Starting phenix.real_space_refine (version: dev) on Mon Feb 27 21:44:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xb1_6714/02_2023/5xb1_6714.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xb1_6714/02_2023/5xb1_6714.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xb1_6714/02_2023/5xb1_6714.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xb1_6714/02_2023/5xb1_6714.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xb1_6714/02_2023/5xb1_6714.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5xb1_6714/02_2023/5xb1_6714.pdb" } resolution = 3.0 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= 0.017 sd= 0.165 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 30847 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "B" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "C" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "D" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "E" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "F" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "G" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "H" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "I" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "J" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "K" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "L" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "M" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "N" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "O" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "P" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "Q" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "R" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "S" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "T" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "U" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "V" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "W" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "X" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1283 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 2, 'TRANS': 152} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "P" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "S" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "W" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 17.27, per 1000 atoms: 0.56 Number of scatterers: 30847 At special positions: 0 Unit cell: (132.744, 132.744, 132.744, 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 168 16.00 O 5959 8.00 N 5472 7.00 C 19248 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: 10.96 Conformation dependent library (CDL) restraints added in 4.1 seconds 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7200 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 0 sheets defined 76.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.60 Creating SS restraints... Processing helix chain 'A' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN A 22 " --> pdb=" O GLU A 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA A 31 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU A 36 " --> pdb=" O SER A 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER A 37 " --> pdb=" O TYR A 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 77 removed outlier: 3.737A pdb=" N HIS A 58 " --> pdb=" O LYS A 54 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG A 64 " --> pdb=" O SER A 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU A 65 " --> pdb=" O HIS A 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA A 67 " --> pdb=" O GLU A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 125 removed outlier: 3.508A pdb=" N ALA A 100 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU A 117 " --> pdb=" O GLN A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 158 removed outlier: 4.249A pdb=" N LEU A 139 " --> pdb=" O GLU A 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN A 140 " --> pdb=" O THR A 136 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU A 141 " --> pdb=" O HIS A 137 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP A 151 " --> pdb=" O LYS A 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN A 155 " --> pdb=" O ASP A 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN B 22 " --> pdb=" O GLU B 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA B 31 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 36 " --> pdb=" O SER B 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER B 37 " --> pdb=" O TYR B 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR B 40 " --> pdb=" O LEU B 36 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 77 removed outlier: 3.705A pdb=" N HIS B 58 " --> pdb=" O LYS B 54 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ARG B 64 " --> pdb=" O SER B 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU B 65 " --> pdb=" O HIS B 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 125 removed outlier: 3.515A pdb=" N ALA B 100 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU B 117 " --> pdb=" O GLN B 113 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 158 removed outlier: 4.249A pdb=" N LEU B 139 " --> pdb=" O GLU B 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN B 140 " --> pdb=" O THR B 136 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU B 141 " --> pdb=" O HIS B 137 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL B 143 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP B 151 " --> pdb=" O LYS B 147 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR B 154 " --> pdb=" O GLY B 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN B 155 " --> pdb=" O ASP B 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN C 22 " --> pdb=" O GLU C 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA C 31 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR C 33 " --> pdb=" O LEU C 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU C 36 " --> pdb=" O SER C 32 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER C 37 " --> pdb=" O TYR C 33 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR C 40 " --> pdb=" O LEU C 36 " (cutoff:3.500A) Processing helix chain 'C' and resid 49 through 77 removed outlier: 3.730A pdb=" N HIS C 58 " --> pdb=" O LYS C 54 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG C 64 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU C 65 " --> pdb=" O HIS C 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA C 67 " --> pdb=" O GLU C 63 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 125 removed outlier: 3.515A pdb=" N ALA C 100 " --> pdb=" O SER C 96 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU C 117 " --> pdb=" O GLN C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 159 removed outlier: 4.250A pdb=" N LEU C 139 " --> pdb=" O GLU C 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN C 140 " --> pdb=" O THR C 136 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU C 141 " --> pdb=" O HIS C 137 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL C 143 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP C 151 " --> pdb=" O LYS C 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR C 154 " --> pdb=" O GLY C 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN C 155 " --> pdb=" O ASP C 151 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET C 159 " --> pdb=" O ASN C 155 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN D 22 " --> pdb=" O GLU D 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA D 31 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR D 33 " --> pdb=" O LEU D 29 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU D 36 " --> pdb=" O SER D 32 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER D 37 " --> pdb=" O TYR D 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR D 40 " --> pdb=" O LEU D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 49 through 77 removed outlier: 3.731A pdb=" N HIS D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG D 64 " --> pdb=" O SER D 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU D 65 " --> pdb=" O HIS D 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA D 67 " --> pdb=" O GLU D 63 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 125 removed outlier: 3.511A pdb=" N ALA D 100 " --> pdb=" O SER D 96 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU D 117 " --> pdb=" O GLN D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 158 removed outlier: 4.249A pdb=" N LEU D 139 " --> pdb=" O GLU D 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN D 140 " --> pdb=" O THR D 136 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU D 141 " --> pdb=" O HIS D 137 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL D 143 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP D 151 " --> pdb=" O LYS D 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR D 154 " --> pdb=" O GLY D 150 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN D 155 " --> pdb=" O ASP D 151 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA E 31 " --> pdb=" O LEU E 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR E 33 " --> pdb=" O LEU E 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU E 36 " --> pdb=" O SER E 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER E 37 " --> pdb=" O TYR E 33 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR E 40 " --> pdb=" O LEU E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 49 through 77 removed outlier: 3.739A pdb=" N HIS E 58 " --> pdb=" O LYS E 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG E 64 " --> pdb=" O SER E 60 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU E 65 " --> pdb=" O HIS E 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA E 67 " --> pdb=" O GLU E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 125 removed outlier: 3.506A pdb=" N ALA E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU E 117 " --> pdb=" O GLN E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 159 removed outlier: 4.249A pdb=" N LEU E 139 " --> pdb=" O GLU E 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN E 140 " --> pdb=" O THR E 136 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLU E 141 " --> pdb=" O HIS E 137 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL E 143 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP E 151 " --> pdb=" O LYS E 147 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR E 154 " --> pdb=" O GLY E 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN E 155 " --> pdb=" O ASP E 151 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET E 159 " --> pdb=" O ASN E 155 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN F 22 " --> pdb=" O GLU F 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA F 31 " --> pdb=" O LEU F 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR F 33 " --> pdb=" O LEU F 29 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU F 36 " --> pdb=" O SER F 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER F 37 " --> pdb=" O TYR F 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR F 40 " --> pdb=" O LEU F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 77 removed outlier: 3.694A pdb=" N HIS F 58 " --> pdb=" O LYS F 54 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG F 64 " --> pdb=" O SER F 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU F 65 " --> pdb=" O HIS F 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 125 removed outlier: 3.518A pdb=" N ALA F 100 " --> pdb=" O SER F 96 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU F 117 " --> pdb=" O GLN F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 159 removed outlier: 4.249A pdb=" N LEU F 139 " --> pdb=" O GLU F 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN F 140 " --> pdb=" O THR F 136 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU F 141 " --> pdb=" O HIS F 137 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL F 143 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP F 151 " --> pdb=" O LYS F 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR F 154 " --> pdb=" O GLY F 150 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN F 155 " --> pdb=" O ASP F 151 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET F 159 " --> pdb=" O ASN F 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN G 22 " --> pdb=" O GLU G 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA G 31 " --> pdb=" O LEU G 27 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR G 33 " --> pdb=" O LEU G 29 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU G 36 " --> pdb=" O SER G 32 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER G 37 " --> pdb=" O TYR G 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR G 40 " --> pdb=" O LEU G 36 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 77 removed outlier: 3.730A pdb=" N HIS G 58 " --> pdb=" O LYS G 54 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ARG G 64 " --> pdb=" O SER G 60 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU G 65 " --> pdb=" O HIS G 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA G 67 " --> pdb=" O GLU G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 125 removed outlier: 3.519A pdb=" N ALA G 100 " --> pdb=" O SER G 96 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU G 117 " --> pdb=" O GLN G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 158 removed outlier: 4.250A pdb=" N LEU G 139 " --> pdb=" O GLU G 135 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ASN G 140 " --> pdb=" O THR G 136 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU G 141 " --> pdb=" O HIS G 137 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL G 143 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP G 151 " --> pdb=" O LYS G 147 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR G 154 " --> pdb=" O GLY G 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN G 155 " --> pdb=" O ASP G 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN H 22 " --> pdb=" O GLU H 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA H 31 " --> pdb=" O LEU H 27 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR H 33 " --> pdb=" O LEU H 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU H 36 " --> pdb=" O SER H 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER H 37 " --> pdb=" O TYR H 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR H 40 " --> pdb=" O LEU H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 49 through 77 removed outlier: 3.751A pdb=" N HIS H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG H 64 " --> pdb=" O SER H 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU H 65 " --> pdb=" O HIS H 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA H 67 " --> pdb=" O GLU H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 125 removed outlier: 3.505A pdb=" N ALA H 100 " --> pdb=" O SER H 96 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU H 117 " --> pdb=" O GLN H 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 159 removed outlier: 4.250A pdb=" N LEU H 139 " --> pdb=" O GLU H 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN H 140 " --> pdb=" O THR H 136 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N GLU H 141 " --> pdb=" O HIS H 137 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL H 143 " --> pdb=" O LEU H 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP H 151 " --> pdb=" O LYS H 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR H 154 " --> pdb=" O GLY H 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN H 155 " --> pdb=" O ASP H 151 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET H 159 " --> pdb=" O ASN H 155 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN I 22 " --> pdb=" O GLU I 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA I 31 " --> pdb=" O LEU I 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR I 33 " --> pdb=" O LEU I 29 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU I 36 " --> pdb=" O SER I 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER I 37 " --> pdb=" O TYR I 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR I 40 " --> pdb=" O LEU I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 77 removed outlier: 3.675A pdb=" N HIS I 58 " --> pdb=" O LYS I 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG I 64 " --> pdb=" O SER I 60 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU I 65 " --> pdb=" O HIS I 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA I 67 " --> pdb=" O GLU I 63 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 125 removed outlier: 3.519A pdb=" N ALA I 100 " --> pdb=" O SER I 96 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU I 117 " --> pdb=" O GLN I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 159 removed outlier: 4.250A pdb=" N LEU I 139 " --> pdb=" O GLU I 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN I 140 " --> pdb=" O THR I 136 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N GLU I 141 " --> pdb=" O HIS I 137 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL I 143 " --> pdb=" O LEU I 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP I 151 " --> pdb=" O LYS I 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR I 154 " --> pdb=" O GLY I 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN I 155 " --> pdb=" O ASP I 151 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET I 159 " --> pdb=" O ASN I 155 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN J 22 " --> pdb=" O GLU J 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA J 31 " --> pdb=" O LEU J 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR J 33 " --> pdb=" O LEU J 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU J 36 " --> pdb=" O SER J 32 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER J 37 " --> pdb=" O TYR J 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR J 40 " --> pdb=" O LEU J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 49 through 77 removed outlier: 3.736A pdb=" N HIS J 58 " --> pdb=" O LYS J 54 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG J 64 " --> pdb=" O SER J 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU J 65 " --> pdb=" O HIS J 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA J 67 " --> pdb=" O GLU J 63 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 125 removed outlier: 3.516A pdb=" N ALA J 100 " --> pdb=" O SER J 96 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLU J 117 " --> pdb=" O GLN J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 159 removed outlier: 4.249A pdb=" N LEU J 139 " --> pdb=" O GLU J 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN J 140 " --> pdb=" O THR J 136 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU J 141 " --> pdb=" O HIS J 137 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL J 143 " --> pdb=" O LEU J 139 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP J 151 " --> pdb=" O LYS J 147 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR J 154 " --> pdb=" O GLY J 150 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN J 155 " --> pdb=" O ASP J 151 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET J 159 " --> pdb=" O ASN J 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN K 22 " --> pdb=" O GLU K 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA K 31 " --> pdb=" O LEU K 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR K 33 " --> pdb=" O LEU K 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU K 36 " --> pdb=" O SER K 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER K 37 " --> pdb=" O TYR K 33 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR K 40 " --> pdb=" O LEU K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 49 through 77 removed outlier: 3.716A pdb=" N HIS K 58 " --> pdb=" O LYS K 54 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ARG K 64 " --> pdb=" O SER K 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU K 65 " --> pdb=" O HIS K 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA K 67 " --> pdb=" O GLU K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 125 removed outlier: 3.519A pdb=" N ALA K 100 " --> pdb=" O SER K 96 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU K 117 " --> pdb=" O GLN K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 158 removed outlier: 4.249A pdb=" N LEU K 139 " --> pdb=" O GLU K 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN K 140 " --> pdb=" O THR K 136 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU K 141 " --> pdb=" O HIS K 137 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL K 143 " --> pdb=" O LEU K 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP K 151 " --> pdb=" O LYS K 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR K 154 " --> pdb=" O GLY K 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN K 155 " --> pdb=" O ASP K 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN L 22 " --> pdb=" O GLU L 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA L 31 " --> pdb=" O LEU L 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR L 33 " --> pdb=" O LEU L 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU L 36 " --> pdb=" O SER L 32 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER L 37 " --> pdb=" O TYR L 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR L 40 " --> pdb=" O LEU L 36 " (cutoff:3.500A) Processing helix chain 'L' and resid 49 through 77 removed outlier: 3.686A pdb=" N HIS L 58 " --> pdb=" O LYS L 54 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG L 64 " --> pdb=" O SER L 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU L 65 " --> pdb=" O HIS L 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA L 67 " --> pdb=" O GLU L 63 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 125 removed outlier: 3.513A pdb=" N ALA L 100 " --> pdb=" O SER L 96 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N GLU L 117 " --> pdb=" O GLN L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 159 removed outlier: 4.250A pdb=" N LEU L 139 " --> pdb=" O GLU L 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN L 140 " --> pdb=" O THR L 136 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU L 141 " --> pdb=" O HIS L 137 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL L 143 " --> pdb=" O LEU L 139 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP L 151 " --> pdb=" O LYS L 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR L 154 " --> pdb=" O GLY L 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN L 155 " --> pdb=" O ASP L 151 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET L 159 " --> pdb=" O ASN L 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 40 removed outlier: 3.502A pdb=" N ASN M 22 " --> pdb=" O GLU M 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA M 31 " --> pdb=" O LEU M 27 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR M 33 " --> pdb=" O LEU M 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU M 36 " --> pdb=" O SER M 32 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER M 37 " --> pdb=" O TYR M 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR M 40 " --> pdb=" O LEU M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 49 through 77 removed outlier: 3.715A pdb=" N HIS M 58 " --> pdb=" O LYS M 54 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ARG M 64 " --> pdb=" O SER M 60 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU M 65 " --> pdb=" O HIS M 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA M 67 " --> pdb=" O GLU M 63 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 125 removed outlier: 3.522A pdb=" N ALA M 100 " --> pdb=" O SER M 96 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU M 117 " --> pdb=" O GLN M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 158 removed outlier: 4.249A pdb=" N LEU M 139 " --> pdb=" O GLU M 135 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ASN M 140 " --> pdb=" O THR M 136 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLU M 141 " --> pdb=" O HIS M 137 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VAL M 143 " --> pdb=" O LEU M 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP M 151 " --> pdb=" O LYS M 147 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR M 154 " --> pdb=" O GLY M 150 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN M 155 " --> pdb=" O ASP M 151 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN N 22 " --> pdb=" O GLU N 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA N 31 " --> pdb=" O LEU N 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR N 33 " --> pdb=" O LEU N 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU N 36 " --> pdb=" O SER N 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER N 37 " --> pdb=" O TYR N 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR N 40 " --> pdb=" O LEU N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 49 through 77 removed outlier: 3.726A pdb=" N HIS N 58 " --> pdb=" O LYS N 54 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG N 64 " --> pdb=" O SER N 60 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU N 65 " --> pdb=" O HIS N 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA N 67 " --> pdb=" O GLU N 63 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 125 removed outlier: 3.513A pdb=" N ALA N 100 " --> pdb=" O SER N 96 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU N 117 " --> pdb=" O GLN N 113 " (cutoff:3.500A) Processing helix chain 'N' and resid 127 through 159 removed outlier: 4.249A pdb=" N LEU N 139 " --> pdb=" O GLU N 135 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ASN N 140 " --> pdb=" O THR N 136 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N GLU N 141 " --> pdb=" O HIS N 137 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N VAL N 143 " --> pdb=" O LEU N 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP N 151 " --> pdb=" O LYS N 147 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR N 154 " --> pdb=" O GLY N 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN N 155 " --> pdb=" O ASP N 151 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET N 159 " --> pdb=" O ASN N 155 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN O 22 " --> pdb=" O GLU O 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA O 31 " --> pdb=" O LEU O 27 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR O 33 " --> pdb=" O LEU O 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU O 36 " --> pdb=" O SER O 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER O 37 " --> pdb=" O TYR O 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR O 40 " --> pdb=" O LEU O 36 " (cutoff:3.500A) Processing helix chain 'O' and resid 49 through 77 removed outlier: 3.615A pdb=" N HIS O 58 " --> pdb=" O LYS O 54 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG O 64 " --> pdb=" O SER O 60 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU O 65 " --> pdb=" O HIS O 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA O 67 " --> pdb=" O GLU O 63 " (cutoff:3.500A) Processing helix chain 'O' and resid 96 through 125 removed outlier: 3.518A pdb=" N ALA O 100 " --> pdb=" O SER O 96 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU O 117 " --> pdb=" O GLN O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 158 removed outlier: 4.249A pdb=" N LEU O 139 " --> pdb=" O GLU O 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN O 140 " --> pdb=" O THR O 136 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU O 141 " --> pdb=" O HIS O 137 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N VAL O 143 " --> pdb=" O LEU O 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP O 151 " --> pdb=" O LYS O 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR O 154 " --> pdb=" O GLY O 150 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN O 155 " --> pdb=" O ASP O 151 " (cutoff:3.500A) Processing helix chain 'P' and resid 14 through 40 removed outlier: 3.502A pdb=" N ASN P 22 " --> pdb=" O GLU P 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA P 31 " --> pdb=" O LEU P 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR P 33 " --> pdb=" O LEU P 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU P 36 " --> pdb=" O SER P 32 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER P 37 " --> pdb=" O TYR P 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR P 40 " --> pdb=" O LEU P 36 " (cutoff:3.500A) Processing helix chain 'P' and resid 49 through 77 removed outlier: 3.738A pdb=" N HIS P 58 " --> pdb=" O LYS P 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG P 64 " --> pdb=" O SER P 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU P 65 " --> pdb=" O HIS P 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA P 67 " --> pdb=" O GLU P 63 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 125 removed outlier: 3.514A pdb=" N ALA P 100 " --> pdb=" O SER P 96 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU P 117 " --> pdb=" O GLN P 113 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 159 removed outlier: 4.250A pdb=" N LEU P 139 " --> pdb=" O GLU P 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN P 140 " --> pdb=" O THR P 136 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU P 141 " --> pdb=" O HIS P 137 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL P 143 " --> pdb=" O LEU P 139 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP P 151 " --> pdb=" O LYS P 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR P 154 " --> pdb=" O GLY P 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN P 155 " --> pdb=" O ASP P 151 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET P 159 " --> pdb=" O ASN P 155 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN Q 22 " --> pdb=" O GLU Q 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA Q 31 " --> pdb=" O LEU Q 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR Q 33 " --> pdb=" O LEU Q 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU Q 36 " --> pdb=" O SER Q 32 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER Q 37 " --> pdb=" O TYR Q 33 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR Q 40 " --> pdb=" O LEU Q 36 " (cutoff:3.500A) Processing helix chain 'Q' and resid 49 through 77 removed outlier: 3.685A pdb=" N HIS Q 58 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG Q 64 " --> pdb=" O SER Q 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU Q 65 " --> pdb=" O HIS Q 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA Q 67 " --> pdb=" O GLU Q 63 " (cutoff:3.500A) Processing helix chain 'Q' and resid 96 through 125 removed outlier: 3.512A pdb=" N ALA Q 100 " --> pdb=" O SER Q 96 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLU Q 117 " --> pdb=" O GLN Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 159 removed outlier: 4.250A pdb=" N LEU Q 139 " --> pdb=" O GLU Q 135 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ASN Q 140 " --> pdb=" O THR Q 136 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLU Q 141 " --> pdb=" O HIS Q 137 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL Q 143 " --> pdb=" O LEU Q 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP Q 151 " --> pdb=" O LYS Q 147 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR Q 154 " --> pdb=" O GLY Q 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN Q 155 " --> pdb=" O ASP Q 151 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET Q 159 " --> pdb=" O ASN Q 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 40 removed outlier: 3.504A pdb=" N ASN R 22 " --> pdb=" O GLU R 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA R 31 " --> pdb=" O LEU R 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR R 33 " --> pdb=" O LEU R 29 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU R 36 " --> pdb=" O SER R 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER R 37 " --> pdb=" O TYR R 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR R 40 " --> pdb=" O LEU R 36 " (cutoff:3.500A) Processing helix chain 'R' and resid 49 through 77 removed outlier: 3.693A pdb=" N HIS R 58 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ARG R 64 " --> pdb=" O SER R 60 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU R 65 " --> pdb=" O HIS R 61 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ALA R 67 " --> pdb=" O GLU R 63 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 125 removed outlier: 3.519A pdb=" N ALA R 100 " --> pdb=" O SER R 96 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU R 117 " --> pdb=" O GLN R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 158 removed outlier: 4.249A pdb=" N LEU R 139 " --> pdb=" O GLU R 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN R 140 " --> pdb=" O THR R 136 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N GLU R 141 " --> pdb=" O HIS R 137 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL R 143 " --> pdb=" O LEU R 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP R 151 " --> pdb=" O LYS R 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR R 154 " --> pdb=" O GLY R 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN R 155 " --> pdb=" O ASP R 151 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN S 22 " --> pdb=" O GLU S 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA S 31 " --> pdb=" O LEU S 27 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TYR S 33 " --> pdb=" O LEU S 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU S 36 " --> pdb=" O SER S 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER S 37 " --> pdb=" O TYR S 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR S 40 " --> pdb=" O LEU S 36 " (cutoff:3.500A) Processing helix chain 'S' and resid 49 through 77 removed outlier: 3.690A pdb=" N HIS S 58 " --> pdb=" O LYS S 54 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG S 64 " --> pdb=" O SER S 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU S 65 " --> pdb=" O HIS S 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA S 67 " --> pdb=" O GLU S 63 " (cutoff:3.500A) Processing helix chain 'S' and resid 96 through 125 removed outlier: 3.515A pdb=" N ALA S 100 " --> pdb=" O SER S 96 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU S 117 " --> pdb=" O GLN S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 127 through 159 removed outlier: 4.249A pdb=" N LEU S 139 " --> pdb=" O GLU S 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN S 140 " --> pdb=" O THR S 136 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N GLU S 141 " --> pdb=" O HIS S 137 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL S 143 " --> pdb=" O LEU S 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP S 151 " --> pdb=" O LYS S 147 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR S 154 " --> pdb=" O GLY S 150 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN S 155 " --> pdb=" O ASP S 151 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET S 159 " --> pdb=" O ASN S 155 " (cutoff:3.500A) Processing helix chain 'T' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN T 22 " --> pdb=" O GLU T 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA T 31 " --> pdb=" O LEU T 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR T 33 " --> pdb=" O LEU T 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU T 36 " --> pdb=" O SER T 32 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N SER T 37 " --> pdb=" O TYR T 33 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR T 40 " --> pdb=" O LEU T 36 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 77 removed outlier: 3.738A pdb=" N HIS T 58 " --> pdb=" O LYS T 54 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG T 64 " --> pdb=" O SER T 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU T 65 " --> pdb=" O HIS T 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA T 67 " --> pdb=" O GLU T 63 " (cutoff:3.500A) Processing helix chain 'T' and resid 96 through 125 removed outlier: 3.514A pdb=" N ALA T 100 " --> pdb=" O SER T 96 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU T 117 " --> pdb=" O GLN T 113 " (cutoff:3.500A) Processing helix chain 'T' and resid 127 through 158 removed outlier: 4.250A pdb=" N LEU T 139 " --> pdb=" O GLU T 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN T 140 " --> pdb=" O THR T 136 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU T 141 " --> pdb=" O HIS T 137 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N VAL T 143 " --> pdb=" O LEU T 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP T 151 " --> pdb=" O LYS T 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR T 154 " --> pdb=" O GLY T 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN T 155 " --> pdb=" O ASP T 151 " (cutoff:3.500A) Processing helix chain 'U' and resid 14 through 40 removed outlier: 3.504A pdb=" N ASN U 22 " --> pdb=" O GLU U 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA U 31 " --> pdb=" O LEU U 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR U 33 " --> pdb=" O LEU U 29 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU U 36 " --> pdb=" O SER U 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER U 37 " --> pdb=" O TYR U 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR U 40 " --> pdb=" O LEU U 36 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 77 removed outlier: 3.722A pdb=" N HIS U 58 " --> pdb=" O LYS U 54 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG U 64 " --> pdb=" O SER U 60 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N GLU U 65 " --> pdb=" O HIS U 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA U 67 " --> pdb=" O GLU U 63 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 125 removed outlier: 3.508A pdb=" N ALA U 100 " --> pdb=" O SER U 96 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU U 117 " --> pdb=" O GLN U 113 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 159 removed outlier: 4.249A pdb=" N LEU U 139 " --> pdb=" O GLU U 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN U 140 " --> pdb=" O THR U 136 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLU U 141 " --> pdb=" O HIS U 137 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N VAL U 143 " --> pdb=" O LEU U 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP U 151 " --> pdb=" O LYS U 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR U 154 " --> pdb=" O GLY U 150 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN U 155 " --> pdb=" O ASP U 151 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET U 159 " --> pdb=" O ASN U 155 " (cutoff:3.500A) Processing helix chain 'V' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN V 22 " --> pdb=" O GLU V 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA V 31 " --> pdb=" O LEU V 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR V 33 " --> pdb=" O LEU V 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU V 36 " --> pdb=" O SER V 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER V 37 " --> pdb=" O TYR V 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR V 40 " --> pdb=" O LEU V 36 " (cutoff:3.500A) Processing helix chain 'V' and resid 49 through 77 removed outlier: 3.690A pdb=" N HIS V 58 " --> pdb=" O LYS V 54 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ARG V 64 " --> pdb=" O SER V 60 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU V 65 " --> pdb=" O HIS V 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA V 67 " --> pdb=" O GLU V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 96 through 125 removed outlier: 3.504A pdb=" N ALA V 100 " --> pdb=" O SER V 96 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLU V 117 " --> pdb=" O GLN V 113 " (cutoff:3.500A) Processing helix chain 'V' and resid 127 through 159 removed outlier: 4.249A pdb=" N LEU V 139 " --> pdb=" O GLU V 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN V 140 " --> pdb=" O THR V 136 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU V 141 " --> pdb=" O HIS V 137 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL V 143 " --> pdb=" O LEU V 139 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP V 151 " --> pdb=" O LYS V 147 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N THR V 154 " --> pdb=" O GLY V 150 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASN V 155 " --> pdb=" O ASP V 151 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET V 159 " --> pdb=" O ASN V 155 " (cutoff:3.500A) Processing helix chain 'W' and resid 14 through 40 removed outlier: 3.503A pdb=" N ASN W 22 " --> pdb=" O GLU W 18 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA W 31 " --> pdb=" O LEU W 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR W 33 " --> pdb=" O LEU W 29 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU W 36 " --> pdb=" O SER W 32 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER W 37 " --> pdb=" O TYR W 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR W 40 " --> pdb=" O LEU W 36 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 77 removed outlier: 3.721A pdb=" N HIS W 58 " --> pdb=" O LYS W 54 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ARG W 64 " --> pdb=" O SER W 60 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU W 65 " --> pdb=" O HIS W 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA W 67 " --> pdb=" O GLU W 63 " (cutoff:3.500A) Processing helix chain 'W' and resid 96 through 125 removed outlier: 3.508A pdb=" N ALA W 100 " --> pdb=" O SER W 96 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU W 117 " --> pdb=" O GLN W 113 " (cutoff:3.500A) Processing helix chain 'W' and resid 127 through 159 removed outlier: 4.250A pdb=" N LEU W 139 " --> pdb=" O GLU W 135 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ASN W 140 " --> pdb=" O THR W 136 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N GLU W 141 " --> pdb=" O HIS W 137 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL W 143 " --> pdb=" O LEU W 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP W 151 " --> pdb=" O LYS W 147 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N THR W 154 " --> pdb=" O GLY W 150 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN W 155 " --> pdb=" O ASP W 151 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET W 159 " --> pdb=" O ASN W 155 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 40 removed outlier: 3.502A pdb=" N ASN X 22 " --> pdb=" O GLU X 18 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA X 31 " --> pdb=" O LEU X 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR X 33 " --> pdb=" O LEU X 29 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU X 36 " --> pdb=" O SER X 32 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N SER X 37 " --> pdb=" O TYR X 33 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR X 40 " --> pdb=" O LEU X 36 " (cutoff:3.500A) Processing helix chain 'X' and resid 49 through 77 removed outlier: 3.693A pdb=" N HIS X 58 " --> pdb=" O LYS X 54 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG X 64 " --> pdb=" O SER X 60 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLU X 65 " --> pdb=" O HIS X 61 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALA X 67 " --> pdb=" O GLU X 63 " (cutoff:3.500A) Processing helix chain 'X' and resid 96 through 125 removed outlier: 3.515A pdb=" N ALA X 100 " --> pdb=" O SER X 96 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N GLU X 117 " --> pdb=" O GLN X 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 127 through 159 removed outlier: 4.250A pdb=" N LEU X 139 " --> pdb=" O GLU X 135 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ASN X 140 " --> pdb=" O THR X 136 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLU X 141 " --> pdb=" O HIS X 137 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL X 143 " --> pdb=" O LEU X 139 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP X 151 " --> pdb=" O LYS X 147 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N THR X 154 " --> pdb=" O GLY X 150 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ASN X 155 " --> pdb=" O ASP X 151 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET X 159 " --> pdb=" O ASN X 155 " (cutoff:3.500A) 1992 hydrogen bonds defined for protein. 5976 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: 8.59 Time building geometry restraints manager: 11.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10532 1.34 - 1.45: 4301 1.45 - 1.57: 16295 1.57 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 31392 Sorted by residual: bond pdb=" CB ARG B 64 " pdb=" CG ARG B 64 " ideal model delta sigma weight residual 1.520 1.429 0.091 3.00e-02 1.11e+03 9.14e+00 bond pdb=" CG ARG J 64 " pdb=" CD ARG J 64 " ideal model delta sigma weight residual 1.520 1.438 0.082 3.00e-02 1.11e+03 7.49e+00 bond pdb=" CG ARG G 64 " pdb=" CD ARG G 64 " ideal model delta sigma weight residual 1.520 1.443 0.077 3.00e-02 1.11e+03 6.66e+00 bond pdb=" CG ARG B 64 " pdb=" CD ARG B 64 " ideal model delta sigma weight residual 1.520 1.456 0.064 3.00e-02 1.11e+03 4.48e+00 bond pdb=" CG ARG N 64 " pdb=" CD ARG N 64 " ideal model delta sigma weight residual 1.520 1.459 0.061 3.00e-02 1.11e+03 4.13e+00 ... (remaining 31387 not shown) Histogram of bond angle deviations from ideal: 100.33 - 107.03: 588 107.03 - 113.72: 17409 113.72 - 120.42: 12630 120.42 - 127.12: 11277 127.12 - 133.82: 336 Bond angle restraints: 42240 Sorted by residual: angle pdb=" NE ARG J 64 " pdb=" CZ ARG J 64 " pdb=" NH1 ARG J 64 " ideal model delta sigma weight residual 121.50 115.95 5.55 1.00e+00 1.00e+00 3.08e+01 angle pdb=" NE ARG G 64 " pdb=" CZ ARG G 64 " pdb=" NH1 ARG G 64 " ideal model delta sigma weight residual 121.50 116.03 5.47 1.00e+00 1.00e+00 2.99e+01 angle pdb=" NE ARG N 64 " pdb=" CZ ARG N 64 " pdb=" NH1 ARG N 64 " ideal model delta sigma weight residual 121.50 116.96 4.54 1.00e+00 1.00e+00 2.06e+01 angle pdb=" C GLU B 63 " pdb=" N ARG B 64 " pdb=" CA ARG B 64 " ideal model delta sigma weight residual 122.06 113.99 8.07 1.86e+00 2.89e-01 1.88e+01 angle pdb=" CG ARG B 64 " pdb=" CD ARG B 64 " pdb=" NE ARG B 64 " ideal model delta sigma weight residual 112.00 102.89 9.11 2.20e+00 2.07e-01 1.71e+01 ... (remaining 42235 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.16: 18514 16.16 - 32.32: 291 32.32 - 48.48: 178 48.48 - 64.64: 49 64.64 - 80.80: 48 Dihedral angle restraints: 19080 sinusoidal: 7992 harmonic: 11088 Sorted by residual: dihedral pdb=" CA ASP P 151 " pdb=" C ASP P 151 " pdb=" N HIS P 152 " pdb=" CA HIS P 152 " ideal model delta harmonic sigma weight residual 180.00 157.48 22.52 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA ASP A 151 " pdb=" C ASP A 151 " pdb=" N HIS A 152 " pdb=" CA HIS A 152 " ideal model delta harmonic sigma weight residual 180.00 157.49 22.51 0 5.00e+00 4.00e-02 2.03e+01 dihedral pdb=" CA ASP R 151 " pdb=" C ASP R 151 " pdb=" N HIS R 152 " pdb=" CA HIS R 152 " ideal model delta harmonic sigma weight residual 180.00 157.49 22.51 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 19077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2808 0.042 - 0.084: 1359 0.084 - 0.126: 221 0.126 - 0.167: 50 0.167 - 0.209: 2 Chirality restraints: 4440 Sorted by residual: chirality pdb=" CA ASN I 140 " pdb=" N ASN I 140 " pdb=" C ASN I 140 " pdb=" CB ASN I 140 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" CA ASN H 140 " pdb=" N ASN H 140 " pdb=" C ASN H 140 " pdb=" CB ASN H 140 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CA GLU I 141 " pdb=" N GLU I 141 " pdb=" C GLU I 141 " pdb=" CB GLU I 141 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.68e-01 ... (remaining 4437 not shown) Planarity restraints: 5568 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR U 33 " -0.026 2.00e-02 2.50e+03 1.92e-02 7.40e+00 pdb=" CG TYR U 33 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR U 33 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR U 33 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR U 33 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR U 33 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR U 33 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR U 33 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR T 33 " -0.026 2.00e-02 2.50e+03 1.92e-02 7.38e+00 pdb=" CG TYR T 33 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR T 33 " -0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR T 33 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR T 33 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR T 33 " -0.003 2.00e-02 2.50e+03 pdb=" CZ TYR T 33 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR T 33 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR V 33 " 0.026 2.00e-02 2.50e+03 1.92e-02 7.38e+00 pdb=" CG TYR V 33 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR V 33 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR V 33 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR V 33 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR V 33 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR V 33 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR V 33 " 0.005 2.00e-02 2.50e+03 ... (remaining 5565 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1257 2.72 - 3.26: 30137 3.26 - 3.81: 44501 3.81 - 4.35: 64149 4.35 - 4.90: 105510 Nonbonded interactions: 245554 Sorted by model distance: nonbonded pdb=" OG SER B 7 " pdb=" OD2 ASP N 45 " model vdw 2.173 2.440 nonbonded pdb=" OG SER H 7 " pdb=" OD2 ASP T 45 " model vdw 2.173 2.440 nonbonded pdb=" OD2 ASP E 45 " pdb=" OG SER Q 7 " model vdw 2.177 2.440 nonbonded pdb=" OE1 GLU B 28 " pdb=" O HOH B 201 " model vdw 2.178 2.440 nonbonded pdb=" OE1 GLU D 28 " pdb=" O HOH D 201 " model vdw 2.187 2.440 ... (remaining 245549 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 19248 2.51 5 N 5472 2.21 5 O 5959 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: 0.170 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 3.810 Check model and map are aligned: 0.510 Process input model: 72.750 Find NCS groups from input model: 2.130 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Set scattering table: 0.270 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8789 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.091 31392 Z= 0.463 Angle : 0.712 9.107 42240 Z= 0.390 Chirality : 0.045 0.209 4440 Planarity : 0.004 0.037 5568 Dihedral : 10.819 80.801 11880 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -6.31 (0.08), residues: 3672 helix: -4.34 (0.04), residues: 2904 sheet: None (None), residues: 0 loop : -2.03 (0.20), residues: 768 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1192 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1192 time to evaluate : 3.942 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 1192 average time/residue: 1.8819 time to fit residues: 2538.2211 Evaluate side-chains 765 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 765 time to evaluate : 4.209 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.8654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 303 optimal weight: 10.0000 chunk 272 optimal weight: 7.9990 chunk 151 optimal weight: 6.9990 chunk 93 optimal weight: 6.9990 chunk 184 optimal weight: 5.9990 chunk 145 optimal weight: 0.4980 chunk 282 optimal weight: 7.9990 chunk 109 optimal weight: 2.9990 chunk 171 optimal weight: 0.7980 chunk 210 optimal weight: 0.0980 chunk 326 optimal weight: 10.0000 overall best weight: 2.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 GLN A 84 GLN ** B 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 24 GLN B 74 GLN B 84 GLN ** C 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN C 61 HIS C 74 GLN C 84 GLN ** D 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 24 GLN D 61 HIS D 74 GLN D 76 GLN D 84 GLN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 24 GLN E 74 GLN ** F 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 24 GLN F 74 GLN F 84 GLN ** G 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN G 61 HIS G 74 GLN ** H 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 74 GLN H 84 GLN ** I 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 24 GLN I 74 GLN I 76 GLN I 84 GLN J 11 GLN ** J 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 24 GLN J 61 HIS J 74 GLN J 84 GLN ** K 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 24 GLN K 74 GLN K 76 GLN K 84 GLN ** L 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 24 GLN L 74 GLN L 84 GLN ** M 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 24 GLN M 74 GLN M 84 GLN ** N 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 24 GLN N 74 GLN N 84 GLN ** O 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 24 GLN O 74 GLN O 84 GLN ** P 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 24 GLN P 61 HIS P 74 GLN P 84 GLN ** Q 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 24 GLN Q 74 GLN Q 84 GLN ** R 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 74 GLN R 84 GLN S 11 GLN ** S 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 24 GLN S 74 GLN S 84 GLN ** T 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 24 GLN T 74 GLN T 84 GLN ** U 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 24 GLN U 61 HIS U 74 GLN U 84 GLN ** V 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 GLN V 74 GLN V 84 GLN ** W 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 24 GLN W 74 GLN W 76 GLN W 84 GLN ** X 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 24 GLN X 74 GLN X 84 GLN Total number of N/Q/H flips: 79 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.017 31392 Z= 0.158 Angle : 0.490 3.607 42240 Z= 0.283 Chirality : 0.035 0.118 4440 Planarity : 0.005 0.031 5568 Dihedral : 4.650 20.841 4056 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 2.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer Outliers : 2.86 % 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: -1.55 (0.11), residues: 3672 helix: -0.72 (0.08), residues: 2880 sheet: None (None), residues: 0 loop : -1.58 (0.18), residues: 792 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 918 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 96 poor density : 822 time to evaluate : 4.220 Fit side-chains outliers start: 96 outliers final: 42 residues processed: 888 average time/residue: 1.8852 time to fit residues: 1896.7848 Evaluate side-chains 724 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 682 time to evaluate : 3.887 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 41 residues processed: 1 average time/residue: 0.4598 time to fit residues: 6.3518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 181 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 272 optimal weight: 10.0000 chunk 222 optimal weight: 9.9990 chunk 90 optimal weight: 20.0000 chunk 327 optimal weight: 9.9990 chunk 353 optimal weight: 20.0000 chunk 291 optimal weight: 1.9990 chunk 324 optimal weight: 20.0000 chunk 111 optimal weight: 10.0000 chunk 262 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN A 126 ASN B 84 GLN C 84 GLN D 84 GLN D 126 ASN E 126 ASN F 84 GLN F 126 ASN G 126 ASN H 84 GLN I 84 GLN J 84 GLN J 126 ASN K 84 GLN K 126 ASN L 84 GLN L 126 ASN M 11 GLN M 84 GLN N 84 GLN O 76 GLN O 84 GLN O 126 ASN P 84 GLN P 126 ASN Q 84 GLN R 84 GLN S 84 GLN S 126 ASN T 11 GLN T 84 GLN U 84 GLN U 126 ASN V 84 GLN V 126 ASN W 84 GLN W 126 ASN X 84 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8788 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.030 31392 Z= 0.343 Angle : 0.630 6.455 42240 Z= 0.341 Chirality : 0.042 0.126 4440 Planarity : 0.004 0.045 5568 Dihedral : 4.730 21.420 4056 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer Outliers : 2.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.13), residues: 3672 helix: 1.04 (0.09), residues: 2904 sheet: None (None), residues: 0 loop : -1.03 (0.20), residues: 768 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 526 time to evaluate : 4.143 Fit side-chains outliers start: 78 outliers final: 48 residues processed: 588 average time/residue: 2.4434 time to fit residues: 1589.1862 Evaluate side-chains 573 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 525 time to evaluate : 4.017 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 43 residues processed: 6 average time/residue: 1.6261 time to fit residues: 16.8174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 323 optimal weight: 20.0000 chunk 246 optimal weight: 3.9990 chunk 169 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 156 optimal weight: 2.9990 chunk 219 optimal weight: 0.9990 chunk 328 optimal weight: 10.0000 chunk 347 optimal weight: 9.9990 chunk 171 optimal weight: 10.0000 chunk 311 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN B 84 GLN C 84 GLN D 84 GLN F 84 GLN H 84 GLN I 84 GLN J 84 GLN K 84 GLN L 84 GLN M 84 GLN N 84 GLN O 84 GLN P 84 GLN Q 84 GLN R 84 GLN S 84 GLN T 84 GLN U 84 GLN U 126 ASN V 84 GLN V 126 ASN W 84 GLN X 84 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.4295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 31392 Z= 0.153 Angle : 0.429 3.269 42240 Z= 0.247 Chirality : 0.035 0.118 4440 Planarity : 0.003 0.023 5568 Dihedral : 4.247 18.632 4056 Min Nonbonded Distance : 2.199 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer Outliers : 2.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.40 (0.13), residues: 3672 helix: 2.15 (0.09), residues: 2904 sheet: None (None), residues: 0 loop : -0.60 (0.21), residues: 768 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 704 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 605 time to evaluate : 4.273 Fit side-chains outliers start: 99 outliers final: 60 residues processed: 692 average time/residue: 2.2327 time to fit residues: 1720.2961 Evaluate side-chains 616 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 556 time to evaluate : 3.799 Switching outliers to nearest non-outliers outliers start: 60 outliers final: 56 residues processed: 4 average time/residue: 2.0588 time to fit residues: 14.4016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 289 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 5 optimal weight: 8.9990 chunk 259 optimal weight: 6.9990 chunk 143 optimal weight: 0.0770 chunk 296 optimal weight: 1.9990 chunk 240 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 177 optimal weight: 9.9990 chunk 312 optimal weight: 2.9990 chunk 87 optimal weight: 9.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 84 GLN B 24 GLN B 84 GLN C 24 GLN C 84 GLN D 24 GLN D 84 GLN E 24 GLN E 126 ASN F 24 GLN F 84 GLN G 24 GLN H 84 GLN I 24 GLN I 84 GLN J 24 GLN J 84 GLN K 24 GLN K 84 GLN L 24 GLN L 84 GLN L 126 ASN M 24 GLN M 84 GLN N 24 GLN N 84 GLN O 24 GLN O 84 GLN P 24 GLN P 84 GLN Q 24 GLN Q 84 GLN R 84 GLN S 24 GLN S 84 GLN T 24 GLN T 84 GLN U 24 GLN U 84 GLN U 126 ASN V 24 GLN V 84 GLN V 126 ASN W 24 GLN W 84 GLN X 24 GLN X 84 GLN Total number of N/Q/H flips: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.4243 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 31392 Z= 0.188 Angle : 0.464 3.852 42240 Z= 0.261 Chirality : 0.036 0.119 4440 Planarity : 0.003 0.021 5568 Dihedral : 4.175 17.926 4056 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer Outliers : 3.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.13), residues: 3672 helix: 2.45 (0.09), residues: 2904 sheet: None (None), residues: 0 loop : -0.36 (0.22), residues: 768 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 559 time to evaluate : 3.969 Fit side-chains outliers start: 113 outliers final: 106 residues processed: 667 average time/residue: 2.2740 time to fit residues: 1684.5544 Evaluate side-chains 657 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 551 time to evaluate : 3.865 Switching outliers to nearest non-outliers outliers start: 106 outliers final: 101 residues processed: 5 average time/residue: 2.5740 time to fit residues: 19.5071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 117 optimal weight: 7.9990 chunk 313 optimal weight: 4.9990 chunk 68 optimal weight: 0.2980 chunk 204 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 348 optimal weight: 10.0000 chunk 289 optimal weight: 5.9990 chunk 161 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 115 optimal weight: 3.9990 chunk 182 optimal weight: 10.0000 overall best weight: 3.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN C 126 ASN D 84 GLN F 84 GLN F 126 ASN J 84 GLN J 126 ASN K 84 GLN K 126 ASN L 84 GLN M 84 GLN M 126 ASN P 84 GLN Q 84 GLN Q 126 ASN S 84 GLN T 84 GLN T 126 ASN V 84 GLN W 84 GLN X 84 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.4388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 31392 Z= 0.165 Angle : 0.431 3.790 42240 Z= 0.247 Chirality : 0.035 0.119 4440 Planarity : 0.002 0.020 5568 Dihedral : 4.056 16.945 4056 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 3.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer Outliers : 3.24 % 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: 3.25 (0.13), residues: 3672 helix: 2.74 (0.09), residues: 2904 sheet: None (None), residues: 0 loop : -0.26 (0.22), residues: 768 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 587 time to evaluate : 3.741 Fit side-chains outliers start: 109 outliers final: 105 residues processed: 691 average time/residue: 2.2916 time to fit residues: 1759.4997 Evaluate side-chains 687 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 582 time to evaluate : 3.870 Switching outliers to nearest non-outliers outliers start: 105 outliers final: 96 residues processed: 9 average time/residue: 0.9951 time to fit residues: 16.2710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 335 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 198 optimal weight: 1.9990 chunk 254 optimal weight: 4.9990 chunk 197 optimal weight: 8.9990 chunk 293 optimal weight: 8.9990 chunk 194 optimal weight: 7.9990 chunk 346 optimal weight: 9.9990 chunk 217 optimal weight: 20.0000 chunk 211 optimal weight: 6.9990 chunk 160 optimal weight: 5.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN G 126 ASN K 84 GLN L 84 GLN P 126 ASN Q 84 GLN T 84 GLN V 84 GLN W 84 GLN W 126 ASN X 84 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 31392 Z= 0.256 Angle : 0.524 4.831 42240 Z= 0.289 Chirality : 0.039 0.120 4440 Planarity : 0.003 0.034 5568 Dihedral : 4.210 18.358 4056 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 3.39 % 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: 2.93 (0.13), residues: 3672 helix: 2.49 (0.09), residues: 2904 sheet: None (None), residues: 0 loop : -0.29 (0.23), residues: 768 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 672 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 558 time to evaluate : 4.542 Fit side-chains outliers start: 114 outliers final: 106 residues processed: 660 average time/residue: 2.3219 time to fit residues: 1702.3065 Evaluate side-chains 665 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 559 time to evaluate : 4.127 Switching outliers to nearest non-outliers outliers start: 106 outliers final: 97 residues processed: 9 average time/residue: 1.9423 time to fit residues: 25.2937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 214 optimal weight: 7.9990 chunk 138 optimal weight: 10.0000 chunk 207 optimal weight: 7.9990 chunk 104 optimal weight: 9.9990 chunk 68 optimal weight: 0.9990 chunk 67 optimal weight: 4.9990 chunk 220 optimal weight: 2.9990 chunk 236 optimal weight: 0.9980 chunk 171 optimal weight: 9.9990 chunk 32 optimal weight: 9.9990 chunk 272 optimal weight: 10.0000 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN K 84 GLN L 84 GLN Q 84 GLN T 84 GLN U 126 ASN V 84 GLN V 126 ASN W 84 GLN X 84 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8728 moved from start: 0.4402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 31392 Z= 0.179 Angle : 0.448 3.925 42240 Z= 0.255 Chirality : 0.036 0.118 4440 Planarity : 0.002 0.019 5568 Dihedral : 4.061 17.701 4056 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer Outliers : 3.30 % 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: 3.28 (0.13), residues: 3672 helix: 2.75 (0.09), residues: 2904 sheet: None (None), residues: 0 loop : -0.21 (0.23), residues: 768 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 634 time to evaluate : 3.989 Fit side-chains outliers start: 111 outliers final: 95 residues processed: 742 average time/residue: 2.1435 time to fit residues: 1777.7962 Evaluate side-chains 714 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 619 time to evaluate : 4.104 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 93 residues processed: 2 average time/residue: 0.4550 time to fit residues: 7.1195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 315 optimal weight: 20.0000 chunk 332 optimal weight: 9.9990 chunk 303 optimal weight: 10.0000 chunk 323 optimal weight: 0.7980 chunk 194 optimal weight: 7.9990 chunk 140 optimal weight: 3.9990 chunk 253 optimal weight: 5.9990 chunk 99 optimal weight: 20.0000 chunk 292 optimal weight: 5.9990 chunk 305 optimal weight: 8.9990 chunk 322 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN D 126 ASN K 84 GLN L 84 GLN Q 84 GLN S 126 ASN V 84 GLN W 84 GLN X 84 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.4361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 31392 Z= 0.215 Angle : 0.489 4.320 42240 Z= 0.273 Chirality : 0.037 0.120 4440 Planarity : 0.003 0.029 5568 Dihedral : 4.092 17.826 4056 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer Outliers : 3.51 % 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: 3.20 (0.13), residues: 3672 helix: 2.69 (0.09), residues: 2904 sheet: None (None), residues: 0 loop : -0.22 (0.23), residues: 768 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 723 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 605 time to evaluate : 3.892 Fit side-chains outliers start: 118 outliers final: 100 residues processed: 715 average time/residue: 2.2219 time to fit residues: 1771.6645 Evaluate side-chains 700 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 600 time to evaluate : 4.127 Switching outliers to nearest non-outliers outliers start: 100 outliers final: 93 residues processed: 7 average time/residue: 1.9244 time to fit residues: 20.5845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 212 optimal weight: 10.0000 chunk 341 optimal weight: 3.9990 chunk 208 optimal weight: 7.9990 chunk 162 optimal weight: 6.9990 chunk 237 optimal weight: 0.3980 chunk 358 optimal weight: 4.9990 chunk 330 optimal weight: 20.0000 chunk 285 optimal weight: 20.0000 chunk 29 optimal weight: 9.9990 chunk 220 optimal weight: 10.0000 chunk 175 optimal weight: 4.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN K 84 GLN L 84 GLN Q 84 GLN V 84 GLN W 84 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 31392 Z= 0.205 Angle : 0.477 4.067 42240 Z= 0.268 Chirality : 0.037 0.119 4440 Planarity : 0.003 0.026 5568 Dihedral : 4.077 17.773 4056 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 2.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer Outliers : 3.33 % 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: 3.29 (0.13), residues: 3672 helix: 2.77 (0.09), residues: 2904 sheet: None (None), residues: 0 loop : -0.23 (0.23), residues: 768 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7344 Ramachandran restraints generated. 3672 Oldfield, 0 Emsley, 3672 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 609 time to evaluate : 4.197 Fit side-chains outliers start: 112 outliers final: 95 residues processed: 719 average time/residue: 2.2259 time to fit residues: 1786.9200 Evaluate side-chains 696 residues out of total 3360 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 601 time to evaluate : 3.920 Switching outliers to nearest non-outliers outliers start: 95 outliers final: 93 residues processed: 2 average time/residue: 0.4238 time to fit residues: 6.6134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 226 optimal weight: 4.9990 chunk 304 optimal weight: 3.9990 chunk 87 optimal weight: 0.9990 chunk 263 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 79 optimal weight: 10.0000 chunk 286 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 chunk 293 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 52 optimal weight: 6.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 GLN K 84 GLN L 84 GLN Q 84 GLN V 84 GLN W 84 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.148741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.139782 restraints weight = 30609.215| |-----------------------------------------------------------------------------| r_work (start): 0.3451 rms_B_bonded: 0.69 r_work: 0.3340 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 2.56 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.4444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 31392 Z= 0.179 Angle : 0.447 3.946 42240 Z= 0.255 Chirality : 0.036 0.118 4440 Planarity : 0.002 0.019 5568 Dihedral : 4.008 17.696 4056 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 3.36 % 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: 3.51 (0.13), residues: 3672 helix: 2.93 (0.09), residues: 2904 sheet: None (None), residues: 0 loop : -0.21 (0.23), residues: 768 =============================================================================== Job complete usr+sys time: 20757.01 seconds wall clock time: 365 minutes 33.72 seconds (21933.72 seconds total)