Starting phenix.real_space_refine on Sun Mar 24 23:10:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5s_0142/03_2024/6h5s_0142.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5s_0142/03_2024/6h5s_0142.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5s_0142/03_2024/6h5s_0142.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5s_0142/03_2024/6h5s_0142.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5s_0142/03_2024/6h5s_0142.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6h5s_0142/03_2024/6h5s_0142.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 75 5.49 5 S 180 5.16 5 C 28185 2.51 5 N 7740 2.21 5 O 8520 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C ARG 54": "NH1" <-> "NH2" Residue "C ARG 57": "NH1" <-> "NH2" Residue "C ARG 100": "NH1" <-> "NH2" Residue "C ARG 194": "NH1" <-> "NH2" Residue "C ARG 195": "NH1" <-> "NH2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C ARG 213": "NH1" <-> "NH2" Residue "C ARG 222": "NH1" <-> "NH2" Residue "C ARG 230": "NH1" <-> "NH2" Residue "C PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 370": "NH1" <-> "NH2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ARG 57": "NH1" <-> "NH2" Residue "A ARG 100": "NH1" <-> "NH2" Residue "A ARG 194": "NH1" <-> "NH2" Residue "A ARG 195": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A ARG 204": "NH1" <-> "NH2" Residue "A ARG 213": "NH1" <-> "NH2" Residue "A ARG 222": "NH1" <-> "NH2" Residue "A ARG 230": "NH1" <-> "NH2" Residue "A PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 370": "NH1" <-> "NH2" Residue "D ARG 54": "NH1" <-> "NH2" Residue "D ARG 57": "NH1" <-> "NH2" Residue "D ARG 100": "NH1" <-> "NH2" Residue "D ARG 194": "NH1" <-> "NH2" Residue "D ARG 195": "NH1" <-> "NH2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D ARG 204": "NH1" <-> "NH2" Residue "D ARG 213": "NH1" <-> "NH2" Residue "D ARG 222": "NH1" <-> "NH2" Residue "D ARG 230": "NH1" <-> "NH2" Residue "D PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 370": "NH1" <-> "NH2" Residue "G ARG 54": "NH1" <-> "NH2" Residue "G ARG 57": "NH1" <-> "NH2" Residue "G ARG 100": "NH1" <-> "NH2" Residue "G ARG 194": "NH1" <-> "NH2" Residue "G ARG 195": "NH1" <-> "NH2" Residue "G ARG 203": "NH1" <-> "NH2" Residue "G ARG 204": "NH1" <-> "NH2" Residue "G ARG 213": "NH1" <-> "NH2" Residue "G ARG 222": "NH1" <-> "NH2" Residue "G ARG 230": "NH1" <-> "NH2" Residue "G PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 370": "NH1" <-> "NH2" Residue "I ARG 54": "NH1" <-> "NH2" Residue "I ARG 57": "NH1" <-> "NH2" Residue "I ARG 100": "NH1" <-> "NH2" Residue "I ARG 194": "NH1" <-> "NH2" Residue "I ARG 195": "NH1" <-> "NH2" Residue "I ARG 203": "NH1" <-> "NH2" Residue "I ARG 204": "NH1" <-> "NH2" Residue "I ARG 213": "NH1" <-> "NH2" Residue "I ARG 222": "NH1" <-> "NH2" Residue "I ARG 230": "NH1" <-> "NH2" Residue "I PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 370": "NH1" <-> "NH2" Residue "K ARG 54": "NH1" <-> "NH2" Residue "K ARG 57": "NH1" <-> "NH2" Residue "K ARG 100": "NH1" <-> "NH2" Residue "K ARG 194": "NH1" <-> "NH2" Residue "K ARG 195": "NH1" <-> "NH2" Residue "K ARG 203": "NH1" <-> "NH2" Residue "K ARG 204": "NH1" <-> "NH2" Residue "K ARG 213": "NH1" <-> "NH2" Residue "K ARG 222": "NH1" <-> "NH2" Residue "K ARG 230": "NH1" <-> "NH2" Residue "K PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 370": "NH1" <-> "NH2" Residue "M ARG 54": "NH1" <-> "NH2" Residue "M ARG 57": "NH1" <-> "NH2" Residue "M ARG 100": "NH1" <-> "NH2" Residue "M ARG 194": "NH1" <-> "NH2" Residue "M ARG 195": "NH1" <-> "NH2" Residue "M ARG 203": "NH1" <-> "NH2" Residue "M ARG 204": "NH1" <-> "NH2" Residue "M ARG 213": "NH1" <-> "NH2" Residue "M ARG 222": "NH1" <-> "NH2" Residue "M ARG 230": "NH1" <-> "NH2" Residue "M PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 370": "NH1" <-> "NH2" Residue "O ARG 54": "NH1" <-> "NH2" Residue "O ARG 57": "NH1" <-> "NH2" Residue "O ARG 100": "NH1" <-> "NH2" Residue "O ARG 194": "NH1" <-> "NH2" Residue "O ARG 195": "NH1" <-> "NH2" Residue "O ARG 203": "NH1" <-> "NH2" Residue "O ARG 204": "NH1" <-> "NH2" Residue "O ARG 213": "NH1" <-> "NH2" Residue "O ARG 222": "NH1" <-> "NH2" Residue "O ARG 230": "NH1" <-> "NH2" Residue "O PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 370": "NH1" <-> "NH2" Residue "Q ARG 54": "NH1" <-> "NH2" Residue "Q ARG 57": "NH1" <-> "NH2" Residue "Q ARG 100": "NH1" <-> "NH2" Residue "Q ARG 194": "NH1" <-> "NH2" Residue "Q ARG 195": "NH1" <-> "NH2" Residue "Q ARG 203": "NH1" <-> "NH2" Residue "Q ARG 204": "NH1" <-> "NH2" Residue "Q ARG 213": "NH1" <-> "NH2" Residue "Q ARG 222": "NH1" <-> "NH2" Residue "Q ARG 230": "NH1" <-> "NH2" Residue "Q PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 370": "NH1" <-> "NH2" Residue "S ARG 54": "NH1" <-> "NH2" Residue "S ARG 57": "NH1" <-> "NH2" Residue "S ARG 100": "NH1" <-> "NH2" Residue "S ARG 194": "NH1" <-> "NH2" Residue "S ARG 195": "NH1" <-> "NH2" Residue "S ARG 203": "NH1" <-> "NH2" Residue "S ARG 204": "NH1" <-> "NH2" Residue "S ARG 213": "NH1" <-> "NH2" Residue "S ARG 222": "NH1" <-> "NH2" Residue "S ARG 230": "NH1" <-> "NH2" Residue "S PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 370": "NH1" <-> "NH2" Residue "U ARG 54": "NH1" <-> "NH2" Residue "U ARG 57": "NH1" <-> "NH2" Residue "U ARG 100": "NH1" <-> "NH2" Residue "U ARG 194": "NH1" <-> "NH2" Residue "U ARG 195": "NH1" <-> "NH2" Residue "U ARG 203": "NH1" <-> "NH2" Residue "U ARG 204": "NH1" <-> "NH2" Residue "U ARG 213": "NH1" <-> "NH2" Residue "U ARG 222": "NH1" <-> "NH2" Residue "U ARG 230": "NH1" <-> "NH2" Residue "U PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 370": "NH1" <-> "NH2" Residue "W ARG 54": "NH1" <-> "NH2" Residue "W ARG 57": "NH1" <-> "NH2" Residue "W ARG 100": "NH1" <-> "NH2" Residue "W ARG 194": "NH1" <-> "NH2" Residue "W ARG 195": "NH1" <-> "NH2" Residue "W ARG 203": "NH1" <-> "NH2" Residue "W ARG 204": "NH1" <-> "NH2" Residue "W ARG 213": "NH1" <-> "NH2" Residue "W ARG 222": "NH1" <-> "NH2" Residue "W ARG 230": "NH1" <-> "NH2" Residue "W PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 370": "NH1" <-> "NH2" Residue "Y ARG 54": "NH1" <-> "NH2" Residue "Y ARG 57": "NH1" <-> "NH2" Residue "Y ARG 100": "NH1" <-> "NH2" Residue "Y ARG 194": "NH1" <-> "NH2" Residue "Y ARG 195": "NH1" <-> "NH2" Residue "Y ARG 203": "NH1" <-> "NH2" Residue "Y ARG 204": "NH1" <-> "NH2" Residue "Y ARG 213": "NH1" <-> "NH2" Residue "Y ARG 222": "NH1" <-> "NH2" Residue "Y ARG 230": "NH1" <-> "NH2" Residue "Y PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 370": "NH1" <-> "NH2" Residue "0 ARG 54": "NH1" <-> "NH2" Residue "0 ARG 57": "NH1" <-> "NH2" Residue "0 ARG 100": "NH1" <-> "NH2" Residue "0 ARG 194": "NH1" <-> "NH2" Residue "0 ARG 195": "NH1" <-> "NH2" Residue "0 ARG 203": "NH1" <-> "NH2" Residue "0 ARG 204": "NH1" <-> "NH2" Residue "0 ARG 213": "NH1" <-> "NH2" Residue "0 ARG 222": "NH1" <-> "NH2" Residue "0 ARG 230": "NH1" <-> "NH2" Residue "0 PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 ARG 370": "NH1" <-> "NH2" Residue "2 ARG 54": "NH1" <-> "NH2" Residue "2 ARG 57": "NH1" <-> "NH2" Residue "2 ARG 100": "NH1" <-> "NH2" Residue "2 ARG 194": "NH1" <-> "NH2" Residue "2 ARG 195": "NH1" <-> "NH2" Residue "2 ARG 203": "NH1" <-> "NH2" Residue "2 ARG 204": "NH1" <-> "NH2" Residue "2 ARG 213": "NH1" <-> "NH2" Residue "2 ARG 222": "NH1" <-> "NH2" Residue "2 ARG 230": "NH1" <-> "NH2" Residue "2 PHE 352": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "2 ARG 370": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 44700 Number of models: 1 Model: "" Number of chains: 30 Chain: "C" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "E" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "A" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "B" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "D" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "F" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "G" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "H" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "I" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "J" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "K" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "L" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "M" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "N" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "O" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "P" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "Q" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "R" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "S" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "T" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "U" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "V" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "W" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "X" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "Y" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "Z" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "0" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "1" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 4} Chain: "2" Number of atoms: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 2854 Classifications: {'peptide': 363} Link IDs: {'PTRANS': 16, 'TRANS': 346} Chain breaks: 2 Chain: "3" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 126 Classifications: {'RNA': 6} Modifications used: {'5*END': 1, 'rna2p_pyr': 1, 'rna3p_pur': 4, 'rna3p_pyr': 1} Link IDs: {'rna2p': 1, 'rna3p': 4} Time building chain proxies: 22.85, per 1000 atoms: 0.51 Number of scatterers: 44700 At special positions: 0 Unit cell: (204, 204.816, 129.744, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 180 16.00 P 75 15.00 O 8520 8.00 N 7740 7.00 C 28185 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 17.00 Conformation dependent library (CDL) restraints added in 8.0 seconds 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10020 Finding SS restraints... Secondary structure from input PDB file: 330 helices and 15 sheets defined 61.7% alpha, 4.4% beta 0 base pairs and 45 stacking pairs defined. Time for finding SS restraints: 15.63 Creating SS restraints... Processing helix chain 'C' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG C 6 " --> pdb=" O ALA C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG C 48 " --> pdb=" O SER C 44 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG C 57 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE C 59 " --> pdb=" O LEU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 65 through 77 Processing helix chain 'C' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN C 89 " --> pdb=" O GLY C 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG C 90 " --> pdb=" O GLN C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 132 Processing helix chain 'C' and resid 159 through 172 Processing helix chain 'C' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS C 180 " --> pdb=" O LEU C 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA C 181 " --> pdb=" O LEU C 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 177 through 181' Processing helix chain 'C' and resid 185 through 187 No H-bonds generated for 'chain 'C' and resid 185 through 187' Processing helix chain 'C' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU C 193 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG C 194 " --> pdb=" O ASP C 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG C 195 " --> pdb=" O SER C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 226 Processing helix chain 'C' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE C 237 " --> pdb=" O MET C 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG C 242 " --> pdb=" O LEU C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 248 through 258 Processing helix chain 'C' and resid 259 through 261 No H-bonds generated for 'chain 'C' and resid 259 through 261' Processing helix chain 'C' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU C 271 " --> pdb=" O ALA C 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR C 272 " --> pdb=" O SER C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY C 291 " --> pdb=" O HIS C 287 " (cutoff:3.500A) Processing helix chain 'C' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU C 299 " --> pdb=" O THR C 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN C 304 " --> pdb=" O MET C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR C 309 " --> pdb=" O MET C 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA C 310 " --> pdb=" O GLY C 307 " (cutoff:3.500A) Proline residue: C 311 - end of helix No H-bonds generated for 'chain 'C' and resid 306 through 313' Processing helix chain 'C' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN C 321 " --> pdb=" O ASN C 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN C 322 " --> pdb=" O SER C 319 " (cutoff:3.500A) Processing helix chain 'C' and resid 325 through 328 removed outlier: 3.516A pdb=" N SER C 328 " --> pdb=" O SER C 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 325 through 328' Processing helix chain 'C' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER C 334 " --> pdb=" O PRO C 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU C 342 " --> pdb=" O GLY C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE C 362 " --> pdb=" O ASP C 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL C 369 " --> pdb=" O GLY C 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG A 6 " --> pdb=" O ALA A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG A 48 " --> pdb=" O SER A 44 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG A 57 " --> pdb=" O ASP A 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE A 59 " --> pdb=" O LEU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 77 Processing helix chain 'A' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN A 89 " --> pdb=" O GLY A 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 132 Processing helix chain 'A' and resid 159 through 172 Processing helix chain 'A' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS A 180 " --> pdb=" O LEU A 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA A 181 " --> pdb=" O LEU A 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 177 through 181' Processing helix chain 'A' and resid 185 through 187 No H-bonds generated for 'chain 'A' and resid 185 through 187' Processing helix chain 'A' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU A 193 " --> pdb=" O ALA A 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG A 194 " --> pdb=" O ASP A 190 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 226 Processing helix chain 'A' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE A 237 " --> pdb=" O MET A 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG A 242 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 258 Processing helix chain 'A' and resid 259 through 261 No H-bonds generated for 'chain 'A' and resid 259 through 261' Processing helix chain 'A' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU A 271 " --> pdb=" O ALA A 267 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR A 272 " --> pdb=" O SER A 268 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY A 291 " --> pdb=" O HIS A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU A 299 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN A 304 " --> pdb=" O MET A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR A 309 " --> pdb=" O MET A 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA A 310 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Proline residue: A 311 - end of helix No H-bonds generated for 'chain 'A' and resid 306 through 313' Processing helix chain 'A' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN A 321 " --> pdb=" O ASN A 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN A 322 " --> pdb=" O SER A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER A 328 " --> pdb=" O SER A 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 325 through 328' Processing helix chain 'A' and resid 329 through 344 removed outlier: 3.852A pdb=" N SER A 334 " --> pdb=" O PRO A 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU A 342 " --> pdb=" O GLY A 338 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 358 through 372 removed outlier: 3.823A pdb=" N PHE A 362 " --> pdb=" O ASP A 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL A 369 " --> pdb=" O GLY A 365 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 13 removed outlier: 4.184A pdb=" N ARG D 6 " --> pdb=" O ALA D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG D 48 " --> pdb=" O SER D 44 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG D 57 " --> pdb=" O ASP D 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE D 59 " --> pdb=" O LEU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 65 through 77 Processing helix chain 'D' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN D 89 " --> pdb=" O GLY D 85 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG D 90 " --> pdb=" O GLN D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 132 Processing helix chain 'D' and resid 159 through 172 Processing helix chain 'D' and resid 177 through 181 removed outlier: 3.533A pdb=" N LYS D 180 " --> pdb=" O LEU D 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA D 181 " --> pdb=" O LEU D 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 177 through 181' Processing helix chain 'D' and resid 185 through 187 No H-bonds generated for 'chain 'D' and resid 185 through 187' Processing helix chain 'D' and resid 188 through 202 removed outlier: 3.674A pdb=" N LEU D 193 " --> pdb=" O ALA D 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG D 194 " --> pdb=" O ASP D 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG D 195 " --> pdb=" O SER D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 226 Processing helix chain 'D' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE D 237 " --> pdb=" O MET D 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG D 242 " --> pdb=" O LEU D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 258 Processing helix chain 'D' and resid 259 through 261 No H-bonds generated for 'chain 'D' and resid 259 through 261' Processing helix chain 'D' and resid 266 through 276 removed outlier: 3.562A pdb=" N LEU D 271 " --> pdb=" O ALA D 267 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR D 272 " --> pdb=" O SER D 268 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY D 291 " --> pdb=" O HIS D 287 " (cutoff:3.500A) Processing helix chain 'D' and resid 293 through 305 removed outlier: 4.278A pdb=" N LEU D 299 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN D 304 " --> pdb=" O MET D 300 " (cutoff:3.500A) Processing helix chain 'D' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR D 309 " --> pdb=" O MET D 306 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA D 310 " --> pdb=" O GLY D 307 " (cutoff:3.500A) Proline residue: D 311 - end of helix No H-bonds generated for 'chain 'D' and resid 306 through 313' Processing helix chain 'D' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN D 321 " --> pdb=" O ASN D 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN D 322 " --> pdb=" O SER D 319 " (cutoff:3.500A) Processing helix chain 'D' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER D 328 " --> pdb=" O SER D 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 325 through 328' Processing helix chain 'D' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER D 334 " --> pdb=" O PRO D 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU D 342 " --> pdb=" O GLY D 338 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 358 through 372 removed outlier: 3.823A pdb=" N PHE D 362 " --> pdb=" O ASP D 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL D 369 " --> pdb=" O GLY D 365 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG G 6 " --> pdb=" O ALA G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG G 48 " --> pdb=" O SER G 44 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG G 57 " --> pdb=" O ASP G 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU G 58 " --> pdb=" O ARG G 54 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 65 through 77 Processing helix chain 'G' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN G 89 " --> pdb=" O GLY G 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG G 90 " --> pdb=" O GLN G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 132 Processing helix chain 'G' and resid 159 through 172 Processing helix chain 'G' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS G 180 " --> pdb=" O LEU G 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA G 181 " --> pdb=" O LEU G 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 177 through 181' Processing helix chain 'G' and resid 185 through 187 No H-bonds generated for 'chain 'G' and resid 185 through 187' Processing helix chain 'G' and resid 188 through 202 removed outlier: 3.674A pdb=" N LEU G 193 " --> pdb=" O ALA G 189 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG G 194 " --> pdb=" O ASP G 190 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG G 195 " --> pdb=" O SER G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 212 through 226 Processing helix chain 'G' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE G 237 " --> pdb=" O MET G 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG G 242 " --> pdb=" O LEU G 238 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 258 Processing helix chain 'G' and resid 259 through 261 No H-bonds generated for 'chain 'G' and resid 259 through 261' Processing helix chain 'G' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU G 271 " --> pdb=" O ALA G 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR G 272 " --> pdb=" O SER G 268 " (cutoff:3.500A) Processing helix chain 'G' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY G 291 " --> pdb=" O HIS G 287 " (cutoff:3.500A) Processing helix chain 'G' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU G 299 " --> pdb=" O THR G 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN G 304 " --> pdb=" O MET G 300 " (cutoff:3.500A) Processing helix chain 'G' and resid 306 through 313 removed outlier: 4.167A pdb=" N THR G 309 " --> pdb=" O MET G 306 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA G 310 " --> pdb=" O GLY G 307 " (cutoff:3.500A) Proline residue: G 311 - end of helix No H-bonds generated for 'chain 'G' and resid 306 through 313' Processing helix chain 'G' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN G 321 " --> pdb=" O ASN G 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN G 322 " --> pdb=" O SER G 319 " (cutoff:3.500A) Processing helix chain 'G' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER G 328 " --> pdb=" O SER G 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 325 through 328' Processing helix chain 'G' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER G 334 " --> pdb=" O PRO G 330 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU G 342 " --> pdb=" O GLY G 338 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 350 Processing helix chain 'G' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE G 362 " --> pdb=" O ASP G 358 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL G 369 " --> pdb=" O GLY G 365 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG I 6 " --> pdb=" O ALA I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG I 48 " --> pdb=" O SER I 44 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG I 57 " --> pdb=" O ASP I 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU I 58 " --> pdb=" O ARG I 54 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE I 59 " --> pdb=" O LEU I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 65 through 77 Processing helix chain 'I' and resid 84 through 92 removed outlier: 3.681A pdb=" N GLN I 89 " --> pdb=" O GLY I 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG I 90 " --> pdb=" O GLN I 86 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 132 Processing helix chain 'I' and resid 159 through 172 Processing helix chain 'I' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS I 180 " --> pdb=" O LEU I 177 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA I 181 " --> pdb=" O LEU I 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 177 through 181' Processing helix chain 'I' and resid 185 through 187 No H-bonds generated for 'chain 'I' and resid 185 through 187' Processing helix chain 'I' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU I 193 " --> pdb=" O ALA I 189 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG I 194 " --> pdb=" O ASP I 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG I 195 " --> pdb=" O SER I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 212 through 226 Processing helix chain 'I' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE I 237 " --> pdb=" O MET I 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG I 242 " --> pdb=" O LEU I 238 " (cutoff:3.500A) Processing helix chain 'I' and resid 248 through 258 Processing helix chain 'I' and resid 259 through 261 No H-bonds generated for 'chain 'I' and resid 259 through 261' Processing helix chain 'I' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU I 271 " --> pdb=" O ALA I 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR I 272 " --> pdb=" O SER I 268 " (cutoff:3.500A) Processing helix chain 'I' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY I 291 " --> pdb=" O HIS I 287 " (cutoff:3.500A) Processing helix chain 'I' and resid 293 through 305 removed outlier: 4.278A pdb=" N LEU I 299 " --> pdb=" O THR I 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN I 304 " --> pdb=" O MET I 300 " (cutoff:3.500A) Processing helix chain 'I' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR I 309 " --> pdb=" O MET I 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA I 310 " --> pdb=" O GLY I 307 " (cutoff:3.500A) Proline residue: I 311 - end of helix No H-bonds generated for 'chain 'I' and resid 306 through 313' Processing helix chain 'I' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN I 321 " --> pdb=" O ASN I 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN I 322 " --> pdb=" O SER I 319 " (cutoff:3.500A) Processing helix chain 'I' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER I 328 " --> pdb=" O SER I 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 325 through 328' Processing helix chain 'I' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER I 334 " --> pdb=" O PRO I 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU I 342 " --> pdb=" O GLY I 338 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 350 Processing helix chain 'I' and resid 358 through 372 removed outlier: 3.823A pdb=" N PHE I 362 " --> pdb=" O ASP I 358 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL I 369 " --> pdb=" O GLY I 365 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG K 6 " --> pdb=" O ALA K 2 " (cutoff:3.500A) Processing helix chain 'K' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG K 48 " --> pdb=" O SER K 44 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG K 57 " --> pdb=" O ASP K 53 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU K 58 " --> pdb=" O ARG K 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE K 59 " --> pdb=" O LEU K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 77 Processing helix chain 'K' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN K 89 " --> pdb=" O GLY K 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG K 90 " --> pdb=" O GLN K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 132 Processing helix chain 'K' and resid 159 through 172 Processing helix chain 'K' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS K 180 " --> pdb=" O LEU K 177 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA K 181 " --> pdb=" O LEU K 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 177 through 181' Processing helix chain 'K' and resid 185 through 187 No H-bonds generated for 'chain 'K' and resid 185 through 187' Processing helix chain 'K' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU K 193 " --> pdb=" O ALA K 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG K 194 " --> pdb=" O ASP K 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG K 195 " --> pdb=" O SER K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 212 through 226 Processing helix chain 'K' and resid 227 through 242 removed outlier: 3.512A pdb=" N ILE K 237 " --> pdb=" O MET K 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG K 242 " --> pdb=" O LEU K 238 " (cutoff:3.500A) Processing helix chain 'K' and resid 248 through 258 Processing helix chain 'K' and resid 259 through 261 No H-bonds generated for 'chain 'K' and resid 259 through 261' Processing helix chain 'K' and resid 266 through 276 removed outlier: 3.562A pdb=" N LEU K 271 " --> pdb=" O ALA K 267 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N THR K 272 " --> pdb=" O SER K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY K 291 " --> pdb=" O HIS K 287 " (cutoff:3.500A) Processing helix chain 'K' and resid 293 through 305 removed outlier: 4.278A pdb=" N LEU K 299 " --> pdb=" O THR K 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN K 304 " --> pdb=" O MET K 300 " (cutoff:3.500A) Processing helix chain 'K' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR K 309 " --> pdb=" O MET K 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA K 310 " --> pdb=" O GLY K 307 " (cutoff:3.500A) Proline residue: K 311 - end of helix No H-bonds generated for 'chain 'K' and resid 306 through 313' Processing helix chain 'K' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN K 321 " --> pdb=" O ASN K 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN K 322 " --> pdb=" O SER K 319 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER K 328 " --> pdb=" O SER K 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 325 through 328' Processing helix chain 'K' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER K 334 " --> pdb=" O PRO K 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU K 342 " --> pdb=" O GLY K 338 " (cutoff:3.500A) Processing helix chain 'K' and resid 345 through 350 Processing helix chain 'K' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE K 362 " --> pdb=" O ASP K 358 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL K 369 " --> pdb=" O GLY K 365 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG M 6 " --> pdb=" O ALA M 2 " (cutoff:3.500A) Processing helix chain 'M' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG M 48 " --> pdb=" O SER M 44 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG M 57 " --> pdb=" O ASP M 53 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU M 58 " --> pdb=" O ARG M 54 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE M 59 " --> pdb=" O LEU M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 65 through 77 Processing helix chain 'M' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN M 89 " --> pdb=" O GLY M 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG M 90 " --> pdb=" O GLN M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 132 Processing helix chain 'M' and resid 159 through 172 Processing helix chain 'M' and resid 177 through 181 removed outlier: 3.533A pdb=" N LYS M 180 " --> pdb=" O LEU M 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA M 181 " --> pdb=" O LEU M 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 177 through 181' Processing helix chain 'M' and resid 185 through 187 No H-bonds generated for 'chain 'M' and resid 185 through 187' Processing helix chain 'M' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU M 193 " --> pdb=" O ALA M 189 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG M 194 " --> pdb=" O ASP M 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG M 195 " --> pdb=" O SER M 191 " (cutoff:3.500A) Processing helix chain 'M' and resid 212 through 226 Processing helix chain 'M' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE M 237 " --> pdb=" O MET M 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG M 242 " --> pdb=" O LEU M 238 " (cutoff:3.500A) Processing helix chain 'M' and resid 248 through 258 Processing helix chain 'M' and resid 259 through 261 No H-bonds generated for 'chain 'M' and resid 259 through 261' Processing helix chain 'M' and resid 266 through 276 removed outlier: 3.562A pdb=" N LEU M 271 " --> pdb=" O ALA M 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR M 272 " --> pdb=" O SER M 268 " (cutoff:3.500A) Processing helix chain 'M' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY M 291 " --> pdb=" O HIS M 287 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU M 299 " --> pdb=" O THR M 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN M 304 " --> pdb=" O MET M 300 " (cutoff:3.500A) Processing helix chain 'M' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR M 309 " --> pdb=" O MET M 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA M 310 " --> pdb=" O GLY M 307 " (cutoff:3.500A) Proline residue: M 311 - end of helix No H-bonds generated for 'chain 'M' and resid 306 through 313' Processing helix chain 'M' and resid 318 through 323 removed outlier: 3.921A pdb=" N GLN M 321 " --> pdb=" O ASN M 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN M 322 " --> pdb=" O SER M 319 " (cutoff:3.500A) Processing helix chain 'M' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER M 328 " --> pdb=" O SER M 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 325 through 328' Processing helix chain 'M' and resid 329 through 344 removed outlier: 3.852A pdb=" N SER M 334 " --> pdb=" O PRO M 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU M 342 " --> pdb=" O GLY M 338 " (cutoff:3.500A) Processing helix chain 'M' and resid 345 through 350 Processing helix chain 'M' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE M 362 " --> pdb=" O ASP M 358 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL M 369 " --> pdb=" O GLY M 365 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 13 removed outlier: 4.184A pdb=" N ARG O 6 " --> pdb=" O ALA O 2 " (cutoff:3.500A) Processing helix chain 'O' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG O 48 " --> pdb=" O SER O 44 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG O 57 " --> pdb=" O ASP O 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU O 58 " --> pdb=" O ARG O 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE O 59 " --> pdb=" O LEU O 55 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 77 Processing helix chain 'O' and resid 84 through 92 removed outlier: 3.681A pdb=" N GLN O 89 " --> pdb=" O GLY O 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG O 90 " --> pdb=" O GLN O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 132 Processing helix chain 'O' and resid 159 through 172 Processing helix chain 'O' and resid 177 through 181 removed outlier: 3.533A pdb=" N LYS O 180 " --> pdb=" O LEU O 177 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA O 181 " --> pdb=" O LEU O 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 177 through 181' Processing helix chain 'O' and resid 185 through 187 No H-bonds generated for 'chain 'O' and resid 185 through 187' Processing helix chain 'O' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU O 193 " --> pdb=" O ALA O 189 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG O 194 " --> pdb=" O ASP O 190 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG O 195 " --> pdb=" O SER O 191 " (cutoff:3.500A) Processing helix chain 'O' and resid 212 through 226 Processing helix chain 'O' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE O 237 " --> pdb=" O MET O 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG O 242 " --> pdb=" O LEU O 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 248 through 258 Processing helix chain 'O' and resid 259 through 261 No H-bonds generated for 'chain 'O' and resid 259 through 261' Processing helix chain 'O' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU O 271 " --> pdb=" O ALA O 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR O 272 " --> pdb=" O SER O 268 " (cutoff:3.500A) Processing helix chain 'O' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY O 291 " --> pdb=" O HIS O 287 " (cutoff:3.500A) Processing helix chain 'O' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU O 299 " --> pdb=" O THR O 295 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN O 304 " --> pdb=" O MET O 300 " (cutoff:3.500A) Processing helix chain 'O' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR O 309 " --> pdb=" O MET O 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA O 310 " --> pdb=" O GLY O 307 " (cutoff:3.500A) Proline residue: O 311 - end of helix No H-bonds generated for 'chain 'O' and resid 306 through 313' Processing helix chain 'O' and resid 318 through 323 removed outlier: 3.921A pdb=" N GLN O 321 " --> pdb=" O ASN O 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN O 322 " --> pdb=" O SER O 319 " (cutoff:3.500A) Processing helix chain 'O' and resid 325 through 328 removed outlier: 3.516A pdb=" N SER O 328 " --> pdb=" O SER O 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 325 through 328' Processing helix chain 'O' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER O 334 " --> pdb=" O PRO O 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU O 342 " --> pdb=" O GLY O 338 " (cutoff:3.500A) Processing helix chain 'O' and resid 345 through 350 Processing helix chain 'O' and resid 358 through 372 removed outlier: 3.823A pdb=" N PHE O 362 " --> pdb=" O ASP O 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL O 369 " --> pdb=" O GLY O 365 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 13 removed outlier: 4.184A pdb=" N ARG Q 6 " --> pdb=" O ALA Q 2 " (cutoff:3.500A) Processing helix chain 'Q' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG Q 48 " --> pdb=" O SER Q 44 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG Q 57 " --> pdb=" O ASP Q 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU Q 58 " --> pdb=" O ARG Q 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE Q 59 " --> pdb=" O LEU Q 55 " (cutoff:3.500A) Processing helix chain 'Q' and resid 65 through 77 Processing helix chain 'Q' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN Q 89 " --> pdb=" O GLY Q 85 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG Q 90 " --> pdb=" O GLN Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 132 Processing helix chain 'Q' and resid 159 through 172 Processing helix chain 'Q' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS Q 180 " --> pdb=" O LEU Q 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA Q 181 " --> pdb=" O LEU Q 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 177 through 181' Processing helix chain 'Q' and resid 185 through 187 No H-bonds generated for 'chain 'Q' and resid 185 through 187' Processing helix chain 'Q' and resid 188 through 202 removed outlier: 3.674A pdb=" N LEU Q 193 " --> pdb=" O ALA Q 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG Q 194 " --> pdb=" O ASP Q 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG Q 195 " --> pdb=" O SER Q 191 " (cutoff:3.500A) Processing helix chain 'Q' and resid 212 through 226 Processing helix chain 'Q' and resid 227 through 242 removed outlier: 3.510A pdb=" N ILE Q 237 " --> pdb=" O MET Q 233 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG Q 242 " --> pdb=" O LEU Q 238 " (cutoff:3.500A) Processing helix chain 'Q' and resid 248 through 258 Processing helix chain 'Q' and resid 259 through 261 No H-bonds generated for 'chain 'Q' and resid 259 through 261' Processing helix chain 'Q' and resid 266 through 276 removed outlier: 3.562A pdb=" N LEU Q 271 " --> pdb=" O ALA Q 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR Q 272 " --> pdb=" O SER Q 268 " (cutoff:3.500A) Processing helix chain 'Q' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY Q 291 " --> pdb=" O HIS Q 287 " (cutoff:3.500A) Processing helix chain 'Q' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU Q 299 " --> pdb=" O THR Q 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN Q 304 " --> pdb=" O MET Q 300 " (cutoff:3.500A) Processing helix chain 'Q' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR Q 309 " --> pdb=" O MET Q 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA Q 310 " --> pdb=" O GLY Q 307 " (cutoff:3.500A) Proline residue: Q 311 - end of helix No H-bonds generated for 'chain 'Q' and resid 306 through 313' Processing helix chain 'Q' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN Q 321 " --> pdb=" O ASN Q 318 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASN Q 322 " --> pdb=" O SER Q 319 " (cutoff:3.500A) Processing helix chain 'Q' and resid 325 through 328 removed outlier: 3.516A pdb=" N SER Q 328 " --> pdb=" O SER Q 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 325 through 328' Processing helix chain 'Q' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER Q 334 " --> pdb=" O PRO Q 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU Q 342 " --> pdb=" O GLY Q 338 " (cutoff:3.500A) Processing helix chain 'Q' and resid 345 through 350 Processing helix chain 'Q' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE Q 362 " --> pdb=" O ASP Q 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL Q 369 " --> pdb=" O GLY Q 365 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 13 removed outlier: 4.184A pdb=" N ARG S 6 " --> pdb=" O ALA S 2 " (cutoff:3.500A) Processing helix chain 'S' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG S 48 " --> pdb=" O SER S 44 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG S 57 " --> pdb=" O ASP S 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU S 58 " --> pdb=" O ARG S 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE S 59 " --> pdb=" O LEU S 55 " (cutoff:3.500A) Processing helix chain 'S' and resid 65 through 77 Processing helix chain 'S' and resid 84 through 92 removed outlier: 3.681A pdb=" N GLN S 89 " --> pdb=" O GLY S 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG S 90 " --> pdb=" O GLN S 86 " (cutoff:3.500A) Processing helix chain 'S' and resid 127 through 132 Processing helix chain 'S' and resid 159 through 172 Processing helix chain 'S' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS S 180 " --> pdb=" O LEU S 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA S 181 " --> pdb=" O LEU S 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 177 through 181' Processing helix chain 'S' and resid 185 through 187 No H-bonds generated for 'chain 'S' and resid 185 through 187' Processing helix chain 'S' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU S 193 " --> pdb=" O ALA S 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG S 194 " --> pdb=" O ASP S 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG S 195 " --> pdb=" O SER S 191 " (cutoff:3.500A) Processing helix chain 'S' and resid 212 through 226 Processing helix chain 'S' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE S 237 " --> pdb=" O MET S 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG S 242 " --> pdb=" O LEU S 238 " (cutoff:3.500A) Processing helix chain 'S' and resid 248 through 258 Processing helix chain 'S' and resid 259 through 261 No H-bonds generated for 'chain 'S' and resid 259 through 261' Processing helix chain 'S' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU S 271 " --> pdb=" O ALA S 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR S 272 " --> pdb=" O SER S 268 " (cutoff:3.500A) Processing helix chain 'S' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY S 291 " --> pdb=" O HIS S 287 " (cutoff:3.500A) Processing helix chain 'S' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU S 299 " --> pdb=" O THR S 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN S 304 " --> pdb=" O MET S 300 " (cutoff:3.500A) Processing helix chain 'S' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR S 309 " --> pdb=" O MET S 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA S 310 " --> pdb=" O GLY S 307 " (cutoff:3.500A) Proline residue: S 311 - end of helix No H-bonds generated for 'chain 'S' and resid 306 through 313' Processing helix chain 'S' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN S 321 " --> pdb=" O ASN S 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN S 322 " --> pdb=" O SER S 319 " (cutoff:3.500A) Processing helix chain 'S' and resid 325 through 328 removed outlier: 3.516A pdb=" N SER S 328 " --> pdb=" O SER S 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 325 through 328' Processing helix chain 'S' and resid 329 through 344 removed outlier: 3.852A pdb=" N SER S 334 " --> pdb=" O PRO S 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU S 342 " --> pdb=" O GLY S 338 " (cutoff:3.500A) Processing helix chain 'S' and resid 345 through 350 Processing helix chain 'S' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE S 362 " --> pdb=" O ASP S 358 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N VAL S 369 " --> pdb=" O GLY S 365 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 13 removed outlier: 4.184A pdb=" N ARG U 6 " --> pdb=" O ALA U 2 " (cutoff:3.500A) Processing helix chain 'U' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG U 48 " --> pdb=" O SER U 44 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG U 57 " --> pdb=" O ASP U 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU U 58 " --> pdb=" O ARG U 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE U 59 " --> pdb=" O LEU U 55 " (cutoff:3.500A) Processing helix chain 'U' and resid 65 through 77 Processing helix chain 'U' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN U 89 " --> pdb=" O GLY U 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG U 90 " --> pdb=" O GLN U 86 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 132 Processing helix chain 'U' and resid 159 through 172 Processing helix chain 'U' and resid 177 through 181 removed outlier: 3.533A pdb=" N LYS U 180 " --> pdb=" O LEU U 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA U 181 " --> pdb=" O LEU U 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 177 through 181' Processing helix chain 'U' and resid 185 through 187 No H-bonds generated for 'chain 'U' and resid 185 through 187' Processing helix chain 'U' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU U 193 " --> pdb=" O ALA U 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG U 194 " --> pdb=" O ASP U 190 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG U 195 " --> pdb=" O SER U 191 " (cutoff:3.500A) Processing helix chain 'U' and resid 212 through 226 Processing helix chain 'U' and resid 227 through 242 removed outlier: 3.512A pdb=" N ILE U 237 " --> pdb=" O MET U 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG U 242 " --> pdb=" O LEU U 238 " (cutoff:3.500A) Processing helix chain 'U' and resid 248 through 258 Processing helix chain 'U' and resid 259 through 261 No H-bonds generated for 'chain 'U' and resid 259 through 261' Processing helix chain 'U' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU U 271 " --> pdb=" O ALA U 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR U 272 " --> pdb=" O SER U 268 " (cutoff:3.500A) Processing helix chain 'U' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY U 291 " --> pdb=" O HIS U 287 " (cutoff:3.500A) Processing helix chain 'U' and resid 293 through 305 removed outlier: 4.278A pdb=" N LEU U 299 " --> pdb=" O THR U 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN U 304 " --> pdb=" O MET U 300 " (cutoff:3.500A) Processing helix chain 'U' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR U 309 " --> pdb=" O MET U 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA U 310 " --> pdb=" O GLY U 307 " (cutoff:3.500A) Proline residue: U 311 - end of helix No H-bonds generated for 'chain 'U' and resid 306 through 313' Processing helix chain 'U' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN U 321 " --> pdb=" O ASN U 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN U 322 " --> pdb=" O SER U 319 " (cutoff:3.500A) Processing helix chain 'U' and resid 325 through 328 removed outlier: 3.516A pdb=" N SER U 328 " --> pdb=" O SER U 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 325 through 328' Processing helix chain 'U' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER U 334 " --> pdb=" O PRO U 330 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N GLU U 342 " --> pdb=" O GLY U 338 " (cutoff:3.500A) Processing helix chain 'U' and resid 345 through 350 Processing helix chain 'U' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE U 362 " --> pdb=" O ASP U 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL U 369 " --> pdb=" O GLY U 365 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG W 6 " --> pdb=" O ALA W 2 " (cutoff:3.500A) Processing helix chain 'W' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG W 48 " --> pdb=" O SER W 44 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG W 57 " --> pdb=" O ASP W 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU W 58 " --> pdb=" O ARG W 54 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE W 59 " --> pdb=" O LEU W 55 " (cutoff:3.500A) Processing helix chain 'W' and resid 65 through 77 Processing helix chain 'W' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN W 89 " --> pdb=" O GLY W 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG W 90 " --> pdb=" O GLN W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 127 through 132 Processing helix chain 'W' and resid 159 through 172 Processing helix chain 'W' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS W 180 " --> pdb=" O LEU W 177 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ALA W 181 " --> pdb=" O LEU W 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 177 through 181' Processing helix chain 'W' and resid 185 through 187 No H-bonds generated for 'chain 'W' and resid 185 through 187' Processing helix chain 'W' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU W 193 " --> pdb=" O ALA W 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG W 194 " --> pdb=" O ASP W 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG W 195 " --> pdb=" O SER W 191 " (cutoff:3.500A) Processing helix chain 'W' and resid 212 through 226 Processing helix chain 'W' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE W 237 " --> pdb=" O MET W 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG W 242 " --> pdb=" O LEU W 238 " (cutoff:3.500A) Processing helix chain 'W' and resid 248 through 258 Processing helix chain 'W' and resid 259 through 261 No H-bonds generated for 'chain 'W' and resid 259 through 261' Processing helix chain 'W' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU W 271 " --> pdb=" O ALA W 267 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N THR W 272 " --> pdb=" O SER W 268 " (cutoff:3.500A) Processing helix chain 'W' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY W 291 " --> pdb=" O HIS W 287 " (cutoff:3.500A) Processing helix chain 'W' and resid 293 through 305 removed outlier: 4.278A pdb=" N LEU W 299 " --> pdb=" O THR W 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN W 304 " --> pdb=" O MET W 300 " (cutoff:3.500A) Processing helix chain 'W' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR W 309 " --> pdb=" O MET W 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA W 310 " --> pdb=" O GLY W 307 " (cutoff:3.500A) Proline residue: W 311 - end of helix No H-bonds generated for 'chain 'W' and resid 306 through 313' Processing helix chain 'W' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN W 321 " --> pdb=" O ASN W 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN W 322 " --> pdb=" O SER W 319 " (cutoff:3.500A) Processing helix chain 'W' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER W 328 " --> pdb=" O SER W 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 325 through 328' Processing helix chain 'W' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER W 334 " --> pdb=" O PRO W 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU W 342 " --> pdb=" O GLY W 338 " (cutoff:3.500A) Processing helix chain 'W' and resid 345 through 350 Processing helix chain 'W' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE W 362 " --> pdb=" O ASP W 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL W 369 " --> pdb=" O GLY W 365 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 13 removed outlier: 4.184A pdb=" N ARG Y 6 " --> pdb=" O ALA Y 2 " (cutoff:3.500A) Processing helix chain 'Y' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG Y 48 " --> pdb=" O SER Y 44 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG Y 57 " --> pdb=" O ASP Y 53 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU Y 58 " --> pdb=" O ARG Y 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE Y 59 " --> pdb=" O LEU Y 55 " (cutoff:3.500A) Processing helix chain 'Y' and resid 65 through 77 Processing helix chain 'Y' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN Y 89 " --> pdb=" O GLY Y 85 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N ARG Y 90 " --> pdb=" O GLN Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 127 through 132 Processing helix chain 'Y' and resid 159 through 172 Processing helix chain 'Y' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS Y 180 " --> pdb=" O LEU Y 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA Y 181 " --> pdb=" O LEU Y 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 177 through 181' Processing helix chain 'Y' and resid 185 through 187 No H-bonds generated for 'chain 'Y' and resid 185 through 187' Processing helix chain 'Y' and resid 188 through 202 removed outlier: 3.674A pdb=" N LEU Y 193 " --> pdb=" O ALA Y 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG Y 194 " --> pdb=" O ASP Y 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG Y 195 " --> pdb=" O SER Y 191 " (cutoff:3.500A) Processing helix chain 'Y' and resid 212 through 226 Processing helix chain 'Y' and resid 227 through 242 removed outlier: 3.512A pdb=" N ILE Y 237 " --> pdb=" O MET Y 233 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG Y 242 " --> pdb=" O LEU Y 238 " (cutoff:3.500A) Processing helix chain 'Y' and resid 248 through 258 Processing helix chain 'Y' and resid 259 through 261 No H-bonds generated for 'chain 'Y' and resid 259 through 261' Processing helix chain 'Y' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU Y 271 " --> pdb=" O ALA Y 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR Y 272 " --> pdb=" O SER Y 268 " (cutoff:3.500A) Processing helix chain 'Y' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY Y 291 " --> pdb=" O HIS Y 287 " (cutoff:3.500A) Processing helix chain 'Y' and resid 293 through 305 removed outlier: 4.278A pdb=" N LEU Y 299 " --> pdb=" O THR Y 295 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLN Y 304 " --> pdb=" O MET Y 300 " (cutoff:3.500A) Processing helix chain 'Y' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR Y 309 " --> pdb=" O MET Y 306 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA Y 310 " --> pdb=" O GLY Y 307 " (cutoff:3.500A) Proline residue: Y 311 - end of helix No H-bonds generated for 'chain 'Y' and resid 306 through 313' Processing helix chain 'Y' and resid 318 through 323 removed outlier: 3.921A pdb=" N GLN Y 321 " --> pdb=" O ASN Y 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN Y 322 " --> pdb=" O SER Y 319 " (cutoff:3.500A) Processing helix chain 'Y' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER Y 328 " --> pdb=" O SER Y 325 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 325 through 328' Processing helix chain 'Y' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER Y 334 " --> pdb=" O PRO Y 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU Y 342 " --> pdb=" O GLY Y 338 " (cutoff:3.500A) Processing helix chain 'Y' and resid 345 through 350 Processing helix chain 'Y' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE Y 362 " --> pdb=" O ASP Y 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL Y 369 " --> pdb=" O GLY Y 365 " (cutoff:3.500A) Processing helix chain '0' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG 0 6 " --> pdb=" O ALA 0 2 " (cutoff:3.500A) Processing helix chain '0' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG 0 48 " --> pdb=" O SER 0 44 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ARG 0 57 " --> pdb=" O ASP 0 53 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU 0 58 " --> pdb=" O ARG 0 54 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ILE 0 59 " --> pdb=" O LEU 0 55 " (cutoff:3.500A) Processing helix chain '0' and resid 65 through 77 Processing helix chain '0' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN 0 89 " --> pdb=" O GLY 0 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG 0 90 " --> pdb=" O GLN 0 86 " (cutoff:3.500A) Processing helix chain '0' and resid 127 through 132 Processing helix chain '0' and resid 159 through 172 Processing helix chain '0' and resid 177 through 181 removed outlier: 3.532A pdb=" N LYS 0 180 " --> pdb=" O LEU 0 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA 0 181 " --> pdb=" O LEU 0 178 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 177 through 181' Processing helix chain '0' and resid 185 through 187 No H-bonds generated for 'chain '0' and resid 185 through 187' Processing helix chain '0' and resid 188 through 202 removed outlier: 3.674A pdb=" N LEU 0 193 " --> pdb=" O ALA 0 189 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ARG 0 194 " --> pdb=" O ASP 0 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG 0 195 " --> pdb=" O SER 0 191 " (cutoff:3.500A) Processing helix chain '0' and resid 212 through 226 Processing helix chain '0' and resid 227 through 242 removed outlier: 3.510A pdb=" N ILE 0 237 " --> pdb=" O MET 0 233 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ARG 0 242 " --> pdb=" O LEU 0 238 " (cutoff:3.500A) Processing helix chain '0' and resid 248 through 258 Processing helix chain '0' and resid 259 through 261 No H-bonds generated for 'chain '0' and resid 259 through 261' Processing helix chain '0' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU 0 271 " --> pdb=" O ALA 0 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR 0 272 " --> pdb=" O SER 0 268 " (cutoff:3.500A) Processing helix chain '0' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY 0 291 " --> pdb=" O HIS 0 287 " (cutoff:3.500A) Processing helix chain '0' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU 0 299 " --> pdb=" O THR 0 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN 0 304 " --> pdb=" O MET 0 300 " (cutoff:3.500A) Processing helix chain '0' and resid 306 through 313 removed outlier: 4.166A pdb=" N THR 0 309 " --> pdb=" O MET 0 306 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ALA 0 310 " --> pdb=" O GLY 0 307 " (cutoff:3.500A) Proline residue: 0 311 - end of helix No H-bonds generated for 'chain '0' and resid 306 through 313' Processing helix chain '0' and resid 318 through 323 removed outlier: 3.921A pdb=" N GLN 0 321 " --> pdb=" O ASN 0 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN 0 322 " --> pdb=" O SER 0 319 " (cutoff:3.500A) Processing helix chain '0' and resid 325 through 328 removed outlier: 3.515A pdb=" N SER 0 328 " --> pdb=" O SER 0 325 " (cutoff:3.500A) No H-bonds generated for 'chain '0' and resid 325 through 328' Processing helix chain '0' and resid 329 through 344 removed outlier: 3.851A pdb=" N SER 0 334 " --> pdb=" O PRO 0 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU 0 342 " --> pdb=" O GLY 0 338 " (cutoff:3.500A) Processing helix chain '0' and resid 345 through 350 Processing helix chain '0' and resid 358 through 372 removed outlier: 3.824A pdb=" N PHE 0 362 " --> pdb=" O ASP 0 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL 0 369 " --> pdb=" O GLY 0 365 " (cutoff:3.500A) Processing helix chain '2' and resid 2 through 13 removed outlier: 4.183A pdb=" N ARG 2 6 " --> pdb=" O ALA 2 2 " (cutoff:3.500A) Processing helix chain '2' and resid 44 through 60 removed outlier: 4.121A pdb=" N ARG 2 48 " --> pdb=" O SER 2 44 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG 2 57 " --> pdb=" O ASP 2 53 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU 2 58 " --> pdb=" O ARG 2 54 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE 2 59 " --> pdb=" O LEU 2 55 " (cutoff:3.500A) Processing helix chain '2' and resid 65 through 77 Processing helix chain '2' and resid 84 through 92 removed outlier: 3.682A pdb=" N GLN 2 89 " --> pdb=" O GLY 2 85 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ARG 2 90 " --> pdb=" O GLN 2 86 " (cutoff:3.500A) Processing helix chain '2' and resid 127 through 132 Processing helix chain '2' and resid 159 through 172 Processing helix chain '2' and resid 177 through 181 removed outlier: 3.533A pdb=" N LYS 2 180 " --> pdb=" O LEU 2 177 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ALA 2 181 " --> pdb=" O LEU 2 178 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 177 through 181' Processing helix chain '2' and resid 185 through 187 No H-bonds generated for 'chain '2' and resid 185 through 187' Processing helix chain '2' and resid 188 through 202 removed outlier: 3.675A pdb=" N LEU 2 193 " --> pdb=" O ALA 2 189 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ARG 2 194 " --> pdb=" O ASP 2 190 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ARG 2 195 " --> pdb=" O SER 2 191 " (cutoff:3.500A) Processing helix chain '2' and resid 212 through 226 Processing helix chain '2' and resid 227 through 242 removed outlier: 3.511A pdb=" N ILE 2 237 " --> pdb=" O MET 2 233 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ARG 2 242 " --> pdb=" O LEU 2 238 " (cutoff:3.500A) Processing helix chain '2' and resid 248 through 258 Processing helix chain '2' and resid 259 through 261 No H-bonds generated for 'chain '2' and resid 259 through 261' Processing helix chain '2' and resid 266 through 276 removed outlier: 3.563A pdb=" N LEU 2 271 " --> pdb=" O ALA 2 267 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N THR 2 272 " --> pdb=" O SER 2 268 " (cutoff:3.500A) Processing helix chain '2' and resid 286 through 291 removed outlier: 3.961A pdb=" N GLY 2 291 " --> pdb=" O HIS 2 287 " (cutoff:3.500A) Processing helix chain '2' and resid 293 through 305 removed outlier: 4.277A pdb=" N LEU 2 299 " --> pdb=" O THR 2 295 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN 2 304 " --> pdb=" O MET 2 300 " (cutoff:3.500A) Processing helix chain '2' and resid 306 through 313 removed outlier: 4.165A pdb=" N THR 2 309 " --> pdb=" O MET 2 306 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA 2 310 " --> pdb=" O GLY 2 307 " (cutoff:3.500A) Proline residue: 2 311 - end of helix No H-bonds generated for 'chain '2' and resid 306 through 313' Processing helix chain '2' and resid 318 through 323 removed outlier: 3.920A pdb=" N GLN 2 321 " --> pdb=" O ASN 2 318 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ASN 2 322 " --> pdb=" O SER 2 319 " (cutoff:3.500A) Processing helix chain '2' and resid 325 through 328 removed outlier: 3.516A pdb=" N SER 2 328 " --> pdb=" O SER 2 325 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 325 through 328' Processing helix chain '2' and resid 329 through 344 removed outlier: 3.852A pdb=" N SER 2 334 " --> pdb=" O PRO 2 330 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N GLU 2 342 " --> pdb=" O GLY 2 338 " (cutoff:3.500A) Processing helix chain '2' and resid 345 through 350 Processing helix chain '2' and resid 358 through 372 removed outlier: 3.823A pdb=" N PHE 2 362 " --> pdb=" O ASP 2 358 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N VAL 2 369 " --> pdb=" O GLY 2 365 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'C' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE C 35 " --> pdb=" O ARG C 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU C 102 " --> pdb=" O ILE C 35 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL C 37 " --> pdb=" O LEU C 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL C 104 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE C 39 " --> pdb=" O VAL C 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN C 106 " --> pdb=" O ILE C 39 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE A 35 " --> pdb=" O ARG A 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU A 102 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL A 37 " --> pdb=" O LEU A 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL A 104 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE A 39 " --> pdb=" O VAL A 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN A 106 " --> pdb=" O ILE A 39 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'D' and resid 34 through 40 removed outlier: 5.502A pdb=" N ILE D 35 " --> pdb=" O ARG D 100 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU D 102 " --> pdb=" O ILE D 35 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL D 37 " --> pdb=" O LEU D 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL D 104 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE D 39 " --> pdb=" O VAL D 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN D 106 " --> pdb=" O ILE D 39 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'G' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE G 35 " --> pdb=" O ARG G 100 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU G 102 " --> pdb=" O ILE G 35 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL G 37 " --> pdb=" O LEU G 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL G 104 " --> pdb=" O VAL G 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE G 39 " --> pdb=" O VAL G 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN G 106 " --> pdb=" O ILE G 39 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'I' and resid 34 through 40 removed outlier: 5.502A pdb=" N ILE I 35 " --> pdb=" O ARG I 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU I 102 " --> pdb=" O ILE I 35 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL I 37 " --> pdb=" O LEU I 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL I 104 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE I 39 " --> pdb=" O VAL I 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN I 106 " --> pdb=" O ILE I 39 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'K' and resid 34 through 40 removed outlier: 5.502A pdb=" N ILE K 35 " --> pdb=" O ARG K 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU K 102 " --> pdb=" O ILE K 35 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL K 37 " --> pdb=" O LEU K 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL K 104 " --> pdb=" O VAL K 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE K 39 " --> pdb=" O VAL K 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN K 106 " --> pdb=" O ILE K 39 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'M' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE M 35 " --> pdb=" O ARG M 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU M 102 " --> pdb=" O ILE M 35 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL M 37 " --> pdb=" O LEU M 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL M 104 " --> pdb=" O VAL M 37 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE M 39 " --> pdb=" O VAL M 104 " (cutoff:3.500A) removed outlier: 8.463A pdb=" N GLN M 106 " --> pdb=" O ILE M 39 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'O' and resid 34 through 40 removed outlier: 5.502A pdb=" N ILE O 35 " --> pdb=" O ARG O 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU O 102 " --> pdb=" O ILE O 35 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL O 37 " --> pdb=" O LEU O 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL O 104 " --> pdb=" O VAL O 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE O 39 " --> pdb=" O VAL O 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN O 106 " --> pdb=" O ILE O 39 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'Q' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE Q 35 " --> pdb=" O ARG Q 100 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU Q 102 " --> pdb=" O ILE Q 35 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL Q 37 " --> pdb=" O LEU Q 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL Q 104 " --> pdb=" O VAL Q 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE Q 39 " --> pdb=" O VAL Q 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN Q 106 " --> pdb=" O ILE Q 39 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'S' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE S 35 " --> pdb=" O ARG S 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU S 102 " --> pdb=" O ILE S 35 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL S 37 " --> pdb=" O LEU S 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL S 104 " --> pdb=" O VAL S 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE S 39 " --> pdb=" O VAL S 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN S 106 " --> pdb=" O ILE S 39 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'U' and resid 34 through 40 removed outlier: 5.502A pdb=" N ILE U 35 " --> pdb=" O ARG U 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU U 102 " --> pdb=" O ILE U 35 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N VAL U 37 " --> pdb=" O LEU U 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL U 104 " --> pdb=" O VAL U 37 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N ILE U 39 " --> pdb=" O VAL U 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN U 106 " --> pdb=" O ILE U 39 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'W' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE W 35 " --> pdb=" O ARG W 100 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N LEU W 102 " --> pdb=" O ILE W 35 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL W 37 " --> pdb=" O LEU W 102 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N VAL W 104 " --> pdb=" O VAL W 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE W 39 " --> pdb=" O VAL W 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN W 106 " --> pdb=" O ILE W 39 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'Y' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE Y 35 " --> pdb=" O ARG Y 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU Y 102 " --> pdb=" O ILE Y 35 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL Y 37 " --> pdb=" O LEU Y 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL Y 104 " --> pdb=" O VAL Y 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE Y 39 " --> pdb=" O VAL Y 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN Y 106 " --> pdb=" O ILE Y 39 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain '0' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE 0 35 " --> pdb=" O ARG 0 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU 0 102 " --> pdb=" O ILE 0 35 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL 0 37 " --> pdb=" O LEU 0 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL 0 104 " --> pdb=" O VAL 0 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE 0 39 " --> pdb=" O VAL 0 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN 0 106 " --> pdb=" O ILE 0 39 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain '2' and resid 34 through 40 removed outlier: 5.501A pdb=" N ILE 2 35 " --> pdb=" O ARG 2 100 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU 2 102 " --> pdb=" O ILE 2 35 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL 2 37 " --> pdb=" O LEU 2 102 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N VAL 2 104 " --> pdb=" O VAL 2 37 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE 2 39 " --> pdb=" O VAL 2 104 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN 2 106 " --> pdb=" O ILE 2 39 " (cutoff:3.500A) 1710 hydrogen bonds defined for protein. 4950 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 45 stacking parallelities Total time for adding SS restraints: 16.39 Time building geometry restraints manager: 18.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 13813 1.33 - 1.45: 6869 1.45 - 1.57: 24513 1.57 - 1.69: 150 1.69 - 1.80: 345 Bond restraints: 45690 Sorted by residual: bond pdb=" CB VAL Q 314 " pdb=" CG1 VAL Q 314 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.18e+00 bond pdb=" CB VAL 2 314 " pdb=" CG1 VAL 2 314 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.18e+00 bond pdb=" CB VAL G 314 " pdb=" CG1 VAL G 314 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.15e+00 bond pdb=" CB VAL A 314 " pdb=" CG1 VAL A 314 " ideal model delta sigma weight residual 1.521 1.462 0.059 3.30e-02 9.18e+02 3.15e+00 bond pdb=" CB VAL K 314 " pdb=" CG1 VAL K 314 " ideal model delta sigma weight residual 1.521 1.463 0.058 3.30e-02 9.18e+02 3.13e+00 ... (remaining 45685 not shown) Histogram of bond angle deviations from ideal: 97.29 - 104.65: 1110 104.65 - 112.00: 21326 112.00 - 119.36: 17087 119.36 - 126.72: 21831 126.72 - 134.07: 791 Bond angle restraints: 62145 Sorted by residual: angle pdb=" N ILE M 28 " pdb=" CA ILE M 28 " pdb=" C ILE M 28 " ideal model delta sigma weight residual 113.71 106.84 6.87 9.50e-01 1.11e+00 5.22e+01 angle pdb=" N ILE 0 28 " pdb=" CA ILE 0 28 " pdb=" C ILE 0 28 " ideal model delta sigma weight residual 113.71 106.86 6.85 9.50e-01 1.11e+00 5.21e+01 angle pdb=" N ILE Y 28 " pdb=" CA ILE Y 28 " pdb=" C ILE Y 28 " ideal model delta sigma weight residual 113.71 106.87 6.84 9.50e-01 1.11e+00 5.19e+01 angle pdb=" N ILE I 28 " pdb=" CA ILE I 28 " pdb=" C ILE I 28 " ideal model delta sigma weight residual 113.71 106.87 6.84 9.50e-01 1.11e+00 5.19e+01 angle pdb=" N ILE Q 28 " pdb=" CA ILE Q 28 " pdb=" C ILE Q 28 " ideal model delta sigma weight residual 113.71 106.88 6.83 9.50e-01 1.11e+00 5.18e+01 ... (remaining 62140 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.16: 25486 15.16 - 30.32: 1664 30.32 - 45.47: 330 45.47 - 60.63: 90 60.63 - 75.79: 75 Dihedral angle restraints: 27645 sinusoidal: 12075 harmonic: 15570 Sorted by residual: dihedral pdb=" CA LYS Q 150 " pdb=" C LYS Q 150 " pdb=" N GLU Q 151 " pdb=" CA GLU Q 151 " ideal model delta harmonic sigma weight residual 180.00 155.03 24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA LYS K 150 " pdb=" C LYS K 150 " pdb=" N GLU K 151 " pdb=" CA GLU K 151 " ideal model delta harmonic sigma weight residual 180.00 155.03 24.97 0 5.00e+00 4.00e-02 2.49e+01 dihedral pdb=" CA LYS 2 150 " pdb=" C LYS 2 150 " pdb=" N GLU 2 151 " pdb=" CA GLU 2 151 " ideal model delta harmonic sigma weight residual 180.00 155.04 24.96 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 27642 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 5736 0.075 - 0.151: 1224 0.151 - 0.226: 120 0.226 - 0.301: 15 0.301 - 0.376: 15 Chirality restraints: 7110 Sorted by residual: chirality pdb=" CA ASP O 42 " pdb=" N ASP O 42 " pdb=" C ASP O 42 " pdb=" CB ASP O 42 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.54e+00 chirality pdb=" CA ASP I 42 " pdb=" N ASP I 42 " pdb=" C ASP I 42 " pdb=" CB ASP I 42 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA ASP Y 42 " pdb=" N ASP Y 42 " pdb=" C ASP Y 42 " pdb=" CB ASP Y 42 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.51e+00 ... (remaining 7107 not shown) Planarity restraints: 7650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR S 281 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.93e+00 pdb=" N PRO S 282 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO S 282 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO S 282 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR 0 281 " 0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO 0 282 " -0.096 5.00e-02 4.00e+02 pdb=" CA PRO 0 282 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO 0 282 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TYR A 281 " -0.037 5.00e-02 4.00e+02 5.55e-02 4.92e+00 pdb=" N PRO A 282 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO A 282 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 282 " -0.031 5.00e-02 4.00e+02 ... (remaining 7647 not shown) Histogram of nonbonded interaction distances: 1.82 - 2.43: 155 2.43 - 3.05: 26373 3.05 - 3.67: 70679 3.67 - 4.28: 108488 4.28 - 4.90: 175370 Nonbonded interactions: 381065 Sorted by model distance: nonbonded pdb=" O GLY A 23 " pdb=" OE2 GLU 0 342 " model vdw 1.817 3.040 nonbonded pdb=" O GLY D 23 " pdb=" OE2 GLU 2 342 " model vdw 1.817 3.040 nonbonded pdb=" OG SER Y 334 " pdb=" O PHE Y 357 " model vdw 2.272 2.440 nonbonded pdb=" OG SER W 334 " pdb=" O PHE W 357 " model vdw 2.272 2.440 nonbonded pdb=" OG SER 2 334 " pdb=" O PHE 2 357 " model vdw 2.272 2.440 ... (remaining 381060 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '2' selection = chain 'A' selection = chain 'C' selection = chain 'D' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'U' selection = chain 'W' selection = chain 'Y' } ncs_group { reference = chain '1' selection = chain '3' selection = chain 'B' selection = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'V' selection = chain 'X' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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: 1.610 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: 0.030 Extract box with map and model: 9.580 Check model and map are aligned: 0.670 Set scattering table: 0.410 Process input model: 123.920 Find NCS groups from input model: 3.240 Set up NCS constraints: 0.460 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.700 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8502 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.060 45690 Z= 0.619 Angle : 1.118 13.127 62145 Z= 0.607 Chirality : 0.063 0.376 7110 Planarity : 0.007 0.056 7650 Dihedral : 11.844 75.788 17625 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 0.65 % Allowed : 4.19 % Favored : 95.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.39 (0.08), residues: 5355 helix: -4.22 (0.04), residues: 3030 sheet: -1.96 (0.26), residues: 390 loop : -2.39 (0.12), residues: 1935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP Y 215 HIS 0.004 0.001 HIS O 287 PHE 0.020 0.004 PHE G 324 TYR 0.029 0.005 TYR O 281 ARG 0.011 0.001 ARG D 370 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1274 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1244 time to evaluate : 4.833 Fit side-chains revert: symmetry clash REVERT: C 29 ARG cc_start: 0.8344 (ptp-110) cc_final: 0.8029 (ptp-110) REVERT: C 143 ARG cc_start: 0.7223 (pmt170) cc_final: 0.6689 (ptm-80) REVERT: C 166 ILE cc_start: 0.9019 (mm) cc_final: 0.8814 (mt) REVERT: C 256 ASP cc_start: 0.8847 (t70) cc_final: 0.8252 (t0) REVERT: C 306 MET cc_start: 0.8949 (mtp) cc_final: 0.8705 (mtp) REVERT: A 143 ARG cc_start: 0.7317 (pmt170) cc_final: 0.6829 (ttp-110) REVERT: A 156 GLU cc_start: 0.7123 (tm-30) cc_final: 0.6601 (tm-30) REVERT: A 320 ILE cc_start: 0.9108 (tt) cc_final: 0.8776 (tt) REVERT: A 367 GLU cc_start: 0.7353 (tt0) cc_final: 0.7031 (tt0) REVERT: D 29 ARG cc_start: 0.8407 (ptp-110) cc_final: 0.8067 (ptp-110) REVERT: D 53 ASP cc_start: 0.8341 (t0) cc_final: 0.7861 (t0) REVERT: D 76 ILE cc_start: 0.8588 (pt) cc_final: 0.8245 (pt) REVERT: D 143 ARG cc_start: 0.7375 (pmt170) cc_final: 0.6961 (ptt-90) REVERT: D 297 GLU cc_start: 0.7808 (tt0) cc_final: 0.7576 (tt0) REVERT: D 320 ILE cc_start: 0.9164 (tt) cc_final: 0.8869 (tt) REVERT: G 13 ARG cc_start: 0.7384 (mtm-85) cc_final: 0.7156 (mtm110) REVERT: G 156 GLU cc_start: 0.7225 (tm-30) cc_final: 0.6656 (tm-30) REVERT: G 297 GLU cc_start: 0.7905 (tt0) cc_final: 0.7629 (tt0) REVERT: G 306 MET cc_start: 0.8946 (mtp) cc_final: 0.8675 (mtp) REVERT: I 53 ASP cc_start: 0.8188 (t0) cc_final: 0.7979 (t0) REVERT: I 57 ARG cc_start: 0.8188 (ptp-110) cc_final: 0.7927 (ttp-170) REVERT: I 123 MET cc_start: 0.6115 (mtm) cc_final: 0.5910 (ptt) REVERT: I 143 ARG cc_start: 0.7443 (pmt170) cc_final: 0.7143 (ptt-90) REVERT: I 159 ASP cc_start: 0.8641 (p0) cc_final: 0.8378 (p0) REVERT: I 297 GLU cc_start: 0.7795 (tt0) cc_final: 0.7552 (tt0) REVERT: I 320 ILE cc_start: 0.9104 (tt) cc_final: 0.8855 (tt) REVERT: K 156 GLU cc_start: 0.7162 (tm-30) cc_final: 0.6555 (tm-30) REVERT: K 158 GLN cc_start: 0.7966 (mp10) cc_final: 0.7602 (mm-40) REVERT: K 252 GLU cc_start: 0.8119 (tp30) cc_final: 0.7818 (tp30) REVERT: K 297 GLU cc_start: 0.7735 (tt0) cc_final: 0.7442 (tt0) REVERT: K 320 ILE cc_start: 0.9068 (tt) cc_final: 0.8827 (tt) REVERT: M 3 THR cc_start: 0.8878 (t) cc_final: 0.8632 (m) REVERT: M 29 ARG cc_start: 0.8372 (ptp-110) cc_final: 0.8148 (ptp-110) REVERT: M 53 ASP cc_start: 0.8202 (t0) cc_final: 0.7989 (t0) REVERT: M 143 ARG cc_start: 0.7484 (pmt170) cc_final: 0.7110 (ptt-90) REVERT: M 156 GLU cc_start: 0.7025 (tm-30) cc_final: 0.6144 (tm-30) REVERT: M 158 GLN cc_start: 0.8036 (mp10) cc_final: 0.7767 (mm-40) REVERT: M 166 ILE cc_start: 0.8987 (mm) cc_final: 0.8775 (mt) REVERT: M 263 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7850 (mt-10) REVERT: M 320 ILE cc_start: 0.9049 (tt) cc_final: 0.8748 (tt) REVERT: M 371 ARG cc_start: 0.7307 (mtp180) cc_final: 0.7085 (mtp180) REVERT: O 29 ARG cc_start: 0.8453 (ptp-110) cc_final: 0.7938 (ptp-110) REVERT: O 53 ASP cc_start: 0.8342 (t0) cc_final: 0.8057 (t0) REVERT: O 143 ARG cc_start: 0.7332 (pmt170) cc_final: 0.6890 (ptm-80) REVERT: O 217 ASP cc_start: 0.7574 (m-30) cc_final: 0.7208 (m-30) REVERT: O 320 ILE cc_start: 0.9103 (tt) cc_final: 0.8842 (tt) REVERT: O 371 ARG cc_start: 0.7138 (mtp180) cc_final: 0.6871 (mtp180) REVERT: Q 10 LEU cc_start: 0.9043 (mt) cc_final: 0.8803 (mp) REVERT: Q 29 ARG cc_start: 0.8393 (ptp-110) cc_final: 0.8060 (ptp-110) REVERT: Q 53 ASP cc_start: 0.8358 (t0) cc_final: 0.7935 (t0) REVERT: Q 109 GLN cc_start: 0.7236 (tm-30) cc_final: 0.7035 (tm-30) REVERT: Q 143 ARG cc_start: 0.7297 (pmt170) cc_final: 0.7038 (ptm-80) REVERT: Q 217 ASP cc_start: 0.7541 (m-30) cc_final: 0.7083 (m-30) REVERT: Q 253 MET cc_start: 0.8187 (ttm) cc_final: 0.7968 (ttp) REVERT: Q 371 ARG cc_start: 0.7311 (mtp180) cc_final: 0.7043 (mtp180) REVERT: S 13 ARG cc_start: 0.7283 (mtm-85) cc_final: 0.7053 (mtm110) REVERT: S 166 ILE cc_start: 0.9061 (mm) cc_final: 0.8836 (mt) REVERT: S 256 ASP cc_start: 0.8764 (t70) cc_final: 0.8106 (t0) REVERT: S 304 GLN cc_start: 0.7935 (pt0) cc_final: 0.7710 (pt0) REVERT: U 29 ARG cc_start: 0.8391 (ptp-110) cc_final: 0.8148 (ptp-110) REVERT: U 143 ARG cc_start: 0.7374 (pmt170) cc_final: 0.6981 (mtp-110) REVERT: U 159 ASP cc_start: 0.8672 (p0) cc_final: 0.8409 (p0) REVERT: U 166 ILE cc_start: 0.9116 (mm) cc_final: 0.8890 (mt) REVERT: U 256 ASP cc_start: 0.8707 (t70) cc_final: 0.7959 (t0) REVERT: U 306 MET cc_start: 0.8921 (mtp) cc_final: 0.8670 (mtm) REVERT: U 371 ARG cc_start: 0.7160 (mtp180) cc_final: 0.6899 (mtp180) REVERT: W 5 LEU cc_start: 0.8707 (mm) cc_final: 0.8507 (mm) REVERT: W 10 LEU cc_start: 0.8950 (mt) cc_final: 0.8665 (mt) REVERT: W 111 GLN cc_start: 0.8082 (tp-100) cc_final: 0.7538 (tp40) REVERT: W 143 ARG cc_start: 0.7218 (pmt170) cc_final: 0.6645 (ptm-80) REVERT: W 367 GLU cc_start: 0.7472 (tt0) cc_final: 0.7271 (tt0) REVERT: W 371 ARG cc_start: 0.7317 (mtp180) cc_final: 0.7066 (mtp180) REVERT: Y 31 ILE cc_start: 0.8835 (tp) cc_final: 0.8571 (tp) REVERT: Y 53 ASP cc_start: 0.8570 (t0) cc_final: 0.8333 (t0) REVERT: Y 123 MET cc_start: 0.5922 (mtm) cc_final: 0.5454 (mtp) REVERT: Y 166 ILE cc_start: 0.9054 (mm) cc_final: 0.8814 (mt) REVERT: Y 209 PHE cc_start: 0.8582 (m-10) cc_final: 0.8321 (m-80) REVERT: Y 337 MET cc_start: 0.8494 (mmp) cc_final: 0.8275 (mmp) REVERT: Y 367 GLU cc_start: 0.7488 (tt0) cc_final: 0.7262 (tt0) REVERT: Y 371 ARG cc_start: 0.7322 (mtp180) cc_final: 0.6934 (mtp180) REVERT: 0 53 ASP cc_start: 0.8687 (t0) cc_final: 0.8300 (t0) REVERT: 0 337 MET cc_start: 0.8589 (mmp) cc_final: 0.8310 (mmp) REVERT: 0 371 ARG cc_start: 0.7213 (mtp180) cc_final: 0.6742 (mtp180) REVERT: 2 3 THR cc_start: 0.8554 (t) cc_final: 0.8256 (m) REVERT: 2 10 LEU cc_start: 0.9044 (mt) cc_final: 0.8808 (mt) REVERT: 2 29 ARG cc_start: 0.8365 (ptp-110) cc_final: 0.7918 (ptp90) REVERT: 2 256 ASP cc_start: 0.8711 (t70) cc_final: 0.8005 (t0) REVERT: 2 274 LYS cc_start: 0.8670 (tttp) cc_final: 0.8439 (ttmt) REVERT: 2 320 ILE cc_start: 0.9108 (tt) cc_final: 0.8887 (tt) REVERT: 2 371 ARG cc_start: 0.7273 (mtp180) cc_final: 0.6887 (mtp180) outliers start: 30 outliers final: 7 residues processed: 1267 average time/residue: 0.6087 time to fit residues: 1222.5260 Evaluate side-chains 844 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 837 time to evaluate : 5.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain G residue 42 ASP Chi-restraints excluded: chain I residue 236 LEU Chi-restraints excluded: chain K residue 236 LEU Chi-restraints excluded: chain Q residue 236 LEU Chi-restraints excluded: chain S residue 236 LEU Chi-restraints excluded: chain 0 residue 236 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 455 optimal weight: 0.9980 chunk 409 optimal weight: 5.9990 chunk 227 optimal weight: 9.9990 chunk 139 optimal weight: 0.9980 chunk 276 optimal weight: 0.9980 chunk 218 optimal weight: 0.9980 chunk 423 optimal weight: 2.9990 chunk 163 optimal weight: 3.9990 chunk 257 optimal weight: 0.9990 chunk 315 optimal weight: 2.9990 chunk 490 optimal weight: 0.7980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 14 ASN C 33 HIS C 61 ASN C 164 ASN C 351 ASN A 33 HIS A 61 ASN A 304 GLN A 351 ASN D 61 ASN D 246 ASN ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 351 ASN G 33 HIS G 61 ASN G 246 ASN G 351 ASN ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 61 ASN ** I 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 149 ASN I 351 ASN K 33 HIS K 61 ASN K 149 ASN K 164 ASN K 246 ASN ** K 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 351 ASN M 33 HIS M 61 ASN M 149 ASN ** M 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 246 ASN M 351 ASN O 33 HIS O 61 ASN O 164 ASN O 246 ASN O 304 GLN O 351 ASN ** Q 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 HIS Q 61 ASN Q 351 ASN S 33 HIS S 61 ASN S 351 ASN U 33 HIS U 61 ASN U 164 ASN U 351 ASN W 14 ASN W 33 HIS W 61 ASN W 351 ASN Y 14 ASN Y 33 HIS Y 61 ASN Y 111 GLN ** Y 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 351 ASN 0 14 ASN 0 33 HIS 0 61 ASN ** 0 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 14 ASN 2 33 HIS 2 61 ASN 2 164 ASN 2 351 ASN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 45690 Z= 0.172 Angle : 0.613 9.746 62145 Z= 0.319 Chirality : 0.044 0.242 7110 Planarity : 0.005 0.048 7650 Dihedral : 10.664 73.571 7184 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.24 % Allowed : 8.88 % Favored : 88.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.21 (0.10), residues: 5355 helix: -1.93 (0.08), residues: 3120 sheet: -1.76 (0.26), residues: 390 loop : -2.25 (0.13), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP W 333 HIS 0.005 0.001 HIS S 33 PHE 0.018 0.002 PHE O 163 TYR 0.011 0.001 TYR 0 361 ARG 0.005 0.000 ARG O 249 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 936 time to evaluate : 5.291 Fit side-chains revert: symmetry clash REVERT: C 29 ARG cc_start: 0.8420 (ptp-110) cc_final: 0.8111 (ptp-110) REVERT: C 53 ASP cc_start: 0.8364 (t0) cc_final: 0.7971 (t0) REVERT: C 143 ARG cc_start: 0.7294 (pmt170) cc_final: 0.6649 (ptm-80) REVERT: C 209 PHE cc_start: 0.8765 (m-10) cc_final: 0.8547 (m-10) REVERT: C 217 ASP cc_start: 0.7332 (m-30) cc_final: 0.6669 (m-30) REVERT: C 320 ILE cc_start: 0.9231 (tt) cc_final: 0.8985 (tt) REVERT: C 371 ARG cc_start: 0.7098 (mtp180) cc_final: 0.6823 (mtp180) REVERT: A 100 ARG cc_start: 0.8184 (ttp80) cc_final: 0.7892 (tmm160) REVERT: A 130 TYR cc_start: 0.9064 (t80) cc_final: 0.8852 (t80) REVERT: A 320 ILE cc_start: 0.9100 (tt) cc_final: 0.8876 (tt) REVERT: D 53 ASP cc_start: 0.8235 (t0) cc_final: 0.7918 (t0) REVERT: D 143 ARG cc_start: 0.7468 (pmt170) cc_final: 0.7143 (ptt-90) REVERT: D 320 ILE cc_start: 0.9164 (tt) cc_final: 0.8956 (tt) REVERT: D 344 GLU cc_start: 0.7946 (mp0) cc_final: 0.7659 (mp0) REVERT: G 53 ASP cc_start: 0.8387 (t0) cc_final: 0.8100 (t0) REVERT: G 192 GLU cc_start: 0.7626 (mt-10) cc_final: 0.7395 (mt-10) REVERT: G 306 MET cc_start: 0.8774 (mtp) cc_final: 0.8471 (mtp) REVERT: G 337 MET cc_start: 0.8440 (mmp) cc_final: 0.8157 (mmp) REVERT: I 57 ARG cc_start: 0.8120 (ptp-110) cc_final: 0.7846 (ttp-170) REVERT: I 129 GLN cc_start: 0.8256 (mp10) cc_final: 0.8030 (mp10) REVERT: I 143 ARG cc_start: 0.7538 (pmt170) cc_final: 0.7113 (ptt-90) REVERT: I 271 LEU cc_start: 0.8600 (mt) cc_final: 0.8334 (mt) REVERT: I 344 GLU cc_start: 0.7907 (mp0) cc_final: 0.7703 (mp0) REVERT: K 13 ARG cc_start: 0.7539 (mtp180) cc_final: 0.7291 (mtm110) REVERT: K 29 ARG cc_start: 0.8445 (ptp-110) cc_final: 0.8119 (ptp90) REVERT: K 156 GLU cc_start: 0.7088 (tm-30) cc_final: 0.6538 (tm-30) REVERT: K 159 ASP cc_start: 0.8226 (p0) cc_final: 0.7873 (p0) REVERT: K 246 ASN cc_start: 0.8726 (m110) cc_final: 0.8474 (m-40) REVERT: K 256 ASP cc_start: 0.8738 (t70) cc_final: 0.8168 (t0) REVERT: K 306 MET cc_start: 0.8907 (mtp) cc_final: 0.8640 (mtm) REVERT: K 320 ILE cc_start: 0.9090 (tt) cc_final: 0.8732 (tt) REVERT: K 344 GLU cc_start: 0.7816 (mp0) cc_final: 0.7549 (mm-30) REVERT: K 371 ARG cc_start: 0.7348 (mtp180) cc_final: 0.7055 (mtp180) REVERT: M 53 ASP cc_start: 0.8198 (t0) cc_final: 0.7889 (t0) REVERT: M 143 ARG cc_start: 0.7529 (pmt170) cc_final: 0.6916 (ptt-90) REVERT: M 156 GLU cc_start: 0.6938 (tm-30) cc_final: 0.6177 (tm-30) REVERT: M 158 GLN cc_start: 0.8100 (mp10) cc_final: 0.7873 (mm-40) REVERT: M 217 ASP cc_start: 0.7197 (m-30) cc_final: 0.6717 (m-30) REVERT: M 263 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7808 (mt-10) REVERT: M 371 ARG cc_start: 0.7216 (mtp180) cc_final: 0.6732 (mtp180) REVERT: O 6 ARG cc_start: 0.7995 (ptp90) cc_final: 0.7603 (ttp-110) REVERT: O 53 ASP cc_start: 0.8322 (t0) cc_final: 0.8086 (t0) REVERT: O 82 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7639 (mt-10) REVERT: O 86 GLN cc_start: 0.8448 (pt0) cc_final: 0.8226 (pt0) REVERT: O 100 ARG cc_start: 0.8343 (ttp80) cc_final: 0.8112 (tmm160) REVERT: O 143 ARG cc_start: 0.7328 (pmt170) cc_final: 0.6881 (ptm-80) REVERT: O 212 GLU cc_start: 0.8176 (pt0) cc_final: 0.7972 (pt0) REVERT: O 217 ASP cc_start: 0.7365 (m-30) cc_final: 0.6974 (m-30) REVERT: O 320 ILE cc_start: 0.9069 (tt) cc_final: 0.8836 (tt) REVERT: O 367 GLU cc_start: 0.7627 (tt0) cc_final: 0.7106 (tt0) REVERT: O 371 ARG cc_start: 0.7100 (mtp180) cc_final: 0.6789 (mtp180) REVERT: Q 53 ASP cc_start: 0.8345 (t0) cc_final: 0.8001 (t0) REVERT: Q 57 ARG cc_start: 0.8254 (ptp-110) cc_final: 0.8045 (ptm160) REVERT: Q 109 GLN cc_start: 0.7140 (tm-30) cc_final: 0.6924 (tm-30) REVERT: Q 143 ARG cc_start: 0.7273 (pmt170) cc_final: 0.6915 (ptm-80) REVERT: Q 213 ARG cc_start: 0.7672 (mtp-110) cc_final: 0.7198 (mtp-110) REVERT: Q 217 ASP cc_start: 0.7240 (m-30) cc_final: 0.6824 (m-30) REVERT: Q 371 ARG cc_start: 0.7216 (mtp180) cc_final: 0.6890 (mtp180) REVERT: S 143 ARG cc_start: 0.7155 (ptt-90) cc_final: 0.6345 (ttp-110) REVERT: S 280 MET cc_start: 0.8339 (mmm) cc_final: 0.7880 (mmt) REVERT: S 371 ARG cc_start: 0.7033 (mtp180) cc_final: 0.6832 (mtp180) REVERT: U 143 ARG cc_start: 0.7400 (pmt170) cc_final: 0.6947 (ttp-110) REVERT: U 371 ARG cc_start: 0.7137 (mtp180) cc_final: 0.6778 (mtp180) REVERT: W 111 GLN cc_start: 0.8127 (tp-100) cc_final: 0.7615 (tp40) REVERT: W 143 ARG cc_start: 0.7217 (pmt170) cc_final: 0.6608 (ptm-80) REVERT: W 371 ARG cc_start: 0.7241 (mtp180) cc_final: 0.6920 (mtp180) REVERT: Y 6 ARG cc_start: 0.8202 (ptp90) cc_final: 0.7786 (mtm110) REVERT: Y 10 LEU cc_start: 0.8750 (mt) cc_final: 0.8498 (mt) REVERT: Y 100 ARG cc_start: 0.7803 (ttp-110) cc_final: 0.7474 (tmm160) REVERT: Y 123 MET cc_start: 0.5873 (mtm) cc_final: 0.5444 (mtp) REVERT: Y 371 ARG cc_start: 0.7181 (mtp180) cc_final: 0.6665 (mtp180) REVERT: 0 53 ASP cc_start: 0.8647 (t0) cc_final: 0.8392 (t0) REVERT: 0 371 ARG cc_start: 0.7163 (mtp180) cc_final: 0.6670 (mtp180) REVERT: 2 10 LEU cc_start: 0.9028 (mt) cc_final: 0.8735 (mm) REVERT: 2 53 ASP cc_start: 0.8594 (t0) cc_final: 0.8148 (t0) REVERT: 2 274 LYS cc_start: 0.8613 (tttp) cc_final: 0.8382 (ttmt) REVERT: 2 317 GLU cc_start: 0.5571 (tm-30) cc_final: 0.4879 (tm-30) REVERT: 2 371 ARG cc_start: 0.7231 (mtp180) cc_final: 0.6789 (mtp180) outliers start: 104 outliers final: 53 residues processed: 1016 average time/residue: 0.6337 time to fit residues: 1008.5046 Evaluate side-chains 876 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 822 time to evaluate : 4.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 225 GLU Chi-restraints excluded: chain C residue 227 LEU Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 227 LEU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain D residue 45 ILE Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain G residue 45 ILE Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 355 SER Chi-restraints excluded: chain I residue 45 ILE Chi-restraints excluded: chain I residue 150 LYS Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain K residue 57 ARG Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 123 MET Chi-restraints excluded: chain K residue 150 LYS Chi-restraints excluded: chain K residue 225 GLU Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 86 GLN Chi-restraints excluded: chain M residue 225 GLU Chi-restraints excluded: chain M residue 355 SER Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 82 GLU Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain Q residue 86 GLN Chi-restraints excluded: chain Q residue 150 LYS Chi-restraints excluded: chain Q residue 225 GLU Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain S residue 355 SER Chi-restraints excluded: chain U residue 227 LEU Chi-restraints excluded: chain U residue 355 SER Chi-restraints excluded: chain U residue 367 GLU Chi-restraints excluded: chain W residue 86 GLN Chi-restraints excluded: chain W residue 150 LYS Chi-restraints excluded: chain W residue 227 LEU Chi-restraints excluded: chain W residue 355 SER Chi-restraints excluded: chain Y residue 86 GLN Chi-restraints excluded: chain Y residue 111 GLN Chi-restraints excluded: chain Y residue 227 LEU Chi-restraints excluded: chain Y residue 355 SER Chi-restraints excluded: chain 0 residue 86 GLN Chi-restraints excluded: chain 0 residue 186 ASP Chi-restraints excluded: chain 0 residue 225 GLU Chi-restraints excluded: chain 2 residue 150 LYS Chi-restraints excluded: chain 2 residue 227 LEU Chi-restraints excluded: chain 2 residue 355 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 272 optimal weight: 7.9990 chunk 152 optimal weight: 0.4980 chunk 408 optimal weight: 10.0000 chunk 333 optimal weight: 0.0870 chunk 135 optimal weight: 8.9990 chunk 491 optimal weight: 6.9990 chunk 530 optimal weight: 9.9990 chunk 437 optimal weight: 5.9990 chunk 487 optimal weight: 9.9990 chunk 167 optimal weight: 7.9990 chunk 394 optimal weight: 1.9990 overall best weight: 3.1164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 HIS ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 33 HIS A 304 GLN D 33 HIS ** D 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN G 33 HIS ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 33 HIS K 14 ASN K 33 HIS M 33 HIS M 246 ASN O 33 HIS O 164 ASN O 246 ASN ** O 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 33 HIS ** Q 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 14 ASN S 33 HIS U 33 HIS U 304 GLN W 33 HIS W 304 GLN Y 33 HIS ** Y 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 33 HIS 2 33 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.090 45690 Z= 0.300 Angle : 0.599 6.991 62145 Z= 0.307 Chirality : 0.045 0.209 7110 Planarity : 0.004 0.037 7650 Dihedral : 10.299 73.578 7170 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.69 % Allowed : 9.33 % Favored : 87.98 % 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: -1.93 (0.11), residues: 5355 helix: -0.80 (0.09), residues: 3195 sheet: -1.50 (0.27), residues: 390 loop : -1.88 (0.14), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 333 HIS 0.005 0.001 HIS I 33 PHE 0.012 0.002 PHE U 324 TYR 0.016 0.002 TYR 0 361 ARG 0.006 0.001 ARG S 100 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 971 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 846 time to evaluate : 5.513 Fit side-chains revert: symmetry clash REVERT: C 29 ARG cc_start: 0.8518 (ptp-110) cc_final: 0.8157 (ptp-110) REVERT: C 53 ASP cc_start: 0.8478 (t0) cc_final: 0.8172 (t0) REVERT: C 143 ARG cc_start: 0.7349 (pmt170) cc_final: 0.6835 (ptt-90) REVERT: C 201 GLN cc_start: 0.8842 (OUTLIER) cc_final: 0.7561 (mt0) REVERT: C 371 ARG cc_start: 0.7080 (mtp180) cc_final: 0.6726 (mtp180) REVERT: A 100 ARG cc_start: 0.8227 (ttp80) cc_final: 0.7982 (tmm160) REVERT: A 280 MET cc_start: 0.8396 (mmt) cc_final: 0.7997 (mmt) REVERT: A 297 GLU cc_start: 0.6788 (tt0) cc_final: 0.6512 (tt0) REVERT: A 320 ILE cc_start: 0.9139 (tt) cc_final: 0.8826 (tt) REVERT: A 371 ARG cc_start: 0.7184 (mtp180) cc_final: 0.6706 (mtp180) REVERT: D 53 ASP cc_start: 0.8372 (t0) cc_final: 0.8051 (t0) REVERT: D 143 ARG cc_start: 0.7472 (pmt170) cc_final: 0.7043 (ptt-90) REVERT: D 201 GLN cc_start: 0.8801 (OUTLIER) cc_final: 0.7435 (mp10) REVERT: D 320 ILE cc_start: 0.9221 (tt) cc_final: 0.8969 (tt) REVERT: G 53 ASP cc_start: 0.8508 (t0) cc_final: 0.8239 (t0) REVERT: G 201 GLN cc_start: 0.8772 (OUTLIER) cc_final: 0.7462 (mt0) REVERT: G 227 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8505 (tp) REVERT: I 53 ASP cc_start: 0.8150 (t0) cc_final: 0.7869 (t0) REVERT: I 57 ARG cc_start: 0.8162 (ptp-110) cc_final: 0.7854 (ttp-170) REVERT: I 143 ARG cc_start: 0.7575 (pmt170) cc_final: 0.7259 (ptt-90) REVERT: I 201 GLN cc_start: 0.8809 (OUTLIER) cc_final: 0.7486 (mt0) REVERT: I 227 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8563 (tp) REVERT: I 271 LEU cc_start: 0.8617 (mt) cc_final: 0.8318 (mt) REVERT: K 5 LEU cc_start: 0.8738 (mm) cc_final: 0.8503 (mm) REVERT: K 10 LEU cc_start: 0.8812 (mt) cc_final: 0.8479 (mt) REVERT: K 29 ARG cc_start: 0.8488 (ptp-110) cc_final: 0.8113 (ptp90) REVERT: K 102 LEU cc_start: 0.8676 (OUTLIER) cc_final: 0.8394 (pp) REVERT: K 201 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.7444 (mt0) REVERT: K 297 GLU cc_start: 0.7461 (tt0) cc_final: 0.7180 (tt0) REVERT: K 320 ILE cc_start: 0.9057 (tt) cc_final: 0.8822 (tt) REVERT: K 371 ARG cc_start: 0.7331 (mtp180) cc_final: 0.7088 (mtp180) REVERT: M 53 ASP cc_start: 0.8291 (t0) cc_final: 0.7994 (t0) REVERT: M 143 ARG cc_start: 0.7571 (pmt170) cc_final: 0.7145 (ptt-90) REVERT: M 156 GLU cc_start: 0.7177 (tm-30) cc_final: 0.6342 (tm-30) REVERT: M 158 GLN cc_start: 0.8135 (mp10) cc_final: 0.7855 (mm-40) REVERT: M 201 GLN cc_start: 0.8904 (OUTLIER) cc_final: 0.7682 (mt0) REVERT: M 217 ASP cc_start: 0.7119 (m-30) cc_final: 0.6620 (m-30) REVERT: M 371 ARG cc_start: 0.7162 (mtp180) cc_final: 0.6712 (mtp180) REVERT: O 6 ARG cc_start: 0.8043 (ptp90) cc_final: 0.7657 (ttp-110) REVERT: O 53 ASP cc_start: 0.8390 (t0) cc_final: 0.8181 (t0) REVERT: O 93 ASP cc_start: 0.7411 (p0) cc_final: 0.7195 (t70) REVERT: O 100 ARG cc_start: 0.8397 (ttp80) cc_final: 0.8130 (tmm160) REVERT: O 143 ARG cc_start: 0.7386 (pmt170) cc_final: 0.6993 (ptt-90) REVERT: O 212 GLU cc_start: 0.8298 (pt0) cc_final: 0.7953 (pt0) REVERT: O 217 ASP cc_start: 0.7357 (m-30) cc_final: 0.7020 (m-30) REVERT: O 280 MET cc_start: 0.8544 (mmt) cc_final: 0.8318 (mmm) REVERT: O 320 ILE cc_start: 0.9152 (tt) cc_final: 0.8878 (tt) REVERT: O 367 GLU cc_start: 0.7700 (tt0) cc_final: 0.7199 (tt0) REVERT: O 371 ARG cc_start: 0.7099 (mtp180) cc_final: 0.6821 (mtp180) REVERT: Q 53 ASP cc_start: 0.8390 (t0) cc_final: 0.8037 (t0) REVERT: Q 109 GLN cc_start: 0.7137 (tm-30) cc_final: 0.6920 (tm-30) REVERT: Q 143 ARG cc_start: 0.7316 (pmt170) cc_final: 0.6871 (ptm-80) REVERT: Q 217 ASP cc_start: 0.7263 (m-30) cc_final: 0.6846 (m-30) REVERT: Q 371 ARG cc_start: 0.7295 (mtp180) cc_final: 0.6955 (mtp180) REVERT: S 6 ARG cc_start: 0.8158 (ttp-170) cc_final: 0.7945 (ttp-110) REVERT: S 143 ARG cc_start: 0.7168 (ptt-90) cc_final: 0.6557 (ptm-80) REVERT: S 201 GLN cc_start: 0.8887 (OUTLIER) cc_final: 0.7360 (mt0) REVERT: S 280 MET cc_start: 0.8377 (mmm) cc_final: 0.7950 (mmt) REVERT: S 371 ARG cc_start: 0.7073 (mtp180) cc_final: 0.6676 (mtp180) REVERT: U 143 ARG cc_start: 0.7447 (pmt170) cc_final: 0.6909 (ttp-110) REVERT: U 201 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.7445 (mt0) REVERT: U 313 MET cc_start: 0.8397 (ptp) cc_final: 0.8192 (ptm) REVERT: U 371 ARG cc_start: 0.7084 (mtp180) cc_final: 0.6620 (mtp180) REVERT: W 10 LEU cc_start: 0.8871 (mt) cc_final: 0.8576 (mm) REVERT: W 111 GLN cc_start: 0.8179 (tp-100) cc_final: 0.7659 (tp40) REVERT: W 143 ARG cc_start: 0.7385 (pmt170) cc_final: 0.6682 (ptm-80) REVERT: W 371 ARG cc_start: 0.7188 (mtp180) cc_final: 0.6911 (mtp180) REVERT: Y 6 ARG cc_start: 0.8220 (ptp90) cc_final: 0.7682 (mtm110) REVERT: Y 123 MET cc_start: 0.5877 (mtm) cc_final: 0.5425 (mtp) REVERT: Y 225 GLU cc_start: 0.8016 (tt0) cc_final: 0.7560 (tt0) REVERT: Y 371 ARG cc_start: 0.7211 (mtp180) cc_final: 0.6718 (mtp180) REVERT: 0 201 GLN cc_start: 0.9059 (OUTLIER) cc_final: 0.7583 (mp10) REVERT: 0 217 ASP cc_start: 0.7128 (m-30) cc_final: 0.6927 (m-30) REVERT: 0 371 ARG cc_start: 0.7123 (mtp180) cc_final: 0.6543 (mtp180) REVERT: 2 10 LEU cc_start: 0.8970 (mt) cc_final: 0.8699 (mm) REVERT: 2 161 GLU cc_start: 0.7940 (pt0) cc_final: 0.7705 (pt0) REVERT: 2 201 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.7629 (mp10) REVERT: 2 274 LYS cc_start: 0.8637 (tttp) cc_final: 0.8409 (ttmt) REVERT: 2 317 GLU cc_start: 0.5611 (tm-30) cc_final: 0.4910 (tm-30) REVERT: 2 371 ARG cc_start: 0.7204 (mtp180) cc_final: 0.6826 (mtp180) outliers start: 125 outliers final: 66 residues processed: 937 average time/residue: 0.6048 time to fit residues: 896.7244 Evaluate side-chains 857 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 778 time to evaluate : 5.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 150 LYS Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 201 GLN Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 225 GLU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 355 SER Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain I residue 213 ARG Chi-restraints excluded: chain I residue 225 GLU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 57 ARG Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 201 GLN Chi-restraints excluded: chain M residue 82 GLU Chi-restraints excluded: chain M residue 86 GLN Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 108 ASP Chi-restraints excluded: chain M residue 201 GLN Chi-restraints excluded: chain M residue 225 GLU Chi-restraints excluded: chain M residue 355 SER Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 55 LEU Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain Q residue 86 GLN Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 150 LYS Chi-restraints excluded: chain Q residue 225 GLU Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain S residue 150 LYS Chi-restraints excluded: chain S residue 186 ASP Chi-restraints excluded: chain S residue 201 GLN Chi-restraints excluded: chain S residue 225 GLU Chi-restraints excluded: chain S residue 355 SER Chi-restraints excluded: chain U residue 186 ASP Chi-restraints excluded: chain U residue 201 GLN Chi-restraints excluded: chain U residue 341 VAL Chi-restraints excluded: chain U residue 355 SER Chi-restraints excluded: chain W residue 86 GLN Chi-restraints excluded: chain W residue 150 LYS Chi-restraints excluded: chain W residue 355 SER Chi-restraints excluded: chain Y residue 86 GLN Chi-restraints excluded: chain Y residue 91 ILE Chi-restraints excluded: chain Y residue 227 LEU Chi-restraints excluded: chain Y residue 304 GLN Chi-restraints excluded: chain Y residue 355 SER Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 0 residue 86 GLN Chi-restraints excluded: chain 0 residue 186 ASP Chi-restraints excluded: chain 0 residue 201 GLN Chi-restraints excluded: chain 0 residue 225 GLU Chi-restraints excluded: chain 2 residue 150 LYS Chi-restraints excluded: chain 2 residue 186 ASP Chi-restraints excluded: chain 2 residue 201 GLN Chi-restraints excluded: chain 2 residue 227 LEU Chi-restraints excluded: chain 2 residue 355 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 485 optimal weight: 5.9990 chunk 369 optimal weight: 1.9990 chunk 254 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 234 optimal weight: 4.9990 chunk 329 optimal weight: 0.8980 chunk 493 optimal weight: 2.9990 chunk 521 optimal weight: 0.4980 chunk 257 optimal weight: 2.9990 chunk 467 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 HIS ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 GLN A 33 HIS A 304 GLN D 33 HIS D 246 ASN G 33 HIS G 246 ASN G 301 ASN G 304 GLN I 33 HIS K 149 ASN K 164 ASN K 246 ASN M 33 HIS M 246 ASN M 304 GLN O 33 HIS O 86 GLN O 246 ASN Q 33 HIS ** Q 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 301 ASN S 33 HIS U 33 HIS U 164 ASN W 33 HIS W 304 GLN Y 33 HIS ** Y 322 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 33 HIS Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.2813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 45690 Z= 0.178 Angle : 0.528 9.122 62145 Z= 0.272 Chirality : 0.043 0.188 7110 Planarity : 0.003 0.034 7650 Dihedral : 10.128 73.556 7170 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.57 % Favored : 96.36 % Rotamer: Outliers : 2.43 % Allowed : 10.00 % Favored : 87.57 % 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: -1.10 (0.12), residues: 5355 helix: -0.11 (0.10), residues: 3120 sheet: -1.56 (0.26), residues: 390 loop : -1.45 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 333 HIS 0.005 0.001 HIS S 33 PHE 0.013 0.001 PHE Q 324 TYR 0.011 0.001 TYR C 303 ARG 0.008 0.000 ARG K 249 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 957 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 113 poor density : 844 time to evaluate : 5.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 ARG cc_start: 0.8507 (ptp-110) cc_final: 0.8179 (ptp-110) REVERT: C 53 ASP cc_start: 0.8471 (t0) cc_final: 0.8034 (t0) REVERT: C 143 ARG cc_start: 0.7320 (pmt170) cc_final: 0.6800 (ptt-90) REVERT: C 201 GLN cc_start: 0.8800 (OUTLIER) cc_final: 0.7358 (mt0) REVERT: A 100 ARG cc_start: 0.8197 (ttp80) cc_final: 0.7939 (tmm160) REVERT: A 256 ASP cc_start: 0.8391 (t70) cc_final: 0.7931 (t70) REVERT: A 280 MET cc_start: 0.8393 (mmt) cc_final: 0.8038 (mmt) REVERT: A 297 GLU cc_start: 0.6846 (tt0) cc_final: 0.6605 (tt0) REVERT: A 371 ARG cc_start: 0.7340 (mtp180) cc_final: 0.6949 (mtp180) REVERT: D 53 ASP cc_start: 0.8427 (t0) cc_final: 0.8117 (t0) REVERT: D 143 ARG cc_start: 0.7441 (pmt170) cc_final: 0.7022 (ptt-90) REVERT: D 150 LYS cc_start: 0.8601 (ptpp) cc_final: 0.8000 (mtpt) REVERT: D 320 ILE cc_start: 0.9182 (tt) cc_final: 0.8875 (tt) REVERT: G 13 ARG cc_start: 0.7670 (ttp-110) cc_final: 0.7469 (ttp-110) REVERT: G 53 ASP cc_start: 0.8514 (t0) cc_final: 0.8271 (t0) REVERT: G 165 MET cc_start: 0.8467 (tpt) cc_final: 0.8200 (tpt) REVERT: G 201 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.7459 (mt0) REVERT: I 53 ASP cc_start: 0.8188 (t0) cc_final: 0.7881 (t0) REVERT: I 57 ARG cc_start: 0.8154 (ptp-110) cc_final: 0.7885 (ttp-170) REVERT: I 143 ARG cc_start: 0.7521 (pmt170) cc_final: 0.7216 (ptt-90) REVERT: I 159 ASP cc_start: 0.8056 (p0) cc_final: 0.7752 (p0) REVERT: I 201 GLN cc_start: 0.8812 (OUTLIER) cc_final: 0.7430 (mt0) REVERT: I 227 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8515 (tp) REVERT: I 271 LEU cc_start: 0.8555 (mt) cc_final: 0.8272 (mt) REVERT: K 5 LEU cc_start: 0.8761 (mm) cc_final: 0.8544 (mm) REVERT: K 29 ARG cc_start: 0.8453 (ptp-110) cc_final: 0.7948 (ptp90) REVERT: K 102 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8239 (pp) REVERT: K 159 ASP cc_start: 0.8128 (p0) cc_final: 0.7794 (p0) REVERT: K 201 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.7438 (mt0) REVERT: K 306 MET cc_start: 0.8518 (mtm) cc_final: 0.8080 (mtp) REVERT: K 320 ILE cc_start: 0.9044 (tt) cc_final: 0.8743 (tt) REVERT: M 102 LEU cc_start: 0.8518 (OUTLIER) cc_final: 0.8281 (pp) REVERT: M 143 ARG cc_start: 0.7560 (pmt170) cc_final: 0.7140 (ptt-90) REVERT: M 156 GLU cc_start: 0.7212 (tm-30) cc_final: 0.6401 (tm-30) REVERT: M 158 GLN cc_start: 0.8090 (mp10) cc_final: 0.7851 (mm-40) REVERT: M 212 GLU cc_start: 0.8281 (pt0) cc_final: 0.7889 (pt0) REVERT: M 371 ARG cc_start: 0.7129 (mtp180) cc_final: 0.6741 (mtp180) REVERT: O 6 ARG cc_start: 0.8040 (ptp90) cc_final: 0.7759 (ttp-170) REVERT: O 53 ASP cc_start: 0.8356 (t0) cc_final: 0.8070 (t0) REVERT: O 54 ARG cc_start: 0.7841 (mmp80) cc_final: 0.7553 (mmp80) REVERT: O 82 GLU cc_start: 0.7885 (tt0) cc_final: 0.7642 (mt-10) REVERT: O 93 ASP cc_start: 0.7394 (p0) cc_final: 0.7159 (t70) REVERT: O 100 ARG cc_start: 0.8324 (ttp80) cc_final: 0.8046 (tmm160) REVERT: O 143 ARG cc_start: 0.7376 (pmt170) cc_final: 0.6970 (ptt-90) REVERT: O 212 GLU cc_start: 0.8251 (pt0) cc_final: 0.7958 (pt0) REVERT: O 280 MET cc_start: 0.8545 (mmt) cc_final: 0.8189 (mmt) REVERT: O 320 ILE cc_start: 0.9108 (tt) cc_final: 0.8862 (tt) REVERT: O 371 ARG cc_start: 0.7111 (mtp180) cc_final: 0.6825 (mtp180) REVERT: Q 53 ASP cc_start: 0.8365 (t0) cc_final: 0.8085 (t0) REVERT: Q 143 ARG cc_start: 0.7258 (pmt170) cc_final: 0.6780 (ptm-80) REVERT: Q 217 ASP cc_start: 0.7244 (m-30) cc_final: 0.6799 (m-30) REVERT: Q 371 ARG cc_start: 0.7298 (mtp180) cc_final: 0.6967 (mtp180) REVERT: S 6 ARG cc_start: 0.8159 (ttp-170) cc_final: 0.7957 (ttp-110) REVERT: S 143 ARG cc_start: 0.7108 (ptt-90) cc_final: 0.6251 (ttp-110) REVERT: S 371 ARG cc_start: 0.7094 (mtp180) cc_final: 0.6735 (mtp180) REVERT: U 143 ARG cc_start: 0.7406 (pmt170) cc_final: 0.6862 (ttp-110) REVERT: U 201 GLN cc_start: 0.8897 (OUTLIER) cc_final: 0.7397 (mt0) REVERT: U 225 GLU cc_start: 0.8144 (tt0) cc_final: 0.7914 (tt0) REVERT: U 371 ARG cc_start: 0.6995 (mtp180) cc_final: 0.6652 (mtp180) REVERT: W 31 ILE cc_start: 0.8959 (tp) cc_final: 0.8758 (tp) REVERT: W 111 GLN cc_start: 0.8197 (tp-100) cc_final: 0.7673 (tp40) REVERT: W 143 ARG cc_start: 0.7364 (pmt170) cc_final: 0.6638 (ptm-80) REVERT: W 225 GLU cc_start: 0.7991 (tt0) cc_final: 0.7703 (tt0) REVERT: W 371 ARG cc_start: 0.7130 (mtp180) cc_final: 0.6752 (mtp180) REVERT: Y 6 ARG cc_start: 0.8189 (ptp90) cc_final: 0.7711 (mtm110) REVERT: Y 123 MET cc_start: 0.5873 (mtm) cc_final: 0.5478 (mtp) REVERT: Y 225 GLU cc_start: 0.8004 (tt0) cc_final: 0.7607 (tt0) REVERT: Y 301 ASN cc_start: 0.8045 (m-40) cc_final: 0.7657 (m-40) REVERT: Y 371 ARG cc_start: 0.7275 (mtp180) cc_final: 0.6790 (mtp180) REVERT: 0 53 ASP cc_start: 0.8691 (t0) cc_final: 0.8399 (t0) REVERT: 0 123 MET cc_start: 0.6816 (OUTLIER) cc_final: 0.6444 (mtp) REVERT: 0 201 GLN cc_start: 0.9022 (OUTLIER) cc_final: 0.7422 (mp10) REVERT: 0 217 ASP cc_start: 0.7087 (m-30) cc_final: 0.6823 (m-30) REVERT: 0 225 GLU cc_start: 0.7950 (OUTLIER) cc_final: 0.7712 (tt0) REVERT: 0 371 ARG cc_start: 0.7198 (mtp180) cc_final: 0.6700 (mtp180) REVERT: 2 10 LEU cc_start: 0.8936 (mt) cc_final: 0.8711 (mm) REVERT: 2 31 ILE cc_start: 0.8897 (tp) cc_final: 0.8680 (tp) REVERT: 2 53 ASP cc_start: 0.8738 (t0) cc_final: 0.8345 (t0) REVERT: 2 100 ARG cc_start: 0.7890 (tmm160) cc_final: 0.7676 (tmm160) REVERT: 2 102 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8315 (pp) REVERT: 2 274 LYS cc_start: 0.8601 (tttp) cc_final: 0.8388 (ttmt) REVERT: 2 317 GLU cc_start: 0.5398 (tm-30) cc_final: 0.4563 (tm-30) REVERT: 2 371 ARG cc_start: 0.7178 (mtp180) cc_final: 0.6830 (mtp180) outliers start: 113 outliers final: 58 residues processed: 919 average time/residue: 0.6321 time to fit residues: 912.9256 Evaluate side-chains 833 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 763 time to evaluate : 5.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 225 GLU Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 246 ASN Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 213 ARG Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain I residue 14 ASN Chi-restraints excluded: chain I residue 158 GLN Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain I residue 225 GLU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain K residue 57 ARG Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 201 GLN Chi-restraints excluded: chain K residue 225 GLU Chi-restraints excluded: chain M residue 86 GLN Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 225 GLU Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain Q residue 86 GLN Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain Q residue 367 GLU Chi-restraints excluded: chain S residue 150 LYS Chi-restraints excluded: chain S residue 164 ASN Chi-restraints excluded: chain S residue 186 ASP Chi-restraints excluded: chain S residue 304 GLN Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain U residue 186 ASP Chi-restraints excluded: chain U residue 201 GLN Chi-restraints excluded: chain U residue 341 VAL Chi-restraints excluded: chain W residue 86 GLN Chi-restraints excluded: chain Y residue 86 GLN Chi-restraints excluded: chain Y residue 91 ILE Chi-restraints excluded: chain Y residue 129 GLN Chi-restraints excluded: chain Y residue 227 LEU Chi-restraints excluded: chain 0 residue 3 THR Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 0 residue 86 GLN Chi-restraints excluded: chain 0 residue 123 MET Chi-restraints excluded: chain 0 residue 186 ASP Chi-restraints excluded: chain 0 residue 201 GLN Chi-restraints excluded: chain 0 residue 225 GLU Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 150 LYS Chi-restraints excluded: chain 2 residue 186 ASP Chi-restraints excluded: chain 2 residue 227 LEU Chi-restraints excluded: chain 2 residue 228 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 434 optimal weight: 9.9990 chunk 296 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 388 optimal weight: 3.9990 chunk 215 optimal weight: 3.9990 chunk 445 optimal weight: 6.9990 chunk 360 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 266 optimal weight: 1.9990 chunk 468 optimal weight: 10.0000 chunk 131 optimal weight: 7.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 33 HIS ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 14 ASN A 33 HIS D 33 HIS G 33 HIS K 33 HIS K 322 ASN M 33 HIS O 33 HIS Q 33 HIS Q 246 ASN S 33 HIS U 14 ASN U 33 HIS U 304 GLN U 322 ASN W 33 HIS Y 33 HIS ** Y 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 33 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.2961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 45690 Z= 0.295 Angle : 0.574 8.053 62145 Z= 0.292 Chirality : 0.045 0.176 7110 Planarity : 0.004 0.034 7650 Dihedral : 10.153 73.582 7170 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.26 % Favored : 95.61 % Rotamer: Outliers : 3.05 % Allowed : 10.80 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.12), residues: 5355 helix: 0.07 (0.10), residues: 3195 sheet: -1.56 (0.26), residues: 390 loop : -1.36 (0.15), residues: 1770 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP U 333 HIS 0.005 0.001 HIS S 33 PHE 0.017 0.002 PHE 0 209 TYR 0.015 0.001 TYR 0 361 ARG 0.007 0.000 ARG G 143 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 978 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 836 time to evaluate : 5.138 Fit side-chains revert: symmetry clash REVERT: C 29 ARG cc_start: 0.8539 (ptp-110) cc_final: 0.8252 (ptp-110) REVERT: C 53 ASP cc_start: 0.8501 (t0) cc_final: 0.8196 (t0) REVERT: C 143 ARG cc_start: 0.7311 (pmt170) cc_final: 0.6799 (ptt-90) REVERT: C 201 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.7529 (mt0) REVERT: A 100 ARG cc_start: 0.8227 (ttp80) cc_final: 0.7997 (tmm160) REVERT: A 212 GLU cc_start: 0.8507 (pt0) cc_final: 0.8129 (pt0) REVERT: A 280 MET cc_start: 0.8404 (mmt) cc_final: 0.8040 (mmt) REVERT: A 297 GLU cc_start: 0.6815 (tt0) cc_final: 0.6586 (tt0) REVERT: A 371 ARG cc_start: 0.7341 (mtp180) cc_final: 0.6869 (mtp180) REVERT: D 53 ASP cc_start: 0.8455 (t0) cc_final: 0.8088 (t0) REVERT: D 143 ARG cc_start: 0.7440 (pmt170) cc_final: 0.7019 (ptt-90) REVERT: D 150 LYS cc_start: 0.8619 (ptpp) cc_final: 0.8141 (mtpt) REVERT: D 320 ILE cc_start: 0.9191 (tt) cc_final: 0.8916 (tt) REVERT: D 367 GLU cc_start: 0.7593 (tt0) cc_final: 0.7388 (tt0) REVERT: G 53 ASP cc_start: 0.8541 (t0) cc_final: 0.8262 (t0) REVERT: G 201 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8043 (mp10) REVERT: I 53 ASP cc_start: 0.8246 (t0) cc_final: 0.7899 (t0) REVERT: I 57 ARG cc_start: 0.8216 (ptp-110) cc_final: 0.7893 (ttp-170) REVERT: I 143 ARG cc_start: 0.7559 (pmt170) cc_final: 0.7254 (ptt-90) REVERT: I 159 ASP cc_start: 0.8086 (p0) cc_final: 0.7753 (p0) REVERT: I 201 GLN cc_start: 0.8823 (OUTLIER) cc_final: 0.7474 (mt0) REVERT: I 227 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8568 (tp) REVERT: I 271 LEU cc_start: 0.8605 (mt) cc_final: 0.8285 (mt) REVERT: I 322 ASN cc_start: 0.8215 (m-40) cc_final: 0.7987 (m110) REVERT: I 371 ARG cc_start: 0.7322 (mtp180) cc_final: 0.7042 (mtp180) REVERT: K 53 ASP cc_start: 0.8360 (t0) cc_final: 0.8098 (t0) REVERT: K 102 LEU cc_start: 0.8671 (OUTLIER) cc_final: 0.8351 (pp) REVERT: K 159 ASP cc_start: 0.8151 (p0) cc_final: 0.7787 (p0) REVERT: K 201 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.7424 (mt0) REVERT: K 306 MET cc_start: 0.8687 (mtm) cc_final: 0.8351 (mtm) REVERT: M 102 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8425 (pp) REVERT: M 143 ARG cc_start: 0.7545 (pmt170) cc_final: 0.7113 (ptt-90) REVERT: M 212 GLU cc_start: 0.8316 (pt0) cc_final: 0.8104 (pt0) REVERT: M 371 ARG cc_start: 0.7102 (mtp180) cc_final: 0.6743 (mtp180) REVERT: O 6 ARG cc_start: 0.8064 (ptp90) cc_final: 0.7758 (ttp-110) REVERT: O 53 ASP cc_start: 0.8349 (t0) cc_final: 0.8076 (t0) REVERT: O 54 ARG cc_start: 0.7883 (mmp80) cc_final: 0.7628 (mmp80) REVERT: O 82 GLU cc_start: 0.7935 (tt0) cc_final: 0.7683 (mt-10) REVERT: O 93 ASP cc_start: 0.7398 (p0) cc_final: 0.7176 (t70) REVERT: O 100 ARG cc_start: 0.8423 (ttp80) cc_final: 0.8121 (tmm160) REVERT: O 143 ARG cc_start: 0.7332 (pmt170) cc_final: 0.6919 (ptt-90) REVERT: O 212 GLU cc_start: 0.8260 (pt0) cc_final: 0.7981 (pt0) REVERT: O 371 ARG cc_start: 0.7205 (mtp180) cc_final: 0.6922 (mtp180) REVERT: Q 53 ASP cc_start: 0.8401 (t0) cc_final: 0.8006 (t0) REVERT: Q 143 ARG cc_start: 0.7257 (pmt170) cc_final: 0.6761 (ptm-80) REVERT: Q 217 ASP cc_start: 0.7259 (m-30) cc_final: 0.6837 (m-30) REVERT: S 6 ARG cc_start: 0.8204 (ttp-170) cc_final: 0.7992 (ttp-110) REVERT: S 150 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8017 (mttm) REVERT: S 256 ASP cc_start: 0.8574 (t70) cc_final: 0.7892 (t0) REVERT: S 371 ARG cc_start: 0.7106 (mtp180) cc_final: 0.6773 (mtp180) REVERT: U 143 ARG cc_start: 0.7434 (pmt170) cc_final: 0.6862 (ttp-110) REVERT: U 201 GLN cc_start: 0.8886 (OUTLIER) cc_final: 0.7444 (mt0) REVERT: U 371 ARG cc_start: 0.7070 (mtp180) cc_final: 0.6703 (mtp180) REVERT: W 111 GLN cc_start: 0.8212 (tp-100) cc_final: 0.7683 (tp40) REVERT: W 143 ARG cc_start: 0.7427 (pmt170) cc_final: 0.6654 (ptm-80) REVERT: W 225 GLU cc_start: 0.8010 (tt0) cc_final: 0.7768 (tt0) REVERT: W 371 ARG cc_start: 0.7154 (mtp180) cc_final: 0.6775 (mtp180) REVERT: Y 6 ARG cc_start: 0.8202 (ptp90) cc_final: 0.7730 (mtm110) REVERT: Y 123 MET cc_start: 0.5836 (mtm) cc_final: 0.5414 (mtp) REVERT: Y 225 GLU cc_start: 0.8060 (tt0) cc_final: 0.7749 (tt0) REVERT: Y 371 ARG cc_start: 0.7317 (mtp180) cc_final: 0.6793 (mtp180) REVERT: 0 201 GLN cc_start: 0.9038 (OUTLIER) cc_final: 0.7565 (mp10) REVERT: 0 225 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7753 (tt0) REVERT: 0 292 GLU cc_start: 0.7810 (OUTLIER) cc_final: 0.7582 (tt0) REVERT: 0 371 ARG cc_start: 0.7182 (mtp180) cc_final: 0.6761 (mtp180) REVERT: 2 31 ILE cc_start: 0.8934 (tp) cc_final: 0.8704 (tp) REVERT: 2 102 LEU cc_start: 0.8620 (OUTLIER) cc_final: 0.8412 (pp) REVERT: 2 201 GLN cc_start: 0.8921 (OUTLIER) cc_final: 0.7928 (mt0) REVERT: 2 217 ASP cc_start: 0.7285 (m-30) cc_final: 0.7049 (m-30) REVERT: 2 274 LYS cc_start: 0.8635 (tttp) cc_final: 0.8409 (ttmt) REVERT: 2 317 GLU cc_start: 0.5566 (tm-30) cc_final: 0.4237 (tm-30) REVERT: 2 371 ARG cc_start: 0.7259 (mtp180) cc_final: 0.6796 (mtp180) outliers start: 142 outliers final: 91 residues processed: 936 average time/residue: 0.6240 time to fit residues: 923.4773 Evaluate side-chains 896 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 791 time to evaluate : 5.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 35 ILE Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 213 ARG Chi-restraints excluded: chain G residue 225 GLU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 355 SER Chi-restraints excluded: chain I residue 35 ILE Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 123 MET Chi-restraints excluded: chain I residue 158 GLN Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain I residue 213 ARG Chi-restraints excluded: chain I residue 225 GLU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 57 ARG Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 201 GLN Chi-restraints excluded: chain K residue 225 GLU Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 86 GLN Chi-restraints excluded: chain M residue 98 SER Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 108 ASP Chi-restraints excluded: chain M residue 225 GLU Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 355 SER Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain Q residue 35 ILE Chi-restraints excluded: chain Q residue 86 GLN Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 186 ASP Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 57 ARG Chi-restraints excluded: chain S residue 91 ILE Chi-restraints excluded: chain S residue 150 LYS Chi-restraints excluded: chain S residue 164 ASN Chi-restraints excluded: chain S residue 355 SER Chi-restraints excluded: chain U residue 98 SER Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 123 MET Chi-restraints excluded: chain U residue 164 ASN Chi-restraints excluded: chain U residue 186 ASP Chi-restraints excluded: chain U residue 187 THR Chi-restraints excluded: chain U residue 201 GLN Chi-restraints excluded: chain U residue 341 VAL Chi-restraints excluded: chain U residue 355 SER Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain W residue 86 GLN Chi-restraints excluded: chain W residue 150 LYS Chi-restraints excluded: chain W residue 187 THR Chi-restraints excluded: chain W residue 355 SER Chi-restraints excluded: chain Y residue 14 ASN Chi-restraints excluded: chain Y residue 86 GLN Chi-restraints excluded: chain Y residue 227 LEU Chi-restraints excluded: chain Y residue 355 SER Chi-restraints excluded: chain 0 residue 3 THR Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 0 residue 86 GLN Chi-restraints excluded: chain 0 residue 186 ASP Chi-restraints excluded: chain 0 residue 201 GLN Chi-restraints excluded: chain 0 residue 225 GLU Chi-restraints excluded: chain 0 residue 259 THR Chi-restraints excluded: chain 0 residue 292 GLU Chi-restraints excluded: chain 2 residue 35 ILE Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 150 LYS Chi-restraints excluded: chain 2 residue 186 ASP Chi-restraints excluded: chain 2 residue 201 GLN Chi-restraints excluded: chain 2 residue 227 LEU Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 355 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 175 optimal weight: 5.9990 chunk 470 optimal weight: 10.0000 chunk 103 optimal weight: 6.9990 chunk 306 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 522 optimal weight: 2.9990 chunk 433 optimal weight: 0.0670 chunk 241 optimal weight: 1.9990 chunk 43 optimal weight: 0.9980 chunk 172 optimal weight: 0.9990 chunk 274 optimal weight: 1.9990 overall best weight: 1.2124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS ** C 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 304 GLN G 33 HIS I 86 GLN K 304 GLN K 322 ASN M 33 HIS M 246 ASN O 33 HIS O 246 ASN O 304 GLN Q 33 HIS ** Q 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 33 HIS U 304 GLN U 322 ASN W 33 HIS ** Y 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 33 HIS ** 0 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 33 HIS 2 89 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 45690 Z= 0.169 Angle : 0.515 6.386 62145 Z= 0.264 Chirality : 0.042 0.159 7110 Planarity : 0.003 0.036 7650 Dihedral : 10.115 73.475 7170 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.45 % Favored : 96.43 % Rotamer: Outliers : 2.37 % Allowed : 12.09 % Favored : 85.55 % 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: -0.54 (0.12), residues: 5355 helix: 0.35 (0.10), residues: 3135 sheet: -1.54 (0.26), residues: 390 loop : -1.18 (0.15), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 333 HIS 0.005 0.001 HIS S 33 PHE 0.017 0.001 PHE 0 209 TYR 0.014 0.001 TYR C 303 ARG 0.008 0.000 ARG M 249 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 940 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 830 time to evaluate : 5.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 29 ARG cc_start: 0.8508 (ptp-110) cc_final: 0.8232 (ptp-110) REVERT: C 53 ASP cc_start: 0.8500 (t0) cc_final: 0.8144 (t0) REVERT: C 143 ARG cc_start: 0.7274 (pmt170) cc_final: 0.6777 (ptt-90) REVERT: C 150 LYS cc_start: 0.8637 (mtmm) cc_final: 0.7903 (mttp) REVERT: C 201 GLN cc_start: 0.8795 (OUTLIER) cc_final: 0.7340 (mt0) REVERT: A 100 ARG cc_start: 0.8175 (ttp80) cc_final: 0.7927 (tmm160) REVERT: A 159 ASP cc_start: 0.8252 (p0) cc_final: 0.7975 (p0) REVERT: A 212 GLU cc_start: 0.8425 (pt0) cc_final: 0.7930 (pt0) REVERT: A 280 MET cc_start: 0.8419 (mmt) cc_final: 0.8064 (mmt) REVERT: A 371 ARG cc_start: 0.7313 (mtp180) cc_final: 0.6913 (mtp180) REVERT: D 53 ASP cc_start: 0.8469 (t0) cc_final: 0.8113 (t0) REVERT: D 143 ARG cc_start: 0.7412 (pmt170) cc_final: 0.6991 (ptt-90) REVERT: D 150 LYS cc_start: 0.8573 (ptpp) cc_final: 0.8133 (mttt) REVERT: D 320 ILE cc_start: 0.9153 (tt) cc_final: 0.8909 (tt) REVERT: G 53 ASP cc_start: 0.8533 (t0) cc_final: 0.8301 (t0) REVERT: G 150 LYS cc_start: 0.8633 (ptpp) cc_final: 0.7865 (mttp) REVERT: G 201 GLN cc_start: 0.8680 (OUTLIER) cc_final: 0.7435 (mt0) REVERT: I 53 ASP cc_start: 0.8237 (t0) cc_final: 0.7918 (t0) REVERT: I 57 ARG cc_start: 0.8167 (ptp-110) cc_final: 0.7864 (ttp-170) REVERT: I 143 ARG cc_start: 0.7535 (pmt170) cc_final: 0.7230 (ptt-90) REVERT: I 159 ASP cc_start: 0.7986 (p0) cc_final: 0.7635 (p0) REVERT: I 201 GLN cc_start: 0.8792 (OUTLIER) cc_final: 0.7395 (mt0) REVERT: I 227 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8486 (tp) REVERT: I 271 LEU cc_start: 0.8549 (mt) cc_final: 0.8263 (mt) REVERT: K 5 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8494 (mm) REVERT: K 53 ASP cc_start: 0.8351 (t0) cc_final: 0.8079 (t0) REVERT: K 102 LEU cc_start: 0.8575 (OUTLIER) cc_final: 0.8231 (pp) REVERT: K 103 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7655 (mt-10) REVERT: K 159 ASP cc_start: 0.8108 (p0) cc_final: 0.7774 (p0) REVERT: K 201 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.7383 (mt0) REVERT: K 306 MET cc_start: 0.8444 (mtm) cc_final: 0.8193 (mtm) REVERT: K 313 MET cc_start: 0.8488 (ptp) cc_final: 0.8236 (ptp) REVERT: M 102 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8351 (pp) REVERT: M 143 ARG cc_start: 0.7496 (pmt170) cc_final: 0.7057 (ptt-90) REVERT: M 371 ARG cc_start: 0.7032 (mtp180) cc_final: 0.6610 (mtp180) REVERT: O 6 ARG cc_start: 0.8012 (ptp90) cc_final: 0.7759 (ttp-110) REVERT: O 53 ASP cc_start: 0.8282 (t0) cc_final: 0.8024 (t0) REVERT: O 82 GLU cc_start: 0.7929 (tt0) cc_final: 0.7688 (mt-10) REVERT: O 100 ARG cc_start: 0.8307 (ttp80) cc_final: 0.8019 (tmm160) REVERT: O 143 ARG cc_start: 0.7307 (pmt170) cc_final: 0.6884 (ptt-90) REVERT: O 212 GLU cc_start: 0.8159 (pt0) cc_final: 0.7860 (pt0) REVERT: O 280 MET cc_start: 0.8513 (mmt) cc_final: 0.8259 (mmm) REVERT: O 320 ILE cc_start: 0.9077 (tt) cc_final: 0.8828 (tt) REVERT: O 371 ARG cc_start: 0.7179 (mtp180) cc_final: 0.6926 (mtp180) REVERT: Q 53 ASP cc_start: 0.8385 (t0) cc_final: 0.8033 (t0) REVERT: Q 143 ARG cc_start: 0.7225 (pmt170) cc_final: 0.6706 (ptm-80) REVERT: Q 217 ASP cc_start: 0.7200 (m-30) cc_final: 0.6763 (m-30) REVERT: S 6 ARG cc_start: 0.8176 (ttp-170) cc_final: 0.7972 (ttp-110) REVERT: S 111 GLN cc_start: 0.8316 (tp40) cc_final: 0.7787 (tp40) REVERT: S 143 ARG cc_start: 0.7246 (ptt-90) cc_final: 0.6686 (ptm-80) REVERT: S 150 LYS cc_start: 0.8638 (OUTLIER) cc_final: 0.8053 (mttm) REVERT: S 161 GLU cc_start: 0.7489 (pt0) cc_final: 0.7236 (pt0) REVERT: S 371 ARG cc_start: 0.7083 (mtp180) cc_final: 0.6791 (mtp180) REVERT: U 143 ARG cc_start: 0.7374 (pmt170) cc_final: 0.6803 (ttp-110) REVERT: U 201 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.7419 (mt0) REVERT: U 209 PHE cc_start: 0.8374 (m-10) cc_final: 0.8131 (m-10) REVERT: U 371 ARG cc_start: 0.7024 (mtp180) cc_final: 0.6710 (mtp180) REVERT: W 111 GLN cc_start: 0.8226 (tp-100) cc_final: 0.7698 (tp40) REVERT: W 123 MET cc_start: 0.5781 (OUTLIER) cc_final: 0.5329 (mtm) REVERT: W 143 ARG cc_start: 0.7354 (pmt170) cc_final: 0.6629 (ptm-80) REVERT: W 371 ARG cc_start: 0.7055 (mtp180) cc_final: 0.6758 (mtp180) REVERT: Y 6 ARG cc_start: 0.8133 (ptp90) cc_final: 0.7682 (mtm110) REVERT: Y 123 MET cc_start: 0.5819 (mtm) cc_final: 0.5414 (mtp) REVERT: Y 201 GLN cc_start: 0.8875 (OUTLIER) cc_final: 0.7515 (mp10) REVERT: Y 225 GLU cc_start: 0.8021 (tt0) cc_final: 0.7760 (tt0) REVERT: Y 301 ASN cc_start: 0.7955 (m-40) cc_final: 0.7691 (m110) REVERT: Y 371 ARG cc_start: 0.7361 (mtp180) cc_final: 0.6923 (mtp180) REVERT: 0 123 MET cc_start: 0.6689 (mtp) cc_final: 0.6411 (mtp) REVERT: 0 201 GLN cc_start: 0.9008 (OUTLIER) cc_final: 0.7560 (mp10) REVERT: 0 371 ARG cc_start: 0.7252 (mtp180) cc_final: 0.6866 (mtp180) REVERT: 2 10 LEU cc_start: 0.8917 (mp) cc_final: 0.8647 (mm) REVERT: 2 31 ILE cc_start: 0.8928 (tp) cc_final: 0.8710 (tp) REVERT: 2 102 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8298 (pp) REVERT: 2 201 GLN cc_start: 0.8907 (OUTLIER) cc_final: 0.7925 (mt0) REVERT: 2 209 PHE cc_start: 0.7681 (m-10) cc_final: 0.7257 (m-80) REVERT: 2 274 LYS cc_start: 0.8633 (tttp) cc_final: 0.8409 (ttmt) REVERT: 2 317 GLU cc_start: 0.5409 (tm-30) cc_final: 0.3611 (tm-30) REVERT: 2 371 ARG cc_start: 0.7245 (mtp180) cc_final: 0.6983 (mtp180) outliers start: 110 outliers final: 63 residues processed: 902 average time/residue: 0.6180 time to fit residues: 874.2469 Evaluate side-chains 858 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 780 time to evaluate : 4.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 35 ILE Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 201 GLN Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain A residue 57 ARG Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 197 ILE Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain I residue 14 ASN Chi-restraints excluded: chain I residue 98 SER Chi-restraints excluded: chain I residue 158 GLN Chi-restraints excluded: chain I residue 201 GLN Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 57 ARG Chi-restraints excluded: chain K residue 98 SER Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 201 GLN Chi-restraints excluded: chain M residue 86 GLN Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 355 SER Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 98 SER Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain Q residue 86 GLN Chi-restraints excluded: chain Q residue 186 ASP Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain Q residue 367 GLU Chi-restraints excluded: chain S residue 91 ILE Chi-restraints excluded: chain S residue 129 GLN Chi-restraints excluded: chain S residue 150 LYS Chi-restraints excluded: chain S residue 164 ASN Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 123 MET Chi-restraints excluded: chain U residue 164 ASN Chi-restraints excluded: chain U residue 186 ASP Chi-restraints excluded: chain U residue 201 GLN Chi-restraints excluded: chain U residue 228 SER Chi-restraints excluded: chain U residue 341 VAL Chi-restraints excluded: chain W residue 86 GLN Chi-restraints excluded: chain W residue 123 MET Chi-restraints excluded: chain W residue 320 ILE Chi-restraints excluded: chain Y residue 14 ASN Chi-restraints excluded: chain Y residue 86 GLN Chi-restraints excluded: chain Y residue 129 GLN Chi-restraints excluded: chain Y residue 201 GLN Chi-restraints excluded: chain Y residue 227 LEU Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 0 residue 14 ASN Chi-restraints excluded: chain 0 residue 55 LEU Chi-restraints excluded: chain 0 residue 86 GLN Chi-restraints excluded: chain 0 residue 186 ASP Chi-restraints excluded: chain 0 residue 201 GLN Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 150 LYS Chi-restraints excluded: chain 2 residue 186 ASP Chi-restraints excluded: chain 2 residue 201 GLN Chi-restraints excluded: chain 2 residue 227 LEU Chi-restraints excluded: chain 2 residue 228 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 503 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 297 optimal weight: 0.7980 chunk 381 optimal weight: 10.0000 chunk 295 optimal weight: 0.0040 chunk 439 optimal weight: 5.9990 chunk 291 optimal weight: 0.0970 chunk 520 optimal weight: 4.9990 chunk 325 optimal weight: 2.9990 chunk 317 optimal weight: 3.9990 chunk 240 optimal weight: 0.8980 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS C 246 ASN C 304 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 HIS I 14 ASN K 164 ASN K 304 GLN M 14 ASN M 33 HIS O 33 HIS Q 33 HIS ** Q 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 322 ASN ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 304 GLN U 322 ASN W 33 HIS Y 33 HIS Y 246 ASN Y 304 GLN 0 33 HIS 2 33 HIS 2 89 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 45690 Z= 0.135 Angle : 0.499 8.349 62145 Z= 0.256 Chirality : 0.041 0.126 7110 Planarity : 0.003 0.037 7650 Dihedral : 10.056 73.385 7170 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.12 % Favored : 96.79 % Rotamer: Outliers : 2.26 % Allowed : 12.97 % Favored : 84.77 % 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: -0.31 (0.12), residues: 5355 helix: 0.49 (0.10), residues: 3150 sheet: -1.39 (0.26), residues: 390 loop : -1.02 (0.15), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 215 HIS 0.007 0.001 HIS U 33 PHE 0.017 0.001 PHE 0 209 TYR 0.017 0.001 TYR K 281 ARG 0.009 0.000 ARG A 249 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 987 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 882 time to evaluate : 4.857 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 53 ASP cc_start: 0.8448 (t0) cc_final: 0.8100 (t0) REVERT: C 143 ARG cc_start: 0.7235 (pmt170) cc_final: 0.6748 (ptt-90) REVERT: C 150 LYS cc_start: 0.8653 (mtmm) cc_final: 0.7978 (mttp) REVERT: A 100 ARG cc_start: 0.8110 (ttp80) cc_final: 0.7774 (tmm160) REVERT: A 150 LYS cc_start: 0.8509 (mtmm) cc_final: 0.8211 (mttt) REVERT: A 159 ASP cc_start: 0.8147 (p0) cc_final: 0.7864 (p0) REVERT: A 201 GLN cc_start: 0.8733 (OUTLIER) cc_final: 0.7334 (mp10) REVERT: A 212 GLU cc_start: 0.8442 (pt0) cc_final: 0.7796 (pt0) REVERT: A 256 ASP cc_start: 0.8280 (t70) cc_final: 0.7830 (t70) REVERT: A 280 MET cc_start: 0.8445 (mmt) cc_final: 0.8110 (mmt) REVERT: A 371 ARG cc_start: 0.7273 (mtp180) cc_final: 0.6898 (mtp180) REVERT: D 53 ASP cc_start: 0.8501 (t0) cc_final: 0.8117 (t0) REVERT: D 143 ARG cc_start: 0.7418 (pmt170) cc_final: 0.7004 (ptt-90) REVERT: D 150 LYS cc_start: 0.8537 (ptpp) cc_final: 0.8236 (mtpt) REVERT: D 212 GLU cc_start: 0.8270 (pt0) cc_final: 0.8013 (pt0) REVERT: D 320 ILE cc_start: 0.9136 (tt) cc_final: 0.8897 (tt) REVERT: G 53 ASP cc_start: 0.8477 (t0) cc_final: 0.8184 (t0) REVERT: G 150 LYS cc_start: 0.8597 (ptpp) cc_final: 0.7928 (mttp) REVERT: G 201 GLN cc_start: 0.8681 (OUTLIER) cc_final: 0.7451 (mt0) REVERT: I 53 ASP cc_start: 0.8244 (t0) cc_final: 0.7962 (t0) REVERT: I 57 ARG cc_start: 0.8098 (ptp-110) cc_final: 0.7854 (ttp-170) REVERT: I 103 GLU cc_start: 0.7764 (mp0) cc_final: 0.7432 (mp0) REVERT: I 143 ARG cc_start: 0.7546 (pmt170) cc_final: 0.7241 (ptt-90) REVERT: I 150 LYS cc_start: 0.8692 (mtmm) cc_final: 0.8322 (mttt) REVERT: I 158 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7523 (mm-40) REVERT: I 159 ASP cc_start: 0.7905 (p0) cc_final: 0.7560 (p0) REVERT: I 227 LEU cc_start: 0.8723 (OUTLIER) cc_final: 0.8410 (tp) REVERT: I 271 LEU cc_start: 0.8507 (mt) cc_final: 0.8258 (mt) REVERT: K 5 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8453 (mm) REVERT: K 57 ARG cc_start: 0.8423 (OUTLIER) cc_final: 0.7860 (ttp-170) REVERT: K 102 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8078 (pp) REVERT: K 150 LYS cc_start: 0.8745 (mtmm) cc_final: 0.8353 (mtpt) REVERT: K 159 ASP cc_start: 0.8022 (p0) cc_final: 0.7681 (p0) REVERT: K 201 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.7268 (mt0) REVERT: M 102 LEU cc_start: 0.8452 (OUTLIER) cc_final: 0.8225 (pp) REVERT: M 103 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7661 (mt-10) REVERT: M 143 ARG cc_start: 0.7488 (pmt170) cc_final: 0.7070 (ptt-90) REVERT: M 371 ARG cc_start: 0.7130 (mtp180) cc_final: 0.6715 (mtp180) REVERT: O 6 ARG cc_start: 0.7988 (ptp90) cc_final: 0.7783 (ttp-110) REVERT: O 53 ASP cc_start: 0.8239 (t0) cc_final: 0.8009 (t0) REVERT: O 54 ARG cc_start: 0.7763 (mmp80) cc_final: 0.7398 (mmp80) REVERT: O 82 GLU cc_start: 0.7901 (tt0) cc_final: 0.7668 (mt-10) REVERT: O 100 ARG cc_start: 0.8224 (ttp80) cc_final: 0.7937 (tmm160) REVERT: O 143 ARG cc_start: 0.7276 (pmt170) cc_final: 0.6865 (ptt-90) REVERT: O 150 LYS cc_start: 0.8623 (mtmm) cc_final: 0.8071 (mmmt) REVERT: O 212 GLU cc_start: 0.8059 (pt0) cc_final: 0.7652 (pt0) REVERT: O 280 MET cc_start: 0.8538 (mmt) cc_final: 0.8123 (mmt) REVERT: O 320 ILE cc_start: 0.9106 (tt) cc_final: 0.8878 (tt) REVERT: O 371 ARG cc_start: 0.7123 (mtp180) cc_final: 0.6876 (mtp180) REVERT: Q 53 ASP cc_start: 0.8393 (t0) cc_final: 0.8104 (t0) REVERT: Q 143 ARG cc_start: 0.7213 (pmt170) cc_final: 0.6701 (ptm-80) REVERT: S 143 ARG cc_start: 0.7181 (ptt-90) cc_final: 0.6618 (ptm-80) REVERT: S 150 LYS cc_start: 0.8629 (OUTLIER) cc_final: 0.8294 (mtpt) REVERT: S 161 GLU cc_start: 0.7473 (pt0) cc_final: 0.7231 (pt0) REVERT: S 256 ASP cc_start: 0.8438 (t70) cc_final: 0.8214 (t0) REVERT: S 371 ARG cc_start: 0.7092 (mtp180) cc_final: 0.6869 (mtp180) REVERT: U 31 ILE cc_start: 0.8904 (tp) cc_final: 0.8697 (tp) REVERT: U 143 ARG cc_start: 0.7303 (pmt170) cc_final: 0.6736 (ttp-110) REVERT: U 201 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.7410 (mt0) REVERT: U 371 ARG cc_start: 0.7051 (mtp180) cc_final: 0.6787 (mtp180) REVERT: W 111 GLN cc_start: 0.8186 (tp-100) cc_final: 0.7686 (tp40) REVERT: W 143 ARG cc_start: 0.7315 (pmt170) cc_final: 0.6538 (ptm-80) REVERT: W 371 ARG cc_start: 0.7056 (mtp180) cc_final: 0.6672 (mtp180) REVERT: Y 6 ARG cc_start: 0.8092 (ptp90) cc_final: 0.7698 (mtm110) REVERT: Y 15 LYS cc_start: 0.8645 (ptmm) cc_final: 0.8395 (ptmm) REVERT: Y 123 MET cc_start: 0.5877 (mtm) cc_final: 0.5479 (mtp) REVERT: Y 150 LYS cc_start: 0.8387 (ptpp) cc_final: 0.8068 (mtpt) REVERT: Y 201 GLN cc_start: 0.8879 (OUTLIER) cc_final: 0.8571 (mp10) REVERT: Y 301 ASN cc_start: 0.7890 (m-40) cc_final: 0.7661 (m110) REVERT: Y 371 ARG cc_start: 0.7327 (mtp180) cc_final: 0.6961 (mtp180) REVERT: 0 53 ASP cc_start: 0.8718 (t0) cc_final: 0.8460 (t0) REVERT: 0 123 MET cc_start: 0.6708 (mtp) cc_final: 0.6454 (mtp) REVERT: 0 201 GLN cc_start: 0.8999 (OUTLIER) cc_final: 0.7505 (mp10) REVERT: 0 371 ARG cc_start: 0.7278 (mtp180) cc_final: 0.6938 (mtp180) REVERT: 2 102 LEU cc_start: 0.8445 (OUTLIER) cc_final: 0.8198 (pp) REVERT: 2 201 GLN cc_start: 0.8895 (OUTLIER) cc_final: 0.7925 (mt0) REVERT: 2 256 ASP cc_start: 0.8611 (t70) cc_final: 0.7995 (t0) REVERT: 2 274 LYS cc_start: 0.8602 (tttp) cc_final: 0.8401 (ttmt) REVERT: 2 317 GLU cc_start: 0.5398 (tm-30) cc_final: 0.3539 (tm-30) REVERT: 2 371 ARG cc_start: 0.7289 (mtp180) cc_final: 0.7018 (mtp180) outliers start: 105 outliers final: 57 residues processed: 952 average time/residue: 0.6199 time to fit residues: 930.8394 Evaluate side-chains 864 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 792 time to evaluate : 5.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 367 GLU Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 367 GLU Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 213 ARG Chi-restraints excluded: chain G residue 225 GLU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 328 SER Chi-restraints excluded: chain I residue 14 ASN Chi-restraints excluded: chain I residue 158 GLN Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 304 GLN Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 57 ARG Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 201 GLN Chi-restraints excluded: chain M residue 86 GLN Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 332 LEU Chi-restraints excluded: chain M residue 355 SER Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain Q residue 86 GLN Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain Q residue 367 GLU Chi-restraints excluded: chain S residue 150 LYS Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 123 MET Chi-restraints excluded: chain U residue 150 LYS Chi-restraints excluded: chain U residue 164 ASN Chi-restraints excluded: chain U residue 186 ASP Chi-restraints excluded: chain U residue 187 THR Chi-restraints excluded: chain U residue 201 GLN Chi-restraints excluded: chain U residue 237 ILE Chi-restraints excluded: chain U residue 341 VAL Chi-restraints excluded: chain U residue 355 SER Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain W residue 86 GLN Chi-restraints excluded: chain W residue 355 SER Chi-restraints excluded: chain Y residue 14 ASN Chi-restraints excluded: chain Y residue 86 GLN Chi-restraints excluded: chain Y residue 91 ILE Chi-restraints excluded: chain Y residue 201 GLN Chi-restraints excluded: chain Y residue 227 LEU Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 0 residue 14 ASN Chi-restraints excluded: chain 0 residue 86 GLN Chi-restraints excluded: chain 0 residue 201 GLN Chi-restraints excluded: chain 0 residue 259 THR Chi-restraints excluded: chain 2 residue 102 LEU Chi-restraints excluded: chain 2 residue 150 LYS Chi-restraints excluded: chain 2 residue 186 ASP Chi-restraints excluded: chain 2 residue 201 GLN Chi-restraints excluded: chain 2 residue 227 LEU Chi-restraints excluded: chain 2 residue 228 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 321 optimal weight: 6.9990 chunk 207 optimal weight: 8.9990 chunk 310 optimal weight: 5.9990 chunk 156 optimal weight: 10.0000 chunk 102 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 330 optimal weight: 0.0980 chunk 354 optimal weight: 0.9980 chunk 257 optimal weight: 7.9990 chunk 48 optimal weight: 7.9990 chunk 409 optimal weight: 7.9990 overall best weight: 3.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS C 304 GLN A 33 HIS A 164 ASN D 33 HIS ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN G 33 HIS ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 33 HIS ** K 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 HIS M 246 ASN O 33 HIS O 164 ASN Q 33 HIS ** Q 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 322 ASN ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 304 GLN ** U 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 33 HIS Y 33 HIS 0 33 HIS ** 0 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 33 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.3369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 45690 Z= 0.329 Angle : 0.588 10.637 62145 Z= 0.298 Chirality : 0.045 0.134 7110 Planarity : 0.004 0.047 7650 Dihedral : 10.178 73.624 7170 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.26 % Favored : 95.67 % Rotamer: Outliers : 2.62 % Allowed : 13.68 % Favored : 83.70 % 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: -0.41 (0.12), residues: 5355 helix: 0.39 (0.10), residues: 3150 sheet: -1.41 (0.26), residues: 390 loop : -1.03 (0.15), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP M 196 HIS 0.007 0.001 HIS U 33 PHE 0.021 0.002 PHE Y 209 TYR 0.028 0.002 TYR Q 303 ARG 0.023 0.001 ARG I 13 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 962 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 840 time to evaluate : 5.014 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 6 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7574 (ttm110) REVERT: C 29 ARG cc_start: 0.8564 (ptp-110) cc_final: 0.8310 (ptp-110) REVERT: C 103 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7902 (mt-10) REVERT: C 143 ARG cc_start: 0.7224 (pmt170) cc_final: 0.6698 (ptt-90) REVERT: A 100 ARG cc_start: 0.8235 (ttp80) cc_final: 0.7995 (tmm160) REVERT: A 150 LYS cc_start: 0.8513 (mtmm) cc_final: 0.8167 (mttt) REVERT: A 159 ASP cc_start: 0.8275 (p0) cc_final: 0.8000 (p0) REVERT: A 201 GLN cc_start: 0.8729 (OUTLIER) cc_final: 0.7275 (mp10) REVERT: A 212 GLU cc_start: 0.8497 (pt0) cc_final: 0.7688 (pt0) REVERT: A 256 ASP cc_start: 0.8350 (t70) cc_final: 0.7906 (t70) REVERT: A 371 ARG cc_start: 0.7295 (mtp180) cc_final: 0.6849 (mtp180) REVERT: D 53 ASP cc_start: 0.8519 (t0) cc_final: 0.8088 (t0) REVERT: D 143 ARG cc_start: 0.7470 (pmt170) cc_final: 0.7039 (ptt-90) REVERT: D 150 LYS cc_start: 0.8544 (ptpp) cc_final: 0.8224 (mtpt) REVERT: D 320 ILE cc_start: 0.9182 (OUTLIER) cc_final: 0.8940 (tt) REVERT: G 150 LYS cc_start: 0.8595 (ptpp) cc_final: 0.7882 (mttp) REVERT: G 201 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8165 (mp10) REVERT: I 143 ARG cc_start: 0.7529 (pmt170) cc_final: 0.7234 (ptt-90) REVERT: I 158 GLN cc_start: 0.8134 (OUTLIER) cc_final: 0.7448 (mm-40) REVERT: I 159 ASP cc_start: 0.7989 (p0) cc_final: 0.7626 (p0) REVERT: I 227 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8572 (tp) REVERT: I 271 LEU cc_start: 0.8599 (mt) cc_final: 0.8281 (mt) REVERT: K 102 LEU cc_start: 0.8663 (OUTLIER) cc_final: 0.8329 (pp) REVERT: K 150 LYS cc_start: 0.8808 (mtmm) cc_final: 0.8340 (mttt) REVERT: K 159 ASP cc_start: 0.8122 (p0) cc_final: 0.7764 (p0) REVERT: K 201 GLN cc_start: 0.8769 (OUTLIER) cc_final: 0.7328 (mt0) REVERT: K 280 MET cc_start: 0.8324 (mmm) cc_final: 0.8112 (mmt) REVERT: M 102 LEU cc_start: 0.8622 (OUTLIER) cc_final: 0.8418 (pp) REVERT: M 103 GLU cc_start: 0.8001 (mt-10) cc_final: 0.7755 (mt-10) REVERT: M 143 ARG cc_start: 0.7541 (pmt170) cc_final: 0.7102 (ptt-90) REVERT: M 371 ARG cc_start: 0.7158 (mtp180) cc_final: 0.6865 (mtp180) REVERT: O 6 ARG cc_start: 0.8040 (ptp90) cc_final: 0.7827 (ttp-110) REVERT: O 53 ASP cc_start: 0.8331 (t0) cc_final: 0.8043 (t0) REVERT: O 54 ARG cc_start: 0.7998 (mmp80) cc_final: 0.7624 (mmp80) REVERT: O 82 GLU cc_start: 0.7934 (tt0) cc_final: 0.7705 (mt-10) REVERT: O 100 ARG cc_start: 0.8344 (ttp80) cc_final: 0.8055 (tmm160) REVERT: O 143 ARG cc_start: 0.7279 (pmt170) cc_final: 0.6856 (ptt-90) REVERT: O 144 PHE cc_start: 0.7930 (m-10) cc_final: 0.7661 (m-10) REVERT: O 201 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.7179 (mp10) REVERT: O 212 GLU cc_start: 0.8115 (pt0) cc_final: 0.7756 (pt0) REVERT: O 320 ILE cc_start: 0.9138 (tt) cc_final: 0.8856 (tt) REVERT: O 371 ARG cc_start: 0.7199 (mtp180) cc_final: 0.6700 (mtp180) REVERT: Q 53 ASP cc_start: 0.8452 (t0) cc_final: 0.8051 (t0) REVERT: Q 143 ARG cc_start: 0.7299 (pmt170) cc_final: 0.6652 (ttp-110) REVERT: Q 201 GLN cc_start: 0.8774 (OUTLIER) cc_final: 0.6948 (mp10) REVERT: Q 217 ASP cc_start: 0.7213 (m-30) cc_final: 0.6777 (m-30) REVERT: S 150 LYS cc_start: 0.8609 (OUTLIER) cc_final: 0.8188 (mttt) REVERT: S 161 GLU cc_start: 0.7536 (pt0) cc_final: 0.7265 (pt0) REVERT: S 228 SER cc_start: 0.8792 (p) cc_final: 0.8527 (m) REVERT: S 371 ARG cc_start: 0.7211 (mtp180) cc_final: 0.6927 (mtp180) REVERT: U 143 ARG cc_start: 0.7358 (pmt170) cc_final: 0.6766 (ttp-110) REVERT: U 201 GLN cc_start: 0.8864 (OUTLIER) cc_final: 0.7439 (mt0) REVERT: U 371 ARG cc_start: 0.7102 (mtp180) cc_final: 0.6797 (mtp180) REVERT: W 111 GLN cc_start: 0.8206 (tp-100) cc_final: 0.7699 (tp40) REVERT: W 143 ARG cc_start: 0.7403 (pmt170) cc_final: 0.6656 (ptm-80) REVERT: W 371 ARG cc_start: 0.7156 (mtp180) cc_final: 0.6733 (mtp180) REVERT: Y 6 ARG cc_start: 0.8124 (ptp90) cc_final: 0.7754 (mtm110) REVERT: Y 150 LYS cc_start: 0.8355 (ptpp) cc_final: 0.7998 (mtpt) REVERT: Y 201 GLN cc_start: 0.8909 (OUTLIER) cc_final: 0.7410 (mp10) REVERT: Y 301 ASN cc_start: 0.8001 (m-40) cc_final: 0.7679 (m110) REVERT: Y 371 ARG cc_start: 0.7282 (mtp180) cc_final: 0.6877 (mtp180) REVERT: 0 29 ARG cc_start: 0.8710 (ptp-170) cc_final: 0.8464 (ptp90) REVERT: 0 123 MET cc_start: 0.6710 (mtp) cc_final: 0.6480 (mtp) REVERT: 0 201 GLN cc_start: 0.9005 (OUTLIER) cc_final: 0.7677 (mp10) REVERT: 0 371 ARG cc_start: 0.7293 (mtp180) cc_final: 0.6935 (mtp180) REVERT: 2 201 GLN cc_start: 0.8900 (OUTLIER) cc_final: 0.8023 (mt0) REVERT: 2 274 LYS cc_start: 0.8660 (tttp) cc_final: 0.8449 (ttmt) REVERT: 2 317 GLU cc_start: 0.5543 (tm-30) cc_final: 0.4039 (tm-30) REVERT: 2 371 ARG cc_start: 0.7352 (mtp180) cc_final: 0.6951 (mtp180) outliers start: 122 outliers final: 81 residues processed: 931 average time/residue: 0.6081 time to fit residues: 895.8604 Evaluate side-chains 878 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 781 time to evaluate : 4.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain C residue 186 ASP Chi-restraints excluded: chain C residue 355 SER Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 108 ASP Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 355 SER Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain D residue 5 LEU Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 108 ASP Chi-restraints excluded: chain D residue 186 ASP Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain D residue 320 ILE Chi-restraints excluded: chain G residue 186 ASP Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 213 ARG Chi-restraints excluded: chain G residue 225 GLU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain G residue 355 SER Chi-restraints excluded: chain I residue 158 GLN Chi-restraints excluded: chain I residue 225 GLU Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 304 GLN Chi-restraints excluded: chain I residue 355 SER Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 57 ARG Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 201 GLN Chi-restraints excluded: chain M residue 35 ILE Chi-restraints excluded: chain M residue 86 GLN Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 228 SER Chi-restraints excluded: chain M residue 355 SER Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 108 ASP Chi-restraints excluded: chain O residue 186 ASP Chi-restraints excluded: chain O residue 201 GLN Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain Q residue 35 ILE Chi-restraints excluded: chain Q residue 86 GLN Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 186 ASP Chi-restraints excluded: chain Q residue 201 GLN Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain Q residue 355 SER Chi-restraints excluded: chain S residue 91 ILE Chi-restraints excluded: chain S residue 150 LYS Chi-restraints excluded: chain S residue 164 ASN Chi-restraints excluded: chain S residue 225 GLU Chi-restraints excluded: chain S residue 256 ASP Chi-restraints excluded: chain S residue 355 SER Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 35 ILE Chi-restraints excluded: chain U residue 96 ASP Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 164 ASN Chi-restraints excluded: chain U residue 186 ASP Chi-restraints excluded: chain U residue 187 THR Chi-restraints excluded: chain U residue 201 GLN Chi-restraints excluded: chain U residue 228 SER Chi-restraints excluded: chain U residue 355 SER Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain W residue 86 GLN Chi-restraints excluded: chain W residue 123 MET Chi-restraints excluded: chain W residue 164 ASN Chi-restraints excluded: chain W residue 186 ASP Chi-restraints excluded: chain W residue 213 ARG Chi-restraints excluded: chain W residue 355 SER Chi-restraints excluded: chain Y residue 14 ASN Chi-restraints excluded: chain Y residue 86 GLN Chi-restraints excluded: chain Y residue 91 ILE Chi-restraints excluded: chain Y residue 201 GLN Chi-restraints excluded: chain Y residue 227 LEU Chi-restraints excluded: chain Y residue 355 SER Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 0 residue 14 ASN Chi-restraints excluded: chain 0 residue 86 GLN Chi-restraints excluded: chain 0 residue 186 ASP Chi-restraints excluded: chain 0 residue 201 GLN Chi-restraints excluded: chain 0 residue 228 SER Chi-restraints excluded: chain 0 residue 259 THR Chi-restraints excluded: chain 0 residue 292 GLU Chi-restraints excluded: chain 2 residue 150 LYS Chi-restraints excluded: chain 2 residue 186 ASP Chi-restraints excluded: chain 2 residue 201 GLN Chi-restraints excluded: chain 2 residue 227 LEU Chi-restraints excluded: chain 2 residue 228 SER Chi-restraints excluded: chain 2 residue 355 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 473 optimal weight: 0.7980 chunk 498 optimal weight: 0.9990 chunk 454 optimal weight: 2.9990 chunk 485 optimal weight: 0.0570 chunk 291 optimal weight: 6.9990 chunk 211 optimal weight: 0.9980 chunk 380 optimal weight: 4.9990 chunk 148 optimal weight: 8.9990 chunk 438 optimal weight: 0.8980 chunk 458 optimal weight: 3.9990 chunk 483 optimal weight: 0.9980 overall best weight: 0.7498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS C 246 ASN C 304 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN G 33 HIS I 86 GLN K 164 ASN K 322 ASN M 33 HIS M 246 ASN O 33 HIS Q 33 HIS ** Q 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 14 ASN ** U 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 246 ASN U 322 ASN ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 304 GLN W 322 ASN Y 33 HIS Y 246 ASN 0 33 HIS ** 0 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 33 HIS 2 86 GLN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 45690 Z= 0.153 Angle : 0.518 7.544 62145 Z= 0.266 Chirality : 0.042 0.141 7110 Planarity : 0.003 0.040 7650 Dihedral : 10.099 73.445 7170 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.16 % Favored : 96.83 % Rotamer: Outliers : 1.68 % Allowed : 14.90 % Favored : 83.42 % 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: -0.24 (0.12), residues: 5355 helix: 0.49 (0.10), residues: 3210 sheet: -1.42 (0.26), residues: 390 loop : -0.89 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP S 333 HIS 0.008 0.001 HIS U 33 PHE 0.017 0.001 PHE 0 209 TYR 0.020 0.001 TYR Q 303 ARG 0.010 0.000 ARG K 249 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 890 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 812 time to evaluate : 4.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 ARG cc_start: 0.7962 (OUTLIER) cc_final: 0.7583 (ttm110) REVERT: C 29 ARG cc_start: 0.8546 (ptp-110) cc_final: 0.8290 (ptp-110) REVERT: C 143 ARG cc_start: 0.7226 (pmt170) cc_final: 0.6704 (ptt-90) REVERT: C 150 LYS cc_start: 0.8687 (mtmm) cc_final: 0.8252 (mttt) REVERT: A 100 ARG cc_start: 0.8200 (ttp80) cc_final: 0.7949 (tmm160) REVERT: A 159 ASP cc_start: 0.8180 (p0) cc_final: 0.7893 (p0) REVERT: A 201 GLN cc_start: 0.8730 (OUTLIER) cc_final: 0.7219 (mp10) REVERT: A 212 GLU cc_start: 0.8416 (pt0) cc_final: 0.7703 (pt0) REVERT: A 280 MET cc_start: 0.8468 (mmt) cc_final: 0.8201 (mmt) REVERT: A 371 ARG cc_start: 0.7300 (mtp180) cc_final: 0.6899 (mtp180) REVERT: D 53 ASP cc_start: 0.8515 (t0) cc_final: 0.8087 (t0) REVERT: D 123 MET cc_start: 0.6006 (ptt) cc_final: 0.5747 (ptp) REVERT: D 143 ARG cc_start: 0.7422 (pmt170) cc_final: 0.7000 (ptt-90) REVERT: D 150 LYS cc_start: 0.8473 (ptpp) cc_final: 0.8178 (mttt) REVERT: D 212 GLU cc_start: 0.8326 (pt0) cc_final: 0.8012 (pt0) REVERT: G 150 LYS cc_start: 0.8555 (ptpp) cc_final: 0.8053 (mttp) REVERT: G 201 GLN cc_start: 0.8676 (OUTLIER) cc_final: 0.7449 (mt0) REVERT: I 53 ASP cc_start: 0.8123 (t0) cc_final: 0.7894 (t0) REVERT: I 143 ARG cc_start: 0.7510 (pmt170) cc_final: 0.7220 (ptt-90) REVERT: I 158 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7447 (mm-40) REVERT: I 159 ASP cc_start: 0.7937 (p0) cc_final: 0.7390 (p0) REVERT: I 227 LEU cc_start: 0.8698 (OUTLIER) cc_final: 0.8405 (tp) REVERT: I 271 LEU cc_start: 0.8518 (mt) cc_final: 0.8257 (mt) REVERT: I 304 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.8091 (pp30) REVERT: K 5 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8481 (mm) REVERT: K 53 ASP cc_start: 0.8351 (t0) cc_final: 0.8090 (t0) REVERT: K 57 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7854 (ttp-170) REVERT: K 102 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8098 (pp) REVERT: K 150 LYS cc_start: 0.8756 (mtmm) cc_final: 0.8363 (mttt) REVERT: K 159 ASP cc_start: 0.8050 (p0) cc_final: 0.7732 (p0) REVERT: K 201 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.7216 (mt0) REVERT: K 325 SER cc_start: 0.9100 (t) cc_final: 0.8897 (p) REVERT: K 371 ARG cc_start: 0.7209 (mtp180) cc_final: 0.6911 (mtp180) REVERT: M 102 LEU cc_start: 0.8482 (OUTLIER) cc_final: 0.8277 (pp) REVERT: M 103 GLU cc_start: 0.7921 (mt-10) cc_final: 0.7663 (mt-10) REVERT: M 111 GLN cc_start: 0.8127 (tp40) cc_final: 0.7920 (tp40) REVERT: M 143 ARG cc_start: 0.7520 (pmt170) cc_final: 0.7083 (ptt-90) REVERT: M 371 ARG cc_start: 0.7131 (mtp180) cc_final: 0.6738 (mtp180) REVERT: O 6 ARG cc_start: 0.8000 (ptp90) cc_final: 0.7794 (ttp-110) REVERT: O 82 GLU cc_start: 0.7930 (tt0) cc_final: 0.7707 (mt-10) REVERT: O 100 ARG cc_start: 0.8272 (ttp80) cc_final: 0.8009 (tmm160) REVERT: O 143 ARG cc_start: 0.7199 (pmt170) cc_final: 0.6800 (ptt-90) REVERT: O 144 PHE cc_start: 0.7896 (m-10) cc_final: 0.7641 (m-10) REVERT: O 150 LYS cc_start: 0.8562 (mtmm) cc_final: 0.8044 (mmtm) REVERT: O 201 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.7139 (mp10) REVERT: O 212 GLU cc_start: 0.8031 (pt0) cc_final: 0.7677 (pt0) REVERT: O 320 ILE cc_start: 0.9134 (tt) cc_final: 0.8857 (tt) REVERT: O 371 ARG cc_start: 0.7129 (mtp180) cc_final: 0.6884 (mtp180) REVERT: Q 13 ARG cc_start: 0.7375 (mtp180) cc_final: 0.7075 (mtm110) REVERT: Q 53 ASP cc_start: 0.8453 (t0) cc_final: 0.8134 (t0) REVERT: Q 143 ARG cc_start: 0.7253 (pmt170) cc_final: 0.6619 (ttp-110) REVERT: Q 201 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.6992 (mp10) REVERT: Q 322 ASN cc_start: 0.7922 (m-40) cc_final: 0.7708 (m110) REVERT: S 143 ARG cc_start: 0.7230 (ptt-90) cc_final: 0.6437 (ttp-110) REVERT: S 150 LYS cc_start: 0.8503 (OUTLIER) cc_final: 0.8190 (mttt) REVERT: S 161 GLU cc_start: 0.7481 (pt0) cc_final: 0.7235 (pt0) REVERT: S 256 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8228 (t0) REVERT: U 31 ILE cc_start: 0.8882 (tp) cc_final: 0.8682 (tp) REVERT: U 143 ARG cc_start: 0.7299 (pmt170) cc_final: 0.6721 (ttp-110) REVERT: U 150 LYS cc_start: 0.8341 (ptpp) cc_final: 0.7833 (mttt) REVERT: U 201 GLN cc_start: 0.8829 (OUTLIER) cc_final: 0.7333 (mt0) REVERT: U 209 PHE cc_start: 0.8338 (m-10) cc_final: 0.8048 (m-10) REVERT: U 371 ARG cc_start: 0.7063 (mtp180) cc_final: 0.6785 (mtp180) REVERT: W 111 GLN cc_start: 0.8163 (tp-100) cc_final: 0.7670 (tp40) REVERT: W 143 ARG cc_start: 0.7346 (pmt170) cc_final: 0.6641 (ptm-80) REVERT: W 371 ARG cc_start: 0.7121 (mtp180) cc_final: 0.6748 (mtp180) REVERT: Y 6 ARG cc_start: 0.8077 (ptp90) cc_final: 0.7696 (mtm110) REVERT: Y 150 LYS cc_start: 0.8254 (ptpp) cc_final: 0.8012 (mtpt) REVERT: Y 301 ASN cc_start: 0.7918 (m-40) cc_final: 0.7648 (m110) REVERT: Y 323 LYS cc_start: 0.9041 (ttmm) cc_final: 0.8838 (ttmt) REVERT: Y 371 ARG cc_start: 0.7183 (mtp180) cc_final: 0.6835 (mtp180) REVERT: 0 29 ARG cc_start: 0.8692 (ptp-170) cc_final: 0.8444 (ptp-170) REVERT: 0 123 MET cc_start: 0.6764 (mtp) cc_final: 0.6509 (mtp) REVERT: 0 201 GLN cc_start: 0.8979 (OUTLIER) cc_final: 0.7533 (mp10) REVERT: 0 371 ARG cc_start: 0.7277 (mtp180) cc_final: 0.6896 (mtp180) REVERT: 2 150 LYS cc_start: 0.8562 (OUTLIER) cc_final: 0.8070 (mttm) REVERT: 2 161 GLU cc_start: 0.7795 (pt0) cc_final: 0.7467 (pt0) REVERT: 2 201 GLN cc_start: 0.8881 (OUTLIER) cc_final: 0.8003 (mt0) REVERT: 2 209 PHE cc_start: 0.8311 (m-80) cc_final: 0.7949 (m-10) REVERT: 2 274 LYS cc_start: 0.8647 (tttp) cc_final: 0.8436 (ttmt) REVERT: 2 317 GLU cc_start: 0.5522 (tm-30) cc_final: 0.4017 (tm-30) REVERT: 2 371 ARG cc_start: 0.7345 (mtp180) cc_final: 0.7112 (mtp180) outliers start: 78 outliers final: 47 residues processed: 866 average time/residue: 0.6246 time to fit residues: 855.5600 Evaluate side-chains 850 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 784 time to evaluate : 5.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 158 GLN Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain I residue 304 GLN Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 57 ARG Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 201 GLN Chi-restraints excluded: chain M residue 86 GLN Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 225 GLU Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 201 GLN Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain Q residue 86 GLN Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 201 GLN Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain S residue 150 LYS Chi-restraints excluded: chain S residue 164 ASN Chi-restraints excluded: chain S residue 225 GLU Chi-restraints excluded: chain S residue 256 ASP Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 35 ILE Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 164 ASN Chi-restraints excluded: chain U residue 186 ASP Chi-restraints excluded: chain U residue 187 THR Chi-restraints excluded: chain U residue 201 GLN Chi-restraints excluded: chain U residue 228 SER Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain W residue 86 GLN Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 14 ASN Chi-restraints excluded: chain Y residue 86 GLN Chi-restraints excluded: chain Y residue 91 ILE Chi-restraints excluded: chain Y residue 227 LEU Chi-restraints excluded: chain Y residue 306 MET Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 0 residue 14 ASN Chi-restraints excluded: chain 0 residue 201 GLN Chi-restraints excluded: chain 0 residue 259 THR Chi-restraints excluded: chain 0 residue 292 GLU Chi-restraints excluded: chain 2 residue 150 LYS Chi-restraints excluded: chain 2 residue 186 ASP Chi-restraints excluded: chain 2 residue 201 GLN Chi-restraints excluded: chain 2 residue 227 LEU Chi-restraints excluded: chain 2 residue 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 318 optimal weight: 4.9990 chunk 512 optimal weight: 9.9990 chunk 313 optimal weight: 0.9990 chunk 243 optimal weight: 8.9990 chunk 356 optimal weight: 4.9990 chunk 537 optimal weight: 3.9990 chunk 495 optimal weight: 0.8980 chunk 428 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 330 optimal weight: 0.0370 chunk 262 optimal weight: 8.9990 overall best weight: 2.1864 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS C 304 GLN A 33 HIS ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 14 ASN G 33 HIS K 33 HIS M 33 HIS O 33 HIS O 164 ASN Q 33 HIS ** Q 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 14 ASN ** U 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 322 ASN ** W 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 33 HIS 0 33 HIS ** 0 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 33 HIS Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.3562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 45690 Z= 0.230 Angle : 0.544 7.926 62145 Z= 0.277 Chirality : 0.043 0.132 7110 Planarity : 0.004 0.041 7650 Dihedral : 10.120 73.532 7170 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.83 % Favored : 96.13 % Rotamer: Outliers : 1.83 % Allowed : 14.97 % Favored : 83.20 % 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: -0.25 (0.12), residues: 5355 helix: 0.49 (0.10), residues: 3210 sheet: -1.41 (0.26), residues: 390 loop : -0.90 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP W 333 HIS 0.007 0.001 HIS U 33 PHE 0.023 0.001 PHE 0 209 TYR 0.023 0.001 TYR Q 303 ARG 0.010 0.000 ARG K 249 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10710 Ramachandran restraints generated. 5355 Oldfield, 0 Emsley, 5355 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 894 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 809 time to evaluate : 5.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 ARG cc_start: 0.7957 (OUTLIER) cc_final: 0.7590 (ttm110) REVERT: C 143 ARG cc_start: 0.7239 (pmt170) cc_final: 0.6711 (ptt-90) REVERT: C 150 LYS cc_start: 0.8729 (mtmm) cc_final: 0.8300 (mmmt) REVERT: A 100 ARG cc_start: 0.8221 (ttp80) cc_final: 0.7965 (tmm160) REVERT: A 123 MET cc_start: 0.6445 (ptt) cc_final: 0.6122 (ptp) REVERT: A 159 ASP cc_start: 0.8212 (p0) cc_final: 0.7917 (p0) REVERT: A 201 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.7290 (mp10) REVERT: A 212 GLU cc_start: 0.8307 (pt0) cc_final: 0.7899 (pt0) REVERT: A 256 ASP cc_start: 0.8351 (t70) cc_final: 0.7905 (t70) REVERT: A 280 MET cc_start: 0.8467 (mmt) cc_final: 0.8188 (mmt) REVERT: A 371 ARG cc_start: 0.7273 (mtp180) cc_final: 0.6872 (mtp180) REVERT: D 53 ASP cc_start: 0.8553 (t0) cc_final: 0.8173 (t0) REVERT: D 123 MET cc_start: 0.6113 (ptt) cc_final: 0.5879 (ptp) REVERT: D 143 ARG cc_start: 0.7430 (pmt170) cc_final: 0.7000 (ptt-90) REVERT: D 150 LYS cc_start: 0.8453 (ptpp) cc_final: 0.8209 (mttt) REVERT: D 212 GLU cc_start: 0.8336 (pt0) cc_final: 0.7981 (pt0) REVERT: D 320 ILE cc_start: 0.9158 (tt) cc_final: 0.8846 (tt) REVERT: G 150 LYS cc_start: 0.8545 (ptpp) cc_final: 0.8084 (mttp) REVERT: G 201 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8131 (mp10) REVERT: G 351 ASN cc_start: 0.8717 (t0) cc_final: 0.8511 (t0) REVERT: I 53 ASP cc_start: 0.8133 (t0) cc_final: 0.7906 (t0) REVERT: I 123 MET cc_start: 0.5803 (ptt) cc_final: 0.5557 (ptp) REVERT: I 143 ARG cc_start: 0.7556 (pmt170) cc_final: 0.7261 (ptt-90) REVERT: I 158 GLN cc_start: 0.8148 (OUTLIER) cc_final: 0.7421 (mm-40) REVERT: I 159 ASP cc_start: 0.7938 (p0) cc_final: 0.7398 (p0) REVERT: I 227 LEU cc_start: 0.8820 (OUTLIER) cc_final: 0.8520 (tp) REVERT: I 271 LEU cc_start: 0.8552 (mt) cc_final: 0.8282 (mt) REVERT: I 320 ILE cc_start: 0.9173 (tt) cc_final: 0.8940 (tt) REVERT: K 5 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8478 (mm) REVERT: K 53 ASP cc_start: 0.8372 (t0) cc_final: 0.8162 (t0) REVERT: K 102 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.8187 (pp) REVERT: K 150 LYS cc_start: 0.8720 (mtmm) cc_final: 0.8336 (mttt) REVERT: K 159 ASP cc_start: 0.8056 (p0) cc_final: 0.7703 (p0) REVERT: K 201 GLN cc_start: 0.8706 (OUTLIER) cc_final: 0.7188 (mt0) REVERT: K 371 ARG cc_start: 0.7253 (mtp180) cc_final: 0.6969 (mtp180) REVERT: M 102 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8329 (pp) REVERT: M 103 GLU cc_start: 0.7979 (mt-10) cc_final: 0.7713 (mt-10) REVERT: M 111 GLN cc_start: 0.8130 (tp40) cc_final: 0.7925 (tp40) REVERT: M 143 ARG cc_start: 0.7534 (pmt170) cc_final: 0.7102 (ptt-90) REVERT: M 371 ARG cc_start: 0.7229 (mtp180) cc_final: 0.6942 (mtp180) REVERT: O 6 ARG cc_start: 0.8020 (ptp90) cc_final: 0.7818 (ttp-110) REVERT: O 82 GLU cc_start: 0.7945 (tt0) cc_final: 0.7727 (mt-10) REVERT: O 100 ARG cc_start: 0.8330 (ttp80) cc_final: 0.8046 (tmm160) REVERT: O 143 ARG cc_start: 0.7236 (pmt170) cc_final: 0.6836 (ptt-90) REVERT: O 144 PHE cc_start: 0.7901 (m-10) cc_final: 0.7642 (m-10) REVERT: O 150 LYS cc_start: 0.8573 (mtmm) cc_final: 0.8066 (mmtm) REVERT: O 201 GLN cc_start: 0.8712 (OUTLIER) cc_final: 0.7130 (mp10) REVERT: O 212 GLU cc_start: 0.8070 (pt0) cc_final: 0.7709 (pt0) REVERT: O 320 ILE cc_start: 0.9141 (tt) cc_final: 0.8851 (tt) REVERT: O 371 ARG cc_start: 0.7146 (mtp180) cc_final: 0.6880 (mtp180) REVERT: Q 53 ASP cc_start: 0.8457 (t0) cc_final: 0.8084 (t0) REVERT: Q 143 ARG cc_start: 0.7272 (pmt170) cc_final: 0.6632 (ttp-110) REVERT: Q 201 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.6937 (mp10) REVERT: Q 217 ASP cc_start: 0.7239 (m-30) cc_final: 0.6777 (m-30) REVERT: Q 301 ASN cc_start: 0.7850 (m-40) cc_final: 0.7485 (m110) REVERT: S 143 ARG cc_start: 0.7258 (ptt-90) cc_final: 0.6177 (ttp-110) REVERT: S 150 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8210 (mttt) REVERT: S 161 GLU cc_start: 0.7504 (pt0) cc_final: 0.7225 (pt0) REVERT: S 201 GLN cc_start: 0.8874 (OUTLIER) cc_final: 0.7141 (mp10) REVERT: S 256 ASP cc_start: 0.8502 (OUTLIER) cc_final: 0.8238 (t0) REVERT: S 371 ARG cc_start: 0.7187 (mtp180) cc_final: 0.6909 (mtp180) REVERT: U 31 ILE cc_start: 0.8907 (tp) cc_final: 0.8696 (tp) REVERT: U 143 ARG cc_start: 0.7249 (pmt170) cc_final: 0.6657 (ttp-110) REVERT: U 150 LYS cc_start: 0.8328 (ptpp) cc_final: 0.7844 (mttt) REVERT: U 201 GLN cc_start: 0.8840 (OUTLIER) cc_final: 0.7392 (mt0) REVERT: U 209 PHE cc_start: 0.8313 (m-10) cc_final: 0.8022 (m-10) REVERT: U 253 MET cc_start: 0.8455 (ttm) cc_final: 0.8210 (ttp) REVERT: U 371 ARG cc_start: 0.7097 (mtp180) cc_final: 0.6806 (mtp180) REVERT: W 111 GLN cc_start: 0.8150 (tp-100) cc_final: 0.7667 (tp40) REVERT: W 143 ARG cc_start: 0.7346 (pmt170) cc_final: 0.6614 (ptm-80) REVERT: W 371 ARG cc_start: 0.7179 (mtp180) cc_final: 0.6775 (mtp180) REVERT: Y 6 ARG cc_start: 0.8054 (ptp90) cc_final: 0.7684 (mtm110) REVERT: Y 201 GLN cc_start: 0.8926 (OUTLIER) cc_final: 0.7495 (mp10) REVERT: Y 301 ASN cc_start: 0.8013 (m-40) cc_final: 0.7683 (m110) REVERT: Y 371 ARG cc_start: 0.7128 (mtp180) cc_final: 0.6766 (mtp180) REVERT: 0 29 ARG cc_start: 0.8682 (ptp-170) cc_final: 0.8383 (ptp-170) REVERT: 0 123 MET cc_start: 0.6778 (mtp) cc_final: 0.6507 (mtp) REVERT: 0 201 GLN cc_start: 0.8985 (OUTLIER) cc_final: 0.7547 (mp10) REVERT: 0 313 MET cc_start: 0.8215 (ptp) cc_final: 0.7946 (ptm) REVERT: 0 371 ARG cc_start: 0.7375 (mtp180) cc_final: 0.7107 (mtp180) REVERT: 2 89 GLN cc_start: 0.8766 (mm110) cc_final: 0.8448 (mm110) REVERT: 2 100 ARG cc_start: 0.7859 (tmm160) cc_final: 0.7658 (tmm160) REVERT: 2 150 LYS cc_start: 0.8598 (OUTLIER) cc_final: 0.8212 (mttt) REVERT: 2 161 GLU cc_start: 0.7822 (pt0) cc_final: 0.7448 (pt0) REVERT: 2 201 GLN cc_start: 0.8899 (OUTLIER) cc_final: 0.8023 (mt0) REVERT: 2 209 PHE cc_start: 0.8414 (m-80) cc_final: 0.8074 (m-10) REVERT: 2 274 LYS cc_start: 0.8664 (tttp) cc_final: 0.8450 (ttmt) REVERT: 2 317 GLU cc_start: 0.5485 (tm-30) cc_final: 0.3958 (tm-30) REVERT: 2 371 ARG cc_start: 0.7360 (mtp180) cc_final: 0.6936 (mtp180) outliers start: 85 outliers final: 56 residues processed: 872 average time/residue: 0.6138 time to fit residues: 847.1144 Evaluate side-chains 860 residues out of total 4650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 785 time to evaluate : 4.851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 LEU Chi-restraints excluded: chain C residue 6 ARG Chi-restraints excluded: chain A residue 35 ILE Chi-restraints excluded: chain A residue 86 GLN Chi-restraints excluded: chain A residue 186 ASP Chi-restraints excluded: chain A residue 201 GLN Chi-restraints excluded: chain A residue 376 VAL Chi-restraints excluded: chain D residue 35 ILE Chi-restraints excluded: chain D residue 86 GLN Chi-restraints excluded: chain D residue 227 LEU Chi-restraints excluded: chain G residue 201 GLN Chi-restraints excluded: chain G residue 213 ARG Chi-restraints excluded: chain G residue 225 GLU Chi-restraints excluded: chain G residue 227 LEU Chi-restraints excluded: chain I residue 91 ILE Chi-restraints excluded: chain I residue 158 GLN Chi-restraints excluded: chain I residue 227 LEU Chi-restraints excluded: chain I residue 228 SER Chi-restraints excluded: chain K residue 3 THR Chi-restraints excluded: chain K residue 5 LEU Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 57 ARG Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 186 ASP Chi-restraints excluded: chain K residue 201 GLN Chi-restraints excluded: chain K residue 228 SER Chi-restraints excluded: chain M residue 86 GLN Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 228 SER Chi-restraints excluded: chain O residue 3 THR Chi-restraints excluded: chain O residue 5 LEU Chi-restraints excluded: chain O residue 102 LEU Chi-restraints excluded: chain O residue 201 GLN Chi-restraints excluded: chain O residue 227 LEU Chi-restraints excluded: chain Q residue 86 GLN Chi-restraints excluded: chain Q residue 91 ILE Chi-restraints excluded: chain Q residue 201 GLN Chi-restraints excluded: chain Q residue 227 LEU Chi-restraints excluded: chain Q residue 367 GLU Chi-restraints excluded: chain S residue 150 LYS Chi-restraints excluded: chain S residue 164 ASN Chi-restraints excluded: chain S residue 201 GLN Chi-restraints excluded: chain S residue 225 GLU Chi-restraints excluded: chain S residue 256 ASP Chi-restraints excluded: chain U residue 34 ILE Chi-restraints excluded: chain U residue 35 ILE Chi-restraints excluded: chain U residue 102 LEU Chi-restraints excluded: chain U residue 123 MET Chi-restraints excluded: chain U residue 164 ASN Chi-restraints excluded: chain U residue 186 ASP Chi-restraints excluded: chain U residue 187 THR Chi-restraints excluded: chain U residue 201 GLN Chi-restraints excluded: chain U residue 228 SER Chi-restraints excluded: chain U residue 355 SER Chi-restraints excluded: chain W residue 5 LEU Chi-restraints excluded: chain W residue 86 GLN Chi-restraints excluded: chain W residue 355 SER Chi-restraints excluded: chain Y residue 5 LEU Chi-restraints excluded: chain Y residue 14 ASN Chi-restraints excluded: chain Y residue 86 GLN Chi-restraints excluded: chain Y residue 91 ILE Chi-restraints excluded: chain Y residue 201 GLN Chi-restraints excluded: chain Y residue 227 LEU Chi-restraints excluded: chain 0 residue 5 LEU Chi-restraints excluded: chain 0 residue 14 ASN Chi-restraints excluded: chain 0 residue 201 GLN Chi-restraints excluded: chain 0 residue 228 SER Chi-restraints excluded: chain 0 residue 259 THR Chi-restraints excluded: chain 0 residue 292 GLU Chi-restraints excluded: chain 2 residue 35 ILE Chi-restraints excluded: chain 2 residue 150 LYS Chi-restraints excluded: chain 2 residue 186 ASP Chi-restraints excluded: chain 2 residue 201 GLN Chi-restraints excluded: chain 2 residue 227 LEU Chi-restraints excluded: chain 2 residue 228 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 540 random chunks: chunk 340 optimal weight: 5.9990 chunk 456 optimal weight: 0.8980 chunk 131 optimal weight: 2.9990 chunk 395 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 429 optimal weight: 0.8980 chunk 179 optimal weight: 0.7980 chunk 440 optimal weight: 5.9990 chunk 54 optimal weight: 0.7980 chunk 79 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 33 HIS C 246 ASN C 304 GLN A 33 HIS A 301 ASN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 33 HIS I 86 GLN ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 HIS M 246 ASN O 33 HIS Q 33 HIS ** Q 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 322 ASN ** U 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 322 ASN W 33 HIS W 322 ASN Y 33 HIS ** Y 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 33 HIS 2 33 HIS Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.119236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.102484 restraints weight = 65947.726| |-----------------------------------------------------------------------------| r_work (start): 0.2965 rms_B_bonded: 1.93 r_work: 0.2852 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.3691 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 45690 Z= 0.155 Angle : 0.513 7.868 62145 Z= 0.263 Chirality : 0.041 0.124 7110 Planarity : 0.003 0.042 7650 Dihedral : 10.083 73.418 7170 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.21 % Favored : 96.77 % Rotamer: Outliers : 1.81 % Allowed : 15.33 % Favored : 82.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.12), residues: 5355 helix: 0.56 (0.10), residues: 3210 sheet: -1.34 (0.25), residues: 390 loop : -0.82 (0.15), residues: 1755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP S 333 HIS 0.007 0.001 HIS U 33 PHE 0.020 0.001 PHE 0 209 TYR 0.020 0.001 TYR Q 303 ARG 0.010 0.000 ARG K 249 =============================================================================== Job complete usr+sys time: 14442.83 seconds wall clock time: 261 minutes 36.18 seconds (15696.18 seconds total)