Starting phenix.real_space_refine (version: dev) on Sat Apr 9 11:49:44 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5s_0142/04_2022/6h5s_0142.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5s_0142/04_2022/6h5s_0142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5s_0142/04_2022/6h5s_0142.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5s_0142/04_2022/6h5s_0142.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5s_0142/04_2022/6h5s_0142.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5s_0142/04_2022/6h5s_0142.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "C ARG 54": "NH1" <-> "NH2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C ARG 100": "NH1" <-> "NH2" Residue "C ARG 194": "NH1" <-> "NH2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C ARG 222": "NH1" <-> "NH2" Residue "C ARG 230": "NH1" <-> "NH2" Residue "C PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 370": "NH1" <-> "NH2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A ARG 194": "NH1" <-> "NH2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 204": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "D ARG 54": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D ARG 194": "NH1" <-> "NH2" Residue "D ARG 195": "NH1" <-> "NH2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D ARG 204": "NH1" <-> "NH2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "D ARG 222": "NH1" <-> "NH2" Residue "D ARG 230": "NH1" <-> "NH2" Residue "D PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 370": "NH1" <-> "NH2" Residue "G ARG 54": "NH1" <-> "NH2" Residue "G ARG 57": "NH1" <-> "NH2" Residue "G ARG 100": "NH1" <-> "NH2" Residue "G ARG 194": "NH1" <-> "NH2" Residue "G ARG 195": "NH1" <-> "NH2" Residue "G ARG 203": "NH1" <-> "NH2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "G ARG 213": "NH1" <-> "NH2" Residue "G ARG 222": "NH1" <-> "NH2" Residue "G ARG 230": "NH1" <-> "NH2" Residue "G PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 370": "NH1" <-> "NH2" Residue "I ARG 54": "NH1" <-> "NH2" Residue "I ARG 57": "NH1" <-> "NH2" Residue "I ARG 100": "NH1" <-> "NH2" Residue "I ARG 194": "NH1" <-> "NH2" Residue "I ARG 195": "NH1" <-> "NH2" Residue "I ARG 203": "NH1" <-> "NH2" Residue "I ARG 204": "NH1" <-> "NH2" Residue "I ARG 213": "NH1" <-> "NH2" Residue "I ARG 222": "NH1" <-> "NH2" Residue "I ARG 230": "NH1" <-> "NH2" Residue "I PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 370": "NH1" <-> "NH2" Residue "K ARG 54": "NH1" <-> "NH2" Residue "K ARG 57": "NH1" <-> "NH2" Residue "K ARG 100": "NH1" <-> "NH2" Residue "K ARG 194": "NH1" <-> "NH2" Residue "K ARG 195": "NH1" <-> "NH2" Residue "K ARG 203": "NH1" <-> "NH2" Residue "K ARG 204": "NH1" <-> "NH2" Residue "K ARG 213": "NH1" <-> "NH2" Residue "K ARG 222": "NH1" <-> "NH2" Residue "K ARG 230": "NH1" <-> "NH2" Residue "K PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 370": "NH1" <-> "NH2" Residue "M ARG 54": "NH1" <-> "NH2" Residue "M ARG 57": "NH1" <-> "NH2" Residue "M ARG 100": "NH1" <-> "NH2" Residue "M ARG 194": "NH1" <-> "NH2" Residue "M ARG 195": "NH1" <-> "NH2" Residue "M ARG 203": "NH1" <-> "NH2" Residue "M ARG 204": "NH1" <-> "NH2" Residue "M ARG 213": "NH1" <-> "NH2" Residue "M ARG 222": "NH1" <-> "NH2" Residue "M ARG 230": "NH1" <-> "NH2" Residue "M PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 370": "NH1" <-> "NH2" Residue "O ARG 54": "NH1" <-> "NH2" Residue "O ARG 57": "NH1" <-> "NH2" Residue "O ARG 100": "NH1" <-> "NH2" Residue "O ARG 194": "NH1" <-> "NH2" Residue "O ARG 195": "NH1" <-> "NH2" Residue "O ARG 203": "NH1" <-> "NH2" Residue "O ARG 204": "NH1" <-> "NH2" Residue "O ARG 213": "NH1" <-> "NH2" Residue "O ARG 222": "NH1" <-> "NH2" Residue "O ARG 230": "NH1" <-> "NH2" Residue "O PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 370": "NH1" <-> "NH2" Residue "Q ARG 54": "NH1" <-> "NH2" Residue "Q ARG 57": "NH1" <-> "NH2" Residue "Q ARG 100": "NH1" <-> "NH2" Residue "Q ARG 194": "NH1" <-> "NH2" Residue "Q ARG 195": "NH1" <-> "NH2" Residue "Q ARG 203": "NH1" <-> "NH2" Residue "Q ARG 204": "NH1" <-> "NH2" Residue "Q ARG 213": "NH1" <-> "NH2" Residue "Q ARG 222": "NH1" <-> "NH2" Residue "Q ARG 230": "NH1" <-> "NH2" Residue "Q PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 370": "NH1" <-> "NH2" Residue "S ARG 54": "NH1" <-> "NH2" Residue "S ARG 57": "NH1" <-> "NH2" Residue "S ARG 100": "NH1" <-> "NH2" Residue "S ARG 194": "NH1" <-> "NH2" Residue "S ARG 195": "NH1" <-> "NH2" Residue "S ARG 203": "NH1" <-> "NH2" Residue "S ARG 204": "NH1" <-> "NH2" Residue "S ARG 213": "NH1" <-> "NH2" Residue "S ARG 222": "NH1" <-> "NH2" Residue "S ARG 230": "NH1" <-> "NH2" Residue "S PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 370": "NH1" <-> "NH2" Residue "U ARG 54": "NH1" <-> "NH2" Residue "U ARG 57": "NH1" <-> "NH2" Residue "U ARG 100": "NH1" <-> "NH2" Residue "U ARG 194": "NH1" <-> "NH2" Residue "U ARG 195": "NH1" <-> "NH2" Residue "U ARG 203": "NH1" <-> "NH2" Residue "U ARG 204": "NH1" <-> "NH2" Residue "U ARG 213": "NH1" <-> "NH2" Residue "U ARG 222": "NH1" <-> "NH2" Residue "U ARG 230": "NH1" <-> "NH2" Residue "U PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 370": "NH1" <-> "NH2" Residue "W ARG 54": "NH1" <-> "NH2" Residue "W ARG 57": "NH1" <-> "NH2" Residue "W ARG 100": "NH1" <-> "NH2" Residue "W ARG 194": "NH1" <-> "NH2" Residue "W ARG 195": "NH1" <-> "NH2" Residue "W ARG 203": "NH1" <-> "NH2" Residue "W ARG 204": "NH1" <-> "NH2" Residue "W ARG 213": "NH1" <-> "NH2" Residue "W ARG 222": "NH1" <-> "NH2" Residue "W ARG 230": "NH1" <-> "NH2" Residue "W PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 370": "NH1" <-> "NH2" Residue "Y ARG 54": "NH1" <-> "NH2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y ARG 100": "NH1" <-> "NH2" Residue "Y ARG 194": "NH1" <-> "NH2" Residue "Y ARG 195": "NH1" <-> "NH2" Residue "Y ARG 203": "NH1" <-> "NH2" Residue "Y ARG 204": "NH1" <-> "NH2" Residue "Y ARG 213": "NH1" <-> "NH2" Residue "Y ARG 222": "NH1" <-> "NH2" Residue "Y ARG 230": "NH1" <-> "NH2" Residue "Y PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 370": "NH1" <-> "NH2" Residue "0 ARG 54": "NH1" <-> "NH2" Residue "0 ARG 57": "NH1" <-> "NH2" Residue "0 ARG 100": "NH1" <-> "NH2" Residue "0 ARG 194": "NH1" <-> "NH2" Residue "0 ARG 195": "NH1" <-> "NH2" Residue "0 ARG 203": "NH1" <-> "NH2" Residue "0 ARG 204": "NH1" <-> "NH2" Residue "0 ARG 213": "NH1" <-> "NH2" Residue "0 ARG 222": "NH1" <-> "NH2" Residue "0 ARG 230": "NH1" <-> "NH2" Residue "0 PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 370": "NH1" <-> "NH2" Residue "2 ARG 54": "NH1" <-> "NH2" Residue "2 ARG 57": "NH1" <-> "NH2" Residue "2 ARG 100": "NH1" <-> "NH2" Residue "2 ARG 194": "NH1" <-> "NH2" Residue "2 ARG 195": "NH1" <-> "NH2" Residue "2 ARG 203": "NH1" <-> "NH2" Residue "2 ARG 204": "NH1" <-> "NH2" Residue "2 ARG 213": "NH1" <-> "NH2" Residue "2 ARG 222": "NH1" <-> "NH2" Residue "2 ARG 230": "NH1" <-> "NH2" Residue "2 PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 370": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 44700 Number of models: 1 Model: "" Number of chains: 30 Chain: "C" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "A" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "D" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "F" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "G" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "H" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "I" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "J" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "K" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "L" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "M" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "N" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "O" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "P" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "Q" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "R" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "S" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "T" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "U" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "V" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "W" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "X" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "Y" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "Z" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "0" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "1" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "2" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "3" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna3p_pur': 4, 'rna2p_pyr': 1, 'rna3p_pyr': 1} Link IDs: {'rna3p': 4, 'rna2p': 1} Time building chain proxies: 24.52, per 1000 atoms: 0.55 Number of scatterers: 44700 At special positions: 0 Unit cell: (204, 204.816, 129.744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 P 75 15.00 O 8520 8.00 N 7740 7.00 C 28185 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: 18.55 Conformation dependent library (CDL) restraints added in 6.5 seconds 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10020 Finding SS restraints... Secondary structure from input PDB file: 330 helices and 15 sheets defined 61.7% alpha, 4.4% beta 0 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 13.01 Creating SS restraints... Processing helix chain 'C' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG C 6 " --> pdb=" O ALA C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG C 48 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG C 57 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 77 Processing helix chain 'C' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG C 90 " --> pdb=" O GLN C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 132 Processing helix chain 'C' and resid 159 through 172 Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS C 180 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C 181 " --> pdb=" O LEU C 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 181' Processing helix chain 'C' and resid 185 through 187 No H-bonds generated for 'chain 'C' and resid 185 through 187' Processing helix chain 'C' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 194 " --> pdb=" O ASP C 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG C 195 " --> pdb=" O SER C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 Processing helix chain 'C' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE C 237 " --> pdb=" O MET C 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG C 242 " --> pdb=" O LEU C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 258 Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR C 272 " --> pdb=" O SER C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY C 291 " --> pdb=" O HIS C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU C 299 " --> pdb=" O THR C 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN C 304 " --> pdb=" O MET C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR C 309 " --> pdb=" O MET C 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 310 " --> pdb=" O GLY C 307 " (cutoff:3.500A) Proline residue: C 311 - end of helix No H-bonds generated for 'chain 'C' and resid 306 through 313' Processing helix chain 'C' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN C 321 " --> pdb=" O ASN C 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN C 322 " --> pdb=" O SER C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 328 removed outlier: 3.516A pdb=" N SER C 328 " --> pdb=" O SER C 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 325 through 328' Processing helix chain 'C' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER C 334 " --> pdb=" O PRO C 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU C 342 " --> pdb=" O GLY C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE C 362 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL C 369 " --> pdb=" O GLY C 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN A 89 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 159 through 172 Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS A 180 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 181 " --> pdb=" O LEU A 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 177 through 181' Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 258 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY A 291 " --> pdb=" O HIS A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 304 " --> pdb=" O MET A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR A 309 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 310 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Proline residue: A 311 - end of helix No H-bonds generated for 'chain 'A' and resid 306 through 313' Processing helix chain 'A' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN A 321 " --> pdb=" O ASN A 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 322 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER A 328 " --> pdb=" O SER A 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 325 through 328' Processing helix chain 'A' and resid 329 through 344 removed outlier: 3.852A pdb=" N SER A 334 " --> pdb=" O PRO A 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 358 through 372 removed outlier: 3.823A pdb=" N PHE A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 369 " --> pdb=" O GLY A 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 13 removed outlier: 4.184A pdb=" N ARG D 6 " --> pdb=" O ALA D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG D 48 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG D 57 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 77 Processing helix chain 'D' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG D 90 " --> pdb=" O GLN D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 159 through 172 Processing helix chain 'D' and resid 177 through 181 removed outlier: 3.533A pdb=" N LYS D 180 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA D 181 " --> pdb=" O LEU D 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 177 through 181' Processing helix chain 'D' and resid 185 through 187 No H-bonds generated for 'chain 'D' and resid 185 through 187' Processing helix chain 'D' and resid 188 through 202 removed outlier: 3.674A pdb=" N LEU D 193 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG D 194 " --> pdb=" O ASP D 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG D 195 " --> pdb=" O SER D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 226 Processing helix chain 'D' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG D 242 " --> pdb=" O LEU D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 258 Processing helix chain 'D' and resid 259 through 261 No H-bonds generated for 'chain 'D' and resid 259 through 261' Processing helix chain 'D' and resid 266 through 276 removed outlier: 3.562A pdb=" N LEU D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR D 272 " --> pdb=" O SER D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY D 291 " --> pdb=" O HIS D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 305 removed outlier: 4.278A pdb=" N LEU D 299 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN D 304 " --> pdb=" O MET D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR D 309 " --> pdb=" O MET D 306 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA D 310 " --> pdb=" O GLY D 307 " (cutoff:3.500A) Proline residue: D 311 - end of helix No H-bonds generated for 'chain 'D' and resid 306 through 313' Processing helix chain 'D' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN D 321 " --> pdb=" O ASN D 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN D 322 " --> pdb=" O SER D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER D 328 " --> pdb=" O SER D 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 325 through 328' Processing helix chain 'D' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER D 334 " --> pdb=" O PRO D 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU D 342 " --> pdb=" O GLY D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 358 through 372 removed outlier: 3.823A pdb=" N PHE D 362 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL D 369 " --> pdb=" O GLY D 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG G 6 " --> pdb=" O ALA G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG G 48 " --> pdb=" O SER G 44 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG G 57 " --> pdb=" O ASP G 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU G 58 " --> pdb=" O ARG G 54 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 77 Processing helix chain 'G' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN G 89 " --> pdb=" O GLY G 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG G 90 " --> pdb=" O GLN G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 132 Processing helix chain 'G' and resid 159 through 172 Processing helix chain 'G' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS G 180 " --> pdb=" O LEU G 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA G 181 " --> pdb=" O LEU G 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 177 through 181' Processing helix chain 'G' and resid 185 through 187 No H-bonds generated for 'chain 'G' and resid 185 through 187' Processing helix chain 'G' and resid 188 through 202 removed outlier: 3.674A pdb=" N LEU G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG G 194 " --> pdb=" O ASP G 190 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG G 195 " --> pdb=" O SER G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 226 Processing helix chain 'G' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE G 237 " --> pdb=" O MET G 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG G 242 " --> pdb=" O LEU G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 258 Processing helix chain 'G' and resid 259 through 261 No H-bonds generated for 'chain 'G' and resid 259 through 261' Processing helix chain 'G' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU G 271 " --> pdb=" O ALA G 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR G 272 " --> pdb=" O SER G 268 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY G 291 " --> pdb=" O HIS G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU G 299 " --> pdb=" O THR G 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN G 304 " --> pdb=" O MET G 300 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 313 removed outlier: 4.167A pdb=" N THR G 309 " --> pdb=" O MET G 306 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA G 310 " --> pdb=" O GLY G 307 " (cutoff:3.500A) Proline residue: G 311 - end of helix No H-bonds generated for 'chain 'G' and resid 306 through 313' Processing helix chain 'G' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN G 321 " --> pdb=" O ASN G 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN G 322 " --> pdb=" O SER G 319 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER G 328 " --> pdb=" O SER G 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 325 through 328' Processing helix chain 'G' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER G 334 " --> pdb=" O PRO G 330 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU G 342 " --> pdb=" O GLY G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 350 Processing helix chain 'G' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE G 362 " --> pdb=" O ASP G 358 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL G 369 " --> pdb=" O GLY G 365 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG I 6 " --> pdb=" O ALA I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG I 48 " --> pdb=" O SER I 44 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG I 57 " --> pdb=" O ASP I 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU I 58 " --> pdb=" O ARG I 54 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE I 59 " --> pdb=" O LEU I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 77 Processing helix chain 'I' and resid 84 through 92 removed outlier: 3.681A pdb=" N GLN I 89 " --> pdb=" O GLY I 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG I 90 " --> pdb=" O GLN I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 132 Processing helix chain 'I' and resid 159 through 172 Processing helix chain 'I' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS I 180 " --> pdb=" O LEU I 177 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA I 181 " --> pdb=" O LEU I 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 177 through 181' Processing helix chain 'I' and resid 185 through 187 No H-bonds generated for 'chain 'I' and resid 185 through 187' Processing helix chain 'I' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU I 193 " --> pdb=" O ALA I 189 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG I 194 " --> pdb=" O ASP I 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG I 195 " --> pdb=" O SER I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 212 through 226 Processing helix chain 'I' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG I 242 " --> pdb=" O LEU I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 248 through 258 Processing helix chain 'I' and resid 259 through 261 No H-bonds generated for 'chain 'I' and resid 259 through 261' Processing helix chain 'I' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU I 271 " --> pdb=" O ALA I 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR I 272 " --> pdb=" O SER I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY I 291 " --> pdb=" O HIS I 287 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 305 removed outlier: 4.278A pdb=" N LEU I 299 " --> pdb=" O THR I 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN I 304 " --> pdb=" O MET I 300 " (cutoff:3.500A) Processing helix chain 'I' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR I 309 " --> pdb=" O MET I 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA I 310 " --> pdb=" O GLY I 307 " (cutoff:3.500A) Proline residue: I 311 - end of helix No H-bonds generated for 'chain 'I' and resid 306 through 313' Processing helix chain 'I' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN I 321 " --> pdb=" O ASN I 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN I 322 " --> pdb=" O SER I 319 " (cutoff:3.500A) Processing helix chain 'I' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER I 328 " --> pdb=" O SER I 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 325 through 328' Processing helix chain 'I' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER I 334 " --> pdb=" O PRO I 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU I 342 " --> pdb=" O GLY I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 350 Processing helix chain 'I' and resid 358 through 372 removed outlier: 3.823A pdb=" N PHE I 362 " --> pdb=" O ASP I 358 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL I 369 " --> pdb=" O GLY I 365 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG K 6 " --> pdb=" O ALA K 2 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG K 48 " --> pdb=" O SER K 44 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG K 57 " --> pdb=" O ASP K 53 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU K 58 " --> pdb=" O ARG K 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE K 59 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 77 Processing helix chain 'K' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN K 89 " --> pdb=" O GLY K 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG K 90 " --> pdb=" O GLN K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 132 Processing helix chain 'K' and resid 159 through 172 Processing helix chain 'K' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS K 180 " --> pdb=" O LEU K 177 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA K 181 " --> pdb=" O LEU K 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 177 through 181' Processing helix chain 'K' and resid 185 through 187 No H-bonds generated for 'chain 'K' and resid 185 through 187' Processing helix chain 'K' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU K 193 " --> pdb=" O ALA K 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG K 194 " --> pdb=" O ASP K 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG K 195 " --> pdb=" O SER K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 212 through 226 Processing helix chain 'K' and resid 227 through 242 removed outlier: 3.512A pdb=" N ILE K 237 " --> pdb=" O MET K 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG K 242 " --> pdb=" O LEU K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 258 Processing helix chain 'K' and resid 259 through 261 No H-bonds generated for 'chain 'K' and resid 259 through 261' Processing helix chain 'K' and resid 266 through 276 removed outlier: 3.562A pdb=" N LEU K 271 " --> pdb=" O ALA K 267 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR K 272 " --> pdb=" O SER K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY K 291 " --> pdb=" O HIS K 287 " (cutoff:3.500A) Processing helix chain 'K' and resid 293 through 305 removed outlier: 4.278A pdb=" N LEU K 299 " --> pdb=" O THR K 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN K 304 " --> pdb=" O MET K 300 " (cutoff:3.500A) Processing helix chain 'K' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR K 309 " --> pdb=" O MET K 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA K 310 " --> pdb=" O GLY K 307 " (cutoff:3.500A) Proline residue: K 311 - end of helix No H-bonds generated for 'chain 'K' and resid 306 through 313' Processing helix chain 'K' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN K 321 " --> pdb=" O ASN K 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN K 322 " --> pdb=" O SER K 319 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER K 328 " --> pdb=" O SER K 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 325 through 328' Processing helix chain 'K' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER K 334 " --> pdb=" O PRO K 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU K 342 " --> pdb=" O GLY K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 345 through 350 Processing helix chain 'K' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE K 362 " --> pdb=" O ASP K 358 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL K 369 " --> pdb=" O GLY K 365 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG M 6 " --> pdb=" O ALA M 2 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG M 48 " --> pdb=" O SER M 44 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG M 57 " --> pdb=" O ASP M 53 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU M 58 " --> pdb=" O ARG M 54 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE M 59 " --> pdb=" O LEU M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 77 Processing helix chain 'M' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN M 89 " --> pdb=" O GLY M 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG M 90 " --> pdb=" O GLN M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 132 Processing helix chain 'M' and resid 159 through 172 Processing helix chain 'M' and resid 177 through 181 removed outlier: 3.533A pdb=" N LYS M 180 " --> pdb=" O LEU M 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA M 181 " --> pdb=" O LEU M 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 177 through 181' Processing helix chain 'M' and resid 185 through 187 No H-bonds generated for 'chain 'M' and resid 185 through 187' Processing helix chain 'M' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU M 193 " --> pdb=" O ALA M 189 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG M 194 " --> pdb=" O ASP M 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG M 195 " --> pdb=" O SER M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 226 Processing helix chain 'M' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE M 237 " --> pdb=" O MET M 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG M 242 " --> pdb=" O LEU M 238 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 258 Processing helix chain 'M' and resid 259 through 261 No H-bonds generated for 'chain 'M' and resid 259 through 261' Processing helix chain 'M' and resid 266 through 276 removed outlier: 3.562A pdb=" N LEU M 271 " --> pdb=" O ALA M 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR M 272 " --> pdb=" O SER M 268 " (cutoff:3.500A) Processing helix chain 'M' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY M 291 " --> pdb=" O HIS M 287 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU M 299 " --> pdb=" O THR M 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN M 304 " --> pdb=" O MET M 300 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR M 309 " --> pdb=" O MET M 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA M 310 " --> pdb=" O GLY M 307 " (cutoff:3.500A) Proline residue: M 311 - end of helix No H-bonds generated for 'chain 'M' and resid 306 through 313' Processing helix chain 'M' and resid 318 through 323 removed outlier: 3.921A pdb=" N GLN M 321 " --> pdb=" O ASN M 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN M 322 " --> pdb=" O SER M 319 " (cutoff:3.500A) Processing helix chain 'M' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER M 328 " --> pdb=" O SER M 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 325 through 328' Processing helix chain 'M' and resid 329 through 344 removed outlier: 3.852A pdb=" N SER M 334 " --> pdb=" O PRO M 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU M 342 " --> pdb=" O GLY M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 345 through 350 Processing helix chain 'M' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE M 362 " --> pdb=" O ASP M 358 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL M 369 " --> pdb=" O GLY M 365 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 13 removed outlier: 4.184A pdb=" N ARG O 6 " --> pdb=" O ALA O 2 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG O 48 " --> pdb=" O SER O 44 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG O 57 " --> pdb=" O ASP O 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU O 58 " --> pdb=" O ARG O 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE O 59 " --> pdb=" O LEU O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 77 Processing helix chain 'O' and resid 84 through 92 removed outlier: 3.681A pdb=" N GLN O 89 " --> pdb=" O GLY O 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG O 90 " --> pdb=" O GLN O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 132 Processing helix chain 'O' and resid 159 through 172 Processing helix chain 'O' and resid 177 through 181 removed outlier: 3.533A pdb=" N LYS O 180 " --> pdb=" O LEU O 177 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA O 181 " --> pdb=" O LEU O 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 177 through 181' Processing helix chain 'O' and resid 185 through 187 No H-bonds generated for 'chain 'O' and resid 185 through 187' Processing helix chain 'O' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU O 193 " --> pdb=" O ALA O 189 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG O 194 " --> pdb=" O ASP O 190 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG O 195 " --> pdb=" O SER O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 212 through 226 Processing helix chain 'O' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE O 237 " --> pdb=" O MET O 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG O 242 " --> pdb=" O LEU O 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 248 through 258 Processing helix chain 'O' and resid 259 through 261 No H-bonds generated for 'chain 'O' and resid 259 through 261' Processing helix chain 'O' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU O 271 " --> pdb=" O ALA O 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR O 272 " --> pdb=" O SER O 268 " (cutoff:3.500A) Processing helix chain 'O' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY O 291 " --> pdb=" O HIS O 287 " (cutoff:3.500A) Processing helix chain 'O' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU O 299 " --> pdb=" O THR O 295 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN O 304 " --> pdb=" O MET O 300 " (cutoff:3.500A) Processing helix chain 'O' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR O 309 " --> pdb=" O MET O 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA O 310 " --> pdb=" O GLY O 307 " (cutoff:3.500A) Proline residue: O 311 - end of helix No H-bonds generated for 'chain 'O' and resid 306 through 313' Processing helix chain 'O' and resid 318 through 323 removed outlier: 3.921A pdb=" N GLN O 321 " --> pdb=" O ASN O 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN O 322 " --> pdb=" O SER O 319 " (cutoff:3.500A) Processing helix chain 'O' and resid 325 through 328 removed outlier: 3.516A pdb=" N SER O 328 " --> pdb=" O SER O 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 325 through 328' Processing helix chain 'O' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER O 334 " --> pdb=" O PRO O 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU O 342 " --> pdb=" O GLY O 338 " (cutoff:3.500A) Processing helix chain 'O' and resid 345 through 350 Processing helix chain 'O' and resid 358 through 372 removed outlier: 3.823A pdb=" N PHE O 362 " --> pdb=" O ASP O 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL O 369 " --> pdb=" O GLY O 365 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 13 removed outlier: 4.184A pdb=" N ARG Q 6 " --> pdb=" O ALA Q 2 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG Q 48 " --> pdb=" O SER Q 44 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG Q 57 " --> pdb=" O ASP Q 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU Q 58 " --> pdb=" O ARG Q 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE Q 59 " --> pdb=" O LEU Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 65 through 77 Processing helix chain 'Q' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN Q 89 " --> pdb=" O GLY Q 85 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG Q 90 " --> pdb=" O GLN Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 132 Processing helix chain 'Q' and resid 159 through 172 Processing helix chain 'Q' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS Q 180 " --> pdb=" O LEU Q 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA Q 181 " --> pdb=" O LEU Q 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 177 through 181' Processing helix chain 'Q' and resid 185 through 187 No H-bonds generated for 'chain 'Q' and resid 185 through 187' Processing helix chain 'Q' and resid 188 through 202 removed outlier: 3.674A pdb=" N LEU Q 193 " --> pdb=" O ALA Q 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG Q 194 " --> pdb=" O ASP Q 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG Q 195 " --> pdb=" O SER Q 191 " (cutoff:3.500A) Processing helix chain 'Q' and resid 212 through 226 Processing helix chain 'Q' and resid 227 through 242 removed outlier: 3.510A pdb=" N ILE Q 237 " --> pdb=" O MET Q 233 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG Q 242 " --> pdb=" O LEU Q 238 " (cutoff:3.500A) Processing helix chain 'Q' and resid 248 through 258 Processing helix chain 'Q' and resid 259 through 261 No H-bonds generated for 'chain 'Q' and resid 259 through 261' Processing helix chain 'Q' and resid 266 through 276 removed outlier: 3.562A pdb=" N LEU Q 271 " --> pdb=" O ALA Q 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR Q 272 " --> pdb=" O SER Q 268 " (cutoff:3.500A) Processing helix chain 'Q' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY Q 291 " --> pdb=" O HIS Q 287 " (cutoff:3.500A) Processing helix chain 'Q' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU Q 299 " --> pdb=" O THR Q 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN Q 304 " --> pdb=" O MET Q 300 " (cutoff:3.500A) Processing helix chain 'Q' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR Q 309 " --> pdb=" O MET Q 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA Q 310 " --> pdb=" O GLY Q 307 " (cutoff:3.500A) Proline residue: Q 311 - end of helix No H-bonds generated for 'chain 'Q' and resid 306 through 313' Processing helix chain 'Q' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN Q 321 " --> pdb=" O ASN Q 318 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN Q 322 " --> pdb=" O SER Q 319 " (cutoff:3.500A) Processing helix chain 'Q' and resid 325 through 328 removed outlier: 3.516A pdb=" N SER Q 328 " --> pdb=" O SER Q 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 325 through 328' Processing helix chain 'Q' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER Q 334 " --> pdb=" O PRO Q 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU Q 342 " --> pdb=" O GLY Q 338 " (cutoff:3.500A) Processing helix chain 'Q' and resid 345 through 350 Processing helix chain 'Q' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE Q 362 " --> pdb=" O ASP Q 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL Q 369 " --> pdb=" O GLY Q 365 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 13 removed outlier: 4.184A pdb=" N ARG S 6 " --> pdb=" O ALA S 2 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG S 48 " --> pdb=" O SER S 44 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG S 57 " --> pdb=" O ASP S 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU S 58 " --> pdb=" O ARG S 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE S 59 " --> pdb=" O LEU S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 77 Processing helix chain 'S' and resid 84 through 92 removed outlier: 3.681A pdb=" N GLN S 89 " --> pdb=" O GLY S 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG S 90 " --> pdb=" O GLN S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 127 through 132 Processing helix chain 'S' and resid 159 through 172 Processing helix chain 'S' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS S 180 " --> pdb=" O LEU S 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA S 181 " --> pdb=" O LEU S 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 177 through 181' Processing helix chain 'S' and resid 185 through 187 No H-bonds generated for 'chain 'S' and resid 185 through 187' Processing helix chain 'S' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU S 193 " --> pdb=" O ALA S 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG S 194 " --> pdb=" O ASP S 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG S 195 " --> pdb=" O SER S 191 " (cutoff:3.500A) Processing helix chain 'S' and resid 212 through 226 Processing helix chain 'S' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE S 237 " --> pdb=" O MET S 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG S 242 " --> pdb=" O LEU S 238 " (cutoff:3.500A) Processing helix chain 'S' and resid 248 through 258 Processing helix chain 'S' and resid 259 through 261 No H-bonds generated for 'chain 'S' and resid 259 through 261' Processing helix chain 'S' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU S 271 " --> pdb=" O ALA S 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR S 272 " --> pdb=" O SER S 268 " (cutoff:3.500A) Processing helix chain 'S' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY S 291 " --> pdb=" O HIS S 287 " (cutoff:3.500A) Processing helix chain 'S' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU S 299 " --> pdb=" O THR S 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN S 304 " --> pdb=" O MET S 300 " (cutoff:3.500A) Processing helix chain 'S' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR S 309 " --> pdb=" O MET S 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA S 310 " --> pdb=" O GLY S 307 " (cutoff:3.500A) Proline residue: S 311 - end of helix No H-bonds generated for 'chain 'S' and resid 306 through 313' Processing helix chain 'S' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN S 321 " --> pdb=" O ASN S 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN S 322 " --> pdb=" O SER S 319 " (cutoff:3.500A) Processing helix chain 'S' and resid 325 through 328 removed outlier: 3.516A pdb=" N SER S 328 " --> pdb=" O SER S 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 325 through 328' Processing helix chain 'S' and resid 329 through 344 removed outlier: 3.852A pdb=" N SER S 334 " --> pdb=" O PRO S 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU S 342 " --> pdb=" O GLY S 338 " (cutoff:3.500A) Processing helix chain 'S' and resid 345 through 350 Processing helix chain 'S' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE S 362 " --> pdb=" O ASP S 358 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL S 369 " --> pdb=" O GLY S 365 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 13 removed outlier: 4.184A pdb=" N ARG U 6 " --> pdb=" O ALA U 2 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG U 48 " --> pdb=" O SER U 44 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG U 57 " --> pdb=" O ASP U 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU U 58 " --> pdb=" O ARG U 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE U 59 " --> pdb=" O LEU U 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 77 Processing helix chain 'U' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN U 89 " --> pdb=" O GLY U 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG U 90 " --> pdb=" O GLN U 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 132 Processing helix chain 'U' and resid 159 through 172 Processing helix chain 'U' and resid 177 through 181 removed outlier: 3.533A pdb=" N LYS U 180 " --> pdb=" O LEU U 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA U 181 " --> pdb=" O LEU U 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 177 through 181' Processing helix chain 'U' and resid 185 through 187 No H-bonds generated for 'chain 'U' and resid 185 through 187' Processing helix chain 'U' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU U 193 " --> pdb=" O ALA U 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG U 194 " --> pdb=" O ASP U 190 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG U 195 " --> pdb=" O SER U 191 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 226 Processing helix chain 'U' and resid 227 through 242 removed outlier: 3.512A pdb=" N ILE U 237 " --> pdb=" O MET U 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG U 242 " --> pdb=" O LEU U 238 " (cutoff:3.500A) Processing helix chain 'U' and resid 248 through 258 Processing helix chain 'U' and resid 259 through 261 No H-bonds generated for 'chain 'U' and resid 259 through 261' Processing helix chain 'U' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU U 271 " --> pdb=" O ALA U 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR U 272 " --> pdb=" O SER U 268 " (cutoff:3.500A) Processing helix chain 'U' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY U 291 " --> pdb=" O HIS U 287 " (cutoff:3.500A) Processing helix chain 'U' and resid 293 through 305 removed outlier: 4.278A pdb=" N LEU U 299 " --> pdb=" O THR U 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN U 304 " --> pdb=" O MET U 300 " (cutoff:3.500A) Processing helix chain 'U' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR U 309 " --> pdb=" O MET U 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA U 310 " --> pdb=" O GLY U 307 " (cutoff:3.500A) Proline residue: U 311 - end of helix No H-bonds generated for 'chain 'U' and resid 306 through 313' Processing helix chain 'U' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN U 321 " --> pdb=" O ASN U 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN U 322 " --> pdb=" O SER U 319 " (cutoff:3.500A) Processing helix chain 'U' and resid 325 through 328 removed outlier: 3.516A pdb=" N SER U 328 " --> pdb=" O SER U 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 325 through 328' Processing helix chain 'U' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER U 334 " --> pdb=" O PRO U 330 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU U 342 " --> pdb=" O GLY U 338 " (cutoff:3.500A) Processing helix chain 'U' and resid 345 through 350 Processing helix chain 'U' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE U 362 " --> pdb=" O ASP U 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL U 369 " --> pdb=" O GLY U 365 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG W 6 " --> pdb=" O ALA W 2 " (cutoff:3.500A) Processing helix chain 'W' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG W 48 " --> pdb=" O SER W 44 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG W 57 " --> pdb=" O ASP W 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU W 58 " --> pdb=" O ARG W 54 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE W 59 " --> pdb=" O LEU W 55 " (cutoff:3.500A) Processing helix chain 'W' and resid 65 through 77 Processing helix chain 'W' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN W 89 " --> pdb=" O GLY W 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG W 90 " --> pdb=" O GLN W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 127 through 132 Processing helix chain 'W' and resid 159 through 172 Processing helix chain 'W' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS W 180 " --> pdb=" O LEU W 177 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA W 181 " --> pdb=" O LEU W 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 177 through 181' Processing helix chain 'W' and resid 185 through 187 No H-bonds generated for 'chain 'W' and resid 185 through 187' Processing helix chain 'W' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU W 193 " --> pdb=" O ALA W 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG W 194 " --> pdb=" O ASP W 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG W 195 " --> pdb=" O SER W 191 " (cutoff:3.500A) Processing helix chain 'W' and resid 212 through 226 Processing helix chain 'W' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE W 237 " --> pdb=" O MET W 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG W 242 " --> pdb=" O LEU W 238 " (cutoff:3.500A) Processing helix chain 'W' and resid 248 through 258 Processing helix chain 'W' and resid 259 through 261 No H-bonds generated for 'chain 'W' and resid 259 through 261' Processing helix chain 'W' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU W 271 " --> pdb=" O ALA W 267 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR W 272 " --> pdb=" O SER W 268 " (cutoff:3.500A) Processing helix chain 'W' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY W 291 " --> pdb=" O HIS W 287 " (cutoff:3.500A) Processing helix chain 'W' and resid 293 through 305 removed outlier: 4.278A pdb=" N LEU W 299 " --> pdb=" O THR W 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN W 304 " --> pdb=" O MET W 300 " (cutoff:3.500A) Processing helix chain 'W' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR W 309 " --> pdb=" O MET W 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA W 310 " --> pdb=" O GLY W 307 " (cutoff:3.500A) Proline residue: W 311 - end of helix No H-bonds generated for 'chain 'W' and resid 306 through 313' Processing helix chain 'W' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN W 321 " --> pdb=" O ASN W 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN W 322 " --> pdb=" O SER W 319 " (cutoff:3.500A) Processing helix chain 'W' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER W 328 " --> pdb=" O SER W 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 325 through 328' Processing helix chain 'W' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER W 334 " --> pdb=" O PRO W 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU W 342 " --> pdb=" O GLY W 338 " (cutoff:3.500A) Processing helix chain 'W' and resid 345 through 350 Processing helix chain 'W' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE W 362 " --> pdb=" O ASP W 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL W 369 " --> pdb=" O GLY W 365 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 13 removed outlier: 4.184A pdb=" N ARG Y 6 " --> pdb=" O ALA Y 2 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG Y 48 " --> pdb=" O SER Y 44 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG Y 57 " --> pdb=" O ASP Y 53 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU Y 58 " --> pdb=" O ARG Y 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE Y 59 " --> pdb=" O LEU Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 65 through 77 Processing helix chain 'Y' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN Y 89 " --> pdb=" O GLY Y 85 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG Y 90 " --> pdb=" O GLN Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 127 through 132 Processing helix chain 'Y' and resid 159 through 172 Processing helix chain 'Y' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS Y 180 " --> pdb=" O LEU Y 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA Y 181 " --> pdb=" O LEU Y 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 177 through 181' Processing helix chain 'Y' and resid 185 through 187 No H-bonds generated for 'chain 'Y' and resid 185 through 187' Processing helix chain 'Y' and resid 188 through 202 removed outlier: 3.674A pdb=" N LEU Y 193 " --> pdb=" O ALA Y 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG Y 194 " --> pdb=" O ASP Y 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG Y 195 " --> pdb=" O SER Y 191 " (cutoff:3.500A) Processing helix chain 'Y' and resid 212 through 226 Processing helix chain 'Y' and resid 227 through 242 removed outlier: 3.512A pdb=" N ILE Y 237 " --> pdb=" O MET Y 233 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG Y 242 " --> pdb=" O LEU Y 238 " (cutoff:3.500A) Processing helix chain 'Y' and resid 248 through 258 Processing helix chain 'Y' and resid 259 through 261 No H-bonds generated for 'chain 'Y' and resid 259 through 261' Processing helix chain 'Y' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU Y 271 " --> pdb=" O ALA Y 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR Y 272 " --> pdb=" O SER Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY Y 291 " --> pdb=" O HIS Y 287 " (cutoff:3.500A) Processing helix chain 'Y' and resid 293 through 305 removed outlier: 4.278A pdb=" N LEU Y 299 " --> pdb=" O THR Y 295 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN Y 304 " --> pdb=" O MET Y 300 " (cutoff:3.500A) Processing helix chain 'Y' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR Y 309 " --> pdb=" O MET Y 306 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA Y 310 " --> pdb=" O GLY Y 307 " (cutoff:3.500A) Proline residue: Y 311 - end of helix No H-bonds generated for 'chain 'Y' and resid 306 through 313' Processing helix chain 'Y' and resid 318 through 323 removed outlier: 3.921A pdb=" N GLN Y 321 " --> pdb=" O ASN Y 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN Y 322 " --> pdb=" O SER Y 319 " (cutoff:3.500A) Processing helix chain 'Y' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER Y 328 " --> pdb=" O SER Y 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 325 through 328' Processing helix chain 'Y' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER Y 334 " --> pdb=" O PRO Y 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU Y 342 " --> pdb=" O GLY Y 338 " (cutoff:3.500A) Processing helix chain 'Y' and resid 345 through 350 Processing helix chain 'Y' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE Y 362 " --> pdb=" O ASP Y 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL Y 369 " --> pdb=" O GLY Y 365 " (cutoff:3.500A) Processing helix chain '0' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG 0 6 " --> pdb=" O ALA 0 2 " (cutoff:3.500A) Processing helix chain '0' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG 0 48 " --> pdb=" O SER 0 44 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG 0 57 " --> pdb=" O ASP 0 53 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU 0 58 " --> pdb=" O ARG 0 54 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE 0 59 " --> pdb=" O LEU 0 55 " (cutoff:3.500A) Processing helix chain '0' and resid 65 through 77 Processing helix chain '0' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN 0 89 " --> pdb=" O GLY 0 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG 0 90 " --> pdb=" O GLN 0 86 " (cutoff:3.500A) Processing helix chain '0' and resid 127 through 132 Processing helix chain '0' and resid 159 through 172 Processing helix chain '0' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS 0 180 " --> pdb=" O LEU 0 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA 0 181 " --> pdb=" O LEU 0 178 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 177 through 181' Processing helix chain '0' and resid 185 through 187 No H-bonds generated for 'chain '0' and resid 185 through 187' Processing helix chain '0' and resid 188 through 202 removed outlier: 3.674A pdb=" N LEU 0 193 " --> pdb=" O ALA 0 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG 0 194 " --> pdb=" O ASP 0 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG 0 195 " --> pdb=" O SER 0 191 " (cutoff:3.500A) Processing helix chain '0' and resid 212 through 226 Processing helix chain '0' and resid 227 through 242 removed outlier: 3.510A pdb=" N ILE 0 237 " --> pdb=" O MET 0 233 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG 0 242 " --> pdb=" O LEU 0 238 " (cutoff:3.500A) Processing helix chain '0' and resid 248 through 258 Processing helix chain '0' and resid 259 through 261 No H-bonds generated for 'chain '0' and resid 259 through 261' Processing helix chain '0' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU 0 271 " --> pdb=" O ALA 0 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR 0 272 " --> pdb=" O SER 0 268 " (cutoff:3.500A) Processing helix chain '0' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY 0 291 " --> pdb=" O HIS 0 287 " (cutoff:3.500A) Processing helix chain '0' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU 0 299 " --> pdb=" O THR 0 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN 0 304 " --> pdb=" O MET 0 300 " (cutoff:3.500A) Processing helix chain '0' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR 0 309 " --> pdb=" O MET 0 306 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA 0 310 " --> pdb=" O GLY 0 307 " (cutoff:3.500A) Proline residue: 0 311 - end of helix No H-bonds generated for 'chain '0' and resid 306 through 313' Processing helix chain '0' and resid 318 through 323 removed outlier: 3.921A pdb=" N GLN 0 321 " --> pdb=" O ASN 0 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN 0 322 " --> pdb=" O SER 0 319 " (cutoff:3.500A) Processing helix chain '0' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER 0 328 " --> pdb=" O SER 0 325 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 325 through 328' Processing helix chain '0' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER 0 334 " --> pdb=" O PRO 0 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU 0 342 " --> pdb=" O GLY 0 338 " (cutoff:3.500A) Processing helix chain '0' and resid 345 through 350 Processing helix chain '0' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE 0 362 " --> pdb=" O ASP 0 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL 0 369 " --> pdb=" O GLY 0 365 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG 2 6 " --> pdb=" O ALA 2 2 " (cutoff:3.500A) Processing helix chain '2' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG 2 48 " --> pdb=" O SER 2 44 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG 2 57 " --> pdb=" O ASP 2 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU 2 58 " --> pdb=" O ARG 2 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE 2 59 " --> pdb=" O LEU 2 55 " (cutoff:3.500A) Processing helix chain '2' and resid 65 through 77 Processing helix chain '2' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN 2 89 " --> pdb=" O GLY 2 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG 2 90 " --> pdb=" O GLN 2 86 " (cutoff:3.500A) Processing helix chain '2' and resid 127 through 132 Processing helix chain '2' and resid 159 through 172 Processing helix chain '2' and resid 177 through 181 removed outlier: 3.533A pdb=" N LYS 2 180 " --> pdb=" O LEU 2 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA 2 181 " --> pdb=" O LEU 2 178 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 177 through 181' Processing helix chain '2' and resid 185 through 187 No H-bonds generated for 'chain '2' and resid 185 through 187' Processing helix chain '2' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU 2 193 " --> pdb=" O ALA 2 189 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG 2 194 " --> pdb=" O ASP 2 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG 2 195 " --> pdb=" O SER 2 191 " (cutoff:3.500A) Processing helix chain '2' and resid 212 through 226 Processing helix chain '2' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE 2 237 " --> pdb=" O MET 2 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG 2 242 " --> pdb=" O LEU 2 238 " (cutoff:3.500A) Processing helix chain '2' and resid 248 through 258 Processing helix chain '2' and resid 259 through 261 No H-bonds generated for 'chain '2' and resid 259 through 261' Processing helix chain '2' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU 2 271 " --> pdb=" O ALA 2 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR 2 272 " --> pdb=" O SER 2 268 " (cutoff:3.500A) Processing helix chain '2' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY 2 291 " --> pdb=" O HIS 2 287 " (cutoff:3.500A) Processing helix chain '2' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU 2 299 " --> pdb=" O THR 2 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN 2 304 " --> pdb=" O MET 2 300 " (cutoff:3.500A) Processing helix chain '2' and resid 306 through 313 removed outlier: 4.165A pdb=" N THR 2 309 " --> pdb=" O MET 2 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA 2 310 " --> pdb=" O GLY 2 307 " (cutoff:3.500A) Proline residue: 2 311 - end of helix No H-bonds generated for 'chain '2' and resid 306 through 313' Processing helix chain '2' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN 2 321 " --> pdb=" O ASN 2 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN 2 322 " --> pdb=" O SER 2 319 " (cutoff:3.500A) Processing helix chain '2' and resid 325 through 328 removed outlier: 3.516A pdb=" N SER 2 328 " --> pdb=" O SER 2 325 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 325 through 328' Processing helix chain '2' and resid 329 through 344 removed outlier: 3.852A pdb=" N SER 2 334 " --> pdb=" O PRO 2 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU 2 342 " --> pdb=" O GLY 2 338 " (cutoff:3.500A) Processing helix chain '2' and resid 345 through 350 Processing helix chain '2' and resid 358 through 372 removed outlier: 3.823A pdb=" N PHE 2 362 " --> pdb=" O ASP 2 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL 2 369 " --> pdb=" O GLY 2 365 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'C' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE C 35 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU C 102 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL C 37 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL C 104 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE C 39 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN C 106 " --> pdb=" O ILE C 39 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE A 35 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 102 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL A 37 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL A 104 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 39 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN A 106 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'D' and resid 34 through 40 removed outlier: 5.502A pdb=" N ILE D 35 " --> pdb=" O ARG D 100 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU D 102 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL D 37 " --> pdb=" O LEU D 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL D 104 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE D 39 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN D 106 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'G' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE G 35 " --> pdb=" O ARG G 100 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU G 102 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL G 37 " --> pdb=" O LEU G 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL G 104 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE G 39 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN G 106 " --> pdb=" O ILE G 39 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'I' and resid 34 through 40 removed outlier: 5.502A pdb=" N ILE I 35 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU I 102 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL I 37 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL I 104 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE I 39 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN I 106 " --> pdb=" O ILE I 39 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'K' and resid 34 through 40 removed outlier: 5.502A pdb=" N ILE K 35 " --> pdb=" O ARG K 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU K 102 " --> pdb=" O ILE K 35 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL K 37 " --> pdb=" O LEU K 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL K 104 " --> pdb=" O VAL K 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE K 39 " --> pdb=" O VAL K 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN K 106 " --> pdb=" O ILE K 39 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'M' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE M 35 " --> pdb=" O ARG M 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU M 102 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL M 37 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL M 104 " --> pdb=" O VAL M 37 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE M 39 " --> pdb=" O VAL M 104 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N GLN M 106 " --> pdb=" O ILE M 39 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'O' and resid 34 through 40 removed outlier: 5.502A pdb=" N ILE O 35 " --> pdb=" O ARG O 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU O 102 " --> pdb=" O ILE O 35 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL O 37 " --> pdb=" O LEU O 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL O 104 " --> pdb=" O VAL O 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE O 39 " --> pdb=" O VAL O 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN O 106 " --> pdb=" O ILE O 39 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'Q' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE Q 35 " --> pdb=" O ARG Q 100 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU Q 102 " --> pdb=" O ILE Q 35 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL Q 37 " --> pdb=" O LEU Q 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL Q 104 " --> pdb=" O VAL Q 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE Q 39 " --> pdb=" O VAL Q 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN Q 106 " --> pdb=" O ILE Q 39 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'S' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE S 35 " --> pdb=" O ARG S 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU S 102 " --> pdb=" O ILE S 35 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL S 37 " --> pdb=" O LEU S 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL S 104 " --> pdb=" O VAL S 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE S 39 " --> pdb=" O VAL S 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN S 106 " --> pdb=" O ILE S 39 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'U' and resid 34 through 40 removed outlier: 5.502A pdb=" N ILE U 35 " --> pdb=" O ARG U 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU U 102 " --> pdb=" O ILE U 35 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL U 37 " --> pdb=" O LEU U 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL U 104 " --> pdb=" O VAL U 37 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE U 39 " --> pdb=" O VAL U 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN U 106 " --> pdb=" O ILE U 39 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'W' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE W 35 " --> pdb=" O ARG W 100 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU W 102 " --> pdb=" O ILE W 35 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL W 37 " --> pdb=" O LEU W 102 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL W 104 " --> pdb=" O VAL W 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE W 39 " --> pdb=" O VAL W 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN W 106 " --> pdb=" O ILE W 39 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'Y' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE Y 35 " --> pdb=" O ARG Y 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU Y 102 " --> pdb=" O ILE Y 35 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL Y 37 " --> pdb=" O LEU Y 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL Y 104 " --> pdb=" O VAL Y 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE Y 39 " --> pdb=" O VAL Y 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN Y 106 " --> pdb=" O ILE Y 39 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '0' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE 0 35 " --> pdb=" O ARG 0 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU 0 102 " --> pdb=" O ILE 0 35 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL 0 37 " --> pdb=" O LEU 0 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL 0 104 " --> pdb=" O VAL 0 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE 0 39 " --> pdb=" O VAL 0 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN 0 106 " --> pdb=" O ILE 0 39 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '2' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE 2 35 " --> pdb=" O ARG 2 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU 2 102 " --> pdb=" O ILE 2 35 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL 2 37 " --> pdb=" O LEU 2 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL 2 104 " --> pdb=" O VAL 2 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE 2 39 " --> pdb=" O VAL 2 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN 2 106 " --> pdb=" O ILE 2 39 " (cutoff:3.500A) 1710 hydrogen bonds defined for protein. 4950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 15.75 Time building geometry restraints manager: 19.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 13813 1.33 - 1.45: 6869 1.45 - 1.57: 24513 1.57 - 1.69: 150 1.69 - 1.80: 345 Bond restraints: 45690 Sorted by residual: bond pdb=" CB VAL Q 314 " pdb=" CG1 VAL Q 314 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.18e+00 bond pdb=" CB VAL 2 314 " pdb=" CG1 VAL 2 314 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.18e+00 bond pdb=" CB VAL G 314 " pdb=" CG1 VAL G 314 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.15e+00 bond pdb=" CB VAL A 314 " pdb=" CG1 VAL A 314 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.15e+00 bond pdb=" CB VAL K 314 " pdb=" CG1 VAL K 314 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.13e+00 ... (remaining 45685 not shown) Histogram of bond angle deviations from ideal: 97.29 - 104.65: 1110 104.65 - 112.00: 21326 112.00 - 119.36: 17087 119.36 - 126.72: 21831 126.72 - 134.07: 791 Bond angle restraints: 62145 Sorted by residual: angle pdb=" N ILE M 28 " pdb=" CA ILE M 28 " pdb=" C ILE M 28 " ideal model delta sigma weight residual 113.71 106.84 6.87 9.50e-01 1.11e+00 5.22e+01 angle pdb=" N ILE 0 28 " pdb=" CA ILE 0 28 " pdb=" C ILE 0 28 " ideal model delta sigma weight residual 113.71 106.86 6.85 9.50e-01 1.11e+00 5.21e+01 angle pdb=" N ILE Y 28 " pdb=" CA ILE Y 28 " pdb=" C ILE Y 28 " ideal model delta sigma weight residual 113.71 106.87 6.84 9.50e-01 1.11e+00 5.19e+01 angle pdb=" N ILE I 28 " pdb=" CA ILE I 28 " pdb=" C ILE I 28 " ideal model delta sigma weight residual 113.71 106.87 6.84 9.50e-01 1.11e+00 5.19e+01 angle pdb=" N ILE Q 28 " pdb=" CA ILE Q 28 " pdb=" C ILE Q 28 " ideal model delta sigma weight residual 113.71 106.88 6.83 9.50e-01 1.11e+00 5.18e+01 ... (remaining 62140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.16: 25426 15.16 - 30.32: 1649 30.32 - 45.47: 285 45.47 - 60.63: 60 60.63 - 75.79: 15 Dihedral angle restraints: 27435 sinusoidal: 11865 harmonic: 15570 Sorted by residual: dihedral pdb=" CA LYS Q 150 " pdb=" C LYS Q 150 " pdb=" N GLU Q 151 " pdb=" CA GLU Q 151 " ideal model delta harmonic sigma weight residual 180.00 155.03 24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA LYS K 150 " pdb=" C LYS K 150 " pdb=" N GLU K 151 " pdb=" CA GLU K 151 " ideal model delta harmonic sigma weight residual 180.00 155.03 24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA LYS 2 150 " pdb=" C LYS 2 150 " pdb=" N GLU 2 151 " pdb=" CA GLU 2 151 " ideal model delta harmonic sigma weight residual 180.00 155.04 24.96 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 27432 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 5736 0.075 - 0.151: 1224 0.151 - 0.226: 120 0.226 - 0.301: 15 0.301 - 0.376: 15 Chirality restraints: 7110 Sorted by residual: chirality pdb=" CA ASP O 42 " pdb=" N ASP O 42 " pdb=" C ASP O 42 " pdb=" CB ASP O 42 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA ASP I 42 " pdb=" N ASP I 42 " pdb=" C ASP I 42 " pdb=" CB ASP I 42 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA ASP Y 42 " pdb=" N ASP Y 42 " pdb=" C ASP Y 42 " pdb=" CB ASP Y 42 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 ... (remaining 7107 not shown) Planarity restraints: 7650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR S 281 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO S 282 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO S 282 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO S 282 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR 0 281 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO 0 282 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO 0 282 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO 0 282 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 281 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO A 282 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " -0.031 5.00e-02 4.00e+02 ... (remaining 7647 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 155 2.43 - 3.05: 26373 3.05 - 3.67: 70679 3.67 - 4.28: 108488 4.28 - 4.90: 175370 Nonbonded interactions: 381065 Sorted by model distance: nonbonded pdb=" O GLY A 23 " pdb=" OE2 GLU 0 342 " model vdw 1.817 3.040 nonbonded pdb=" O GLY D 23 " pdb=" OE2 GLU 2 342 " model vdw 1.817 3.040 nonbonded pdb=" OG SER Y 334 " pdb=" O PHE Y 357 " model vdw 2.272 2.440 nonbonded pdb=" OG SER W 334 " pdb=" O PHE W 357 " model vdw 2.272 2.440 nonbonded pdb=" OG SER 2 334 " pdb=" O PHE 2 357 " model vdw 2.272 2.440 ... (remaining 381060 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '2' selection = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain '1' selection = chain '3' selection = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 75 5.49 5 S 180 5.16 5 C 28185 2.51 5 N 7740 2.21 5 O 8520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.590 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: 0.040 Extract box with map and model: 11.120 Check model and map are aligned: 0.680 Convert atoms to be neutral: 0.380 Process input model: 118.180 Find NCS groups from input model: 3.290 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 138.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8783 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 : 0.010 0.060 45690 Z= 0.619 Angle : 1.118 13.127 62145 Z= 0.607 Chirality : 0.063 0.376 7110 Planarity : 0.007 0.056 7650 Dihedral : 10.773 75.788 17415 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.39 (0.08), residues: 5355 helix: -4.22 (0.04), residues: 3030 sheet: -1.96 (0.26), residues: 390 loop : -2.39 (0.12), residues: 1935 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1274 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1244 time to evaluate : 5.659 Fit side-chains revert: symmetry clash outliers start: 30 outliers final: 7 residues processed: 1267 average time/residue: 0.6003 time to fit residues: 1208.1009 Evaluate side-chains 820 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 813 time to evaluate : 5.662 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.3848 time to fit residues: 12.6387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 455 optimal weight: 0.9980 chunk 409 optimal weight: 2.9990 chunk 227 optimal weight: 9.9990 chunk 139 optimal weight: 0.9980 chunk 276 optimal weight: 0.9980 chunk 218 optimal weight: 2.9990 chunk 423 optimal weight: 2.9990 chunk 163 optimal weight: 4.9990 chunk 257 optimal weight: 0.9980 chunk 315 optimal weight: 2.9990 chunk 490 optimal weight: 0.7980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN C 33 HIS C 61 ASN C 164 ASN C 351 ASN A 33 HIS A 61 ASN A 304 GLN A 351 ASN D 61 ASN D 246 ASN ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 ASN G 33 HIS G 61 ASN G 246 ASN G 351 ASN ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 ASN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 149 ASN I 351 ASN K 33 HIS K 61 ASN K 149 ASN K 164 ASN K 246 ASN ** K 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 351 ASN M 33 HIS M 61 ASN M 149 ASN ** M 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 246 ASN M 351 ASN O 33 HIS O 61 ASN O 164 ASN O 246 ASN O 304 GLN O 351 ASN ** Q 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 HIS Q 61 ASN Q 351 ASN S 33 HIS S 61 ASN S 351 ASN U 33 HIS U 61 ASN U 164 ASN U 351 ASN W 14 ASN W 33 HIS W 61 ASN W 351 ASN Y 14 ASN Y 33 HIS Y 61 ASN Y 111 GLN ** Y 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 351 ASN 0 14 ASN 0 33 HIS 0 61 ASN ** 0 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 14 ASN 2 33 HIS 2 61 ASN 2 164 ASN 2 351 ASN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.2196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 45690 Z= 0.174 Angle : 0.622 7.669 62145 Z= 0.325 Chirality : 0.044 0.231 7110 Planarity : 0.006 0.066 7650 Dihedral : 7.258 54.161 6960 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.10), residues: 5355 helix: -1.89 (0.08), residues: 3120 sheet: -1.81 (0.26), residues: 390 loop : -2.24 (0.13), residues: 1845 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1037 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 927 time to evaluate : 5.740 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 110 outliers final: 56 residues processed: 1010 average time/residue: 0.6404 time to fit residues: 1017.1967 Evaluate side-chains 849 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 793 time to evaluate : 4.893 Switching outliers to nearest non-outliers outliers start: 56 outliers final: 0 residues processed: 56 average time/residue: 0.4778 time to fit residues: 53.8232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 272 optimal weight: 7.9990 chunk 152 optimal weight: 0.9990 chunk 408 optimal weight: 9.9990 chunk 333 optimal weight: 9.9990 chunk 135 optimal weight: 8.9990 chunk 491 optimal weight: 6.9990 chunk 530 optimal weight: 6.9990 chunk 437 optimal weight: 4.9990 chunk 487 optimal weight: 9.9990 chunk 167 optimal weight: 5.9990 chunk 394 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 HIS ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 322 ASN A 14 ASN A 33 HIS A 304 GLN D 33 HIS G 14 ASN G 33 HIS ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS K 14 ASN K 33 HIS K 246 ASN M 33 HIS M 246 ASN O 33 HIS O 86 GLN O 164 ASN O 246 ASN ** O 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 HIS Q 246 ASN S 14 ASN S 33 HIS U 33 HIS U 164 ASN U 304 GLN W 33 HIS W 111 GLN W 304 GLN Y 33 HIS Y 246 ASN ** Y 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 33 HIS 2 33 HIS Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8828 moved from start: 0.2609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.059 45690 Z= 0.388 Angle : 0.659 7.133 62145 Z= 0.335 Chirality : 0.047 0.203 7110 Planarity : 0.005 0.056 7650 Dihedral : 7.115 52.740 6960 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 9.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.11), residues: 5355 helix: -0.89 (0.09), residues: 3255 sheet: -1.75 (0.26), residues: 390 loop : -1.93 (0.14), residues: 1710 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 909 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 829 time to evaluate : 5.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 80 outliers final: 35 residues processed: 882 average time/residue: 0.6225 time to fit residues: 870.4181 Evaluate side-chains 790 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 755 time to evaluate : 5.260 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.4772 time to fit residues: 35.9174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 485 optimal weight: 4.9990 chunk 369 optimal weight: 0.1980 chunk 254 optimal weight: 0.0000 chunk 54 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 329 optimal weight: 0.6980 chunk 493 optimal weight: 0.9990 chunk 521 optimal weight: 0.4980 chunk 257 optimal weight: 0.9980 chunk 467 optimal weight: 3.9990 chunk 140 optimal weight: 0.8980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN C 33 HIS ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 HIS A 304 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 HIS G 246 ASN G 304 GLN I 33 HIS K 246 ASN K 322 ASN M 33 HIS M 246 ASN M 304 GLN O 33 HIS O 246 ASN Q 33 HIS Q 246 ASN Q 301 ASN S 33 HIS U 33 HIS U 164 ASN U 322 ASN W 33 HIS ** W 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 33 HIS Y 164 ASN 0 33 HIS 0 304 GLN ** 2 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.3000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 45690 Z= 0.140 Angle : 0.533 9.284 62145 Z= 0.275 Chirality : 0.042 0.174 7110 Planarity : 0.004 0.037 7650 Dihedral : 6.830 55.447 6960 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.31 % Favored : 96.68 % Rotamer Outliers : 1.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.12), residues: 5355 helix: -0.10 (0.10), residues: 3180 sheet: -1.76 (0.25), residues: 390 loop : -1.38 (0.14), residues: 1785 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 871 time to evaluate : 5.337 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 14 residues processed: 901 average time/residue: 0.6112 time to fit residues: 874.0354 Evaluate side-chains 777 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 763 time to evaluate : 5.131 Switching outliers to nearest non-outliers outliers start: 14 outliers final: 0 residues processed: 14 average time/residue: 0.5008 time to fit residues: 18.9053 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 434 optimal weight: 9.9990 chunk 296 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 3.9990 chunk 445 optimal weight: 0.0870 chunk 360 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 266 optimal weight: 0.0870 chunk 468 optimal weight: 10.0000 chunk 131 optimal weight: 10.0000 overall best weight: 1.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN C 33 HIS C 246 ASN ** C 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 33 HIS ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 HIS I 33 HIS M 33 HIS M 246 ASN O 33 HIS O 304 GLN Q 33 HIS Q 246 ASN Q 301 ASN S 33 HIS U 14 ASN U 33 HIS U 164 ASN U 304 GLN W 33 HIS ** Y 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 33 HIS Y 164 ASN 0 33 HIS 0 109 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8759 moved from start: 0.3149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 45690 Z= 0.190 Angle : 0.534 8.418 62145 Z= 0.272 Chirality : 0.043 0.145 7110 Planarity : 0.004 0.049 7650 Dihedral : 6.691 53.682 6960 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.81 % Favored : 96.10 % Rotamer Outliers : 0.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.12), residues: 5355 helix: 0.24 (0.10), residues: 3135 sheet: -1.78 (0.25), residues: 390 loop : -1.30 (0.14), residues: 1830 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 865 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 821 time to evaluate : 5.022 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 19 residues processed: 846 average time/residue: 0.6365 time to fit residues: 853.9049 Evaluate side-chains 775 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 756 time to evaluate : 5.304 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.4793 time to fit residues: 23.3168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 175 optimal weight: 0.9990 chunk 470 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 306 optimal weight: 6.9990 chunk 128 optimal weight: 7.9990 chunk 522 optimal weight: 5.9990 chunk 433 optimal weight: 7.9990 chunk 241 optimal weight: 0.9980 chunk 43 optimal weight: 7.9990 chunk 172 optimal weight: 0.8980 chunk 274 optimal weight: 5.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS C 246 ASN C 304 GLN A 14 ASN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 HIS K 33 HIS K 304 GLN M 33 HIS M 246 ASN O 33 HIS O 246 ASN ** O 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 HIS Q 246 ASN ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 304 GLN U 33 HIS U 164 ASN U 246 ASN U 304 GLN W 33 HIS Y 33 HIS Y 164 ASN 0 33 HIS ** 0 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 89 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.3239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.041 45690 Z= 0.273 Angle : 0.568 6.940 62145 Z= 0.289 Chirality : 0.044 0.139 7110 Planarity : 0.004 0.040 7650 Dihedral : 6.725 52.663 6960 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.00 % Favored : 95.89 % Rotamer Outliers : 1.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.62 (0.12), residues: 5355 helix: 0.32 (0.10), residues: 3135 sheet: -1.76 (0.25), residues: 390 loop : -1.23 (0.15), residues: 1830 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 799 time to evaluate : 5.642 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 26 residues processed: 837 average time/residue: 0.6162 time to fit residues: 818.3677 Evaluate side-chains 772 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 746 time to evaluate : 5.450 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.3820 time to fit residues: 26.0807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 503 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 297 optimal weight: 8.9990 chunk 381 optimal weight: 2.9990 chunk 295 optimal weight: 0.9990 chunk 439 optimal weight: 2.9990 chunk 291 optimal weight: 4.9990 chunk 520 optimal weight: 0.6980 chunk 325 optimal weight: 4.9990 chunk 317 optimal weight: 3.9990 chunk 240 optimal weight: 1.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS C 246 ASN C 304 GLN D 86 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 HIS ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 HIS O 33 HIS Q 33 HIS Q 246 ASN ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 345 ASN U 33 HIS U 164 ASN U 246 ASN U 304 GLN W 33 HIS Y 33 HIS Y 164 ASN Y 304 GLN 0 33 HIS ** 0 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 89 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8756 moved from start: 0.3408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.058 45690 Z= 0.171 Angle : 0.527 8.457 62145 Z= 0.269 Chirality : 0.042 0.160 7110 Planarity : 0.003 0.042 7650 Dihedral : 6.644 54.211 6960 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.16 % Favored : 96.75 % Rotamer Outliers : 0.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.12), residues: 5355 helix: 0.47 (0.10), residues: 3135 sheet: -1.72 (0.25), residues: 390 loop : -1.10 (0.15), residues: 1830 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 822 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 794 time to evaluate : 5.286 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 10 residues processed: 813 average time/residue: 0.6374 time to fit residues: 821.6042 Evaluate side-chains 750 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 740 time to evaluate : 5.234 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.5720 time to fit residues: 17.2949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 321 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 310 optimal weight: 1.9990 chunk 156 optimal weight: 5.9990 chunk 102 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 330 optimal weight: 5.9990 chunk 354 optimal weight: 1.9990 chunk 257 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 409 optimal weight: 7.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS C 246 ASN C 304 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 HIS ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS ** K 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 HIS M 246 ASN O 33 HIS Q 33 HIS Q 246 ASN ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 33 HIS U 164 ASN U 304 GLN W 33 HIS Y 33 HIS Y 164 ASN 0 33 HIS ** 0 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 45690 Z= 0.188 Angle : 0.529 9.022 62145 Z= 0.269 Chirality : 0.042 0.141 7110 Planarity : 0.004 0.040 7650 Dihedral : 6.590 53.520 6960 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.06 % Allowed : 3.44 % Favored : 96.51 % Rotamer Outliers : 0.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.12), residues: 5355 helix: 0.54 (0.10), residues: 3135 sheet: -1.67 (0.25), residues: 390 loop : -1.04 (0.15), residues: 1830 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 811 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 787 time to evaluate : 5.056 Fit side-chains revert: symmetry clash outliers start: 24 outliers final: 13 residues processed: 801 average time/residue: 0.6433 time to fit residues: 815.2489 Evaluate side-chains 770 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 757 time to evaluate : 5.159 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 0 residues processed: 13 average time/residue: 0.4207 time to fit residues: 17.0694 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 473 optimal weight: 1.9990 chunk 498 optimal weight: 8.9990 chunk 454 optimal weight: 4.9990 chunk 485 optimal weight: 0.0010 chunk 291 optimal weight: 8.9990 chunk 211 optimal weight: 4.9990 chunk 380 optimal weight: 6.9990 chunk 148 optimal weight: 4.9990 chunk 438 optimal weight: 0.9990 chunk 458 optimal weight: 0.9990 chunk 483 optimal weight: 3.9990 overall best weight: 1.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS C 304 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 HIS ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS K 201 GLN ** K 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 HIS M 246 ASN O 33 HIS Q 33 HIS ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 33 HIS U 304 GLN W 322 ASN Y 33 HIS Y 164 ASN 0 33 HIS ** 0 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 33 HIS 2 86 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8755 moved from start: 0.3577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 45690 Z= 0.188 Angle : 0.529 6.494 62145 Z= 0.269 Chirality : 0.042 0.131 7110 Planarity : 0.004 0.042 7650 Dihedral : 6.572 53.514 6960 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.36 % Favored : 96.60 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.12), residues: 5355 helix: 0.56 (0.10), residues: 3120 sheet: -1.63 (0.25), residues: 390 loop : -0.98 (0.15), residues: 1845 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 786 time to evaluate : 5.083 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 7 residues processed: 796 average time/residue: 0.6550 time to fit residues: 828.3707 Evaluate side-chains 762 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 755 time to evaluate : 5.481 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.4414 time to fit residues: 12.9547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 318 optimal weight: 2.9990 chunk 512 optimal weight: 8.9990 chunk 313 optimal weight: 5.9990 chunk 243 optimal weight: 5.9990 chunk 356 optimal weight: 8.9990 chunk 537 optimal weight: 3.9990 chunk 495 optimal weight: 0.6980 chunk 428 optimal weight: 5.9990 chunk 44 optimal weight: 0.1980 chunk 330 optimal weight: 0.0070 chunk 262 optimal weight: 0.0470 overall best weight: 0.7898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS C 246 ASN C 304 GLN A 33 HIS ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 HIS ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS ** K 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 HIS M 246 ASN O 33 HIS O 201 GLN Q 33 HIS S 304 GLN ** U 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 164 ASN U 322 ASN W 33 HIS Y 33 HIS 0 33 HIS 2 33 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.3713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.110 45690 Z= 0.155 Angle : 0.522 11.029 62145 Z= 0.266 Chirality : 0.041 0.133 7110 Planarity : 0.004 0.089 7650 Dihedral : 6.544 53.846 6960 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.21 % Favored : 96.77 % Rotamer Outliers : 0.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.12), residues: 5355 helix: 0.63 (0.10), residues: 3120 sheet: -1.54 (0.25), residues: 390 loop : -0.92 (0.15), residues: 1845 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 830 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 823 time to evaluate : 5.654 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 825 average time/residue: 0.6369 time to fit residues: 831.4130 Evaluate side-chains 767 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 765 time to evaluate : 5.030 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.4650 time to fit residues: 8.6313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 340 optimal weight: 4.9990 chunk 456 optimal weight: 3.9990 chunk 131 optimal weight: 8.9990 chunk 395 optimal weight: 3.9990 chunk 63 optimal weight: 8.9990 chunk 119 optimal weight: 7.9990 chunk 429 optimal weight: 9.9990 chunk 179 optimal weight: 2.9990 chunk 440 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 79 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS C 304 GLN ** A 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 322 ASN G 33 HIS ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS I 86 GLN I 201 GLN ** K 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 HIS M 246 ASN O 33 HIS O 164 ASN Q 33 HIS S 304 GLN ** U 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 164 ASN U 322 ASN W 33 HIS Y 33 HIS Y 246 ASN Y 304 GLN 0 33 HIS 2 89 GLN 2 301 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.111654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.093964 restraints weight = 67422.107| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 2.06 r_work: 0.3084 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3070 rms_B_bonded: 1.82 restraints_weight: 0.2500 r_work: 0.3056 rms_B_bonded: 1.87 restraints_weight: 0.1250 r_work: 0.3041 rms_B_bonded: 1.99 restraints_weight: 0.0625 r_work: 0.3025 rms_B_bonded: 2.15 restraints_weight: 0.0312 r_work: 0.3008 rms_B_bonded: 2.35 restraints_weight: 0.0156 r_work: 0.2989 rms_B_bonded: 2.60 restraints_weight: 0.0078 r_work: 0.2969 rms_B_bonded: 2.90 restraints_weight: 0.0039 r_work: 0.2946 rms_B_bonded: 3.25 restraints_weight: 0.0020 r_work: 0.2922 rms_B_bonded: 3.66 restraints_weight: 0.0010 r_work: 0.2895 rms_B_bonded: 4.13 restraints_weight: 0.0005 r_work: 0.2865 rms_B_bonded: 4.68 restraints_weight: 0.0002 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8974 moved from start: 0.3717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.096 45690 Z= 0.230 Angle : 0.551 9.322 62145 Z= 0.280 Chirality : 0.043 0.135 7110 Planarity : 0.004 0.073 7650 Dihedral : 6.540 52.442 6960 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 0.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.12), residues: 5355 helix: 0.60 (0.10), residues: 3120 sheet: -1.51 (0.25), residues: 390 loop : -0.91 (0.15), residues: 1845 =============================================================================== Job complete usr+sys time: 13034.59 seconds wall clock time: 233 minutes 53.76 seconds (14033.76 seconds total)