU A 240 " --> pdb=" O LEU A 236 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 67 Processing helix chain 'B' and resid 165 through 177 removed outlier: 4.453A pdb=" N ILE B 169 " --> pdb=" O PRO B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 193 removed outlier: 3.898A pdb=" N GLY B 192 " --> pdb=" O ALA B 188 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 240 removed outlier: 3.579A pdb=" N LEU B 240 " --> pdb=" O LEU B 236 " (cutoff:3.500A) Processing helix chain 'C' and resid 63 through 67 Processing helix chain 'C' and resid 165 through 177 removed outlier: 4.453A pdb=" N ILE C 169 " --> pdb=" O PRO C 165 " (cutoff:3.500A) Processing helix chain 'C' and resid 188 through 193 removed outlier: 3.898A pdb=" N GLY C 192 " --> pdb=" O ALA C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 240 removed outlier: 3.579A pdb=" N LEU C 240 " --> pdb=" O LEU C 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 67 Processing helix chain 'D' and resid 165 through 177 removed outlier: 4.453A pdb=" N ILE D 169 " --> pdb=" O PRO D 165 " (cutoff:3.500A) Processing helix chain 'D' and resid 188 through 193 removed outlier: 3.898A pdb=" N GLY D 192 " --> pdb=" O ALA D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 240 removed outlier: 3.580A pdb=" N LEU D 240 " --> pdb=" O LEU D 236 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 67 Processing helix chain 'E' and resid 165 through 177 removed outlier: 4.453A pdb=" N ILE E 169 " --> pdb=" O PRO E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 188 through 193 removed outlier: 3.899A pdb=" N GLY E 192 " --> pdb=" O ALA E 188 " (cutoff:3.500A) Processing helix chain 'E' and resid 233 through 240 removed outlier: 3.579A pdb=" N LEU E 240 " --> pdb=" O LEU E 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 63 through 67 Processing helix chain 'F' and resid 165 through 177 removed outlier: 4.453A pdb=" N ILE F 169 " --> pdb=" O PRO F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 193 removed outlier: 3.898A pdb=" N GLY F 192 " --> pdb=" O ALA F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 240 removed outlier: 3.579A pdb=" N LEU F 240 " --> pdb=" O LEU F 236 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 67 Processing helix chain 'G' and resid 165 through 177 removed outlier: 4.453A pdb=" N ILE G 169 " --> pdb=" O PRO G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 188 through 193 removed outlier: 3.898A pdb=" N GLY G 192 " --> pdb=" O ALA G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 233 through 240 removed outlier: 3.579A pdb=" N LEU G 240 " --> pdb=" O LEU G 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 67 Processing helix chain 'H' and resid 165 through 177 removed outlier: 4.453A pdb=" N ILE H 169 " --> pdb=" O PRO H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 188 through 193 removed outlier: 3.898A pdb=" N GLY H 192 " --> pdb=" O ALA H 188 " (cutoff:3.500A) Processing helix chain 'H' and resid 233 through 240 removed outlier: 3.579A pdb=" N LEU H 240 " --> pdb=" O LEU H 236 " (cutoff:3.500A) Processing helix chain 'I' and resid 63 through 67 Processing helix chain 'I' and resid 165 through 177 removed outlier: 4.453A pdb=" N ILE I 169 " --> pdb=" O PRO I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 188 through 193 removed outlier: 3.898A pdb=" N GLY I 192 " --> pdb=" O ALA I 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 233 through 240 removed outlier: 3.578A pdb=" N LEU I 240 " --> pdb=" O LEU I 236 " (cutoff:3.500A) Processing helix chain 'J' and resid 63 through 67 Processing helix chain 'J' and resid 165 through 177 removed outlier: 4.453A pdb=" N ILE J 169 " --> pdb=" O PRO J 165 " (cutoff:3.500A) Processing helix chain 'J' and resid 188 through 193 removed outlier: 3.899A pdb=" N GLY J 192 " --> pdb=" O ALA J 188 " (cutoff:3.500A) Processing helix chain 'J' and resid 233 through 240 removed outlier: 3.579A pdb=" N LEU J 240 " --> pdb=" O LEU J 236 " (cutoff:3.500A) Processing helix chain 'K' and resid 63 through 67 Processing helix chain 'K' and resid 165 through 177 removed outlier: 4.453A pdb=" N ILE K 169 " --> pdb=" O PRO K 165 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 193 removed outlier: 3.898A pdb=" N GLY K 192 " --> pdb=" O ALA K 188 " (cutoff:3.500A) Processing helix chain 'K' and resid 233 through 240 removed outlier: 3.580A pdb=" N LEU K 240 " --> pdb=" O LEU K 236 " (cutoff:3.500A) Processing helix chain 'L' and resid 63 through 67 Processing helix chain 'L' and resid 165 through 177 removed outlier: 4.453A pdb=" N ILE L 169 " --> pdb=" O PRO L 165 " (cutoff:3.500A) Processing helix chain 'L' and resid 188 through 193 removed outlier: 3.898A pdb=" N GLY L 192 " --> pdb=" O ALA L 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 233 through 240 removed outlier: 3.580A pdb=" N LEU L 240 " --> pdb=" O LEU L 236 " (cutoff:3.500A) Processing helix chain 'M' and resid 63 through 67 Processing helix chain 'M' and resid 165 through 177 removed outlier: 4.453A pdb=" N ILE M 169 " --> pdb=" O PRO M 165 " (cutoff:3.500A) Processing helix chain 'M' and resid 188 through 193 removed outlier: 3.898A pdb=" N GLY M 192 " --> pdb=" O ALA M 188 " (cutoff:3.500A) Processing helix chain 'M' and resid 233 through 240 removed outlier: 3.579A pdb=" N LEU M 240 " --> pdb=" O LEU M 236 " (cutoff:3.500A) Processing helix chain 'N' and resid 63 through 67 Processing helix chain 'N' and resid 165 through 177 removed outlier: 4.453A pdb=" N ILE N 169 " --> pdb=" O PRO N 165 " (cutoff:3.500A) Processing helix chain 'N' and resid 188 through 193 removed outlier: 3.898A pdb=" N GLY N 192 " --> pdb=" O ALA N 188 " (cutoff:3.500A) Processing helix chain 'N' and resid 233 through 240 removed outlier: 3.579A pdb=" N LEU N 240 " --> pdb=" O LEU N 236 " (cutoff:3.500A) Processing helix chain 'O' and resid 63 through 67 Processing helix chain 'O' and resid 165 through 177 removed outlier: 4.453A pdb=" N ILE O 169 " --> pdb=" O PRO O 165 " (cutoff:3.500A) Processing helix chain 'O' and resid 188 through 193 removed outlier: 3.898A pdb=" N GLY O 192 " --> pdb=" O ALA O 188 " (cutoff:3.500A) Processing helix chain 'O' and resid 233 through 240 removed outlier: 3.579A pdb=" N LEU O 240 " --> pdb=" O LEU O 236 " (cutoff:3.500A) Processing helix chain 'P' and resid 63 through 67 Processing helix chain 'P' and resid 165 through 177 removed outlier: 4.453A pdb=" N ILE P 169 " --> pdb=" O PRO P 165 " (cutoff:3.500A) Processing helix chain 'P' and resid 188 through 193 removed outlier: 3.898A pdb=" N GLY P 192 " --> pdb=" O ALA P 188 " (cutoff:3.500A) Processing helix chain 'P' and resid 233 through 240 removed outlier: 3.580A pdb=" N LEU P 240 " --> pdb=" O LEU P 236 " (cutoff:3.500A) Processing helix chain 'Q' and resid 63 through 67 Processing helix chain 'Q' and resid 165 through 177 removed outlier: 4.453A pdb=" N ILE Q 169 " --> pdb=" O PRO Q 165 " (cutoff:3.500A) Processing helix chain 'Q' and resid 188 through 193 removed outlier: 3.899A pdb=" N GLY Q 192 " --> pdb=" O ALA Q 188 " (cutoff:3.500A) Processing helix chain 'Q' and resid 233 through 240 removed outlier: 3.579A pdb=" N LEU Q 240 " --> pdb=" O LEU Q 236 " (cutoff:3.500A) Processing helix chain 'R' and resid 63 through 67 Processing helix chain 'R' and resid 165 through 177 removed outlier: 4.453A pdb=" N ILE R 169 " --> pdb=" O PRO R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 188 through 193 removed outlier: 3.898A pdb=" N GLY R 192 " --> pdb=" O ALA R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 233 through 240 removed outlier: 3.579A pdb=" N LEU R 240 " --> pdb=" O LEU R 236 " (cutoff:3.500A) Processing helix chain 'S' and resid 63 through 67 Processing helix chain 'S' and resid 165 through 177 removed outlier: 4.453A pdb=" N ILE S 169 " --> pdb=" O PRO S 165 " (cutoff:3.500A) Processing helix chain 'S' and resid 188 through 193 removed outlier: 3.898A pdb=" N GLY S 192 " --> pdb=" O ALA S 188 " (cutoff:3.500A) Processing helix chain 'S' and resid 233 through 240 removed outlier: 3.579A pdb=" N LEU S 240 " --> pdb=" O LEU S 236 " (cutoff:3.500A) Processing helix chain 'T' and resid 63 through 67 Processing helix chain 'T' and resid 165 through 177 removed outlier: 4.453A pdb=" N ILE T 169 " --> pdb=" O PRO T 165 " (cutoff:3.500A) Processing helix chain 'T' and resid 188 through 193 removed outlier: 3.898A pdb=" N GLY T 192 " --> pdb=" O ALA T 188 " (cutoff:3.500A) Processing helix chain 'T' and resid 233 through 240 removed outlier: 3.579A pdb=" N LEU T 240 " --> pdb=" O LEU T 236 " (cutoff:3.500A) Processing helix chain 'U' and resid 63 through 67 Processing helix chain 'U' and resid 165 through 177 removed outlier: 4.453A pdb=" N ILE U 169 " --> pdb=" O PRO U 165 " (cutoff:3.500A) Processing helix chain 'U' and resid 188 through 193 removed outlier: 3.898A pdb=" N GLY U 192 " --> pdb=" O ALA U 188 " (cutoff:3.500A) Processing helix chain 'U' and resid 233 through 240 removed outlier: 3.578A pdb=" N LEU U 240 " --> pdb=" O LEU U 236 " (cutoff:3.500A) Processing helix chain 'V' and resid 63 through 67 Processing helix chain 'V' and resid 165 through 177 removed outlier: 4.453A pdb=" N ILE V 169 " --> pdb=" O PRO V 165 " (cutoff:3.500A) Processing helix chain 'V' and resid 188 through 193 removed outlier: 3.899A pdb=" N GLY V 192 " --> pdb=" O ALA V 188 " (cutoff:3.500A) Processing helix chain 'V' and resid 233 through 240 removed outlier: 3.579A pdb=" N LEU V 240 " --> pdb=" O LEU V 236 " (cutoff:3.500A) Processing helix chain 'W' and resid 63 through 67 Processing helix chain 'W' and resid 165 through 177 removed outlier: 4.453A pdb=" N ILE W 169 " --> pdb=" O PRO W 165 " (cutoff:3.500A) Processing helix chain 'W' and resid 188 through 193 removed outlier: 3.898A pdb=" N GLY W 192 " --> pdb=" O ALA W 188 " (cutoff:3.500A) Processing helix chain 'W' and resid 233 through 240 removed outlier: 3.580A pdb=" N LEU W 240 " --> pdb=" O LEU W 236 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 67 Processing helix chain 'X' and resid 165 through 177 removed outlier: 4.453A pdb=" N ILE X 169 " --> pdb=" O PRO X 165 " (cutoff:3.500A) Processing helix chain 'X' and resid 188 through 193 removed outlier: 3.898A pdb=" N GLY X 192 " --> pdb=" O ALA X 188 " (cutoff:3.500A) Processing helix chain 'X' and resid 233 through 240 removed outlier: 3.580A pdb=" N LEU X 240 " --> pdb=" O LEU X 236 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 12 through 14 Processing sheet with id=2, first strand: chain 'A' and resid 17 through 26 removed outlier: 6.797A pdb=" N THR A 43 " --> pdb=" O THR A 24 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA A 26 " --> pdb=" O VAL A 41 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL A 41 " --> pdb=" O ALA A 26 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS A 40 " --> pdb=" O LEU A 83 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS A 75 " --> pdb=" O THR A 82 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA A 84 " --> pdb=" O VAL A 73 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL A 73 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL A 55 " --> pdb=" O VAL A 110 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU A 106 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS A 109 " --> pdb=" O SER A 19 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N SER A 19 " --> pdb=" O LYS A 109 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR A 157 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL A 122 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR A 155 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL A 124 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A 153 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU A 152 " --> pdb=" O MET A 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN A 220 " --> pdb=" O GLN A 206 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR A 199 " --> pdb=" O ILE A 182 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR A 157 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL A 122 " --> pdb=" O THR A 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR A 155 " --> pdb=" O VAL A 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL A 124 " --> pdb=" O VAL A 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL A 153 " --> pdb=" O VAL A 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU A 152 " --> pdb=" O MET A 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN A 220 " --> pdb=" O GLN A 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 196 " --> pdb=" O TYR A 232 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'A' and resid 129 through 134 removed outlier: 4.214A pdb=" N THR A 148 " --> pdb=" O GLN A 130 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR A 132 " --> pdb=" O ASN A 146 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ASN A 146 " --> pdb=" O THR A 132 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE A 134 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER A 144 " --> pdb=" O PHE A 134 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 12 through 14 Processing sheet with id=7, first strand: chain 'B' and resid 17 through 26 removed outlier: 6.797A pdb=" N THR B 43 " --> pdb=" O THR B 24 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA B 26 " --> pdb=" O VAL B 41 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL B 41 " --> pdb=" O ALA B 26 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS B 40 " --> pdb=" O LEU B 83 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS B 75 " --> pdb=" O THR B 82 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA B 84 " --> pdb=" O VAL B 73 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL B 73 " --> pdb=" O ALA B 84 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL B 55 " --> pdb=" O VAL B 110 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU B 106 " --> pdb=" O THR B 59 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS B 109 " --> pdb=" O SER B 19 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N SER B 19 " --> pdb=" O LYS B 109 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'B' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR B 157 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL B 122 " --> pdb=" O THR B 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR B 155 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL B 124 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 153 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU B 152 " --> pdb=" O MET B 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN B 220 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR B 199 " --> pdb=" O ILE B 182 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'B' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR B 157 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL B 122 " --> pdb=" O THR B 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR B 155 " --> pdb=" O VAL B 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL B 124 " --> pdb=" O VAL B 153 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL B 153 " --> pdb=" O VAL B 124 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU B 152 " --> pdb=" O MET B 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN B 220 " --> pdb=" O GLN B 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 196 " --> pdb=" O TYR B 232 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'B' and resid 129 through 134 removed outlier: 4.214A pdb=" N THR B 148 " --> pdb=" O GLN B 130 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N THR B 132 " --> pdb=" O ASN B 146 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASN B 146 " --> pdb=" O THR B 132 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE B 134 " --> pdb=" O SER B 144 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N SER B 144 " --> pdb=" O PHE B 134 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'C' and resid 12 through 14 Processing sheet with id=12, first strand: chain 'C' and resid 17 through 26 removed outlier: 6.797A pdb=" N THR C 43 " --> pdb=" O THR C 24 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA C 26 " --> pdb=" O VAL C 41 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL C 41 " --> pdb=" O ALA C 26 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS C 40 " --> pdb=" O LEU C 83 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS C 75 " --> pdb=" O THR C 82 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ALA C 84 " --> pdb=" O VAL C 73 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL C 73 " --> pdb=" O ALA C 84 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL C 55 " --> pdb=" O VAL C 110 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU C 106 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS C 109 " --> pdb=" O SER C 19 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N SER C 19 " --> pdb=" O LYS C 109 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'C' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR C 157 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL C 122 " --> pdb=" O THR C 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR C 155 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL C 124 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL C 153 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU C 152 " --> pdb=" O MET C 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN C 220 " --> pdb=" O GLN C 206 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR C 199 " --> pdb=" O ILE C 182 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'C' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR C 157 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL C 122 " --> pdb=" O THR C 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR C 155 " --> pdb=" O VAL C 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL C 124 " --> pdb=" O VAL C 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL C 153 " --> pdb=" O VAL C 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU C 152 " --> pdb=" O MET C 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN C 220 " --> pdb=" O GLN C 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE C 196 " --> pdb=" O TYR C 232 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'C' and resid 129 through 134 removed outlier: 4.214A pdb=" N THR C 148 " --> pdb=" O GLN C 130 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR C 132 " --> pdb=" O ASN C 146 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ASN C 146 " --> pdb=" O THR C 132 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE C 134 " --> pdb=" O SER C 144 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER C 144 " --> pdb=" O PHE C 134 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'D' and resid 12 through 14 Processing sheet with id=17, first strand: chain 'D' and resid 17 through 26 removed outlier: 6.797A pdb=" N THR D 43 " --> pdb=" O THR D 24 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA D 26 " --> pdb=" O VAL D 41 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL D 41 " --> pdb=" O ALA D 26 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS D 40 " --> pdb=" O LEU D 83 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS D 75 " --> pdb=" O THR D 82 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA D 84 " --> pdb=" O VAL D 73 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL D 73 " --> pdb=" O ALA D 84 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL D 55 " --> pdb=" O VAL D 110 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU D 106 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS D 109 " --> pdb=" O SER D 19 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N SER D 19 " --> pdb=" O LYS D 109 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'D' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR D 157 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL D 122 " --> pdb=" O THR D 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR D 155 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL D 124 " --> pdb=" O VAL D 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL D 153 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU D 152 " --> pdb=" O MET D 225 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN D 220 " --> pdb=" O GLN D 206 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR D 199 " --> pdb=" O ILE D 182 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'D' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR D 157 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL D 122 " --> pdb=" O THR D 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR D 155 " --> pdb=" O VAL D 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL D 124 " --> pdb=" O VAL D 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL D 153 " --> pdb=" O VAL D 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU D 152 " --> pdb=" O MET D 225 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN D 220 " --> pdb=" O GLN D 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE D 196 " --> pdb=" O TYR D 232 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'D' and resid 129 through 134 removed outlier: 4.214A pdb=" N THR D 148 " --> pdb=" O GLN D 130 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N THR D 132 " --> pdb=" O ASN D 146 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ASN D 146 " --> pdb=" O THR D 132 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE D 134 " --> pdb=" O SER D 144 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER D 144 " --> pdb=" O PHE D 134 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'E' and resid 12 through 14 Processing sheet with id=22, first strand: chain 'E' and resid 17 through 26 removed outlier: 6.797A pdb=" N THR E 43 " --> pdb=" O THR E 24 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA E 26 " --> pdb=" O VAL E 41 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL E 41 " --> pdb=" O ALA E 26 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS E 40 " --> pdb=" O LEU E 83 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS E 75 " --> pdb=" O THR E 82 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA E 84 " --> pdb=" O VAL E 73 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL E 73 " --> pdb=" O ALA E 84 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL E 55 " --> pdb=" O VAL E 110 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU E 106 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS E 109 " --> pdb=" O SER E 19 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N SER E 19 " --> pdb=" O LYS E 109 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'E' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR E 157 " --> pdb=" O THR E 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL E 122 " --> pdb=" O THR E 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR E 155 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL E 124 " --> pdb=" O VAL E 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL E 153 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU E 152 " --> pdb=" O MET E 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN E 220 " --> pdb=" O GLN E 206 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR E 199 " --> pdb=" O ILE E 182 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'E' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR E 157 " --> pdb=" O THR E 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL E 122 " --> pdb=" O THR E 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR E 155 " --> pdb=" O VAL E 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL E 124 " --> pdb=" O VAL E 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL E 153 " --> pdb=" O VAL E 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU E 152 " --> pdb=" O MET E 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN E 220 " --> pdb=" O GLN E 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE E 196 " --> pdb=" O TYR E 232 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'E' and resid 129 through 134 removed outlier: 4.213A pdb=" N THR E 148 " --> pdb=" O GLN E 130 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR E 132 " --> pdb=" O ASN E 146 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ASN E 146 " --> pdb=" O THR E 132 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE E 134 " --> pdb=" O SER E 144 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER E 144 " --> pdb=" O PHE E 134 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'F' and resid 12 through 14 Processing sheet with id=27, first strand: chain 'F' and resid 17 through 26 removed outlier: 6.797A pdb=" N THR F 43 " --> pdb=" O THR F 24 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA F 26 " --> pdb=" O VAL F 41 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL F 41 " --> pdb=" O ALA F 26 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS F 40 " --> pdb=" O LEU F 83 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS F 75 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ALA F 84 " --> pdb=" O VAL F 73 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL F 73 " --> pdb=" O ALA F 84 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL F 55 " --> pdb=" O VAL F 110 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU F 106 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS F 109 " --> pdb=" O SER F 19 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N SER F 19 " --> pdb=" O LYS F 109 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'F' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR F 157 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL F 122 " --> pdb=" O THR F 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR F 155 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL F 124 " --> pdb=" O VAL F 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL F 153 " --> pdb=" O VAL F 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU F 152 " --> pdb=" O MET F 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN F 220 " --> pdb=" O GLN F 206 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR F 199 " --> pdb=" O ILE F 182 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'F' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR F 157 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL F 122 " --> pdb=" O THR F 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR F 155 " --> pdb=" O VAL F 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL F 124 " --> pdb=" O VAL F 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL F 153 " --> pdb=" O VAL F 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU F 152 " --> pdb=" O MET F 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN F 220 " --> pdb=" O GLN F 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE F 196 " --> pdb=" O TYR F 232 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'F' and resid 129 through 134 removed outlier: 4.214A pdb=" N THR F 148 " --> pdb=" O GLN F 130 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR F 132 " --> pdb=" O ASN F 146 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASN F 146 " --> pdb=" O THR F 132 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE F 134 " --> pdb=" O SER F 144 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER F 144 " --> pdb=" O PHE F 134 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'G' and resid 12 through 14 Processing sheet with id=32, first strand: chain 'G' and resid 17 through 26 removed outlier: 6.797A pdb=" N THR G 43 " --> pdb=" O THR G 24 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA G 26 " --> pdb=" O VAL G 41 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL G 41 " --> pdb=" O ALA G 26 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS G 40 " --> pdb=" O LEU G 83 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS G 75 " --> pdb=" O THR G 82 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA G 84 " --> pdb=" O VAL G 73 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL G 73 " --> pdb=" O ALA G 84 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL G 55 " --> pdb=" O VAL G 110 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU G 106 " --> pdb=" O THR G 59 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS G 109 " --> pdb=" O SER G 19 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N SER G 19 " --> pdb=" O LYS G 109 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'G' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR G 157 " --> pdb=" O THR G 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL G 122 " --> pdb=" O THR G 155 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR G 155 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL G 124 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL G 153 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU G 152 " --> pdb=" O MET G 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN G 220 " --> pdb=" O GLN G 206 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR G 199 " --> pdb=" O ILE G 182 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'G' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR G 157 " --> pdb=" O THR G 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL G 122 " --> pdb=" O THR G 155 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR G 155 " --> pdb=" O VAL G 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL G 124 " --> pdb=" O VAL G 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL G 153 " --> pdb=" O VAL G 124 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU G 152 " --> pdb=" O MET G 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN G 220 " --> pdb=" O GLN G 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE G 196 " --> pdb=" O TYR G 232 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'G' and resid 129 through 134 removed outlier: 4.214A pdb=" N THR G 148 " --> pdb=" O GLN G 130 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR G 132 " --> pdb=" O ASN G 146 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASN G 146 " --> pdb=" O THR G 132 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE G 134 " --> pdb=" O SER G 144 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER G 144 " --> pdb=" O PHE G 134 " (cutoff:3.500A) Processing sheet with id=36, first strand: chain 'H' and resid 12 through 14 Processing sheet with id=37, first strand: chain 'H' and resid 17 through 26 removed outlier: 6.797A pdb=" N THR H 43 " --> pdb=" O THR H 24 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA H 26 " --> pdb=" O VAL H 41 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL H 41 " --> pdb=" O ALA H 26 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS H 40 " --> pdb=" O LEU H 83 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS H 75 " --> pdb=" O THR H 82 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ALA H 84 " --> pdb=" O VAL H 73 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL H 73 " --> pdb=" O ALA H 84 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL H 55 " --> pdb=" O VAL H 110 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU H 106 " --> pdb=" O THR H 59 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS H 109 " --> pdb=" O SER H 19 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N SER H 19 " --> pdb=" O LYS H 109 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'H' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR H 157 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL H 122 " --> pdb=" O THR H 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR H 155 " --> pdb=" O VAL H 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL H 124 " --> pdb=" O VAL H 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL H 153 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU H 152 " --> pdb=" O MET H 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN H 220 " --> pdb=" O GLN H 206 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR H 199 " --> pdb=" O ILE H 182 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'H' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR H 157 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL H 122 " --> pdb=" O THR H 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR H 155 " --> pdb=" O VAL H 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL H 124 " --> pdb=" O VAL H 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL H 153 " --> pdb=" O VAL H 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU H 152 " --> pdb=" O MET H 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN H 220 " --> pdb=" O GLN H 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE H 196 " --> pdb=" O TYR H 232 " (cutoff:3.500A) Processing sheet with id=40, first strand: chain 'H' and resid 129 through 134 removed outlier: 4.214A pdb=" N THR H 148 " --> pdb=" O GLN H 130 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR H 132 " --> pdb=" O ASN H 146 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ASN H 146 " --> pdb=" O THR H 132 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE H 134 " --> pdb=" O SER H 144 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N SER H 144 " --> pdb=" O PHE H 134 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'I' and resid 12 through 14 Processing sheet with id=42, first strand: chain 'I' and resid 17 through 26 removed outlier: 6.797A pdb=" N THR I 43 " --> pdb=" O THR I 24 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA I 26 " --> pdb=" O VAL I 41 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL I 41 " --> pdb=" O ALA I 26 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS I 40 " --> pdb=" O LEU I 83 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS I 75 " --> pdb=" O THR I 82 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA I 84 " --> pdb=" O VAL I 73 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL I 73 " --> pdb=" O ALA I 84 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL I 55 " --> pdb=" O VAL I 110 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU I 106 " --> pdb=" O THR I 59 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS I 109 " --> pdb=" O SER I 19 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N SER I 19 " --> pdb=" O LYS I 109 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'I' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR I 157 " --> pdb=" O THR I 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL I 122 " --> pdb=" O THR I 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR I 155 " --> pdb=" O VAL I 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL I 124 " --> pdb=" O VAL I 153 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL I 153 " --> pdb=" O VAL I 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU I 152 " --> pdb=" O MET I 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN I 220 " --> pdb=" O GLN I 206 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR I 199 " --> pdb=" O ILE I 182 " (cutoff:3.500A) Processing sheet with id=44, first strand: chain 'I' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR I 157 " --> pdb=" O THR I 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL I 122 " --> pdb=" O THR I 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR I 155 " --> pdb=" O VAL I 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL I 124 " --> pdb=" O VAL I 153 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL I 153 " --> pdb=" O VAL I 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU I 152 " --> pdb=" O MET I 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN I 220 " --> pdb=" O GLN I 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE I 196 " --> pdb=" O TYR I 232 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'I' and resid 129 through 134 removed outlier: 4.213A pdb=" N THR I 148 " --> pdb=" O GLN I 130 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR I 132 " --> pdb=" O ASN I 146 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ASN I 146 " --> pdb=" O THR I 132 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE I 134 " --> pdb=" O SER I 144 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER I 144 " --> pdb=" O PHE I 134 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'J' and resid 12 through 14 Processing sheet with id=47, first strand: chain 'J' and resid 17 through 26 removed outlier: 6.797A pdb=" N THR J 43 " --> pdb=" O THR J 24 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA J 26 " --> pdb=" O VAL J 41 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL J 41 " --> pdb=" O ALA J 26 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS J 40 " --> pdb=" O LEU J 83 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS J 75 " --> pdb=" O THR J 82 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ALA J 84 " --> pdb=" O VAL J 73 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL J 73 " --> pdb=" O ALA J 84 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL J 55 " --> pdb=" O VAL J 110 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU J 106 " --> pdb=" O THR J 59 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS J 109 " --> pdb=" O SER J 19 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N SER J 19 " --> pdb=" O LYS J 109 " (cutoff:3.500A) Processing sheet with id=48, first strand: chain 'J' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR J 157 " --> pdb=" O THR J 120 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL J 122 " --> pdb=" O THR J 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR J 155 " --> pdb=" O VAL J 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL J 124 " --> pdb=" O VAL J 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL J 153 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU J 152 " --> pdb=" O MET J 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN J 220 " --> pdb=" O GLN J 206 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR J 199 " --> pdb=" O ILE J 182 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'J' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR J 157 " --> pdb=" O THR J 120 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL J 122 " --> pdb=" O THR J 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR J 155 " --> pdb=" O VAL J 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL J 124 " --> pdb=" O VAL J 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL J 153 " --> pdb=" O VAL J 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU J 152 " --> pdb=" O MET J 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN J 220 " --> pdb=" O GLN J 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE J 196 " --> pdb=" O TYR J 232 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'J' and resid 129 through 134 removed outlier: 4.213A pdb=" N THR J 148 " --> pdb=" O GLN J 130 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N THR J 132 " --> pdb=" O ASN J 146 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ASN J 146 " --> pdb=" O THR J 132 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE J 134 " --> pdb=" O SER J 144 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER J 144 " --> pdb=" O PHE J 134 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'K' and resid 12 through 14 Processing sheet with id=52, first strand: chain 'K' and resid 17 through 26 removed outlier: 6.797A pdb=" N THR K 43 " --> pdb=" O THR K 24 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA K 26 " --> pdb=" O VAL K 41 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL K 41 " --> pdb=" O ALA K 26 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS K 40 " --> pdb=" O LEU K 83 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS K 75 " --> pdb=" O THR K 82 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA K 84 " --> pdb=" O VAL K 73 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL K 73 " --> pdb=" O ALA K 84 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL K 55 " --> pdb=" O VAL K 110 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU K 106 " --> pdb=" O THR K 59 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS K 109 " --> pdb=" O SER K 19 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N SER K 19 " --> pdb=" O LYS K 109 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'K' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR K 157 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL K 122 " --> pdb=" O THR K 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR K 155 " --> pdb=" O VAL K 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL K 124 " --> pdb=" O VAL K 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL K 153 " --> pdb=" O VAL K 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU K 152 " --> pdb=" O MET K 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN K 220 " --> pdb=" O GLN K 206 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR K 199 " --> pdb=" O ILE K 182 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'K' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR K 157 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL K 122 " --> pdb=" O THR K 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR K 155 " --> pdb=" O VAL K 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL K 124 " --> pdb=" O VAL K 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL K 153 " --> pdb=" O VAL K 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU K 152 " --> pdb=" O MET K 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN K 220 " --> pdb=" O GLN K 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE K 196 " --> pdb=" O TYR K 232 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'K' and resid 129 through 134 removed outlier: 4.213A pdb=" N THR K 148 " --> pdb=" O GLN K 130 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR K 132 " --> pdb=" O ASN K 146 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ASN K 146 " --> pdb=" O THR K 132 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE K 134 " --> pdb=" O SER K 144 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N SER K 144 " --> pdb=" O PHE K 134 " (cutoff:3.500A) Processing sheet with id=56, first strand: chain 'L' and resid 12 through 14 Processing sheet with id=57, first strand: chain 'L' and resid 17 through 26 removed outlier: 6.797A pdb=" N THR L 43 " --> pdb=" O THR L 24 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA L 26 " --> pdb=" O VAL L 41 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL L 41 " --> pdb=" O ALA L 26 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS L 40 " --> pdb=" O LEU L 83 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS L 75 " --> pdb=" O THR L 82 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA L 84 " --> pdb=" O VAL L 73 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL L 73 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL L 55 " --> pdb=" O VAL L 110 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU L 106 " --> pdb=" O THR L 59 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS L 109 " --> pdb=" O SER L 19 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N SER L 19 " --> pdb=" O LYS L 109 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'L' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR L 157 " --> pdb=" O THR L 120 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL L 122 " --> pdb=" O THR L 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR L 155 " --> pdb=" O VAL L 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL L 124 " --> pdb=" O VAL L 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL L 153 " --> pdb=" O VAL L 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU L 152 " --> pdb=" O MET L 225 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN L 220 " --> pdb=" O GLN L 206 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR L 199 " --> pdb=" O ILE L 182 " (cutoff:3.500A) Processing sheet with id=59, first strand: chain 'L' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR L 157 " --> pdb=" O THR L 120 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL L 122 " --> pdb=" O THR L 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR L 155 " --> pdb=" O VAL L 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL L 124 " --> pdb=" O VAL L 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL L 153 " --> pdb=" O VAL L 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU L 152 " --> pdb=" O MET L 225 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN L 220 " --> pdb=" O GLN L 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE L 196 " --> pdb=" O TYR L 232 " (cutoff:3.500A) Processing sheet with id=60, first strand: chain 'L' and resid 129 through 134 removed outlier: 4.214A pdb=" N THR L 148 " --> pdb=" O GLN L 130 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR L 132 " --> pdb=" O ASN L 146 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASN L 146 " --> pdb=" O THR L 132 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE L 134 " --> pdb=" O SER L 144 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER L 144 " --> pdb=" O PHE L 134 " (cutoff:3.500A) Processing sheet with id=61, first strand: chain 'M' and resid 12 through 14 Processing sheet with id=62, first strand: chain 'M' and resid 17 through 26 removed outlier: 6.797A pdb=" N THR M 43 " --> pdb=" O THR M 24 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA M 26 " --> pdb=" O VAL M 41 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL M 41 " --> pdb=" O ALA M 26 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS M 40 " --> pdb=" O LEU M 83 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS M 75 " --> pdb=" O THR M 82 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA M 84 " --> pdb=" O VAL M 73 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL M 73 " --> pdb=" O ALA M 84 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL M 55 " --> pdb=" O VAL M 110 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU M 106 " --> pdb=" O THR M 59 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS M 109 " --> pdb=" O SER M 19 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N SER M 19 " --> pdb=" O LYS M 109 " (cutoff:3.500A) Processing sheet with id=63, first strand: chain 'M' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR M 157 " --> pdb=" O THR M 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL M 122 " --> pdb=" O THR M 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR M 155 " --> pdb=" O VAL M 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL M 124 " --> pdb=" O VAL M 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL M 153 " --> pdb=" O VAL M 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU M 152 " --> pdb=" O MET M 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN M 220 " --> pdb=" O GLN M 206 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR M 199 " --> pdb=" O ILE M 182 " (cutoff:3.500A) Processing sheet with id=64, first strand: chain 'M' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR M 157 " --> pdb=" O THR M 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL M 122 " --> pdb=" O THR M 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR M 155 " --> pdb=" O VAL M 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL M 124 " --> pdb=" O VAL M 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL M 153 " --> pdb=" O VAL M 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU M 152 " --> pdb=" O MET M 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN M 220 " --> pdb=" O GLN M 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE M 196 " --> pdb=" O TYR M 232 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain 'M' and resid 129 through 134 removed outlier: 4.214A pdb=" N THR M 148 " --> pdb=" O GLN M 130 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR M 132 " --> pdb=" O ASN M 146 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ASN M 146 " --> pdb=" O THR M 132 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE M 134 " --> pdb=" O SER M 144 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER M 144 " --> pdb=" O PHE M 134 " (cutoff:3.500A) Processing sheet with id=66, first strand: chain 'N' and resid 12 through 14 Processing sheet with id=67, first strand: chain 'N' and resid 17 through 26 removed outlier: 6.797A pdb=" N THR N 43 " --> pdb=" O THR N 24 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA N 26 " --> pdb=" O VAL N 41 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL N 41 " --> pdb=" O ALA N 26 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS N 40 " --> pdb=" O LEU N 83 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS N 75 " --> pdb=" O THR N 82 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA N 84 " --> pdb=" O VAL N 73 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL N 73 " --> pdb=" O ALA N 84 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL N 55 " --> pdb=" O VAL N 110 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU N 106 " --> pdb=" O THR N 59 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS N 109 " --> pdb=" O SER N 19 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N SER N 19 " --> pdb=" O LYS N 109 " (cutoff:3.500A) Processing sheet with id=68, first strand: chain 'N' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR N 157 " --> pdb=" O THR N 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL N 122 " --> pdb=" O THR N 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR N 155 " --> pdb=" O VAL N 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL N 124 " --> pdb=" O VAL N 153 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL N 153 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU N 152 " --> pdb=" O MET N 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN N 220 " --> pdb=" O GLN N 206 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR N 199 " --> pdb=" O ILE N 182 " (cutoff:3.500A) Processing sheet with id=69, first strand: chain 'N' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR N 157 " --> pdb=" O THR N 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL N 122 " --> pdb=" O THR N 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR N 155 " --> pdb=" O VAL N 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL N 124 " --> pdb=" O VAL N 153 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL N 153 " --> pdb=" O VAL N 124 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU N 152 " --> pdb=" O MET N 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN N 220 " --> pdb=" O GLN N 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE N 196 " --> pdb=" O TYR N 232 " (cutoff:3.500A) Processing sheet with id=70, first strand: chain 'N' and resid 129 through 134 removed outlier: 4.214A pdb=" N THR N 148 " --> pdb=" O GLN N 130 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N THR N 132 " --> pdb=" O ASN N 146 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASN N 146 " --> pdb=" O THR N 132 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE N 134 " --> pdb=" O SER N 144 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N SER N 144 " --> pdb=" O PHE N 134 " (cutoff:3.500A) Processing sheet with id=71, first strand: chain 'O' and resid 12 through 14 Processing sheet with id=72, first strand: chain 'O' and resid 17 through 26 removed outlier: 6.797A pdb=" N THR O 43 " --> pdb=" O THR O 24 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA O 26 " --> pdb=" O VAL O 41 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL O 41 " --> pdb=" O ALA O 26 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS O 40 " --> pdb=" O LEU O 83 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS O 75 " --> pdb=" O THR O 82 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ALA O 84 " --> pdb=" O VAL O 73 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL O 73 " --> pdb=" O ALA O 84 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL O 55 " --> pdb=" O VAL O 110 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU O 106 " --> pdb=" O THR O 59 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS O 109 " --> pdb=" O SER O 19 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N SER O 19 " --> pdb=" O LYS O 109 " (cutoff:3.500A) Processing sheet with id=73, first strand: chain 'O' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR O 157 " --> pdb=" O THR O 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL O 122 " --> pdb=" O THR O 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR O 155 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL O 124 " --> pdb=" O VAL O 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL O 153 " --> pdb=" O VAL O 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU O 152 " --> pdb=" O MET O 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN O 220 " --> pdb=" O GLN O 206 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR O 199 " --> pdb=" O ILE O 182 " (cutoff:3.500A) Processing sheet with id=74, first strand: chain 'O' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR O 157 " --> pdb=" O THR O 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL O 122 " --> pdb=" O THR O 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR O 155 " --> pdb=" O VAL O 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL O 124 " --> pdb=" O VAL O 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL O 153 " --> pdb=" O VAL O 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU O 152 " --> pdb=" O MET O 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN O 220 " --> pdb=" O GLN O 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE O 196 " --> pdb=" O TYR O 232 " (cutoff:3.500A) Processing sheet with id=75, first strand: chain 'O' and resid 129 through 134 removed outlier: 4.214A pdb=" N THR O 148 " --> pdb=" O GLN O 130 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR O 132 " --> pdb=" O ASN O 146 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ASN O 146 " --> pdb=" O THR O 132 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE O 134 " --> pdb=" O SER O 144 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER O 144 " --> pdb=" O PHE O 134 " (cutoff:3.500A) Processing sheet with id=76, first strand: chain 'P' and resid 12 through 14 Processing sheet with id=77, first strand: chain 'P' and resid 17 through 26 removed outlier: 6.797A pdb=" N THR P 43 " --> pdb=" O THR P 24 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA P 26 " --> pdb=" O VAL P 41 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL P 41 " --> pdb=" O ALA P 26 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS P 40 " --> pdb=" O LEU P 83 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS P 75 " --> pdb=" O THR P 82 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA P 84 " --> pdb=" O VAL P 73 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL P 73 " --> pdb=" O ALA P 84 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL P 55 " --> pdb=" O VAL P 110 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU P 106 " --> pdb=" O THR P 59 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS P 109 " --> pdb=" O SER P 19 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N SER P 19 " --> pdb=" O LYS P 109 " (cutoff:3.500A) Processing sheet with id=78, first strand: chain 'P' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR P 157 " --> pdb=" O THR P 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL P 122 " --> pdb=" O THR P 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR P 155 " --> pdb=" O VAL P 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL P 124 " --> pdb=" O VAL P 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL P 153 " --> pdb=" O VAL P 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU P 152 " --> pdb=" O MET P 225 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN P 220 " --> pdb=" O GLN P 206 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR P 199 " --> pdb=" O ILE P 182 " (cutoff:3.500A) Processing sheet with id=79, first strand: chain 'P' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR P 157 " --> pdb=" O THR P 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL P 122 " --> pdb=" O THR P 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR P 155 " --> pdb=" O VAL P 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL P 124 " --> pdb=" O VAL P 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL P 153 " --> pdb=" O VAL P 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU P 152 " --> pdb=" O MET P 225 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN P 220 " --> pdb=" O GLN P 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE P 196 " --> pdb=" O TYR P 232 " (cutoff:3.500A) Processing sheet with id=80, first strand: chain 'P' and resid 129 through 134 removed outlier: 4.214A pdb=" N THR P 148 " --> pdb=" O GLN P 130 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N THR P 132 " --> pdb=" O ASN P 146 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ASN P 146 " --> pdb=" O THR P 132 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE P 134 " --> pdb=" O SER P 144 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER P 144 " --> pdb=" O PHE P 134 " (cutoff:3.500A) Processing sheet with id=81, first strand: chain 'Q' and resid 12 through 14 Processing sheet with id=82, first strand: chain 'Q' and resid 17 through 26 removed outlier: 6.797A pdb=" N THR Q 43 " --> pdb=" O THR Q 24 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA Q 26 " --> pdb=" O VAL Q 41 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL Q 41 " --> pdb=" O ALA Q 26 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS Q 40 " --> pdb=" O LEU Q 83 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS Q 75 " --> pdb=" O THR Q 82 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA Q 84 " --> pdb=" O VAL Q 73 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL Q 73 " --> pdb=" O ALA Q 84 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL Q 55 " --> pdb=" O VAL Q 110 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU Q 106 " --> pdb=" O THR Q 59 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS Q 109 " --> pdb=" O SER Q 19 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N SER Q 19 " --> pdb=" O LYS Q 109 " (cutoff:3.500A) Processing sheet with id=83, first strand: chain 'Q' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR Q 157 " --> pdb=" O THR Q 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL Q 122 " --> pdb=" O THR Q 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR Q 155 " --> pdb=" O VAL Q 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL Q 124 " --> pdb=" O VAL Q 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL Q 153 " --> pdb=" O VAL Q 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU Q 152 " --> pdb=" O MET Q 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN Q 220 " --> pdb=" O GLN Q 206 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR Q 199 " --> pdb=" O ILE Q 182 " (cutoff:3.500A) Processing sheet with id=84, first strand: chain 'Q' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR Q 157 " --> pdb=" O THR Q 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL Q 122 " --> pdb=" O THR Q 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR Q 155 " --> pdb=" O VAL Q 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL Q 124 " --> pdb=" O VAL Q 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL Q 153 " --> pdb=" O VAL Q 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU Q 152 " --> pdb=" O MET Q 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN Q 220 " --> pdb=" O GLN Q 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE Q 196 " --> pdb=" O TYR Q 232 " (cutoff:3.500A) Processing sheet with id=85, first strand: chain 'Q' and resid 129 through 134 removed outlier: 4.213A pdb=" N THR Q 148 " --> pdb=" O GLN Q 130 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR Q 132 " --> pdb=" O ASN Q 146 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ASN Q 146 " --> pdb=" O THR Q 132 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE Q 134 " --> pdb=" O SER Q 144 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER Q 144 " --> pdb=" O PHE Q 134 " (cutoff:3.500A) Processing sheet with id=86, first strand: chain 'R' and resid 12 through 14 Processing sheet with id=87, first strand: chain 'R' and resid 17 through 26 removed outlier: 6.797A pdb=" N THR R 43 " --> pdb=" O THR R 24 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA R 26 " --> pdb=" O VAL R 41 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL R 41 " --> pdb=" O ALA R 26 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS R 40 " --> pdb=" O LEU R 83 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS R 75 " --> pdb=" O THR R 82 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ALA R 84 " --> pdb=" O VAL R 73 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL R 73 " --> pdb=" O ALA R 84 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL R 55 " --> pdb=" O VAL R 110 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU R 106 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS R 109 " --> pdb=" O SER R 19 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N SER R 19 " --> pdb=" O LYS R 109 " (cutoff:3.500A) Processing sheet with id=88, first strand: chain 'R' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR R 157 " --> pdb=" O THR R 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL R 122 " --> pdb=" O THR R 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR R 155 " --> pdb=" O VAL R 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL R 124 " --> pdb=" O VAL R 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL R 153 " --> pdb=" O VAL R 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU R 152 " --> pdb=" O MET R 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN R 220 " --> pdb=" O GLN R 206 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR R 199 " --> pdb=" O ILE R 182 " (cutoff:3.500A) Processing sheet with id=89, first strand: chain 'R' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR R 157 " --> pdb=" O THR R 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL R 122 " --> pdb=" O THR R 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR R 155 " --> pdb=" O VAL R 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL R 124 " --> pdb=" O VAL R 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL R 153 " --> pdb=" O VAL R 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU R 152 " --> pdb=" O MET R 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN R 220 " --> pdb=" O GLN R 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE R 196 " --> pdb=" O TYR R 232 " (cutoff:3.500A) Processing sheet with id=90, first strand: chain 'R' and resid 129 through 134 removed outlier: 4.214A pdb=" N THR R 148 " --> pdb=" O GLN R 130 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR R 132 " --> pdb=" O ASN R 146 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASN R 146 " --> pdb=" O THR R 132 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE R 134 " --> pdb=" O SER R 144 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER R 144 " --> pdb=" O PHE R 134 " (cutoff:3.500A) Processing sheet with id=91, first strand: chain 'S' and resid 12 through 14 Processing sheet with id=92, first strand: chain 'S' and resid 17 through 26 removed outlier: 6.797A pdb=" N THR S 43 " --> pdb=" O THR S 24 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA S 26 " --> pdb=" O VAL S 41 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL S 41 " --> pdb=" O ALA S 26 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS S 40 " --> pdb=" O LEU S 83 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LYS S 75 " --> pdb=" O THR S 82 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA S 84 " --> pdb=" O VAL S 73 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL S 73 " --> pdb=" O ALA S 84 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL S 55 " --> pdb=" O VAL S 110 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU S 106 " --> pdb=" O THR S 59 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS S 109 " --> pdb=" O SER S 19 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N SER S 19 " --> pdb=" O LYS S 109 " (cutoff:3.500A) Processing sheet with id=93, first strand: chain 'S' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR S 157 " --> pdb=" O THR S 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL S 122 " --> pdb=" O THR S 155 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR S 155 " --> pdb=" O VAL S 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL S 124 " --> pdb=" O VAL S 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL S 153 " --> pdb=" O VAL S 124 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU S 152 " --> pdb=" O MET S 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN S 220 " --> pdb=" O GLN S 206 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR S 199 " --> pdb=" O ILE S 182 " (cutoff:3.500A) Processing sheet with id=94, first strand: chain 'S' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR S 157 " --> pdb=" O THR S 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL S 122 " --> pdb=" O THR S 155 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N THR S 155 " --> pdb=" O VAL S 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL S 124 " --> pdb=" O VAL S 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL S 153 " --> pdb=" O VAL S 124 " (cutoff:3.500A) removed outlier: 4.986A pdb=" N LEU S 152 " --> pdb=" O MET S 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN S 220 " --> pdb=" O GLN S 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE S 196 " --> pdb=" O TYR S 232 " (cutoff:3.500A) Processing sheet with id=95, first strand: chain 'S' and resid 129 through 134 removed outlier: 4.214A pdb=" N THR S 148 " --> pdb=" O GLN S 130 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR S 132 " --> pdb=" O ASN S 146 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASN S 146 " --> pdb=" O THR S 132 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE S 134 " --> pdb=" O SER S 144 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER S 144 " --> pdb=" O PHE S 134 " (cutoff:3.500A) Processing sheet with id=96, first strand: chain 'T' and resid 12 through 14 Processing sheet with id=97, first strand: chain 'T' and resid 17 through 26 removed outlier: 6.797A pdb=" N THR T 43 " --> pdb=" O THR T 24 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA T 26 " --> pdb=" O VAL T 41 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL T 41 " --> pdb=" O ALA T 26 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS T 40 " --> pdb=" O LEU T 83 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS T 75 " --> pdb=" O THR T 82 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ALA T 84 " --> pdb=" O VAL T 73 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL T 73 " --> pdb=" O ALA T 84 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL T 55 " --> pdb=" O VAL T 110 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU T 106 " --> pdb=" O THR T 59 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS T 109 " --> pdb=" O SER T 19 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N SER T 19 " --> pdb=" O LYS T 109 " (cutoff:3.500A) Processing sheet with id=98, first strand: chain 'T' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR T 157 " --> pdb=" O THR T 120 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL T 122 " --> pdb=" O THR T 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR T 155 " --> pdb=" O VAL T 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL T 124 " --> pdb=" O VAL T 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL T 153 " --> pdb=" O VAL T 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU T 152 " --> pdb=" O MET T 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN T 220 " --> pdb=" O GLN T 206 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR T 199 " --> pdb=" O ILE T 182 " (cutoff:3.500A) Processing sheet with id=99, first strand: chain 'T' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR T 157 " --> pdb=" O THR T 120 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL T 122 " --> pdb=" O THR T 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR T 155 " --> pdb=" O VAL T 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL T 124 " --> pdb=" O VAL T 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL T 153 " --> pdb=" O VAL T 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU T 152 " --> pdb=" O MET T 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN T 220 " --> pdb=" O GLN T 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE T 196 " --> pdb=" O TYR T 232 " (cutoff:3.500A) Processing sheet with id=100, first strand: chain 'T' and resid 129 through 134 removed outlier: 4.214A pdb=" N THR T 148 " --> pdb=" O GLN T 130 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR T 132 " --> pdb=" O ASN T 146 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ASN T 146 " --> pdb=" O THR T 132 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE T 134 " --> pdb=" O SER T 144 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N SER T 144 " --> pdb=" O PHE T 134 " (cutoff:3.500A) Processing sheet with id=101, first strand: chain 'U' and resid 12 through 14 Processing sheet with id=102, first strand: chain 'U' and resid 17 through 26 removed outlier: 6.797A pdb=" N THR U 43 " --> pdb=" O THR U 24 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA U 26 " --> pdb=" O VAL U 41 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL U 41 " --> pdb=" O ALA U 26 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS U 40 " --> pdb=" O LEU U 83 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS U 75 " --> pdb=" O THR U 82 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA U 84 " --> pdb=" O VAL U 73 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL U 73 " --> pdb=" O ALA U 84 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL U 55 " --> pdb=" O VAL U 110 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU U 106 " --> pdb=" O THR U 59 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS U 109 " --> pdb=" O SER U 19 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N SER U 19 " --> pdb=" O LYS U 109 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain 'U' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR U 157 " --> pdb=" O THR U 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL U 122 " --> pdb=" O THR U 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR U 155 " --> pdb=" O VAL U 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL U 124 " --> pdb=" O VAL U 153 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL U 153 " --> pdb=" O VAL U 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU U 152 " --> pdb=" O MET U 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN U 220 " --> pdb=" O GLN U 206 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR U 199 " --> pdb=" O ILE U 182 " (cutoff:3.500A) Processing sheet with id=104, first strand: chain 'U' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR U 157 " --> pdb=" O THR U 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL U 122 " --> pdb=" O THR U 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR U 155 " --> pdb=" O VAL U 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL U 124 " --> pdb=" O VAL U 153 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL U 153 " --> pdb=" O VAL U 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU U 152 " --> pdb=" O MET U 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN U 220 " --> pdb=" O GLN U 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE U 196 " --> pdb=" O TYR U 232 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain 'U' and resid 129 through 134 removed outlier: 4.213A pdb=" N THR U 148 " --> pdb=" O GLN U 130 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR U 132 " --> pdb=" O ASN U 146 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ASN U 146 " --> pdb=" O THR U 132 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE U 134 " --> pdb=" O SER U 144 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER U 144 " --> pdb=" O PHE U 134 " (cutoff:3.500A) Processing sheet with id=106, first strand: chain 'V' and resid 12 through 14 Processing sheet with id=107, first strand: chain 'V' and resid 17 through 26 removed outlier: 6.797A pdb=" N THR V 43 " --> pdb=" O THR V 24 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA V 26 " --> pdb=" O VAL V 41 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL V 41 " --> pdb=" O ALA V 26 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS V 40 " --> pdb=" O LEU V 83 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS V 75 " --> pdb=" O THR V 82 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ALA V 84 " --> pdb=" O VAL V 73 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL V 73 " --> pdb=" O ALA V 84 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL V 55 " --> pdb=" O VAL V 110 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU V 106 " --> pdb=" O THR V 59 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS V 109 " --> pdb=" O SER V 19 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N SER V 19 " --> pdb=" O LYS V 109 " (cutoff:3.500A) Processing sheet with id=108, first strand: chain 'V' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR V 157 " --> pdb=" O THR V 120 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL V 122 " --> pdb=" O THR V 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR V 155 " --> pdb=" O VAL V 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL V 124 " --> pdb=" O VAL V 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL V 153 " --> pdb=" O VAL V 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU V 152 " --> pdb=" O MET V 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN V 220 " --> pdb=" O GLN V 206 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR V 199 " --> pdb=" O ILE V 182 " (cutoff:3.500A) Processing sheet with id=109, first strand: chain 'V' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR V 157 " --> pdb=" O THR V 120 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL V 122 " --> pdb=" O THR V 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR V 155 " --> pdb=" O VAL V 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL V 124 " --> pdb=" O VAL V 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL V 153 " --> pdb=" O VAL V 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU V 152 " --> pdb=" O MET V 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN V 220 " --> pdb=" O GLN V 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE V 196 " --> pdb=" O TYR V 232 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain 'V' and resid 129 through 134 removed outlier: 4.213A pdb=" N THR V 148 " --> pdb=" O GLN V 130 " (cutoff:3.500A) removed outlier: 6.132A pdb=" N THR V 132 " --> pdb=" O ASN V 146 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ASN V 146 " --> pdb=" O THR V 132 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE V 134 " --> pdb=" O SER V 144 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER V 144 " --> pdb=" O PHE V 134 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain 'W' and resid 12 through 14 Processing sheet with id=112, first strand: chain 'W' and resid 17 through 26 removed outlier: 6.797A pdb=" N THR W 43 " --> pdb=" O THR W 24 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA W 26 " --> pdb=" O VAL W 41 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL W 41 " --> pdb=" O ALA W 26 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS W 40 " --> pdb=" O LEU W 83 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS W 75 " --> pdb=" O THR W 82 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA W 84 " --> pdb=" O VAL W 73 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL W 73 " --> pdb=" O ALA W 84 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL W 55 " --> pdb=" O VAL W 110 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU W 106 " --> pdb=" O THR W 59 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LYS W 109 " --> pdb=" O SER W 19 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N SER W 19 " --> pdb=" O LYS W 109 " (cutoff:3.500A) Processing sheet with id=113, first strand: chain 'W' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR W 157 " --> pdb=" O THR W 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL W 122 " --> pdb=" O THR W 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR W 155 " --> pdb=" O VAL W 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL W 124 " --> pdb=" O VAL W 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL W 153 " --> pdb=" O VAL W 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU W 152 " --> pdb=" O MET W 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN W 220 " --> pdb=" O GLN W 206 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR W 199 " --> pdb=" O ILE W 182 " (cutoff:3.500A) Processing sheet with id=114, first strand: chain 'W' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR W 157 " --> pdb=" O THR W 120 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL W 122 " --> pdb=" O THR W 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR W 155 " --> pdb=" O VAL W 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL W 124 " --> pdb=" O VAL W 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL W 153 " --> pdb=" O VAL W 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU W 152 " --> pdb=" O MET W 225 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLN W 220 " --> pdb=" O GLN W 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE W 196 " --> pdb=" O TYR W 232 " (cutoff:3.500A) Processing sheet with id=115, first strand: chain 'W' and resid 129 through 134 removed outlier: 4.213A pdb=" N THR W 148 " --> pdb=" O GLN W 130 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR W 132 " --> pdb=" O ASN W 146 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N ASN W 146 " --> pdb=" O THR W 132 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE W 134 " --> pdb=" O SER W 144 " (cutoff:3.500A) removed outlier: 5.581A pdb=" N SER W 144 " --> pdb=" O PHE W 134 " (cutoff:3.500A) Processing sheet with id=116, first strand: chain 'X' and resid 12 through 14 Processing sheet with id=117, first strand: chain 'X' and resid 17 through 26 removed outlier: 6.797A pdb=" N THR X 43 " --> pdb=" O THR X 24 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N ALA X 26 " --> pdb=" O VAL X 41 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VAL X 41 " --> pdb=" O ALA X 26 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N CYS X 40 " --> pdb=" O LEU X 83 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N LYS X 75 " --> pdb=" O THR X 82 " (cutoff:3.500A) removed outlier: 5.736A pdb=" N ALA X 84 " --> pdb=" O VAL X 73 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL X 73 " --> pdb=" O ALA X 84 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N VAL X 55 " --> pdb=" O VAL X 110 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU X 106 " --> pdb=" O THR X 59 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N LYS X 109 " --> pdb=" O SER X 19 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N SER X 19 " --> pdb=" O LYS X 109 " (cutoff:3.500A) Processing sheet with id=118, first strand: chain 'X' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR X 157 " --> pdb=" O THR X 120 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL X 122 " --> pdb=" O THR X 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR X 155 " --> pdb=" O VAL X 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL X 124 " --> pdb=" O VAL X 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL X 153 " --> pdb=" O VAL X 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU X 152 " --> pdb=" O MET X 225 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN X 220 " --> pdb=" O GLN X 206 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N TYR X 199 " --> pdb=" O ILE X 182 " (cutoff:3.500A) Processing sheet with id=119, first strand: chain 'X' and resid 119 through 126 removed outlier: 7.109A pdb=" N THR X 157 " --> pdb=" O THR X 120 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N VAL X 122 " --> pdb=" O THR X 155 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N THR X 155 " --> pdb=" O VAL X 122 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N VAL X 124 " --> pdb=" O VAL X 153 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N VAL X 153 " --> pdb=" O VAL X 124 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N LEU X 152 " --> pdb=" O MET X 225 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN X 220 " --> pdb=" O GLN X 206 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE X 196 " --> pdb=" O TYR X 232 " (cutoff:3.500A) Processing sheet with id=120, first strand: chain 'X' and resid 129 through 134 removed outlier: 4.214A pdb=" N THR X 148 " --> pdb=" O GLN X 130 " (cutoff:3.500A) removed outlier: 6.133A pdb=" N THR X 132 " --> pdb=" O ASN X 146 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N ASN X 146 " --> pdb=" O THR X 132 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N PHE X 134 " --> pdb=" O SER X 144 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER X 144 " --> pdb=" O PHE X 134 " (cutoff:3.500A) 1536 hydrogen bonds defined for protein. 4320 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: 11.83 Time building geometry restraints manager: 4.66 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: 14088 1.34 - 1.46: 8778 1.46 - 1.58: 20334 1.58 - 1.69: 0 1.69 - 1.81: 192 Bond restraints: 43392 Sorted by residual: bond pdb=" N GLU Q 212 " pdb=" CA GLU Q 212 " ideal model delta sigma weight residual 1.455 1.479 -0.024 1.27e-02 6.20e+03 3.62e+00 bond pdb=" N GLU E 212 " pdb=" CA GLU E 212 " ideal model delta sigma weight residual 1.455 1.479 -0.024 1.27e-02 6.20e+03 3.62e+00 bond pdb=" N GLU K 212 " pdb=" CA GLU K 212 " ideal model delta sigma weight residual 1.455 1.479 -0.024 1.27e-02 6.20e+03 3.59e+00 bond pdb=" N GLU W 212 " pdb=" CA GLU W 212 " ideal model delta sigma weight residual 1.455 1.479 -0.024 1.27e-02 6.20e+03 3.59e+00 bond pdb=" N GLU F 212 " pdb=" CA GLU F 212 " ideal model delta sigma weight residual 1.455 1.479 -0.024 1.27e-02 6.20e+03 3.56e+00 ... (remaining 43387 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 58102 1.45 - 2.91: 728 2.91 - 4.36: 378 4.36 - 5.82: 72 5.82 - 7.27: 24 Bond angle restraints: 59304 Sorted by residual: angle pdb=" CA GLN B 4 " pdb=" C GLN B 4 " pdb=" O GLN B 4 " ideal model delta sigma weight residual 121.60 116.48 5.12 1.21e+00 6.83e-01 1.79e+01 angle pdb=" CA GLN N 4 " pdb=" C GLN N 4 " pdb=" O GLN N 4 " ideal model delta sigma weight residual 121.60 116.48 5.12 1.21e+00 6.83e-01 1.79e+01 angle pdb=" CA GLN I 4 " pdb=" C GLN I 4 " pdb=" O GLN I 4 " ideal model delta sigma weight residual 121.60 116.50 5.10 1.21e+00 6.83e-01 1.78e+01 angle pdb=" CA GLN U 4 " pdb=" C GLN U 4 " pdb=" O GLN U 4 " ideal model delta sigma weight residual 121.60 116.50 5.10 1.21e+00 6.83e-01 1.78e+01 angle pdb=" CA GLN G 4 " pdb=" C GLN G 4 " pdb=" O GLN G 4 " ideal model delta sigma weight residual 121.60 116.51 5.09 1.21e+00 6.83e-01 1.77e+01 ... (remaining 59299 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 23544 17.27 - 34.53: 1752 34.53 - 51.80: 426 51.80 - 69.06: 30 69.06 - 86.33: 120 Dihedral angle restraints: 25872 sinusoidal: 9408 harmonic: 16464 Sorted by residual: dihedral pdb=" C GLU J 212 " pdb=" N GLU J 212 " pdb=" CA GLU J 212 " pdb=" CB GLU J 212 " ideal model delta harmonic sigma weight residual -122.60 -114.01 -8.59 0 2.50e+00 1.60e-01 1.18e+01 dihedral pdb=" C GLU V 212 " pdb=" N GLU V 212 " pdb=" CA GLU V 212 " pdb=" CB GLU V 212 " ideal model delta harmonic sigma weight residual -122.60 -114.01 -8.59 0 2.50e+00 1.60e-01 1.18e+01 dihedral pdb=" C GLU K 212 " pdb=" N GLU K 212 " pdb=" CA GLU K 212 " pdb=" CB GLU K 212 " ideal model delta harmonic sigma weight residual -122.60 -114.02 -8.58 0 2.50e+00 1.60e-01 1.18e+01 ... (remaining 25869 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 4460 0.033 - 0.065: 1764 0.065 - 0.098: 434 0.098 - 0.130: 640 0.130 - 0.163: 46 Chirality restraints: 7344 Sorted by residual: chirality pdb=" CA GLU K 212 " pdb=" N GLU K 212 " pdb=" C GLU K 212 " pdb=" CB GLU K 212 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CA GLU W 212 " pdb=" N GLU W 212 " pdb=" C GLU W 212 " pdb=" CB GLU W 212 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CA GLU J 212 " pdb=" N GLU J 212 " pdb=" C GLU J 212 " pdb=" CB GLU J 212 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 7341 not shown) Planarity restraints: 7656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR N 3 " -0.009 2.00e-02 2.50e+03 6.63e-03 8.78e-01 pdb=" CG TYR N 3 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR N 3 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR N 3 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR N 3 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR N 3 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR N 3 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR N 3 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 3 " 0.009 2.00e-02 2.50e+03 6.63e-03 8.78e-01 pdb=" CG TYR B 3 " -0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR B 3 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR B 3 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR B 3 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 3 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 3 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 3 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 3 " -0.009 2.00e-02 2.50e+03 6.60e-03 8.71e-01 pdb=" CG TYR L 3 " 0.016 2.00e-02 2.50e+03 pdb=" CD1 TYR L 3 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR L 3 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR L 3 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR L 3 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR L 3 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR L 3 " -0.002 2.00e-02 2.50e+03 ... (remaining 7653 not shown) Histogram of nonbonded interaction distances: 1.98 - 2.57: 168 2.57 - 3.15: 34198 3.15 - 3.73: 57728 3.73 - 4.32: 81790 4.32 - 4.90: 143521 Nonbonded interactions: 317405 Sorted by model distance: nonbonded pdb=" OE1 GLU P 217 " pdb=" NE2 GLN T 4 " model vdw 1.982 3.120 nonbonded pdb=" OE1 GLU D 217 " pdb=" NE2 GLN H 4 " model vdw 1.982 3.120 nonbonded pdb=" OE1 GLU O 217 " pdb=" NE2 GLN S 4 " model vdw 1.982 3.120 nonbonded pdb=" OE1 GLU C 217 " pdb=" NE2 GLN G 4 " model vdw 1.982 3.120 nonbonded pdb=" OE1 GLU I 217 " pdb=" NE2 GLN M 4 " model vdw 1.982 3.120 ... (remaining 317400 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: 0.18 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 5.550 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: 0.030 Extract box with map and model: 0.880 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 35.470 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.190 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 43392 Z= 0.142 Angle : 0.543 7.271 59304 Z= 0.310 Chirality : 0.048 0.163 7344 Planarity : 0.002 0.017 7656 Dihedral : 14.720 86.330 15264 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.51 % Allowed : 9.69 % Favored : 89.80 % 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: 0.00 (0.11), residues: 5712 helix: 2.67 (0.26), residues: 432 sheet: 0.09 (0.10), residues: 2520 loop : -0.44 (0.12), residues: 2760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 85 TYR 0.016 0.002 TYR N 3 PHE 0.010 0.001 PHE L 158 TRP 0.003 0.001 TRP W 63 HIS 0.001 0.000 HIS R 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.14 (43392) covalent geometry : angle 0.54299 / 0.31 (59304) hydrogen bonds : bond 0.21548 / 14.76 ( 1224) hydrogen bonds : angle 8.45547 / 5.74 ( 4320) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11424 Ramachandran restraints generated. 5712 Oldfield, 0 Emsley, 5712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11424 Ramachandran restraints generated. 5712 Oldfield, 0 Emsley, 5712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 4872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 590 time to evaluate : 1.637 Fit side-chains REVERT: A 60 LYS cc_start: 0.8197 (pttp) cc_final: 0.7972 (pttm) REVERT: A 106 GLU cc_start: 0.7591 (tt0) cc_final: 0.7048 (tt0) REVERT: B 139 VAL cc_start: 0.9224 (t) cc_final: 0.8974 (p) REVERT: B 183 LYS cc_start: 0.8574 (tttt) cc_final: 0.8362 (tttm) REVERT: B 193 LYS cc_start: 0.8903 (mtpt) cc_final: 0.8702 (ttmt) REVERT: D 16 VAL cc_start: 0.8811 (OUTLIER) cc_final: 0.8569 (p) REVERT: D 35 ASP cc_start: 0.7953 (t0) cc_final: 0.7667 (t0) REVERT: E 60 LYS cc_start: 0.8134 (pttp) cc_final: 0.7892 (pttm) REVERT: E 106 GLU cc_start: 0.7615 (tt0) cc_final: 0.6971 (tt0) REVERT: F 60 LYS cc_start: 0.8603 (pttp) cc_final: 0.8340 (ptpt) REVERT: F 139 VAL cc_start: 0.9274 (t) cc_final: 0.9055 (p) REVERT: H 16 VAL cc_start: 0.8788 (OUTLIER) cc_final: 0.8550 (p) REVERT: J 57 MET cc_start: 0.8832 (ttp) cc_final: 0.8614 (ttp) REVERT: J 60 LYS cc_start: 0.8584 (pttp) cc_final: 0.8341 (ptpt) REVERT: J 139 VAL cc_start: 0.9290 (t) cc_final: 0.9064 (p) REVERT: L 75 LYS cc_start: 0.8515 (tttt) cc_final: 0.8294 (ttpp) REVERT: M 60 LYS cc_start: 0.8194 (pttp) cc_final: 0.7969 (pttm) REVERT: M 106 GLU cc_start: 0.7586 (tt0) cc_final: 0.7039 (tt0) REVERT: N 139 VAL cc_start: 0.9227 (t) cc_final: 0.8985 (p) REVERT: N 183 LYS cc_start: 0.8556 (tttt) cc_final: 0.8343 (tttm) REVERT: P 16 VAL cc_start: 0.8816 (OUTLIER) cc_final: 0.8581 (p) REVERT: P 35 ASP cc_start: 0.7960 (t0) cc_final: 0.7655 (t0) REVERT: Q 60 LYS cc_start: 0.8145 (pttp) cc_final: 0.7895 (pttm) REVERT: Q 106 GLU cc_start: 0.7618 (tt0) cc_final: 0.6985 (tt0) REVERT: R 60 LYS cc_start: 0.8601 (pttp) cc_final: 0.8339 (ptpt) REVERT: R 139 VAL cc_start: 0.9271 (t) cc_final: 0.9054 (p) REVERT: T 16 VAL cc_start: 0.8789 (OUTLIER) cc_final: 0.8553 (p) REVERT: V 57 MET cc_start: 0.8840 (ttp) cc_final: 0.8622 (ttp) REVERT: V 60 LYS cc_start: 0.8590 (pttp) cc_final: 0.8346 (ptpt) REVERT: V 139 VAL cc_start: 0.9276 (t) cc_final: 0.9056 (p) REVERT: X 75 LYS cc_start: 0.8514 (tttt) cc_final: 0.8292 (ttpp) outliers start: 24 outliers final: 2 residues processed: 614 average time/residue: 0.2424 time to fit residues: 239.9984 Evaluate side-chains 446 residues out of total 4872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 440 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain G residue 16 VAL Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain S residue 16 VAL Chi-restraints excluded: chain T residue 16 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 394 optimal weight: 9.9990 chunk 430 optimal weight: 4.9990 chunk 41 optimal weight: 7.9990 chunk 265 optimal weight: 10.0000 chunk 523 optimal weight: 3.9990 chunk 497 optimal weight: 9.9990 chunk 414 optimal weight: 8.9990 chunk 310 optimal weight: 9.9990 chunk 488 optimal weight: 7.9990 chunk 366 optimal weight: 9.9990 chunk 223 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.111195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.080114 restraints weight = 62845.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.083290 restraints weight = 37304.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.084578 restraints weight = 24110.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.084931 restraints weight = 23478.054| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.084894 restraints weight = 20511.378| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.071 43392 Z= 0.393 Angle : 0.722 8.891 59304 Z= 0.383 Chirality : 0.055 0.146 7344 Planarity : 0.005 0.028 7656 Dihedral : 5.530 53.345 6006 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 2.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 2.13 % Allowed : 11.31 % Favored : 86.56 % 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: -0.61 (0.11), residues: 5712 helix: 1.07 (0.23), residues: 456 sheet: -0.36 (0.10), residues: 2568 loop : -0.57 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 65 TYR 0.020 0.003 TYR R 199 PHE 0.028 0.004 PHE I 158 TRP 0.009 0.002 TRP D 63 HIS 0.003 0.001 HIS U 48 Details of bonding type rmsd/Z covalent geometry : bond 0.01006 / 0.39 (43392) covalent geometry : angle 0.72215 / 0.38 (59304) hydrogen bonds : bond 0.04912 / 3.32 ( 1224) hydrogen bonds : angle 5.45718 / 3.67 ( 4320) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11424 Ramachandran restraints generated. 5712 Oldfield, 0 Emsley, 5712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11424 Ramachandran restraints generated. 5712 Oldfield, 0 Emsley, 5712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 4872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 500 time to evaluate : 1.593 Fit side-chains REVERT: A 35 ASP cc_start: 0.8155 (t0) cc_final: 0.7831 (t0) REVERT: A 60 LYS cc_start: 0.8784 (pttp) cc_final: 0.8549 (pttm) REVERT: B 193 LYS cc_start: 0.8950 (mtpt) cc_final: 0.8626 (ttmt) REVERT: C 206 GLN cc_start: 0.8144 (OUTLIER) cc_final: 0.7246 (tm-30) REVERT: D 35 ASP cc_start: 0.8428 (t0) cc_final: 0.7981 (t0) REVERT: D 161 ASP cc_start: 0.8751 (t0) cc_final: 0.8510 (t0) REVERT: E 35 ASP cc_start: 0.8174 (t0) cc_final: 0.7849 (t0) REVERT: E 60 LYS cc_start: 0.8709 (pttp) cc_final: 0.8459 (pttp) REVERT: E 77 ASP cc_start: 0.8415 (t0) cc_final: 0.8126 (t70) REVERT: F 60 LYS cc_start: 0.8970 (pttp) cc_final: 0.8583 (ptpt) REVERT: G 206 GLN cc_start: 0.8044 (OUTLIER) cc_final: 0.7174 (tm-30) REVERT: H 191 SER cc_start: 0.9168 (m) cc_final: 0.8917 (t) REVERT: H 193 LYS cc_start: 0.8889 (mmmm) cc_final: 0.8442 (tppt) REVERT: I 35 ASP cc_start: 0.8166 (t0) cc_final: 0.7875 (t0) REVERT: I 191 SER cc_start: 0.9156 (m) cc_final: 0.8947 (p) REVERT: J 60 LYS cc_start: 0.8998 (pttp) cc_final: 0.8667 (ptpt) REVERT: J 65 ARG cc_start: 0.7624 (mmm-85) cc_final: 0.7340 (mmm-85) REVERT: L 75 LYS cc_start: 0.8829 (tttt) cc_final: 0.8178 (ttpt) REVERT: L 115 ASP cc_start: 0.7875 (t0) cc_final: 0.7629 (t0) REVERT: L 191 SER cc_start: 0.9094 (m) cc_final: 0.8857 (t) REVERT: L 193 LYS cc_start: 0.8784 (mmmm) cc_final: 0.8433 (tppt) REVERT: M 35 ASP cc_start: 0.8155 (t0) cc_final: 0.7827 (t0) REVERT: M 60 LYS cc_start: 0.8790 (pttp) cc_final: 0.8555 (pttm) REVERT: O 206 GLN cc_start: 0.8142 (OUTLIER) cc_final: 0.7246 (tm-30) REVERT: P 35 ASP cc_start: 0.8434 (t0) cc_final: 0.7980 (t0) REVERT: P 161 ASP cc_start: 0.8751 (t0) cc_final: 0.8507 (t0) REVERT: Q 35 ASP cc_start: 0.8181 (t0) cc_final: 0.7853 (t0) REVERT: Q 60 LYS cc_start: 0.8703 (pttp) cc_final: 0.8455 (pttp) REVERT: Q 77 ASP cc_start: 0.8408 (t0) cc_final: 0.8121 (t70) REVERT: R 60 LYS cc_start: 0.8969 (pttp) cc_final: 0.8584 (ptpt) REVERT: S 206 GLN cc_start: 0.8053 (OUTLIER) cc_final: 0.7180 (tm-30) REVERT: T 191 SER cc_start: 0.9172 (m) cc_final: 0.8917 (t) REVERT: T 193 LYS cc_start: 0.8887 (mmmm) cc_final: 0.8438 (tppt) REVERT: U 35 ASP cc_start: 0.8168 (t0) cc_final: 0.7879 (t0) REVERT: U 191 SER cc_start: 0.9154 (m) cc_final: 0.8946 (p) REVERT: V 60 LYS cc_start: 0.9004 (pttp) cc_final: 0.8666 (ptpt) REVERT: V 65 ARG cc_start: 0.7627 (mmm-85) cc_final: 0.7339 (mmm-85) REVERT: X 75 LYS cc_start: 0.8816 (tttt) cc_final: 0.8160 (ttpt) REVERT: X 115 ASP cc_start: 0.7875 (t0) cc_final: 0.7632 (t0) REVERT: X 191 SER cc_start: 0.9092 (m) cc_final: 0.8853 (t) REVERT: X 193 LYS cc_start: 0.8781 (mmmm) cc_final: 0.8432 (tppt) outliers start: 100 outliers final: 44 residues processed: 582 average time/residue: 0.2364 time to fit residues: 229.8407 Evaluate side-chains 506 residues out of total 4872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 458 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 THR Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 206 GLN Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 133 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 206 GLN Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 133 THR Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain M residue 61 THR Chi-restraints excluded: chain N residue 44 CYS Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 206 GLN Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 114 ILE Chi-restraints excluded: chain P residue 133 THR Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 206 GLN Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 114 ILE Chi-restraints excluded: chain T residue 133 THR Chi-restraints excluded: chain V residue 44 CYS Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 114 ILE Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 114 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 124 optimal weight: 7.9990 chunk 296 optimal weight: 1.9990 chunk 571 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 405 optimal weight: 0.9980 chunk 278 optimal weight: 1.9990 chunk 192 optimal weight: 0.9990 chunk 262 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 471 optimal weight: 3.9990 chunk 431 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 130 GLN I 130 GLN M 130 GLN U 130 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.116625 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.084597 restraints weight = 60956.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.087768 restraints weight = 35084.373| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.089834 restraints weight = 24979.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.091169 restraints weight = 20176.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.091997 restraints weight = 17604.457| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.2302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 43392 Z= 0.095 Angle : 0.518 11.109 59304 Z= 0.258 Chirality : 0.046 0.125 7344 Planarity : 0.003 0.023 7656 Dihedral : 4.533 51.807 6004 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 1.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.11 % Allowed : 13.95 % Favored : 84.95 % 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: -0.17 (0.11), residues: 5712 helix: 1.89 (0.25), residues: 456 sheet: -0.02 (0.10), residues: 2448 loop : -0.44 (0.12), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 65 TYR 0.007 0.001 TYR V 199 PHE 0.015 0.001 PHE E 158 TRP 0.004 0.001 TRP H 63 HIS 0.002 0.001 HIS O 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00232 / 0.10 (43392) covalent geometry : angle 0.51798 / 0.26 (59304) hydrogen bonds : bond 0.02647 / 1.78 ( 1224) hydrogen bonds : angle 4.63114 / 3.11 ( 4320) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11424 Ramachandran restraints generated. 5712 Oldfield, 0 Emsley, 5712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11424 Ramachandran restraints generated. 5712 Oldfield, 0 Emsley, 5712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 518 residues out of total 4872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 466 time to evaluate : 1.724 Fit side-chains REVERT: A 35 ASP cc_start: 0.7990 (t0) cc_final: 0.7696 (t0) REVERT: A 139 VAL cc_start: 0.9256 (t) cc_final: 0.8907 (p) REVERT: B 193 LYS cc_start: 0.8827 (mtpt) cc_final: 0.8587 (ttmt) REVERT: D 16 VAL cc_start: 0.8770 (OUTLIER) cc_final: 0.8480 (p) REVERT: D 35 ASP cc_start: 0.8350 (t0) cc_final: 0.7654 (t0) REVERT: E 35 ASP cc_start: 0.8053 (t0) cc_final: 0.7726 (t0) REVERT: E 60 LYS cc_start: 0.8694 (pttp) cc_final: 0.8446 (pttp) REVERT: E 77 ASP cc_start: 0.8256 (t0) cc_final: 0.8018 (t0) REVERT: F 60 LYS cc_start: 0.8952 (pttp) cc_final: 0.8594 (ptpt) REVERT: G 193 LYS cc_start: 0.8997 (mtpt) cc_final: 0.8756 (mtpt) REVERT: H 16 VAL cc_start: 0.8701 (OUTLIER) cc_final: 0.8423 (p) REVERT: H 232 TYR cc_start: 0.8929 (m-80) cc_final: 0.8620 (m-80) REVERT: I 33 ILE cc_start: 0.9124 (OUTLIER) cc_final: 0.8893 (tp) REVERT: I 35 ASP cc_start: 0.8025 (t0) cc_final: 0.7770 (t0) REVERT: J 60 LYS cc_start: 0.8903 (pttp) cc_final: 0.8553 (ptpt) REVERT: J 65 ARG cc_start: 0.7564 (mmm-85) cc_final: 0.7286 (mmm-85) REVERT: L 75 LYS cc_start: 0.8776 (tttt) cc_final: 0.8150 (ttpt) REVERT: L 193 LYS cc_start: 0.8795 (mmmm) cc_final: 0.8442 (tppt) REVERT: M 35 ASP cc_start: 0.7995 (t0) cc_final: 0.7699 (t0) REVERT: M 139 VAL cc_start: 0.9260 (t) cc_final: 0.8917 (p) REVERT: P 16 VAL cc_start: 0.8769 (OUTLIER) cc_final: 0.8476 (p) REVERT: P 35 ASP cc_start: 0.8356 (t0) cc_final: 0.7651 (t0) REVERT: Q 35 ASP cc_start: 0.8053 (t0) cc_final: 0.7726 (t0) REVERT: Q 60 LYS cc_start: 0.8698 (pttp) cc_final: 0.8444 (pttp) REVERT: Q 77 ASP cc_start: 0.8256 (t0) cc_final: 0.8018 (t0) REVERT: R 60 LYS cc_start: 0.8947 (pttp) cc_final: 0.8591 (ptpt) REVERT: S 193 LYS cc_start: 0.8998 (mtpt) cc_final: 0.8755 (mtpt) REVERT: T 16 VAL cc_start: 0.8706 (OUTLIER) cc_final: 0.8428 (p) REVERT: T 232 TYR cc_start: 0.8929 (m-80) cc_final: 0.8625 (m-80) REVERT: U 33 ILE cc_start: 0.9127 (OUTLIER) cc_final: 0.8895 (tp) REVERT: U 35 ASP cc_start: 0.8029 (t0) cc_final: 0.7771 (t0) REVERT: V 60 LYS cc_start: 0.8908 (pttp) cc_final: 0.8555 (ptpt) REVERT: V 65 ARG cc_start: 0.7566 (mmm-85) cc_final: 0.7289 (mmm-85) REVERT: X 75 LYS cc_start: 0.8768 (tttt) cc_final: 0.8132 (ttpt) REVERT: X 193 LYS cc_start: 0.8787 (mmmm) cc_final: 0.8435 (tppt) outliers start: 52 outliers final: 30 residues processed: 504 average time/residue: 0.2724 time to fit residues: 225.9622 Evaluate side-chains 466 residues out of total 4872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 430 time to evaluate : 1.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain E residue 48 HIS Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 48 HIS Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 48 HIS Chi-restraints excluded: chain N residue 44 CYS Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 114 ILE Chi-restraints excluded: chain Q residue 48 HIS Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 114 ILE Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 48 HIS Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 114 ILE Chi-restraints excluded: chain V residue 44 CYS Chi-restraints excluded: chain W residue 114 ILE Chi-restraints excluded: chain X residue 114 ILE Chi-restraints excluded: chain X residue 180 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 50 optimal weight: 20.0000 chunk 82 optimal weight: 9.9990 chunk 203 optimal weight: 0.8980 chunk 542 optimal weight: 0.9990 chunk 467 optimal weight: 0.9990 chunk 449 optimal weight: 3.9990 chunk 331 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 436 optimal weight: 9.9990 chunk 78 optimal weight: 3.9990 chunk 514 optimal weight: 9.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.115158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.083098 restraints weight = 61274.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.086198 restraints weight = 35429.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.088236 restraints weight = 25374.092| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.089481 restraints weight = 20560.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.090370 restraints weight = 18045.436| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2417 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 43392 Z= 0.145 Angle : 0.531 10.503 59304 Z= 0.268 Chirality : 0.046 0.131 7344 Planarity : 0.003 0.024 7656 Dihedral : 4.467 32.503 6004 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.04 % Allowed : 14.18 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.22 (0.11), residues: 5712 helix: 1.83 (0.25), residues: 456 sheet: -0.03 (0.10), residues: 2448 loop : -0.49 (0.12), residues: 2808 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 65 TYR 0.011 0.001 TYR J 199 PHE 0.015 0.002 PHE I 158 TRP 0.004 0.001 TRP T 63 HIS 0.001 0.000 HIS E 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00373 / 0.15 (43392) covalent geometry : angle 0.53107 / 0.27 (59304) hydrogen bonds : bond 0.02951 / 1.99 ( 1224) hydrogen bonds : angle 4.50453 / 3.03 ( 4320) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11424 Ramachandran restraints generated. 5712 Oldfield, 0 Emsley, 5712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11424 Ramachandran restraints generated. 5712 Oldfield, 0 Emsley, 5712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 540 residues out of total 4872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 444 time to evaluate : 1.590 Fit side-chains REVERT: A 35 ASP cc_start: 0.8005 (t0) cc_final: 0.7697 (t0) REVERT: A 139 VAL cc_start: 0.9265 (t) cc_final: 0.9021 (m) REVERT: B 193 LYS cc_start: 0.8846 (mtpt) cc_final: 0.8576 (ttmt) REVERT: D 16 VAL cc_start: 0.8713 (OUTLIER) cc_final: 0.8470 (p) REVERT: D 35 ASP cc_start: 0.8350 (t0) cc_final: 0.7650 (t0) REVERT: E 35 ASP cc_start: 0.8102 (t0) cc_final: 0.7778 (t0) REVERT: E 57 MET cc_start: 0.8764 (ttp) cc_final: 0.8519 (ttm) REVERT: E 60 LYS cc_start: 0.8695 (pttp) cc_final: 0.8431 (pttp) REVERT: E 77 ASP cc_start: 0.8200 (t0) cc_final: 0.7932 (t0) REVERT: F 60 LYS cc_start: 0.8926 (pttp) cc_final: 0.8583 (ptpt) REVERT: H 16 VAL cc_start: 0.8778 (OUTLIER) cc_final: 0.8528 (p) REVERT: H 193 LYS cc_start: 0.8691 (mmmm) cc_final: 0.8292 (tppp) REVERT: H 232 TYR cc_start: 0.8937 (m-80) cc_final: 0.8655 (m-80) REVERT: I 35 ASP cc_start: 0.8073 (t0) cc_final: 0.7802 (t0) REVERT: J 60 LYS cc_start: 0.8901 (pttp) cc_final: 0.8544 (ptpt) REVERT: L 75 LYS cc_start: 0.8777 (tttt) cc_final: 0.8088 (ttpt) REVERT: M 35 ASP cc_start: 0.8008 (t0) cc_final: 0.7697 (t0) REVERT: M 139 VAL cc_start: 0.9269 (t) cc_final: 0.9029 (m) REVERT: P 16 VAL cc_start: 0.8716 (OUTLIER) cc_final: 0.8472 (p) REVERT: P 35 ASP cc_start: 0.8357 (t0) cc_final: 0.7645 (t0) REVERT: Q 35 ASP cc_start: 0.8102 (t0) cc_final: 0.7775 (t0) REVERT: Q 57 MET cc_start: 0.8765 (ttp) cc_final: 0.8520 (ttm) REVERT: Q 60 LYS cc_start: 0.8700 (pttp) cc_final: 0.8435 (pttp) REVERT: Q 77 ASP cc_start: 0.8198 (t0) cc_final: 0.7933 (t0) REVERT: R 60 LYS cc_start: 0.8926 (pttp) cc_final: 0.8581 (ptpt) REVERT: T 16 VAL cc_start: 0.8776 (OUTLIER) cc_final: 0.8525 (p) REVERT: T 193 LYS cc_start: 0.8690 (mmmm) cc_final: 0.8290 (tppp) REVERT: T 232 TYR cc_start: 0.8937 (m-80) cc_final: 0.8656 (m-80) REVERT: U 35 ASP cc_start: 0.8079 (t0) cc_final: 0.7807 (t0) REVERT: V 60 LYS cc_start: 0.8904 (pttp) cc_final: 0.8546 (ptpt) REVERT: X 75 LYS cc_start: 0.8769 (tttt) cc_final: 0.8070 (ttpt) outliers start: 96 outliers final: 60 residues processed: 514 average time/residue: 0.2436 time to fit residues: 208.2440 Evaluate side-chains 488 residues out of total 4872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 424 time to evaluate : 1.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain D residue 16 VAL Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain H residue 16 VAL Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain I residue 48 HIS Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain N residue 44 CYS Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain P residue 16 VAL Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 114 ILE Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 114 ILE Chi-restraints excluded: chain R residue 44 CYS Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 180 THR Chi-restraints excluded: chain T residue 16 VAL Chi-restraints excluded: chain T residue 114 ILE Chi-restraints excluded: chain T residue 180 THR Chi-restraints excluded: chain U residue 48 HIS Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 114 ILE Chi-restraints excluded: chain V residue 34 SER Chi-restraints excluded: chain V residue 44 CYS Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 114 ILE Chi-restraints excluded: chain W residue 180 THR Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 114 ILE Chi-restraints excluded: chain X residue 180 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 70 optimal weight: 8.9990 chunk 12 optimal weight: 8.9990 chunk 500 optimal weight: 6.9990 chunk 179 optimal weight: 0.5980 chunk 76 optimal weight: 0.0030 chunk 453 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 chunk 405 optimal weight: 4.9990 chunk 63 optimal weight: 1.9990 chunk 426 optimal weight: 4.9990 chunk 234 optimal weight: 4.9990 overall best weight: 2.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.114973 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.083096 restraints weight = 61005.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.086173 restraints weight = 35456.875| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.088206 restraints weight = 25420.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.089513 restraints weight = 20572.241| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.090357 restraints weight = 18012.967| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 43392 Z= 0.152 Angle : 0.535 11.600 59304 Z= 0.268 Chirality : 0.046 0.130 7344 Planarity : 0.003 0.026 7656 Dihedral : 4.458 18.524 6004 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 2.42 % Allowed : 14.73 % Favored : 82.84 % 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: -0.26 (0.11), residues: 5712 helix: 1.84 (0.25), residues: 456 sheet: -0.16 (0.10), residues: 2568 loop : -0.43 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 65 TYR 0.014 0.001 TYR U 232 PHE 0.016 0.002 PHE L 158 TRP 0.004 0.001 TRP T 63 HIS 0.002 0.000 HIS E 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.15 (43392) covalent geometry : angle 0.53458 / 0.27 (59304) hydrogen bonds : bond 0.02924 / 1.97 ( 1224) hydrogen bonds : angle 4.40734 / 2.97 ( 4320) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11424 Ramachandran restraints generated. 5712 Oldfield, 0 Emsley, 5712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11424 Ramachandran restraints generated. 5712 Oldfield, 0 Emsley, 5712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 568 residues out of total 4872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 454 time to evaluate : 1.637 Fit side-chains REVERT: A 35 ASP cc_start: 0.8025 (t0) cc_final: 0.7719 (t0) REVERT: A 139 VAL cc_start: 0.9269 (OUTLIER) cc_final: 0.8984 (p) REVERT: B 193 LYS cc_start: 0.8872 (mtpt) cc_final: 0.8598 (ttmt) REVERT: D 35 ASP cc_start: 0.8355 (t0) cc_final: 0.7658 (t0) REVERT: E 35 ASP cc_start: 0.8116 (t0) cc_final: 0.7789 (t0) REVERT: E 57 MET cc_start: 0.8777 (ttp) cc_final: 0.8560 (ttm) REVERT: E 60 LYS cc_start: 0.8710 (pttp) cc_final: 0.8458 (pttp) REVERT: E 77 ASP cc_start: 0.8184 (t0) cc_final: 0.7929 (t0) REVERT: F 60 LYS cc_start: 0.8878 (pttp) cc_final: 0.8505 (ptpt) REVERT: H 193 LYS cc_start: 0.8705 (mmmm) cc_final: 0.8300 (tppp) REVERT: I 35 ASP cc_start: 0.8084 (t0) cc_final: 0.7792 (t0) REVERT: J 60 LYS cc_start: 0.8917 (pttp) cc_final: 0.8570 (ptpt) REVERT: L 75 LYS cc_start: 0.8757 (tttt) cc_final: 0.8083 (ttpt) REVERT: L 193 LYS cc_start: 0.8709 (mmmm) cc_final: 0.8324 (tppp) REVERT: M 35 ASP cc_start: 0.8027 (t0) cc_final: 0.7719 (t0) REVERT: M 139 VAL cc_start: 0.9271 (OUTLIER) cc_final: 0.8985 (p) REVERT: P 35 ASP cc_start: 0.8355 (t0) cc_final: 0.7653 (t0) REVERT: Q 35 ASP cc_start: 0.8123 (t0) cc_final: 0.7790 (t0) REVERT: Q 57 MET cc_start: 0.8778 (ttp) cc_final: 0.8560 (ttm) REVERT: Q 60 LYS cc_start: 0.8720 (pttp) cc_final: 0.8462 (pttp) REVERT: Q 77 ASP cc_start: 0.8186 (t0) cc_final: 0.7930 (t0) REVERT: R 60 LYS cc_start: 0.8873 (pttp) cc_final: 0.8501 (ptpt) REVERT: T 193 LYS cc_start: 0.8706 (mmmm) cc_final: 0.8299 (tppp) REVERT: U 35 ASP cc_start: 0.8100 (t0) cc_final: 0.7806 (t0) REVERT: V 60 LYS cc_start: 0.8921 (pttp) cc_final: 0.8571 (ptpt) REVERT: X 75 LYS cc_start: 0.8750 (tttt) cc_final: 0.8065 (ttpt) REVERT: X 193 LYS cc_start: 0.8700 (mmmm) cc_final: 0.8314 (tppp) outliers start: 114 outliers final: 76 residues processed: 536 average time/residue: 0.2458 time to fit residues: 219.3718 Evaluate side-chains 502 residues out of total 4872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 424 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain D residue 61 THR Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 238 GLU Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain N residue 44 CYS Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain P residue 61 THR Chi-restraints excluded: chain P residue 114 ILE Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 114 ILE Chi-restraints excluded: chain Q residue 180 THR Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain R residue 44 CYS Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 180 THR Chi-restraints excluded: chain T residue 114 ILE Chi-restraints excluded: chain T residue 180 THR Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 114 ILE Chi-restraints excluded: chain U residue 238 GLU Chi-restraints excluded: chain V residue 34 SER Chi-restraints excluded: chain V residue 44 CYS Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 114 ILE Chi-restraints excluded: chain W residue 180 THR Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 114 ILE Chi-restraints excluded: chain X residue 180 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 172 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 565 optimal weight: 1.9990 chunk 445 optimal weight: 0.1980 chunk 2 optimal weight: 20.0000 chunk 464 optimal weight: 10.0000 chunk 520 optimal weight: 0.8980 chunk 485 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 98 optimal weight: 20.0000 chunk 513 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.117903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.085343 restraints weight = 60767.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.088638 restraints weight = 34834.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.090799 restraints weight = 24665.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.092194 restraints weight = 19850.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.093033 restraints weight = 17278.907| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 43392 Z= 0.088 Angle : 0.498 11.851 59304 Z= 0.245 Chirality : 0.045 0.122 7344 Planarity : 0.003 0.025 7656 Dihedral : 4.086 17.674 6000 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.04 % Allowed : 15.62 % Favored : 82.33 % 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: -0.16 (0.11), residues: 5712 helix: 2.00 (0.26), residues: 456 sheet: -0.05 (0.10), residues: 2520 loop : -0.42 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 65 TYR 0.007 0.001 TYR I 199 PHE 0.012 0.001 PHE X 158 TRP 0.003 0.000 TRP H 63 HIS 0.001 0.000 HIS E 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.09 (43392) covalent geometry : angle 0.49819 / 0.25 (59304) hydrogen bonds : bond 0.02268 / 1.53 ( 1224) hydrogen bonds : angle 4.13387 / 2.79 ( 4320) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11424 Ramachandran restraints generated. 5712 Oldfield, 0 Emsley, 5712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11424 Ramachandran restraints generated. 5712 Oldfield, 0 Emsley, 5712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 4872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 468 time to evaluate : 1.662 Fit side-chains REVERT: A 35 ASP cc_start: 0.7996 (t0) cc_final: 0.7674 (t0) REVERT: A 139 VAL cc_start: 0.9184 (t) cc_final: 0.8900 (p) REVERT: B 193 LYS cc_start: 0.8790 (mtpt) cc_final: 0.8574 (ttmt) REVERT: D 35 ASP cc_start: 0.8295 (t0) cc_final: 0.7914 (t0) REVERT: D 106 GLU cc_start: 0.7633 (tt0) cc_final: 0.7124 (tp30) REVERT: E 35 ASP cc_start: 0.8042 (t0) cc_final: 0.7717 (t0) REVERT: E 60 LYS cc_start: 0.8671 (pttp) cc_final: 0.8448 (pttp) REVERT: E 77 ASP cc_start: 0.8169 (t0) cc_final: 0.7905 (t0) REVERT: F 60 LYS cc_start: 0.8808 (pttp) cc_final: 0.8553 (ptpt) REVERT: G 79 ASN cc_start: 0.8777 (OUTLIER) cc_final: 0.8403 (t0) REVERT: H 193 LYS cc_start: 0.8655 (mmmm) cc_final: 0.8176 (tppp) REVERT: I 35 ASP cc_start: 0.8056 (t0) cc_final: 0.7737 (t0) REVERT: I 87 ASP cc_start: 0.8248 (t0) cc_final: 0.7866 (m-30) REVERT: J 60 LYS cc_start: 0.8873 (pttp) cc_final: 0.8574 (ptpt) REVERT: L 75 LYS cc_start: 0.8694 (tttt) cc_final: 0.7961 (ttpp) REVERT: L 193 LYS cc_start: 0.8670 (mmmm) cc_final: 0.8453 (tppp) REVERT: M 35 ASP cc_start: 0.7994 (t0) cc_final: 0.7675 (t0) REVERT: M 139 VAL cc_start: 0.9184 (t) cc_final: 0.8895 (p) REVERT: P 35 ASP cc_start: 0.8293 (t0) cc_final: 0.7915 (t0) REVERT: P 106 GLU cc_start: 0.7633 (tt0) cc_final: 0.7127 (tp30) REVERT: Q 35 ASP cc_start: 0.8041 (t0) cc_final: 0.7714 (t0) REVERT: Q 60 LYS cc_start: 0.8683 (pttp) cc_final: 0.8449 (pttp) REVERT: Q 77 ASP cc_start: 0.8174 (t0) cc_final: 0.7910 (t0) REVERT: R 60 LYS cc_start: 0.8807 (pttp) cc_final: 0.8553 (ptpt) REVERT: S 79 ASN cc_start: 0.8779 (OUTLIER) cc_final: 0.8403 (t0) REVERT: T 193 LYS cc_start: 0.8658 (mmmm) cc_final: 0.8180 (tppp) REVERT: U 35 ASP cc_start: 0.8059 (t0) cc_final: 0.7740 (t0) REVERT: U 87 ASP cc_start: 0.8253 (t0) cc_final: 0.7867 (m-30) REVERT: V 60 LYS cc_start: 0.8876 (pttp) cc_final: 0.8575 (ptpt) REVERT: X 75 LYS cc_start: 0.8684 (tttt) cc_final: 0.7946 (ttpp) REVERT: X 193 LYS cc_start: 0.8663 (mmmm) cc_final: 0.8455 (tppp) outliers start: 96 outliers final: 64 residues processed: 540 average time/residue: 0.2439 time to fit residues: 217.1991 Evaluate side-chains 502 residues out of total 4872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 436 time to evaluate : 1.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ILE Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain E residue 114 ILE Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 180 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 79 ASN Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain I residue 48 HIS Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain I residue 114 ILE Chi-restraints excluded: chain I residue 238 GLU Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain M residue 114 ILE Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain N residue 44 CYS Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain P residue 114 ILE Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain Q residue 114 ILE Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 180 THR Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain R residue 44 CYS Chi-restraints excluded: chain R residue 180 THR Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain S residue 79 ASN Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 180 THR Chi-restraints excluded: chain T residue 114 ILE Chi-restraints excluded: chain T residue 180 THR Chi-restraints excluded: chain U residue 48 HIS Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 114 ILE Chi-restraints excluded: chain U residue 238 GLU Chi-restraints excluded: chain V residue 44 CYS Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 114 ILE Chi-restraints excluded: chain W residue 180 THR Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 114 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 282 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 437 optimal weight: 6.9990 chunk 19 optimal weight: 5.9990 chunk 178 optimal weight: 9.9990 chunk 238 optimal weight: 3.9990 chunk 109 optimal weight: 0.9980 chunk 222 optimal weight: 4.9990 chunk 435 optimal weight: 0.9990 chunk 547 optimal weight: 3.9990 chunk 492 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.114799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.082527 restraints weight = 61011.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.085595 restraints weight = 35651.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.087637 restraints weight = 25661.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.088933 restraints weight = 20832.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.089748 restraints weight = 18255.209| |-----------------------------------------------------------------------------| r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 43392 Z= 0.178 Angle : 0.547 11.432 59304 Z= 0.275 Chirality : 0.047 0.136 7344 Planarity : 0.003 0.026 7656 Dihedral : 4.440 19.074 6000 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 2.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 2.17 % Allowed : 16.28 % Favored : 81.55 % 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: -0.29 (0.11), residues: 5712 helix: 1.83 (0.25), residues: 456 sheet: -0.13 (0.10), residues: 2568 loop : -0.49 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 65 TYR 0.012 0.002 TYR B 232 PHE 0.016 0.002 PHE I 158 TRP 0.004 0.001 TRP H 63 HIS 0.002 0.001 HIS E 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00458 / 0.18 (43392) covalent geometry : angle 0.54748 / 0.27 (59304) hydrogen bonds : bond 0.03028 / 2.04 ( 1224) hydrogen bonds : angle 4.33634 / 2.93 ( 4320) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11424 Ramachandran restraints generated. 5712 Oldfield, 0 Emsley, 5712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11424 Ramachandran restraints generated. 5712 Oldfield, 0 Emsley, 5712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 536 residues out of total 4872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 434 time to evaluate : 1.662 Fit side-chains REVERT: A 35 ASP cc_start: 0.8040 (t0) cc_final: 0.7705 (t0) REVERT: A 139 VAL cc_start: 0.9253 (OUTLIER) cc_final: 0.8989 (p) REVERT: B 193 LYS cc_start: 0.8846 (mtpt) cc_final: 0.8585 (ttmt) REVERT: D 35 ASP cc_start: 0.8186 (t0) cc_final: 0.7833 (t0) REVERT: E 35 ASP cc_start: 0.8137 (t0) cc_final: 0.7808 (t0) REVERT: E 60 LYS cc_start: 0.8703 (pttp) cc_final: 0.8478 (pttp) REVERT: E 77 ASP cc_start: 0.8176 (t0) cc_final: 0.7912 (t0) REVERT: F 60 LYS cc_start: 0.8805 (pttp) cc_final: 0.8463 (ptpt) REVERT: G 79 ASN cc_start: 0.8730 (OUTLIER) cc_final: 0.8506 (t0) REVERT: H 191 SER cc_start: 0.9180 (m) cc_final: 0.8937 (t) REVERT: I 35 ASP cc_start: 0.8125 (t0) cc_final: 0.7819 (t0) REVERT: I 87 ASP cc_start: 0.8219 (t0) cc_final: 0.7776 (p0) REVERT: J 60 LYS cc_start: 0.8863 (pttp) cc_final: 0.8552 (ptpt) REVERT: L 75 LYS cc_start: 0.8745 (tttt) cc_final: 0.8004 (ttpp) REVERT: L 193 LYS cc_start: 0.8679 (mmmm) cc_final: 0.8361 (ttmm) REVERT: M 35 ASP cc_start: 0.8041 (t0) cc_final: 0.7703 (t0) REVERT: M 139 VAL cc_start: 0.9253 (OUTLIER) cc_final: 0.8986 (p) REVERT: P 35 ASP cc_start: 0.8185 (t0) cc_final: 0.7827 (t0) REVERT: Q 35 ASP cc_start: 0.8137 (t0) cc_final: 0.7805 (t0) REVERT: Q 60 LYS cc_start: 0.8717 (pttp) cc_final: 0.8481 (pttp) REVERT: Q 77 ASP cc_start: 0.8178 (t0) cc_final: 0.7914 (t0) REVERT: R 60 LYS cc_start: 0.8804 (pttp) cc_final: 0.8463 (ptpt) REVERT: S 79 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8507 (t0) REVERT: T 191 SER cc_start: 0.9180 (m) cc_final: 0.8938 (t) REVERT: U 35 ASP cc_start: 0.8128 (t0) cc_final: 0.7822 (t0) REVERT: U 87 ASP cc_start: 0.8222 (t0) cc_final: 0.7777 (p0) REVERT: V 60 LYS cc_start: 0.8868 (pttp) cc_final: 0.8556 (ptpt) REVERT: X 75 LYS cc_start: 0.8737 (tttt) cc_final: 0.7988 (ttpp) REVERT: X 193 LYS cc_start: 0.8675 (mmmm) cc_final: 0.8362 (ttmm) outliers start: 102 outliers final: 76 residues processed: 510 average time/residue: 0.2496 time to fit residues: 211.4659 Evaluate side-chains 500 residues out of total 4872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 420 time to evaluate : 1.808 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 79 ASN Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain I residue 33 ILE Chi-restraints excluded: chain I residue 48 HIS Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 238 GLU Chi-restraints excluded: chain J residue 34 SER Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 79 ASN Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain M residue 139 VAL Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain N residue 44 CYS Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain P residue 114 ILE Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 180 THR Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain R residue 44 CYS Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 79 ASN Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 180 THR Chi-restraints excluded: chain T residue 114 ILE Chi-restraints excluded: chain T residue 180 THR Chi-restraints excluded: chain U residue 33 ILE Chi-restraints excluded: chain U residue 48 HIS Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 180 THR Chi-restraints excluded: chain U residue 238 GLU Chi-restraints excluded: chain V residue 34 SER Chi-restraints excluded: chain V residue 44 CYS Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 79 ASN Chi-restraints excluded: chain W residue 114 ILE Chi-restraints excluded: chain W residue 180 THR Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 114 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 79 optimal weight: 3.9990 chunk 390 optimal weight: 0.8980 chunk 33 optimal weight: 0.0970 chunk 556 optimal weight: 3.9990 chunk 232 optimal weight: 0.8980 chunk 167 optimal weight: 0.9990 chunk 334 optimal weight: 6.9990 chunk 476 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 134 optimal weight: 9.9990 chunk 74 optimal weight: 20.0000 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.118656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3004 r_free = 0.3004 target = 0.086017 restraints weight = 60608.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.089265 restraints weight = 34711.042| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.091453 restraints weight = 24666.537| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.092882 restraints weight = 19843.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.093728 restraints weight = 17252.670| |-----------------------------------------------------------------------------| r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8646 moved from start: 0.2764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 43392 Z= 0.084 Angle : 0.503 12.105 59304 Z= 0.244 Chirality : 0.044 0.123 7344 Planarity : 0.003 0.029 7656 Dihedral : 4.030 17.628 6000 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.53 % Allowed : 17.37 % Favored : 81.10 % 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: -0.15 (0.11), residues: 5712 helix: 2.03 (0.26), residues: 456 sheet: -0.03 (0.10), residues: 2520 loop : -0.43 (0.12), residues: 2736 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 65 TYR 0.013 0.001 TYR B 232 PHE 0.011 0.001 PHE E 158 TRP 0.002 0.000 TRP T 63 HIS 0.001 0.000 HIS N 160 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.08 (43392) covalent geometry : angle 0.50298 / 0.24 (59304) hydrogen bonds : bond 0.02149 / 1.45 ( 1224) hydrogen bonds : angle 4.02580 / 2.72 ( 4320) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11424 Ramachandran restraints generated. 5712 Oldfield, 0 Emsley, 5712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11424 Ramachandran restraints generated. 5712 Oldfield, 0 Emsley, 5712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 4872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 467 time to evaluate : 1.712 Fit side-chains REVERT: A 35 ASP cc_start: 0.7974 (t0) cc_final: 0.7654 (t0) REVERT: A 139 VAL cc_start: 0.9163 (t) cc_final: 0.8889 (p) REVERT: B 193 LYS cc_start: 0.8779 (mtpt) cc_final: 0.8561 (ttmt) REVERT: D 35 ASP cc_start: 0.8073 (t0) cc_final: 0.7687 (t0) REVERT: D 106 GLU cc_start: 0.7573 (tt0) cc_final: 0.7130 (tp30) REVERT: E 35 ASP cc_start: 0.7999 (t0) cc_final: 0.7693 (t0) REVERT: E 60 LYS cc_start: 0.8656 (pttp) cc_final: 0.8431 (pttp) REVERT: E 77 ASP cc_start: 0.8149 (t0) cc_final: 0.7892 (t0) REVERT: F 60 LYS cc_start: 0.8755 (pttp) cc_final: 0.8487 (ptpt) REVERT: G 193 LYS cc_start: 0.8934 (mtpt) cc_final: 0.8727 (mtpt) REVERT: H 106 GLU cc_start: 0.7747 (tt0) cc_final: 0.7334 (tp30) REVERT: H 193 LYS cc_start: 0.8532 (mmmm) cc_final: 0.8101 (tppp) REVERT: I 35 ASP cc_start: 0.8029 (t0) cc_final: 0.7728 (t0) REVERT: J 60 LYS cc_start: 0.8833 (pttp) cc_final: 0.8514 (ptpt) REVERT: L 75 LYS cc_start: 0.8725 (tttt) cc_final: 0.7967 (ttpp) REVERT: L 193 LYS cc_start: 0.8679 (mmmm) cc_final: 0.8369 (ttmm) REVERT: M 35 ASP cc_start: 0.7981 (t0) cc_final: 0.7657 (t0) REVERT: M 139 VAL cc_start: 0.9162 (t) cc_final: 0.8885 (p) REVERT: P 35 ASP cc_start: 0.8074 (t0) cc_final: 0.7682 (t0) REVERT: P 106 GLU cc_start: 0.7577 (tt0) cc_final: 0.7135 (tp30) REVERT: Q 35 ASP cc_start: 0.7999 (t0) cc_final: 0.7688 (t0) REVERT: Q 60 LYS cc_start: 0.8665 (pttp) cc_final: 0.8434 (pttp) REVERT: Q 77 ASP cc_start: 0.8158 (t0) cc_final: 0.7901 (t0) REVERT: R 60 LYS cc_start: 0.8749 (pttp) cc_final: 0.8486 (ptpt) REVERT: S 193 LYS cc_start: 0.8936 (mtpt) cc_final: 0.8727 (mtpt) REVERT: T 106 GLU cc_start: 0.7743 (tt0) cc_final: 0.7334 (tp30) REVERT: T 193 LYS cc_start: 0.8534 (mmmm) cc_final: 0.8100 (tppp) REVERT: U 35 ASP cc_start: 0.8034 (t0) cc_final: 0.7733 (t0) REVERT: V 60 LYS cc_start: 0.8838 (pttp) cc_final: 0.8515 (ptpt) REVERT: X 75 LYS cc_start: 0.8719 (tttt) cc_final: 0.7956 (ttpp) REVERT: X 193 LYS cc_start: 0.8671 (mmmm) cc_final: 0.8365 (ttmm) outliers start: 72 outliers final: 58 residues processed: 523 average time/residue: 0.2772 time to fit residues: 238.2393 Evaluate side-chains 491 residues out of total 4872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 433 time to evaluate : 1.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain I residue 48 HIS Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 238 GLU Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain N residue 44 CYS Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain P residue 114 ILE Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 180 THR Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain R residue 44 CYS Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 180 THR Chi-restraints excluded: chain T residue 114 ILE Chi-restraints excluded: chain T residue 180 THR Chi-restraints excluded: chain U residue 48 HIS Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 180 THR Chi-restraints excluded: chain U residue 238 GLU Chi-restraints excluded: chain V residue 44 CYS Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain W residue 114 ILE Chi-restraints excluded: chain W residue 180 THR Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 114 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 113 optimal weight: 2.9990 chunk 343 optimal weight: 0.9980 chunk 530 optimal weight: 8.9990 chunk 222 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 354 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 525 optimal weight: 5.9990 chunk 387 optimal weight: 0.0070 chunk 497 optimal weight: 7.9990 chunk 442 optimal weight: 9.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.116568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.084219 restraints weight = 60553.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.087372 restraints weight = 35094.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.089455 restraints weight = 25123.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.090811 restraints weight = 20276.429| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.091658 restraints weight = 17718.642| |-----------------------------------------------------------------------------| r_work (final): 0.3121 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 43392 Z= 0.129 Angle : 0.526 11.441 59304 Z= 0.263 Chirality : 0.046 0.133 7344 Planarity : 0.003 0.029 7656 Dihedral : 4.188 18.311 6000 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.74 % Allowed : 17.41 % Favored : 80.85 % 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: -0.16 (0.11), residues: 5712 helix: 1.90 (0.25), residues: 456 sheet: -0.02 (0.10), residues: 2568 loop : -0.44 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 65 TYR 0.016 0.001 TYR E 232 PHE 0.013 0.001 PHE I 158 TRP 0.003 0.001 TRP T 63 HIS 0.001 0.000 HIS M 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.13 (43392) covalent geometry : angle 0.52586 / 0.26 (59304) hydrogen bonds : bond 0.02619 / 1.77 ( 1224) hydrogen bonds : angle 4.13466 / 2.79 ( 4320) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11424 Ramachandran restraints generated. 5712 Oldfield, 0 Emsley, 5712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11424 Ramachandran restraints generated. 5712 Oldfield, 0 Emsley, 5712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 4872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 430 time to evaluate : 1.809 Fit side-chains REVERT: A 35 ASP cc_start: 0.8002 (t0) cc_final: 0.7655 (t0) REVERT: A 87 ASP cc_start: 0.8181 (t0) cc_final: 0.7954 (m-30) REVERT: A 139 VAL cc_start: 0.9198 (t) cc_final: 0.8983 (p) REVERT: B 65 ARG cc_start: 0.7696 (mmm-85) cc_final: 0.7432 (mmm-85) REVERT: B 193 LYS cc_start: 0.8808 (mtpt) cc_final: 0.8563 (ttmt) REVERT: D 35 ASP cc_start: 0.8079 (t0) cc_final: 0.7704 (t0) REVERT: D 106 GLU cc_start: 0.7603 (tt0) cc_final: 0.7139 (tp30) REVERT: E 35 ASP cc_start: 0.8066 (t0) cc_final: 0.7744 (t0) REVERT: E 60 LYS cc_start: 0.8687 (pttp) cc_final: 0.8476 (pttp) REVERT: E 77 ASP cc_start: 0.8163 (t0) cc_final: 0.7900 (t0) REVERT: F 60 LYS cc_start: 0.8766 (pttp) cc_final: 0.8490 (ptpt) REVERT: H 193 LYS cc_start: 0.8563 (mmmm) cc_final: 0.8153 (tppp) REVERT: I 35 ASP cc_start: 0.7975 (t0) cc_final: 0.7685 (t0) REVERT: I 232 TYR cc_start: 0.8885 (m-80) cc_final: 0.8584 (m-80) REVERT: J 60 LYS cc_start: 0.8827 (pttp) cc_final: 0.8512 (ptpt) REVERT: L 75 LYS cc_start: 0.8749 (tttt) cc_final: 0.7975 (ttpp) REVERT: L 193 LYS cc_start: 0.8689 (mmmm) cc_final: 0.8395 (ttmm) REVERT: M 35 ASP cc_start: 0.8008 (t0) cc_final: 0.7655 (t0) REVERT: M 87 ASP cc_start: 0.8183 (t0) cc_final: 0.7947 (m-30) REVERT: M 139 VAL cc_start: 0.9199 (t) cc_final: 0.8981 (p) REVERT: N 65 ARG cc_start: 0.7691 (mmm-85) cc_final: 0.7428 (mmm-85) REVERT: P 35 ASP cc_start: 0.8080 (t0) cc_final: 0.7698 (t0) REVERT: P 106 GLU cc_start: 0.7611 (tt0) cc_final: 0.7143 (tp30) REVERT: Q 35 ASP cc_start: 0.8068 (t0) cc_final: 0.7740 (t0) REVERT: Q 60 LYS cc_start: 0.8697 (pttp) cc_final: 0.8477 (pttp) REVERT: Q 77 ASP cc_start: 0.8171 (t0) cc_final: 0.7909 (t0) REVERT: R 60 LYS cc_start: 0.8766 (pttp) cc_final: 0.8491 (ptpt) REVERT: T 193 LYS cc_start: 0.8564 (mmmm) cc_final: 0.8152 (tppp) REVERT: U 35 ASP cc_start: 0.7977 (t0) cc_final: 0.7687 (t0) REVERT: U 232 TYR cc_start: 0.8884 (m-80) cc_final: 0.8583 (m-80) REVERT: V 60 LYS cc_start: 0.8831 (pttp) cc_final: 0.8513 (ptpt) REVERT: X 75 LYS cc_start: 0.8745 (tttt) cc_final: 0.7962 (ttpp) REVERT: X 193 LYS cc_start: 0.8683 (mmmm) cc_final: 0.8392 (ttmm) outliers start: 82 outliers final: 68 residues processed: 492 average time/residue: 0.2670 time to fit residues: 217.5891 Evaluate side-chains 492 residues out of total 4872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 424 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain I residue 48 HIS Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 238 GLU Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain N residue 44 CYS Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain P residue 114 ILE Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 180 THR Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain R residue 44 CYS Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 180 THR Chi-restraints excluded: chain T residue 114 ILE Chi-restraints excluded: chain T residue 180 THR Chi-restraints excluded: chain U residue 48 HIS Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 180 THR Chi-restraints excluded: chain U residue 238 GLU Chi-restraints excluded: chain V residue 44 CYS Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 114 ILE Chi-restraints excluded: chain W residue 180 THR Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 114 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 165 optimal weight: 3.9990 chunk 488 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 297 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 chunk 358 optimal weight: 3.9990 chunk 409 optimal weight: 6.9990 chunk 340 optimal weight: 8.9990 chunk 262 optimal weight: 0.5980 chunk 193 optimal weight: 9.9990 chunk 327 optimal weight: 4.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.115368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.083003 restraints weight = 61282.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.086128 restraints weight = 35624.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.088167 restraints weight = 25535.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.089470 restraints weight = 20715.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.090279 restraints weight = 18170.573| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 43392 Z= 0.165 Angle : 0.555 12.319 59304 Z= 0.277 Chirality : 0.047 0.136 7344 Planarity : 0.003 0.029 7656 Dihedral : 4.427 19.154 6000 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.70 % Allowed : 17.71 % Favored : 80.59 % 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: -0.32 (0.11), residues: 5712 helix: 1.76 (0.25), residues: 456 sheet: -0.14 (0.10), residues: 2568 loop : -0.52 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 65 TYR 0.014 0.002 TYR A 199 PHE 0.015 0.002 PHE Q 158 TRP 0.004 0.001 TRP P 63 HIS 0.002 0.000 HIS M 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00425 / 0.17 (43392) covalent geometry : angle 0.55513 / 0.28 (59304) hydrogen bonds : bond 0.02904 / 1.96 ( 1224) hydrogen bonds : angle 4.24869 / 2.87 ( 4320) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11424 Ramachandran restraints generated. 5712 Oldfield, 0 Emsley, 5712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11424 Ramachandran restraints generated. 5712 Oldfield, 0 Emsley, 5712 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 4872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 432 time to evaluate : 1.768 Fit side-chains REVERT: A 35 ASP cc_start: 0.8022 (t0) cc_final: 0.7644 (t0) REVERT: A 87 ASP cc_start: 0.8131 (t0) cc_final: 0.7916 (m-30) REVERT: A 139 VAL cc_start: 0.9237 (t) cc_final: 0.9022 (p) REVERT: B 193 LYS cc_start: 0.8836 (mtpt) cc_final: 0.8586 (ttmt) REVERT: D 35 ASP cc_start: 0.8090 (t0) cc_final: 0.7725 (t0) REVERT: E 35 ASP cc_start: 0.8136 (t0) cc_final: 0.7793 (t0) REVERT: E 60 LYS cc_start: 0.8658 (pttp) cc_final: 0.8443 (pttp) REVERT: E 77 ASP cc_start: 0.8161 (t0) cc_final: 0.7899 (t0) REVERT: F 60 LYS cc_start: 0.8777 (pttp) cc_final: 0.8449 (ptpt) REVERT: H 191 SER cc_start: 0.9175 (m) cc_final: 0.8922 (t) REVERT: H 193 LYS cc_start: 0.8577 (mmmm) cc_final: 0.8180 (tppp) REVERT: I 35 ASP cc_start: 0.8050 (t0) cc_final: 0.7776 (t0) REVERT: J 60 LYS cc_start: 0.8858 (pttp) cc_final: 0.8546 (ptpt) REVERT: L 75 LYS cc_start: 0.8734 (tttt) cc_final: 0.7946 (ttpp) REVERT: L 193 LYS cc_start: 0.8697 (mmmm) cc_final: 0.8374 (ttmm) REVERT: M 35 ASP cc_start: 0.8026 (t0) cc_final: 0.7648 (t0) REVERT: M 87 ASP cc_start: 0.8128 (t0) cc_final: 0.7913 (m-30) REVERT: M 139 VAL cc_start: 0.9239 (t) cc_final: 0.9019 (p) REVERT: P 35 ASP cc_start: 0.8094 (t0) cc_final: 0.7720 (t0) REVERT: Q 35 ASP cc_start: 0.8141 (t0) cc_final: 0.7794 (t0) REVERT: Q 60 LYS cc_start: 0.8666 (pttp) cc_final: 0.8447 (pttp) REVERT: Q 77 ASP cc_start: 0.8166 (t0) cc_final: 0.7905 (t0) REVERT: R 60 LYS cc_start: 0.8776 (pttp) cc_final: 0.8447 (ptpt) REVERT: T 191 SER cc_start: 0.9176 (m) cc_final: 0.8925 (t) REVERT: T 193 LYS cc_start: 0.8577 (mmmm) cc_final: 0.8179 (tppp) REVERT: U 35 ASP cc_start: 0.8054 (t0) cc_final: 0.7778 (t0) REVERT: V 60 LYS cc_start: 0.8860 (pttp) cc_final: 0.8548 (ptpt) REVERT: X 75 LYS cc_start: 0.8725 (tttt) cc_final: 0.7934 (ttpp) REVERT: X 193 LYS cc_start: 0.8690 (mmmm) cc_final: 0.8371 (ttmm) outliers start: 80 outliers final: 78 residues processed: 496 average time/residue: 0.2673 time to fit residues: 220.1767 Evaluate side-chains 496 residues out of total 4872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 418 time to evaluate : 1.694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 MET Chi-restraints excluded: chain A residue 180 THR Chi-restraints excluded: chain B residue 34 SER Chi-restraints excluded: chain B residue 44 CYS Chi-restraints excluded: chain B residue 61 THR Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain C residue 61 THR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 229 MET Chi-restraints excluded: chain D residue 38 GLN Chi-restraints excluded: chain D residue 114 ILE Chi-restraints excluded: chain D residue 180 THR Chi-restraints excluded: chain E residue 61 THR Chi-restraints excluded: chain E residue 131 THR Chi-restraints excluded: chain E residue 139 VAL Chi-restraints excluded: chain E residue 180 THR Chi-restraints excluded: chain F residue 34 SER Chi-restraints excluded: chain F residue 44 CYS Chi-restraints excluded: chain F residue 61 THR Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain G residue 61 THR Chi-restraints excluded: chain G residue 114 ILE Chi-restraints excluded: chain G residue 180 THR Chi-restraints excluded: chain H residue 114 ILE Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain I residue 48 HIS Chi-restraints excluded: chain I residue 61 THR Chi-restraints excluded: chain I residue 139 VAL Chi-restraints excluded: chain I residue 180 THR Chi-restraints excluded: chain I residue 238 GLU Chi-restraints excluded: chain J residue 44 CYS Chi-restraints excluded: chain J residue 61 THR Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain K residue 61 THR Chi-restraints excluded: chain K residue 79 ASN Chi-restraints excluded: chain K residue 114 ILE Chi-restraints excluded: chain K residue 180 THR Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 114 ILE Chi-restraints excluded: chain M residue 57 MET Chi-restraints excluded: chain M residue 180 THR Chi-restraints excluded: chain N residue 34 SER Chi-restraints excluded: chain N residue 44 CYS Chi-restraints excluded: chain N residue 61 THR Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain O residue 61 THR Chi-restraints excluded: chain O residue 180 THR Chi-restraints excluded: chain O residue 229 MET Chi-restraints excluded: chain P residue 38 GLN Chi-restraints excluded: chain P residue 114 ILE Chi-restraints excluded: chain P residue 180 THR Chi-restraints excluded: chain Q residue 61 THR Chi-restraints excluded: chain Q residue 131 THR Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain Q residue 180 THR Chi-restraints excluded: chain R residue 34 SER Chi-restraints excluded: chain R residue 44 CYS Chi-restraints excluded: chain R residue 61 THR Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain S residue 61 THR Chi-restraints excluded: chain S residue 114 ILE Chi-restraints excluded: chain S residue 180 THR Chi-restraints excluded: chain T residue 114 ILE Chi-restraints excluded: chain T residue 180 THR Chi-restraints excluded: chain U residue 48 HIS Chi-restraints excluded: chain U residue 61 THR Chi-restraints excluded: chain U residue 139 VAL Chi-restraints excluded: chain U residue 180 THR Chi-restraints excluded: chain U residue 238 GLU Chi-restraints excluded: chain V residue 44 CYS Chi-restraints excluded: chain V residue 61 THR Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain W residue 61 THR Chi-restraints excluded: chain W residue 79 ASN Chi-restraints excluded: chain W residue 114 ILE Chi-restraints excluded: chain W residue 180 THR Chi-restraints excluded: chain X residue 81 VAL Chi-restraints excluded: chain X residue 114 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 576 random chunks: chunk 197 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 276 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 222 optimal weight: 0.0470 chunk 189 optimal weight: 6.9990 chunk 23 optimal weight: 0.0040 chunk 515 optimal weight: 0.7980 chunk 344 optimal weight: 6.9990 chunk 386 optimal weight: 6.9990 chunk 425 optimal weight: 0.9990 overall best weight: 1.5694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.116618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.084263 restraints weight = 61083.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.087459 restraints weight = 35314.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.089532 restraints weight = 25188.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.090873 restraints weight = 20384.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.091739 restraints weight = 17800.710| |-----------------------------------------------------------------------------| r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 43392 Z= 0.118 Angle : 0.533 12.818 59304 Z= 0.262 Chirality : 0.045 0.127 7344 Planarity : 0.003 0.030 7656 Dihedral : 4.231 18.433 6000 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.70 % Allowed : 17.71 % Favored : 80.59 % 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: -0.26 (0.11), residues: 5712 helix: 1.87 (0.25), residues: 456 sheet: -0.10 (0.10), residues: 2568 loop : -0.48 (0.12), residues: 2688 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 65 TYR 0.011 0.001 TYR B 232 PHE 0.013 0.001 PHE E 158 TRP 0.003 0.000 TRP T 63 HIS 0.001 0.000 HIS E 48 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 (43392) covalent geometry : angle 0.53313 / 0.26 (59304) hydrogen bonds : bond 0.02522 / 1.70 ( 1224) hydrogen bonds : angle 4.11998 / 2.79 ( 4320) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6938.78 seconds wall clock time: 120 minutes 39.83 seconds (7239.83 seconds total)