Starting phenix.real_space_refine (version: dev) on Wed May 18 07:30:32 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh3_11212/05_2022/6zh3_11212.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh3_11212/05_2022/6zh3_11212.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh3_11212/05_2022/6zh3_11212.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh3_11212/05_2022/6zh3_11212.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh3_11212/05_2022/6zh3_11212.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zh3_11212/05_2022/6zh3_11212.pdb" } resolution = 3.2 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 ------------------------------------------------------------------------------- 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= 0.015 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 49716 Number of models: 1 Model: "" Number of chains: 36 Chain: "B" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "A" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "C" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "D" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "E" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "F" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "G" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "H" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "I" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "J" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "K" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "L" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "M" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "N" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "O" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "P" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "Q" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "R" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "S" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "T" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "U" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "V" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "W" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "X" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "Y" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "Z" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "0" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "1" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "2" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "3" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "4" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "5" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "6" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "7" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "8" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Chain: "9" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1381 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 3, 'TRANS': 166} Time building chain proxies: 27.50, per 1000 atoms: 0.55 Number of scatterers: 49716 At special positions: 0 Unit cell: (172.64, 171.6, 307.84, 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 396 16.00 O 9684 8.00 N 9072 7.00 C 30564 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 - 3.50 Amino acid : False - 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: 21.94 Conformation dependent library (CDL) restraints added in 7.4 seconds 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11808 Finding SS restraints... Secondary structure from input PDB file: 297 helices and 0 sheets defined 87.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.86 Creating SS restraints... Processing helix chain 'B' and resid 2 through 10 Processing helix chain 'B' and resid 12 through 56 removed outlier: 3.709A pdb=" N ARG B 18 " --> pdb=" O LYS B 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG B 25 " --> pdb=" O ARG B 21 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY B 28 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU B 32 " --> pdb=" O GLY B 28 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL B 40 " --> pdb=" O ARG B 36 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU B 41 " --> pdb=" O GLU B 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN B 47 " --> pdb=" O ASN B 43 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS B 54 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS B 55 " --> pdb=" O LYS B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 57 through 98 removed outlier: 4.757A pdb=" N LEU B 63 " --> pdb=" O ARG B 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B 66 " --> pdb=" O ARG B 62 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU B 67 " --> pdb=" O LEU B 63 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR B 69 " --> pdb=" O ALA B 65 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN B 70 " --> pdb=" O LYS B 66 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN B 74 " --> pdb=" O GLN B 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG B 77 " --> pdb=" O LYS B 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA B 83 " --> pdb=" O TYR B 79 " (cutoff:3.500A) Processing helix chain 'B' and resid 100 through 120 removed outlier: 3.723A pdb=" N LEU B 111 " --> pdb=" O ASP B 107 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU B 114 " --> pdb=" O GLY B 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU B 118 " --> pdb=" O GLU B 114 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG B 120 " --> pdb=" O ASN B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 123 No H-bonds generated for 'chain 'B' and resid 121 through 123' Processing helix chain 'B' and resid 124 through 135 removed outlier: 3.783A pdb=" N GLU B 130 " --> pdb=" O ASN B 126 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 145 Processing helix chain 'B' and resid 162 through 170 Processing helix chain 'A' and resid 2 through 10 removed outlier: 3.816A pdb=" N LYS A 6 " --> pdb=" O ASP A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 56 removed outlier: 3.785A pdb=" N ARG A 18 " --> pdb=" O LYS A 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER A 22 " --> pdb=" O ARG A 18 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG A 25 " --> pdb=" O ARG A 21 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY A 28 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU A 32 " --> pdb=" O GLY A 28 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU A 38 " --> pdb=" O SER A 34 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL A 40 " --> pdb=" O ARG A 36 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU A 41 " --> pdb=" O GLU A 37 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS A 50 " --> pdb=" O GLN A 46 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER A 52 " --> pdb=" O LEU A 48 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS A 54 " --> pdb=" O LYS A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 98 removed outlier: 4.036A pdb=" N LEU A 63 " --> pdb=" O ARG A 59 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS A 66 " --> pdb=" O ARG A 62 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU A 67 " --> pdb=" O LEU A 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR A 80 " --> pdb=" O ASP A 76 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA A 83 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing helix chain 'A' and resid 100 through 119 removed outlier: 3.535A pdb=" N GLY A 110 " --> pdb=" O ALA A 106 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU A 111 " --> pdb=" O ASP A 107 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU A 114 " --> pdb=" O GLY A 110 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU A 118 " --> pdb=" O GLU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 123 No H-bonds generated for 'chain 'A' and resid 121 through 123' Processing helix chain 'A' and resid 124 through 135 removed outlier: 3.681A pdb=" N GLU A 130 " --> pdb=" O ASN A 126 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 146 removed outlier: 3.605A pdb=" N ASP A 146 " --> pdb=" O SER A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 162 through 170 removed outlier: 4.006A pdb=" N VAL A 167 " --> pdb=" O VAL A 163 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN A 168 " --> pdb=" O ASP A 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 10 removed outlier: 3.676A pdb=" N LYS C 6 " --> pdb=" O ASP C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 56 removed outlier: 3.576A pdb=" N ARG C 18 " --> pdb=" O LYS C 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG C 25 " --> pdb=" O ARG C 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY C 28 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU C 32 " --> pdb=" O GLY C 28 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU C 38 " --> pdb=" O SER C 34 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL C 40 " --> pdb=" O ARG C 36 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU C 41 " --> pdb=" O GLU C 37 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS C 54 " --> pdb=" O LYS C 50 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS C 55 " --> pdb=" O LYS C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 57 through 98 removed outlier: 4.484A pdb=" N LEU C 63 " --> pdb=" O ARG C 59 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU C 67 " --> pdb=" O LEU C 63 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR C 69 " --> pdb=" O ALA C 65 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN C 70 " --> pdb=" O LYS C 66 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG C 77 " --> pdb=" O LYS C 73 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA C 83 " --> pdb=" O TYR C 79 " (cutoff:3.500A) Processing helix chain 'C' and resid 100 through 120 removed outlier: 3.536A pdb=" N ARG C 113 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU C 114 " --> pdb=" O GLY C 110 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU C 118 " --> pdb=" O GLU C 114 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG C 120 " --> pdb=" O ASN C 116 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 123 No H-bonds generated for 'chain 'C' and resid 121 through 123' Processing helix chain 'C' and resid 124 through 133 removed outlier: 3.633A pdb=" N GLU C 130 " --> pdb=" O ASN C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 145 Processing helix chain 'C' and resid 146 through 150 removed outlier: 3.723A pdb=" N MET C 149 " --> pdb=" O ASP C 146 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU C 150 " --> pdb=" O ASP C 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 146 through 150' Processing helix chain 'C' and resid 162 through 170 Processing helix chain 'D' and resid 2 through 10 Processing helix chain 'D' and resid 12 through 56 removed outlier: 3.646A pdb=" N ARG D 18 " --> pdb=" O LYS D 14 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL D 23 " --> pdb=" O ARG D 19 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG D 25 " --> pdb=" O ARG D 21 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY D 28 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU D 32 " --> pdb=" O GLY D 28 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU D 38 " --> pdb=" O SER D 34 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL D 40 " --> pdb=" O ARG D 36 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU D 41 " --> pdb=" O GLU D 37 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN D 47 " --> pdb=" O ASN D 43 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS D 50 " --> pdb=" O GLN D 46 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS D 54 " --> pdb=" O LYS D 50 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS D 55 " --> pdb=" O LYS D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 57 through 98 removed outlier: 4.253A pdb=" N LEU D 63 " --> pdb=" O ARG D 59 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS D 66 " --> pdb=" O ARG D 62 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU D 67 " --> pdb=" O LEU D 63 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN D 70 " --> pdb=" O LYS D 66 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG D 77 " --> pdb=" O LYS D 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA D 83 " --> pdb=" O TYR D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 120 removed outlier: 3.535A pdb=" N SER D 108 " --> pdb=" O GLN D 104 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG D 113 " --> pdb=" O ALA D 109 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU D 114 " --> pdb=" O GLY D 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG D 120 " --> pdb=" O ASN D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 123 No H-bonds generated for 'chain 'D' and resid 121 through 123' Processing helix chain 'D' and resid 124 through 135 removed outlier: 3.713A pdb=" N GLU D 130 " --> pdb=" O ASN D 126 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU D 134 " --> pdb=" O GLU D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 145 Processing helix chain 'D' and resid 162 through 170 removed outlier: 3.616A pdb=" N VAL D 167 " --> pdb=" O VAL D 163 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS D 169 " --> pdb=" O GLU D 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 10 Processing helix chain 'E' and resid 12 through 56 removed outlier: 3.709A pdb=" N ARG E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL E 23 " --> pdb=" O ARG E 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG E 25 " --> pdb=" O ARG E 21 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY E 28 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU E 32 " --> pdb=" O GLY E 28 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU E 38 " --> pdb=" O SER E 34 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL E 40 " --> pdb=" O ARG E 36 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU E 41 " --> pdb=" O GLU E 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN E 47 " --> pdb=" O ASN E 43 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS E 54 " --> pdb=" O LYS E 50 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS E 55 " --> pdb=" O LYS E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 98 removed outlier: 4.757A pdb=" N LEU E 63 " --> pdb=" O ARG E 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS E 66 " --> pdb=" O ARG E 62 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU E 67 " --> pdb=" O LEU E 63 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR E 69 " --> pdb=" O ALA E 65 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN E 70 " --> pdb=" O LYS E 66 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN E 74 " --> pdb=" O GLN E 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG E 77 " --> pdb=" O LYS E 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA E 83 " --> pdb=" O TYR E 79 " (cutoff:3.500A) Processing helix chain 'E' and resid 100 through 120 removed outlier: 3.722A pdb=" N LEU E 111 " --> pdb=" O ASP E 107 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU E 114 " --> pdb=" O GLY E 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU E 118 " --> pdb=" O GLU E 114 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG E 120 " --> pdb=" O ASN E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 123 No H-bonds generated for 'chain 'E' and resid 121 through 123' Processing helix chain 'E' and resid 124 through 135 removed outlier: 3.783A pdb=" N GLU E 130 " --> pdb=" O ASN E 126 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 145 Processing helix chain 'E' and resid 162 through 170 Processing helix chain 'F' and resid 2 through 10 removed outlier: 3.816A pdb=" N LYS F 6 " --> pdb=" O ASP F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 56 removed outlier: 3.785A pdb=" N ARG F 18 " --> pdb=" O LYS F 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER F 22 " --> pdb=" O ARG F 18 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL F 23 " --> pdb=" O ARG F 19 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG F 25 " --> pdb=" O ARG F 21 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY F 28 " --> pdb=" O LEU F 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU F 32 " --> pdb=" O GLY F 28 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU F 38 " --> pdb=" O SER F 34 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL F 40 " --> pdb=" O ARG F 36 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU F 41 " --> pdb=" O GLU F 37 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS F 50 " --> pdb=" O GLN F 46 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER F 52 " --> pdb=" O LEU F 48 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS F 54 " --> pdb=" O LYS F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 57 through 98 removed outlier: 4.036A pdb=" N LEU F 63 " --> pdb=" O ARG F 59 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS F 66 " --> pdb=" O ARG F 62 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU F 67 " --> pdb=" O LEU F 63 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR F 69 " --> pdb=" O ALA F 65 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG F 77 " --> pdb=" O LYS F 73 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR F 80 " --> pdb=" O ASP F 76 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA F 83 " --> pdb=" O TYR F 79 " (cutoff:3.500A) Processing helix chain 'F' and resid 100 through 119 removed outlier: 3.536A pdb=" N GLY F 110 " --> pdb=" O ALA F 106 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU F 111 " --> pdb=" O ASP F 107 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU F 114 " --> pdb=" O GLY F 110 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU F 118 " --> pdb=" O GLU F 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 123 No H-bonds generated for 'chain 'F' and resid 121 through 123' Processing helix chain 'F' and resid 124 through 135 removed outlier: 3.681A pdb=" N GLU F 130 " --> pdb=" O ASN F 126 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 146 removed outlier: 3.605A pdb=" N ASP F 146 " --> pdb=" O SER F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 162 through 170 removed outlier: 4.006A pdb=" N VAL F 167 " --> pdb=" O VAL F 163 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN F 168 " --> pdb=" O ASP F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 10 removed outlier: 3.676A pdb=" N LYS G 6 " --> pdb=" O ASP G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 56 removed outlier: 3.576A pdb=" N ARG G 18 " --> pdb=" O LYS G 14 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG G 25 " --> pdb=" O ARG G 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY G 28 " --> pdb=" O LEU G 24 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU G 32 " --> pdb=" O GLY G 28 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU G 38 " --> pdb=" O SER G 34 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL G 40 " --> pdb=" O ARG G 36 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU G 41 " --> pdb=" O GLU G 37 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS G 54 " --> pdb=" O LYS G 50 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS G 55 " --> pdb=" O LYS G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 57 through 98 removed outlier: 4.483A pdb=" N LEU G 63 " --> pdb=" O ARG G 59 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU G 67 " --> pdb=" O LEU G 63 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN G 70 " --> pdb=" O LYS G 66 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG G 77 " --> pdb=" O LYS G 73 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA G 83 " --> pdb=" O TYR G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 100 through 120 removed outlier: 3.537A pdb=" N ARG G 113 " --> pdb=" O ALA G 109 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU G 114 " --> pdb=" O GLY G 110 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU G 118 " --> pdb=" O GLU G 114 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG G 120 " --> pdb=" O ASN G 116 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 123 No H-bonds generated for 'chain 'G' and resid 121 through 123' Processing helix chain 'G' and resid 124 through 133 removed outlier: 3.633A pdb=" N GLU G 130 " --> pdb=" O ASN G 126 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 145 Processing helix chain 'G' and resid 146 through 150 removed outlier: 3.723A pdb=" N MET G 149 " --> pdb=" O ASP G 146 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU G 150 " --> pdb=" O ASP G 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 146 through 150' Processing helix chain 'G' and resid 162 through 170 Processing helix chain 'H' and resid 2 through 10 Processing helix chain 'H' and resid 12 through 56 removed outlier: 3.647A pdb=" N ARG H 18 " --> pdb=" O LYS H 14 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL H 23 " --> pdb=" O ARG H 19 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG H 25 " --> pdb=" O ARG H 21 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY H 28 " --> pdb=" O LEU H 24 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU H 32 " --> pdb=" O GLY H 28 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU H 38 " --> pdb=" O SER H 34 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL H 40 " --> pdb=" O ARG H 36 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU H 41 " --> pdb=" O GLU H 37 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN H 47 " --> pdb=" O ASN H 43 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS H 50 " --> pdb=" O GLN H 46 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS H 54 " --> pdb=" O LYS H 50 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS H 55 " --> pdb=" O LYS H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 98 removed outlier: 4.253A pdb=" N LEU H 63 " --> pdb=" O ARG H 59 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS H 66 " --> pdb=" O ARG H 62 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU H 67 " --> pdb=" O LEU H 63 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN H 70 " --> pdb=" O LYS H 66 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG H 77 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA H 83 " --> pdb=" O TYR H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 120 removed outlier: 3.535A pdb=" N SER H 108 " --> pdb=" O GLN H 104 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG H 113 " --> pdb=" O ALA H 109 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU H 114 " --> pdb=" O GLY H 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU H 118 " --> pdb=" O GLU H 114 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG H 120 " --> pdb=" O ASN H 116 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 123 No H-bonds generated for 'chain 'H' and resid 121 through 123' Processing helix chain 'H' and resid 124 through 135 removed outlier: 3.713A pdb=" N GLU H 130 " --> pdb=" O ASN H 126 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU H 134 " --> pdb=" O GLU H 130 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 145 Processing helix chain 'H' and resid 162 through 170 removed outlier: 3.616A pdb=" N VAL H 167 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS H 169 " --> pdb=" O GLU H 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 10 Processing helix chain 'I' and resid 12 through 56 removed outlier: 3.709A pdb=" N ARG I 18 " --> pdb=" O LYS I 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL I 23 " --> pdb=" O ARG I 19 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ARG I 25 " --> pdb=" O ARG I 21 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY I 28 " --> pdb=" O LEU I 24 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU I 32 " --> pdb=" O GLY I 28 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU I 38 " --> pdb=" O SER I 34 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL I 40 " --> pdb=" O ARG I 36 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU I 41 " --> pdb=" O GLU I 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN I 47 " --> pdb=" O ASN I 43 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS I 54 " --> pdb=" O LYS I 50 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS I 55 " --> pdb=" O LYS I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 57 through 98 removed outlier: 4.757A pdb=" N LEU I 63 " --> pdb=" O ARG I 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS I 66 " --> pdb=" O ARG I 62 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU I 67 " --> pdb=" O LEU I 63 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR I 69 " --> pdb=" O ALA I 65 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN I 70 " --> pdb=" O LYS I 66 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN I 74 " --> pdb=" O GLN I 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG I 77 " --> pdb=" O LYS I 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA I 83 " --> pdb=" O TYR I 79 " (cutoff:3.500A) Processing helix chain 'I' and resid 100 through 120 removed outlier: 3.722A pdb=" N LEU I 111 " --> pdb=" O ASP I 107 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU I 114 " --> pdb=" O GLY I 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU I 118 " --> pdb=" O GLU I 114 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG I 120 " --> pdb=" O ASN I 116 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 123 No H-bonds generated for 'chain 'I' and resid 121 through 123' Processing helix chain 'I' and resid 124 through 135 removed outlier: 3.783A pdb=" N GLU I 130 " --> pdb=" O ASN I 126 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 145 Processing helix chain 'I' and resid 162 through 170 Processing helix chain 'J' and resid 2 through 10 removed outlier: 3.816A pdb=" N LYS J 6 " --> pdb=" O ASP J 2 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 56 removed outlier: 3.784A pdb=" N ARG J 18 " --> pdb=" O LYS J 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER J 22 " --> pdb=" O ARG J 18 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL J 23 " --> pdb=" O ARG J 19 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG J 25 " --> pdb=" O ARG J 21 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY J 28 " --> pdb=" O LEU J 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU J 32 " --> pdb=" O GLY J 28 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU J 38 " --> pdb=" O SER J 34 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL J 40 " --> pdb=" O ARG J 36 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU J 41 " --> pdb=" O GLU J 37 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS J 50 " --> pdb=" O GLN J 46 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER J 52 " --> pdb=" O LEU J 48 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS J 54 " --> pdb=" O LYS J 50 " (cutoff:3.500A) Processing helix chain 'J' and resid 57 through 98 removed outlier: 4.035A pdb=" N LEU J 63 " --> pdb=" O ARG J 59 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS J 66 " --> pdb=" O ARG J 62 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU J 67 " --> pdb=" O LEU J 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR J 69 " --> pdb=" O ALA J 65 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG J 77 " --> pdb=" O LYS J 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR J 80 " --> pdb=" O ASP J 76 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA J 83 " --> pdb=" O TYR J 79 " (cutoff:3.500A) Processing helix chain 'J' and resid 100 through 119 removed outlier: 3.535A pdb=" N GLY J 110 " --> pdb=" O ALA J 106 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU J 111 " --> pdb=" O ASP J 107 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N GLU J 114 " --> pdb=" O GLY J 110 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU J 118 " --> pdb=" O GLU J 114 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 123 No H-bonds generated for 'chain 'J' and resid 121 through 123' Processing helix chain 'J' and resid 124 through 135 removed outlier: 3.682A pdb=" N GLU J 130 " --> pdb=" O ASN J 126 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 146 removed outlier: 3.605A pdb=" N ASP J 146 " --> pdb=" O SER J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 162 through 170 removed outlier: 4.006A pdb=" N VAL J 167 " --> pdb=" O VAL J 163 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN J 168 " --> pdb=" O ASP J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 10 removed outlier: 3.675A pdb=" N LYS K 6 " --> pdb=" O ASP K 2 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 56 removed outlier: 3.576A pdb=" N ARG K 18 " --> pdb=" O LYS K 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG K 25 " --> pdb=" O ARG K 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY K 28 " --> pdb=" O LEU K 24 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU K 32 " --> pdb=" O GLY K 28 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU K 38 " --> pdb=" O SER K 34 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL K 40 " --> pdb=" O ARG K 36 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU K 41 " --> pdb=" O GLU K 37 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS K 54 " --> pdb=" O LYS K 50 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS K 55 " --> pdb=" O LYS K 51 " (cutoff:3.500A) Processing helix chain 'K' and resid 57 through 98 removed outlier: 4.483A pdb=" N LEU K 63 " --> pdb=" O ARG K 59 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU K 67 " --> pdb=" O LEU K 63 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR K 69 " --> pdb=" O ALA K 65 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN K 70 " --> pdb=" O LYS K 66 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG K 77 " --> pdb=" O LYS K 73 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA K 83 " --> pdb=" O TYR K 79 " (cutoff:3.500A) Processing helix chain 'K' and resid 100 through 120 removed outlier: 3.536A pdb=" N ARG K 113 " --> pdb=" O ALA K 109 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU K 114 " --> pdb=" O GLY K 110 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N LEU K 118 " --> pdb=" O GLU K 114 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG K 120 " --> pdb=" O ASN K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 123 No H-bonds generated for 'chain 'K' and resid 121 through 123' Processing helix chain 'K' and resid 124 through 133 removed outlier: 3.633A pdb=" N GLU K 130 " --> pdb=" O ASN K 126 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 145 Processing helix chain 'K' and resid 146 through 150 removed outlier: 3.722A pdb=" N MET K 149 " --> pdb=" O ASP K 146 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU K 150 " --> pdb=" O ASP K 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 146 through 150' Processing helix chain 'K' and resid 162 through 170 Processing helix chain 'L' and resid 2 through 10 Processing helix chain 'L' and resid 12 through 56 removed outlier: 3.645A pdb=" N ARG L 18 " --> pdb=" O LYS L 14 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N VAL L 23 " --> pdb=" O ARG L 19 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG L 25 " --> pdb=" O ARG L 21 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY L 28 " --> pdb=" O LEU L 24 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU L 32 " --> pdb=" O GLY L 28 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU L 38 " --> pdb=" O SER L 34 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL L 40 " --> pdb=" O ARG L 36 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU L 41 " --> pdb=" O GLU L 37 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN L 47 " --> pdb=" O ASN L 43 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS L 50 " --> pdb=" O GLN L 46 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS L 54 " --> pdb=" O LYS L 50 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS L 55 " --> pdb=" O LYS L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 57 through 98 removed outlier: 4.254A pdb=" N LEU L 63 " --> pdb=" O ARG L 59 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS L 66 " --> pdb=" O ARG L 62 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU L 67 " --> pdb=" O LEU L 63 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN L 70 " --> pdb=" O LYS L 66 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG L 77 " --> pdb=" O LYS L 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA L 83 " --> pdb=" O TYR L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 100 through 120 removed outlier: 3.536A pdb=" N SER L 108 " --> pdb=" O GLN L 104 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG L 113 " --> pdb=" O ALA L 109 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU L 114 " --> pdb=" O GLY L 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU L 118 " --> pdb=" O GLU L 114 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG L 120 " --> pdb=" O ASN L 116 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 123 No H-bonds generated for 'chain 'L' and resid 121 through 123' Processing helix chain 'L' and resid 124 through 135 removed outlier: 3.713A pdb=" N GLU L 130 " --> pdb=" O ASN L 126 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU L 134 " --> pdb=" O GLU L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 145 Processing helix chain 'L' and resid 162 through 170 removed outlier: 3.616A pdb=" N VAL L 167 " --> pdb=" O VAL L 163 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS L 169 " --> pdb=" O GLU L 165 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 10 Processing helix chain 'M' and resid 12 through 56 removed outlier: 3.709A pdb=" N ARG M 18 " --> pdb=" O LYS M 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL M 23 " --> pdb=" O ARG M 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG M 25 " --> pdb=" O ARG M 21 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY M 28 " --> pdb=" O LEU M 24 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU M 32 " --> pdb=" O GLY M 28 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU M 38 " --> pdb=" O SER M 34 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL M 40 " --> pdb=" O ARG M 36 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU M 41 " --> pdb=" O GLU M 37 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN M 47 " --> pdb=" O ASN M 43 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS M 54 " --> pdb=" O LYS M 50 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS M 55 " --> pdb=" O LYS M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 57 through 98 removed outlier: 4.756A pdb=" N LEU M 63 " --> pdb=" O ARG M 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS M 66 " --> pdb=" O ARG M 62 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU M 67 " --> pdb=" O LEU M 63 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR M 69 " --> pdb=" O ALA M 65 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN M 70 " --> pdb=" O LYS M 66 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN M 74 " --> pdb=" O GLN M 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG M 77 " --> pdb=" O LYS M 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA M 83 " --> pdb=" O TYR M 79 " (cutoff:3.500A) Processing helix chain 'M' and resid 100 through 120 removed outlier: 3.723A pdb=" N LEU M 111 " --> pdb=" O ASP M 107 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU M 114 " --> pdb=" O GLY M 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU M 118 " --> pdb=" O GLU M 114 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG M 120 " --> pdb=" O ASN M 116 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 123 No H-bonds generated for 'chain 'M' and resid 121 through 123' Processing helix chain 'M' and resid 124 through 135 removed outlier: 3.783A pdb=" N GLU M 130 " --> pdb=" O ASN M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 139 through 145 Processing helix chain 'M' and resid 162 through 170 Processing helix chain 'N' and resid 2 through 10 removed outlier: 3.816A pdb=" N LYS N 6 " --> pdb=" O ASP N 2 " (cutoff:3.500A) Processing helix chain 'N' and resid 12 through 56 removed outlier: 3.784A pdb=" N ARG N 18 " --> pdb=" O LYS N 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER N 22 " --> pdb=" O ARG N 18 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL N 23 " --> pdb=" O ARG N 19 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG N 25 " --> pdb=" O ARG N 21 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY N 28 " --> pdb=" O LEU N 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU N 32 " --> pdb=" O GLY N 28 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU N 38 " --> pdb=" O SER N 34 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL N 40 " --> pdb=" O ARG N 36 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU N 41 " --> pdb=" O GLU N 37 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS N 50 " --> pdb=" O GLN N 46 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER N 52 " --> pdb=" O LEU N 48 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS N 54 " --> pdb=" O LYS N 50 " (cutoff:3.500A) Processing helix chain 'N' and resid 57 through 98 removed outlier: 4.036A pdb=" N LEU N 63 " --> pdb=" O ARG N 59 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS N 66 " --> pdb=" O ARG N 62 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU N 67 " --> pdb=" O LEU N 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR N 69 " --> pdb=" O ALA N 65 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG N 77 " --> pdb=" O LYS N 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR N 80 " --> pdb=" O ASP N 76 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA N 83 " --> pdb=" O TYR N 79 " (cutoff:3.500A) Processing helix chain 'N' and resid 100 through 119 removed outlier: 3.535A pdb=" N GLY N 110 " --> pdb=" O ALA N 106 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU N 111 " --> pdb=" O ASP N 107 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU N 114 " --> pdb=" O GLY N 110 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU N 118 " --> pdb=" O GLU N 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 123 No H-bonds generated for 'chain 'N' and resid 121 through 123' Processing helix chain 'N' and resid 124 through 135 removed outlier: 3.682A pdb=" N GLU N 130 " --> pdb=" O ASN N 126 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 146 removed outlier: 3.605A pdb=" N ASP N 146 " --> pdb=" O SER N 142 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 170 removed outlier: 4.006A pdb=" N VAL N 167 " --> pdb=" O VAL N 163 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN N 168 " --> pdb=" O ASP N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 10 removed outlier: 3.676A pdb=" N LYS O 6 " --> pdb=" O ASP O 2 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 56 removed outlier: 3.576A pdb=" N ARG O 18 " --> pdb=" O LYS O 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG O 25 " --> pdb=" O ARG O 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY O 28 " --> pdb=" O LEU O 24 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU O 32 " --> pdb=" O GLY O 28 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU O 38 " --> pdb=" O SER O 34 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL O 40 " --> pdb=" O ARG O 36 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU O 41 " --> pdb=" O GLU O 37 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS O 54 " --> pdb=" O LYS O 50 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS O 55 " --> pdb=" O LYS O 51 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 98 removed outlier: 4.484A pdb=" N LEU O 63 " --> pdb=" O ARG O 59 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU O 67 " --> pdb=" O LEU O 63 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR O 69 " --> pdb=" O ALA O 65 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN O 70 " --> pdb=" O LYS O 66 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG O 77 " --> pdb=" O LYS O 73 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA O 83 " --> pdb=" O TYR O 79 " (cutoff:3.500A) Processing helix chain 'O' and resid 100 through 120 removed outlier: 3.536A pdb=" N ARG O 113 " --> pdb=" O ALA O 109 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU O 114 " --> pdb=" O GLY O 110 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU O 118 " --> pdb=" O GLU O 114 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG O 120 " --> pdb=" O ASN O 116 " (cutoff:3.500A) Processing helix chain 'O' and resid 121 through 123 No H-bonds generated for 'chain 'O' and resid 121 through 123' Processing helix chain 'O' and resid 124 through 133 removed outlier: 3.633A pdb=" N GLU O 130 " --> pdb=" O ASN O 126 " (cutoff:3.500A) Processing helix chain 'O' and resid 139 through 145 Processing helix chain 'O' and resid 146 through 150 removed outlier: 3.722A pdb=" N MET O 149 " --> pdb=" O ASP O 146 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU O 150 " --> pdb=" O ASP O 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 146 through 150' Processing helix chain 'O' and resid 162 through 170 Processing helix chain 'P' and resid 2 through 10 Processing helix chain 'P' and resid 12 through 56 removed outlier: 3.646A pdb=" N ARG P 18 " --> pdb=" O LYS P 14 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL P 23 " --> pdb=" O ARG P 19 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG P 25 " --> pdb=" O ARG P 21 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY P 28 " --> pdb=" O LEU P 24 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU P 32 " --> pdb=" O GLY P 28 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU P 38 " --> pdb=" O SER P 34 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL P 40 " --> pdb=" O ARG P 36 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU P 41 " --> pdb=" O GLU P 37 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN P 47 " --> pdb=" O ASN P 43 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS P 50 " --> pdb=" O GLN P 46 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS P 54 " --> pdb=" O LYS P 50 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS P 55 " --> pdb=" O LYS P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 57 through 98 removed outlier: 4.253A pdb=" N LEU P 63 " --> pdb=" O ARG P 59 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS P 66 " --> pdb=" O ARG P 62 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU P 67 " --> pdb=" O LEU P 63 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN P 70 " --> pdb=" O LYS P 66 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG P 77 " --> pdb=" O LYS P 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA P 83 " --> pdb=" O TYR P 79 " (cutoff:3.500A) Processing helix chain 'P' and resid 100 through 120 removed outlier: 3.535A pdb=" N SER P 108 " --> pdb=" O GLN P 104 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG P 113 " --> pdb=" O ALA P 109 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU P 114 " --> pdb=" O GLY P 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU P 118 " --> pdb=" O GLU P 114 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG P 120 " --> pdb=" O ASN P 116 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 123 No H-bonds generated for 'chain 'P' and resid 121 through 123' Processing helix chain 'P' and resid 124 through 135 removed outlier: 3.714A pdb=" N GLU P 130 " --> pdb=" O ASN P 126 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU P 134 " --> pdb=" O GLU P 130 " (cutoff:3.500A) Processing helix chain 'P' and resid 139 through 145 Processing helix chain 'P' and resid 162 through 170 removed outlier: 3.616A pdb=" N VAL P 167 " --> pdb=" O VAL P 163 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS P 169 " --> pdb=" O GLU P 165 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 10 Processing helix chain 'Q' and resid 12 through 56 removed outlier: 3.710A pdb=" N ARG Q 18 " --> pdb=" O LYS Q 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL Q 23 " --> pdb=" O ARG Q 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG Q 25 " --> pdb=" O ARG Q 21 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY Q 28 " --> pdb=" O LEU Q 24 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU Q 32 " --> pdb=" O GLY Q 28 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU Q 38 " --> pdb=" O SER Q 34 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL Q 40 " --> pdb=" O ARG Q 36 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU Q 41 " --> pdb=" O GLU Q 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN Q 47 " --> pdb=" O ASN Q 43 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS Q 54 " --> pdb=" O LYS Q 50 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS Q 55 " --> pdb=" O LYS Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 57 through 98 removed outlier: 4.757A pdb=" N LEU Q 63 " --> pdb=" O ARG Q 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS Q 66 " --> pdb=" O ARG Q 62 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU Q 67 " --> pdb=" O LEU Q 63 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR Q 69 " --> pdb=" O ALA Q 65 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN Q 70 " --> pdb=" O LYS Q 66 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN Q 74 " --> pdb=" O GLN Q 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG Q 77 " --> pdb=" O LYS Q 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA Q 83 " --> pdb=" O TYR Q 79 " (cutoff:3.500A) Processing helix chain 'Q' and resid 100 through 120 removed outlier: 3.723A pdb=" N LEU Q 111 " --> pdb=" O ASP Q 107 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU Q 114 " --> pdb=" O GLY Q 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU Q 118 " --> pdb=" O GLU Q 114 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG Q 120 " --> pdb=" O ASN Q 116 " (cutoff:3.500A) Processing helix chain 'Q' and resid 121 through 123 No H-bonds generated for 'chain 'Q' and resid 121 through 123' Processing helix chain 'Q' and resid 124 through 135 removed outlier: 3.782A pdb=" N GLU Q 130 " --> pdb=" O ASN Q 126 " (cutoff:3.500A) Processing helix chain 'Q' and resid 139 through 145 Processing helix chain 'Q' and resid 162 through 170 Processing helix chain 'R' and resid 2 through 10 removed outlier: 3.816A pdb=" N LYS R 6 " --> pdb=" O ASP R 2 " (cutoff:3.500A) Processing helix chain 'R' and resid 12 through 56 removed outlier: 3.785A pdb=" N ARG R 18 " --> pdb=" O LYS R 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER R 22 " --> pdb=" O ARG R 18 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL R 23 " --> pdb=" O ARG R 19 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ARG R 25 " --> pdb=" O ARG R 21 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY R 28 " --> pdb=" O LEU R 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU R 32 " --> pdb=" O GLY R 28 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU R 38 " --> pdb=" O SER R 34 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL R 40 " --> pdb=" O ARG R 36 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU R 41 " --> pdb=" O GLU R 37 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS R 50 " --> pdb=" O GLN R 46 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER R 52 " --> pdb=" O LEU R 48 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS R 54 " --> pdb=" O LYS R 50 " (cutoff:3.500A) Processing helix chain 'R' and resid 57 through 98 removed outlier: 4.035A pdb=" N LEU R 63 " --> pdb=" O ARG R 59 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS R 66 " --> pdb=" O ARG R 62 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU R 67 " --> pdb=" O LEU R 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR R 69 " --> pdb=" O ALA R 65 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG R 77 " --> pdb=" O LYS R 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR R 80 " --> pdb=" O ASP R 76 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA R 83 " --> pdb=" O TYR R 79 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 119 removed outlier: 3.535A pdb=" N GLY R 110 " --> pdb=" O ALA R 106 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU R 111 " --> pdb=" O ASP R 107 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU R 114 " --> pdb=" O GLY R 110 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU R 118 " --> pdb=" O GLU R 114 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 123 No H-bonds generated for 'chain 'R' and resid 121 through 123' Processing helix chain 'R' and resid 124 through 135 removed outlier: 3.681A pdb=" N GLU R 130 " --> pdb=" O ASN R 126 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 146 removed outlier: 3.604A pdb=" N ASP R 146 " --> pdb=" O SER R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 162 through 170 removed outlier: 4.006A pdb=" N VAL R 167 " --> pdb=" O VAL R 163 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN R 168 " --> pdb=" O ASP R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 10 removed outlier: 3.676A pdb=" N LYS S 6 " --> pdb=" O ASP S 2 " (cutoff:3.500A) Processing helix chain 'S' and resid 12 through 56 removed outlier: 3.576A pdb=" N ARG S 18 " --> pdb=" O LYS S 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG S 25 " --> pdb=" O ARG S 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY S 28 " --> pdb=" O LEU S 24 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU S 32 " --> pdb=" O GLY S 28 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU S 38 " --> pdb=" O SER S 34 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL S 40 " --> pdb=" O ARG S 36 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LEU S 41 " --> pdb=" O GLU S 37 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS S 54 " --> pdb=" O LYS S 50 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS S 55 " --> pdb=" O LYS S 51 " (cutoff:3.500A) Processing helix chain 'S' and resid 57 through 98 removed outlier: 4.483A pdb=" N LEU S 63 " --> pdb=" O ARG S 59 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU S 67 " --> pdb=" O LEU S 63 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR S 69 " --> pdb=" O ALA S 65 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN S 70 " --> pdb=" O LYS S 66 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG S 77 " --> pdb=" O LYS S 73 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA S 83 " --> pdb=" O TYR S 79 " (cutoff:3.500A) Processing helix chain 'S' and resid 100 through 120 removed outlier: 3.537A pdb=" N ARG S 113 " --> pdb=" O ALA S 109 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU S 114 " --> pdb=" O GLY S 110 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU S 118 " --> pdb=" O GLU S 114 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARG S 120 " --> pdb=" O ASN S 116 " (cutoff:3.500A) Processing helix chain 'S' and resid 121 through 123 No H-bonds generated for 'chain 'S' and resid 121 through 123' Processing helix chain 'S' and resid 124 through 133 removed outlier: 3.633A pdb=" N GLU S 130 " --> pdb=" O ASN S 126 " (cutoff:3.500A) Processing helix chain 'S' and resid 139 through 145 Processing helix chain 'S' and resid 146 through 150 removed outlier: 3.722A pdb=" N MET S 149 " --> pdb=" O ASP S 146 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU S 150 " --> pdb=" O ASP S 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 146 through 150' Processing helix chain 'S' and resid 162 through 170 Processing helix chain 'T' and resid 2 through 10 Processing helix chain 'T' and resid 12 through 56 removed outlier: 3.646A pdb=" N ARG T 18 " --> pdb=" O LYS T 14 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL T 23 " --> pdb=" O ARG T 19 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG T 25 " --> pdb=" O ARG T 21 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY T 28 " --> pdb=" O LEU T 24 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU T 32 " --> pdb=" O GLY T 28 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU T 38 " --> pdb=" O SER T 34 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL T 40 " --> pdb=" O ARG T 36 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU T 41 " --> pdb=" O GLU T 37 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN T 47 " --> pdb=" O ASN T 43 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS T 50 " --> pdb=" O GLN T 46 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS T 54 " --> pdb=" O LYS T 50 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS T 55 " --> pdb=" O LYS T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 57 through 98 removed outlier: 4.253A pdb=" N LEU T 63 " --> pdb=" O ARG T 59 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS T 66 " --> pdb=" O ARG T 62 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU T 67 " --> pdb=" O LEU T 63 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN T 70 " --> pdb=" O LYS T 66 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG T 77 " --> pdb=" O LYS T 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA T 83 " --> pdb=" O TYR T 79 " (cutoff:3.500A) Processing helix chain 'T' and resid 100 through 120 removed outlier: 3.535A pdb=" N SER T 108 " --> pdb=" O GLN T 104 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG T 113 " --> pdb=" O ALA T 109 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU T 114 " --> pdb=" O GLY T 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU T 118 " --> pdb=" O GLU T 114 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG T 120 " --> pdb=" O ASN T 116 " (cutoff:3.500A) Processing helix chain 'T' and resid 121 through 123 No H-bonds generated for 'chain 'T' and resid 121 through 123' Processing helix chain 'T' and resid 124 through 135 removed outlier: 3.713A pdb=" N GLU T 130 " --> pdb=" O ASN T 126 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU T 134 " --> pdb=" O GLU T 130 " (cutoff:3.500A) Processing helix chain 'T' and resid 139 through 145 Processing helix chain 'T' and resid 162 through 170 removed outlier: 3.616A pdb=" N VAL T 167 " --> pdb=" O VAL T 163 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS T 169 " --> pdb=" O GLU T 165 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 10 Processing helix chain 'U' and resid 12 through 56 removed outlier: 3.709A pdb=" N ARG U 18 " --> pdb=" O LYS U 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL U 23 " --> pdb=" O ARG U 19 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG U 25 " --> pdb=" O ARG U 21 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLY U 28 " --> pdb=" O LEU U 24 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU U 32 " --> pdb=" O GLY U 28 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU U 38 " --> pdb=" O SER U 34 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL U 40 " --> pdb=" O ARG U 36 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU U 41 " --> pdb=" O GLU U 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN U 47 " --> pdb=" O ASN U 43 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS U 54 " --> pdb=" O LYS U 50 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS U 55 " --> pdb=" O LYS U 51 " (cutoff:3.500A) Processing helix chain 'U' and resid 57 through 98 removed outlier: 4.757A pdb=" N LEU U 63 " --> pdb=" O ARG U 59 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS U 66 " --> pdb=" O ARG U 62 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU U 67 " --> pdb=" O LEU U 63 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR U 69 " --> pdb=" O ALA U 65 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN U 70 " --> pdb=" O LYS U 66 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN U 74 " --> pdb=" O GLN U 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG U 77 " --> pdb=" O LYS U 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA U 83 " --> pdb=" O TYR U 79 " (cutoff:3.500A) Processing helix chain 'U' and resid 100 through 120 removed outlier: 3.723A pdb=" N LEU U 111 " --> pdb=" O ASP U 107 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU U 114 " --> pdb=" O GLY U 110 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU U 118 " --> pdb=" O GLU U 114 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG U 120 " --> pdb=" O ASN U 116 " (cutoff:3.500A) Processing helix chain 'U' and resid 121 through 123 No H-bonds generated for 'chain 'U' and resid 121 through 123' Processing helix chain 'U' and resid 124 through 135 removed outlier: 3.782A pdb=" N GLU U 130 " --> pdb=" O ASN U 126 " (cutoff:3.500A) Processing helix chain 'U' and resid 139 through 145 Processing helix chain 'U' and resid 162 through 170 Processing helix chain 'V' and resid 2 through 10 removed outlier: 3.816A pdb=" N LYS V 6 " --> pdb=" O ASP V 2 " (cutoff:3.500A) Processing helix chain 'V' and resid 12 through 56 removed outlier: 3.785A pdb=" N ARG V 18 " --> pdb=" O LYS V 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER V 22 " --> pdb=" O ARG V 18 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL V 23 " --> pdb=" O ARG V 19 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG V 25 " --> pdb=" O ARG V 21 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY V 28 " --> pdb=" O LEU V 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU V 32 " --> pdb=" O GLY V 28 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU V 38 " --> pdb=" O SER V 34 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL V 40 " --> pdb=" O ARG V 36 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU V 41 " --> pdb=" O GLU V 37 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS V 50 " --> pdb=" O GLN V 46 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER V 52 " --> pdb=" O LEU V 48 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS V 54 " --> pdb=" O LYS V 50 " (cutoff:3.500A) Processing helix chain 'V' and resid 57 through 98 removed outlier: 4.036A pdb=" N LEU V 63 " --> pdb=" O ARG V 59 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS V 66 " --> pdb=" O ARG V 62 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU V 67 " --> pdb=" O LEU V 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR V 69 " --> pdb=" O ALA V 65 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG V 77 " --> pdb=" O LYS V 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR V 80 " --> pdb=" O ASP V 76 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA V 83 " --> pdb=" O TYR V 79 " (cutoff:3.500A) Processing helix chain 'V' and resid 100 through 119 removed outlier: 3.535A pdb=" N GLY V 110 " --> pdb=" O ALA V 106 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU V 111 " --> pdb=" O ASP V 107 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU V 114 " --> pdb=" O GLY V 110 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU V 118 " --> pdb=" O GLU V 114 " (cutoff:3.500A) Processing helix chain 'V' and resid 121 through 123 No H-bonds generated for 'chain 'V' and resid 121 through 123' Processing helix chain 'V' and resid 124 through 135 removed outlier: 3.680A pdb=" N GLU V 130 " --> pdb=" O ASN V 126 " (cutoff:3.500A) Processing helix chain 'V' and resid 139 through 146 removed outlier: 3.605A pdb=" N ASP V 146 " --> pdb=" O SER V 142 " (cutoff:3.500A) Processing helix chain 'V' and resid 162 through 170 removed outlier: 4.005A pdb=" N VAL V 167 " --> pdb=" O VAL V 163 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN V 168 " --> pdb=" O ASP V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 10 removed outlier: 3.676A pdb=" N LYS W 6 " --> pdb=" O ASP W 2 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 56 removed outlier: 3.577A pdb=" N ARG W 18 " --> pdb=" O LYS W 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG W 25 " --> pdb=" O ARG W 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY W 28 " --> pdb=" O LEU W 24 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU W 32 " --> pdb=" O GLY W 28 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU W 38 " --> pdb=" O SER W 34 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL W 40 " --> pdb=" O ARG W 36 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU W 41 " --> pdb=" O GLU W 37 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS W 54 " --> pdb=" O LYS W 50 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS W 55 " --> pdb=" O LYS W 51 " (cutoff:3.500A) Processing helix chain 'W' and resid 57 through 98 removed outlier: 4.484A pdb=" N LEU W 63 " --> pdb=" O ARG W 59 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU W 67 " --> pdb=" O LEU W 63 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR W 69 " --> pdb=" O ALA W 65 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N GLN W 70 " --> pdb=" O LYS W 66 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG W 77 " --> pdb=" O LYS W 73 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA W 83 " --> pdb=" O TYR W 79 " (cutoff:3.500A) Processing helix chain 'W' and resid 100 through 120 removed outlier: 3.537A pdb=" N ARG W 113 " --> pdb=" O ALA W 109 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU W 114 " --> pdb=" O GLY W 110 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU W 118 " --> pdb=" O GLU W 114 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG W 120 " --> pdb=" O ASN W 116 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 123 No H-bonds generated for 'chain 'W' and resid 121 through 123' Processing helix chain 'W' and resid 124 through 133 removed outlier: 3.634A pdb=" N GLU W 130 " --> pdb=" O ASN W 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 139 through 145 Processing helix chain 'W' and resid 146 through 150 removed outlier: 3.723A pdb=" N MET W 149 " --> pdb=" O ASP W 146 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU W 150 " --> pdb=" O ASP W 147 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 146 through 150' Processing helix chain 'W' and resid 162 through 170 Processing helix chain 'X' and resid 2 through 10 Processing helix chain 'X' and resid 12 through 56 removed outlier: 3.647A pdb=" N ARG X 18 " --> pdb=" O LYS X 14 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL X 23 " --> pdb=" O ARG X 19 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG X 25 " --> pdb=" O ARG X 21 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY X 28 " --> pdb=" O LEU X 24 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU X 32 " --> pdb=" O GLY X 28 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LEU X 38 " --> pdb=" O SER X 34 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL X 40 " --> pdb=" O ARG X 36 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU X 41 " --> pdb=" O GLU X 37 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN X 47 " --> pdb=" O ASN X 43 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS X 50 " --> pdb=" O GLN X 46 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS X 54 " --> pdb=" O LYS X 50 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS X 55 " --> pdb=" O LYS X 51 " (cutoff:3.500A) Processing helix chain 'X' and resid 57 through 98 removed outlier: 4.253A pdb=" N LEU X 63 " --> pdb=" O ARG X 59 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS X 66 " --> pdb=" O ARG X 62 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU X 67 " --> pdb=" O LEU X 63 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN X 70 " --> pdb=" O LYS X 66 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG X 77 " --> pdb=" O LYS X 73 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA X 83 " --> pdb=" O TYR X 79 " (cutoff:3.500A) Processing helix chain 'X' and resid 100 through 120 removed outlier: 3.535A pdb=" N SER X 108 " --> pdb=" O GLN X 104 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG X 113 " --> pdb=" O ALA X 109 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU X 114 " --> pdb=" O GLY X 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU X 118 " --> pdb=" O GLU X 114 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG X 120 " --> pdb=" O ASN X 116 " (cutoff:3.500A) Processing helix chain 'X' and resid 121 through 123 No H-bonds generated for 'chain 'X' and resid 121 through 123' Processing helix chain 'X' and resid 124 through 135 removed outlier: 3.713A pdb=" N GLU X 130 " --> pdb=" O ASN X 126 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU X 134 " --> pdb=" O GLU X 130 " (cutoff:3.500A) Processing helix chain 'X' and resid 139 through 145 Processing helix chain 'X' and resid 162 through 170 removed outlier: 3.616A pdb=" N VAL X 167 " --> pdb=" O VAL X 163 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS X 169 " --> pdb=" O GLU X 165 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 10 Processing helix chain 'Y' and resid 12 through 56 removed outlier: 3.709A pdb=" N ARG Y 18 " --> pdb=" O LYS Y 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL Y 23 " --> pdb=" O ARG Y 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG Y 25 " --> pdb=" O ARG Y 21 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY Y 28 " --> pdb=" O LEU Y 24 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLU Y 32 " --> pdb=" O GLY Y 28 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU Y 38 " --> pdb=" O SER Y 34 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL Y 40 " --> pdb=" O ARG Y 36 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU Y 41 " --> pdb=" O GLU Y 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN Y 47 " --> pdb=" O ASN Y 43 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS Y 54 " --> pdb=" O LYS Y 50 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS Y 55 " --> pdb=" O LYS Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 57 through 98 removed outlier: 4.757A pdb=" N LEU Y 63 " --> pdb=" O ARG Y 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS Y 66 " --> pdb=" O ARG Y 62 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU Y 67 " --> pdb=" O LEU Y 63 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR Y 69 " --> pdb=" O ALA Y 65 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN Y 70 " --> pdb=" O LYS Y 66 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN Y 74 " --> pdb=" O GLN Y 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG Y 77 " --> pdb=" O LYS Y 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA Y 83 " --> pdb=" O TYR Y 79 " (cutoff:3.500A) Processing helix chain 'Y' and resid 100 through 120 removed outlier: 3.723A pdb=" N LEU Y 111 " --> pdb=" O ASP Y 107 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU Y 114 " --> pdb=" O GLY Y 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU Y 118 " --> pdb=" O GLU Y 114 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG Y 120 " --> pdb=" O ASN Y 116 " (cutoff:3.500A) Processing helix chain 'Y' and resid 121 through 123 No H-bonds generated for 'chain 'Y' and resid 121 through 123' Processing helix chain 'Y' and resid 124 through 135 removed outlier: 3.783A pdb=" N GLU Y 130 " --> pdb=" O ASN Y 126 " (cutoff:3.500A) Processing helix chain 'Y' and resid 139 through 145 Processing helix chain 'Y' and resid 162 through 170 Processing helix chain 'Z' and resid 2 through 10 removed outlier: 3.816A pdb=" N LYS Z 6 " --> pdb=" O ASP Z 2 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 56 removed outlier: 3.785A pdb=" N ARG Z 18 " --> pdb=" O LYS Z 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER Z 22 " --> pdb=" O ARG Z 18 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N VAL Z 23 " --> pdb=" O ARG Z 19 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG Z 25 " --> pdb=" O ARG Z 21 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY Z 28 " --> pdb=" O LEU Z 24 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU Z 32 " --> pdb=" O GLY Z 28 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N LEU Z 38 " --> pdb=" O SER Z 34 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL Z 40 " --> pdb=" O ARG Z 36 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU Z 41 " --> pdb=" O GLU Z 37 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS Z 50 " --> pdb=" O GLN Z 46 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N SER Z 52 " --> pdb=" O LEU Z 48 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS Z 54 " --> pdb=" O LYS Z 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 57 through 98 removed outlier: 4.035A pdb=" N LEU Z 63 " --> pdb=" O ARG Z 59 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS Z 66 " --> pdb=" O ARG Z 62 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU Z 67 " --> pdb=" O LEU Z 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR Z 69 " --> pdb=" O ALA Z 65 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG Z 77 " --> pdb=" O LYS Z 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR Z 80 " --> pdb=" O ASP Z 76 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA Z 83 " --> pdb=" O TYR Z 79 " (cutoff:3.500A) Processing helix chain 'Z' and resid 100 through 119 removed outlier: 3.535A pdb=" N GLY Z 110 " --> pdb=" O ALA Z 106 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU Z 111 " --> pdb=" O ASP Z 107 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU Z 114 " --> pdb=" O GLY Z 110 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU Z 118 " --> pdb=" O GLU Z 114 " (cutoff:3.500A) Processing helix chain 'Z' and resid 121 through 123 No H-bonds generated for 'chain 'Z' and resid 121 through 123' Processing helix chain 'Z' and resid 124 through 135 removed outlier: 3.681A pdb=" N GLU Z 130 " --> pdb=" O ASN Z 126 " (cutoff:3.500A) Processing helix chain 'Z' and resid 139 through 146 removed outlier: 3.605A pdb=" N ASP Z 146 " --> pdb=" O SER Z 142 " (cutoff:3.500A) Processing helix chain 'Z' and resid 162 through 170 removed outlier: 4.006A pdb=" N VAL Z 167 " --> pdb=" O VAL Z 163 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN Z 168 " --> pdb=" O ASP Z 164 " (cutoff:3.500A) Processing helix chain '0' and resid 2 through 10 removed outlier: 3.676A pdb=" N LYS 0 6 " --> pdb=" O ASP 0 2 " (cutoff:3.500A) Processing helix chain '0' and resid 12 through 56 removed outlier: 3.576A pdb=" N ARG 0 18 " --> pdb=" O LYS 0 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG 0 25 " --> pdb=" O ARG 0 21 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLY 0 28 " --> pdb=" O LEU 0 24 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU 0 32 " --> pdb=" O GLY 0 28 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N LEU 0 38 " --> pdb=" O SER 0 34 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL 0 40 " --> pdb=" O ARG 0 36 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU 0 41 " --> pdb=" O GLU 0 37 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS 0 54 " --> pdb=" O LYS 0 50 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N LYS 0 55 " --> pdb=" O LYS 0 51 " (cutoff:3.500A) Processing helix chain '0' and resid 57 through 98 removed outlier: 4.484A pdb=" N LEU 0 63 " --> pdb=" O ARG 0 59 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU 0 67 " --> pdb=" O LEU 0 63 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR 0 69 " --> pdb=" O ALA 0 65 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN 0 70 " --> pdb=" O LYS 0 66 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG 0 77 " --> pdb=" O LYS 0 73 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA 0 83 " --> pdb=" O TYR 0 79 " (cutoff:3.500A) Processing helix chain '0' and resid 100 through 120 removed outlier: 3.536A pdb=" N ARG 0 113 " --> pdb=" O ALA 0 109 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU 0 114 " --> pdb=" O GLY 0 110 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU 0 118 " --> pdb=" O GLU 0 114 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG 0 120 " --> pdb=" O ASN 0 116 " (cutoff:3.500A) Processing helix chain '0' and resid 121 through 123 No H-bonds generated for 'chain '0' and resid 121 through 123' Processing helix chain '0' and resid 124 through 133 removed outlier: 3.634A pdb=" N GLU 0 130 " --> pdb=" O ASN 0 126 " (cutoff:3.500A) Processing helix chain '0' and resid 139 through 145 Processing helix chain '0' and resid 146 through 150 removed outlier: 3.722A pdb=" N MET 0 149 " --> pdb=" O ASP 0 146 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU 0 150 " --> pdb=" O ASP 0 147 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 146 through 150' Processing helix chain '0' and resid 162 through 170 Processing helix chain '1' and resid 2 through 10 Processing helix chain '1' and resid 12 through 56 removed outlier: 3.646A pdb=" N ARG 1 18 " --> pdb=" O LYS 1 14 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL 1 23 " --> pdb=" O ARG 1 19 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARG 1 25 " --> pdb=" O ARG 1 21 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY 1 28 " --> pdb=" O LEU 1 24 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU 1 32 " --> pdb=" O GLY 1 28 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU 1 38 " --> pdb=" O SER 1 34 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL 1 40 " --> pdb=" O ARG 1 36 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU 1 41 " --> pdb=" O GLU 1 37 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN 1 47 " --> pdb=" O ASN 1 43 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS 1 50 " --> pdb=" O GLN 1 46 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N LYS 1 54 " --> pdb=" O LYS 1 50 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS 1 55 " --> pdb=" O LYS 1 51 " (cutoff:3.500A) Processing helix chain '1' and resid 57 through 98 removed outlier: 4.254A pdb=" N LEU 1 63 " --> pdb=" O ARG 1 59 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS 1 66 " --> pdb=" O ARG 1 62 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU 1 67 " --> pdb=" O LEU 1 63 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN 1 70 " --> pdb=" O LYS 1 66 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG 1 77 " --> pdb=" O LYS 1 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA 1 83 " --> pdb=" O TYR 1 79 " (cutoff:3.500A) Processing helix chain '1' and resid 100 through 120 removed outlier: 3.536A pdb=" N SER 1 108 " --> pdb=" O GLN 1 104 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG 1 113 " --> pdb=" O ALA 1 109 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU 1 114 " --> pdb=" O GLY 1 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU 1 118 " --> pdb=" O GLU 1 114 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG 1 120 " --> pdb=" O ASN 1 116 " (cutoff:3.500A) Processing helix chain '1' and resid 121 through 123 No H-bonds generated for 'chain '1' and resid 121 through 123' Processing helix chain '1' and resid 124 through 135 removed outlier: 3.713A pdb=" N GLU 1 130 " --> pdb=" O ASN 1 126 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU 1 134 " --> pdb=" O GLU 1 130 " (cutoff:3.500A) Processing helix chain '1' and resid 139 through 145 Processing helix chain '1' and resid 162 through 170 removed outlier: 3.616A pdb=" N VAL 1 167 " --> pdb=" O VAL 1 163 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS 1 169 " --> pdb=" O GLU 1 165 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 10 Processing helix chain '2' and resid 12 through 56 removed outlier: 3.709A pdb=" N ARG 2 18 " --> pdb=" O LYS 2 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N VAL 2 23 " --> pdb=" O ARG 2 19 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ARG 2 25 " --> pdb=" O ARG 2 21 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY 2 28 " --> pdb=" O LEU 2 24 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU 2 32 " --> pdb=" O GLY 2 28 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU 2 38 " --> pdb=" O SER 2 34 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL 2 40 " --> pdb=" O ARG 2 36 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU 2 41 " --> pdb=" O GLU 2 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN 2 47 " --> pdb=" O ASN 2 43 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS 2 54 " --> pdb=" O LYS 2 50 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS 2 55 " --> pdb=" O LYS 2 51 " (cutoff:3.500A) Processing helix chain '2' and resid 57 through 98 removed outlier: 4.757A pdb=" N LEU 2 63 " --> pdb=" O ARG 2 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS 2 66 " --> pdb=" O ARG 2 62 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N GLU 2 67 " --> pdb=" O LEU 2 63 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N TYR 2 69 " --> pdb=" O ALA 2 65 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLN 2 70 " --> pdb=" O LYS 2 66 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN 2 74 " --> pdb=" O GLN 2 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG 2 77 " --> pdb=" O LYS 2 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA 2 83 " --> pdb=" O TYR 2 79 " (cutoff:3.500A) Processing helix chain '2' and resid 100 through 120 removed outlier: 3.722A pdb=" N LEU 2 111 " --> pdb=" O ASP 2 107 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU 2 114 " --> pdb=" O GLY 2 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU 2 118 " --> pdb=" O GLU 2 114 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG 2 120 " --> pdb=" O ASN 2 116 " (cutoff:3.500A) Processing helix chain '2' and resid 121 through 123 No H-bonds generated for 'chain '2' and resid 121 through 123' Processing helix chain '2' and resid 124 through 135 removed outlier: 3.782A pdb=" N GLU 2 130 " --> pdb=" O ASN 2 126 " (cutoff:3.500A) Processing helix chain '2' and resid 139 through 145 Processing helix chain '2' and resid 162 through 170 Processing helix chain '3' and resid 2 through 10 removed outlier: 3.816A pdb=" N LYS 3 6 " --> pdb=" O ASP 3 2 " (cutoff:3.500A) Processing helix chain '3' and resid 12 through 56 removed outlier: 3.784A pdb=" N ARG 3 18 " --> pdb=" O LYS 3 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER 3 22 " --> pdb=" O ARG 3 18 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL 3 23 " --> pdb=" O ARG 3 19 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG 3 25 " --> pdb=" O ARG 3 21 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N GLY 3 28 " --> pdb=" O LEU 3 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU 3 32 " --> pdb=" O GLY 3 28 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU 3 38 " --> pdb=" O SER 3 34 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N VAL 3 40 " --> pdb=" O ARG 3 36 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU 3 41 " --> pdb=" O GLU 3 37 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS 3 50 " --> pdb=" O GLN 3 46 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER 3 52 " --> pdb=" O LEU 3 48 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N LYS 3 54 " --> pdb=" O LYS 3 50 " (cutoff:3.500A) Processing helix chain '3' and resid 57 through 98 removed outlier: 4.036A pdb=" N LEU 3 63 " --> pdb=" O ARG 3 59 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS 3 66 " --> pdb=" O ARG 3 62 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU 3 67 " --> pdb=" O LEU 3 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR 3 69 " --> pdb=" O ALA 3 65 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ARG 3 77 " --> pdb=" O LYS 3 73 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N THR 3 80 " --> pdb=" O ASP 3 76 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA 3 83 " --> pdb=" O TYR 3 79 " (cutoff:3.500A) Processing helix chain '3' and resid 100 through 119 removed outlier: 3.535A pdb=" N GLY 3 110 " --> pdb=" O ALA 3 106 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU 3 111 " --> pdb=" O ASP 3 107 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU 3 114 " --> pdb=" O GLY 3 110 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU 3 118 " --> pdb=" O GLU 3 114 " (cutoff:3.500A) Processing helix chain '3' and resid 121 through 123 No H-bonds generated for 'chain '3' and resid 121 through 123' Processing helix chain '3' and resid 124 through 135 removed outlier: 3.681A pdb=" N GLU 3 130 " --> pdb=" O ASN 3 126 " (cutoff:3.500A) Processing helix chain '3' and resid 139 through 146 removed outlier: 3.605A pdb=" N ASP 3 146 " --> pdb=" O SER 3 142 " (cutoff:3.500A) Processing helix chain '3' and resid 162 through 170 removed outlier: 4.006A pdb=" N VAL 3 167 " --> pdb=" O VAL 3 163 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN 3 168 " --> pdb=" O ASP 3 164 " (cutoff:3.500A) Processing helix chain '4' and resid 2 through 10 removed outlier: 3.676A pdb=" N LYS 4 6 " --> pdb=" O ASP 4 2 " (cutoff:3.500A) Processing helix chain '4' and resid 12 through 56 removed outlier: 3.576A pdb=" N ARG 4 18 " --> pdb=" O LYS 4 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG 4 25 " --> pdb=" O ARG 4 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY 4 28 " --> pdb=" O LEU 4 24 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLU 4 32 " --> pdb=" O GLY 4 28 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU 4 38 " --> pdb=" O SER 4 34 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL 4 40 " --> pdb=" O ARG 4 36 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU 4 41 " --> pdb=" O GLU 4 37 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS 4 54 " --> pdb=" O LYS 4 50 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS 4 55 " --> pdb=" O LYS 4 51 " (cutoff:3.500A) Processing helix chain '4' and resid 57 through 98 removed outlier: 4.484A pdb=" N LEU 4 63 " --> pdb=" O ARG 4 59 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU 4 67 " --> pdb=" O LEU 4 63 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR 4 69 " --> pdb=" O ALA 4 65 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN 4 70 " --> pdb=" O LYS 4 66 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG 4 77 " --> pdb=" O LYS 4 73 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA 4 83 " --> pdb=" O TYR 4 79 " (cutoff:3.500A) Processing helix chain '4' and resid 100 through 120 removed outlier: 3.537A pdb=" N ARG 4 113 " --> pdb=" O ALA 4 109 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU 4 114 " --> pdb=" O GLY 4 110 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU 4 118 " --> pdb=" O GLU 4 114 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG 4 120 " --> pdb=" O ASN 4 116 " (cutoff:3.500A) Processing helix chain '4' and resid 121 through 123 No H-bonds generated for 'chain '4' and resid 121 through 123' Processing helix chain '4' and resid 124 through 133 removed outlier: 3.634A pdb=" N GLU 4 130 " --> pdb=" O ASN 4 126 " (cutoff:3.500A) Processing helix chain '4' and resid 139 through 145 Processing helix chain '4' and resid 146 through 150 removed outlier: 3.723A pdb=" N MET 4 149 " --> pdb=" O ASP 4 146 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N GLU 4 150 " --> pdb=" O ASP 4 147 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 146 through 150' Processing helix chain '4' and resid 162 through 170 Processing helix chain '5' and resid 2 through 10 Processing helix chain '5' and resid 12 through 56 removed outlier: 3.647A pdb=" N ARG 5 18 " --> pdb=" O LYS 5 14 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL 5 23 " --> pdb=" O ARG 5 19 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG 5 25 " --> pdb=" O ARG 5 21 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N GLY 5 28 " --> pdb=" O LEU 5 24 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLU 5 32 " --> pdb=" O GLY 5 28 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU 5 38 " --> pdb=" O SER 5 34 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL 5 40 " --> pdb=" O ARG 5 36 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LEU 5 41 " --> pdb=" O GLU 5 37 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLN 5 47 " --> pdb=" O ASN 5 43 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS 5 50 " --> pdb=" O GLN 5 46 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS 5 54 " --> pdb=" O LYS 5 50 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LYS 5 55 " --> pdb=" O LYS 5 51 " (cutoff:3.500A) Processing helix chain '5' and resid 57 through 98 removed outlier: 4.253A pdb=" N LEU 5 63 " --> pdb=" O ARG 5 59 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS 5 66 " --> pdb=" O ARG 5 62 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N GLU 5 67 " --> pdb=" O LEU 5 63 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN 5 70 " --> pdb=" O LYS 5 66 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG 5 77 " --> pdb=" O LYS 5 73 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA 5 83 " --> pdb=" O TYR 5 79 " (cutoff:3.500A) Processing helix chain '5' and resid 100 through 120 removed outlier: 3.535A pdb=" N SER 5 108 " --> pdb=" O GLN 5 104 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG 5 113 " --> pdb=" O ALA 5 109 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU 5 114 " --> pdb=" O GLY 5 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU 5 118 " --> pdb=" O GLU 5 114 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N ARG 5 120 " --> pdb=" O ASN 5 116 " (cutoff:3.500A) Processing helix chain '5' and resid 121 through 123 No H-bonds generated for 'chain '5' and resid 121 through 123' Processing helix chain '5' and resid 124 through 135 removed outlier: 3.713A pdb=" N GLU 5 130 " --> pdb=" O ASN 5 126 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU 5 134 " --> pdb=" O GLU 5 130 " (cutoff:3.500A) Processing helix chain '5' and resid 139 through 145 Processing helix chain '5' and resid 162 through 170 removed outlier: 3.616A pdb=" N VAL 5 167 " --> pdb=" O VAL 5 163 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS 5 169 " --> pdb=" O GLU 5 165 " (cutoff:3.500A) Processing helix chain '6' and resid 2 through 10 Processing helix chain '6' and resid 12 through 56 removed outlier: 3.709A pdb=" N ARG 6 18 " --> pdb=" O LYS 6 14 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL 6 23 " --> pdb=" O ARG 6 19 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ARG 6 25 " --> pdb=" O ARG 6 21 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY 6 28 " --> pdb=" O LEU 6 24 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N GLU 6 32 " --> pdb=" O GLY 6 28 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU 6 38 " --> pdb=" O SER 6 34 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL 6 40 " --> pdb=" O ARG 6 36 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N LEU 6 41 " --> pdb=" O GLU 6 37 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLN 6 47 " --> pdb=" O ASN 6 43 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LYS 6 54 " --> pdb=" O LYS 6 50 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LYS 6 55 " --> pdb=" O LYS 6 51 " (cutoff:3.500A) Processing helix chain '6' and resid 57 through 98 removed outlier: 4.757A pdb=" N LEU 6 63 " --> pdb=" O ARG 6 59 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS 6 66 " --> pdb=" O ARG 6 62 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N GLU 6 67 " --> pdb=" O LEU 6 63 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N TYR 6 69 " --> pdb=" O ALA 6 65 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLN 6 70 " --> pdb=" O LYS 6 66 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN 6 74 " --> pdb=" O GLN 6 70 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ARG 6 77 " --> pdb=" O LYS 6 73 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ALA 6 83 " --> pdb=" O TYR 6 79 " (cutoff:3.500A) Processing helix chain '6' and resid 100 through 120 removed outlier: 3.723A pdb=" N LEU 6 111 " --> pdb=" O ASP 6 107 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLU 6 114 " --> pdb=" O GLY 6 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU 6 118 " --> pdb=" O GLU 6 114 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ARG 6 120 " --> pdb=" O ASN 6 116 " (cutoff:3.500A) Processing helix chain '6' and resid 121 through 123 No H-bonds generated for 'chain '6' and resid 121 through 123' Processing helix chain '6' and resid 124 through 135 removed outlier: 3.782A pdb=" N GLU 6 130 " --> pdb=" O ASN 6 126 " (cutoff:3.500A) Processing helix chain '6' and resid 139 through 145 Processing helix chain '6' and resid 162 through 170 Processing helix chain '7' and resid 2 through 10 removed outlier: 3.816A pdb=" N LYS 7 6 " --> pdb=" O ASP 7 2 " (cutoff:3.500A) Processing helix chain '7' and resid 12 through 56 removed outlier: 3.785A pdb=" N ARG 7 18 " --> pdb=" O LYS 7 14 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER 7 22 " --> pdb=" O ARG 7 18 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL 7 23 " --> pdb=" O ARG 7 19 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ARG 7 25 " --> pdb=" O ARG 7 21 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLY 7 28 " --> pdb=" O LEU 7 24 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N GLU 7 32 " --> pdb=" O GLY 7 28 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N LEU 7 38 " --> pdb=" O SER 7 34 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N VAL 7 40 " --> pdb=" O ARG 7 36 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N LEU 7 41 " --> pdb=" O GLU 7 37 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LYS 7 50 " --> pdb=" O GLN 7 46 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER 7 52 " --> pdb=" O LEU 7 48 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS 7 54 " --> pdb=" O LYS 7 50 " (cutoff:3.500A) Processing helix chain '7' and resid 57 through 98 removed outlier: 4.037A pdb=" N LEU 7 63 " --> pdb=" O ARG 7 59 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS 7 66 " --> pdb=" O ARG 7 62 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N GLU 7 67 " --> pdb=" O LEU 7 63 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N TYR 7 69 " --> pdb=" O ALA 7 65 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG 7 77 " --> pdb=" O LYS 7 73 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N THR 7 80 " --> pdb=" O ASP 7 76 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA 7 83 " --> pdb=" O TYR 7 79 " (cutoff:3.500A) Processing helix chain '7' and resid 100 through 119 removed outlier: 3.535A pdb=" N GLY 7 110 " --> pdb=" O ALA 7 106 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LEU 7 111 " --> pdb=" O ASP 7 107 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N GLU 7 114 " --> pdb=" O GLY 7 110 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LEU 7 118 " --> pdb=" O GLU 7 114 " (cutoff:3.500A) Processing helix chain '7' and resid 121 through 123 No H-bonds generated for 'chain '7' and resid 121 through 123' Processing helix chain '7' and resid 124 through 135 removed outlier: 3.681A pdb=" N GLU 7 130 " --> pdb=" O ASN 7 126 " (cutoff:3.500A) Processing helix chain '7' and resid 139 through 146 removed outlier: 3.605A pdb=" N ASP 7 146 " --> pdb=" O SER 7 142 " (cutoff:3.500A) Processing helix chain '7' and resid 162 through 170 removed outlier: 4.006A pdb=" N VAL 7 167 " --> pdb=" O VAL 7 163 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ASN 7 168 " --> pdb=" O ASP 7 164 " (cutoff:3.500A) Processing helix chain '8' and resid 2 through 10 removed outlier: 3.676A pdb=" N LYS 8 6 " --> pdb=" O ASP 8 2 " (cutoff:3.500A) Processing helix chain '8' and resid 12 through 56 removed outlier: 3.576A pdb=" N ARG 8 18 " --> pdb=" O LYS 8 14 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG 8 25 " --> pdb=" O ARG 8 21 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLY 8 28 " --> pdb=" O LEU 8 24 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU 8 32 " --> pdb=" O GLY 8 28 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU 8 38 " --> pdb=" O SER 8 34 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL 8 40 " --> pdb=" O ARG 8 36 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N LEU 8 41 " --> pdb=" O GLU 8 37 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N LYS 8 54 " --> pdb=" O LYS 8 50 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N LYS 8 55 " --> pdb=" O LYS 8 51 " (cutoff:3.500A) Processing helix chain '8' and resid 57 through 98 removed outlier: 4.483A pdb=" N LEU 8 63 " --> pdb=" O ARG 8 59 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU 8 67 " --> pdb=" O LEU 8 63 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N TYR 8 69 " --> pdb=" O ALA 8 65 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N GLN 8 70 " --> pdb=" O LYS 8 66 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ARG 8 77 " --> pdb=" O LYS 8 73 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ALA 8 83 " --> pdb=" O TYR 8 79 " (cutoff:3.500A) Processing helix chain '8' and resid 100 through 120 removed outlier: 3.536A pdb=" N ARG 8 113 " --> pdb=" O ALA 8 109 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLU 8 114 " --> pdb=" O GLY 8 110 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU 8 118 " --> pdb=" O GLU 8 114 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N ARG 8 120 " --> pdb=" O ASN 8 116 " (cutoff:3.500A) Processing helix chain '8' and resid 121 through 123 No H-bonds generated for 'chain '8' and resid 121 through 123' Processing helix chain '8' and resid 124 through 133 removed outlier: 3.633A pdb=" N GLU 8 130 " --> pdb=" O ASN 8 126 " (cutoff:3.500A) Processing helix chain '8' and resid 139 through 145 Processing helix chain '8' and resid 146 through 150 removed outlier: 3.723A pdb=" N MET 8 149 " --> pdb=" O ASP 8 146 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLU 8 150 " --> pdb=" O ASP 8 147 " (cutoff:3.500A) No H-bonds generated for 'chain '8' and resid 146 through 150' Processing helix chain '8' and resid 162 through 170 Processing helix chain '9' and resid 2 through 10 Processing helix chain '9' and resid 12 through 56 removed outlier: 3.646A pdb=" N ARG 9 18 " --> pdb=" O LYS 9 14 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL 9 23 " --> pdb=" O ARG 9 19 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG 9 25 " --> pdb=" O ARG 9 21 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY 9 28 " --> pdb=" O LEU 9 24 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLU 9 32 " --> pdb=" O GLY 9 28 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU 9 38 " --> pdb=" O SER 9 34 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N VAL 9 40 " --> pdb=" O ARG 9 36 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N LEU 9 41 " --> pdb=" O GLU 9 37 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLN 9 47 " --> pdb=" O ASN 9 43 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LYS 9 50 " --> pdb=" O GLN 9 46 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LYS 9 54 " --> pdb=" O LYS 9 50 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N LYS 9 55 " --> pdb=" O LYS 9 51 " (cutoff:3.500A) Processing helix chain '9' and resid 57 through 98 removed outlier: 4.254A pdb=" N LEU 9 63 " --> pdb=" O ARG 9 59 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS 9 66 " --> pdb=" O ARG 9 62 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLU 9 67 " --> pdb=" O LEU 9 63 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN 9 70 " --> pdb=" O LYS 9 66 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ARG 9 77 " --> pdb=" O LYS 9 73 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ALA 9 83 " --> pdb=" O TYR 9 79 " (cutoff:3.500A) Processing helix chain '9' and resid 100 through 120 removed outlier: 3.535A pdb=" N SER 9 108 " --> pdb=" O GLN 9 104 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG 9 113 " --> pdb=" O ALA 9 109 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLU 9 114 " --> pdb=" O GLY 9 110 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU 9 118 " --> pdb=" O GLU 9 114 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ARG 9 120 " --> pdb=" O ASN 9 116 " (cutoff:3.500A) Processing helix chain '9' and resid 121 through 123 No H-bonds generated for 'chain '9' and resid 121 through 123' Processing helix chain '9' and resid 124 through 135 removed outlier: 3.713A pdb=" N GLU 9 130 " --> pdb=" O ASN 9 126 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLU 9 134 " --> pdb=" O GLU 9 130 " (cutoff:3.500A) Processing helix chain '9' and resid 139 through 145 Processing helix chain '9' and resid 162 through 170 removed outlier: 3.616A pdb=" N VAL 9 167 " --> pdb=" O VAL 9 163 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS 9 169 " --> pdb=" O GLU 9 165 " (cutoff:3.500A) 3294 hydrogen bonds defined for protein. 9882 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: 16.68 Time building geometry restraints manager: 23.30 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 12269 1.33 - 1.45: 7526 1.45 - 1.57: 29453 1.57 - 1.69: 0 1.69 - 1.80: 792 Bond restraints: 50040 Sorted by residual: bond pdb=" CG1 ILE O 140 " pdb=" CD1 ILE O 140 " ideal model delta sigma weight residual 1.513 1.418 0.095 3.90e-02 6.57e+02 5.94e+00 bond pdb=" CG1 ILE K 140 " pdb=" CD1 ILE K 140 " ideal model delta sigma weight residual 1.513 1.418 0.095 3.90e-02 6.57e+02 5.92e+00 bond pdb=" CG1 ILE I 140 " pdb=" CD1 ILE I 140 " ideal model delta sigma weight residual 1.513 1.418 0.095 3.90e-02 6.57e+02 5.90e+00 bond pdb=" CG1 ILE 8 140 " pdb=" CD1 ILE 8 140 " ideal model delta sigma weight residual 1.513 1.418 0.095 3.90e-02 6.57e+02 5.90e+00 bond pdb=" CG1 ILE S 140 " pdb=" CD1 ILE S 140 " ideal model delta sigma weight residual 1.513 1.418 0.095 3.90e-02 6.57e+02 5.90e+00 ... (remaining 50035 not shown) Histogram of bond angle deviations from ideal: 98.10 - 105.28: 756 105.28 - 112.46: 24576 112.46 - 119.64: 19573 119.64 - 126.82: 21695 126.82 - 133.99: 252 Bond angle restraints: 66852 Sorted by residual: angle pdb=" C ARG 1 97 " pdb=" N MET 1 98 " pdb=" CA MET 1 98 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C ARG T 97 " pdb=" N MET T 98 " pdb=" CA MET T 98 " ideal model delta sigma weight residual 121.54 129.44 -7.90 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C ARG H 97 " pdb=" N MET H 98 " pdb=" CA MET H 98 " ideal model delta sigma weight residual 121.54 129.43 -7.89 1.91e+00 2.74e-01 1.71e+01 angle pdb=" C ARG D 97 " pdb=" N MET D 98 " pdb=" CA MET D 98 " ideal model delta sigma weight residual 121.54 129.42 -7.88 1.91e+00 2.74e-01 1.70e+01 angle pdb=" C ARG P 97 " pdb=" N MET P 98 " pdb=" CA MET P 98 " ideal model delta sigma weight residual 121.54 129.41 -7.87 1.91e+00 2.74e-01 1.70e+01 ... (remaining 66847 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.10: 29034 15.10 - 30.21: 2151 30.21 - 45.31: 981 45.31 - 60.41: 90 60.41 - 75.52: 180 Dihedral angle restraints: 32436 sinusoidal: 14364 harmonic: 18072 Sorted by residual: dihedral pdb=" CA ARG 3 21 " pdb=" C ARG 3 21 " pdb=" N SER 3 22 " pdb=" CA SER 3 22 " ideal model delta harmonic sigma weight residual 180.00 159.12 20.88 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ARG J 21 " pdb=" C ARG J 21 " pdb=" N SER J 22 " pdb=" CA SER J 22 " ideal model delta harmonic sigma weight residual 180.00 159.14 20.86 0 5.00e+00 4.00e-02 1.74e+01 dihedral pdb=" CA ARG N 21 " pdb=" C ARG N 21 " pdb=" N SER N 22 " pdb=" CA SER N 22 " ideal model delta harmonic sigma weight residual 180.00 159.15 20.85 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 32433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 4700 0.050 - 0.100: 2445 0.100 - 0.150: 349 0.150 - 0.200: 39 0.200 - 0.250: 27 Chirality restraints: 7560 Sorted by residual: chirality pdb=" CG LEU I 135 " pdb=" CB LEU I 135 " pdb=" CD1 LEU I 135 " pdb=" CD2 LEU I 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CG LEU Q 135 " pdb=" CB LEU Q 135 " pdb=" CD1 LEU Q 135 " pdb=" CD2 LEU Q 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CG LEU Y 135 " pdb=" CB LEU Y 135 " pdb=" CD1 LEU Y 135 " pdb=" CD2 LEU Y 135 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.55e+00 ... (remaining 7557 not shown) Planarity restraints: 8676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET T 98 " -0.013 2.00e-02 2.50e+03 2.67e-02 7.12e+00 pdb=" C MET T 98 " 0.046 2.00e-02 2.50e+03 pdb=" O MET T 98 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN T 99 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET 9 98 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.10e+00 pdb=" C MET 9 98 " 0.046 2.00e-02 2.50e+03 pdb=" O MET 9 98 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN 9 99 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET D 98 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.09e+00 pdb=" C MET D 98 " 0.046 2.00e-02 2.50e+03 pdb=" O MET D 98 " -0.017 2.00e-02 2.50e+03 pdb=" N ASN D 99 " -0.016 2.00e-02 2.50e+03 ... (remaining 8673 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 14773 2.83 - 3.34: 48001 3.34 - 3.86: 77444 3.86 - 4.38: 93135 4.38 - 4.90: 155091 Nonbonded interactions: 388444 Sorted by model distance: nonbonded pdb=" O LEU Q 35 " pdb=" OG1 THR Q 39 " model vdw 2.307 2.440 nonbonded pdb=" O LEU 6 35 " pdb=" OG1 THR 6 39 " model vdw 2.307 2.440 nonbonded pdb=" O LEU M 35 " pdb=" OG1 THR M 39 " model vdw 2.307 2.440 nonbonded pdb=" O LEU 2 35 " pdb=" OG1 THR 2 39 " model vdw 2.307 2.440 nonbonded pdb=" O LEU E 35 " pdb=" OG1 THR E 39 " model vdw 2.307 2.440 ... (remaining 388439 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain '2' selection = chain '3' selection = chain '4' selection = chain '5' selection = chain '6' selection = chain '7' selection = chain '8' selection = chain '9' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 396 5.16 5 C 30564 2.51 5 N 9072 2.21 5 O 9684 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.760 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: 0.060 Extract box with map and model: 8.980 Check model and map are aligned: 0.840 Convert atoms to be neutral: 0.480 Process input model: 120.770 Find NCS groups from input model: 3.720 Set up NCS constraints: 0.570 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 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 : 0.008 0.095 50040 Z= 0.492 Angle : 0.979 8.751 66852 Z= 0.536 Chirality : 0.055 0.250 7560 Planarity : 0.004 0.027 8676 Dihedral : 14.139 75.518 20628 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 1.19 % Allowed : 2.38 % Favored : 96.43 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.47 (0.06), residues: 6048 helix: -4.27 (0.04), residues: 5076 sheet: None (None), residues: 0 loop : -2.20 (0.16), residues: 972 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1721 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1685 time to evaluate : 6.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 2 residues processed: 1700 average time/residue: 0.6763 time to fit residues: 1813.2205 Evaluate side-chains 1079 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1077 time to evaluate : 6.570 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4161 time to fit residues: 10.8683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 516 optimal weight: 7.9990 chunk 463 optimal weight: 5.9990 chunk 257 optimal weight: 0.9980 chunk 158 optimal weight: 40.0000 chunk 312 optimal weight: 6.9990 chunk 247 optimal weight: 2.9990 chunk 479 optimal weight: 6.9990 chunk 185 optimal weight: 0.0000 chunk 291 optimal weight: 0.9990 chunk 357 optimal weight: 0.6980 chunk 555 optimal weight: 4.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 ASN B 99 ASN C 27 ASN C 99 ASN D 42 GLN D 72 ASN E 103 ASN ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 ASN G 74 GLN G 99 ASN H 43 ASN I 27 ASN J 30 ASN K 27 ASN ** K 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 99 ASN L 42 GLN L 43 ASN L 72 ASN L 74 GLN L 123 GLN L 126 ASN M 27 ASN M 42 GLN N 99 ASN O 27 ASN O 99 ASN P 27 ASN P 42 GLN P 43 ASN P 72 ASN P 123 GLN Q 42 GLN Q 99 ASN S 27 ASN S 42 GLN T 27 ASN T 42 GLN T 43 ASN T 72 ASN T 103 ASN V 30 ASN ** W 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 99 ASN X 27 ASN X 43 ASN X 126 ASN Y 42 GLN Z 99 ASN ** 0 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 70 GLN 0 99 ASN 1 43 ASN 1 84 GLN 2 27 ASN 2 42 GLN ** 3 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 99 ASN ** 4 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 99 ASN 5 42 GLN 5 43 ASN 5 72 ASN 8 27 ASN 9 43 ASN 9 126 ASN Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.2943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 50040 Z= 0.197 Angle : 0.645 7.973 66852 Z= 0.347 Chirality : 0.041 0.200 7560 Planarity : 0.005 0.040 8676 Dihedral : 5.210 21.379 6804 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.96 % Allowed : 2.51 % Favored : 96.53 % Rotamer Outliers : 1.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.44 (0.09), residues: 6048 helix: -2.08 (0.06), residues: 5148 sheet: None (None), residues: 0 loop : -1.87 (0.17), residues: 900 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1347 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1245 time to evaluate : 6.314 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 102 outliers final: 59 residues processed: 1291 average time/residue: 0.5754 time to fit residues: 1240.0155 Evaluate side-chains 1062 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1003 time to evaluate : 6.655 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 0 residues processed: 59 average time/residue: 0.4175 time to fit residues: 55.4978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 308 optimal weight: 0.8980 chunk 172 optimal weight: 5.9990 chunk 462 optimal weight: 10.0000 chunk 378 optimal weight: 10.0000 chunk 153 optimal weight: 0.7980 chunk 556 optimal weight: 0.0770 chunk 601 optimal weight: 50.0000 chunk 495 optimal weight: 2.9990 chunk 552 optimal weight: 5.9990 chunk 189 optimal weight: 1.9990 chunk 446 optimal weight: 7.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN B 42 GLN A 42 GLN ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 43 ASN E 27 ASN ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 27 ASN H 27 ASN I 42 GLN ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN L 27 ASN N 27 ASN N 42 GLN ** N 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 126 ASN P 16 GLN Q 27 ASN R 42 GLN S 27 ASN T 42 GLN T 84 GLN T 103 ASN U 27 ASN U 30 ASN U 42 GLN V 27 ASN V 42 GLN W 27 ASN X 16 GLN ** X 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 GLN Y 84 GLN Z 99 ASN 0 27 ASN 0 70 GLN 1 27 ASN 1 123 GLN 3 27 ASN ** 3 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 27 ASN ** 5 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 123 GLN 6 27 ASN 6 72 ASN 8 27 ASN 8 84 GLN 9 123 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 50040 Z= 0.179 Angle : 0.553 7.707 66852 Z= 0.295 Chirality : 0.040 0.151 7560 Planarity : 0.003 0.030 8676 Dihedral : 4.714 18.168 6804 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.66 % Allowed : 2.89 % Favored : 96.45 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.90 (0.10), residues: 6048 helix: -0.99 (0.07), residues: 5112 sheet: None (None), residues: 0 loop : -1.64 (0.17), residues: 936 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1217 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1109 time to evaluate : 6.313 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 108 outliers final: 54 residues processed: 1168 average time/residue: 0.5545 time to fit residues: 1103.0641 Evaluate side-chains 1046 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 992 time to evaluate : 6.425 Switching outliers to nearest non-outliers outliers start: 54 outliers final: 0 residues processed: 54 average time/residue: 0.4238 time to fit residues: 52.5078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 550 optimal weight: 30.0000 chunk 418 optimal weight: 8.9990 chunk 288 optimal weight: 0.4980 chunk 61 optimal weight: 2.9990 chunk 265 optimal weight: 7.9990 chunk 373 optimal weight: 8.9990 chunk 558 optimal weight: 0.7980 chunk 591 optimal weight: 8.9990 chunk 291 optimal weight: 0.6980 chunk 529 optimal weight: 0.8980 chunk 159 optimal weight: 30.0000 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 72 ASN D 72 ASN E 43 ASN I 123 GLN ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 27 ASN N 103 ASN O 72 ASN ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 27 ASN Q 43 ASN R 103 ASN S 27 ASN U 43 ASN ** W 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 27 ASN X 123 GLN Z 42 GLN Z 72 ASN Z 99 ASN Z 103 ASN 0 27 ASN 0 70 GLN 0 84 GLN 1 16 GLN 3 42 GLN 3 72 ASN 4 16 GLN 5 84 GLN 6 43 ASN 7 72 ASN 9 123 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.3859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 50040 Z= 0.163 Angle : 0.528 8.334 66852 Z= 0.279 Chirality : 0.040 0.175 7560 Planarity : 0.002 0.033 8676 Dihedral : 4.399 16.649 6804 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.61 % Allowed : 2.93 % Favored : 96.46 % Rotamer Outliers : 2.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.10), residues: 6048 helix: -0.34 (0.07), residues: 5112 sheet: None (None), residues: 0 loop : -1.43 (0.18), residues: 936 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1214 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 1083 time to evaluate : 6.434 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 131 outliers final: 64 residues processed: 1169 average time/residue: 0.5534 time to fit residues: 1101.8985 Evaluate side-chains 1079 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1015 time to evaluate : 6.476 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 0 residues processed: 64 average time/residue: 0.4262 time to fit residues: 59.9083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 492 optimal weight: 4.9990 chunk 335 optimal weight: 6.9990 chunk 8 optimal weight: 3.9990 chunk 440 optimal weight: 0.0370 chunk 244 optimal weight: 8.9990 chunk 504 optimal weight: 3.9990 chunk 408 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 302 optimal weight: 0.0270 chunk 530 optimal weight: 6.9990 chunk 149 optimal weight: 0.6980 overall best weight: 1.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 43 ASN C 27 ASN C 72 ASN D 72 ASN ** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 GLN G 27 ASN G 74 GLN G 126 ASN H 104 GLN I 43 ASN ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 123 GLN L 126 ASN M 43 ASN N 27 ASN N 103 ASN O 27 ASN O 72 ASN ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 103 ASN ** T 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 27 ASN W 27 ASN W 99 ASN X 99 ASN X 123 GLN Y 43 ASN Z 99 ASN 0 70 GLN 1 123 GLN 2 43 ASN 5 126 ASN 7 42 GLN 8 27 ASN 9 123 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.4065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.074 50040 Z= 0.195 Angle : 0.534 9.346 66852 Z= 0.281 Chirality : 0.041 0.204 7560 Planarity : 0.002 0.026 8676 Dihedral : 4.253 17.844 6804 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.61 % Allowed : 3.08 % Favored : 96.31 % Rotamer Outliers : 1.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.10), residues: 6048 helix: 0.10 (0.07), residues: 5112 sheet: None (None), residues: 0 loop : -1.32 (0.18), residues: 936 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1152 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1061 time to evaluate : 6.498 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 41 residues processed: 1119 average time/residue: 0.5894 time to fit residues: 1124.7372 Evaluate side-chains 1033 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 992 time to evaluate : 6.367 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.4421 time to fit residues: 43.7730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 199 optimal weight: 3.9990 chunk 532 optimal weight: 9.9990 chunk 116 optimal weight: 0.0870 chunk 347 optimal weight: 3.9990 chunk 146 optimal weight: 7.9990 chunk 592 optimal weight: 0.0040 chunk 491 optimal weight: 0.0040 chunk 274 optimal weight: 2.9990 chunk 49 optimal weight: 0.0060 chunk 195 optimal weight: 1.9990 chunk 310 optimal weight: 30.0000 overall best weight: 0.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 72 ASN D 72 ASN ** D 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 16 GLN G 126 ASN ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 103 ASN ** K 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN ** L 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 103 ASN O 84 GLN ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 27 ASN T 123 GLN V 27 ASN W 27 ASN X 16 GLN X 123 GLN Y 16 GLN Z 99 ASN 0 27 ASN 0 70 GLN 1 16 GLN 1 123 GLN 3 103 ASN 4 27 ASN 6 123 GLN 8 27 ASN 9 72 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.4376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.055 50040 Z= 0.132 Angle : 0.511 9.705 66852 Z= 0.267 Chirality : 0.039 0.254 7560 Planarity : 0.002 0.056 8676 Dihedral : 4.062 16.495 6804 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.61 % Allowed : 2.86 % Favored : 96.53 % Rotamer Outliers : 1.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.11), residues: 6048 helix: 0.52 (0.07), residues: 5148 sheet: None (None), residues: 0 loop : -1.08 (0.19), residues: 900 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1195 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 1116 time to evaluate : 6.696 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 33 residues processed: 1159 average time/residue: 0.5500 time to fit residues: 1082.5967 Evaluate side-chains 1056 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1023 time to evaluate : 6.466 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.4391 time to fit residues: 36.1293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 570 optimal weight: 0.5980 chunk 66 optimal weight: 0.0000 chunk 337 optimal weight: 0.9990 chunk 432 optimal weight: 10.0000 chunk 335 optimal weight: 7.9990 chunk 498 optimal weight: 4.9990 chunk 330 optimal weight: 2.9990 chunk 589 optimal weight: 1.9990 chunk 369 optimal weight: 9.9990 chunk 359 optimal weight: 0.9990 chunk 272 optimal weight: 0.3980 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN C 42 GLN E 16 GLN F 103 ASN G 16 GLN G 27 ASN G 126 ASN H 104 GLN ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 16 GLN L 123 GLN ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 27 ASN T 123 GLN V 27 ASN W 27 ASN X 27 ASN X 72 ASN X 104 GLN X 123 GLN ** Y 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 99 ASN 0 27 ASN 1 16 GLN 1 123 GLN 3 72 ASN ** 5 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 123 GLN 6 16 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8023 moved from start: 0.4537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 50040 Z= 0.135 Angle : 0.514 10.716 66852 Z= 0.268 Chirality : 0.039 0.171 7560 Planarity : 0.002 0.029 8676 Dihedral : 3.979 16.287 6804 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.63 % Allowed : 2.88 % Favored : 96.49 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.11), residues: 6048 helix: 0.87 (0.07), residues: 5112 sheet: None (None), residues: 0 loop : -1.00 (0.19), residues: 936 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1137 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1073 time to evaluate : 6.776 Fit side-chains revert: symmetry clash outliers start: 64 outliers final: 36 residues processed: 1103 average time/residue: 0.5449 time to fit residues: 1028.9409 Evaluate side-chains 1049 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1013 time to evaluate : 6.348 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.4468 time to fit residues: 38.5682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 364 optimal weight: 8.9990 chunk 235 optimal weight: 0.0570 chunk 352 optimal weight: 4.9990 chunk 177 optimal weight: 7.9990 chunk 115 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 375 optimal weight: 0.5980 chunk 401 optimal weight: 4.9990 chunk 291 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 463 optimal weight: 0.6980 overall best weight: 1.0500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 99 ASN A 103 ASN ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN C 72 ASN E 16 GLN F 103 ASN G 126 ASN H 104 GLN ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 123 GLN ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 42 GLN T 123 GLN V 27 ASN X 16 GLN X 72 ASN Y 16 GLN Z 99 ASN 0 70 GLN 1 16 GLN ** 1 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 16 GLN 4 27 ASN ** 5 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 123 GLN 8 27 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.056 50040 Z= 0.162 Angle : 0.537 10.439 66852 Z= 0.277 Chirality : 0.041 0.293 7560 Planarity : 0.002 0.056 8676 Dihedral : 3.960 14.028 6804 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.60 % Allowed : 2.94 % Favored : 96.46 % Rotamer Outliers : 0.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.11), residues: 6048 helix: 1.06 (0.07), residues: 5112 sheet: None (None), residues: 0 loop : -0.98 (0.19), residues: 936 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1085 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 1042 time to evaluate : 6.375 Fit side-chains revert: symmetry clash outliers start: 43 outliers final: 22 residues processed: 1065 average time/residue: 0.5492 time to fit residues: 996.8201 Evaluate side-chains 1037 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1015 time to evaluate : 6.684 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.4241 time to fit residues: 27.4564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 536 optimal weight: 0.7980 chunk 565 optimal weight: 1.9990 chunk 515 optimal weight: 20.0000 chunk 549 optimal weight: 7.9990 chunk 564 optimal weight: 5.9990 chunk 330 optimal weight: 10.0000 chunk 239 optimal weight: 3.9990 chunk 431 optimal weight: 8.9990 chunk 168 optimal weight: 7.9990 chunk 496 optimal weight: 6.9990 chunk 519 optimal weight: 0.0980 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN ** E 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 GLN G 27 ASN H 104 GLN ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 72 ASN J 103 ASN ** K 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN L 123 GLN N 103 ASN ** P 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 123 GLN S 16 GLN ** S 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 123 GLN W 27 ASN X 72 ASN X 123 GLN Z 99 ASN Z 103 ASN 0 27 ASN 0 70 GLN ** 1 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 123 GLN 3 103 ASN 4 27 ASN ** 5 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 123 GLN 5 126 ASN ** 6 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.4658 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 50040 Z= 0.254 Angle : 0.580 10.011 66852 Z= 0.300 Chirality : 0.043 0.273 7560 Planarity : 0.003 0.033 8676 Dihedral : 4.097 16.763 6804 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.64 % Allowed : 3.16 % Favored : 96.20 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.05 (0.11), residues: 6048 helix: 1.10 (0.07), residues: 5076 sheet: None (None), residues: 0 loop : -1.13 (0.19), residues: 972 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1063 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1031 time to evaluate : 6.566 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 15 residues processed: 1045 average time/residue: 0.5601 time to fit residues: 997.1933 Evaluate side-chains 1010 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 995 time to evaluate : 6.396 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.4660 time to fit residues: 21.9666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 547 optimal weight: 10.0000 chunk 360 optimal weight: 0.0670 chunk 581 optimal weight: 9.9990 chunk 354 optimal weight: 4.9990 chunk 275 optimal weight: 0.9980 chunk 404 optimal weight: 0.7980 chunk 609 optimal weight: 4.9990 chunk 561 optimal weight: 0.7980 chunk 485 optimal weight: 0.8980 chunk 50 optimal weight: 0.0670 chunk 375 optimal weight: 3.9990 overall best weight: 0.5256 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 42 GLN E 16 GLN F 72 ASN H 84 GLN ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 84 GLN ** K 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 99 ASN M 43 ASN N 103 ASN P 42 GLN ** S 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 27 ASN S 84 GLN T 123 GLN U 123 GLN X 16 GLN X 72 ASN ** X 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 123 GLN Z 99 ASN Z 103 ASN 0 70 GLN 1 16 GLN ** 1 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 123 GLN 6 16 GLN ** 7 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.4862 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 50040 Z= 0.144 Angle : 0.557 12.716 66852 Z= 0.285 Chirality : 0.040 0.200 7560 Planarity : 0.002 0.034 8676 Dihedral : 3.963 15.901 6804 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.63 % Allowed : 2.89 % Favored : 96.48 % Rotamer Outliers : 0.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.11), residues: 6048 helix: 1.28 (0.07), residues: 5076 sheet: None (None), residues: 0 loop : -1.02 (0.19), residues: 972 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12096 Ramachandran restraints generated. 6048 Oldfield, 0 Emsley, 6048 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1069 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1047 time to evaluate : 6.303 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 1056 average time/residue: 0.5648 time to fit residues: 1012.8060 Evaluate side-chains 1020 residues out of total 5616 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1008 time to evaluate : 6.362 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4331 time to fit residues: 18.4810 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 612 random chunks: chunk 297 optimal weight: 6.9990 chunk 385 optimal weight: 0.5980 chunk 517 optimal weight: 7.9990 chunk 148 optimal weight: 5.9990 chunk 447 optimal weight: 0.3980 chunk 71 optimal weight: 7.9990 chunk 134 optimal weight: 20.0000 chunk 486 optimal weight: 6.9990 chunk 203 optimal weight: 9.9990 chunk 499 optimal weight: 9.9990 chunk 61 optimal weight: 0.0770 overall best weight: 2.8142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 99 ASN E 16 GLN G 27 ASN H 104 GLN ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 27 ASN L 99 ASN N 103 ASN O 27 ASN ** P 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 123 GLN V 42 GLN X 72 ASN Z 99 ASN Z 103 ASN 0 27 ASN 0 70 GLN 1 72 ASN ** 1 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 123 GLN ** 5 42 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 16 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4239 r_free = 0.4239 target = 0.186342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.125212 restraints weight = 68922.627| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 3.03 r_work: 0.3418 rms_B_bonded: 2.78 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work: 0.3373 rms_B_bonded: 2.78 restraints_weight: 0.1250 r_work: 0.3346 rms_B_bonded: 2.89 restraints_weight: 0.0625 r_work: 0.3316 rms_B_bonded: 3.09 restraints_weight: 0.0312 r_work: 0.3280 rms_B_bonded: 3.38 restraints_weight: 0.0156 r_work: 0.3236 rms_B_bonded: 3.80 restraints_weight: 0.0078 r_work: 0.3181 rms_B_bonded: 4.42 restraints_weight: 0.0039 r_work (final): 0.3181 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8429 moved from start: 0.4834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.054 50040 Z= 0.274 Angle : 0.601 11.318 66852 Z= 0.309 Chirality : 0.043 0.239 7560 Planarity : 0.003 0.027 8676 Dihedral : 4.102 16.601 6804 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.63 % Allowed : 3.08 % Favored : 96.30 % Rotamer Outliers : 0.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.11), residues: 6048 helix: 1.23 (0.07), residues: 5076 sheet: None (None), residues: 0 loop : -1.02 (0.19), residues: 972 =============================================================================== Job complete usr+sys time: 15885.59 seconds wall clock time: 284 minutes 7.16 seconds (17047.16 seconds total)