Starting phenix.real_space_refine (version: dev) on Sat Apr 9 15:31:48 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5q_0141/04_2022/6h5q_0141.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5q_0141/04_2022/6h5q_0141.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/6h5q_0141/04_2022/6h5q_0141.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5q_0141/04_2022/6h5q_0141.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5q_0141/04_2022/6h5q_0141.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5q_0141/04_2022/6h5q_0141.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= 0.005 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 "B ASP 42": "OD1" <-> "OD2" Residue "B ARG 48": "NH1" <-> "NH2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B ARG 57": "NH1" <-> "NH2" Residue "B ARG 100": "NH1" <-> "NH2" Residue "B ARG 194": "NH1" <-> "NH2" Residue "B ARG 195": "NH1" <-> "NH2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B ARG 204": "NH1" <-> "NH2" Residue "B ARG 213": "NH1" <-> "NH2" Residue "B ARG 222": "NH1" <-> "NH2" Residue "B ARG 230": "NH1" <-> "NH2" Residue "B ARG 370": "NH1" <-> "NH2" Residue "A ASP 42": "OD1" <-> "OD2" Residue "A ARG 48": "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 ARG 370": "NH1" <-> "NH2" Residue "D ASP 42": "OD1" <-> "OD2" Residue "D ARG 48": "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 ARG 370": "NH1" <-> "NH2" Residue "F ASP 42": "OD1" <-> "OD2" Residue "F ARG 48": "NH1" <-> "NH2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F ARG 57": "NH1" <-> "NH2" Residue "F ARG 100": "NH1" <-> "NH2" Residue "F ARG 194": "NH1" <-> "NH2" Residue "F ARG 195": "NH1" <-> "NH2" Residue "F ARG 203": "NH1" <-> "NH2" Residue "F ARG 204": "NH1" <-> "NH2" Residue "F ARG 213": "NH1" <-> "NH2" Residue "F ARG 222": "NH1" <-> "NH2" Residue "F ARG 230": "NH1" <-> "NH2" Residue "F ARG 370": "NH1" <-> "NH2" Residue "H ASP 42": "OD1" <-> "OD2" Residue "H ARG 48": "NH1" <-> "NH2" Residue "H ARG 54": "NH1" <-> "NH2" Residue "H ARG 57": "NH1" <-> "NH2" Residue "H ARG 100": "NH1" <-> "NH2" Residue "H ARG 194": "NH1" <-> "NH2" Residue "H ARG 195": "NH1" <-> "NH2" Residue "H ARG 203": "NH1" <-> "NH2" Residue "H ARG 204": "NH1" <-> "NH2" Residue "H ARG 213": "NH1" <-> "NH2" Residue "H ARG 222": "NH1" <-> "NH2" Residue "H ARG 230": "NH1" <-> "NH2" Residue "H ARG 370": "NH1" <-> "NH2" Residue "J ASP 42": "OD1" <-> "OD2" Residue "J ARG 48": "NH1" <-> "NH2" Residue "J ARG 54": "NH1" <-> "NH2" Residue "J ARG 57": "NH1" <-> "NH2" Residue "J ARG 100": "NH1" <-> "NH2" Residue "J ARG 194": "NH1" <-> "NH2" Residue "J ARG 195": "NH1" <-> "NH2" Residue "J ARG 203": "NH1" <-> "NH2" Residue "J ARG 204": "NH1" <-> "NH2" Residue "J ARG 213": "NH1" <-> "NH2" Residue "J ARG 222": "NH1" <-> "NH2" Residue "J ARG 230": "NH1" <-> "NH2" Residue "J ARG 370": "NH1" <-> "NH2" Residue "L ASP 42": "OD1" <-> "OD2" Residue "L ARG 48": "NH1" <-> "NH2" Residue "L ARG 54": "NH1" <-> "NH2" Residue "L ARG 57": "NH1" <-> "NH2" Residue "L ARG 100": "NH1" <-> "NH2" Residue "L ARG 194": "NH1" <-> "NH2" Residue "L ARG 195": "NH1" <-> "NH2" Residue "L ARG 203": "NH1" <-> "NH2" Residue "L ARG 204": "NH1" <-> "NH2" Residue "L ARG 213": "NH1" <-> "NH2" Residue "L ARG 222": "NH1" <-> "NH2" Residue "L ARG 230": "NH1" <-> "NH2" Residue "L ARG 370": "NH1" <-> "NH2" Residue "N ASP 42": "OD1" <-> "OD2" Residue "N ARG 48": "NH1" <-> "NH2" Residue "N ARG 54": "NH1" <-> "NH2" Residue "N ARG 57": "NH1" <-> "NH2" Residue "N ARG 100": "NH1" <-> "NH2" Residue "N ARG 194": "NH1" <-> "NH2" Residue "N ARG 195": "NH1" <-> "NH2" Residue "N ARG 203": "NH1" <-> "NH2" Residue "N ARG 204": "NH1" <-> "NH2" Residue "N ARG 213": "NH1" <-> "NH2" Residue "N ARG 222": "NH1" <-> "NH2" Residue "N ARG 230": "NH1" <-> "NH2" Residue "N ARG 370": "NH1" <-> "NH2" Residue "P ASP 42": "OD1" <-> "OD2" Residue "P ARG 48": "NH1" <-> "NH2" Residue "P ARG 54": "NH1" <-> "NH2" Residue "P ARG 57": "NH1" <-> "NH2" Residue "P ARG 100": "NH1" <-> "NH2" Residue "P ARG 194": "NH1" <-> "NH2" Residue "P ARG 195": "NH1" <-> "NH2" Residue "P ARG 203": "NH1" <-> "NH2" Residue "P ARG 204": "NH1" <-> "NH2" Residue "P ARG 213": "NH1" <-> "NH2" Residue "P ARG 222": "NH1" <-> "NH2" Residue "P ARG 230": "NH1" <-> "NH2" Residue "P ARG 370": "NH1" <-> "NH2" Residue "S ASP 42": "OD1" <-> "OD2" Residue "S ARG 48": "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 ARG 370": "NH1" <-> "NH2" Residue "U ASP 42": "OD1" <-> "OD2" Residue "U ARG 48": "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 ARG 370": "NH1" <-> "NH2" Residue "W ASP 42": "OD1" <-> "OD2" Residue "W ARG 48": "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 ARG 370": "NH1" <-> "NH2" Residue "Y ASP 42": "OD1" <-> "OD2" Residue "Y ARG 48": "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 ARG 370": "NH1" <-> "NH2" Residue "0 ASP 42": "OD1" <-> "OD2" Residue "0 ARG 48": "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 ARG 370": "NH1" <-> "NH2" Residue "2 ASP 42": "OD1" <-> "OD2" Residue "2 ARG 48": "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 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: 46650 Number of models: 1 Model: "" Number of chains: 30 Chain: "B" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "R" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "A" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "C" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "D" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "E" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "F" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "G" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "H" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "I" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "J" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "K" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "L" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "M" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "N" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "O" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "P" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "Q" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "S" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "T" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "U" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "V" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "W" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "X" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "Y" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "Z" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "0" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "1" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna3p': 4, 'rna2p': 1} Chain: "2" Number of atoms: 2981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 2981 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 16, 'TRANS': 364} Chain breaks: 2 Chain: "3" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 129 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pur': 1, 'rna3p_pur': 5} Link IDs: {'rna3p': 4, 'rna2p': 1} Time building chain proxies: 24.99, per 1000 atoms: 0.54 Number of scatterers: 46650 At special positions: 0 Unit cell: (203.184, 203.184, 135.456, 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 8910 8.00 N 8115 7.00 C 29370 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: 19.49 Conformation dependent library (CDL) restraints added in 6.6 seconds 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10530 Finding SS restraints... Secondary structure from input PDB file: 330 helices and 15 sheets defined 59.1% alpha, 4.7% beta 0 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 12.48 Creating SS restraints... Processing helix chain 'B' and resid 2 through 17 removed outlier: 4.047A pdb=" N ARG B 6 " --> pdb=" O ALA B 2 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN B 14 " --> pdb=" O LEU B 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS B 15 " --> pdb=" O PHE B 11 " (cutoff:3.500A) Processing helix chain 'B' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG B 48 " --> pdb=" O SER B 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG B 57 " --> pdb=" O ASP B 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN B 61 " --> pdb=" O ARG B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU B 69 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 removed outlier: 3.736A pdb=" N LEU B 87 " --> pdb=" O SER B 83 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN B 89 " --> pdb=" O GLY B 85 " (cutoff:3.500A) Processing helix chain 'B' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP B 128 " --> pdb=" O GLU B 124 " (cutoff:3.500A) Processing helix chain 'B' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE B 170 " --> pdb=" O ILE B 166 " (cutoff:3.500A) Processing helix chain 'B' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA B 181 " --> pdb=" O LEU B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA B 189 " --> pdb=" O PRO B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG B 195 " --> pdb=" O SER B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL B 218 " --> pdb=" O LYS B 214 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE B 232 " --> pdb=" O SER B 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE B 237 " --> pdb=" O MET B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP B 256 " --> pdb=" O GLU B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 261 No H-bonds generated for 'chain 'B' and resid 259 through 261' Processing helix chain 'B' and resid 269 through 276 Processing helix chain 'B' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU B 296 " --> pdb=" O GLU B 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER B 298 " --> pdb=" O SER B 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN B 304 " --> pdb=" O MET B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 310 Processing helix chain 'B' and resid 325 through 328 removed outlier: 3.725A pdb=" N SER B 328 " --> pdb=" O SER B 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 325 through 328' Processing helix chain 'B' and resid 329 through 343 removed outlier: 4.462A pdb=" N GLU B 342 " --> pdb=" O GLY B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 350 Processing helix chain 'B' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE B 362 " --> pdb=" O ASP B 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL B 369 " --> pdb=" O GLY B 365 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU B 393 " --> pdb=" O GLU B 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL B 394 " --> pdb=" O ASP B 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 17 removed outlier: 4.047A pdb=" N ARG A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N LYS A 15 " --> pdb=" O PHE A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY A 60 " --> pdb=" O VAL A 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN A 61 " --> pdb=" O ARG A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 removed outlier: 3.538A pdb=" N LEU A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 removed outlier: 3.736A pdb=" N LEU A 87 " --> pdb=" O SER A 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN A 89 " --> pdb=" O GLY A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 132 removed outlier: 3.850A pdb=" N ASP A 128 " --> pdb=" O GLU A 124 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 172 removed outlier: 3.646A pdb=" N ILE A 170 " --> pdb=" O ILE A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA A 181 " --> pdb=" O LEU A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA A 189 " --> pdb=" O PRO A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 224 removed outlier: 3.530A pdb=" N VAL A 218 " --> pdb=" O LYS A 214 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 241 removed outlier: 3.627A pdb=" N PHE A 232 " --> pdb=" O SER A 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP A 256 " --> pdb=" O GLU A 252 " (cutoff:3.500A) 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 269 through 276 Processing helix chain 'A' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU A 296 " --> pdb=" O GLU A 292 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER A 298 " --> pdb=" O SER A 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN A 304 " --> pdb=" O MET A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 310 Processing helix chain 'A' and resid 325 through 328 removed outlier: 3.724A 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 343 removed outlier: 4.463A pdb=" N GLU A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 350 Processing helix chain 'A' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL A 369 " --> pdb=" O GLY A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 385 removed outlier: 3.618A pdb=" N LEU A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 395 removed outlier: 3.832A pdb=" N LEU A 393 " --> pdb=" O GLU A 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL A 394 " --> pdb=" O ASP A 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 17 removed outlier: 4.047A pdb=" N ARG D 6 " --> pdb=" O ALA D 2 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN D 14 " --> pdb=" O LEU D 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS D 15 " --> pdb=" O PHE D 11 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG D 48 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG D 57 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N GLY D 60 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN D 61 " --> pdb=" O ARG D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 77 removed outlier: 3.538A pdb=" N LEU D 69 " --> pdb=" O SER D 65 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 92 removed outlier: 3.737A pdb=" N LEU D 87 " --> pdb=" O SER D 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 132 removed outlier: 3.850A pdb=" N ASP D 128 " --> pdb=" O GLU D 124 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 172 removed outlier: 3.646A pdb=" N ILE D 170 " --> pdb=" O ILE D 166 " (cutoff:3.500A) Processing helix chain 'D' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA D 181 " --> pdb=" O LEU D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA D 189 " --> pdb=" O PRO D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG D 195 " --> pdb=" O SER D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL D 218 " --> pdb=" O LYS D 214 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE D 232 " --> pdb=" O SER D 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 250 through 258 removed outlier: 3.765A pdb=" N ASP D 256 " --> pdb=" O GLU D 252 " (cutoff:3.500A) 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 269 through 276 Processing helix chain 'D' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU D 296 " --> pdb=" O GLU D 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER D 298 " --> pdb=" O SER D 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN D 304 " --> pdb=" O MET D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 307 through 310 Processing helix chain 'D' and resid 325 through 328 removed outlier: 3.725A 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 343 removed outlier: 4.462A pdb=" N GLU D 342 " --> pdb=" O GLY D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 350 Processing helix chain 'D' and resid 358 through 372 removed outlier: 3.602A pdb=" N PHE D 362 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL D 369 " --> pdb=" O GLY D 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU D 384 " --> pdb=" O LEU D 380 " (cutoff:3.500A) Processing helix chain 'D' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU D 393 " --> pdb=" O GLU D 389 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL D 394 " --> pdb=" O ASP D 390 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 17 removed outlier: 4.047A pdb=" N ARG F 6 " --> pdb=" O ALA F 2 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN F 14 " --> pdb=" O LEU F 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS F 15 " --> pdb=" O PHE F 11 " (cutoff:3.500A) Processing helix chain 'F' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG F 48 " --> pdb=" O SER F 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG F 57 " --> pdb=" O ASP F 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY F 60 " --> pdb=" O VAL F 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN F 61 " --> pdb=" O ARG F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU F 69 " --> pdb=" O SER F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 removed outlier: 3.735A pdb=" N LEU F 87 " --> pdb=" O SER F 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN F 89 " --> pdb=" O GLY F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP F 128 " --> pdb=" O GLU F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE F 170 " --> pdb=" O ILE F 166 " (cutoff:3.500A) Processing helix chain 'F' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA F 181 " --> pdb=" O LEU F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA F 189 " --> pdb=" O PRO F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG F 195 " --> pdb=" O SER F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 212 through 224 removed outlier: 3.530A pdb=" N VAL F 218 " --> pdb=" O LYS F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE F 232 " --> pdb=" O SER F 228 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE F 237 " --> pdb=" O MET F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 250 through 258 removed outlier: 3.765A pdb=" N ASP F 256 " --> pdb=" O GLU F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 259 through 261 No H-bonds generated for 'chain 'F' and resid 259 through 261' Processing helix chain 'F' and resid 269 through 276 Processing helix chain 'F' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU F 296 " --> pdb=" O GLU F 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER F 298 " --> pdb=" O SER F 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN F 304 " --> pdb=" O MET F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 310 Processing helix chain 'F' and resid 325 through 328 removed outlier: 3.725A pdb=" N SER F 328 " --> pdb=" O SER F 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 325 through 328' Processing helix chain 'F' and resid 329 through 343 removed outlier: 4.463A pdb=" N GLU F 342 " --> pdb=" O GLY F 338 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 350 Processing helix chain 'F' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE F 362 " --> pdb=" O ASP F 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL F 369 " --> pdb=" O GLY F 365 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 385 removed outlier: 3.616A pdb=" N LEU F 384 " --> pdb=" O LEU F 380 " (cutoff:3.500A) Processing helix chain 'F' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU F 393 " --> pdb=" O GLU F 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL F 394 " --> pdb=" O ASP F 390 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 17 removed outlier: 4.046A pdb=" N ARG H 6 " --> pdb=" O ALA H 2 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN H 14 " --> pdb=" O LEU H 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS H 15 " --> pdb=" O PHE H 11 " (cutoff:3.500A) Processing helix chain 'H' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG H 48 " --> pdb=" O SER H 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG H 57 " --> pdb=" O ASP H 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY H 60 " --> pdb=" O VAL H 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN H 61 " --> pdb=" O ARG H 57 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU H 69 " --> pdb=" O SER H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 83 through 92 removed outlier: 3.736A pdb=" N LEU H 87 " --> pdb=" O SER H 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN H 89 " --> pdb=" O GLY H 85 " (cutoff:3.500A) Processing helix chain 'H' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP H 128 " --> pdb=" O GLU H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 159 through 172 removed outlier: 3.646A pdb=" N ILE H 170 " --> pdb=" O ILE H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 177 through 181 removed outlier: 3.886A pdb=" N ALA H 181 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA H 189 " --> pdb=" O PRO H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG H 195 " --> pdb=" O SER H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL H 218 " --> pdb=" O LYS H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE H 232 " --> pdb=" O SER H 228 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE H 237 " --> pdb=" O MET H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP H 256 " --> pdb=" O GLU H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 261 No H-bonds generated for 'chain 'H' and resid 259 through 261' Processing helix chain 'H' and resid 269 through 276 Processing helix chain 'H' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU H 296 " --> pdb=" O GLU H 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER H 298 " --> pdb=" O SER H 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN H 304 " --> pdb=" O MET H 300 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 310 Processing helix chain 'H' and resid 325 through 328 removed outlier: 3.725A pdb=" N SER H 328 " --> pdb=" O SER H 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 325 through 328' Processing helix chain 'H' and resid 329 through 343 removed outlier: 4.462A pdb=" N GLU H 342 " --> pdb=" O GLY H 338 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 350 Processing helix chain 'H' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE H 362 " --> pdb=" O ASP H 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL H 369 " --> pdb=" O GLY H 365 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU H 384 " --> pdb=" O LEU H 380 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU H 393 " --> pdb=" O GLU H 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL H 394 " --> pdb=" O ASP H 390 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 17 removed outlier: 4.047A pdb=" N ARG J 6 " --> pdb=" O ALA J 2 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN J 14 " --> pdb=" O LEU J 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS J 15 " --> pdb=" O PHE J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG J 48 " --> pdb=" O SER J 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG J 57 " --> pdb=" O ASP J 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY J 60 " --> pdb=" O VAL J 56 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN J 61 " --> pdb=" O ARG J 57 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 77 removed outlier: 3.538A pdb=" N LEU J 69 " --> pdb=" O SER J 65 " (cutoff:3.500A) Processing helix chain 'J' and resid 83 through 92 removed outlier: 3.736A pdb=" N LEU J 87 " --> pdb=" O SER J 83 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN J 89 " --> pdb=" O GLY J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP J 128 " --> pdb=" O GLU J 124 " (cutoff:3.500A) Processing helix chain 'J' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE J 170 " --> pdb=" O ILE J 166 " (cutoff:3.500A) Processing helix chain 'J' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA J 181 " --> pdb=" O LEU J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA J 189 " --> pdb=" O PRO J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 202 removed outlier: 3.542A pdb=" N ARG J 195 " --> pdb=" O SER J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL J 218 " --> pdb=" O LYS J 214 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE J 232 " --> pdb=" O SER J 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE J 237 " --> pdb=" O MET J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP J 256 " --> pdb=" O GLU J 252 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 261 No H-bonds generated for 'chain 'J' and resid 259 through 261' Processing helix chain 'J' and resid 269 through 276 Processing helix chain 'J' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU J 296 " --> pdb=" O GLU J 292 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER J 298 " --> pdb=" O SER J 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN J 304 " --> pdb=" O MET J 300 " (cutoff:3.500A) Processing helix chain 'J' and resid 307 through 310 Processing helix chain 'J' and resid 325 through 328 removed outlier: 3.725A pdb=" N SER J 328 " --> pdb=" O SER J 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 325 through 328' Processing helix chain 'J' and resid 329 through 343 removed outlier: 4.462A pdb=" N GLU J 342 " --> pdb=" O GLY J 338 " (cutoff:3.500A) Processing helix chain 'J' and resid 346 through 350 Processing helix chain 'J' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE J 362 " --> pdb=" O ASP J 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL J 369 " --> pdb=" O GLY J 365 " (cutoff:3.500A) Processing helix chain 'J' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU J 384 " --> pdb=" O LEU J 380 " (cutoff:3.500A) Processing helix chain 'J' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU J 393 " --> pdb=" O GLU J 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL J 394 " --> pdb=" O ASP J 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 17 removed outlier: 4.048A pdb=" N ARG L 6 " --> pdb=" O ALA L 2 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN L 14 " --> pdb=" O LEU L 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS L 15 " --> pdb=" O PHE L 11 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG L 48 " --> pdb=" O SER L 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG L 57 " --> pdb=" O ASP L 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY L 60 " --> pdb=" O VAL L 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN L 61 " --> pdb=" O ARG L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU L 69 " --> pdb=" O SER L 65 " (cutoff:3.500A) Processing helix chain 'L' and resid 83 through 92 removed outlier: 3.737A pdb=" N LEU L 87 " --> pdb=" O SER L 83 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN L 89 " --> pdb=" O GLY L 85 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 132 removed outlier: 3.850A pdb=" N ASP L 128 " --> pdb=" O GLU L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE L 170 " --> pdb=" O ILE L 166 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 181 removed outlier: 3.886A pdb=" N ALA L 181 " --> pdb=" O LEU L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA L 189 " --> pdb=" O PRO L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 191 through 202 removed outlier: 3.542A pdb=" N ARG L 195 " --> pdb=" O SER L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 212 through 224 removed outlier: 3.530A pdb=" N VAL L 218 " --> pdb=" O LYS L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE L 232 " --> pdb=" O SER L 228 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE L 237 " --> pdb=" O MET L 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 250 through 258 removed outlier: 3.765A pdb=" N ASP L 256 " --> pdb=" O GLU L 252 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 261 No H-bonds generated for 'chain 'L' and resid 259 through 261' Processing helix chain 'L' and resid 269 through 276 Processing helix chain 'L' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU L 296 " --> pdb=" O GLU L 292 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER L 298 " --> pdb=" O SER L 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN L 304 " --> pdb=" O MET L 300 " (cutoff:3.500A) Processing helix chain 'L' and resid 307 through 310 Processing helix chain 'L' and resid 325 through 328 removed outlier: 3.725A pdb=" N SER L 328 " --> pdb=" O SER L 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 325 through 328' Processing helix chain 'L' and resid 329 through 343 removed outlier: 4.462A pdb=" N GLU L 342 " --> pdb=" O GLY L 338 " (cutoff:3.500A) Processing helix chain 'L' and resid 346 through 350 Processing helix chain 'L' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE L 362 " --> pdb=" O ASP L 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL L 369 " --> pdb=" O GLY L 365 " (cutoff:3.500A) Processing helix chain 'L' and resid 380 through 385 removed outlier: 3.618A pdb=" N LEU L 384 " --> pdb=" O LEU L 380 " (cutoff:3.500A) Processing helix chain 'L' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU L 393 " --> pdb=" O GLU L 389 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL L 394 " --> pdb=" O ASP L 390 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 17 removed outlier: 4.046A pdb=" N ARG N 6 " --> pdb=" O ALA N 2 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS N 15 " --> pdb=" O PHE N 11 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG N 48 " --> pdb=" O SER N 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG N 57 " --> pdb=" O ASP N 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY N 60 " --> pdb=" O VAL N 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN N 61 " --> pdb=" O ARG N 57 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 77 removed outlier: 3.538A pdb=" N LEU N 69 " --> pdb=" O SER N 65 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 92 removed outlier: 3.736A pdb=" N LEU N 87 " --> pdb=" O SER N 83 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN N 89 " --> pdb=" O GLY N 85 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP N 128 " --> pdb=" O GLU N 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE N 170 " --> pdb=" O ILE N 166 " (cutoff:3.500A) Processing helix chain 'N' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA N 181 " --> pdb=" O LEU N 178 " (cutoff:3.500A) Processing helix chain 'N' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA N 189 " --> pdb=" O PRO N 185 " (cutoff:3.500A) Processing helix chain 'N' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG N 195 " --> pdb=" O SER N 191 " (cutoff:3.500A) Processing helix chain 'N' and resid 212 through 224 removed outlier: 3.530A pdb=" N VAL N 218 " --> pdb=" O LYS N 214 " (cutoff:3.500A) Processing helix chain 'N' and resid 227 through 241 removed outlier: 3.627A pdb=" N PHE N 232 " --> pdb=" O SER N 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE N 237 " --> pdb=" O MET N 233 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP N 256 " --> pdb=" O GLU N 252 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 261 No H-bonds generated for 'chain 'N' and resid 259 through 261' Processing helix chain 'N' and resid 269 through 276 Processing helix chain 'N' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU N 296 " --> pdb=" O GLU N 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER N 298 " --> pdb=" O SER N 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN N 304 " --> pdb=" O MET N 300 " (cutoff:3.500A) Processing helix chain 'N' and resid 307 through 310 Processing helix chain 'N' and resid 325 through 328 removed outlier: 3.724A pdb=" N SER N 328 " --> pdb=" O SER N 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 325 through 328' Processing helix chain 'N' and resid 329 through 343 removed outlier: 4.462A pdb=" N GLU N 342 " --> pdb=" O GLY N 338 " (cutoff:3.500A) Processing helix chain 'N' and resid 346 through 350 Processing helix chain 'N' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE N 362 " --> pdb=" O ASP N 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL N 369 " --> pdb=" O GLY N 365 " (cutoff:3.500A) Processing helix chain 'N' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU N 384 " --> pdb=" O LEU N 380 " (cutoff:3.500A) Processing helix chain 'N' and resid 387 through 395 removed outlier: 3.832A pdb=" N LEU N 393 " --> pdb=" O GLU N 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL N 394 " --> pdb=" O ASP N 390 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 17 removed outlier: 4.047A pdb=" N ARG P 6 " --> pdb=" O ALA P 2 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ASN P 14 " --> pdb=" O LEU P 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS P 15 " --> pdb=" O PHE P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG P 48 " --> pdb=" O SER P 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG P 57 " --> pdb=" O ASP P 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY P 60 " --> pdb=" O VAL P 56 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN P 61 " --> pdb=" O ARG P 57 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU P 69 " --> pdb=" O SER P 65 " (cutoff:3.500A) Processing helix chain 'P' and resid 83 through 92 removed outlier: 3.737A pdb=" N LEU P 87 " --> pdb=" O SER P 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN P 89 " --> pdb=" O GLY P 85 " (cutoff:3.500A) Processing helix chain 'P' and resid 124 through 132 removed outlier: 3.850A pdb=" N ASP P 128 " --> pdb=" O GLU P 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE P 170 " --> pdb=" O ILE P 166 " (cutoff:3.500A) Processing helix chain 'P' and resid 177 through 181 removed outlier: 3.886A pdb=" N ALA P 181 " --> pdb=" O LEU P 178 " (cutoff:3.500A) Processing helix chain 'P' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA P 189 " --> pdb=" O PRO P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG P 195 " --> pdb=" O SER P 191 " (cutoff:3.500A) Processing helix chain 'P' and resid 212 through 224 removed outlier: 3.530A pdb=" N VAL P 218 " --> pdb=" O LYS P 214 " (cutoff:3.500A) Processing helix chain 'P' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE P 232 " --> pdb=" O SER P 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE P 237 " --> pdb=" O MET P 233 " (cutoff:3.500A) Processing helix chain 'P' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP P 256 " --> pdb=" O GLU P 252 " (cutoff:3.500A) Processing helix chain 'P' and resid 259 through 261 No H-bonds generated for 'chain 'P' and resid 259 through 261' Processing helix chain 'P' and resid 269 through 276 Processing helix chain 'P' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU P 296 " --> pdb=" O GLU P 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER P 298 " --> pdb=" O SER P 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN P 304 " --> pdb=" O MET P 300 " (cutoff:3.500A) Processing helix chain 'P' and resid 307 through 310 Processing helix chain 'P' and resid 325 through 328 removed outlier: 3.725A pdb=" N SER P 328 " --> pdb=" O SER P 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 325 through 328' Processing helix chain 'P' and resid 329 through 343 removed outlier: 4.462A pdb=" N GLU P 342 " --> pdb=" O GLY P 338 " (cutoff:3.500A) Processing helix chain 'P' and resid 346 through 350 Processing helix chain 'P' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE P 362 " --> pdb=" O ASP P 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL P 369 " --> pdb=" O GLY P 365 " (cutoff:3.500A) Processing helix chain 'P' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU P 384 " --> pdb=" O LEU P 380 " (cutoff:3.500A) Processing helix chain 'P' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU P 393 " --> pdb=" O GLU P 389 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL P 394 " --> pdb=" O ASP P 390 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 17 removed outlier: 4.047A pdb=" N ARG S 6 " --> pdb=" O ALA S 2 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN S 14 " --> pdb=" O LEU S 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS S 15 " --> pdb=" O PHE S 11 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG S 48 " --> pdb=" O SER S 44 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG S 57 " --> pdb=" O ASP S 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY S 60 " --> pdb=" O VAL S 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN S 61 " --> pdb=" O ARG S 57 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 77 removed outlier: 3.538A pdb=" N LEU S 69 " --> pdb=" O SER S 65 " (cutoff:3.500A) Processing helix chain 'S' and resid 83 through 92 removed outlier: 3.737A pdb=" N LEU S 87 " --> pdb=" O SER S 83 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN S 89 " --> pdb=" O GLY S 85 " (cutoff:3.500A) Processing helix chain 'S' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP S 128 " --> pdb=" O GLU S 124 " (cutoff:3.500A) Processing helix chain 'S' and resid 159 through 172 removed outlier: 3.646A pdb=" N ILE S 170 " --> pdb=" O ILE S 166 " (cutoff:3.500A) Processing helix chain 'S' and resid 177 through 181 removed outlier: 3.886A pdb=" N ALA S 181 " --> pdb=" O LEU S 178 " (cutoff:3.500A) Processing helix chain 'S' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA S 189 " --> pdb=" O PRO S 185 " (cutoff:3.500A) Processing helix chain 'S' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG S 195 " --> pdb=" O SER S 191 " (cutoff:3.500A) Processing helix chain 'S' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL S 218 " --> pdb=" O LYS S 214 " (cutoff:3.500A) Processing helix chain 'S' and resid 227 through 241 removed outlier: 3.627A pdb=" N PHE S 232 " --> pdb=" O SER S 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE S 237 " --> pdb=" O MET S 233 " (cutoff:3.500A) Processing helix chain 'S' and resid 250 through 258 removed outlier: 3.765A pdb=" N ASP S 256 " --> pdb=" O GLU S 252 " (cutoff:3.500A) 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 269 through 276 Processing helix chain 'S' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU S 296 " --> pdb=" O GLU S 292 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER S 298 " --> pdb=" O SER S 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN S 304 " --> pdb=" O MET S 300 " (cutoff:3.500A) Processing helix chain 'S' and resid 307 through 310 Processing helix chain 'S' and resid 325 through 328 removed outlier: 3.725A 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 343 removed outlier: 4.462A pdb=" N GLU S 342 " --> pdb=" O GLY S 338 " (cutoff:3.500A) Processing helix chain 'S' and resid 346 through 350 Processing helix chain 'S' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE S 362 " --> pdb=" O ASP S 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL S 369 " --> pdb=" O GLY S 365 " (cutoff:3.500A) Processing helix chain 'S' and resid 380 through 385 removed outlier: 3.618A pdb=" N LEU S 384 " --> pdb=" O LEU S 380 " (cutoff:3.500A) Processing helix chain 'S' and resid 387 through 395 removed outlier: 3.832A pdb=" N LEU S 393 " --> pdb=" O GLU S 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL S 394 " --> pdb=" O ASP S 390 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 17 removed outlier: 4.046A pdb=" N ARG U 6 " --> pdb=" O ALA U 2 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN U 14 " --> pdb=" O LEU U 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS U 15 " --> pdb=" O PHE U 11 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 61 removed outlier: 3.573A pdb=" N ARG U 48 " --> pdb=" O SER U 44 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG U 57 " --> pdb=" O ASP U 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY U 60 " --> pdb=" O VAL U 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN U 61 " --> pdb=" O ARG U 57 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU U 69 " --> pdb=" O SER U 65 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 92 removed outlier: 3.737A pdb=" N LEU U 87 " --> pdb=" O SER U 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN U 89 " --> pdb=" O GLY U 85 " (cutoff:3.500A) Processing helix chain 'U' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP U 128 " --> pdb=" O GLU U 124 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE U 170 " --> pdb=" O ILE U 166 " (cutoff:3.500A) Processing helix chain 'U' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA U 181 " --> pdb=" O LEU U 178 " (cutoff:3.500A) Processing helix chain 'U' and resid 184 through 189 removed outlier: 4.436A pdb=" N ALA U 189 " --> pdb=" O PRO U 185 " (cutoff:3.500A) Processing helix chain 'U' and resid 191 through 202 removed outlier: 3.542A pdb=" N ARG U 195 " --> pdb=" O SER U 191 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL U 218 " --> pdb=" O LYS U 214 " (cutoff:3.500A) Processing helix chain 'U' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE U 232 " --> pdb=" O SER U 228 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ILE U 237 " --> pdb=" O MET U 233 " (cutoff:3.500A) Processing helix chain 'U' and resid 250 through 258 removed outlier: 3.765A pdb=" N ASP U 256 " --> pdb=" O GLU U 252 " (cutoff:3.500A) 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 269 through 276 Processing helix chain 'U' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU U 296 " --> pdb=" O GLU U 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER U 298 " --> pdb=" O SER U 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN U 304 " --> pdb=" O MET U 300 " (cutoff:3.500A) Processing helix chain 'U' and resid 307 through 310 Processing helix chain 'U' and resid 325 through 328 removed outlier: 3.725A 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 343 removed outlier: 4.463A pdb=" N GLU U 342 " --> pdb=" O GLY U 338 " (cutoff:3.500A) Processing helix chain 'U' and resid 346 through 350 Processing helix chain 'U' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE U 362 " --> pdb=" O ASP U 358 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL U 369 " --> pdb=" O GLY U 365 " (cutoff:3.500A) Processing helix chain 'U' and resid 380 through 385 removed outlier: 3.616A pdb=" N LEU U 384 " --> pdb=" O LEU U 380 " (cutoff:3.500A) Processing helix chain 'U' and resid 387 through 395 removed outlier: 3.832A pdb=" N LEU U 393 " --> pdb=" O GLU U 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL U 394 " --> pdb=" O ASP U 390 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 17 removed outlier: 4.046A pdb=" N ARG W 6 " --> pdb=" O ALA W 2 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ASN W 14 " --> pdb=" O LEU W 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS W 15 " --> pdb=" O PHE W 11 " (cutoff:3.500A) Processing helix chain 'W' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG W 48 " --> pdb=" O SER W 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG W 57 " --> pdb=" O ASP W 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY W 60 " --> pdb=" O VAL W 56 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN W 61 " --> pdb=" O ARG W 57 " (cutoff:3.500A) Processing helix chain 'W' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU W 69 " --> pdb=" O SER W 65 " (cutoff:3.500A) Processing helix chain 'W' and resid 83 through 92 removed outlier: 3.735A pdb=" N LEU W 87 " --> pdb=" O SER W 83 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN W 89 " --> pdb=" O GLY W 85 " (cutoff:3.500A) Processing helix chain 'W' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP W 128 " --> pdb=" O GLU W 124 " (cutoff:3.500A) Processing helix chain 'W' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE W 170 " --> pdb=" O ILE W 166 " (cutoff:3.500A) Processing helix chain 'W' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA W 181 " --> pdb=" O LEU W 178 " (cutoff:3.500A) Processing helix chain 'W' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA W 189 " --> pdb=" O PRO W 185 " (cutoff:3.500A) Processing helix chain 'W' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG W 195 " --> pdb=" O SER W 191 " (cutoff:3.500A) Processing helix chain 'W' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL W 218 " --> pdb=" O LYS W 214 " (cutoff:3.500A) Processing helix chain 'W' and resid 227 through 241 removed outlier: 3.627A pdb=" N PHE W 232 " --> pdb=" O SER W 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE W 237 " --> pdb=" O MET W 233 " (cutoff:3.500A) Processing helix chain 'W' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP W 256 " --> pdb=" O GLU W 252 " (cutoff:3.500A) 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 269 through 276 Processing helix chain 'W' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU W 296 " --> pdb=" O GLU W 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER W 298 " --> pdb=" O SER W 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN W 304 " --> pdb=" O MET W 300 " (cutoff:3.500A) Processing helix chain 'W' and resid 307 through 310 Processing helix chain 'W' and resid 325 through 328 removed outlier: 3.724A 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 343 removed outlier: 4.461A pdb=" N GLU W 342 " --> pdb=" O GLY W 338 " (cutoff:3.500A) Processing helix chain 'W' and resid 346 through 350 Processing helix chain 'W' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE W 362 " --> pdb=" O ASP W 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL W 369 " --> pdb=" O GLY W 365 " (cutoff:3.500A) Processing helix chain 'W' and resid 380 through 385 removed outlier: 3.618A pdb=" N LEU W 384 " --> pdb=" O LEU W 380 " (cutoff:3.500A) Processing helix chain 'W' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU W 393 " --> pdb=" O GLU W 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL W 394 " --> pdb=" O ASP W 390 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 17 removed outlier: 4.046A pdb=" N ARG Y 6 " --> pdb=" O ALA Y 2 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN Y 14 " --> pdb=" O LEU Y 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS Y 15 " --> pdb=" O PHE Y 11 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG Y 48 " --> pdb=" O SER Y 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG Y 57 " --> pdb=" O ASP Y 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY Y 60 " --> pdb=" O VAL Y 56 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN Y 61 " --> pdb=" O ARG Y 57 " (cutoff:3.500A) Processing helix chain 'Y' and resid 65 through 77 removed outlier: 3.538A pdb=" N LEU Y 69 " --> pdb=" O SER Y 65 " (cutoff:3.500A) Processing helix chain 'Y' and resid 83 through 92 removed outlier: 3.737A pdb=" N LEU Y 87 " --> pdb=" O SER Y 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN Y 89 " --> pdb=" O GLY Y 85 " (cutoff:3.500A) Processing helix chain 'Y' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP Y 128 " --> pdb=" O GLU Y 124 " (cutoff:3.500A) Processing helix chain 'Y' and resid 159 through 172 removed outlier: 3.646A pdb=" N ILE Y 170 " --> pdb=" O ILE Y 166 " (cutoff:3.500A) Processing helix chain 'Y' and resid 177 through 181 removed outlier: 3.886A pdb=" N ALA Y 181 " --> pdb=" O LEU Y 178 " (cutoff:3.500A) Processing helix chain 'Y' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA Y 189 " --> pdb=" O PRO Y 185 " (cutoff:3.500A) Processing helix chain 'Y' and resid 191 through 202 removed outlier: 3.542A pdb=" N ARG Y 195 " --> pdb=" O SER Y 191 " (cutoff:3.500A) Processing helix chain 'Y' and resid 212 through 224 removed outlier: 3.530A pdb=" N VAL Y 218 " --> pdb=" O LYS Y 214 " (cutoff:3.500A) Processing helix chain 'Y' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE Y 232 " --> pdb=" O SER Y 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE Y 237 " --> pdb=" O MET Y 233 " (cutoff:3.500A) Processing helix chain 'Y' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP Y 256 " --> pdb=" O GLU Y 252 " (cutoff:3.500A) 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 269 through 276 Processing helix chain 'Y' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU Y 296 " --> pdb=" O GLU Y 292 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER Y 298 " --> pdb=" O SER Y 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN Y 304 " --> pdb=" O MET Y 300 " (cutoff:3.500A) Processing helix chain 'Y' and resid 307 through 310 Processing helix chain 'Y' and resid 325 through 328 removed outlier: 3.725A 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 343 removed outlier: 4.462A pdb=" N GLU Y 342 " --> pdb=" O GLY Y 338 " (cutoff:3.500A) Processing helix chain 'Y' and resid 346 through 350 Processing helix chain 'Y' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE Y 362 " --> pdb=" O ASP Y 358 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL Y 369 " --> pdb=" O GLY Y 365 " (cutoff:3.500A) Processing helix chain 'Y' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU Y 384 " --> pdb=" O LEU Y 380 " (cutoff:3.500A) Processing helix chain 'Y' and resid 387 through 395 removed outlier: 3.833A pdb=" N LEU Y 393 " --> pdb=" O GLU Y 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL Y 394 " --> pdb=" O ASP Y 390 " (cutoff:3.500A) Processing helix chain '0' and resid 2 through 17 removed outlier: 4.047A pdb=" N ARG 0 6 " --> pdb=" O ALA 0 2 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN 0 14 " --> pdb=" O LEU 0 10 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N LYS 0 15 " --> pdb=" O PHE 0 11 " (cutoff:3.500A) Processing helix chain '0' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG 0 48 " --> pdb=" O SER 0 44 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ARG 0 57 " --> pdb=" O ASP 0 53 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY 0 60 " --> pdb=" O VAL 0 56 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN 0 61 " --> pdb=" O ARG 0 57 " (cutoff:3.500A) Processing helix chain '0' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU 0 69 " --> pdb=" O SER 0 65 " (cutoff:3.500A) Processing helix chain '0' and resid 83 through 92 removed outlier: 3.736A pdb=" N LEU 0 87 " --> pdb=" O SER 0 83 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N GLN 0 89 " --> pdb=" O GLY 0 85 " (cutoff:3.500A) Processing helix chain '0' and resid 124 through 132 removed outlier: 3.851A pdb=" N ASP 0 128 " --> pdb=" O GLU 0 124 " (cutoff:3.500A) Processing helix chain '0' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE 0 170 " --> pdb=" O ILE 0 166 " (cutoff:3.500A) Processing helix chain '0' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA 0 181 " --> pdb=" O LEU 0 178 " (cutoff:3.500A) Processing helix chain '0' and resid 184 through 189 removed outlier: 4.436A pdb=" N ALA 0 189 " --> pdb=" O PRO 0 185 " (cutoff:3.500A) Processing helix chain '0' and resid 191 through 202 removed outlier: 3.541A pdb=" N ARG 0 195 " --> pdb=" O SER 0 191 " (cutoff:3.500A) Processing helix chain '0' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL 0 218 " --> pdb=" O LYS 0 214 " (cutoff:3.500A) Processing helix chain '0' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE 0 232 " --> pdb=" O SER 0 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE 0 237 " --> pdb=" O MET 0 233 " (cutoff:3.500A) Processing helix chain '0' and resid 250 through 258 removed outlier: 3.765A pdb=" N ASP 0 256 " --> pdb=" O GLU 0 252 " (cutoff:3.500A) 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 269 through 276 Processing helix chain '0' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU 0 296 " --> pdb=" O GLU 0 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER 0 298 " --> pdb=" O SER 0 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN 0 304 " --> pdb=" O MET 0 300 " (cutoff:3.500A) Processing helix chain '0' and resid 307 through 310 Processing helix chain '0' and resid 325 through 328 removed outlier: 3.724A 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 343 removed outlier: 4.461A pdb=" N GLU 0 342 " --> pdb=" O GLY 0 338 " (cutoff:3.500A) Processing helix chain '0' and resid 346 through 350 Processing helix chain '0' and resid 358 through 372 removed outlier: 3.603A pdb=" N PHE 0 362 " --> pdb=" O ASP 0 358 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N VAL 0 369 " --> pdb=" O GLY 0 365 " (cutoff:3.500A) Processing helix chain '0' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU 0 384 " --> pdb=" O LEU 0 380 " (cutoff:3.500A) Processing helix chain '0' and resid 387 through 395 removed outlier: 3.832A pdb=" N LEU 0 393 " --> pdb=" O GLU 0 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL 0 394 " --> pdb=" O ASP 0 390 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 17 removed outlier: 4.046A pdb=" N ARG 2 6 " --> pdb=" O ALA 2 2 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ASN 2 14 " --> pdb=" O LEU 2 10 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS 2 15 " --> pdb=" O PHE 2 11 " (cutoff:3.500A) Processing helix chain '2' and resid 44 through 61 removed outlier: 3.574A pdb=" N ARG 2 48 " --> pdb=" O SER 2 44 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ARG 2 57 " --> pdb=" O ASP 2 53 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLY 2 60 " --> pdb=" O VAL 2 56 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASN 2 61 " --> pdb=" O ARG 2 57 " (cutoff:3.500A) Processing helix chain '2' and resid 65 through 77 removed outlier: 3.537A pdb=" N LEU 2 69 " --> pdb=" O SER 2 65 " (cutoff:3.500A) Processing helix chain '2' and resid 83 through 92 removed outlier: 3.737A pdb=" N LEU 2 87 " --> pdb=" O SER 2 83 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N GLN 2 89 " --> pdb=" O GLY 2 85 " (cutoff:3.500A) Processing helix chain '2' and resid 124 through 132 removed outlier: 3.850A pdb=" N ASP 2 128 " --> pdb=" O GLU 2 124 " (cutoff:3.500A) Processing helix chain '2' and resid 159 through 172 removed outlier: 3.645A pdb=" N ILE 2 170 " --> pdb=" O ILE 2 166 " (cutoff:3.500A) Processing helix chain '2' and resid 177 through 181 removed outlier: 3.887A pdb=" N ALA 2 181 " --> pdb=" O LEU 2 178 " (cutoff:3.500A) Processing helix chain '2' and resid 184 through 189 removed outlier: 4.437A pdb=" N ALA 2 189 " --> pdb=" O PRO 2 185 " (cutoff:3.500A) Processing helix chain '2' and resid 191 through 202 removed outlier: 3.542A pdb=" N ARG 2 195 " --> pdb=" O SER 2 191 " (cutoff:3.500A) Processing helix chain '2' and resid 212 through 224 removed outlier: 3.529A pdb=" N VAL 2 218 " --> pdb=" O LYS 2 214 " (cutoff:3.500A) Processing helix chain '2' and resid 227 through 241 removed outlier: 3.628A pdb=" N PHE 2 232 " --> pdb=" O SER 2 228 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE 2 237 " --> pdb=" O MET 2 233 " (cutoff:3.500A) Processing helix chain '2' and resid 250 through 258 removed outlier: 3.766A pdb=" N ASP 2 256 " --> pdb=" O GLU 2 252 " (cutoff:3.500A) 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 269 through 276 Processing helix chain '2' and resid 291 through 306 removed outlier: 3.513A pdb=" N LEU 2 296 " --> pdb=" O GLU 2 292 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER 2 298 " --> pdb=" O SER 2 294 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N GLN 2 304 " --> pdb=" O MET 2 300 " (cutoff:3.500A) Processing helix chain '2' and resid 307 through 310 Processing helix chain '2' and resid 325 through 328 removed outlier: 3.725A 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 343 removed outlier: 4.461A pdb=" N GLU 2 342 " --> pdb=" O GLY 2 338 " (cutoff:3.500A) Processing helix chain '2' and resid 346 through 350 Processing helix chain '2' and resid 358 through 372 removed outlier: 3.604A pdb=" N PHE 2 362 " --> pdb=" O ASP 2 358 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N VAL 2 369 " --> pdb=" O GLY 2 365 " (cutoff:3.500A) Processing helix chain '2' and resid 380 through 385 removed outlier: 3.617A pdb=" N LEU 2 384 " --> pdb=" O LEU 2 380 " (cutoff:3.500A) Processing helix chain '2' and resid 387 through 395 removed outlier: 3.832A pdb=" N LEU 2 393 " --> pdb=" O GLU 2 389 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N VAL 2 394 " --> pdb=" O ASP 2 390 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'B' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS B 33 " --> pdb=" O SER B 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG B 100 " --> pdb=" O HIS B 33 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE B 35 " --> pdb=" O ARG B 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU B 102 " --> pdb=" O ILE B 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL B 37 " --> pdb=" O LEU B 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL B 104 " --> pdb=" O VAL B 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE B 39 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN B 106 " --> pdb=" O ILE B 39 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS A 33 " --> pdb=" O SER A 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG A 100 " --> pdb=" O HIS A 33 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE A 35 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU A 102 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL A 37 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL A 104 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE A 39 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN A 106 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'D' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS D 33 " --> pdb=" O SER D 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG D 100 " --> pdb=" O HIS D 33 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE D 35 " --> pdb=" O ARG D 100 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU D 102 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL D 37 " --> pdb=" O LEU D 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL D 104 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE D 39 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N GLN D 106 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'F' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS F 33 " --> pdb=" O SER F 98 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG F 100 " --> pdb=" O HIS F 33 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE F 35 " --> pdb=" O ARG F 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU F 102 " --> pdb=" O ILE F 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL F 37 " --> pdb=" O LEU F 102 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL F 104 " --> pdb=" O VAL F 37 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE F 39 " --> pdb=" O VAL F 104 " (cutoff:3.500A) removed outlier: 8.614A pdb=" N GLN F 106 " --> pdb=" O ILE F 39 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'H' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS H 33 " --> pdb=" O SER H 98 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ARG H 100 " --> pdb=" O HIS H 33 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE H 35 " --> pdb=" O ARG H 100 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU H 102 " --> pdb=" O ILE H 35 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL H 37 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL H 104 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE H 39 " --> pdb=" O VAL H 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN H 106 " --> pdb=" O ILE H 39 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'J' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS J 33 " --> pdb=" O SER J 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG J 100 " --> pdb=" O HIS J 33 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE J 35 " --> pdb=" O ARG J 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU J 102 " --> pdb=" O ILE J 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL J 37 " --> pdb=" O LEU J 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL J 104 " --> pdb=" O VAL J 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE J 39 " --> pdb=" O VAL J 104 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N GLN J 106 " --> pdb=" O ILE J 39 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'L' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS L 33 " --> pdb=" O SER L 98 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG L 100 " --> pdb=" O HIS L 33 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE L 35 " --> pdb=" O ARG L 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU L 102 " --> pdb=" O ILE L 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL L 37 " --> pdb=" O LEU L 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL L 104 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE L 39 " --> pdb=" O VAL L 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN L 106 " --> pdb=" O ILE L 39 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'N' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS N 33 " --> pdb=" O SER N 98 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG N 100 " --> pdb=" O HIS N 33 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE N 35 " --> pdb=" O ARG N 100 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU N 102 " --> pdb=" O ILE N 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL N 37 " --> pdb=" O LEU N 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL N 104 " --> pdb=" O VAL N 37 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ILE N 39 " --> pdb=" O VAL N 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN N 106 " --> pdb=" O ILE N 39 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'P' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS P 33 " --> pdb=" O SER P 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG P 100 " --> pdb=" O HIS P 33 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE P 35 " --> pdb=" O ARG P 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU P 102 " --> pdb=" O ILE P 35 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N VAL P 37 " --> pdb=" O LEU P 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL P 104 " --> pdb=" O VAL P 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE P 39 " --> pdb=" O VAL P 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN P 106 " --> pdb=" O ILE P 39 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'S' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS S 33 " --> pdb=" O SER S 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG S 100 " --> pdb=" O HIS S 33 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE S 35 " --> pdb=" O ARG S 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU S 102 " --> pdb=" O ILE S 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL S 37 " --> pdb=" O LEU S 102 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL S 104 " --> pdb=" O VAL S 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE S 39 " --> pdb=" O VAL S 104 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N GLN S 106 " --> pdb=" O ILE S 39 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'U' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS U 33 " --> pdb=" O SER U 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG U 100 " --> pdb=" O HIS U 33 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE U 35 " --> pdb=" O ARG U 100 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU U 102 " --> pdb=" O ILE U 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL U 37 " --> pdb=" O LEU U 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL U 104 " --> pdb=" O VAL U 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE U 39 " --> pdb=" O VAL U 104 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N GLN U 106 " --> pdb=" O ILE U 39 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'W' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS W 33 " --> pdb=" O SER W 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG W 100 " --> pdb=" O HIS W 33 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE W 35 " --> pdb=" O ARG W 100 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU W 102 " --> pdb=" O ILE W 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL W 37 " --> pdb=" O LEU W 102 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL W 104 " --> pdb=" O VAL W 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE W 39 " --> pdb=" O VAL W 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN W 106 " --> pdb=" O ILE W 39 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'Y' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS Y 33 " --> pdb=" O SER Y 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG Y 100 " --> pdb=" O HIS Y 33 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE Y 35 " --> pdb=" O ARG Y 100 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LEU Y 102 " --> pdb=" O ILE Y 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL Y 37 " --> pdb=" O LEU Y 102 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N VAL Y 104 " --> pdb=" O VAL Y 37 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE Y 39 " --> pdb=" O VAL Y 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN Y 106 " --> pdb=" O ILE Y 39 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '0' and resid 33 through 40 removed outlier: 5.818A pdb=" N HIS 0 33 " --> pdb=" O SER 0 98 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N ARG 0 100 " --> pdb=" O HIS 0 33 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N ILE 0 35 " --> pdb=" O ARG 0 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU 0 102 " --> pdb=" O ILE 0 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL 0 37 " --> pdb=" O LEU 0 102 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL 0 104 " --> pdb=" O VAL 0 37 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ILE 0 39 " --> pdb=" O VAL 0 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN 0 106 " --> pdb=" O ILE 0 39 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '2' and resid 33 through 40 removed outlier: 5.817A pdb=" N HIS 2 33 " --> pdb=" O SER 2 98 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ARG 2 100 " --> pdb=" O HIS 2 33 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N ILE 2 35 " --> pdb=" O ARG 2 100 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LEU 2 102 " --> pdb=" O ILE 2 35 " (cutoff:3.500A) removed outlier: 6.145A pdb=" N VAL 2 37 " --> pdb=" O LEU 2 102 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N VAL 2 104 " --> pdb=" O VAL 2 37 " (cutoff:3.500A) removed outlier: 6.467A pdb=" N ILE 2 39 " --> pdb=" O VAL 2 104 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N GLN 2 106 " --> pdb=" O ILE 2 39 " (cutoff:3.500A) 1725 hydrogen bonds defined for protein. 4995 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: 15.47 Time building geometry restraints manager: 20.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 13736 1.33 - 1.45: 8355 1.45 - 1.57: 25084 1.57 - 1.69: 150 1.69 - 1.81: 345 Bond restraints: 47670 Sorted by residual: bond pdb=" CB PRO A 311 " pdb=" CG PRO A 311 " ideal model delta sigma weight residual 1.492 1.409 0.083 5.00e-02 4.00e+02 2.74e+00 bond pdb=" CB PRO L 311 " pdb=" CG PRO L 311 " ideal model delta sigma weight residual 1.492 1.409 0.083 5.00e-02 4.00e+02 2.74e+00 bond pdb=" CB PRO 0 311 " pdb=" CG PRO 0 311 " ideal model delta sigma weight residual 1.492 1.409 0.083 5.00e-02 4.00e+02 2.73e+00 bond pdb=" CB PRO H 311 " pdb=" CG PRO H 311 " ideal model delta sigma weight residual 1.492 1.409 0.083 5.00e-02 4.00e+02 2.73e+00 bond pdb=" CB PRO F 311 " pdb=" CG PRO F 311 " ideal model delta sigma weight residual 1.492 1.409 0.083 5.00e-02 4.00e+02 2.73e+00 ... (remaining 47665 not shown) Histogram of bond angle deviations from ideal: 98.02 - 105.23: 1335 105.23 - 112.43: 23658 112.43 - 119.64: 17300 119.64 - 126.84: 21663 126.84 - 134.04: 904 Bond angle restraints: 64860 Sorted by residual: angle pdb=" C ASN 2 61 " pdb=" N PRO 2 62 " pdb=" CA PRO 2 62 " ideal model delta sigma weight residual 119.28 129.33 -10.05 1.10e+00 8.26e-01 8.35e+01 angle pdb=" C ASN H 61 " pdb=" N PRO H 62 " pdb=" CA PRO H 62 " ideal model delta sigma weight residual 119.28 129.33 -10.05 1.10e+00 8.26e-01 8.34e+01 angle pdb=" C ASN U 61 " pdb=" N PRO U 62 " pdb=" CA PRO U 62 " ideal model delta sigma weight residual 119.28 129.32 -10.04 1.10e+00 8.26e-01 8.32e+01 angle pdb=" C ASN N 61 " pdb=" N PRO N 62 " pdb=" CA PRO N 62 " ideal model delta sigma weight residual 119.28 129.31 -10.03 1.10e+00 8.26e-01 8.32e+01 angle pdb=" C ASN S 61 " pdb=" N PRO S 62 " pdb=" CA PRO S 62 " ideal model delta sigma weight residual 119.28 129.31 -10.03 1.10e+00 8.26e-01 8.32e+01 ... (remaining 64855 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.07: 25486 13.07 - 26.14: 2194 26.14 - 39.21: 655 39.21 - 52.28: 195 52.28 - 65.35: 90 Dihedral angle restraints: 28620 sinusoidal: 12270 harmonic: 16350 Sorted by residual: dihedral pdb=" CA THR J 187 " pdb=" C THR J 187 " pdb=" N ALA J 188 " pdb=" CA ALA J 188 " ideal model delta harmonic sigma weight residual 180.00 -158.40 -21.60 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA THR Y 187 " pdb=" C THR Y 187 " pdb=" N ALA Y 188 " pdb=" CA ALA Y 188 " ideal model delta harmonic sigma weight residual -180.00 -158.42 -21.58 0 5.00e+00 4.00e-02 1.86e+01 dihedral pdb=" CA THR 0 187 " pdb=" C THR 0 187 " pdb=" N ALA 0 188 " pdb=" CA ALA 0 188 " ideal model delta harmonic sigma weight residual -180.00 -158.43 -21.57 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 28617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 5069 0.055 - 0.110: 1905 0.110 - 0.166: 411 0.166 - 0.221: 70 0.221 - 0.276: 15 Chirality restraints: 7470 Sorted by residual: chirality pdb=" CB VAL J 314 " pdb=" CA VAL J 314 " pdb=" CG1 VAL J 314 " pdb=" CG2 VAL J 314 " both_signs ideal model delta sigma weight residual False -2.63 -2.35 -0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CB VAL 2 314 " pdb=" CA VAL 2 314 " pdb=" CG1 VAL 2 314 " pdb=" CG2 VAL 2 314 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 chirality pdb=" CB VAL 0 314 " pdb=" CA VAL 0 314 " pdb=" CG1 VAL 0 314 " pdb=" CG2 VAL 0 314 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.87e+00 ... (remaining 7467 not shown) Planarity restraints: 7980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS N 375 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.70e+00 pdb=" C LYS N 375 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS N 375 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL N 376 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS L 375 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.69e+00 pdb=" C LYS L 375 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS L 375 " -0.016 2.00e-02 2.50e+03 pdb=" N VAL L 376 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS U 375 " 0.012 2.00e-02 2.50e+03 2.38e-02 5.67e+00 pdb=" C LYS U 375 " -0.041 2.00e-02 2.50e+03 pdb=" O LYS U 375 " 0.016 2.00e-02 2.50e+03 pdb=" N VAL U 376 " 0.014 2.00e-02 2.50e+03 ... (remaining 7977 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 54 2.28 - 2.94: 20209 2.94 - 3.59: 68204 3.59 - 4.25: 116601 4.25 - 4.90: 190536 Nonbonded interactions: 395604 Sorted by model distance: nonbonded pdb=" N GLY A 26 " pdb=" ND2 ASN 0 345 " model vdw 1.628 3.200 nonbonded pdb=" N GLY D 26 " pdb=" ND2 ASN 2 345 " model vdw 1.628 3.200 nonbonded pdb=" C GLY D 25 " pdb=" ND2 ASN 2 345 " model vdw 1.880 3.350 nonbonded pdb=" C GLY A 25 " pdb=" ND2 ASN 0 345 " model vdw 1.881 3.350 nonbonded pdb=" CA GLY D 26 " pdb=" ND2 ASN 2 345 " model vdw 2.105 3.520 ... (remaining 395599 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 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain '1' selection = chain '3' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' 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 29370 2.51 5 N 8115 2.21 5 O 8910 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: 1.160 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: 11.200 Check model and map are aligned: 0.670 Convert atoms to be neutral: 0.410 Process input model: 121.470 Find NCS groups from input model: 3.080 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Set scattering table: 0.040 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 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 0.083 47670 Z= 0.631 Angle : 1.145 12.492 64860 Z= 0.660 Chirality : 0.059 0.276 7470 Planarity : 0.007 0.049 7980 Dihedral : 11.787 65.352 18090 Min Nonbonded Distance : 1.628 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 1.54 % 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: -4.31 (0.09), residues: 5625 helix: -3.84 (0.05), residues: 3150 sheet: -0.57 (0.25), residues: 375 loop : -1.25 (0.13), residues: 2100 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1580 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1505 time to evaluate : 5.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 75 outliers final: 18 residues processed: 1553 average time/residue: 0.5953 time to fit residues: 1483.7521 Evaluate side-chains 1134 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 1116 time to evaluate : 5.418 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.3943 time to fit residues: 20.9729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 481 optimal weight: 0.2980 chunk 432 optimal weight: 9.9990 chunk 239 optimal weight: 5.9990 chunk 147 optimal weight: 4.9990 chunk 291 optimal weight: 0.9990 chunk 230 optimal weight: 10.0000 chunk 446 optimal weight: 0.8980 chunk 172 optimal weight: 2.9990 chunk 271 optimal weight: 2.9990 chunk 332 optimal weight: 0.8980 chunk 517 optimal weight: 7.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 ASN B 322 ASN B 351 ASN A 61 ASN A 221 ASN A 322 ASN A 351 ASN D 149 ASN D 221 ASN D 305 GLN D 322 ASN D 351 ASN F 305 GLN F 351 ASN H 149 ASN ** H 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 221 ASN H 351 ASN J 149 ASN J 164 ASN J 351 ASN L 221 ASN L 322 ASN L 351 ASN N 221 ASN N 322 ASN N 351 ASN P 221 ASN P 322 ASN P 351 ASN S 322 ASN S 351 ASN U 149 ASN U 221 ASN U 322 ASN U 351 ASN W 149 ASN W 221 ASN W 321 GLN W 322 ASN W 351 ASN Y 221 ASN Y 322 ASN Y 351 ASN 0 221 ASN 0 351 ASN 2 351 ASN Total number of N/Q/H flips: 46 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.2344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 47670 Z= 0.201 Angle : 0.654 9.487 64860 Z= 0.340 Chirality : 0.042 0.180 7470 Planarity : 0.005 0.049 7980 Dihedral : 8.835 65.360 7245 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 2.74 % 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: -2.36 (0.10), residues: 5625 helix: -2.06 (0.08), residues: 3165 sheet: 0.40 (0.28), residues: 375 loop : -0.77 (0.13), residues: 2085 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1363 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1230 time to evaluate : 5.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 133 outliers final: 69 residues processed: 1310 average time/residue: 0.5769 time to fit residues: 1245.9758 Evaluate side-chains 1097 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 1028 time to evaluate : 5.794 Switching outliers to nearest non-outliers outliers start: 69 outliers final: 0 residues processed: 69 average time/residue: 0.4650 time to fit residues: 67.3601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 287 optimal weight: 6.9990 chunk 160 optimal weight: 8.9990 chunk 430 optimal weight: 4.9990 chunk 352 optimal weight: 7.9990 chunk 142 optimal weight: 3.9990 chunk 518 optimal weight: 4.9990 chunk 560 optimal weight: 3.9990 chunk 461 optimal weight: 6.9990 chunk 514 optimal weight: 7.9990 chunk 176 optimal weight: 0.9990 chunk 416 optimal weight: 6.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 321 GLN A 149 ASN F 33 HIS F 321 GLN F 322 ASN H 164 ASN J 321 GLN L 321 GLN P 86 GLN S 321 GLN U 321 GLN W 221 ASN Y 321 GLN 0 321 GLN 0 322 ASN 0 345 ASN 2 221 ASN 2 345 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 47670 Z= 0.345 Angle : 0.648 9.913 64860 Z= 0.332 Chirality : 0.044 0.179 7470 Planarity : 0.006 0.118 7980 Dihedral : 8.562 66.872 7245 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer Outliers : 2.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.11), residues: 5625 helix: -1.08 (0.09), residues: 3195 sheet: 0.42 (0.28), residues: 375 loop : -0.54 (0.13), residues: 2055 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1227 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 1102 time to evaluate : 5.400 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 125 outliers final: 77 residues processed: 1172 average time/residue: 0.5884 time to fit residues: 1134.3389 Evaluate side-chains 1062 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 985 time to evaluate : 5.359 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 0 residues processed: 77 average time/residue: 0.4040 time to fit residues: 67.1313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 512 optimal weight: 5.9990 chunk 389 optimal weight: 5.9990 chunk 269 optimal weight: 6.9990 chunk 57 optimal weight: 4.9990 chunk 247 optimal weight: 6.9990 chunk 348 optimal weight: 8.9990 chunk 520 optimal weight: 0.9990 chunk 550 optimal weight: 7.9990 chunk 271 optimal weight: 5.9990 chunk 493 optimal weight: 8.9990 chunk 148 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 GLN H 164 ASN H 321 GLN J 321 GLN N 321 GLN W 221 ASN 2 86 GLN 2 221 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 47670 Z= 0.395 Angle : 0.660 8.992 64860 Z= 0.336 Chirality : 0.045 0.192 7470 Planarity : 0.006 0.102 7980 Dihedral : 8.483 68.327 7245 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer Outliers : 3.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.11), residues: 5625 helix: -0.53 (0.09), residues: 3150 sheet: 0.17 (0.28), residues: 375 loop : -0.47 (0.14), residues: 2100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1202 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1056 time to evaluate : 5.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 146 outliers final: 78 residues processed: 1147 average time/residue: 0.5958 time to fit residues: 1120.0949 Evaluate side-chains 1052 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 974 time to evaluate : 5.514 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 0 residues processed: 78 average time/residue: 0.4549 time to fit residues: 71.3099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 458 optimal weight: 10.0000 chunk 312 optimal weight: 0.6980 chunk 8 optimal weight: 6.9990 chunk 410 optimal weight: 2.9990 chunk 227 optimal weight: 0.3980 chunk 470 optimal weight: 7.9990 chunk 380 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 281 optimal weight: 0.5980 chunk 494 optimal weight: 10.0000 chunk 139 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 GLN H 164 ASN H 202 GLN P 202 GLN S 321 GLN W 202 GLN ** W 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 321 GLN 0 321 GLN 2 221 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8673 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 47670 Z= 0.170 Angle : 0.572 9.123 64860 Z= 0.291 Chirality : 0.040 0.135 7470 Planarity : 0.005 0.096 7980 Dihedral : 8.429 70.952 7245 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 2.02 % 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: -0.40 (0.11), residues: 5625 helix: -0.17 (0.09), residues: 3165 sheet: 0.18 (0.28), residues: 375 loop : -0.23 (0.14), residues: 2085 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1205 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1107 time to evaluate : 5.406 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 98 outliers final: 41 residues processed: 1157 average time/residue: 0.5757 time to fit residues: 1096.1193 Evaluate side-chains 1045 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1004 time to evaluate : 5.325 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 0 residues processed: 41 average time/residue: 0.4133 time to fit residues: 38.9644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 185 optimal weight: 0.7980 chunk 496 optimal weight: 20.0000 chunk 108 optimal weight: 3.9990 chunk 323 optimal weight: 10.0000 chunk 136 optimal weight: 0.8980 chunk 551 optimal weight: 10.0000 chunk 457 optimal weight: 4.9990 chunk 255 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 182 optimal weight: 5.9990 chunk 289 optimal weight: 10.0000 overall best weight: 3.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 86 GLN H 149 ASN H 202 GLN P 202 GLN S 321 GLN W 202 GLN ** W 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 321 GLN 0 321 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.089 47670 Z= 0.306 Angle : 0.616 9.244 64860 Z= 0.309 Chirality : 0.043 0.147 7470 Planarity : 0.005 0.093 7980 Dihedral : 8.316 70.749 7245 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.12), residues: 5625 helix: -0.04 (0.09), residues: 3165 sheet: 0.10 (0.28), residues: 375 loop : -0.22 (0.14), residues: 2085 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1130 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1044 time to evaluate : 5.566 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 86 outliers final: 43 residues processed: 1092 average time/residue: 0.5939 time to fit residues: 1064.8220 Evaluate side-chains 1013 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 970 time to evaluate : 5.443 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 0 residues processed: 43 average time/residue: 0.4076 time to fit residues: 40.9505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 531 optimal weight: 20.0000 chunk 62 optimal weight: 0.8980 chunk 314 optimal weight: 3.9990 chunk 402 optimal weight: 0.9980 chunk 312 optimal weight: 1.9990 chunk 464 optimal weight: 4.9990 chunk 307 optimal weight: 0.0050 chunk 549 optimal weight: 7.9990 chunk 343 optimal weight: 10.0000 chunk 334 optimal weight: 4.9990 chunk 253 optimal weight: 0.9990 overall best weight: 0.9798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 ASN ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 305 GLN H 86 GLN H 202 GLN L 202 GLN U 202 GLN ** W 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 321 GLN 2 86 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.063 47670 Z= 0.172 Angle : 0.577 10.120 64860 Z= 0.290 Chirality : 0.040 0.137 7470 Planarity : 0.005 0.084 7980 Dihedral : 8.328 71.972 7245 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer Outliers : 1.13 % 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: 0.04 (0.12), residues: 5625 helix: 0.25 (0.09), residues: 3150 sheet: 0.06 (0.28), residues: 375 loop : -0.09 (0.15), residues: 2100 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1130 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1075 time to evaluate : 5.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 32 residues processed: 1100 average time/residue: 0.5953 time to fit residues: 1077.2370 Evaluate side-chains 1028 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 996 time to evaluate : 5.365 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 0.4210 time to fit residues: 32.7278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 339 optimal weight: 6.9990 chunk 219 optimal weight: 2.9990 chunk 328 optimal weight: 8.9990 chunk 165 optimal weight: 8.9990 chunk 107 optimal weight: 4.9990 chunk 106 optimal weight: 9.9990 chunk 349 optimal weight: 5.9990 chunk 374 optimal weight: 5.9990 chunk 271 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 431 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 ASN ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 305 GLN H 202 GLN L 202 GLN ** L 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 86 GLN ** W 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 321 GLN 2 345 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.064 47670 Z= 0.257 Angle : 0.609 10.624 64860 Z= 0.306 Chirality : 0.042 0.147 7470 Planarity : 0.005 0.108 7980 Dihedral : 8.251 71.518 7245 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer Outliers : 0.70 % 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: 0.28 (0.12), residues: 5625 helix: 0.54 (0.10), residues: 3075 sheet: 0.01 (0.29), residues: 375 loop : -0.11 (0.14), residues: 2175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1080 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1046 time to evaluate : 5.322 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 21 residues processed: 1057 average time/residue: 0.5916 time to fit residues: 1027.0910 Evaluate side-chains 982 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 961 time to evaluate : 5.923 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.4219 time to fit residues: 24.1565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 499 optimal weight: 3.9990 chunk 526 optimal weight: 7.9990 chunk 480 optimal weight: 6.9990 chunk 511 optimal weight: 9.9990 chunk 308 optimal weight: 3.9990 chunk 223 optimal weight: 0.0670 chunk 402 optimal weight: 3.9990 chunk 157 optimal weight: 0.9980 chunk 462 optimal weight: 6.9990 chunk 484 optimal weight: 0.9980 chunk 510 optimal weight: 8.9990 overall best weight: 2.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 ASN ** A 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 86 GLN ** W 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.3867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 47670 Z= 0.220 Angle : 0.593 10.894 64860 Z= 0.298 Chirality : 0.041 0.131 7470 Planarity : 0.005 0.120 7980 Dihedral : 8.257 71.858 7245 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.68 % 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: 0.39 (0.12), residues: 5625 helix: 0.65 (0.10), residues: 3090 sheet: -0.04 (0.28), residues: 375 loop : -0.07 (0.15), residues: 2160 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1041 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 1008 time to evaluate : 5.713 Fit side-chains outliers start: 33 outliers final: 23 residues processed: 1022 average time/residue: 0.6426 time to fit residues: 1084.2511 Evaluate side-chains 997 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 974 time to evaluate : 5.521 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.4455 time to fit residues: 27.6950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 336 optimal weight: 0.8980 chunk 541 optimal weight: 5.9990 chunk 330 optimal weight: 0.9990 chunk 256 optimal weight: 0.9980 chunk 376 optimal weight: 7.9990 chunk 567 optimal weight: 7.9990 chunk 522 optimal weight: 2.9990 chunk 452 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 349 optimal weight: 5.9990 chunk 277 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 ASN ** J 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 86 GLN ** W 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 86 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.077 47670 Z= 0.205 Angle : 0.589 11.712 64860 Z= 0.298 Chirality : 0.041 0.175 7470 Planarity : 0.005 0.124 7980 Dihedral : 8.248 72.150 7245 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer Outliers : 0.21 % 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: 0.49 (0.12), residues: 5625 helix: 0.72 (0.10), residues: 3090 sheet: -0.08 (0.28), residues: 375 loop : 0.02 (0.15), residues: 2160 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11250 Ramachandran restraints generated. 5625 Oldfield, 0 Emsley, 5625 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1024 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1014 time to evaluate : 5.640 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 1016 average time/residue: 0.5955 time to fit residues: 992.0757 Evaluate side-chains 942 residues out of total 4860 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 939 time to evaluate : 5.200 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.4124 time to fit residues: 9.4674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 570 random chunks: chunk 359 optimal weight: 10.0000 chunk 481 optimal weight: 0.9990 chunk 138 optimal weight: 5.9990 chunk 416 optimal weight: 9.9990 chunk 66 optimal weight: 0.9990 chunk 125 optimal weight: 4.9990 chunk 452 optimal weight: 2.9990 chunk 189 optimal weight: 5.9990 chunk 465 optimal weight: 20.0000 chunk 57 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 221 ASN ** J 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 149 ASN ** W 221 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.115828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.095522 restraints weight = 64271.697| |-----------------------------------------------------------------------------| r_work (start): 0.2944 rms_B_bonded: 1.93 r_work: 0.2927 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2912 rms_B_bonded: 1.69 restraints_weight: 0.2500 r_work: 0.2897 rms_B_bonded: 1.76 restraints_weight: 0.1250 r_work: 0.2881 rms_B_bonded: 1.88 restraints_weight: 0.0625 r_work: 0.2863 rms_B_bonded: 2.05 restraints_weight: 0.0312 r_work: 0.2843 rms_B_bonded: 2.27 restraints_weight: 0.0156 r_work: 0.2821 rms_B_bonded: 2.54 restraints_weight: 0.0078 r_work: 0.2797 rms_B_bonded: 2.87 restraints_weight: 0.0039 r_work: 0.2770 rms_B_bonded: 3.26 restraints_weight: 0.0020 r_work: 0.2740 rms_B_bonded: 3.72 restraints_weight: 0.0010 r_work: 0.2706 rms_B_bonded: 4.27 restraints_weight: 0.0005 r_work: 0.2667 rms_B_bonded: 4.92 restraints_weight: 0.0002 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8942 moved from start: 0.3962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 47670 Z= 0.267 Angle : 0.615 11.486 64860 Z= 0.310 Chirality : 0.042 0.188 7470 Planarity : 0.005 0.106 7980 Dihedral : 8.226 71.708 7245 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.12), residues: 5625 helix: 0.60 (0.10), residues: 3180 sheet: -0.11 (0.28), residues: 375 loop : -0.08 (0.15), residues: 2070 =============================================================================== Job complete usr+sys time: 15554.91 seconds wall clock time: 277 minutes 28.52 seconds (16648.52 seconds total)