Starting phenix.real_space_refine on Fri Dec 8 22:49:47 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n09_9313/12_2023/6n09_9313.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n09_9313/12_2023/6n09_9313.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n09_9313/12_2023/6n09_9313.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n09_9313/12_2023/6n09_9313.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n09_9313/12_2023/6n09_9313.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6n09_9313/12_2023/6n09_9313.pdb" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 180 5.16 5 C 38205 2.51 5 N 10682 2.21 5 O 11258 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 115": "NH1" <-> "NH2" Residue "C TYR 120": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HA ARG 78": "NH1" <-> "NH2" Residue "I ARG 50": "NH1" <-> "NH2" Residue "I ARG 115": "NH1" <-> "NH2" Residue "J TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 199": "NH1" <-> "NH2" Residue "K ARG 70": "NH1" <-> "NH2" Residue "L ARG 99": "NH1" <-> "NH2" Residue "L TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 50": "NH1" <-> "NH2" Residue "O ARG 115": "NH1" <-> "NH2" Residue "P PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 199": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "Q TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 99": "NH1" <-> "NH2" Residue "R TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 50": "NH1" <-> "NH2" Residue "U ARG 115": "NH1" <-> "NH2" Residue "V ARG 199": "NH1" <-> "NH2" Residue "W ARG 70": "NH1" <-> "NH2" Residue "W TYR 172": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 99": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 60325 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "B" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "C" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "D" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "E" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "F" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1520 Classifications: {'peptide': 201} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 191} Chain: "GA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "GF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "HF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "ID" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "IF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "JF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "KF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LA" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LB" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LC" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LD" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LE" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "LF" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 658 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 4, 'TRANS': 87} Chain: "G" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "H" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1533 Classifications: {'peptide': 203} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 193} Chain: "I" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1533 Classifications: {'peptide': 203} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 193} Chain: "J" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1533 Classifications: {'peptide': 203} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 193} Chain: "K" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1520 Classifications: {'peptide': 201} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 191} Chain: "L" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1520 Classifications: {'peptide': 201} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 191} Chain: "M" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "N" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1533 Classifications: {'peptide': 203} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 193} Chain: "O" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1533 Classifications: {'peptide': 203} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 193} Chain: "P" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1533 Classifications: {'peptide': 203} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 193} Chain: "Q" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1520 Classifications: {'peptide': 201} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 191} Chain: "R" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1520 Classifications: {'peptide': 201} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 191} Chain: "S" Number of atoms: 1525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1525 Classifications: {'peptide': 202} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 192} Chain: "T" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1533 Classifications: {'peptide': 203} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 193} Chain: "U" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1533 Classifications: {'peptide': 203} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 193} Chain: "V" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1533 Classifications: {'peptide': 203} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 193} Chain: "W" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1520 Classifications: {'peptide': 201} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 191} Chain: "X" Number of atoms: 1520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1520 Classifications: {'peptide': 201} Link IDs: {'PCIS': 2, 'PTRANS': 7, 'TRANS': 191} Time building chain proxies: 22.79, per 1000 atoms: 0.38 Number of scatterers: 60325 At special positions: 0 Unit cell: (158.62, 294.58, 257.5, 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 180 16.00 O 11258 8.00 N 10682 7.00 C 38205 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: 18.26 Conformation dependent library (CDL) restraints added in 8.8 seconds 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14812 Finding SS restraints... Secondary structure from input PDB file: 291 helices and 84 sheets defined 44.2% alpha, 25.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.96 Creating SS restraints... Processing helix chain 'A' and resid 15 through 25 Processing helix chain 'A' and resid 48 through 59 removed outlier: 3.666A pdb=" N ASP A 53 " --> pdb=" O ASN A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 97 Processing helix chain 'A' and resid 118 through 128 removed outlier: 4.181A pdb=" N ILE A 124 " --> pdb=" O TYR A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 149 No H-bonds generated for 'chain 'A' and resid 147 through 149' Processing helix chain 'A' and resid 150 through 162 Processing helix chain 'A' and resid 183 through 199 Processing helix chain 'B' and resid 15 through 25 Processing helix chain 'B' and resid 47 through 59 Processing helix chain 'B' and resid 81 through 97 Processing helix chain 'B' and resid 118 through 128 removed outlier: 4.177A pdb=" N ILE B 124 " --> pdb=" O TYR B 120 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN B 128 " --> pdb=" O ILE B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 149 No H-bonds generated for 'chain 'B' and resid 147 through 149' Processing helix chain 'B' and resid 150 through 162 removed outlier: 3.746A pdb=" N ALA B 158 " --> pdb=" O ALA B 154 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ALA B 162 " --> pdb=" O ALA B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 199 removed outlier: 3.549A pdb=" N ARG B 199 " --> pdb=" O GLU B 195 " (cutoff:3.500A) Processing helix chain 'C' and resid 15 through 25 Processing helix chain 'C' and resid 47 through 59 Processing helix chain 'C' and resid 81 through 97 Processing helix chain 'C' and resid 118 through 128 removed outlier: 3.590A pdb=" N GLN C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ILE C 124 " --> pdb=" O TYR C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 149 No H-bonds generated for 'chain 'C' and resid 147 through 149' Processing helix chain 'C' and resid 150 through 162 removed outlier: 3.800A pdb=" N ALA C 158 " --> pdb=" O ALA C 154 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 199 removed outlier: 3.559A pdb=" N ARG C 199 " --> pdb=" O GLU C 195 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 25 Processing helix chain 'D' and resid 47 through 59 Processing helix chain 'D' and resid 81 through 97 removed outlier: 3.784A pdb=" N VAL D 85 " --> pdb=" O ASP D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 103 removed outlier: 3.889A pdb=" N ARG D 103 " --> pdb=" O GLU D 100 " (cutoff:3.500A) Processing helix chain 'D' and resid 118 through 126 removed outlier: 3.913A pdb=" N ILE D 124 " --> pdb=" O TYR D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 149 No H-bonds generated for 'chain 'D' and resid 147 through 149' Processing helix chain 'D' and resid 150 through 160 removed outlier: 3.774A pdb=" N ALA D 158 " --> pdb=" O ALA D 154 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 199 Processing helix chain 'E' and resid 15 through 25 Processing helix chain 'E' and resid 47 through 59 Processing helix chain 'E' and resid 81 through 97 removed outlier: 3.526A pdb=" N VAL E 85 " --> pdb=" O ASP E 81 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 103 removed outlier: 4.001A pdb=" N ARG E 103 " --> pdb=" O GLU E 100 " (cutoff:3.500A) Processing helix chain 'E' and resid 118 through 126 removed outlier: 3.915A pdb=" N ILE E 124 " --> pdb=" O TYR E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 149 No H-bonds generated for 'chain 'E' and resid 147 through 149' Processing helix chain 'E' and resid 150 through 161 removed outlier: 3.525A pdb=" N GLU E 157 " --> pdb=" O LEU E 153 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA E 158 " --> pdb=" O ALA E 154 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 199 Processing helix chain 'F' and resid 15 through 26 Processing helix chain 'F' and resid 44 through 46 No H-bonds generated for 'chain 'F' and resid 44 through 46' Processing helix chain 'F' and resid 47 through 59 Processing helix chain 'F' and resid 81 through 97 removed outlier: 3.549A pdb=" N VAL F 85 " --> pdb=" O ASP F 81 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 103 removed outlier: 3.992A pdb=" N ARG F 103 " --> pdb=" O GLU F 100 " (cutoff:3.500A) Processing helix chain 'F' and resid 118 through 126 removed outlier: 3.823A pdb=" N ILE F 124 " --> pdb=" O TYR F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 149 No H-bonds generated for 'chain 'F' and resid 147 through 149' Processing helix chain 'F' and resid 150 through 160 removed outlier: 3.627A pdb=" N ALA F 158 " --> pdb=" O ALA F 154 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 199 Processing helix chain 'GA' and resid 12 through 27 removed outlier: 3.752A pdb=" N VALGA 24 " --> pdb=" O ALAGA 20 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALAGA 27 " --> pdb=" O METGA 23 " (cutoff:3.500A) Processing helix chain 'GA' and resid 49 through 65 removed outlier: 3.962A pdb=" N ALAGA 55 " --> pdb=" O ALAGA 51 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ARGGA 62 " --> pdb=" O GLUGA 58 " (cutoff:3.500A) Processing helix chain 'GA' and resid 80 through 87 removed outlier: 3.550A pdb=" N ASPGA 84 " --> pdb=" O HISGA 80 " (cutoff:3.500A) Processing helix chain 'GB' and resid 12 through 27 removed outlier: 3.592A pdb=" N VALGB 24 " --> pdb=" O ALAGB 20 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALAGB 27 " --> pdb=" O METGB 23 " (cutoff:3.500A) Processing helix chain 'GB' and resid 49 through 65 removed outlier: 3.794A pdb=" N ALAGB 55 " --> pdb=" O ALAGB 51 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLUGB 58 " --> pdb=" O LYSGB 54 " (cutoff:3.500A) Processing helix chain 'GB' and resid 80 through 87 Processing helix chain 'GC' and resid 12 through 27 removed outlier: 3.826A pdb=" N VALGC 24 " --> pdb=" O ALAGC 20 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALAGC 27 " --> pdb=" O METGC 23 " (cutoff:3.500A) Processing helix chain 'GC' and resid 49 through 65 removed outlier: 3.521A pdb=" N ALAGC 55 " --> pdb=" O ALAGC 51 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLUGC 58 " --> pdb=" O LYSGC 54 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALAGC 59 " --> pdb=" O ALAGC 55 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARGGC 62 " --> pdb=" O GLUGC 58 " (cutoff:3.500A) Processing helix chain 'GC' and resid 80 through 87 removed outlier: 3.582A pdb=" N ALAGC 86 " --> pdb=" O ASNGC 82 " (cutoff:3.500A) Processing helix chain 'GD' and resid 12 through 26 removed outlier: 3.873A pdb=" N VALGD 24 " --> pdb=" O ALAGD 20 " (cutoff:3.500A) Processing helix chain 'GD' and resid 49 through 65 removed outlier: 3.612A pdb=" N GLUGD 58 " --> pdb=" O LYSGD 54 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARGGD 62 " --> pdb=" O GLUGD 58 " (cutoff:3.500A) Processing helix chain 'GD' and resid 80 through 87 removed outlier: 3.523A pdb=" N ASPGD 84 " --> pdb=" O HISGD 80 " (cutoff:3.500A) Processing helix chain 'GE' and resid 12 through 27 removed outlier: 3.638A pdb=" N ALAGE 27 " --> pdb=" O METGE 23 " (cutoff:3.500A) Processing helix chain 'GE' and resid 49 through 65 removed outlier: 4.064A pdb=" N GLUGE 58 " --> pdb=" O LYSGE 54 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ALAGE 59 " --> pdb=" O ALAGE 55 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARGGE 62 " --> pdb=" O GLUGE 58 " (cutoff:3.500A) Processing helix chain 'GE' and resid 80 through 87 Processing helix chain 'GF' and resid 12 through 27 removed outlier: 3.697A pdb=" N VALGF 24 " --> pdb=" O ALAGF 20 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ALAGF 27 " --> pdb=" O METGF 23 " (cutoff:3.500A) Processing helix chain 'GF' and resid 49 through 68 removed outlier: 3.671A pdb=" N LYSGF 54 " --> pdb=" O VALGF 50 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALAGF 55 " --> pdb=" O ALAGF 51 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N GLUGF 58 " --> pdb=" O LYSGF 54 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALAGF 59 " --> pdb=" O ALAGF 55 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ARGGF 62 " --> pdb=" O GLUGF 58 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARGGF 66 " --> pdb=" O ARGGF 62 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N VALGF 67 " --> pdb=" O ALAGF 63 " (cutoff:3.500A) Processing helix chain 'GF' and resid 80 through 87 Processing helix chain 'HA' and resid 12 through 27 removed outlier: 3.710A pdb=" N METHA 16 " --> pdb=" O GLYHA 12 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N VALHA 24 " --> pdb=" O ALAHA 20 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALAHA 27 " --> pdb=" O METHA 23 " (cutoff:3.500A) Processing helix chain 'HA' and resid 49 through 68 removed outlier: 3.599A pdb=" N ALAHA 55 " --> pdb=" O ALAHA 51 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N GLUHA 58 " --> pdb=" O LYSHA 54 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ARGHA 62 " --> pdb=" O GLUHA 58 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ARGHA 66 " --> pdb=" O ARGHA 62 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N VALHA 67 " --> pdb=" O ALAHA 63 " (cutoff:3.500A) Processing helix chain 'HA' and resid 80 through 87 Processing helix chain 'HB' and resid 12 through 27 removed outlier: 3.787A pdb=" N METHB 16 " --> pdb=" O GLYHB 12 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VALHB 24 " --> pdb=" O ALAHB 20 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALAHB 27 " --> pdb=" O METHB 23 " (cutoff:3.500A) Processing helix chain 'HB' and resid 49 through 68 removed outlier: 3.917A pdb=" N LYSHB 54 " --> pdb=" O VALHB 50 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N ALAHB 55 " --> pdb=" O ALAHB 51 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALAHB 59 " --> pdb=" O ALAHB 55 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ARGHB 62 " --> pdb=" O GLUHB 58 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARGHB 66 " --> pdb=" O ARGHB 62 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N VALHB 67 " --> pdb=" O ALAHB 63 " (cutoff:3.500A) Processing helix chain 'HB' and resid 80 through 87 Processing helix chain 'HC' and resid 12 through 27 removed outlier: 3.789A pdb=" N VALHC 24 " --> pdb=" O ALAHC 20 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALAHC 27 " --> pdb=" O METHC 23 " (cutoff:3.500A) Processing helix chain 'HC' and resid 49 through 65 removed outlier: 3.982A pdb=" N ALAHC 55 " --> pdb=" O ALAHC 51 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALAHC 59 " --> pdb=" O ALAHC 55 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ARGHC 62 " --> pdb=" O GLUHC 58 " (cutoff:3.500A) Processing helix chain 'HC' and resid 80 through 87 Processing helix chain 'HD' and resid 12 through 27 removed outlier: 3.607A pdb=" N VALHD 24 " --> pdb=" O ALAHD 20 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALAHD 27 " --> pdb=" O METHD 23 " (cutoff:3.500A) Processing helix chain 'HD' and resid 49 through 65 removed outlier: 3.978A pdb=" N ALAHD 55 " --> pdb=" O ALAHD 51 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLUHD 58 " --> pdb=" O LYSHD 54 " (cutoff:3.500A) Processing helix chain 'HD' and resid 80 through 87 Processing helix chain 'HE' and resid 12 through 27 removed outlier: 3.704A pdb=" N ALAHE 27 " --> pdb=" O METHE 23 " (cutoff:3.500A) Processing helix chain 'HE' and resid 49 through 65 removed outlier: 3.555A pdb=" N GLUHE 58 " --> pdb=" O LYSHE 54 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N ALAHE 59 " --> pdb=" O ALAHE 55 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARGHE 62 " --> pdb=" O GLUHE 58 " (cutoff:3.500A) Processing helix chain 'HE' and resid 80 through 87 Processing helix chain 'HF' and resid 12 through 27 removed outlier: 3.803A pdb=" N VALHF 24 " --> pdb=" O ALAHF 20 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALAHF 27 " --> pdb=" O METHF 23 " (cutoff:3.500A) Processing helix chain 'HF' and resid 49 through 65 removed outlier: 3.676A pdb=" N ALAHF 55 " --> pdb=" O ALAHF 51 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLUHF 58 " --> pdb=" O LYSHF 54 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ARGHF 62 " --> pdb=" O GLUHF 58 " (cutoff:3.500A) Processing helix chain 'HF' and resid 80 through 87 removed outlier: 3.584A pdb=" N ASPHF 84 " --> pdb=" O HISHF 80 " (cutoff:3.500A) Processing helix chain 'IA' and resid 12 through 27 removed outlier: 3.565A pdb=" N METIA 16 " --> pdb=" O GLYIA 12 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N VALIA 24 " --> pdb=" O ALAIA 20 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALAIA 27 " --> pdb=" O METIA 23 " (cutoff:3.500A) Processing helix chain 'IA' and resid 49 through 68 removed outlier: 4.033A pdb=" N ALAIA 55 " --> pdb=" O ALAIA 51 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N GLUIA 58 " --> pdb=" O LYSIA 54 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ARGIA 62 " --> pdb=" O GLUIA 58 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ARGIA 66 " --> pdb=" O ARGIA 62 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N VALIA 67 " --> pdb=" O ALAIA 63 " (cutoff:3.500A) Processing helix chain 'IA' and resid 80 through 87 removed outlier: 3.582A pdb=" N ASPIA 84 " --> pdb=" O HISIA 80 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALAIA 85 " --> pdb=" O VALIA 81 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALAIA 86 " --> pdb=" O ASNIA 82 " (cutoff:3.500A) Processing helix chain 'IB' and resid 12 through 27 removed outlier: 3.614A pdb=" N VALIB 24 " --> pdb=" O ALAIB 20 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALAIB 27 " --> pdb=" O METIB 23 " (cutoff:3.500A) Processing helix chain 'IB' and resid 49 through 65 removed outlier: 3.567A pdb=" N LYSIB 54 " --> pdb=" O VALIB 50 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ALAIB 55 " --> pdb=" O ALAIB 51 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLUIB 58 " --> pdb=" O LYSIB 54 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALAIB 59 " --> pdb=" O ALAIB 55 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARGIB 62 " --> pdb=" O GLUIB 58 " (cutoff:3.500A) Processing helix chain 'IB' and resid 80 through 87 removed outlier: 3.505A pdb=" N ASPIB 84 " --> pdb=" O HISIB 80 " (cutoff:3.500A) Processing helix chain 'IC' and resid 12 through 27 removed outlier: 3.849A pdb=" N VALIC 24 " --> pdb=" O ALAIC 20 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALAIC 27 " --> pdb=" O METIC 23 " (cutoff:3.500A) Processing helix chain 'IC' and resid 49 through 65 removed outlier: 3.926A pdb=" N ALAIC 55 " --> pdb=" O ALAIC 51 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLUIC 58 " --> pdb=" O LYSIC 54 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ALAIC 59 " --> pdb=" O ALAIC 55 " (cutoff:3.500A) Processing helix chain 'IC' and resid 80 through 87 Processing helix chain 'ID' and resid 12 through 27 removed outlier: 3.669A pdb=" N VALID 24 " --> pdb=" O ALAID 20 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALAID 27 " --> pdb=" O METID 23 " (cutoff:3.500A) Processing helix chain 'ID' and resid 49 through 65 removed outlier: 3.572A pdb=" N GLUID 58 " --> pdb=" O LYSID 54 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ARGID 62 " --> pdb=" O GLUID 58 " (cutoff:3.500A) Processing helix chain 'ID' and resid 80 through 87 removed outlier: 3.515A pdb=" N ASPID 84 " --> pdb=" O HISID 80 " (cutoff:3.500A) Processing helix chain 'IE' and resid 12 through 27 removed outlier: 3.554A pdb=" N VALIE 24 " --> pdb=" O ALAIE 20 " (cutoff:3.500A) Processing helix chain 'IE' and resid 49 through 65 removed outlier: 3.948A pdb=" N GLUIE 58 " --> pdb=" O LYSIE 54 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ARGIE 62 " --> pdb=" O GLUIE 58 " (cutoff:3.500A) Processing helix chain 'IE' and resid 80 through 87 Processing helix chain 'IF' and resid 12 through 27 removed outlier: 3.768A pdb=" N VALIF 24 " --> pdb=" O ALAIF 20 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALAIF 27 " --> pdb=" O METIF 23 " (cutoff:3.500A) Processing helix chain 'IF' and resid 49 through 65 removed outlier: 3.796A pdb=" N ALAIF 55 " --> pdb=" O ALAIF 51 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLUIF 58 " --> pdb=" O LYSIF 54 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ARGIF 62 " --> pdb=" O GLUIF 58 " (cutoff:3.500A) Processing helix chain 'IF' and resid 80 through 87 Processing helix chain 'JA' and resid 12 through 27 removed outlier: 3.618A pdb=" N VALJA 24 " --> pdb=" O ALAJA 20 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALAJA 27 " --> pdb=" O METJA 23 " (cutoff:3.500A) Processing helix chain 'JA' and resid 49 through 68 removed outlier: 3.881A pdb=" N ALAJA 55 " --> pdb=" O ALAJA 51 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLUJA 58 " --> pdb=" O LYSJA 54 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ARGJA 62 " --> pdb=" O GLUJA 58 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N ARGJA 66 " --> pdb=" O ARGJA 62 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VALJA 67 " --> pdb=" O ALAJA 63 " (cutoff:3.500A) Processing helix chain 'JA' and resid 80 through 87 Processing helix chain 'JB' and resid 12 through 27 removed outlier: 3.736A pdb=" N METJB 16 " --> pdb=" O GLYJB 12 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N VALJB 24 " --> pdb=" O ALAJB 20 " (cutoff:3.500A) Processing helix chain 'JB' and resid 49 through 65 removed outlier: 3.585A pdb=" N LYSJB 54 " --> pdb=" O VALJB 50 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ALAJB 55 " --> pdb=" O ALAJB 51 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLUJB 58 " --> pdb=" O LYSJB 54 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ALAJB 59 " --> pdb=" O ALAJB 55 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N ARGJB 62 " --> pdb=" O GLUJB 58 " (cutoff:3.500A) Processing helix chain 'JB' and resid 80 through 87 Processing helix chain 'JC' and resid 12 through 27 removed outlier: 3.758A pdb=" N VALJC 24 " --> pdb=" O ALAJC 20 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALAJC 27 " --> pdb=" O METJC 23 " (cutoff:3.500A) Processing helix chain 'JC' and resid 49 through 65 removed outlier: 4.025A pdb=" N ALAJC 55 " --> pdb=" O ALAJC 51 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALAJC 59 " --> pdb=" O ALAJC 55 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ARGJC 62 " --> pdb=" O GLUJC 58 " (cutoff:3.500A) Processing helix chain 'JC' and resid 80 through 87 Processing helix chain 'JD' and resid 12 through 27 removed outlier: 3.885A pdb=" N ALAJD 27 " --> pdb=" O METJD 23 " (cutoff:3.500A) Processing helix chain 'JD' and resid 49 through 65 removed outlier: 4.000A pdb=" N ALAJD 55 " --> pdb=" O ALAJD 51 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLUJD 58 " --> pdb=" O LYSJD 54 " (cutoff:3.500A) Processing helix chain 'JD' and resid 80 through 87 removed outlier: 3.529A pdb=" N ASPJD 84 " --> pdb=" O HISJD 80 " (cutoff:3.500A) Processing helix chain 'JE' and resid 12 through 27 removed outlier: 3.624A pdb=" N VALJE 24 " --> pdb=" O ALAJE 20 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALAJE 27 " --> pdb=" O METJE 23 " (cutoff:3.500A) Processing helix chain 'JE' and resid 49 through 65 removed outlier: 3.586A pdb=" N GLUJE 58 " --> pdb=" O LYSJE 54 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ALAJE 59 " --> pdb=" O ALAJE 55 " (cutoff:3.500A) Processing helix chain 'JE' and resid 80 through 87 Processing helix chain 'JF' and resid 12 through 27 removed outlier: 3.520A pdb=" N METJF 16 " --> pdb=" O GLYJF 12 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N VALJF 24 " --> pdb=" O ALAJF 20 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALAJF 27 " --> pdb=" O METJF 23 " (cutoff:3.500A) Processing helix chain 'JF' and resid 49 through 65 removed outlier: 3.844A pdb=" N ALAJF 55 " --> pdb=" O ALAJF 51 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLUJF 58 " --> pdb=" O LYSJF 54 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARGJF 62 " --> pdb=" O GLUJF 58 " (cutoff:3.500A) Processing helix chain 'JF' and resid 80 through 87 removed outlier: 3.552A pdb=" N ASPJF 84 " --> pdb=" O HISJF 80 " (cutoff:3.500A) Processing helix chain 'KA' and resid 12 through 27 removed outlier: 3.541A pdb=" N METKA 16 " --> pdb=" O GLYKA 12 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VALKA 24 " --> pdb=" O ALAKA 20 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALAKA 27 " --> pdb=" O METKA 23 " (cutoff:3.500A) Processing helix chain 'KA' and resid 49 through 68 removed outlier: 3.758A pdb=" N ALAKA 55 " --> pdb=" O ALAKA 51 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLUKA 58 " --> pdb=" O LYSKA 54 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ALAKA 59 " --> pdb=" O ALAKA 55 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N ARGKA 62 " --> pdb=" O GLUKA 58 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARGKA 66 " --> pdb=" O ARGKA 62 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N VALKA 67 " --> pdb=" O ALAKA 63 " (cutoff:3.500A) Processing helix chain 'KA' and resid 80 through 87 removed outlier: 3.518A pdb=" N ASPKA 84 " --> pdb=" O HISKA 80 " (cutoff:3.500A) Processing helix chain 'KB' and resid 12 through 27 removed outlier: 3.545A pdb=" N VALKB 24 " --> pdb=" O ALAKB 20 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALAKB 27 " --> pdb=" O METKB 23 " (cutoff:3.500A) Processing helix chain 'KB' and resid 49 through 65 removed outlier: 3.579A pdb=" N LYSKB 54 " --> pdb=" O VALKB 50 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLUKB 58 " --> pdb=" O LYSKB 54 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ALAKB 59 " --> pdb=" O ALAKB 55 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARGKB 62 " --> pdb=" O GLUKB 58 " (cutoff:3.500A) Processing helix chain 'KB' and resid 80 through 87 Processing helix chain 'KC' and resid 12 through 27 removed outlier: 3.855A pdb=" N VALKC 24 " --> pdb=" O ALAKC 20 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ALAKC 27 " --> pdb=" O METKC 23 " (cutoff:3.500A) Processing helix chain 'KC' and resid 49 through 65 removed outlier: 3.886A pdb=" N GLUKC 58 " --> pdb=" O LYSKC 54 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N ALAKC 59 " --> pdb=" O ALAKC 55 " (cutoff:3.500A) Processing helix chain 'KC' and resid 80 through 87 removed outlier: 3.956A pdb=" N ALAKC 85 " --> pdb=" O VALKC 81 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALAKC 86 " --> pdb=" O ASNKC 82 " (cutoff:3.500A) Processing helix chain 'KD' and resid 12 through 26 removed outlier: 3.920A pdb=" N VALKD 24 " --> pdb=" O ALAKD 20 " (cutoff:3.500A) Processing helix chain 'KD' and resid 49 through 55 removed outlier: 4.055A pdb=" N ALAKD 55 " --> pdb=" O ALAKD 51 " (cutoff:3.500A) Processing helix chain 'KD' and resid 56 through 68 removed outlier: 3.818A pdb=" N ARGKD 62 " --> pdb=" O GLUKD 58 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ARGKD 66 " --> pdb=" O ARGKD 62 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VALKD 67 " --> pdb=" O ALAKD 63 " (cutoff:3.500A) Processing helix chain 'KD' and resid 80 through 87 removed outlier: 3.584A pdb=" N ASPKD 84 " --> pdb=" O HISKD 80 " (cutoff:3.500A) Processing helix chain 'KE' and resid 12 through 27 removed outlier: 3.527A pdb=" N VALKE 24 " --> pdb=" O ALAKE 20 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALAKE 27 " --> pdb=" O METKE 23 " (cutoff:3.500A) Processing helix chain 'KE' and resid 49 through 65 removed outlier: 3.562A pdb=" N ALAKE 55 " --> pdb=" O ALAKE 51 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N GLUKE 58 " --> pdb=" O LYSKE 54 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALAKE 59 " --> pdb=" O ALAKE 55 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ARGKE 62 " --> pdb=" O GLUKE 58 " (cutoff:3.500A) Processing helix chain 'KE' and resid 80 through 87 Processing helix chain 'KF' and resid 12 through 27 removed outlier: 3.691A pdb=" N VALKF 24 " --> pdb=" O ALAKF 20 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALAKF 27 " --> pdb=" O METKF 23 " (cutoff:3.500A) Processing helix chain 'KF' and resid 49 through 65 removed outlier: 3.530A pdb=" N ALAKF 55 " --> pdb=" O ALAKF 51 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLUKF 58 " --> pdb=" O LYSKF 54 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARGKF 62 " --> pdb=" O GLUKF 58 " (cutoff:3.500A) Processing helix chain 'KF' and resid 80 through 87 Processing helix chain 'LA' and resid 12 through 27 removed outlier: 3.527A pdb=" N METLA 16 " --> pdb=" O GLYLA 12 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N VALLA 24 " --> pdb=" O ALALA 20 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALALA 27 " --> pdb=" O METLA 23 " (cutoff:3.500A) Processing helix chain 'LA' and resid 49 through 68 removed outlier: 4.236A pdb=" N GLULA 58 " --> pdb=" O LYSLA 54 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARGLA 62 " --> pdb=" O GLULA 58 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ARGLA 66 " --> pdb=" O ARGLA 62 " (cutoff:3.500A) removed outlier: 4.431A pdb=" N VALLA 67 " --> pdb=" O ALALA 63 " (cutoff:3.500A) Processing helix chain 'LA' and resid 80 through 87 Processing helix chain 'LB' and resid 12 through 26 removed outlier: 3.771A pdb=" N METLB 16 " --> pdb=" O GLYLB 12 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VALLB 24 " --> pdb=" O ALALB 20 " (cutoff:3.500A) Processing helix chain 'LB' and resid 49 through 65 removed outlier: 3.727A pdb=" N ALALB 55 " --> pdb=" O ALALB 51 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLULB 58 " --> pdb=" O LYSLB 54 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ARGLB 62 " --> pdb=" O GLULB 58 " (cutoff:3.500A) Processing helix chain 'LB' and resid 80 through 87 Processing helix chain 'LC' and resid 12 through 27 removed outlier: 3.766A pdb=" N VALLC 24 " --> pdb=" O ALALC 20 " (cutoff:3.500A) Processing helix chain 'LC' and resid 49 through 65 removed outlier: 3.634A pdb=" N LYSLC 54 " --> pdb=" O VALLC 50 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N ALALC 55 " --> pdb=" O ALALC 51 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLULC 58 " --> pdb=" O LYSLC 54 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALALC 59 " --> pdb=" O ALALC 55 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ARGLC 62 " --> pdb=" O GLULC 58 " (cutoff:3.500A) Processing helix chain 'LC' and resid 80 through 87 Processing helix chain 'LD' and resid 12 through 27 removed outlier: 3.545A pdb=" N VALLD 24 " --> pdb=" O ALALD 20 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALALD 27 " --> pdb=" O METLD 23 " (cutoff:3.500A) Processing helix chain 'LD' and resid 49 through 63 removed outlier: 4.017A pdb=" N ALALD 55 " --> pdb=" O ALALD 51 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N GLULD 58 " --> pdb=" O LYSLD 54 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARGLD 62 " --> pdb=" O GLULD 58 " (cutoff:3.500A) Processing helix chain 'LD' and resid 80 through 87 Processing helix chain 'LE' and resid 12 through 27 removed outlier: 3.619A pdb=" N VALLE 24 " --> pdb=" O ALALE 20 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALALE 27 " --> pdb=" O METLE 23 " (cutoff:3.500A) Processing helix chain 'LE' and resid 49 through 65 removed outlier: 3.637A pdb=" N GLULE 58 " --> pdb=" O LYSLE 54 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ALALE 59 " --> pdb=" O ALALE 55 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ARGLE 62 " --> pdb=" O GLULE 58 " (cutoff:3.500A) Processing helix chain 'LE' and resid 80 through 87 Processing helix chain 'LF' and resid 12 through 27 removed outlier: 3.683A pdb=" N VALLF 24 " --> pdb=" O ALALF 20 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ALALF 27 " --> pdb=" O METLF 23 " (cutoff:3.500A) Processing helix chain 'LF' and resid 49 through 68 removed outlier: 3.699A pdb=" N ALALF 55 " --> pdb=" O ALALF 51 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLULF 58 " --> pdb=" O LYSLF 54 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALALF 59 " --> pdb=" O ALALF 55 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ARGLF 62 " --> pdb=" O GLULF 58 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N ARGLF 66 " --> pdb=" O ARGLF 62 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VALLF 67 " --> pdb=" O ALALF 63 " (cutoff:3.500A) Processing helix chain 'LF' and resid 80 through 85 removed outlier: 3.561A pdb=" N ASPLF 84 " --> pdb=" O HISLF 80 " (cutoff:3.500A) Processing helix chain 'G' and resid 15 through 26 Processing helix chain 'G' and resid 47 through 59 removed outlier: 3.841A pdb=" N ASP G 53 " --> pdb=" O ASN G 49 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA G 54 " --> pdb=" O ARG G 50 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 97 Processing helix chain 'G' and resid 99 through 103 removed outlier: 3.559A pdb=" N GLY G 102 " --> pdb=" O ARG G 99 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ARG G 103 " --> pdb=" O GLU G 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 99 through 103' Processing helix chain 'G' and resid 118 through 128 removed outlier: 4.131A pdb=" N ILE G 124 " --> pdb=" O TYR G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 162 removed outlier: 4.227A pdb=" N LEU G 153 " --> pdb=" O GLY G 149 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ALA G 158 " --> pdb=" O ALA G 154 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU G 159 " --> pdb=" O ALA G 155 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 200 removed outlier: 3.545A pdb=" N SER G 200 " --> pdb=" O ALA G 196 " (cutoff:3.500A) Processing helix chain 'H' and resid 15 through 26 Processing helix chain 'H' and resid 47 through 59 removed outlier: 3.518A pdb=" N VAL H 51 " --> pdb=" O ALA H 47 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ASP H 53 " --> pdb=" O ASN H 49 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N ALA H 58 " --> pdb=" O ALA H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 96 Processing helix chain 'H' and resid 99 through 103 removed outlier: 3.644A pdb=" N GLY H 102 " --> pdb=" O ARG H 99 " (cutoff:3.500A) Processing helix chain 'H' and resid 118 through 129 removed outlier: 4.091A pdb=" N ILE H 124 " --> pdb=" O TYR H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 149 No H-bonds generated for 'chain 'H' and resid 147 through 149' Processing helix chain 'H' and resid 150 through 160 removed outlier: 3.892A pdb=" N ALA H 158 " --> pdb=" O ALA H 154 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 199 Processing helix chain 'I' and resid 15 through 26 Processing helix chain 'I' and resid 47 through 57 removed outlier: 3.635A pdb=" N ASP I 53 " --> pdb=" O ASN I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 96 Processing helix chain 'I' and resid 99 through 103 removed outlier: 3.551A pdb=" N GLY I 102 " --> pdb=" O ARG I 99 " (cutoff:3.500A) Processing helix chain 'I' and resid 118 through 128 removed outlier: 3.638A pdb=" N ILE I 124 " --> pdb=" O TYR I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 162 removed outlier: 4.245A pdb=" N LEU I 153 " --> pdb=" O GLY I 149 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA I 158 " --> pdb=" O ALA I 154 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 200 Processing helix chain 'J' and resid 15 through 26 Processing helix chain 'J' and resid 44 through 46 No H-bonds generated for 'chain 'J' and resid 44 through 46' Processing helix chain 'J' and resid 47 through 57 Processing helix chain 'J' and resid 81 through 97 Processing helix chain 'J' and resid 99 through 103 removed outlier: 3.727A pdb=" N ARG J 103 " --> pdb=" O GLU J 100 " (cutoff:3.500A) Processing helix chain 'J' and resid 118 through 128 removed outlier: 4.313A pdb=" N ILE J 124 " --> pdb=" O TYR J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 149 No H-bonds generated for 'chain 'J' and resid 147 through 149' Processing helix chain 'J' and resid 150 through 160 removed outlier: 3.876A pdb=" N ALA J 158 " --> pdb=" O ALA J 154 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 199 Processing helix chain 'K' and resid 15 through 26 Processing helix chain 'K' and resid 44 through 46 No H-bonds generated for 'chain 'K' and resid 44 through 46' Processing helix chain 'K' and resid 47 through 57 Processing helix chain 'K' and resid 81 through 96 removed outlier: 3.787A pdb=" N VAL K 85 " --> pdb=" O ASP K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 103 removed outlier: 3.621A pdb=" N ARG K 103 " --> pdb=" O GLU K 100 " (cutoff:3.500A) Processing helix chain 'K' and resid 118 through 128 removed outlier: 4.130A pdb=" N ILE K 124 " --> pdb=" O TYR K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 150 through 162 removed outlier: 3.832A pdb=" N ALA K 158 " --> pdb=" O ALA K 154 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 200 Processing helix chain 'L' and resid 15 through 26 Processing helix chain 'L' and resid 47 through 57 removed outlier: 4.029A pdb=" N ASP L 53 " --> pdb=" O ASN L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 97 removed outlier: 3.766A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 103 removed outlier: 3.503A pdb=" N GLY L 102 " --> pdb=" O ARG L 99 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG L 103 " --> pdb=" O GLU L 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 99 through 103' Processing helix chain 'L' and resid 118 through 128 removed outlier: 4.292A pdb=" N ILE L 124 " --> pdb=" O TYR L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 150 through 158 removed outlier: 3.771A pdb=" N ALA L 158 " --> pdb=" O ALA L 154 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 200 Processing helix chain 'M' and resid 15 through 26 Processing helix chain 'M' and resid 47 through 59 removed outlier: 3.534A pdb=" N VAL M 51 " --> pdb=" O ALA M 47 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP M 53 " --> pdb=" O ASN M 49 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA M 54 " --> pdb=" O ARG M 50 " (cutoff:3.500A) Processing helix chain 'M' and resid 81 through 96 Processing helix chain 'M' and resid 118 through 128 removed outlier: 3.803A pdb=" N ILE M 124 " --> pdb=" O TYR M 120 " (cutoff:3.500A) Processing helix chain 'M' and resid 149 through 162 removed outlier: 4.245A pdb=" N LEU M 153 " --> pdb=" O GLY M 149 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ALA M 158 " --> pdb=" O ALA M 154 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLU M 159 " --> pdb=" O ALA M 155 " (cutoff:3.500A) Processing helix chain 'M' and resid 183 through 200 Processing helix chain 'N' and resid 15 through 26 Processing helix chain 'N' and resid 47 through 59 removed outlier: 3.779A pdb=" N ASP N 53 " --> pdb=" O ASN N 49 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA N 58 " --> pdb=" O ALA N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 81 through 97 Processing helix chain 'N' and resid 99 through 103 removed outlier: 3.708A pdb=" N ARG N 103 " --> pdb=" O GLU N 100 " (cutoff:3.500A) Processing helix chain 'N' and resid 118 through 128 removed outlier: 4.074A pdb=" N ILE N 124 " --> pdb=" O TYR N 120 " (cutoff:3.500A) Processing helix chain 'N' and resid 150 through 162 removed outlier: 3.969A pdb=" N ALA N 158 " --> pdb=" O ALA N 154 " (cutoff:3.500A) Processing helix chain 'N' and resid 183 through 200 Processing helix chain 'O' and resid 15 through 26 Processing helix chain 'O' and resid 47 through 59 removed outlier: 3.509A pdb=" N VAL O 51 " --> pdb=" O ALA O 47 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N ASP O 53 " --> pdb=" O ASN O 49 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA O 58 " --> pdb=" O ALA O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 81 through 96 Processing helix chain 'O' and resid 99 through 103 removed outlier: 3.659A pdb=" N GLY O 102 " --> pdb=" O ARG O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 118 through 129 removed outlier: 3.923A pdb=" N ILE O 124 " --> pdb=" O TYR O 120 " (cutoff:3.500A) Processing helix chain 'O' and resid 149 through 162 removed outlier: 4.241A pdb=" N LEU O 153 " --> pdb=" O GLY O 149 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ALA O 158 " --> pdb=" O ALA O 154 " (cutoff:3.500A) Processing helix chain 'O' and resid 183 through 199 Processing helix chain 'P' and resid 15 through 26 Processing helix chain 'P' and resid 44 through 46 No H-bonds generated for 'chain 'P' and resid 44 through 46' Processing helix chain 'P' and resid 47 through 57 removed outlier: 3.579A pdb=" N ASP P 53 " --> pdb=" O ASN P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 81 through 97 removed outlier: 3.633A pdb=" N VAL P 85 " --> pdb=" O ASP P 81 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 103 removed outlier: 3.747A pdb=" N ARG P 103 " --> pdb=" O GLU P 100 " (cutoff:3.500A) Processing helix chain 'P' and resid 118 through 128 removed outlier: 4.273A pdb=" N ILE P 124 " --> pdb=" O TYR P 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 147 through 149 No H-bonds generated for 'chain 'P' and resid 147 through 149' Processing helix chain 'P' and resid 150 through 160 removed outlier: 3.977A pdb=" N ALA P 158 " --> pdb=" O ALA P 154 " (cutoff:3.500A) Processing helix chain 'P' and resid 183 through 199 Processing helix chain 'Q' and resid 15 through 26 Processing helix chain 'Q' and resid 44 through 46 No H-bonds generated for 'chain 'Q' and resid 44 through 46' Processing helix chain 'Q' and resid 47 through 59 removed outlier: 3.746A pdb=" N ALA Q 58 " --> pdb=" O ALA Q 54 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 97 Processing helix chain 'Q' and resid 99 through 103 removed outlier: 3.716A pdb=" N ARG Q 103 " --> pdb=" O GLU Q 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 118 through 128 removed outlier: 4.211A pdb=" N ILE Q 124 " --> pdb=" O TYR Q 120 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 162 removed outlier: 4.044A pdb=" N ALA Q 158 " --> pdb=" O ALA Q 154 " (cutoff:3.500A) Processing helix chain 'Q' and resid 183 through 199 Processing helix chain 'R' and resid 15 through 26 Processing helix chain 'R' and resid 44 through 46 No H-bonds generated for 'chain 'R' and resid 44 through 46' Processing helix chain 'R' and resid 47 through 57 Processing helix chain 'R' and resid 81 through 97 removed outlier: 3.724A pdb=" N VAL R 85 " --> pdb=" O ASP R 81 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 103 removed outlier: 3.614A pdb=" N ARG R 103 " --> pdb=" O GLU R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 118 through 128 Processing helix chain 'R' and resid 150 through 162 removed outlier: 3.815A pdb=" N ALA R 158 " --> pdb=" O ALA R 154 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLU R 159 " --> pdb=" O ALA R 155 " (cutoff:3.500A) Processing helix chain 'R' and resid 183 through 200 removed outlier: 3.607A pdb=" N ILE R 187 " --> pdb=" O SER R 183 " (cutoff:3.500A) Processing helix chain 'S' and resid 15 through 26 Processing helix chain 'S' and resid 47 through 57 removed outlier: 3.631A pdb=" N ASP S 53 " --> pdb=" O ASN S 49 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA S 54 " --> pdb=" O ARG S 50 " (cutoff:3.500A) Processing helix chain 'S' and resid 81 through 96 Processing helix chain 'S' and resid 118 through 128 removed outlier: 3.637A pdb=" N ILE S 124 " --> pdb=" O TYR S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 150 through 162 removed outlier: 3.674A pdb=" N ALA S 158 " --> pdb=" O ALA S 154 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N GLU S 159 " --> pdb=" O ALA S 155 " (cutoff:3.500A) Processing helix chain 'S' and resid 183 through 200 Processing helix chain 'T' and resid 15 through 25 Processing helix chain 'T' and resid 47 through 59 removed outlier: 3.714A pdb=" N ASP T 53 " --> pdb=" O ASN T 49 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ALA T 58 " --> pdb=" O ALA T 54 " (cutoff:3.500A) Processing helix chain 'T' and resid 81 through 97 Processing helix chain 'T' and resid 99 through 103 removed outlier: 3.513A pdb=" N ARG T 103 " --> pdb=" O GLU T 100 " (cutoff:3.500A) Processing helix chain 'T' and resid 118 through 128 removed outlier: 3.759A pdb=" N ILE T 124 " --> pdb=" O TYR T 120 " (cutoff:3.500A) Processing helix chain 'T' and resid 149 through 162 removed outlier: 4.224A pdb=" N LEU T 153 " --> pdb=" O GLY T 149 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ALA T 158 " --> pdb=" O ALA T 154 " (cutoff:3.500A) Processing helix chain 'T' and resid 183 through 200 Processing helix chain 'U' and resid 15 through 25 Processing helix chain 'U' and resid 47 through 59 removed outlier: 3.881A pdb=" N ASP U 53 " --> pdb=" O ASN U 49 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ALA U 58 " --> pdb=" O ALA U 54 " (cutoff:3.500A) Processing helix chain 'U' and resid 81 through 96 Processing helix chain 'U' and resid 99 through 103 removed outlier: 3.607A pdb=" N GLY U 102 " --> pdb=" O ARG U 99 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG U 103 " --> pdb=" O GLU U 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 99 through 103' Processing helix chain 'U' and resid 118 through 129 removed outlier: 4.139A pdb=" N ILE U 124 " --> pdb=" O TYR U 120 " (cutoff:3.500A) Processing helix chain 'U' and resid 149 through 162 removed outlier: 4.201A pdb=" N LEU U 153 " --> pdb=" O GLY U 149 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ALA U 158 " --> pdb=" O ALA U 154 " (cutoff:3.500A) Processing helix chain 'U' and resid 183 through 199 Processing helix chain 'V' and resid 15 through 26 Processing helix chain 'V' and resid 44 through 46 No H-bonds generated for 'chain 'V' and resid 44 through 46' Processing helix chain 'V' and resid 47 through 57 removed outlier: 3.737A pdb=" N ASP V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 81 through 97 removed outlier: 3.660A pdb=" N VAL V 85 " --> pdb=" O ASP V 81 " (cutoff:3.500A) Processing helix chain 'V' and resid 99 through 103 removed outlier: 3.640A pdb=" N ARG V 103 " --> pdb=" O GLU V 100 " (cutoff:3.500A) Processing helix chain 'V' and resid 118 through 128 removed outlier: 4.047A pdb=" N ILE V 124 " --> pdb=" O TYR V 120 " (cutoff:3.500A) Processing helix chain 'V' and resid 147 through 149 No H-bonds generated for 'chain 'V' and resid 147 through 149' Processing helix chain 'V' and resid 150 through 160 removed outlier: 3.847A pdb=" N ALA V 158 " --> pdb=" O ALA V 154 " (cutoff:3.500A) Processing helix chain 'V' and resid 183 through 199 Processing helix chain 'W' and resid 15 through 26 Processing helix chain 'W' and resid 44 through 46 No H-bonds generated for 'chain 'W' and resid 44 through 46' Processing helix chain 'W' and resid 47 through 59 removed outlier: 3.854A pdb=" N ALA W 58 " --> pdb=" O ALA W 54 " (cutoff:3.500A) Processing helix chain 'W' and resid 81 through 97 removed outlier: 3.560A pdb=" N VAL W 85 " --> pdb=" O ASP W 81 " (cutoff:3.500A) Processing helix chain 'W' and resid 99 through 103 removed outlier: 3.629A pdb=" N ARG W 103 " --> pdb=" O GLU W 100 " (cutoff:3.500A) Processing helix chain 'W' and resid 118 through 128 removed outlier: 4.209A pdb=" N ILE W 124 " --> pdb=" O TYR W 120 " (cutoff:3.500A) Processing helix chain 'W' and resid 150 through 162 removed outlier: 4.006A pdb=" N ALA W 158 " --> pdb=" O ALA W 154 " (cutoff:3.500A) Processing helix chain 'W' and resid 183 through 200 Processing helix chain 'X' and resid 15 through 26 Processing helix chain 'X' and resid 44 through 46 No H-bonds generated for 'chain 'X' and resid 44 through 46' Processing helix chain 'X' and resid 47 through 57 Processing helix chain 'X' and resid 81 through 97 removed outlier: 3.671A pdb=" N VAL X 85 " --> pdb=" O ASP X 81 " (cutoff:3.500A) Processing helix chain 'X' and resid 99 through 103 Processing helix chain 'X' and resid 118 through 128 removed outlier: 4.008A pdb=" N ILE X 124 " --> pdb=" O TYR X 120 " (cutoff:3.500A) Processing helix chain 'X' and resid 150 through 162 removed outlier: 3.725A pdb=" N ALA X 158 " --> pdb=" O ALA X 154 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU X 159 " --> pdb=" O ALA X 155 " (cutoff:3.500A) Processing helix chain 'X' and resid 183 through 200 Processing sheet with id=AA1, first strand: chain 'A' and resid 5 through 11 Processing sheet with id=AA2, first strand: chain 'A' and resid 107 through 114 removed outlier: 5.686A pdb=" N VAL A 108 " --> pdb=" O GLN A 146 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N GLN A 146 " --> pdb=" O VAL A 108 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N THR A 110 " --> pdb=" O GLU A 144 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ARG A 177 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N VAL A 169 " --> pdb=" O ARG A 177 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N TYR A 179 " --> pdb=" O VAL A 167 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 5 through 11 Processing sheet with id=AA4, first strand: chain 'B' and resid 107 through 113 removed outlier: 6.434A pdb=" N GLU B 144 " --> pdb=" O MET B 109 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N HIS B 111 " --> pdb=" O ILE B 142 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N ILE B 142 " --> pdb=" O HIS B 111 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE B 113 " --> pdb=" O LEU B 140 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU B 140 " --> pdb=" O ILE B 113 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ARG B 177 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N VAL B 169 " --> pdb=" O ARG B 177 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TYR B 179 " --> pdb=" O VAL B 167 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 5 through 11 removed outlier: 4.137A pdb=" N VAL C 65 " --> pdb=" O GLU C 76 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N HIS C 78 " --> pdb=" O PRO C 63 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 107 through 114 removed outlier: 5.657A pdb=" N VAL C 108 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLN C 146 " --> pdb=" O VAL C 108 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N THR C 110 " --> pdb=" O GLU C 144 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ARG C 177 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N VAL C 169 " --> pdb=" O ARG C 177 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N TYR C 179 " --> pdb=" O VAL C 167 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 5 through 11 Processing sheet with id=AA8, first strand: chain 'D' and resid 107 through 114 removed outlier: 5.502A pdb=" N VAL D 108 " --> pdb=" O GLN D 146 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLN D 146 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N THR D 110 " --> pdb=" O GLU D 144 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ASN D 168 " --> pdb=" O TYR D 179 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA D 181 " --> pdb=" O LEU D 166 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LEU D 166 " --> pdb=" O ALA D 181 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 5 through 11 removed outlier: 4.054A pdb=" N VAL E 65 " --> pdb=" O GLU E 76 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N HIS E 78 " --> pdb=" O PRO E 63 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 107 through 114 removed outlier: 5.714A pdb=" N VAL E 108 " --> pdb=" O GLN E 146 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N GLN E 146 " --> pdb=" O VAL E 108 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N THR E 110 " --> pdb=" O GLU E 144 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN E 112 " --> pdb=" O ILE E 142 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N ARG E 177 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N VAL E 169 " --> pdb=" O ARG E 177 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N TYR E 179 " --> pdb=" O VAL E 167 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 5 through 11 Processing sheet with id=AB3, first strand: chain 'F' and resid 107 through 114 removed outlier: 6.606A pdb=" N GLU F 144 " --> pdb=" O MET F 109 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N HIS F 111 " --> pdb=" O ILE F 142 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE F 142 " --> pdb=" O HIS F 111 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE F 113 " --> pdb=" O LEU F 140 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU F 140 " --> pdb=" O ILE F 113 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N ARG F 177 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL F 169 " --> pdb=" O ARG F 177 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N TYR F 179 " --> pdb=" O VAL F 167 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'GA' and resid 31 through 36 removed outlier: 6.045A pdb=" N LEUGA 31 " --> pdb=" O ARGGA 47 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N ARGGA 47 " --> pdb=" O LEUGA 31 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLYGA 33 " --> pdb=" O VALGA 45 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VALGA 45 " --> pdb=" O GLYGA 33 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N LEUGA 5 " --> pdb=" O VALGA 75 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N VALGA 75 " --> pdb=" O LEUGA 5 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N METGA 7 " --> pdb=" O VALGA 73 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VALGA 73 " --> pdb=" O METGA 7 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLUGA 9 " --> pdb=" O VALGA 71 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'GB' and resid 31 through 38 removed outlier: 6.041A pdb=" N LEUGB 31 " --> pdb=" O ARGGB 47 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ARGGB 47 " --> pdb=" O LEUGB 31 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLYGB 33 " --> pdb=" O VALGB 45 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N TYRGB 41 " --> pdb=" O THRGB 37 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALAGB 72 " --> pdb=" O GLUGB 9 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N ARGGB 11 " --> pdb=" O VALGB 70 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N VALGB 70 " --> pdb=" O ARGGB 11 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'GC' and resid 31 through 36 removed outlier: 4.095A pdb=" N GLYGC 33 " --> pdb=" O VALGC 45 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N VALGC 45 " --> pdb=" O GLYGC 33 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEUGC 5 " --> pdb=" O VALGC 75 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N VALGC 75 " --> pdb=" O LEUGC 5 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N METGC 7 " --> pdb=" O VALGC 73 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N VALGC 73 " --> pdb=" O METGC 7 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N GLUGC 9 " --> pdb=" O VALGC 71 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'GD' and resid 31 through 36 removed outlier: 4.198A pdb=" N GLYGD 33 " --> pdb=" O VALGD 45 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N VALGD 45 " --> pdb=" O GLYGD 33 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALAGD 72 " --> pdb=" O GLUGD 9 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ARGGD 11 " --> pdb=" O VALGD 70 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VALGD 70 " --> pdb=" O ARGGD 11 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'GE' and resid 31 through 38 removed outlier: 6.012A pdb=" N LEUGE 31 " --> pdb=" O ARGGE 47 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N ARGGE 47 " --> pdb=" O LEUGE 31 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N GLYGE 33 " --> pdb=" O VALGE 45 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VALGE 45 " --> pdb=" O GLYGE 33 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N TYRGE 41 " --> pdb=" O THRGE 37 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALAGE 72 " --> pdb=" O GLUGE 9 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ARGGE 11 " --> pdb=" O VALGE 70 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VALGE 70 " --> pdb=" O ARGGE 11 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'GF' and resid 31 through 38 removed outlier: 3.832A pdb=" N GLYGF 33 " --> pdb=" O VALGF 45 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THRGF 37 " --> pdb=" O TYRGF 41 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N TYRGF 41 " --> pdb=" O THRGF 37 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEUGF 5 " --> pdb=" O VALGF 75 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N VALGF 75 " --> pdb=" O LEUGF 5 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N METGF 7 " --> pdb=" O VALGF 73 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N VALGF 73 " --> pdb=" O METGF 7 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLUGF 9 " --> pdb=" O VALGF 71 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'HA' and resid 31 through 38 removed outlier: 5.809A pdb=" N LEUHA 31 " --> pdb=" O ARGHA 47 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ARGHA 47 " --> pdb=" O LEUHA 31 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLYHA 33 " --> pdb=" O VALHA 45 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N VALHA 45 " --> pdb=" O GLYHA 33 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N TYRHA 41 " --> pdb=" O THRHA 37 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALAHA 72 " --> pdb=" O GLUHA 9 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARGHA 11 " --> pdb=" O VALHA 70 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VALHA 70 " --> pdb=" O ARGHA 11 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'HB' and resid 30 through 38 removed outlier: 5.596A pdb=" N LEUHB 31 " --> pdb=" O ARGHB 47 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ARGHB 47 " --> pdb=" O LEUHB 31 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N GLYHB 33 " --> pdb=" O VALHB 45 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N TYRHB 41 " --> pdb=" O THRHB 37 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALAHB 72 " --> pdb=" O GLUHB 9 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N ARGHB 11 " --> pdb=" O VALHB 70 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VALHB 70 " --> pdb=" O ARGHB 11 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'HC' and resid 30 through 36 removed outlier: 5.735A pdb=" N LEUHC 31 " --> pdb=" O ARGHC 47 " (cutoff:3.500A) removed outlier: 7.072A pdb=" N ARGHC 47 " --> pdb=" O LEUHC 31 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLYHC 33 " --> pdb=" O VALHC 45 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N VALHC 45 " --> pdb=" O GLYHC 33 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ALAHC 72 " --> pdb=" O GLUHC 9 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ARGHC 11 " --> pdb=" O VALHC 70 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VALHC 70 " --> pdb=" O ARGHC 11 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'HD' and resid 31 through 36 removed outlier: 5.806A pdb=" N LEUHD 31 " --> pdb=" O ARGHD 47 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N ARGHD 47 " --> pdb=" O LEUHD 31 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLYHD 33 " --> pdb=" O VALHD 45 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VALHD 45 " --> pdb=" O GLYHD 33 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALAHD 72 " --> pdb=" O GLUHD 9 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N ARGHD 11 " --> pdb=" O VALHD 70 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N VALHD 70 " --> pdb=" O ARGHD 11 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'HE' and resid 31 through 36 removed outlier: 5.760A pdb=" N LEUHE 31 " --> pdb=" O ARGHE 47 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ARGHE 47 " --> pdb=" O LEUHE 31 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLYHE 33 " --> pdb=" O VALHE 45 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALAHE 72 " --> pdb=" O GLUHE 9 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N ARGHE 11 " --> pdb=" O VALHE 70 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VALHE 70 " --> pdb=" O ARGHE 11 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'HF' and resid 30 through 36 removed outlier: 5.889A pdb=" N LEUHF 31 " --> pdb=" O ARGHF 47 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N ARGHF 47 " --> pdb=" O LEUHF 31 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLYHF 33 " --> pdb=" O VALHF 45 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N VALHF 45 " --> pdb=" O GLYHF 33 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ALAHF 72 " --> pdb=" O GLUHF 9 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARGHF 11 " --> pdb=" O VALHF 70 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N VALHF 70 " --> pdb=" O ARGHF 11 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'IA' and resid 31 through 38 removed outlier: 5.924A pdb=" N LEUIA 31 " --> pdb=" O ARGIA 47 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N ARGIA 47 " --> pdb=" O LEUIA 31 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLYIA 33 " --> pdb=" O VALIA 45 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VALIA 45 " --> pdb=" O GLYIA 33 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N TYRIA 41 " --> pdb=" O THRIA 37 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ALAIA 72 " --> pdb=" O GLUIA 9 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARGIA 11 " --> pdb=" O VALIA 70 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N VALIA 70 " --> pdb=" O ARGIA 11 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'IB' and resid 31 through 38 removed outlier: 5.856A pdb=" N LEUIB 31 " --> pdb=" O ARGIB 47 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ARGIB 47 " --> pdb=" O LEUIB 31 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N GLYIB 33 " --> pdb=" O VALIB 45 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N TYRIB 41 " --> pdb=" O THRIB 37 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALAIB 72 " --> pdb=" O GLUIB 9 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ARGIB 11 " --> pdb=" O VALIB 70 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N VALIB 70 " --> pdb=" O ARGIB 11 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'IC' and resid 31 through 36 removed outlier: 4.160A pdb=" N GLYIC 33 " --> pdb=" O VALIC 45 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N VALIC 45 " --> pdb=" O GLYIC 33 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ALAIC 72 " --> pdb=" O GLUIC 9 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ARGIC 11 " --> pdb=" O VALIC 70 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N VALIC 70 " --> pdb=" O ARGIC 11 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'ID' and resid 30 through 38 removed outlier: 5.730A pdb=" N LEUID 31 " --> pdb=" O ARGID 47 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N ARGID 47 " --> pdb=" O LEUID 31 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N GLYID 33 " --> pdb=" O VALID 45 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VALID 45 " --> pdb=" O GLYID 33 " (cutoff:3.500A) removed outlier: 6.157A pdb=" N TYRID 41 " --> pdb=" O THRID 37 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ARGID 11 " --> pdb=" O VALID 70 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N VALID 70 " --> pdb=" O ARGID 11 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'IE' and resid 31 through 36 removed outlier: 5.921A pdb=" N LEUIE 31 " --> pdb=" O ARGIE 47 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N ARGIE 47 " --> pdb=" O LEUIE 31 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N GLYIE 33 " --> pdb=" O VALIE 45 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VALIE 45 " --> pdb=" O GLYIE 33 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEUIE 5 " --> pdb=" O VALIE 75 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N VALIE 75 " --> pdb=" O LEUIE 5 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N METIE 7 " --> pdb=" O VALIE 73 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VALIE 73 " --> pdb=" O METIE 7 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLUIE 9 " --> pdb=" O VALIE 71 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'IF' and resid 31 through 36 removed outlier: 5.791A pdb=" N LEUIF 31 " --> pdb=" O ARGIF 47 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N ARGIF 47 " --> pdb=" O LEUIF 31 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N GLYIF 33 " --> pdb=" O VALIF 45 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N VALIF 45 " --> pdb=" O GLYIF 33 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALAIF 72 " --> pdb=" O GLUIF 9 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N ARGIF 11 " --> pdb=" O VALIF 70 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N VALIF 70 " --> pdb=" O ARGIF 11 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'JA' and resid 31 through 36 removed outlier: 4.126A pdb=" N GLYJA 33 " --> pdb=" O VALJA 45 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N VALJA 45 " --> pdb=" O GLYJA 33 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALAJA 72 " --> pdb=" O GLUJA 9 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ARGJA 11 " --> pdb=" O VALJA 70 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N VALJA 70 " --> pdb=" O ARGJA 11 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'JB' and resid 30 through 38 removed outlier: 5.589A pdb=" N LEUJB 31 " --> pdb=" O ARGJB 47 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N ARGJB 47 " --> pdb=" O LEUJB 31 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLYJB 33 " --> pdb=" O VALJB 45 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THRJB 37 " --> pdb=" O TYRJB 41 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N TYRJB 41 " --> pdb=" O THRJB 37 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N HISJB 74 " --> pdb=" O METJB 7 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ALAJB 72 " --> pdb=" O GLUJB 9 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ARGJB 11 " --> pdb=" O VALJB 70 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VALJB 70 " --> pdb=" O ARGJB 11 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'JC' and resid 30 through 36 removed outlier: 5.618A pdb=" N LEUJC 31 " --> pdb=" O ARGJC 47 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N ARGJC 47 " --> pdb=" O LEUJC 31 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N GLYJC 33 " --> pdb=" O VALJC 45 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N VALJC 45 " --> pdb=" O GLYJC 33 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N ALAJC 72 " --> pdb=" O GLUJC 9 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ARGJC 11 " --> pdb=" O VALJC 70 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N VALJC 70 " --> pdb=" O ARGJC 11 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'JD' and resid 31 through 38 removed outlier: 5.766A pdb=" N LEUJD 31 " --> pdb=" O ARGJD 47 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ARGJD 47 " --> pdb=" O LEUJD 31 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLYJD 33 " --> pdb=" O VALJD 45 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VALJD 45 " --> pdb=" O GLYJD 33 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N TYRJD 41 " --> pdb=" O THRJD 37 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEUJD 5 " --> pdb=" O VALJD 75 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VALJD 75 " --> pdb=" O LEUJD 5 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N METJD 7 " --> pdb=" O VALJD 73 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VALJD 73 " --> pdb=" O METJD 7 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N GLUJD 9 " --> pdb=" O VALJD 71 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'JE' and resid 30 through 36 removed outlier: 5.435A pdb=" N LEUJE 31 " --> pdb=" O ARGJE 47 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ARGJE 47 " --> pdb=" O LEUJE 31 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLYJE 33 " --> pdb=" O VALJE 45 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VALJE 45 " --> pdb=" O GLYJE 33 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HISJE 74 " --> pdb=" O METJE 7 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALAJE 72 " --> pdb=" O GLUJE 9 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N ARGJE 11 " --> pdb=" O VALJE 70 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VALJE 70 " --> pdb=" O ARGJE 11 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'JF' and resid 30 through 36 removed outlier: 5.965A pdb=" N LEUJF 31 " --> pdb=" O ARGJF 47 " (cutoff:3.500A) removed outlier: 7.075A pdb=" N ARGJF 47 " --> pdb=" O LEUJF 31 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLYJF 33 " --> pdb=" O VALJF 45 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VALJF 45 " --> pdb=" O GLYJF 33 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ALAJF 72 " --> pdb=" O GLUJF 9 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ARGJF 11 " --> pdb=" O VALJF 70 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N VALJF 70 " --> pdb=" O ARGJF 11 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'KA' and resid 31 through 36 removed outlier: 6.010A pdb=" N LEUKA 31 " --> pdb=" O ARGKA 47 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N ARGKA 47 " --> pdb=" O LEUKA 31 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLYKA 33 " --> pdb=" O VALKA 45 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N VALKA 45 " --> pdb=" O GLYKA 33 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALAKA 72 " --> pdb=" O GLUKA 9 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ARGKA 11 " --> pdb=" O VALKA 70 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N VALKA 70 " --> pdb=" O ARGKA 11 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'KB' and resid 30 through 38 removed outlier: 5.740A pdb=" N LEUKB 31 " --> pdb=" O ARGKB 47 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N ARGKB 47 " --> pdb=" O LEUKB 31 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N GLYKB 33 " --> pdb=" O VALKB 45 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N VALKB 45 " --> pdb=" O GLYKB 33 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N TYRKB 41 " --> pdb=" O THRKB 37 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALAKB 72 " --> pdb=" O GLUKB 9 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N ARGKB 11 " --> pdb=" O VALKB 70 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N VALKB 70 " --> pdb=" O ARGKB 11 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'KC' and resid 30 through 38 removed outlier: 5.660A pdb=" N LEUKC 31 " --> pdb=" O ARGKC 47 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ARGKC 47 " --> pdb=" O LEUKC 31 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N GLYKC 33 " --> pdb=" O VALKC 45 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N VALKC 45 " --> pdb=" O GLYKC 33 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THRKC 37 " --> pdb=" O TYRKC 41 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N TYRKC 41 " --> pdb=" O THRKC 37 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALAKC 72 " --> pdb=" O GLUKC 9 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ARGKC 11 " --> pdb=" O VALKC 70 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VALKC 70 " --> pdb=" O ARGKC 11 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'KD' and resid 30 through 38 removed outlier: 5.739A pdb=" N LEUKD 31 " --> pdb=" O ARGKD 47 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N ARGKD 47 " --> pdb=" O LEUKD 31 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N GLYKD 33 " --> pdb=" O VALKD 45 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VALKD 45 " --> pdb=" O GLYKD 33 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N TYRKD 41 " --> pdb=" O THRKD 37 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEUKD 5 " --> pdb=" O VALKD 75 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VALKD 75 " --> pdb=" O LEUKD 5 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N METKD 7 " --> pdb=" O VALKD 73 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N VALKD 73 " --> pdb=" O METKD 7 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLUKD 9 " --> pdb=" O VALKD 71 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'KE' and resid 31 through 38 removed outlier: 5.876A pdb=" N LEUKE 31 " --> pdb=" O ARGKE 47 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N ARGKE 47 " --> pdb=" O LEUKE 31 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N GLYKE 33 " --> pdb=" O VALKE 45 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N VALKE 45 " --> pdb=" O GLYKE 33 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N TYRKE 41 " --> pdb=" O THRKE 37 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALAKE 72 " --> pdb=" O GLUKE 9 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ARGKE 11 " --> pdb=" O VALKE 70 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VALKE 70 " --> pdb=" O ARGKE 11 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'KF' and resid 30 through 38 removed outlier: 5.557A pdb=" N LEUKF 31 " --> pdb=" O ARGKF 47 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ARGKF 47 " --> pdb=" O LEUKF 31 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N GLYKF 33 " --> pdb=" O VALKF 45 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THRKF 37 " --> pdb=" O TYRKF 41 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N TYRKF 41 " --> pdb=" O THRKF 37 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HISKF 74 " --> pdb=" O METKF 7 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALAKF 72 " --> pdb=" O GLUKF 9 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ARGKF 11 " --> pdb=" O VALKF 70 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N VALKF 70 " --> pdb=" O ARGKF 11 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'LA' and resid 30 through 38 removed outlier: 5.649A pdb=" N LEULA 31 " --> pdb=" O ARGLA 47 " (cutoff:3.500A) removed outlier: 7.068A pdb=" N ARGLA 47 " --> pdb=" O LEULA 31 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N GLYLA 33 " --> pdb=" O VALLA 45 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VALLA 45 " --> pdb=" O GLYLA 33 " (cutoff:3.500A) removed outlier: 6.044A pdb=" N TYRLA 41 " --> pdb=" O THRLA 37 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ARGLA 11 " --> pdb=" O VALLA 70 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N VALLA 70 " --> pdb=" O ARGLA 11 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'LB' and resid 31 through 38 removed outlier: 5.694A pdb=" N LEULB 31 " --> pdb=" O ARGLB 47 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ARGLB 47 " --> pdb=" O LEULB 31 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N GLYLB 33 " --> pdb=" O VALLB 45 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VALLB 45 " --> pdb=" O GLYLB 33 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THRLB 37 " --> pdb=" O TYRLB 41 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N TYRLB 41 " --> pdb=" O THRLB 37 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALALB 72 " --> pdb=" O GLULB 9 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N ARGLB 11 " --> pdb=" O VALLB 70 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VALLB 70 " --> pdb=" O ARGLB 11 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'LC' and resid 30 through 36 removed outlier: 5.664A pdb=" N LEULC 31 " --> pdb=" O ARGLC 47 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N ARGLC 47 " --> pdb=" O LEULC 31 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLYLC 33 " --> pdb=" O VALLC 45 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VALLC 45 " --> pdb=" O GLYLC 33 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALALC 72 " --> pdb=" O GLULC 9 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ARGLC 11 " --> pdb=" O VALLC 70 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N VALLC 70 " --> pdb=" O ARGLC 11 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'LD' and resid 31 through 38 removed outlier: 5.841A pdb=" N LEULD 31 " --> pdb=" O ARGLD 47 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ARGLD 47 " --> pdb=" O LEULD 31 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLYLD 33 " --> pdb=" O VALLD 45 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N VALLD 45 " --> pdb=" O GLYLD 33 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N TYRLD 41 " --> pdb=" O THRLD 37 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ALALD 72 " --> pdb=" O GLULD 9 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ARGLD 11 " --> pdb=" O VALLD 70 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N VALLD 70 " --> pdb=" O ARGLD 11 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'LE' and resid 31 through 36 removed outlier: 5.650A pdb=" N LEULE 31 " --> pdb=" O ARGLE 47 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARGLE 47 " --> pdb=" O LEULE 31 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLYLE 33 " --> pdb=" O VALLE 45 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ALALE 72 " --> pdb=" O GLULE 9 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ARGLE 11 " --> pdb=" O VALLE 70 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VALLE 70 " --> pdb=" O ARGLE 11 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'LF' and resid 31 through 38 removed outlier: 6.187A pdb=" N LEULF 31 " --> pdb=" O ARGLF 47 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ARGLF 47 " --> pdb=" O LEULF 31 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N GLYLF 33 " --> pdb=" O VALLF 45 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N VALLF 45 " --> pdb=" O GLYLF 33 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N TYRLF 41 " --> pdb=" O THRLF 37 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALALF 72 " --> pdb=" O GLULF 9 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ARGLF 11 " --> pdb=" O VALLF 70 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VALLF 70 " --> pdb=" O ARGLF 11 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'G' and resid 5 through 11 removed outlier: 4.314A pdb=" N VAL G 65 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 6.669A pdb=" N HIS G 78 " --> pdb=" O PRO G 63 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'G' and resid 107 through 114 removed outlier: 5.487A pdb=" N VAL G 108 " --> pdb=" O GLN G 146 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N GLN G 146 " --> pdb=" O VAL G 108 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N ARG G 177 " --> pdb=" O VAL G 169 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N VAL G 169 " --> pdb=" O ARG G 177 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N TYR G 179 " --> pdb=" O VAL G 167 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'H' and resid 4 through 11 removed outlier: 5.512A pdb=" N LEU H 5 " --> pdb=" O ALA H 43 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N ALA H 43 " --> pdb=" O LEU H 5 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU H 74 " --> pdb=" O GLN H 66 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N GLN H 66 " --> pdb=" O LEU H 74 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLU H 76 " --> pdb=" O ALA H 64 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ALA H 64 " --> pdb=" O GLU H 76 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'H' and resid 107 through 114 removed outlier: 6.486A pdb=" N GLU H 144 " --> pdb=" O MET H 109 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N HIS H 111 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N ILE H 142 " --> pdb=" O HIS H 111 " (cutoff:3.500A) removed outlier: 4.316A pdb=" N ILE H 113 " --> pdb=" O LEU H 140 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU H 140 " --> pdb=" O ILE H 113 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA H 181 " --> pdb=" O LEU H 166 " (cutoff:3.500A) removed outlier: 5.309A pdb=" N LEU H 166 " --> pdb=" O ALA H 181 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'I' and resid 4 through 11 removed outlier: 5.585A pdb=" N LEU I 5 " --> pdb=" O ALA I 43 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N ALA I 43 " --> pdb=" O LEU I 5 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N VAL I 65 " --> pdb=" O GLU I 76 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N HIS I 78 " --> pdb=" O PRO I 63 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'I' and resid 107 through 114 removed outlier: 5.546A pdb=" N VAL I 108 " --> pdb=" O GLN I 146 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N GLN I 146 " --> pdb=" O VAL I 108 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ARG I 177 " --> pdb=" O VAL I 169 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL I 169 " --> pdb=" O ARG I 177 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N TYR I 179 " --> pdb=" O VAL I 167 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'J' and resid 4 through 11 removed outlier: 6.442A pdb=" N GLU J 41 " --> pdb=" O ARG J 6 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N TYR J 8 " --> pdb=" O TRP J 39 " (cutoff:3.500A) removed outlier: 6.897A pdb=" N TRP J 39 " --> pdb=" O TYR J 8 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N PHE J 10 " --> pdb=" O SER J 37 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N SER J 37 " --> pdb=" O PHE J 10 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N VAL J 65 " --> pdb=" O GLU J 76 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N HIS J 78 " --> pdb=" O PRO J 63 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'J' and resid 107 through 114 removed outlier: 5.616A pdb=" N VAL J 108 " --> pdb=" O GLN J 146 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLN J 146 " --> pdb=" O VAL J 108 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR J 110 " --> pdb=" O GLU J 144 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N ALA J 181 " --> pdb=" O LEU J 166 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N LEU J 166 " --> pdb=" O ALA J 181 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'K' and resid 5 through 11 removed outlier: 4.133A pdb=" N VAL K 65 " --> pdb=" O GLU K 76 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N HIS K 78 " --> pdb=" O PRO K 63 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'K' and resid 107 through 114 removed outlier: 5.545A pdb=" N VAL K 108 " --> pdb=" O GLN K 146 " (cutoff:3.500A) removed outlier: 6.784A pdb=" N GLN K 146 " --> pdb=" O VAL K 108 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N THR K 110 " --> pdb=" O GLU K 144 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ARG K 177 " --> pdb=" O VAL K 169 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N VAL K 169 " --> pdb=" O ARG K 177 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N TYR K 179 " --> pdb=" O VAL K 167 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'L' and resid 5 through 11 removed outlier: 4.105A pdb=" N VAL L 65 " --> pdb=" O GLU L 76 " (cutoff:3.500A) removed outlier: 7.130A pdb=" N HIS L 78 " --> pdb=" O PRO L 63 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'L' and resid 107 through 114 removed outlier: 5.521A pdb=" N VAL L 108 " --> pdb=" O GLN L 146 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N GLN L 146 " --> pdb=" O VAL L 108 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N THR L 110 " --> pdb=" O GLU L 144 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG L 177 " --> pdb=" O VAL L 169 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N VAL L 169 " --> pdb=" O ARG L 177 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N TYR L 179 " --> pdb=" O VAL L 167 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'M' and resid 5 through 11 removed outlier: 4.344A pdb=" N VAL M 65 " --> pdb=" O GLU M 76 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N HIS M 78 " --> pdb=" O PRO M 63 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'M' and resid 107 through 114 removed outlier: 5.546A pdb=" N VAL M 108 " --> pdb=" O GLN M 146 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLN M 146 " --> pdb=" O VAL M 108 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N THR M 110 " --> pdb=" O GLU M 144 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N ARG M 177 " --> pdb=" O VAL M 169 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL M 169 " --> pdb=" O ARG M 177 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N TYR M 179 " --> pdb=" O VAL M 167 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'N' and resid 4 through 11 removed outlier: 5.416A pdb=" N LEU N 5 " --> pdb=" O ALA N 43 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA N 43 " --> pdb=" O LEU N 5 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU N 74 " --> pdb=" O GLN N 66 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN N 66 " --> pdb=" O LEU N 74 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLU N 76 " --> pdb=" O ALA N 64 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'N' and resid 107 through 114 removed outlier: 5.474A pdb=" N VAL N 108 " --> pdb=" O GLN N 146 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N GLN N 146 " --> pdb=" O VAL N 108 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ALA N 181 " --> pdb=" O LEU N 166 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LEU N 166 " --> pdb=" O ALA N 181 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'O' and resid 4 through 11 removed outlier: 5.579A pdb=" N LEU O 5 " --> pdb=" O ALA O 43 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ALA O 43 " --> pdb=" O LEU O 5 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU O 74 " --> pdb=" O GLN O 66 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N GLN O 66 " --> pdb=" O LEU O 74 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N GLU O 76 " --> pdb=" O ALA O 64 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'O' and resid 107 through 114 removed outlier: 5.921A pdb=" N VAL O 108 " --> pdb=" O GLN O 146 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLN O 146 " --> pdb=" O VAL O 108 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ALA O 181 " --> pdb=" O LEU O 166 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N LEU O 166 " --> pdb=" O ALA O 181 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'P' and resid 4 through 11 removed outlier: 5.495A pdb=" N LEU P 5 " --> pdb=" O ALA P 43 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA P 43 " --> pdb=" O LEU P 5 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N VAL P 65 " --> pdb=" O GLU P 76 " (cutoff:3.500A) removed outlier: 7.058A pdb=" N HIS P 78 " --> pdb=" O PRO P 63 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'P' and resid 107 through 114 removed outlier: 5.647A pdb=" N VAL P 108 " --> pdb=" O GLN P 146 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N GLN P 146 " --> pdb=" O VAL P 108 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N THR P 110 " --> pdb=" O GLU P 144 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N ARG P 177 " --> pdb=" O VAL P 169 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N VAL P 169 " --> pdb=" O ARG P 177 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N TYR P 179 " --> pdb=" O VAL P 167 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'Q' and resid 5 through 11 removed outlier: 4.005A pdb=" N VAL Q 65 " --> pdb=" O GLU Q 76 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N HIS Q 78 " --> pdb=" O PRO Q 63 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'Q' and resid 107 through 114 removed outlier: 5.547A pdb=" N VAL Q 108 " --> pdb=" O GLN Q 146 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N GLN Q 146 " --> pdb=" O VAL Q 108 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N THR Q 110 " --> pdb=" O GLU Q 144 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARG Q 177 " --> pdb=" O VAL Q 169 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N VAL Q 169 " --> pdb=" O ARG Q 177 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N TYR Q 179 " --> pdb=" O VAL Q 167 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'R' and resid 5 through 11 removed outlier: 4.017A pdb=" N VAL R 65 " --> pdb=" O GLU R 76 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N HIS R 78 " --> pdb=" O PRO R 63 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'R' and resid 107 through 114 removed outlier: 5.573A pdb=" N VAL R 108 " --> pdb=" O GLN R 146 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N GLN R 146 " --> pdb=" O VAL R 108 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N THR R 110 " --> pdb=" O GLU R 144 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARG R 177 " --> pdb=" O VAL R 169 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N VAL R 169 " --> pdb=" O ARG R 177 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N TYR R 179 " --> pdb=" O VAL R 167 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'S' and resid 5 through 11 removed outlier: 4.100A pdb=" N VAL S 65 " --> pdb=" O GLU S 76 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N HIS S 78 " --> pdb=" O PRO S 63 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'S' and resid 107 through 114 removed outlier: 5.514A pdb=" N VAL S 108 " --> pdb=" O GLN S 146 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N GLN S 146 " --> pdb=" O VAL S 108 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR S 110 " --> pdb=" O GLU S 144 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ARG S 177 " --> pdb=" O VAL S 169 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N VAL S 169 " --> pdb=" O ARG S 177 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N TYR S 179 " --> pdb=" O VAL S 167 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'T' and resid 4 through 11 removed outlier: 5.421A pdb=" N LEU T 5 " --> pdb=" O ALA T 43 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N ALA T 43 " --> pdb=" O LEU T 5 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL T 65 " --> pdb=" O GLU T 76 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N HIS T 78 " --> pdb=" O PRO T 63 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'T' and resid 107 through 114 removed outlier: 5.437A pdb=" N VAL T 108 " --> pdb=" O GLN T 146 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N GLN T 146 " --> pdb=" O VAL T 108 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ARG T 177 " --> pdb=" O VAL T 169 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL T 169 " --> pdb=" O ARG T 177 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N TYR T 179 " --> pdb=" O VAL T 167 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'U' and resid 4 through 11 removed outlier: 5.731A pdb=" N LEU U 5 " --> pdb=" O ALA U 43 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N ALA U 43 " --> pdb=" O LEU U 5 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL U 65 " --> pdb=" O GLU U 76 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N HIS U 78 " --> pdb=" O PRO U 63 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'U' and resid 107 through 114 removed outlier: 6.177A pdb=" N VAL U 108 " --> pdb=" O GLN U 146 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N GLN U 146 " --> pdb=" O VAL U 108 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR U 110 " --> pdb=" O GLU U 144 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ARG U 177 " --> pdb=" O VAL U 169 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N VAL U 169 " --> pdb=" O ARG U 177 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N TYR U 179 " --> pdb=" O VAL U 167 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'V' and resid 4 through 11 removed outlier: 5.473A pdb=" N LEU V 5 " --> pdb=" O ALA V 43 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA V 43 " --> pdb=" O LEU V 5 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N VAL V 65 " --> pdb=" O GLU V 76 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N HIS V 78 " --> pdb=" O PRO V 63 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'V' and resid 107 through 114 removed outlier: 5.539A pdb=" N VAL V 108 " --> pdb=" O GLN V 146 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N GLN V 146 " --> pdb=" O VAL V 108 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N THR V 110 " --> pdb=" O GLU V 144 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ARG V 177 " --> pdb=" O VAL V 169 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N VAL V 169 " --> pdb=" O ARG V 177 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N TYR V 179 " --> pdb=" O VAL V 167 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'W' and resid 5 through 11 removed outlier: 4.222A pdb=" N VAL W 65 " --> pdb=" O GLU W 76 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N HIS W 78 " --> pdb=" O PRO W 63 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'W' and resid 107 through 114 removed outlier: 5.609A pdb=" N VAL W 108 " --> pdb=" O GLN W 146 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N GLN W 146 " --> pdb=" O VAL W 108 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N THR W 110 " --> pdb=" O GLU W 144 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ARG W 177 " --> pdb=" O VAL W 169 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N VAL W 169 " --> pdb=" O ARG W 177 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N TYR W 179 " --> pdb=" O VAL W 167 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'X' and resid 5 through 11 removed outlier: 3.956A pdb=" N VAL X 65 " --> pdb=" O GLU X 76 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N HIS X 78 " --> pdb=" O PRO X 63 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'X' and resid 107 through 114 removed outlier: 6.540A pdb=" N GLU X 144 " --> pdb=" O MET X 109 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N HIS X 111 " --> pdb=" O ILE X 142 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE X 142 " --> pdb=" O HIS X 111 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N ILE X 113 " --> pdb=" O LEU X 140 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU X 140 " --> pdb=" O ILE X 113 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N ARG X 177 " --> pdb=" O VAL X 169 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N VAL X 169 " --> pdb=" O ARG X 177 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N TYR X 179 " --> pdb=" O VAL X 167 " (cutoff:3.500A) 3449 hydrogen bonds defined for protein. 9816 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: 22.80 Time building geometry restraints manager: 20.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 16673 1.33 - 1.45: 8616 1.45 - 1.57: 35588 1.57 - 1.69: 0 1.69 - 1.80: 360 Bond restraints: 61237 Sorted by residual: bond pdb=" C ALALC 86 " pdb=" N LEULC 87 " ideal model delta sigma weight residual 1.331 1.260 0.071 2.07e-02 2.33e+03 1.16e+01 bond pdb=" C ILE C 134 " pdb=" N LEU C 135 " ideal model delta sigma weight residual 1.331 1.256 0.075 2.83e-02 1.25e+03 7.10e+00 bond pdb=" C ALAHE 86 " pdb=" N LEUHE 87 " ideal model delta sigma weight residual 1.331 1.259 0.072 2.83e-02 1.25e+03 6.47e+00 bond pdb=" CB THR B 20 " pdb=" CG2 THR B 20 " ideal model delta sigma weight residual 1.521 1.443 0.078 3.30e-02 9.18e+02 5.62e+00 bond pdb=" C ILE U 134 " pdb=" N LEU U 135 " ideal model delta sigma weight residual 1.340 1.212 0.129 5.87e-02 2.90e+02 4.81e+00 ... (remaining 61232 not shown) Histogram of bond angle deviations from ideal: 95.01 - 102.81: 359 102.81 - 110.60: 19716 110.60 - 118.40: 28799 118.40 - 126.20: 33826 126.20 - 133.99: 558 Bond angle restraints: 83258 Sorted by residual: angle pdb=" C GLU A 69 " pdb=" N ARG A 70 " pdb=" CA ARG A 70 " ideal model delta sigma weight residual 121.19 128.64 -7.45 1.59e+00 3.96e-01 2.20e+01 angle pdb=" C ILE B 114 " pdb=" N ARG B 115 " pdb=" CA ARG B 115 " ideal model delta sigma weight residual 121.31 127.00 -5.69 1.49e+00 4.50e-01 1.46e+01 angle pdb=" CA GLU B 69 " pdb=" CB GLU B 69 " pdb=" CG GLU B 69 " ideal model delta sigma weight residual 114.10 121.14 -7.04 2.00e+00 2.50e-01 1.24e+01 angle pdb=" C ILE T 198 " pdb=" N ARG T 199 " pdb=" CA ARG T 199 " ideal model delta sigma weight residual 122.56 116.59 5.97 1.72e+00 3.38e-01 1.21e+01 angle pdb=" N ARG B 115 " pdb=" CA ARG B 115 " pdb=" C ARG B 115 " ideal model delta sigma weight residual 110.35 114.98 -4.63 1.40e+00 5.10e-01 1.10e+01 ... (remaining 83253 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.15: 35746 17.15 - 34.30: 947 34.30 - 51.45: 169 51.45 - 68.60: 17 68.60 - 85.74: 21 Dihedral angle restraints: 36900 sinusoidal: 13770 harmonic: 23130 Sorted by residual: dihedral pdb=" CA ASN E 126 " pdb=" C ASN E 126 " pdb=" N ARG E 127 " pdb=" CA ARG E 127 " ideal model delta harmonic sigma weight residual 180.00 145.10 34.90 0 5.00e+00 4.00e-02 4.87e+01 dihedral pdb=" CA ASN F 126 " pdb=" C ASN F 126 " pdb=" N ARG F 127 " pdb=" CA ARG F 127 " ideal model delta harmonic sigma weight residual 180.00 147.76 32.24 0 5.00e+00 4.00e-02 4.16e+01 dihedral pdb=" CA ASN D 126 " pdb=" C ASN D 126 " pdb=" N ARG D 127 " pdb=" CA ARG D 127 " ideal model delta harmonic sigma weight residual 180.00 149.51 30.49 0 5.00e+00 4.00e-02 3.72e+01 ... (remaining 36897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 8007 0.068 - 0.136: 1666 0.136 - 0.204: 220 0.204 - 0.272: 40 0.272 - 0.340: 2 Chirality restraints: 9935 Sorted by residual: chirality pdb=" CB VAL A 68 " pdb=" CA VAL A 68 " pdb=" CG1 VAL A 68 " pdb=" CG2 VAL A 68 " both_signs ideal model delta sigma weight residual False -2.63 -2.29 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CG LEUJA 89 " pdb=" CB LEUJA 89 " pdb=" CD1 LEUJA 89 " pdb=" CD2 LEUJA 89 " both_signs ideal model delta sigma weight residual False -2.59 -2.30 -0.29 2.00e-01 2.50e+01 2.04e+00 chirality pdb=" CG LEUKE 89 " pdb=" CB LEUKE 89 " pdb=" CD1 LEUKE 89 " pdb=" CD2 LEUKE 89 " both_signs ideal model delta sigma weight residual False -2.59 -2.33 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 9932 not shown) Planarity restraints: 10910 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 29 " 0.020 2.00e-02 2.50e+03 2.30e-02 9.26e+00 pdb=" CG PHE C 29 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 PHE C 29 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 PHE C 29 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE C 29 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 29 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE C 29 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP B 53 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.23e+00 pdb=" C ASP B 53 " -0.050 2.00e-02 2.50e+03 pdb=" O ASP B 53 " 0.019 2.00e-02 2.50e+03 pdb=" N ALA B 54 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN R 62 " 0.042 5.00e-02 4.00e+02 6.30e-02 6.34e+00 pdb=" N PRO R 63 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO R 63 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO R 63 " 0.035 5.00e-02 4.00e+02 ... (remaining 10907 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 10406 2.77 - 3.30: 54538 3.30 - 3.83: 102117 3.83 - 4.37: 119591 4.37 - 4.90: 211630 Nonbonded interactions: 498282 Sorted by model distance: nonbonded pdb=" OG SER H 37 " pdb=" OE2 GLU H 76 " model vdw 2.233 2.440 nonbonded pdb=" OG SER O 37 " pdb=" OE2 GLU O 76 " model vdw 2.247 2.440 nonbonded pdb=" OG SER G 37 " pdb=" OE2 GLU G 76 " model vdw 2.254 2.440 nonbonded pdb=" O PRO F 16 " pdb=" OG1 THR F 20 " model vdw 2.283 2.440 nonbonded pdb=" OG SER N 37 " pdb=" OE2 GLU N 76 " model vdw 2.288 2.440 ... (remaining 498277 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' and resid 4 through 204) selection = (chain 'B' and resid 4 through 204) selection = (chain 'C' and resid 4 through 204) selection = (chain 'D' and resid 4 through 204) selection = (chain 'E' and resid 4 through 204) selection = chain 'F' selection = (chain 'G' and resid 4 through 204) selection = (chain 'H' and resid 4 through 204) selection = (chain 'I' and resid 4 through 204) selection = (chain 'J' and resid 4 through 204) selection = chain 'K' selection = chain 'L' selection = (chain 'M' and resid 4 through 204) selection = (chain 'N' and resid 4 through 204) selection = (chain 'O' and resid 4 through 204) selection = (chain 'P' and resid 4 through 204) selection = chain 'Q' selection = chain 'R' selection = (chain 'S' and resid 4 through 204) selection = (chain 'T' and resid 4 through 204) selection = (chain 'U' and resid 4 through 204) selection = (chain 'V' and resid 4 through 204) selection = chain 'W' selection = chain 'X' } ncs_group { reference = chain 'GA' selection = chain 'GB' selection = chain 'GC' selection = chain 'GD' selection = chain 'GE' selection = chain 'GF' selection = chain 'HA' selection = chain 'HB' selection = chain 'HC' selection = chain 'HD' selection = chain 'HE' selection = chain 'HF' selection = chain 'IA' selection = chain 'IB' selection = chain 'IC' selection = chain 'ID' selection = chain 'IE' selection = chain 'IF' selection = chain 'JA' selection = chain 'JB' selection = chain 'JC' selection = chain 'JD' selection = chain 'JE' selection = chain 'JF' selection = chain 'KA' selection = chain 'KB' selection = chain 'KC' selection = chain 'KD' selection = chain 'KE' selection = chain 'KF' selection = chain 'LA' selection = chain 'LB' selection = chain 'LC' selection = chain 'LD' selection = chain 'LE' selection = chain 'LF' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 26.680 Check model and map are aligned: 0.680 Set scattering table: 0.420 Process input model: 125.730 Find NCS groups from input model: 3.670 Set up NCS constraints: 0.470 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 166.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8275 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 : 0.009 0.129 61237 Z= 0.579 Angle : 0.864 10.533 83258 Z= 0.488 Chirality : 0.057 0.340 9935 Planarity : 0.008 0.063 10910 Dihedral : 9.203 85.744 22088 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 0.20 % Allowed : 2.78 % Favored : 97.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -3.46 (0.08), residues: 8042 helix: -3.07 (0.06), residues: 3196 sheet: -0.47 (0.11), residues: 2051 loop : -2.49 (0.10), residues: 2795 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.005 TRP B 39 HIS 0.009 0.002 HIS F 78 PHE 0.052 0.003 PHE C 29 TYR 0.036 0.003 TYR O 120 ARG 0.013 0.001 ARGGE 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2292 residues out of total 5973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 2280 time to evaluate : 5.121 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 0 residues processed: 2290 average time/residue: 0.6868 time to fit residues: 2469.1627 Evaluate side-chains 1614 residues out of total 5973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1614 time to evaluate : 5.367 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.7614 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 678 optimal weight: 0.9980 chunk 609 optimal weight: 0.9990 chunk 338 optimal weight: 0.8980 chunk 208 optimal weight: 0.5980 chunk 411 optimal weight: 0.7980 chunk 325 optimal weight: 1.9990 chunk 630 optimal weight: 0.7980 chunk 243 optimal weight: 0.1980 chunk 383 optimal weight: 1.9990 chunk 469 optimal weight: 0.7980 chunk 730 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 79 HIS A 112 GLN A 128 ASN B 78 HIS B 79 HIS C 78 HIS C 79 HIS C 128 ASN D 15 GLN D 78 HIS ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 HIS ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 GLN F 112 GLN ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** GD 82 ASN HA 82 ASN HB 82 ASN HD 82 ASN IA 82 ASN IB 82 ASN IF 82 ASN JB 82 ASN JD 61 GLN KB 82 ASN KD 82 ASN KF 82 ASN LB 82 ASN LD 82 ASN LF 82 ASN G 15 GLN ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 163 ASN G 168 ASN ** I 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 168 ASN J 62 GLN J 107 GLN ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 123 GLN L 128 ASN L 168 ASN M 168 ASN ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 165 HIS ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 78 HIS P 112 GLN P 168 ASN Q 17 GLN Q 111 HIS Q 165 HIS S 15 GLN S 66 GLN S 168 ASN T 66 GLN T 123 GLN T 163 ASN T 165 HIS U 15 GLN ** U 156 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 168 ASN V 15 GLN V 49 ASN V 66 GLN V 78 HIS V 128 ASN V 146 GLN V 165 HIS V 168 ASN W 49 ASN W 165 HIS W 168 ASN X 62 GLN X 78 HIS Total number of N/Q/H flips: 67 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 61237 Z= 0.229 Angle : 0.587 8.437 83258 Z= 0.317 Chirality : 0.044 0.219 9935 Planarity : 0.005 0.044 10910 Dihedral : 4.940 26.345 8774 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.70 % Allowed : 10.82 % Favored : 86.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -1.92 (0.09), residues: 8042 helix: -1.21 (0.08), residues: 3382 sheet: -0.47 (0.11), residues: 2188 loop : -1.79 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP S 39 HIS 0.014 0.001 HIS Q 111 PHE 0.024 0.001 PHE D 10 TYR 0.021 0.002 TYR M 172 ARG 0.010 0.001 ARG E 199 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1914 residues out of total 5973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 1753 time to evaluate : 5.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 161 outliers final: 90 residues processed: 1841 average time/residue: 0.7083 time to fit residues: 2059.9785 Evaluate side-chains 1649 residues out of total 5973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1559 time to evaluate : 5.177 Switching outliers to nearest non-outliers outliers start: 90 outliers final: 0 residues processed: 90 average time/residue: 0.4407 time to fit residues: 81.6042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 405 optimal weight: 3.9990 chunk 226 optimal weight: 0.6980 chunk 607 optimal weight: 1.9990 chunk 497 optimal weight: 0.0980 chunk 201 optimal weight: 2.9990 chunk 731 optimal weight: 5.9990 chunk 790 optimal weight: 0.8980 chunk 651 optimal weight: 5.9990 chunk 725 optimal weight: 0.5980 chunk 249 optimal weight: 0.9980 chunk 586 optimal weight: 5.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 GLN A 128 ASN A 163 ASN C 17 GLN C 128 ASN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 15 GLN ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HD 61 GLN ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 78 HIS I 123 GLN J 17 GLN J 78 HIS J 107 GLN ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 111 HIS ** P 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 112 GLN Q 111 HIS Q 112 GLN Q 165 HIS T 163 ASN ** W 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 168 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8325 moved from start: 0.3204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 61237 Z= 0.224 Angle : 0.555 8.003 83258 Z= 0.298 Chirality : 0.044 0.250 9935 Planarity : 0.004 0.055 10910 Dihedral : 4.538 20.849 8774 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.13 % Allowed : 12.99 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -1.18 (0.09), residues: 8042 helix: -0.42 (0.09), residues: 3389 sheet: -0.24 (0.11), residues: 2153 loop : -1.52 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 39 HIS 0.008 0.001 HIS Q 111 PHE 0.023 0.001 PHE K 10 TYR 0.023 0.002 TYR M 172 ARG 0.013 0.001 ARGIE 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1778 residues out of total 5973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1651 time to evaluate : 5.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 127 outliers final: 61 residues processed: 1712 average time/residue: 0.6900 time to fit residues: 1860.1769 Evaluate side-chains 1568 residues out of total 5973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1507 time to evaluate : 5.110 Switching outliers to nearest non-outliers outliers start: 61 outliers final: 0 residues processed: 61 average time/residue: 0.4452 time to fit residues: 57.4707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 722 optimal weight: 0.8980 chunk 549 optimal weight: 2.9990 chunk 379 optimal weight: 2.9990 chunk 80 optimal weight: 4.9990 chunk 349 optimal weight: 0.9990 chunk 491 optimal weight: 0.5980 chunk 734 optimal weight: 6.9990 chunk 777 optimal weight: 1.9990 chunk 383 optimal weight: 0.0970 chunk 695 optimal weight: 0.6980 chunk 209 optimal weight: 0.8980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 112 GLN ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 15 GLN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 HIS ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** GF 82 ASN KE 82 ASN ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 111 HIS ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 165 HIS J 168 ASN L 112 GLN P 49 ASN P 165 HIS Q 111 HIS T 163 ASN ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 15 GLN W 168 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 61237 Z= 0.216 Angle : 0.545 9.016 83258 Z= 0.291 Chirality : 0.043 0.237 9935 Planarity : 0.004 0.050 10910 Dihedral : 4.346 18.781 8774 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 2.26 % Allowed : 14.13 % Favored : 83.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.75 (0.09), residues: 8042 helix: 0.02 (0.09), residues: 3382 sheet: -0.09 (0.11), residues: 2139 loop : -1.37 (0.12), residues: 2521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 39 HIS 0.011 0.001 HIS J 111 PHE 0.022 0.001 PHE K 10 TYR 0.025 0.001 TYRIC 41 ARG 0.015 0.001 ARGIC 11 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1731 residues out of total 5973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 135 poor density : 1596 time to evaluate : 5.231 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 135 outliers final: 72 residues processed: 1658 average time/residue: 0.7517 time to fit residues: 1979.4716 Evaluate side-chains 1554 residues out of total 5973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 1482 time to evaluate : 5.128 Switching outliers to nearest non-outliers outliers start: 72 outliers final: 0 residues processed: 72 average time/residue: 0.4782 time to fit residues: 73.3470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 647 optimal weight: 4.9990 chunk 441 optimal weight: 0.0040 chunk 11 optimal weight: 2.9990 chunk 578 optimal weight: 1.9990 chunk 320 optimal weight: 0.9990 chunk 663 optimal weight: 1.9990 chunk 537 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 396 optimal weight: 0.9990 chunk 697 optimal weight: 1.9990 chunk 196 optimal weight: 0.8980 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN B 156 ASN E 15 GLN ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 111 HIS ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** IC 82 ASN KE 82 ASN ** G 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 168 ASN ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 78 HIS ** N 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 HIS Q 111 HIS ** S 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 163 ASN ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 112 GLN W 168 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 61237 Z= 0.270 Angle : 0.560 6.578 83258 Z= 0.298 Chirality : 0.044 0.341 9935 Planarity : 0.004 0.055 10910 Dihedral : 4.290 17.568 8774 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.88 % Allowed : 15.32 % Favored : 82.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.50 (0.09), residues: 8042 helix: 0.27 (0.09), residues: 3367 sheet: -0.04 (0.11), residues: 2179 loop : -1.23 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP C 39 HIS 0.008 0.001 HIS F 111 PHE 0.018 0.001 PHE X 10 TYR 0.025 0.002 TYR M 172 ARG 0.012 0.001 ARGKC 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1645 residues out of total 5973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1533 time to evaluate : 5.095 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 67 residues processed: 1579 average time/residue: 0.7188 time to fit residues: 1774.1812 Evaluate side-chains 1514 residues out of total 5973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 1447 time to evaluate : 5.104 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.4649 time to fit residues: 64.1848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 261 optimal weight: 0.9980 chunk 699 optimal weight: 0.7980 chunk 153 optimal weight: 0.7980 chunk 456 optimal weight: 0.8980 chunk 191 optimal weight: 0.0670 chunk 777 optimal weight: 5.9990 chunk 645 optimal weight: 0.7980 chunk 360 optimal weight: 3.9990 chunk 64 optimal weight: 0.0980 chunk 257 optimal weight: 2.9990 chunk 408 optimal weight: 0.9980 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN C 123 GLN ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 78 HIS ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** KE 82 ASN ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 168 ASN J 111 HIS ** O 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 HIS Q 111 HIS ** S 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 163 ASN ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 112 GLN W 168 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 61237 Z= 0.199 Angle : 0.540 7.690 83258 Z= 0.287 Chirality : 0.043 0.297 9935 Planarity : 0.004 0.072 10910 Dihedral : 4.187 17.645 8774 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 1.51 % Allowed : 16.12 % Favored : 82.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.25 (0.09), residues: 8042 helix: 0.51 (0.09), residues: 3367 sheet: 0.07 (0.11), residues: 2161 loop : -1.15 (0.12), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP U 39 HIS 0.004 0.001 HIS F 79 PHE 0.019 0.001 PHE U 175 TYR 0.022 0.001 TYR M 172 ARG 0.017 0.001 ARG W 99 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1602 residues out of total 5973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1512 time to evaluate : 5.169 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 90 outliers final: 48 residues processed: 1552 average time/residue: 0.7236 time to fit residues: 1762.1943 Evaluate side-chains 1481 residues out of total 5973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1433 time to evaluate : 5.112 Switching outliers to nearest non-outliers outliers start: 48 outliers final: 0 residues processed: 48 average time/residue: 0.4297 time to fit residues: 46.4304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 749 optimal weight: 0.5980 chunk 87 optimal weight: 5.9990 chunk 443 optimal weight: 1.9990 chunk 568 optimal weight: 0.5980 chunk 440 optimal weight: 2.9990 chunk 654 optimal weight: 10.0000 chunk 434 optimal weight: 1.9990 chunk 774 optimal weight: 2.9990 chunk 484 optimal weight: 3.9990 chunk 472 optimal weight: 0.7980 chunk 357 optimal weight: 0.6980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN D 79 HIS ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** KE 82 ASN G 78 HIS ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 123 GLN ** N 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 128 ASN ** O 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 17 GLN Q 49 ASN ** Q 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 HIS Q 111 HIS R 78 HIS T 163 ASN ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 112 GLN W 168 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 61237 Z= 0.265 Angle : 0.569 9.051 83258 Z= 0.301 Chirality : 0.044 0.230 9935 Planarity : 0.004 0.077 10910 Dihedral : 4.187 18.988 8774 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 13.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.56 % Allowed : 16.78 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.21 (0.09), residues: 8042 helix: 0.53 (0.09), residues: 3367 sheet: 0.10 (0.11), residues: 2161 loop : -1.10 (0.12), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP U 39 HIS 0.018 0.001 HISLD 74 PHE 0.019 0.001 PHE U 175 TYR 0.025 0.002 TYR M 172 ARG 0.017 0.001 ARG J 99 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1564 residues out of total 5973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1471 time to evaluate : 5.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 93 outliers final: 53 residues processed: 1504 average time/residue: 0.7069 time to fit residues: 1662.1379 Evaluate side-chains 1466 residues out of total 5973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1413 time to evaluate : 5.067 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 0.4515 time to fit residues: 51.2801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 479 optimal weight: 0.8980 chunk 309 optimal weight: 1.9990 chunk 462 optimal weight: 0.8980 chunk 233 optimal weight: 0.8980 chunk 152 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 chunk 492 optimal weight: 0.9980 chunk 527 optimal weight: 0.9990 chunk 383 optimal weight: 0.0980 chunk 72 optimal weight: 3.9990 chunk 609 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 15 GLN ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 GLN ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IA 82 ASN ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 165 HIS J 15 GLN J 111 HIS M 123 GLN ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 128 ASN ** O 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 ASN Q 79 HIS Q 111 HIS ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 168 ASN X 49 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 61237 Z= 0.220 Angle : 0.561 10.273 83258 Z= 0.296 Chirality : 0.043 0.191 9935 Planarity : 0.004 0.067 10910 Dihedral : 4.169 18.393 8774 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 14.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 1.02 % Allowed : 17.34 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.10 (0.09), residues: 8042 helix: 0.62 (0.09), residues: 3367 sheet: 0.15 (0.11), residues: 2161 loop : -1.05 (0.12), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP U 39 HIS 0.008 0.001 HISLD 74 PHE 0.019 0.001 PHE X 10 TYR 0.024 0.001 TYR F 8 ARG 0.014 0.001 ARGJB 62 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1525 residues out of total 5973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 1464 time to evaluate : 5.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 35 residues processed: 1485 average time/residue: 0.7316 time to fit residues: 1711.4259 Evaluate side-chains 1443 residues out of total 5973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1408 time to evaluate : 5.134 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.4640 time to fit residues: 37.2978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 704 optimal weight: 4.9990 chunk 742 optimal weight: 0.9980 chunk 677 optimal weight: 2.9990 chunk 722 optimal weight: 0.9990 chunk 434 optimal weight: 1.9990 chunk 314 optimal weight: 0.8980 chunk 567 optimal weight: 1.9990 chunk 221 optimal weight: 0.1980 chunk 652 optimal weight: 0.6980 chunk 682 optimal weight: 0.9980 chunk 719 optimal weight: 0.7980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 GLN ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 ASN ** Q 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 HIS Q 111 HIS ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 168 ASN X 49 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.4125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 61237 Z= 0.234 Angle : 0.576 10.634 83258 Z= 0.303 Chirality : 0.044 0.275 9935 Planarity : 0.004 0.089 10910 Dihedral : 4.152 18.316 8774 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 14.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.74 % Allowed : 18.11 % Favored : 81.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.03 (0.09), residues: 8042 helix: 0.68 (0.09), residues: 3351 sheet: 0.16 (0.11), residues: 2161 loop : -0.99 (0.12), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 39 HIS 0.007 0.001 HISLD 74 PHE 0.020 0.001 PHE X 10 TYR 0.026 0.002 TYR L 8 ARG 0.018 0.001 ARG W 99 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1492 residues out of total 5973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1448 time to evaluate : 5.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 25 residues processed: 1465 average time/residue: 0.7222 time to fit residues: 1657.4428 Evaluate side-chains 1435 residues out of total 5973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1410 time to evaluate : 5.290 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 25 outliers final: 1 residues processed: 25 average time/residue: 0.4688 time to fit residues: 29.1852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 474 optimal weight: 2.9990 chunk 763 optimal weight: 5.9990 chunk 466 optimal weight: 2.9990 chunk 362 optimal weight: 0.5980 chunk 530 optimal weight: 0.9980 chunk 800 optimal weight: 2.9990 chunk 737 optimal weight: 0.9990 chunk 637 optimal weight: 4.9990 chunk 66 optimal weight: 3.9990 chunk 492 optimal weight: 0.9990 chunk 391 optimal weight: 1.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 78 HIS ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 78 HIS ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 GLN ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 163 ASN J 111 HIS ** M 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 128 ASN O 78 HIS Q 49 ASN ** Q 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 HIS Q 111 HIS ** S 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 78 HIS ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 168 ASN X 49 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8361 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 61237 Z= 0.306 Angle : 0.615 10.712 83258 Z= 0.322 Chirality : 0.045 0.262 9935 Planarity : 0.004 0.095 10910 Dihedral : 4.235 17.822 8774 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 14.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 0.57 % Allowed : 19.02 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.10 (0.09), residues: 8042 helix: 0.61 (0.09), residues: 3351 sheet: 0.14 (0.11), residues: 2161 loop : -1.00 (0.13), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 39 HIS 0.007 0.001 HISLD 74 PHE 0.022 0.001 PHE O 175 TYR 0.026 0.002 TYR L 8 ARG 0.021 0.001 ARG X 99 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16084 Ramachandran restraints generated. 8042 Oldfield, 0 Emsley, 8042 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1472 residues out of total 5973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1438 time to evaluate : 5.166 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 23 residues processed: 1447 average time/residue: 0.7434 time to fit residues: 1687.6373 Evaluate side-chains 1425 residues out of total 5973 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1402 time to evaluate : 5.268 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.4844 time to fit residues: 27.7252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 804 random chunks: chunk 506 optimal weight: 1.9990 chunk 679 optimal weight: 1.9990 chunk 195 optimal weight: 2.9990 chunk 588 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 177 optimal weight: 0.9990 chunk 638 optimal weight: 0.9980 chunk 267 optimal weight: 2.9990 chunk 655 optimal weight: 0.4980 chunk 80 optimal weight: 0.6980 chunk 117 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 66 GLN ** F 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** IF 82 ASN ** G 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 168 ASN ** H 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 165 HIS J 165 HIS ** K 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 126 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 128 ASN ** Q 17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 49 ASN ** Q 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 79 HIS Q 111 HIS ** S 78 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 168 ASN X 49 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.111480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.097753 restraints weight = 107711.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.100397 restraints weight = 49186.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.102076 restraints weight = 28409.360| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 61237 Z= 0.251 Angle : 0.596 10.467 83258 Z= 0.313 Chirality : 0.044 0.265 9935 Planarity : 0.004 0.077 10910 Dihedral : 4.209 20.194 8774 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.60 % Allowed : 18.95 % Favored : 80.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 13.33 % 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: -0.02 (0.10), residues: 8042 helix: 0.69 (0.09), residues: 3351 sheet: 0.17 (0.11), residues: 2161 loop : -0.96 (0.13), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP C 39 HIS 0.006 0.001 HISLD 74 PHE 0.022 0.001 PHE X 10 TYR 0.025 0.002 TYR L 8 ARG 0.019 0.001 ARG X 99 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 23435.21 seconds wall clock time: 405 minutes 28.24 seconds (24328.24 seconds total)