Starting phenix.real_space_refine on Mon Nov 13 15:18:51 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0u_11971/11_2023/7b0u_11971_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0u_11971/11_2023/7b0u_11971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.86 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0u_11971/11_2023/7b0u_11971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0u_11971/11_2023/7b0u_11971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0u_11971/11_2023/7b0u_11971_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0u_11971/11_2023/7b0u_11971_updated.pdb" } resolution = 3.86 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.240 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 32 5.49 5 S 580 5.16 5 C 67536 2.51 5 N 17088 2.21 5 O 20256 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 183": "OE1" <-> "OE2" Residue "B GLU 248": "OE1" <-> "OE2" Residue "F GLU 30": "OE1" <-> "OE2" Residue "F GLU 106": "OE1" <-> "OE2" Residue "I GLU 10": "OE1" <-> "OE2" Residue "N GLU 38": "OE1" <-> "OE2" Residue "K TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 183": "OE1" <-> "OE2" Residue "L GLU 248": "OE1" <-> "OE2" Residue "U GLU 30": "OE1" <-> "OE2" Residue "U GLU 106": "OE1" <-> "OE2" Residue "X GLU 10": "OE1" <-> "OE2" Residue "a GLU 38": "OE1" <-> "OE2" Residue "e TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 183": "OE1" <-> "OE2" Residue "f GLU 248": "OE1" <-> "OE2" Residue "j GLU 30": "OE1" <-> "OE2" Residue "j GLU 106": "OE1" <-> "OE2" Residue "m GLU 10": "OE1" <-> "OE2" Residue "p GLU 38": "OE1" <-> "OE2" Residue "t TYR 96": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u GLU 183": "OE1" <-> "OE2" Residue "u GLU 248": "OE1" <-> "OE2" Residue "y GLU 30": "OE1" <-> "OE2" Residue "y GLU 106": "OE1" <-> "OE2" Residue "1 GLU 10": "OE1" <-> "OE2" Residue "4 GLU 38": "OE1" <-> "OE2" Time to flip residues: 0.21s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib" Total number of atoms: 105492 Number of models: 1 Model: "" Number of chains: 60 Chain: "A" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2192 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Chain: "B" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2196 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2201 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 274, 2192 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Conformer: "B" Number of residues, atoms: 274, 2192 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} bond proxies already assigned to first conformer: 2219 Chain: "D" Number of atoms: 2207 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 274, 2196 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 274, 2196 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2221 Chain: "E" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 881 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "F" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 881 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "G" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2192 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Chain: "H" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2196 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "I" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 881 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "J" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2196 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "M" Number of atoms: 2200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2200 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "N" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 881 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "O" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 881 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "P" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2196 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Q" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2192 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Chain: "K" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2192 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Chain: "L" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2196 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 2201 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 274, 2192 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Conformer: "B" Number of residues, atoms: 274, 2192 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} bond proxies already assigned to first conformer: 2219 Chain: "S" Number of atoms: 2207 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 274, 2196 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 274, 2196 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2221 Chain: "T" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 881 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "U" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 881 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "V" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2192 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Chain: "W" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2196 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "X" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 881 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "Y" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2196 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "Z" Number of atoms: 2200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2200 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "a" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 881 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "b" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 881 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "c" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2196 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "d" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2192 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Chain: "e" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2192 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Chain: "f" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2196 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "g" Number of atoms: 2201 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 274, 2192 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Conformer: "B" Number of residues, atoms: 274, 2192 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} bond proxies already assigned to first conformer: 2219 Chain: "h" Number of atoms: 2207 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 274, 2196 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 274, 2196 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2221 Chain: "i" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 881 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "j" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 881 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "k" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2192 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Chain: "l" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2196 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "m" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 881 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "n" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2196 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "o" Number of atoms: 2200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2200 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "p" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 881 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "q" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 881 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "r" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2196 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "s" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2192 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Chain: "t" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2192 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Chain: "u" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2196 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "v" Number of atoms: 2201 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 274, 2192 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Conformer: "B" Number of residues, atoms: 274, 2192 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} bond proxies already assigned to first conformer: 2219 Chain: "w" Number of atoms: 2207 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 274, 2196 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Conformer: "B" Number of residues, atoms: 274, 2196 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 bond proxies already assigned to first conformer: 2221 Chain: "x" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 881 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "y" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 881 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "z" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2192 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Chain: "0" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2196 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "1" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 881 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "2" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2196 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "3" Number of atoms: 2200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2200 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Planarities with less than four sites: {'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 2 Chain: "4" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 881 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "5" Number of atoms: 881 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 881 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "6" Number of atoms: 2196 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2196 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'TPO:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "7" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 274, 2192 Classifications: {'peptide': 274} Link IDs: {'PTRANS': 9, 'TRANS': 264} Residues with excluded nonbonded symmetry interactions: 5768 residue: pdb=" N MET A 1 " occ=0.00 ... (6 atoms not shown) pdb=" CE MET A 1 " occ=0.00 residue: pdb=" N TYR A 2 " occ=0.00 ... (10 atoms not shown) pdb=" OH TYR A 2 " occ=0.00 residue: pdb=" N LYS A 3 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS A 3 " occ=0.00 residue: pdb=" N ASP A 4 " occ=0.00 ... (6 atoms not shown) pdb=" OD2 ASP A 4 " occ=0.00 residue: pdb=" N PHE A 5 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHE A 5 " occ=0.00 residue: pdb=" N ALA A 6 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA A 6 " occ=0.00 residue: pdb=" N ASN A 7 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN A 7 " occ=0.00 residue: pdb=" N PHE A 8 " occ=0.00 ... (9 atoms not shown) pdb=" CZ PHE A 8 " occ=0.00 residue: pdb=" N ILE A 9 " occ=0.00 ... (6 atoms not shown) pdb=" CD1 ILE A 9 " occ=0.00 residue: pdb=" N ARG A 10 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG A 10 " occ=0.00 residue: pdb=" N THR A 11 " occ=0.00 ... (5 atoms not shown) pdb=" CG2 THR A 11 " occ=0.00 residue: pdb=" N ASN A 12 " occ=0.00 ... (6 atoms not shown) pdb=" ND2 ASN A 12 " occ=0.00 ... (remaining 5756 not shown) Time building chain proxies: 44.07, per 1000 atoms: 0.42 Number of scatterers: 105492 At special positions: 0 Unit cell: (260.558, 303.098, 300.971, 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 580 16.00 P 32 15.00 O 20256 8.00 N 17088 7.00 C 67536 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: 32.14 Conformation dependent library (CDL) restraints added in 15.5 seconds 26256 Ramachandran restraints generated. 13128 Oldfield, 0 Emsley, 13128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 25376 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 484 helices and 60 sheets defined 67.1% alpha, 5.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 23.71 Creating SS restraints... Processing helix chain 'A' and resid 7 through 24 removed outlier: 3.671A pdb=" N THR A 11 " --> pdb=" O ASN A 7 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS A 14 " --> pdb=" O ARG A 10 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP A 15 " --> pdb=" O THR A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 28 through 36 Processing helix chain 'A' and resid 37 through 56 removed outlier: 3.789A pdb=" N LEU A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL A 53 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER A 54 " --> pdb=" O ASP A 50 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN A 55 " --> pdb=" O LEU A 51 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ILE A 56 " --> pdb=" O ILE A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 78 Processing helix chain 'A' and resid 80 through 103 Processing helix chain 'A' and resid 113 through 155 removed outlier: 4.030A pdb=" N TYR A 117 " --> pdb=" O GLU A 113 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU A 121 " --> pdb=" O TYR A 117 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP A 137 " --> pdb=" O THR A 133 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR A 138 " --> pdb=" O ALA A 134 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TRP A 139 " --> pdb=" O TYR A 135 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) removed outlier: 5.160A pdb=" N ALA A 155 " --> pdb=" O GLN A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 193 Processing helix chain 'A' and resid 208 through 226 Processing helix chain 'A' and resid 235 through 246 removed outlier: 3.635A pdb=" N GLY A 246 " --> pdb=" O ILE A 242 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 270 removed outlier: 4.052A pdb=" N ASN A 270 " --> pdb=" O LEU A 266 " (cutoff:3.500A) Processing helix chain 'C' and resid 7 through 24 removed outlier: 4.007A pdb=" N THR C 11 " --> pdb=" O ASN C 7 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N LYS C 14 " --> pdb=" O ARG C 10 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP C 15 " --> pdb=" O THR C 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 36 Processing helix chain 'C' and resid 37 through 56 removed outlier: 4.289A pdb=" N ILE C 52 " --> pdb=" O PHE C 48 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL C 53 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ILE C 56 " --> pdb=" O ILE C 52 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 78 Processing helix chain 'C' and resid 80 through 103 Processing helix chain 'C' and resid 113 through 155 removed outlier: 4.122A pdb=" N TYR C 117 " --> pdb=" O GLU C 113 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA C 136 " --> pdb=" O VAL C 132 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP C 137 " --> pdb=" O THR C 133 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N THR C 138 " --> pdb=" O ALA C 134 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N TRP C 139 " --> pdb=" O TYR C 135 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ALA C 155 " --> pdb=" O GLN C 151 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 193 removed outlier: 5.071A pdb=" N ARG C 193 " --> pdb=" O VAL C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 226 Processing helix chain 'C' and resid 235 through 246 removed outlier: 3.791A pdb=" N GLY C 246 " --> pdb=" O ILE C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 270 Processing helix chain 'G' and resid 7 through 24 removed outlier: 3.631A pdb=" N THR G 11 " --> pdb=" O ASN G 7 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LYS G 14 " --> pdb=" O ARG G 10 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP G 15 " --> pdb=" O THR G 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 36 Processing helix chain 'G' and resid 37 through 56 removed outlier: 3.756A pdb=" N LEU G 51 " --> pdb=" O GLU G 47 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE G 52 " --> pdb=" O PHE G 48 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL G 53 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N SER G 54 " --> pdb=" O ASP G 50 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN G 55 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ILE G 56 " --> pdb=" O ILE G 52 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 78 Processing helix chain 'G' and resid 80 through 103 Processing helix chain 'G' and resid 113 through 155 removed outlier: 3.864A pdb=" N TYR G 117 " --> pdb=" O GLU G 113 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU G 121 " --> pdb=" O TYR G 117 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR G 138 " --> pdb=" O ALA G 134 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TRP G 139 " --> pdb=" O TYR G 135 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N GLU G 140 " --> pdb=" O ALA G 136 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LYS G 141 " --> pdb=" O ASP G 137 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER G 154 " --> pdb=" O LEU G 150 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ALA G 155 " --> pdb=" O GLN G 151 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 193 removed outlier: 5.072A pdb=" N ARG G 193 " --> pdb=" O VAL G 189 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 226 Processing helix chain 'G' and resid 235 through 246 removed outlier: 3.556A pdb=" N GLY G 246 " --> pdb=" O ILE G 242 " (cutoff:3.500A) Processing helix chain 'G' and resid 257 through 270 removed outlier: 4.226A pdb=" N ASN G 270 " --> pdb=" O LEU G 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 7 through 24 removed outlier: 4.596A pdb=" N THR Q 11 " --> pdb=" O ASN Q 7 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LYS Q 14 " --> pdb=" O ARG Q 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 28 through 36 Processing helix chain 'Q' and resid 37 through 56 removed outlier: 3.818A pdb=" N LEU Q 51 " --> pdb=" O GLU Q 47 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE Q 52 " --> pdb=" O PHE Q 48 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL Q 53 " --> pdb=" O VAL Q 49 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N SER Q 54 " --> pdb=" O ASP Q 50 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN Q 55 " --> pdb=" O LEU Q 51 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ILE Q 56 " --> pdb=" O ILE Q 52 " (cutoff:3.500A) Processing helix chain 'Q' and resid 60 through 78 Processing helix chain 'Q' and resid 80 through 103 Processing helix chain 'Q' and resid 113 through 155 removed outlier: 3.800A pdb=" N TYR Q 117 " --> pdb=" O GLU Q 113 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU Q 121 " --> pdb=" O TYR Q 117 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA Q 136 " --> pdb=" O VAL Q 132 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP Q 137 " --> pdb=" O THR Q 133 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N THR Q 138 " --> pdb=" O ALA Q 134 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TRP Q 139 " --> pdb=" O TYR Q 135 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA Q 155 " --> pdb=" O GLN Q 151 " (cutoff:3.500A) Processing helix chain 'Q' and resid 174 through 193 removed outlier: 4.233A pdb=" N ARG Q 193 " --> pdb=" O VAL Q 189 " (cutoff:3.500A) Processing helix chain 'Q' and resid 208 through 226 Processing helix chain 'Q' and resid 235 through 246 removed outlier: 3.810A pdb=" N GLY Q 246 " --> pdb=" O ILE Q 242 " (cutoff:3.500A) Processing helix chain 'Q' and resid 257 through 270 removed outlier: 4.061A pdb=" N GLU Q 263 " --> pdb=" O LYS Q 259 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN Q 270 " --> pdb=" O LEU Q 266 " (cutoff:3.500A) Processing helix chain 'K' and resid 7 through 24 removed outlier: 3.671A pdb=" N THR K 11 " --> pdb=" O ASN K 7 " (cutoff:3.500A) removed outlier: 5.411A pdb=" N LYS K 14 " --> pdb=" O ARG K 10 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP K 15 " --> pdb=" O THR K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 28 through 36 Processing helix chain 'K' and resid 37 through 56 removed outlier: 3.788A pdb=" N LEU K 51 " --> pdb=" O GLU K 47 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE K 52 " --> pdb=" O PHE K 48 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL K 53 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER K 54 " --> pdb=" O ASP K 50 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN K 55 " --> pdb=" O LEU K 51 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ILE K 56 " --> pdb=" O ILE K 52 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 78 Processing helix chain 'K' and resid 80 through 103 Processing helix chain 'K' and resid 113 through 155 removed outlier: 4.031A pdb=" N TYR K 117 " --> pdb=" O GLU K 113 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU K 121 " --> pdb=" O TYR K 117 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP K 137 " --> pdb=" O THR K 133 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR K 138 " --> pdb=" O ALA K 134 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP K 139 " --> pdb=" O TYR K 135 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER K 154 " --> pdb=" O LEU K 150 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA K 155 " --> pdb=" O GLN K 151 " (cutoff:3.500A) Processing helix chain 'K' and resid 174 through 193 Processing helix chain 'K' and resid 208 through 226 Processing helix chain 'K' and resid 235 through 246 removed outlier: 3.635A pdb=" N GLY K 246 " --> pdb=" O ILE K 242 " (cutoff:3.500A) Processing helix chain 'K' and resid 257 through 270 removed outlier: 4.053A pdb=" N ASN K 270 " --> pdb=" O LEU K 266 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 24 removed outlier: 4.007A pdb=" N THR R 11 " --> pdb=" O ASN R 7 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LYS R 14 " --> pdb=" O ARG R 10 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP R 15 " --> pdb=" O THR R 11 " (cutoff:3.500A) Processing helix chain 'R' and resid 28 through 36 Processing helix chain 'R' and resid 37 through 56 removed outlier: 4.289A pdb=" N ILE R 52 " --> pdb=" O PHE R 48 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL R 53 " --> pdb=" O VAL R 49 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ASN R 55 " --> pdb=" O LEU R 51 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ILE R 56 " --> pdb=" O ILE R 52 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 78 Processing helix chain 'R' and resid 80 through 103 Processing helix chain 'R' and resid 113 through 155 removed outlier: 4.121A pdb=" N TYR R 117 " --> pdb=" O GLU R 113 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA R 136 " --> pdb=" O VAL R 132 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP R 137 " --> pdb=" O THR R 133 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N THR R 138 " --> pdb=" O ALA R 134 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N TRP R 139 " --> pdb=" O TYR R 135 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ALA R 155 " --> pdb=" O GLN R 151 " (cutoff:3.500A) Processing helix chain 'R' and resid 174 through 193 removed outlier: 5.071A pdb=" N ARG R 193 " --> pdb=" O VAL R 189 " (cutoff:3.500A) Processing helix chain 'R' and resid 208 through 226 Processing helix chain 'R' and resid 235 through 246 removed outlier: 3.791A pdb=" N GLY R 246 " --> pdb=" O ILE R 242 " (cutoff:3.500A) Processing helix chain 'R' and resid 257 through 270 Processing helix chain 'V' and resid 7 through 24 removed outlier: 3.631A pdb=" N THR V 11 " --> pdb=" O ASN V 7 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LYS V 14 " --> pdb=" O ARG V 10 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASP V 15 " --> pdb=" O THR V 11 " (cutoff:3.500A) Processing helix chain 'V' and resid 28 through 36 Processing helix chain 'V' and resid 37 through 56 removed outlier: 3.756A pdb=" N LEU V 51 " --> pdb=" O GLU V 47 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ILE V 52 " --> pdb=" O PHE V 48 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL V 53 " --> pdb=" O VAL V 49 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER V 54 " --> pdb=" O ASP V 50 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ASN V 55 " --> pdb=" O LEU V 51 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ILE V 56 " --> pdb=" O ILE V 52 " (cutoff:3.500A) Processing helix chain 'V' and resid 60 through 78 Processing helix chain 'V' and resid 80 through 103 Processing helix chain 'V' and resid 113 through 155 removed outlier: 3.864A pdb=" N TYR V 117 " --> pdb=" O GLU V 113 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU V 121 " --> pdb=" O TYR V 117 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR V 138 " --> pdb=" O ALA V 134 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TRP V 139 " --> pdb=" O TYR V 135 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU V 140 " --> pdb=" O ALA V 136 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LYS V 141 " --> pdb=" O ASP V 137 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER V 154 " --> pdb=" O LEU V 150 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ALA V 155 " --> pdb=" O GLN V 151 " (cutoff:3.500A) Processing helix chain 'V' and resid 174 through 193 removed outlier: 5.072A pdb=" N ARG V 193 " --> pdb=" O VAL V 189 " (cutoff:3.500A) Processing helix chain 'V' and resid 208 through 226 Processing helix chain 'V' and resid 235 through 246 removed outlier: 3.556A pdb=" N GLY V 246 " --> pdb=" O ILE V 242 " (cutoff:3.500A) Processing helix chain 'V' and resid 257 through 270 removed outlier: 4.226A pdb=" N ASN V 270 " --> pdb=" O LEU V 266 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 24 removed outlier: 4.595A pdb=" N THR d 11 " --> pdb=" O ASN d 7 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N LYS d 14 " --> pdb=" O ARG d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 28 through 36 Processing helix chain 'd' and resid 37 through 56 removed outlier: 3.817A pdb=" N LEU d 51 " --> pdb=" O GLU d 47 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE d 52 " --> pdb=" O PHE d 48 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL d 53 " --> pdb=" O VAL d 49 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N SER d 54 " --> pdb=" O ASP d 50 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN d 55 " --> pdb=" O LEU d 51 " (cutoff:3.500A) removed outlier: 7.433A pdb=" N ILE d 56 " --> pdb=" O ILE d 52 " (cutoff:3.500A) Processing helix chain 'd' and resid 60 through 78 Processing helix chain 'd' and resid 80 through 103 Processing helix chain 'd' and resid 113 through 155 removed outlier: 3.800A pdb=" N TYR d 117 " --> pdb=" O GLU d 113 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU d 121 " --> pdb=" O TYR d 117 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA d 136 " --> pdb=" O VAL d 132 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP d 137 " --> pdb=" O THR d 133 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N THR d 138 " --> pdb=" O ALA d 134 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N TRP d 139 " --> pdb=" O TYR d 135 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA d 155 " --> pdb=" O GLN d 151 " (cutoff:3.500A) Processing helix chain 'd' and resid 174 through 193 removed outlier: 4.232A pdb=" N ARG d 193 " --> pdb=" O VAL d 189 " (cutoff:3.500A) Processing helix chain 'd' and resid 208 through 226 Processing helix chain 'd' and resid 235 through 246 removed outlier: 3.810A pdb=" N GLY d 246 " --> pdb=" O ILE d 242 " (cutoff:3.500A) Processing helix chain 'd' and resid 257 through 270 removed outlier: 4.062A pdb=" N GLU d 263 " --> pdb=" O LYS d 259 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN d 270 " --> pdb=" O LEU d 266 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 24 removed outlier: 3.670A pdb=" N THR e 11 " --> pdb=" O ASN e 7 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS e 14 " --> pdb=" O ARG e 10 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP e 15 " --> pdb=" O THR e 11 " (cutoff:3.500A) Processing helix chain 'e' and resid 28 through 36 Processing helix chain 'e' and resid 37 through 56 removed outlier: 3.789A pdb=" N LEU e 51 " --> pdb=" O GLU e 47 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ILE e 52 " --> pdb=" O PHE e 48 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL e 53 " --> pdb=" O VAL e 49 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N SER e 54 " --> pdb=" O ASP e 50 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN e 55 " --> pdb=" O LEU e 51 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ILE e 56 " --> pdb=" O ILE e 52 " (cutoff:3.500A) Processing helix chain 'e' and resid 60 through 78 Processing helix chain 'e' and resid 80 through 103 Processing helix chain 'e' and resid 113 through 155 removed outlier: 4.031A pdb=" N TYR e 117 " --> pdb=" O GLU e 113 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU e 121 " --> pdb=" O TYR e 117 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP e 137 " --> pdb=" O THR e 133 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR e 138 " --> pdb=" O ALA e 134 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP e 139 " --> pdb=" O TYR e 135 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER e 154 " --> pdb=" O LEU e 150 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA e 155 " --> pdb=" O GLN e 151 " (cutoff:3.500A) Processing helix chain 'e' and resid 174 through 193 Processing helix chain 'e' and resid 208 through 226 Processing helix chain 'e' and resid 235 through 246 removed outlier: 3.635A pdb=" N GLY e 246 " --> pdb=" O ILE e 242 " (cutoff:3.500A) Processing helix chain 'e' and resid 257 through 270 removed outlier: 4.053A pdb=" N ASN e 270 " --> pdb=" O LEU e 266 " (cutoff:3.500A) Processing helix chain 'g' and resid 7 through 24 removed outlier: 4.007A pdb=" N THR g 11 " --> pdb=" O ASN g 7 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LYS g 14 " --> pdb=" O ARG g 10 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP g 15 " --> pdb=" O THR g 11 " (cutoff:3.500A) Processing helix chain 'g' and resid 28 through 36 Processing helix chain 'g' and resid 37 through 56 removed outlier: 4.290A pdb=" N ILE g 52 " --> pdb=" O PHE g 48 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL g 53 " --> pdb=" O VAL g 49 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN g 55 " --> pdb=" O LEU g 51 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ILE g 56 " --> pdb=" O ILE g 52 " (cutoff:3.500A) Processing helix chain 'g' and resid 60 through 78 Processing helix chain 'g' and resid 80 through 103 Processing helix chain 'g' and resid 113 through 155 removed outlier: 4.122A pdb=" N TYR g 117 " --> pdb=" O GLU g 113 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ALA g 136 " --> pdb=" O VAL g 132 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ASP g 137 " --> pdb=" O THR g 133 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N THR g 138 " --> pdb=" O ALA g 134 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N TRP g 139 " --> pdb=" O TYR g 135 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ALA g 155 " --> pdb=" O GLN g 151 " (cutoff:3.500A) Processing helix chain 'g' and resid 174 through 193 removed outlier: 5.070A pdb=" N ARG g 193 " --> pdb=" O VAL g 189 " (cutoff:3.500A) Processing helix chain 'g' and resid 208 through 226 Processing helix chain 'g' and resid 235 through 246 removed outlier: 3.791A pdb=" N GLY g 246 " --> pdb=" O ILE g 242 " (cutoff:3.500A) Processing helix chain 'g' and resid 257 through 270 Processing helix chain 'k' and resid 7 through 24 removed outlier: 3.631A pdb=" N THR k 11 " --> pdb=" O ASN k 7 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LYS k 14 " --> pdb=" O ARG k 10 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N ASP k 15 " --> pdb=" O THR k 11 " (cutoff:3.500A) Processing helix chain 'k' and resid 28 through 36 Processing helix chain 'k' and resid 37 through 56 removed outlier: 3.755A pdb=" N LEU k 51 " --> pdb=" O GLU k 47 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N ILE k 52 " --> pdb=" O PHE k 48 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL k 53 " --> pdb=" O VAL k 49 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER k 54 " --> pdb=" O ASP k 50 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN k 55 " --> pdb=" O LEU k 51 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ILE k 56 " --> pdb=" O ILE k 52 " (cutoff:3.500A) Processing helix chain 'k' and resid 60 through 78 Processing helix chain 'k' and resid 80 through 103 Processing helix chain 'k' and resid 113 through 155 removed outlier: 3.864A pdb=" N TYR k 117 " --> pdb=" O GLU k 113 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU k 121 " --> pdb=" O TYR k 117 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR k 138 " --> pdb=" O ALA k 134 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TRP k 139 " --> pdb=" O TYR k 135 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU k 140 " --> pdb=" O ALA k 136 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LYS k 141 " --> pdb=" O ASP k 137 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER k 154 " --> pdb=" O LEU k 150 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N ALA k 155 " --> pdb=" O GLN k 151 " (cutoff:3.500A) Processing helix chain 'k' and resid 174 through 193 removed outlier: 5.072A pdb=" N ARG k 193 " --> pdb=" O VAL k 189 " (cutoff:3.500A) Processing helix chain 'k' and resid 208 through 226 Processing helix chain 'k' and resid 235 through 246 removed outlier: 3.556A pdb=" N GLY k 246 " --> pdb=" O ILE k 242 " (cutoff:3.500A) Processing helix chain 'k' and resid 257 through 270 removed outlier: 4.226A pdb=" N ASN k 270 " --> pdb=" O LEU k 266 " (cutoff:3.500A) Processing helix chain 's' and resid 7 through 24 removed outlier: 4.595A pdb=" N THR s 11 " --> pdb=" O ASN s 7 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N LYS s 14 " --> pdb=" O ARG s 10 " (cutoff:3.500A) Processing helix chain 's' and resid 28 through 36 Processing helix chain 's' and resid 37 through 56 removed outlier: 3.818A pdb=" N LEU s 51 " --> pdb=" O GLU s 47 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE s 52 " --> pdb=" O PHE s 48 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL s 53 " --> pdb=" O VAL s 49 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N SER s 54 " --> pdb=" O ASP s 50 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN s 55 " --> pdb=" O LEU s 51 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ILE s 56 " --> pdb=" O ILE s 52 " (cutoff:3.500A) Processing helix chain 's' and resid 60 through 78 Processing helix chain 's' and resid 80 through 103 Processing helix chain 's' and resid 113 through 155 removed outlier: 3.800A pdb=" N TYR s 117 " --> pdb=" O GLU s 113 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU s 121 " --> pdb=" O TYR s 117 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA s 136 " --> pdb=" O VAL s 132 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP s 137 " --> pdb=" O THR s 133 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N THR s 138 " --> pdb=" O ALA s 134 " (cutoff:3.500A) removed outlier: 4.636A pdb=" N TRP s 139 " --> pdb=" O TYR s 135 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N ALA s 155 " --> pdb=" O GLN s 151 " (cutoff:3.500A) Processing helix chain 's' and resid 174 through 193 removed outlier: 4.232A pdb=" N ARG s 193 " --> pdb=" O VAL s 189 " (cutoff:3.500A) Processing helix chain 's' and resid 208 through 226 Processing helix chain 's' and resid 235 through 246 removed outlier: 3.810A pdb=" N GLY s 246 " --> pdb=" O ILE s 242 " (cutoff:3.500A) Processing helix chain 's' and resid 257 through 270 removed outlier: 4.062A pdb=" N GLU s 263 " --> pdb=" O LYS s 259 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN s 270 " --> pdb=" O LEU s 266 " (cutoff:3.500A) Processing helix chain 't' and resid 7 through 24 removed outlier: 3.670A pdb=" N THR t 11 " --> pdb=" O ASN t 7 " (cutoff:3.500A) removed outlier: 5.410A pdb=" N LYS t 14 " --> pdb=" O ARG t 10 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP t 15 " --> pdb=" O THR t 11 " (cutoff:3.500A) Processing helix chain 't' and resid 28 through 36 Processing helix chain 't' and resid 37 through 56 removed outlier: 3.790A pdb=" N LEU t 51 " --> pdb=" O GLU t 47 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N ILE t 52 " --> pdb=" O PHE t 48 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N VAL t 53 " --> pdb=" O VAL t 49 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N SER t 54 " --> pdb=" O ASP t 50 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN t 55 " --> pdb=" O LEU t 51 " (cutoff:3.500A) removed outlier: 5.705A pdb=" N ILE t 56 " --> pdb=" O ILE t 52 " (cutoff:3.500A) Processing helix chain 't' and resid 60 through 78 Processing helix chain 't' and resid 80 through 103 Processing helix chain 't' and resid 113 through 155 removed outlier: 4.030A pdb=" N TYR t 117 " --> pdb=" O GLU t 113 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N GLU t 121 " --> pdb=" O TYR t 117 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ASP t 137 " --> pdb=" O THR t 133 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR t 138 " --> pdb=" O ALA t 134 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N TRP t 139 " --> pdb=" O TYR t 135 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER t 154 " --> pdb=" O LEU t 150 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N ALA t 155 " --> pdb=" O GLN t 151 " (cutoff:3.500A) Processing helix chain 't' and resid 174 through 193 Processing helix chain 't' and resid 208 through 226 Processing helix chain 't' and resid 235 through 246 removed outlier: 3.635A pdb=" N GLY t 246 " --> pdb=" O ILE t 242 " (cutoff:3.500A) Processing helix chain 't' and resid 257 through 270 removed outlier: 4.052A pdb=" N ASN t 270 " --> pdb=" O LEU t 266 " (cutoff:3.500A) Processing helix chain 'v' and resid 7 through 24 removed outlier: 4.007A pdb=" N THR v 11 " --> pdb=" O ASN v 7 " (cutoff:3.500A) removed outlier: 5.208A pdb=" N LYS v 14 " --> pdb=" O ARG v 10 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASP v 15 " --> pdb=" O THR v 11 " (cutoff:3.500A) Processing helix chain 'v' and resid 28 through 36 Processing helix chain 'v' and resid 37 through 56 removed outlier: 4.289A pdb=" N ILE v 52 " --> pdb=" O PHE v 48 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N VAL v 53 " --> pdb=" O VAL v 49 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASN v 55 " --> pdb=" O LEU v 51 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N ILE v 56 " --> pdb=" O ILE v 52 " (cutoff:3.500A) Processing helix chain 'v' and resid 60 through 78 Processing helix chain 'v' and resid 80 through 103 Processing helix chain 'v' and resid 113 through 155 removed outlier: 4.121A pdb=" N TYR v 117 " --> pdb=" O GLU v 113 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ALA v 136 " --> pdb=" O VAL v 132 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N ASP v 137 " --> pdb=" O THR v 133 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N THR v 138 " --> pdb=" O ALA v 134 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N TRP v 139 " --> pdb=" O TYR v 135 " (cutoff:3.500A) removed outlier: 5.147A pdb=" N ALA v 155 " --> pdb=" O GLN v 151 " (cutoff:3.500A) Processing helix chain 'v' and resid 174 through 193 removed outlier: 5.070A pdb=" N ARG v 193 " --> pdb=" O VAL v 189 " (cutoff:3.500A) Processing helix chain 'v' and resid 208 through 226 Processing helix chain 'v' and resid 235 through 246 removed outlier: 3.791A pdb=" N GLY v 246 " --> pdb=" O ILE v 242 " (cutoff:3.500A) Processing helix chain 'v' and resid 257 through 270 Processing helix chain 'z' and resid 7 through 24 removed outlier: 3.630A pdb=" N THR z 11 " --> pdb=" O ASN z 7 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N LYS z 14 " --> pdb=" O ARG z 10 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ASP z 15 " --> pdb=" O THR z 11 " (cutoff:3.500A) Processing helix chain 'z' and resid 28 through 36 Processing helix chain 'z' and resid 37 through 56 removed outlier: 3.756A pdb=" N LEU z 51 " --> pdb=" O GLU z 47 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ILE z 52 " --> pdb=" O PHE z 48 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N VAL z 53 " --> pdb=" O VAL z 49 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER z 54 " --> pdb=" O ASP z 50 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ASN z 55 " --> pdb=" O LEU z 51 " (cutoff:3.500A) removed outlier: 5.474A pdb=" N ILE z 56 " --> pdb=" O ILE z 52 " (cutoff:3.500A) Processing helix chain 'z' and resid 60 through 78 Processing helix chain 'z' and resid 80 through 103 Processing helix chain 'z' and resid 113 through 155 removed outlier: 3.863A pdb=" N TYR z 117 " --> pdb=" O GLU z 113 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLU z 121 " --> pdb=" O TYR z 117 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N THR z 138 " --> pdb=" O ALA z 134 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N TRP z 139 " --> pdb=" O TYR z 135 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLU z 140 " --> pdb=" O ALA z 136 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N LYS z 141 " --> pdb=" O ASP z 137 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N SER z 154 " --> pdb=" O LEU z 150 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ALA z 155 " --> pdb=" O GLN z 151 " (cutoff:3.500A) Processing helix chain 'z' and resid 174 through 193 removed outlier: 5.071A pdb=" N ARG z 193 " --> pdb=" O VAL z 189 " (cutoff:3.500A) Processing helix chain 'z' and resid 208 through 226 Processing helix chain 'z' and resid 235 through 246 removed outlier: 3.555A pdb=" N GLY z 246 " --> pdb=" O ILE z 242 " (cutoff:3.500A) Processing helix chain 'z' and resid 257 through 270 removed outlier: 4.226A pdb=" N ASN z 270 " --> pdb=" O LEU z 266 " (cutoff:3.500A) Processing helix chain '7' and resid 7 through 24 removed outlier: 4.595A pdb=" N THR 7 11 " --> pdb=" O ASN 7 7 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N LYS 7 14 " --> pdb=" O ARG 7 10 " (cutoff:3.500A) Processing helix chain '7' and resid 28 through 36 Processing helix chain '7' and resid 37 through 56 removed outlier: 3.817A pdb=" N LEU 7 51 " --> pdb=" O GLU 7 47 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N ILE 7 52 " --> pdb=" O PHE 7 48 " (cutoff:3.500A) removed outlier: 5.450A pdb=" N VAL 7 53 " --> pdb=" O VAL 7 49 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N SER 7 54 " --> pdb=" O ASP 7 50 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ASN 7 55 " --> pdb=" O LEU 7 51 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N ILE 7 56 " --> pdb=" O ILE 7 52 " (cutoff:3.500A) Processing helix chain '7' and resid 60 through 78 Processing helix chain '7' and resid 80 through 103 Processing helix chain '7' and resid 113 through 155 removed outlier: 3.800A pdb=" N TYR 7 117 " --> pdb=" O GLU 7 113 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N GLU 7 121 " --> pdb=" O TYR 7 117 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA 7 136 " --> pdb=" O VAL 7 132 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N ASP 7 137 " --> pdb=" O THR 7 133 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N THR 7 138 " --> pdb=" O ALA 7 134 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N TRP 7 139 " --> pdb=" O TYR 7 135 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N ALA 7 155 " --> pdb=" O GLN 7 151 " (cutoff:3.500A) Processing helix chain '7' and resid 174 through 193 removed outlier: 4.232A pdb=" N ARG 7 193 " --> pdb=" O VAL 7 189 " (cutoff:3.500A) Processing helix chain '7' and resid 208 through 226 Processing helix chain '7' and resid 235 through 246 removed outlier: 3.810A pdb=" N GLY 7 246 " --> pdb=" O ILE 7 242 " (cutoff:3.500A) Processing helix chain '7' and resid 257 through 270 removed outlier: 4.062A pdb=" N GLU 7 263 " --> pdb=" O LYS 7 259 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N ASN 7 270 " --> pdb=" O LEU 7 266 " (cutoff:3.500A) Processing helix chain 'B' and resid 7 through 20 removed outlier: 4.223A pdb=" N THR B 11 " --> pdb=" O ASN B 7 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LYS B 14 " --> pdb=" O ARG B 10 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 35 Processing helix chain 'B' and resid 37 through 55 removed outlier: 3.800A pdb=" N ILE B 52 " --> pdb=" O PHE B 48 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL B 53 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER B 54 " --> pdb=" O ASP B 50 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASN B 55 " --> pdb=" O LEU B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 78 removed outlier: 3.964A pdb=" N GLU B 65 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY B 78 " --> pdb=" O VAL B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 103 Processing helix chain 'B' and resid 116 through 155 removed outlier: 4.598A pdb=" N GLU B 121 " --> pdb=" O TYR B 117 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR B 138 " --> pdb=" O ALA B 134 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TRP B 139 " --> pdb=" O TYR B 135 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER B 154 " --> pdb=" O LEU B 150 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ALA B 155 " --> pdb=" O GLN B 151 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 193 Processing helix chain 'B' and resid 208 through 226 Processing helix chain 'B' and resid 235 through 240 Processing helix chain 'B' and resid 257 through 270 removed outlier: 3.974A pdb=" N ASN B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 7 through 20 removed outlier: 4.592A pdb=" N THR D 11 " --> pdb=" O ASN D 7 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LYS D 14 " --> pdb=" O ARG D 10 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 35 Processing helix chain 'D' and resid 37 through 55 removed outlier: 3.656A pdb=" N LEU D 51 " --> pdb=" O GLU D 47 " (cutoff:3.500A) removed outlier: 4.369A pdb=" N ILE D 52 " --> pdb=" O PHE D 48 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL D 53 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER D 54 " --> pdb=" O ASP D 50 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ASN D 55 " --> pdb=" O LEU D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 78 Processing helix chain 'D' and resid 80 through 103 removed outlier: 3.697A pdb=" N ASP D 103 " --> pdb=" O MET D 99 " (cutoff:3.500A) Processing helix chain 'D' and resid 116 through 155 removed outlier: 4.502A pdb=" N GLU D 121 " --> pdb=" O TYR D 117 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA D 136 " --> pdb=" O VAL D 132 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP D 137 " --> pdb=" O THR D 133 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N THR D 138 " --> pdb=" O ALA D 134 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TRP D 139 " --> pdb=" O TYR D 135 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA D 155 " --> pdb=" O GLN D 151 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 193 removed outlier: 4.973A pdb=" N ARG D 193 " --> pdb=" O VAL D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 208 through 226 Processing helix chain 'D' and resid 235 through 240 Processing helix chain 'D' and resid 257 through 270 removed outlier: 4.107A pdb=" N ASN D 270 " --> pdb=" O LEU D 266 " (cutoff:3.500A) Processing helix chain 'H' and resid 7 through 20 removed outlier: 4.328A pdb=" N THR H 11 " --> pdb=" O ASN H 7 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LYS H 14 " --> pdb=" O ARG H 10 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 35 Processing helix chain 'H' and resid 37 through 55 removed outlier: 3.655A pdb=" N ILE H 52 " --> pdb=" O PHE H 48 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N VAL H 53 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER H 54 " --> pdb=" O ASP H 50 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ASN H 55 " --> pdb=" O LEU H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 78 removed outlier: 3.650A pdb=" N GLY H 78 " --> pdb=" O VAL H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 80 through 103 Processing helix chain 'H' and resid 116 through 155 removed outlier: 4.504A pdb=" N GLU H 121 " --> pdb=" O TYR H 117 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR H 138 " --> pdb=" O ALA H 134 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP H 139 " --> pdb=" O TYR H 135 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ALA H 155 " --> pdb=" O GLN H 151 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 193 removed outlier: 4.619A pdb=" N ARG H 193 " --> pdb=" O VAL H 189 " (cutoff:3.500A) Processing helix chain 'H' and resid 208 through 226 Processing helix chain 'H' and resid 235 through 240 Processing helix chain 'H' and resid 257 through 270 removed outlier: 4.225A pdb=" N ASN H 270 " --> pdb=" O LEU H 266 " (cutoff:3.500A) Processing helix chain 'J' and resid 7 through 20 removed outlier: 4.614A pdb=" N THR J 11 " --> pdb=" O ASN J 7 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LYS J 14 " --> pdb=" O ARG J 10 " (cutoff:3.500A) Processing helix chain 'J' and resid 28 through 35 Processing helix chain 'J' and resid 37 through 55 removed outlier: 3.616A pdb=" N LEU J 51 " --> pdb=" O GLU J 47 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE J 52 " --> pdb=" O PHE J 48 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N VAL J 53 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER J 54 " --> pdb=" O ASP J 50 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASN J 55 " --> pdb=" O LEU J 51 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 78 removed outlier: 3.556A pdb=" N GLY J 78 " --> pdb=" O VAL J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 80 through 103 removed outlier: 3.569A pdb=" N ASP J 103 " --> pdb=" O MET J 99 " (cutoff:3.500A) Processing helix chain 'J' and resid 116 through 155 removed outlier: 4.596A pdb=" N GLU J 121 " --> pdb=" O TYR J 117 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA J 136 " --> pdb=" O VAL J 132 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP J 137 " --> pdb=" O THR J 133 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N THR J 138 " --> pdb=" O ALA J 134 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TRP J 139 " --> pdb=" O TYR J 135 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ALA J 155 " --> pdb=" O GLN J 151 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 193 removed outlier: 4.764A pdb=" N ARG J 193 " --> pdb=" O VAL J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 208 through 226 Processing helix chain 'J' and resid 235 through 240 Processing helix chain 'J' and resid 257 through 270 removed outlier: 3.706A pdb=" N ASN J 270 " --> pdb=" O LEU J 266 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 20 removed outlier: 4.223A pdb=" N THR L 11 " --> pdb=" O ASN L 7 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N LYS L 14 " --> pdb=" O ARG L 10 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 35 Processing helix chain 'L' and resid 37 through 55 removed outlier: 3.799A pdb=" N ILE L 52 " --> pdb=" O PHE L 48 " (cutoff:3.500A) removed outlier: 5.173A pdb=" N VAL L 53 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N SER L 54 " --> pdb=" O ASP L 50 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASN L 55 " --> pdb=" O LEU L 51 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 78 removed outlier: 3.964A pdb=" N GLU L 65 " --> pdb=" O SER L 61 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N GLY L 78 " --> pdb=" O VAL L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 103 Processing helix chain 'L' and resid 116 through 155 removed outlier: 4.598A pdb=" N GLU L 121 " --> pdb=" O TYR L 117 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N TRP L 139 " --> pdb=" O TYR L 135 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER L 154 " --> pdb=" O LEU L 150 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ALA L 155 " --> pdb=" O GLN L 151 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 193 Processing helix chain 'L' and resid 208 through 226 Processing helix chain 'L' and resid 235 through 240 Processing helix chain 'L' and resid 257 through 270 removed outlier: 3.974A pdb=" N ASN L 270 " --> pdb=" O LEU L 266 " (cutoff:3.500A) Processing helix chain 'S' and resid 7 through 20 removed outlier: 4.593A pdb=" N THR S 11 " --> pdb=" O ASN S 7 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LYS S 14 " --> pdb=" O ARG S 10 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 35 Processing helix chain 'S' and resid 37 through 55 removed outlier: 3.655A pdb=" N LEU S 51 " --> pdb=" O GLU S 47 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE S 52 " --> pdb=" O PHE S 48 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL S 53 " --> pdb=" O VAL S 49 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER S 54 " --> pdb=" O ASP S 50 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ASN S 55 " --> pdb=" O LEU S 51 " (cutoff:3.500A) Processing helix chain 'S' and resid 60 through 78 Processing helix chain 'S' and resid 80 through 103 removed outlier: 3.697A pdb=" N ASP S 103 " --> pdb=" O MET S 99 " (cutoff:3.500A) Processing helix chain 'S' and resid 116 through 155 removed outlier: 4.502A pdb=" N GLU S 121 " --> pdb=" O TYR S 117 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA S 136 " --> pdb=" O VAL S 132 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP S 137 " --> pdb=" O THR S 133 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N THR S 138 " --> pdb=" O ALA S 134 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N TRP S 139 " --> pdb=" O TYR S 135 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA S 155 " --> pdb=" O GLN S 151 " (cutoff:3.500A) Processing helix chain 'S' and resid 174 through 193 removed outlier: 4.972A pdb=" N ARG S 193 " --> pdb=" O VAL S 189 " (cutoff:3.500A) Processing helix chain 'S' and resid 208 through 226 Processing helix chain 'S' and resid 235 through 240 Processing helix chain 'S' and resid 257 through 270 removed outlier: 4.109A pdb=" N ASN S 270 " --> pdb=" O LEU S 266 " (cutoff:3.500A) Processing helix chain 'W' and resid 7 through 20 removed outlier: 4.327A pdb=" N THR W 11 " --> pdb=" O ASN W 7 " (cutoff:3.500A) removed outlier: 5.141A pdb=" N LYS W 14 " --> pdb=" O ARG W 10 " (cutoff:3.500A) Processing helix chain 'W' and resid 28 through 35 Processing helix chain 'W' and resid 37 through 55 removed outlier: 3.656A pdb=" N ILE W 52 " --> pdb=" O PHE W 48 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N VAL W 53 " --> pdb=" O VAL W 49 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N SER W 54 " --> pdb=" O ASP W 50 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ASN W 55 " --> pdb=" O LEU W 51 " (cutoff:3.500A) Processing helix chain 'W' and resid 60 through 78 removed outlier: 3.650A pdb=" N GLY W 78 " --> pdb=" O VAL W 74 " (cutoff:3.500A) Processing helix chain 'W' and resid 80 through 103 Processing helix chain 'W' and resid 116 through 155 removed outlier: 4.504A pdb=" N GLU W 121 " --> pdb=" O TYR W 117 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N THR W 138 " --> pdb=" O ALA W 134 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP W 139 " --> pdb=" O TYR W 135 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ALA W 155 " --> pdb=" O GLN W 151 " (cutoff:3.500A) Processing helix chain 'W' and resid 174 through 193 removed outlier: 4.619A pdb=" N ARG W 193 " --> pdb=" O VAL W 189 " (cutoff:3.500A) Processing helix chain 'W' and resid 208 through 226 Processing helix chain 'W' and resid 235 through 240 Processing helix chain 'W' and resid 257 through 270 removed outlier: 4.226A pdb=" N ASN W 270 " --> pdb=" O LEU W 266 " (cutoff:3.500A) Processing helix chain 'Y' and resid 7 through 20 removed outlier: 4.613A pdb=" N THR Y 11 " --> pdb=" O ASN Y 7 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LYS Y 14 " --> pdb=" O ARG Y 10 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 35 Processing helix chain 'Y' and resid 37 through 55 removed outlier: 3.616A pdb=" N LEU Y 51 " --> pdb=" O GLU Y 47 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE Y 52 " --> pdb=" O PHE Y 48 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N VAL Y 53 " --> pdb=" O VAL Y 49 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER Y 54 " --> pdb=" O ASP Y 50 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ASN Y 55 " --> pdb=" O LEU Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 60 through 78 removed outlier: 3.555A pdb=" N GLY Y 78 " --> pdb=" O VAL Y 74 " (cutoff:3.500A) Processing helix chain 'Y' and resid 80 through 103 removed outlier: 3.569A pdb=" N ASP Y 103 " --> pdb=" O MET Y 99 " (cutoff:3.500A) Processing helix chain 'Y' and resid 116 through 155 removed outlier: 4.596A pdb=" N GLU Y 121 " --> pdb=" O TYR Y 117 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA Y 136 " --> pdb=" O VAL Y 132 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP Y 137 " --> pdb=" O THR Y 133 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N THR Y 138 " --> pdb=" O ALA Y 134 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TRP Y 139 " --> pdb=" O TYR Y 135 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ALA Y 155 " --> pdb=" O GLN Y 151 " (cutoff:3.500A) Processing helix chain 'Y' and resid 174 through 193 removed outlier: 4.763A pdb=" N ARG Y 193 " --> pdb=" O VAL Y 189 " (cutoff:3.500A) Processing helix chain 'Y' and resid 208 through 226 Processing helix chain 'Y' and resid 235 through 240 Processing helix chain 'Y' and resid 257 through 270 removed outlier: 3.706A pdb=" N ASN Y 270 " --> pdb=" O LEU Y 266 " (cutoff:3.500A) Processing helix chain 'f' and resid 7 through 20 removed outlier: 4.224A pdb=" N THR f 11 " --> pdb=" O ASN f 7 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LYS f 14 " --> pdb=" O ARG f 10 " (cutoff:3.500A) Processing helix chain 'f' and resid 28 through 35 Processing helix chain 'f' and resid 37 through 55 removed outlier: 3.799A pdb=" N ILE f 52 " --> pdb=" O PHE f 48 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N VAL f 53 " --> pdb=" O VAL f 49 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER f 54 " --> pdb=" O ASP f 50 " (cutoff:3.500A) removed outlier: 5.362A pdb=" N ASN f 55 " --> pdb=" O LEU f 51 " (cutoff:3.500A) Processing helix chain 'f' and resid 60 through 78 removed outlier: 3.964A pdb=" N GLU f 65 " --> pdb=" O SER f 61 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY f 78 " --> pdb=" O VAL f 74 " (cutoff:3.500A) Processing helix chain 'f' and resid 80 through 103 Processing helix chain 'f' and resid 116 through 155 removed outlier: 4.598A pdb=" N GLU f 121 " --> pdb=" O TYR f 117 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR f 138 " --> pdb=" O ALA f 134 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TRP f 139 " --> pdb=" O TYR f 135 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER f 154 " --> pdb=" O LEU f 150 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N ALA f 155 " --> pdb=" O GLN f 151 " (cutoff:3.500A) Processing helix chain 'f' and resid 174 through 193 Processing helix chain 'f' and resid 208 through 226 Processing helix chain 'f' and resid 235 through 240 Processing helix chain 'f' and resid 257 through 270 removed outlier: 3.973A pdb=" N ASN f 270 " --> pdb=" O LEU f 266 " (cutoff:3.500A) Processing helix chain 'h' and resid 7 through 20 removed outlier: 4.592A pdb=" N THR h 11 " --> pdb=" O ASN h 7 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LYS h 14 " --> pdb=" O ARG h 10 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 35 Processing helix chain 'h' and resid 37 through 55 removed outlier: 3.655A pdb=" N LEU h 51 " --> pdb=" O GLU h 47 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE h 52 " --> pdb=" O PHE h 48 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL h 53 " --> pdb=" O VAL h 49 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER h 54 " --> pdb=" O ASP h 50 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N ASN h 55 " --> pdb=" O LEU h 51 " (cutoff:3.500A) Processing helix chain 'h' and resid 60 through 78 Processing helix chain 'h' and resid 80 through 103 removed outlier: 3.697A pdb=" N ASP h 103 " --> pdb=" O MET h 99 " (cutoff:3.500A) Processing helix chain 'h' and resid 116 through 155 removed outlier: 4.503A pdb=" N GLU h 121 " --> pdb=" O TYR h 117 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N ALA h 136 " --> pdb=" O VAL h 132 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP h 137 " --> pdb=" O THR h 133 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N THR h 138 " --> pdb=" O ALA h 134 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TRP h 139 " --> pdb=" O TYR h 135 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N ALA h 155 " --> pdb=" O GLN h 151 " (cutoff:3.500A) Processing helix chain 'h' and resid 174 through 193 removed outlier: 4.972A pdb=" N ARG h 193 " --> pdb=" O VAL h 189 " (cutoff:3.500A) Processing helix chain 'h' and resid 208 through 226 Processing helix chain 'h' and resid 235 through 240 Processing helix chain 'h' and resid 257 through 270 removed outlier: 4.108A pdb=" N ASN h 270 " --> pdb=" O LEU h 266 " (cutoff:3.500A) Processing helix chain 'l' and resid 7 through 20 removed outlier: 4.328A pdb=" N THR l 11 " --> pdb=" O ASN l 7 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LYS l 14 " --> pdb=" O ARG l 10 " (cutoff:3.500A) Processing helix chain 'l' and resid 28 through 35 Processing helix chain 'l' and resid 37 through 55 removed outlier: 3.656A pdb=" N ILE l 52 " --> pdb=" O PHE l 48 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL l 53 " --> pdb=" O VAL l 49 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N SER l 54 " --> pdb=" O ASP l 50 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ASN l 55 " --> pdb=" O LEU l 51 " (cutoff:3.500A) Processing helix chain 'l' and resid 60 through 78 removed outlier: 3.651A pdb=" N GLY l 78 " --> pdb=" O VAL l 74 " (cutoff:3.500A) Processing helix chain 'l' and resid 80 through 103 Processing helix chain 'l' and resid 116 through 155 removed outlier: 4.503A pdb=" N GLU l 121 " --> pdb=" O TYR l 117 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N THR l 138 " --> pdb=" O ALA l 134 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N TRP l 139 " --> pdb=" O TYR l 135 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ALA l 155 " --> pdb=" O GLN l 151 " (cutoff:3.500A) Processing helix chain 'l' and resid 174 through 193 removed outlier: 4.619A pdb=" N ARG l 193 " --> pdb=" O VAL l 189 " (cutoff:3.500A) Processing helix chain 'l' and resid 208 through 226 Processing helix chain 'l' and resid 235 through 240 Processing helix chain 'l' and resid 257 through 270 removed outlier: 4.225A pdb=" N ASN l 270 " --> pdb=" O LEU l 266 " (cutoff:3.500A) Processing helix chain 'n' and resid 7 through 20 removed outlier: 4.614A pdb=" N THR n 11 " --> pdb=" O ASN n 7 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LYS n 14 " --> pdb=" O ARG n 10 " (cutoff:3.500A) Processing helix chain 'n' and resid 28 through 35 Processing helix chain 'n' and resid 37 through 55 removed outlier: 3.616A pdb=" N LEU n 51 " --> pdb=" O GLU n 47 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE n 52 " --> pdb=" O PHE n 48 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N VAL n 53 " --> pdb=" O VAL n 49 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER n 54 " --> pdb=" O ASP n 50 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N ASN n 55 " --> pdb=" O LEU n 51 " (cutoff:3.500A) Processing helix chain 'n' and resid 60 through 78 removed outlier: 3.555A pdb=" N GLY n 78 " --> pdb=" O VAL n 74 " (cutoff:3.500A) Processing helix chain 'n' and resid 80 through 103 removed outlier: 3.570A pdb=" N ASP n 103 " --> pdb=" O MET n 99 " (cutoff:3.500A) Processing helix chain 'n' and resid 116 through 155 removed outlier: 4.595A pdb=" N GLU n 121 " --> pdb=" O TYR n 117 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA n 136 " --> pdb=" O VAL n 132 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP n 137 " --> pdb=" O THR n 133 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N THR n 138 " --> pdb=" O ALA n 134 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N TRP n 139 " --> pdb=" O TYR n 135 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ALA n 155 " --> pdb=" O GLN n 151 " (cutoff:3.500A) Processing helix chain 'n' and resid 174 through 193 removed outlier: 4.764A pdb=" N ARG n 193 " --> pdb=" O VAL n 189 " (cutoff:3.500A) Processing helix chain 'n' and resid 208 through 226 Processing helix chain 'n' and resid 235 through 240 Processing helix chain 'n' and resid 257 through 270 removed outlier: 3.707A pdb=" N ASN n 270 " --> pdb=" O LEU n 266 " (cutoff:3.500A) Processing helix chain 'u' and resid 7 through 20 removed outlier: 4.224A pdb=" N THR u 11 " --> pdb=" O ASN u 7 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N LYS u 14 " --> pdb=" O ARG u 10 " (cutoff:3.500A) Processing helix chain 'u' and resid 28 through 35 Processing helix chain 'u' and resid 37 through 55 removed outlier: 3.800A pdb=" N ILE u 52 " --> pdb=" O PHE u 48 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N VAL u 53 " --> pdb=" O VAL u 49 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N SER u 54 " --> pdb=" O ASP u 50 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N ASN u 55 " --> pdb=" O LEU u 51 " (cutoff:3.500A) Processing helix chain 'u' and resid 60 through 78 removed outlier: 3.964A pdb=" N GLU u 65 " --> pdb=" O SER u 61 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N GLY u 78 " --> pdb=" O VAL u 74 " (cutoff:3.500A) Processing helix chain 'u' and resid 80 through 103 Processing helix chain 'u' and resid 116 through 155 removed outlier: 4.598A pdb=" N GLU u 121 " --> pdb=" O TYR u 117 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N THR u 138 " --> pdb=" O ALA u 134 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TRP u 139 " --> pdb=" O TYR u 135 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N SER u 154 " --> pdb=" O LEU u 150 " (cutoff:3.500A) removed outlier: 4.964A pdb=" N ALA u 155 " --> pdb=" O GLN u 151 " (cutoff:3.500A) Processing helix chain 'u' and resid 174 through 193 Processing helix chain 'u' and resid 208 through 226 Processing helix chain 'u' and resid 235 through 240 Processing helix chain 'u' and resid 257 through 270 removed outlier: 3.974A pdb=" N ASN u 270 " --> pdb=" O LEU u 266 " (cutoff:3.500A) Processing helix chain 'w' and resid 7 through 20 removed outlier: 4.592A pdb=" N THR w 11 " --> pdb=" O ASN w 7 " (cutoff:3.500A) removed outlier: 4.895A pdb=" N LYS w 14 " --> pdb=" O ARG w 10 " (cutoff:3.500A) Processing helix chain 'w' and resid 28 through 35 Processing helix chain 'w' and resid 37 through 55 removed outlier: 3.655A pdb=" N LEU w 51 " --> pdb=" O GLU w 47 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE w 52 " --> pdb=" O PHE w 48 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL w 53 " --> pdb=" O VAL w 49 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N SER w 54 " --> pdb=" O ASP w 50 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N ASN w 55 " --> pdb=" O LEU w 51 " (cutoff:3.500A) Processing helix chain 'w' and resid 60 through 78 Processing helix chain 'w' and resid 80 through 103 removed outlier: 3.697A pdb=" N ASP w 103 " --> pdb=" O MET w 99 " (cutoff:3.500A) Processing helix chain 'w' and resid 116 through 155 removed outlier: 4.503A pdb=" N GLU w 121 " --> pdb=" O TYR w 117 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ALA w 136 " --> pdb=" O VAL w 132 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ASP w 137 " --> pdb=" O THR w 133 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N THR w 138 " --> pdb=" O ALA w 134 " (cutoff:3.500A) removed outlier: 4.566A pdb=" N TRP w 139 " --> pdb=" O TYR w 135 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N ALA w 155 " --> pdb=" O GLN w 151 " (cutoff:3.500A) Processing helix chain 'w' and resid 174 through 193 removed outlier: 4.972A pdb=" N ARG w 193 " --> pdb=" O VAL w 189 " (cutoff:3.500A) Processing helix chain 'w' and resid 208 through 226 Processing helix chain 'w' and resid 235 through 240 Processing helix chain 'w' and resid 257 through 270 removed outlier: 4.109A pdb=" N ASN w 270 " --> pdb=" O LEU w 266 " (cutoff:3.500A) Processing helix chain '0' and resid 7 through 20 removed outlier: 4.328A pdb=" N THR 0 11 " --> pdb=" O ASN 0 7 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LYS 0 14 " --> pdb=" O ARG 0 10 " (cutoff:3.500A) Processing helix chain '0' and resid 28 through 35 Processing helix chain '0' and resid 37 through 55 removed outlier: 3.655A pdb=" N ILE 0 52 " --> pdb=" O PHE 0 48 " (cutoff:3.500A) removed outlier: 5.126A pdb=" N VAL 0 53 " --> pdb=" O VAL 0 49 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER 0 54 " --> pdb=" O ASP 0 50 " (cutoff:3.500A) removed outlier: 5.113A pdb=" N ASN 0 55 " --> pdb=" O LEU 0 51 " (cutoff:3.500A) Processing helix chain '0' and resid 60 through 78 removed outlier: 3.651A pdb=" N GLY 0 78 " --> pdb=" O VAL 0 74 " (cutoff:3.500A) Processing helix chain '0' and resid 80 through 103 Processing helix chain '0' and resid 116 through 155 removed outlier: 4.504A pdb=" N GLU 0 121 " --> pdb=" O TYR 0 117 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N THR 0 138 " --> pdb=" O ALA 0 134 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TRP 0 139 " --> pdb=" O TYR 0 135 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N ALA 0 155 " --> pdb=" O GLN 0 151 " (cutoff:3.500A) Processing helix chain '0' and resid 174 through 193 removed outlier: 4.620A pdb=" N ARG 0 193 " --> pdb=" O VAL 0 189 " (cutoff:3.500A) Processing helix chain '0' and resid 208 through 226 Processing helix chain '0' and resid 235 through 240 Processing helix chain '0' and resid 257 through 270 removed outlier: 4.226A pdb=" N ASN 0 270 " --> pdb=" O LEU 0 266 " (cutoff:3.500A) Processing helix chain '2' and resid 7 through 20 removed outlier: 4.613A pdb=" N THR 2 11 " --> pdb=" O ASN 2 7 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N LYS 2 14 " --> pdb=" O ARG 2 10 " (cutoff:3.500A) Processing helix chain '2' and resid 28 through 35 Processing helix chain '2' and resid 37 through 55 removed outlier: 3.618A pdb=" N LEU 2 51 " --> pdb=" O GLU 2 47 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N ILE 2 52 " --> pdb=" O PHE 2 48 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N VAL 2 53 " --> pdb=" O VAL 2 49 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER 2 54 " --> pdb=" O ASP 2 50 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ASN 2 55 " --> pdb=" O LEU 2 51 " (cutoff:3.500A) Processing helix chain '2' and resid 60 through 78 removed outlier: 3.555A pdb=" N GLY 2 78 " --> pdb=" O VAL 2 74 " (cutoff:3.500A) Processing helix chain '2' and resid 80 through 103 removed outlier: 3.570A pdb=" N ASP 2 103 " --> pdb=" O MET 2 99 " (cutoff:3.500A) Processing helix chain '2' and resid 116 through 155 removed outlier: 4.595A pdb=" N GLU 2 121 " --> pdb=" O TYR 2 117 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ALA 2 136 " --> pdb=" O VAL 2 132 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASP 2 137 " --> pdb=" O THR 2 133 " (cutoff:3.500A) removed outlier: 5.193A pdb=" N THR 2 138 " --> pdb=" O ALA 2 134 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N TRP 2 139 " --> pdb=" O TYR 2 135 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ALA 2 155 " --> pdb=" O GLN 2 151 " (cutoff:3.500A) Processing helix chain '2' and resid 174 through 193 removed outlier: 4.763A pdb=" N ARG 2 193 " --> pdb=" O VAL 2 189 " (cutoff:3.500A) Processing helix chain '2' and resid 208 through 226 Processing helix chain '2' and resid 235 through 240 Processing helix chain '2' and resid 257 through 270 removed outlier: 3.706A pdb=" N ASN 2 270 " --> pdb=" O LEU 2 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 40 removed outlier: 4.389A pdb=" N SER E 40 " --> pdb=" O ILE E 36 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 73 Processing helix chain 'E' and resid 83 through 93 removed outlier: 4.230A pdb=" N THR E 88 " --> pdb=" O ALA E 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 118 removed outlier: 3.692A pdb=" N GLU E 118 " --> pdb=" O GLN E 114 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 40 removed outlier: 5.244A pdb=" N VAL F 26 " --> pdb=" O ASP F 22 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER F 40 " --> pdb=" O ILE F 36 " (cutoff:3.500A) Processing helix chain 'F' and resid 55 through 73 removed outlier: 3.826A pdb=" N MET F 72 " --> pdb=" O MET F 68 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 Processing helix chain 'F' and resid 104 through 118 removed outlier: 3.965A pdb=" N GLU F 118 " --> pdb=" O GLN F 114 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 40 removed outlier: 4.420A pdb=" N SER I 40 " --> pdb=" O ILE I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 55 through 73 Processing helix chain 'I' and resid 83 through 93 Processing helix chain 'I' and resid 104 through 118 removed outlier: 3.803A pdb=" N GLU I 118 " --> pdb=" O GLN I 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 40 removed outlier: 4.635A pdb=" N SER N 40 " --> pdb=" O ILE N 36 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 73 Processing helix chain 'N' and resid 83 through 93 removed outlier: 4.063A pdb=" N LEU N 92 " --> pdb=" O THR N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 104 through 118 removed outlier: 3.757A pdb=" N GLU N 118 " --> pdb=" O GLN N 114 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 40 removed outlier: 4.464A pdb=" N SER O 40 " --> pdb=" O ILE O 36 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 73 removed outlier: 4.151A pdb=" N MET O 72 " --> pdb=" O MET O 68 " (cutoff:3.500A) Processing helix chain 'O' and resid 83 through 93 Processing helix chain 'O' and resid 104 through 118 Processing helix chain 'T' and resid 22 through 40 removed outlier: 4.390A pdb=" N SER T 40 " --> pdb=" O ILE T 36 " (cutoff:3.500A) Processing helix chain 'T' and resid 55 through 73 Processing helix chain 'T' and resid 83 through 93 removed outlier: 4.231A pdb=" N THR T 88 " --> pdb=" O ALA T 84 " (cutoff:3.500A) Processing helix chain 'T' and resid 104 through 118 removed outlier: 3.691A pdb=" N GLU T 118 " --> pdb=" O GLN T 114 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 40 removed outlier: 5.243A pdb=" N VAL U 26 " --> pdb=" O ASP U 22 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER U 40 " --> pdb=" O ILE U 36 " (cutoff:3.500A) Processing helix chain 'U' and resid 55 through 73 removed outlier: 3.825A pdb=" N MET U 72 " --> pdb=" O MET U 68 " (cutoff:3.500A) Processing helix chain 'U' and resid 83 through 93 Processing helix chain 'U' and resid 104 through 118 removed outlier: 3.966A pdb=" N GLU U 118 " --> pdb=" O GLN U 114 " (cutoff:3.500A) Processing helix chain 'X' and resid 22 through 40 removed outlier: 4.420A pdb=" N SER X 40 " --> pdb=" O ILE X 36 " (cutoff:3.500A) Processing helix chain 'X' and resid 55 through 73 Processing helix chain 'X' and resid 83 through 93 Processing helix chain 'X' and resid 104 through 118 removed outlier: 3.803A pdb=" N GLU X 118 " --> pdb=" O GLN X 114 " (cutoff:3.500A) Processing helix chain 'a' and resid 22 through 40 removed outlier: 4.635A pdb=" N SER a 40 " --> pdb=" O ILE a 36 " (cutoff:3.500A) Processing helix chain 'a' and resid 55 through 73 Processing helix chain 'a' and resid 83 through 93 removed outlier: 4.063A pdb=" N LEU a 92 " --> pdb=" O THR a 88 " (cutoff:3.500A) Processing helix chain 'a' and resid 104 through 118 removed outlier: 3.758A pdb=" N GLU a 118 " --> pdb=" O GLN a 114 " (cutoff:3.500A) Processing helix chain 'b' and resid 22 through 40 removed outlier: 4.464A pdb=" N SER b 40 " --> pdb=" O ILE b 36 " (cutoff:3.500A) Processing helix chain 'b' and resid 55 through 73 removed outlier: 4.152A pdb=" N MET b 72 " --> pdb=" O MET b 68 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 93 Processing helix chain 'b' and resid 104 through 118 Processing helix chain 'i' and resid 22 through 40 removed outlier: 4.389A pdb=" N SER i 40 " --> pdb=" O ILE i 36 " (cutoff:3.500A) Processing helix chain 'i' and resid 55 through 73 Processing helix chain 'i' and resid 83 through 93 removed outlier: 4.230A pdb=" N THR i 88 " --> pdb=" O ALA i 84 " (cutoff:3.500A) Processing helix chain 'i' and resid 104 through 118 removed outlier: 3.691A pdb=" N GLU i 118 " --> pdb=" O GLN i 114 " (cutoff:3.500A) Processing helix chain 'j' and resid 22 through 40 removed outlier: 5.244A pdb=" N VAL j 26 " --> pdb=" O ASP j 22 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N SER j 40 " --> pdb=" O ILE j 36 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 73 removed outlier: 3.826A pdb=" N MET j 72 " --> pdb=" O MET j 68 " (cutoff:3.500A) Processing helix chain 'j' and resid 83 through 93 Processing helix chain 'j' and resid 104 through 118 removed outlier: 3.965A pdb=" N GLU j 118 " --> pdb=" O GLN j 114 " (cutoff:3.500A) Processing helix chain 'm' and resid 22 through 40 removed outlier: 4.420A pdb=" N SER m 40 " --> pdb=" O ILE m 36 " (cutoff:3.500A) Processing helix chain 'm' and resid 55 through 73 Processing helix chain 'm' and resid 83 through 93 Processing helix chain 'm' and resid 104 through 118 removed outlier: 3.803A pdb=" N GLU m 118 " --> pdb=" O GLN m 114 " (cutoff:3.500A) Processing helix chain 'p' and resid 22 through 40 removed outlier: 4.635A pdb=" N SER p 40 " --> pdb=" O ILE p 36 " (cutoff:3.500A) Processing helix chain 'p' and resid 55 through 73 Processing helix chain 'p' and resid 83 through 93 removed outlier: 4.062A pdb=" N LEU p 92 " --> pdb=" O THR p 88 " (cutoff:3.500A) Processing helix chain 'p' and resid 104 through 118 removed outlier: 3.757A pdb=" N GLU p 118 " --> pdb=" O GLN p 114 " (cutoff:3.500A) Processing helix chain 'q' and resid 22 through 40 removed outlier: 4.464A pdb=" N SER q 40 " --> pdb=" O ILE q 36 " (cutoff:3.500A) Processing helix chain 'q' and resid 55 through 73 removed outlier: 4.147A pdb=" N MET q 72 " --> pdb=" O MET q 68 " (cutoff:3.500A) Processing helix chain 'q' and resid 83 through 93 Processing helix chain 'q' and resid 104 through 118 Processing helix chain 'x' and resid 22 through 40 removed outlier: 4.389A pdb=" N SER x 40 " --> pdb=" O ILE x 36 " (cutoff:3.500A) Processing helix chain 'x' and resid 55 through 73 Processing helix chain 'x' and resid 83 through 93 removed outlier: 4.230A pdb=" N THR x 88 " --> pdb=" O ALA x 84 " (cutoff:3.500A) Processing helix chain 'x' and resid 104 through 118 removed outlier: 3.692A pdb=" N GLU x 118 " --> pdb=" O GLN x 114 " (cutoff:3.500A) Processing helix chain 'y' and resid 22 through 40 removed outlier: 5.244A pdb=" N VAL y 26 " --> pdb=" O ASP y 22 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N SER y 40 " --> pdb=" O ILE y 36 " (cutoff:3.500A) Processing helix chain 'y' and resid 55 through 73 removed outlier: 3.825A pdb=" N MET y 72 " --> pdb=" O MET y 68 " (cutoff:3.500A) Processing helix chain 'y' and resid 83 through 93 Processing helix chain 'y' and resid 104 through 118 removed outlier: 3.965A pdb=" N GLU y 118 " --> pdb=" O GLN y 114 " (cutoff:3.500A) Processing helix chain '1' and resid 22 through 40 removed outlier: 4.420A pdb=" N SER 1 40 " --> pdb=" O ILE 1 36 " (cutoff:3.500A) Processing helix chain '1' and resid 55 through 73 Processing helix chain '1' and resid 83 through 93 Processing helix chain '1' and resid 104 through 118 removed outlier: 3.803A pdb=" N GLU 1 118 " --> pdb=" O GLN 1 114 " (cutoff:3.500A) Processing helix chain '4' and resid 22 through 40 removed outlier: 4.635A pdb=" N SER 4 40 " --> pdb=" O ILE 4 36 " (cutoff:3.500A) Processing helix chain '4' and resid 55 through 73 Processing helix chain '4' and resid 83 through 93 removed outlier: 4.063A pdb=" N LEU 4 92 " --> pdb=" O THR 4 88 " (cutoff:3.500A) Processing helix chain '4' and resid 104 through 118 removed outlier: 3.758A pdb=" N GLU 4 118 " --> pdb=" O GLN 4 114 " (cutoff:3.500A) Processing helix chain '5' and resid 22 through 40 removed outlier: 4.464A pdb=" N SER 5 40 " --> pdb=" O ILE 5 36 " (cutoff:3.500A) Processing helix chain '5' and resid 55 through 73 removed outlier: 4.151A pdb=" N MET 5 72 " --> pdb=" O MET 5 68 " (cutoff:3.500A) Processing helix chain '5' and resid 83 through 93 Processing helix chain '5' and resid 104 through 118 Processing helix chain 'M' and resid 3 through 20 removed outlier: 5.063A pdb=" N THR M 11 " --> pdb=" O ASN M 7 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LYS M 14 " --> pdb=" O ARG M 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 23 through 28 removed outlier: 4.003A pdb=" N GLN M 27 " --> pdb=" O GLU M 23 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N SER M 28 " --> pdb=" O MET M 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 23 through 28' Processing helix chain 'M' and resid 29 through 36 Processing helix chain 'M' and resid 37 through 55 removed outlier: 3.697A pdb=" N LEU M 51 " --> pdb=" O GLU M 47 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N ILE M 52 " --> pdb=" O PHE M 48 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL M 53 " --> pdb=" O VAL M 49 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER M 54 " --> pdb=" O ASP M 50 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASN M 55 " --> pdb=" O LEU M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 60 through 78 removed outlier: 3.540A pdb=" N GLY M 78 " --> pdb=" O VAL M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 102 Processing helix chain 'M' and resid 113 through 156 removed outlier: 3.703A pdb=" N TYR M 117 " --> pdb=" O GLU M 113 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU M 121 " --> pdb=" O TYR M 117 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA M 136 " --> pdb=" O VAL M 132 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP M 137 " --> pdb=" O THR M 133 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N THR M 138 " --> pdb=" O ALA M 134 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TRP M 139 " --> pdb=" O TYR M 135 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA M 155 " --> pdb=" O GLN M 151 " (cutoff:3.500A) Proline residue: M 156 - end of helix Processing helix chain 'M' and resid 176 through 193 removed outlier: 4.781A pdb=" N ARG M 193 " --> pdb=" O VAL M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 208 through 226 Processing helix chain 'M' and resid 235 through 240 Processing helix chain 'M' and resid 257 through 270 removed outlier: 3.728A pdb=" N ASN M 270 " --> pdb=" O LEU M 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 3 through 20 removed outlier: 5.063A pdb=" N THR Z 11 " --> pdb=" O ASN Z 7 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LYS Z 14 " --> pdb=" O ARG Z 10 " (cutoff:3.500A) Processing helix chain 'Z' and resid 23 through 28 removed outlier: 4.003A pdb=" N GLN Z 27 " --> pdb=" O GLU Z 23 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N SER Z 28 " --> pdb=" O MET Z 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 23 through 28' Processing helix chain 'Z' and resid 29 through 36 Processing helix chain 'Z' and resid 37 through 55 removed outlier: 3.697A pdb=" N LEU Z 51 " --> pdb=" O GLU Z 47 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE Z 52 " --> pdb=" O PHE Z 48 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL Z 53 " --> pdb=" O VAL Z 49 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N SER Z 54 " --> pdb=" O ASP Z 50 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ASN Z 55 " --> pdb=" O LEU Z 51 " (cutoff:3.500A) Processing helix chain 'Z' and resid 60 through 78 removed outlier: 3.541A pdb=" N GLY Z 78 " --> pdb=" O VAL Z 74 " (cutoff:3.500A) Processing helix chain 'Z' and resid 80 through 102 Processing helix chain 'Z' and resid 113 through 156 removed outlier: 3.703A pdb=" N TYR Z 117 " --> pdb=" O GLU Z 113 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU Z 121 " --> pdb=" O TYR Z 117 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA Z 136 " --> pdb=" O VAL Z 132 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP Z 137 " --> pdb=" O THR Z 133 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N THR Z 138 " --> pdb=" O ALA Z 134 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TRP Z 139 " --> pdb=" O TYR Z 135 " (cutoff:3.500A) removed outlier: 4.706A pdb=" N ALA Z 155 " --> pdb=" O GLN Z 151 " (cutoff:3.500A) Proline residue: Z 156 - end of helix Processing helix chain 'Z' and resid 176 through 193 removed outlier: 4.782A pdb=" N ARG Z 193 " --> pdb=" O VAL Z 189 " (cutoff:3.500A) Processing helix chain 'Z' and resid 208 through 226 Processing helix chain 'Z' and resid 235 through 240 Processing helix chain 'Z' and resid 257 through 270 removed outlier: 3.727A pdb=" N ASN Z 270 " --> pdb=" O LEU Z 266 " (cutoff:3.500A) Processing helix chain 'o' and resid 3 through 20 removed outlier: 5.064A pdb=" N THR o 11 " --> pdb=" O ASN o 7 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LYS o 14 " --> pdb=" O ARG o 10 " (cutoff:3.500A) Processing helix chain 'o' and resid 23 through 28 removed outlier: 4.003A pdb=" N GLN o 27 " --> pdb=" O GLU o 23 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N SER o 28 " --> pdb=" O MET o 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 23 through 28' Processing helix chain 'o' and resid 29 through 36 Processing helix chain 'o' and resid 37 through 55 removed outlier: 3.698A pdb=" N LEU o 51 " --> pdb=" O GLU o 47 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE o 52 " --> pdb=" O PHE o 48 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N VAL o 53 " --> pdb=" O VAL o 49 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER o 54 " --> pdb=" O ASP o 50 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASN o 55 " --> pdb=" O LEU o 51 " (cutoff:3.500A) Processing helix chain 'o' and resid 60 through 78 removed outlier: 3.540A pdb=" N GLY o 78 " --> pdb=" O VAL o 74 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 102 Processing helix chain 'o' and resid 113 through 156 removed outlier: 3.703A pdb=" N TYR o 117 " --> pdb=" O GLU o 113 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU o 121 " --> pdb=" O TYR o 117 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA o 136 " --> pdb=" O VAL o 132 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP o 137 " --> pdb=" O THR o 133 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N THR o 138 " --> pdb=" O ALA o 134 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TRP o 139 " --> pdb=" O TYR o 135 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA o 155 " --> pdb=" O GLN o 151 " (cutoff:3.500A) Proline residue: o 156 - end of helix Processing helix chain 'o' and resid 176 through 193 removed outlier: 4.782A pdb=" N ARG o 193 " --> pdb=" O VAL o 189 " (cutoff:3.500A) Processing helix chain 'o' and resid 208 through 226 Processing helix chain 'o' and resid 235 through 240 Processing helix chain 'o' and resid 257 through 270 removed outlier: 3.728A pdb=" N ASN o 270 " --> pdb=" O LEU o 266 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 20 removed outlier: 5.063A pdb=" N THR 3 11 " --> pdb=" O ASN 3 7 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N LYS 3 14 " --> pdb=" O ARG 3 10 " (cutoff:3.500A) Processing helix chain '3' and resid 23 through 28 removed outlier: 4.003A pdb=" N GLN 3 27 " --> pdb=" O GLU 3 23 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N SER 3 28 " --> pdb=" O MET 3 24 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 23 through 28' Processing helix chain '3' and resid 29 through 36 Processing helix chain '3' and resid 37 through 55 removed outlier: 3.697A pdb=" N LEU 3 51 " --> pdb=" O GLU 3 47 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE 3 52 " --> pdb=" O PHE 3 48 " (cutoff:3.500A) removed outlier: 5.448A pdb=" N VAL 3 53 " --> pdb=" O VAL 3 49 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER 3 54 " --> pdb=" O ASP 3 50 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ASN 3 55 " --> pdb=" O LEU 3 51 " (cutoff:3.500A) Processing helix chain '3' and resid 60 through 78 removed outlier: 3.540A pdb=" N GLY 3 78 " --> pdb=" O VAL 3 74 " (cutoff:3.500A) Processing helix chain '3' and resid 80 through 102 Processing helix chain '3' and resid 113 through 156 removed outlier: 3.703A pdb=" N TYR 3 117 " --> pdb=" O GLU 3 113 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N GLU 3 121 " --> pdb=" O TYR 3 117 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ALA 3 136 " --> pdb=" O VAL 3 132 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ASP 3 137 " --> pdb=" O THR 3 133 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N THR 3 138 " --> pdb=" O ALA 3 134 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TRP 3 139 " --> pdb=" O TYR 3 135 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N ALA 3 155 " --> pdb=" O GLN 3 151 " (cutoff:3.500A) Proline residue: 3 156 - end of helix Processing helix chain '3' and resid 176 through 193 removed outlier: 4.782A pdb=" N ARG 3 193 " --> pdb=" O VAL 3 189 " (cutoff:3.500A) Processing helix chain '3' and resid 208 through 226 Processing helix chain '3' and resid 235 through 240 Processing helix chain '3' and resid 257 through 270 removed outlier: 3.727A pdb=" N ASN 3 270 " --> pdb=" O LEU 3 266 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 24 removed outlier: 3.743A pdb=" N THR P 11 " --> pdb=" O ASN P 7 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LYS P 14 " --> pdb=" O ARG P 10 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP P 15 " --> pdb=" O THR P 11 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 37 removed outlier: 3.619A pdb=" N LYS P 37 " --> pdb=" O ASN P 33 " (cutoff:3.500A) Processing helix chain 'P' and resid 38 through 55 removed outlier: 3.929A pdb=" N ILE P 52 " --> pdb=" O PHE P 48 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL P 53 " --> pdb=" O VAL P 49 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER P 54 " --> pdb=" O ASP P 50 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN P 55 " --> pdb=" O LEU P 51 " (cutoff:3.500A) Processing helix chain 'P' and resid 60 through 78 removed outlier: 3.529A pdb=" N GLY P 78 " --> pdb=" O VAL P 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 80 through 103 Processing helix chain 'P' and resid 113 through 155 removed outlier: 4.146A pdb=" N TYR P 117 " --> pdb=" O GLU P 113 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA P 136 " --> pdb=" O VAL P 132 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP P 137 " --> pdb=" O THR P 133 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N THR P 138 " --> pdb=" O ALA P 134 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TRP P 139 " --> pdb=" O TYR P 135 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ALA P 155 " --> pdb=" O GLN P 151 " (cutoff:3.500A) Processing helix chain 'P' and resid 176 through 193 removed outlier: 4.833A pdb=" N ARG P 193 " --> pdb=" O VAL P 189 " (cutoff:3.500A) Processing helix chain 'P' and resid 208 through 226 Processing helix chain 'P' and resid 235 through 246 removed outlier: 4.230A pdb=" N GLY P 246 " --> pdb=" O ILE P 242 " (cutoff:3.500A) Processing helix chain 'P' and resid 257 through 270 Processing helix chain 'c' and resid 7 through 24 removed outlier: 3.743A pdb=" N THR c 11 " --> pdb=" O ASN c 7 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N LYS c 14 " --> pdb=" O ARG c 10 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP c 15 " --> pdb=" O THR c 11 " (cutoff:3.500A) Processing helix chain 'c' and resid 28 through 37 removed outlier: 3.619A pdb=" N LYS c 37 " --> pdb=" O ASN c 33 " (cutoff:3.500A) Processing helix chain 'c' and resid 38 through 55 removed outlier: 3.929A pdb=" N ILE c 52 " --> pdb=" O PHE c 48 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL c 53 " --> pdb=" O VAL c 49 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER c 54 " --> pdb=" O ASP c 50 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN c 55 " --> pdb=" O LEU c 51 " (cutoff:3.500A) Processing helix chain 'c' and resid 60 through 78 removed outlier: 3.529A pdb=" N GLY c 78 " --> pdb=" O VAL c 74 " (cutoff:3.500A) Processing helix chain 'c' and resid 80 through 103 Processing helix chain 'c' and resid 113 through 155 removed outlier: 4.147A pdb=" N TYR c 117 " --> pdb=" O GLU c 113 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA c 136 " --> pdb=" O VAL c 132 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ASP c 137 " --> pdb=" O THR c 133 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR c 138 " --> pdb=" O ALA c 134 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TRP c 139 " --> pdb=" O TYR c 135 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ALA c 155 " --> pdb=" O GLN c 151 " (cutoff:3.500A) Processing helix chain 'c' and resid 176 through 193 removed outlier: 4.833A pdb=" N ARG c 193 " --> pdb=" O VAL c 189 " (cutoff:3.500A) Processing helix chain 'c' and resid 208 through 226 Processing helix chain 'c' and resid 235 through 246 removed outlier: 4.229A pdb=" N GLY c 246 " --> pdb=" O ILE c 242 " (cutoff:3.500A) Processing helix chain 'c' and resid 257 through 270 Processing helix chain 'r' and resid 7 through 24 removed outlier: 3.744A pdb=" N THR r 11 " --> pdb=" O ASN r 7 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LYS r 14 " --> pdb=" O ARG r 10 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP r 15 " --> pdb=" O THR r 11 " (cutoff:3.500A) Processing helix chain 'r' and resid 28 through 37 removed outlier: 3.618A pdb=" N LYS r 37 " --> pdb=" O ASN r 33 " (cutoff:3.500A) Processing helix chain 'r' and resid 38 through 55 removed outlier: 3.929A pdb=" N ILE r 52 " --> pdb=" O PHE r 48 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N VAL r 53 " --> pdb=" O VAL r 49 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER r 54 " --> pdb=" O ASP r 50 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN r 55 " --> pdb=" O LEU r 51 " (cutoff:3.500A) Processing helix chain 'r' and resid 60 through 78 removed outlier: 3.530A pdb=" N GLY r 78 " --> pdb=" O VAL r 74 " (cutoff:3.500A) Processing helix chain 'r' and resid 80 through 103 Processing helix chain 'r' and resid 113 through 155 removed outlier: 4.147A pdb=" N TYR r 117 " --> pdb=" O GLU r 113 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA r 136 " --> pdb=" O VAL r 132 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP r 137 " --> pdb=" O THR r 133 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR r 138 " --> pdb=" O ALA r 134 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TRP r 139 " --> pdb=" O TYR r 135 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ALA r 155 " --> pdb=" O GLN r 151 " (cutoff:3.500A) Processing helix chain 'r' and resid 176 through 193 removed outlier: 4.833A pdb=" N ARG r 193 " --> pdb=" O VAL r 189 " (cutoff:3.500A) Processing helix chain 'r' and resid 208 through 226 Processing helix chain 'r' and resid 235 through 246 removed outlier: 4.230A pdb=" N GLY r 246 " --> pdb=" O ILE r 242 " (cutoff:3.500A) Processing helix chain 'r' and resid 257 through 270 Processing helix chain '6' and resid 7 through 24 removed outlier: 3.743A pdb=" N THR 6 11 " --> pdb=" O ASN 6 7 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LYS 6 14 " --> pdb=" O ARG 6 10 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ASP 6 15 " --> pdb=" O THR 6 11 " (cutoff:3.500A) Processing helix chain '6' and resid 28 through 37 removed outlier: 3.619A pdb=" N LYS 6 37 " --> pdb=" O ASN 6 33 " (cutoff:3.500A) Processing helix chain '6' and resid 38 through 55 removed outlier: 3.930A pdb=" N ILE 6 52 " --> pdb=" O PHE 6 48 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N VAL 6 53 " --> pdb=" O VAL 6 49 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER 6 54 " --> pdb=" O ASP 6 50 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ASN 6 55 " --> pdb=" O LEU 6 51 " (cutoff:3.500A) Processing helix chain '6' and resid 60 through 78 removed outlier: 3.530A pdb=" N GLY 6 78 " --> pdb=" O VAL 6 74 " (cutoff:3.500A) Processing helix chain '6' and resid 80 through 103 Processing helix chain '6' and resid 113 through 155 removed outlier: 4.148A pdb=" N TYR 6 117 " --> pdb=" O GLU 6 113 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ALA 6 136 " --> pdb=" O VAL 6 132 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP 6 137 " --> pdb=" O THR 6 133 " (cutoff:3.500A) removed outlier: 4.751A pdb=" N THR 6 138 " --> pdb=" O ALA 6 134 " (cutoff:3.500A) removed outlier: 4.571A pdb=" N TRP 6 139 " --> pdb=" O TYR 6 135 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N ALA 6 155 " --> pdb=" O GLN 6 151 " (cutoff:3.500A) Processing helix chain '6' and resid 176 through 193 removed outlier: 4.833A pdb=" N ARG 6 193 " --> pdb=" O VAL 6 189 " (cutoff:3.500A) Processing helix chain '6' and resid 208 through 226 Processing helix chain '6' and resid 235 through 246 removed outlier: 4.230A pdb=" N GLY 6 246 " --> pdb=" O ILE 6 242 " (cutoff:3.500A) Processing helix chain '6' and resid 257 through 270 Processing sheet with id= 1, first strand: chain 'A' and resid 164 through 168 removed outlier: 3.693A pdb=" N ILE A 199 " --> pdb=" O MET A 230 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C' and resid 164 through 168 Processing sheet with id= 3, first strand: chain 'G' and resid 164 through 168 Processing sheet with id= 4, first strand: chain 'Q' and resid 164 through 168 Processing sheet with id= 5, first strand: chain 'K' and resid 164 through 168 removed outlier: 3.693A pdb=" N ILE K 199 " --> pdb=" O MET K 230 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'R' and resid 164 through 168 Processing sheet with id= 7, first strand: chain 'V' and resid 164 through 168 Processing sheet with id= 8, first strand: chain 'd' and resid 164 through 168 Processing sheet with id= 9, first strand: chain 'e' and resid 164 through 168 removed outlier: 3.692A pdb=" N ILE e 199 " --> pdb=" O MET e 230 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'g' and resid 164 through 168 Processing sheet with id= 11, first strand: chain 'k' and resid 164 through 168 Processing sheet with id= 12, first strand: chain 's' and resid 164 through 168 Processing sheet with id= 13, first strand: chain 't' and resid 164 through 168 removed outlier: 3.692A pdb=" N ILE t 199 " --> pdb=" O MET t 230 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'v' and resid 164 through 168 Processing sheet with id= 15, first strand: chain 'z' and resid 164 through 168 Processing sheet with id= 16, first strand: chain '7' and resid 164 through 168 Processing sheet with id= 17, first strand: chain 'B' and resid 164 through 168 Processing sheet with id= 18, first strand: chain 'D' and resid 164 through 168 removed outlier: 3.500A pdb=" N LEU D 198 " --> pdb=" O SER D 165 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'H' and resid 164 through 168 removed outlier: 4.031A pdb=" N ILE H 199 " --> pdb=" O MET H 230 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'J' and resid 164 through 168 removed outlier: 3.743A pdb=" N LEU J 198 " --> pdb=" O SER J 165 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N MET J 230 " --> pdb=" O VAL J 197 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'L' and resid 164 through 168 Processing sheet with id= 22, first strand: chain 'S' and resid 164 through 168 removed outlier: 3.500A pdb=" N LEU S 198 " --> pdb=" O SER S 165 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'W' and resid 164 through 168 removed outlier: 4.032A pdb=" N ILE W 199 " --> pdb=" O MET W 230 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'Y' and resid 164 through 168 removed outlier: 3.743A pdb=" N LEU Y 198 " --> pdb=" O SER Y 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET Y 230 " --> pdb=" O VAL Y 197 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'f' and resid 164 through 168 Processing sheet with id= 26, first strand: chain 'h' and resid 164 through 168 removed outlier: 3.500A pdb=" N LEU h 198 " --> pdb=" O SER h 165 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'l' and resid 164 through 168 removed outlier: 4.031A pdb=" N ILE l 199 " --> pdb=" O MET l 230 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'n' and resid 164 through 168 removed outlier: 3.744A pdb=" N LEU n 198 " --> pdb=" O SER n 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET n 230 " --> pdb=" O VAL n 197 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'u' and resid 164 through 168 Processing sheet with id= 30, first strand: chain 'w' and resid 164 through 168 removed outlier: 3.500A pdb=" N LEU w 198 " --> pdb=" O SER w 165 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain '0' and resid 164 through 168 removed outlier: 4.030A pdb=" N ILE 0 199 " --> pdb=" O MET 0 230 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain '2' and resid 164 through 168 removed outlier: 3.743A pdb=" N LEU 2 198 " --> pdb=" O SER 2 165 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET 2 230 " --> pdb=" O VAL 2 197 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'E' and resid 11 through 15 Processing sheet with id= 34, first strand: chain 'F' and resid 11 through 15 removed outlier: 3.893A pdb=" N ASP F 47 " --> pdb=" O ILE F 14 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'I' and resid 11 through 15 Processing sheet with id= 36, first strand: chain 'N' and resid 11 through 15 removed outlier: 3.648A pdb=" N ASP N 47 " --> pdb=" O ILE N 14 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL N 44 " --> pdb=" O ALA N 74 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE N 46 " --> pdb=" O VAL N 76 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'O' and resid 11 through 15 Processing sheet with id= 38, first strand: chain 'T' and resid 11 through 15 Processing sheet with id= 39, first strand: chain 'U' and resid 11 through 15 removed outlier: 3.893A pdb=" N ASP U 47 " --> pdb=" O ILE U 14 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'X' and resid 11 through 15 Processing sheet with id= 41, first strand: chain 'a' and resid 11 through 15 removed outlier: 3.649A pdb=" N ASP a 47 " --> pdb=" O ILE a 14 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL a 44 " --> pdb=" O ALA a 74 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE a 46 " --> pdb=" O VAL a 76 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'b' and resid 11 through 15 Processing sheet with id= 43, first strand: chain 'i' and resid 11 through 15 Processing sheet with id= 44, first strand: chain 'j' and resid 11 through 15 removed outlier: 3.893A pdb=" N ASP j 47 " --> pdb=" O ILE j 14 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'm' and resid 11 through 15 Processing sheet with id= 46, first strand: chain 'p' and resid 11 through 15 removed outlier: 3.648A pdb=" N ASP p 47 " --> pdb=" O ILE p 14 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL p 44 " --> pdb=" O ALA p 74 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE p 46 " --> pdb=" O VAL p 76 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'q' and resid 11 through 15 Processing sheet with id= 48, first strand: chain 'x' and resid 11 through 15 Processing sheet with id= 49, first strand: chain 'y' and resid 11 through 15 removed outlier: 3.892A pdb=" N ASP y 47 " --> pdb=" O ILE y 14 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain '1' and resid 11 through 15 Processing sheet with id= 51, first strand: chain '4' and resid 11 through 15 removed outlier: 3.649A pdb=" N ASP 4 47 " --> pdb=" O ILE 4 14 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL 4 44 " --> pdb=" O ALA 4 74 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE 4 46 " --> pdb=" O VAL 4 76 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain '5' and resid 11 through 15 Processing sheet with id= 53, first strand: chain 'M' and resid 164 through 168 removed outlier: 4.003A pdb=" N ILE M 199 " --> pdb=" O MET M 230 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'Z' and resid 164 through 168 removed outlier: 4.002A pdb=" N ILE Z 199 " --> pdb=" O MET Z 230 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'o' and resid 164 through 168 removed outlier: 4.003A pdb=" N ILE o 199 " --> pdb=" O MET o 230 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain '3' and resid 164 through 168 removed outlier: 4.003A pdb=" N ILE 3 199 " --> pdb=" O MET 3 230 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'P' and resid 164 through 168 Processing sheet with id= 58, first strand: chain 'c' and resid 164 through 168 Processing sheet with id= 59, first strand: chain 'r' and resid 164 through 168 Processing sheet with id= 60, first strand: chain '6' and resid 164 through 168 6712 hydrogen bonds defined for protein. 20136 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 39.41 Time building geometry restraints manager: 35.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 34230 1.34 - 1.46: 18558 1.46 - 1.58: 53128 1.58 - 1.70: 104 1.70 - 1.81: 1100 Bond restraints: 107120 Sorted by residual: bond pdb=" OG1 TPO B 241 " pdb=" P TPO B 241 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" OG1 TPO u 241 " pdb=" P TPO u 241 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.04e+01 bond pdb=" OG1 TPO L 241 " pdb=" P TPO L 241 " ideal model delta sigma weight residual 1.717 1.607 0.110 2.00e-02 2.50e+03 3.02e+01 bond pdb=" OG1 TPO f 241 " pdb=" P TPO f 241 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.99e+01 bond pdb=" OG1 TPO l 241 " pdb=" P TPO l 241 " ideal model delta sigma weight residual 1.717 1.608 0.109 2.00e-02 2.50e+03 2.99e+01 ... (remaining 107115 not shown) Histogram of bond angle deviations from ideal: 95.41 - 103.15: 936 103.15 - 110.90: 37851 110.90 - 118.64: 50754 118.64 - 126.38: 54375 126.38 - 134.12: 1240 Bond angle restraints: 145156 Sorted by residual: angle pdb=" N GLU a 19 " pdb=" CA GLU a 19 " pdb=" C GLU a 19 " ideal model delta sigma weight residual 111.30 121.45 -10.15 1.36e+00 5.41e-01 5.57e+01 angle pdb=" N GLU N 19 " pdb=" CA GLU N 19 " pdb=" C GLU N 19 " ideal model delta sigma weight residual 111.30 121.27 -9.97 1.36e+00 5.41e-01 5.38e+01 angle pdb=" N GLU 4 19 " pdb=" CA GLU 4 19 " pdb=" C GLU 4 19 " ideal model delta sigma weight residual 111.30 121.25 -9.95 1.36e+00 5.41e-01 5.35e+01 angle pdb=" N GLU p 19 " pdb=" CA GLU p 19 " pdb=" C GLU p 19 " ideal model delta sigma weight residual 111.30 121.22 -9.92 1.36e+00 5.41e-01 5.32e+01 angle pdb=" CA GLU 4 19 " pdb=" CB GLU 4 19 " pdb=" CG GLU 4 19 " ideal model delta sigma weight residual 114.10 127.67 -13.57 2.00e+00 2.50e-01 4.60e+01 ... (remaining 145151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.14: 59792 17.14 - 34.28: 4616 34.28 - 51.42: 898 51.42 - 68.56: 102 68.56 - 85.70: 40 Dihedral angle restraints: 65448 sinusoidal: 26516 harmonic: 38932 Sorted by residual: dihedral pdb=" N GLU a 19 " pdb=" C GLU a 19 " pdb=" CA GLU a 19 " pdb=" CB GLU a 19 " ideal model delta harmonic sigma weight residual 122.80 136.84 -14.04 0 2.50e+00 1.60e-01 3.15e+01 dihedral pdb=" N GLU 4 19 " pdb=" C GLU 4 19 " pdb=" CA GLU 4 19 " pdb=" CB GLU 4 19 " ideal model delta harmonic sigma weight residual 122.80 136.72 -13.92 0 2.50e+00 1.60e-01 3.10e+01 dihedral pdb=" N GLU p 19 " pdb=" C GLU p 19 " pdb=" CA GLU p 19 " pdb=" CB GLU p 19 " ideal model delta harmonic sigma weight residual 122.80 136.66 -13.86 0 2.50e+00 1.60e-01 3.07e+01 ... (remaining 65445 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.114: 17158 0.114 - 0.227: 300 0.227 - 0.341: 10 0.341 - 0.455: 0 0.455 - 0.569: 4 Chirality restraints: 17472 Sorted by residual: chirality pdb=" CA GLU a 19 " pdb=" N GLU a 19 " pdb=" C GLU a 19 " pdb=" CB GLU a 19 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.09e+00 chirality pdb=" CA GLU 4 19 " pdb=" N GLU 4 19 " pdb=" C GLU 4 19 " pdb=" CB GLU 4 19 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.90e+00 chirality pdb=" CA GLU p 19 " pdb=" N GLU p 19 " pdb=" C GLU p 19 " pdb=" CB GLU p 19 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.56 2.00e-01 2.50e+01 7.83e+00 ... (remaining 17469 not shown) Planarity restraints: 18240 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE s 234 " 0.013 2.00e-02 2.50e+03 2.57e-02 6.60e+00 pdb=" C ILE s 234 " -0.044 2.00e-02 2.50e+03 pdb=" O ILE s 234 " 0.017 2.00e-02 2.50e+03 pdb=" N ARG s 235 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 117 " 0.021 2.00e-02 2.50e+03 1.63e-02 5.34e+00 pdb=" CG TYR B 117 " -0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR B 117 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR B 117 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 117 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 117 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR B 117 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR B 117 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR f 117 " -0.021 2.00e-02 2.50e+03 1.62e-02 5.27e+00 pdb=" CG TYR f 117 " 0.040 2.00e-02 2.50e+03 pdb=" CD1 TYR f 117 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 TYR f 117 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR f 117 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR f 117 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR f 117 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR f 117 " -0.001 2.00e-02 2.50e+03 ... (remaining 18237 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 8531 2.74 - 3.28: 119077 3.28 - 3.82: 178640 3.82 - 4.36: 201159 4.36 - 4.90: 339009 Nonbonded interactions: 846416 Sorted by model distance: nonbonded pdb=" O VAL L 207 " pdb=" O2P TPO L 241 " model vdw 2.196 3.040 nonbonded pdb=" O VAL u 207 " pdb=" O1P TPO u 241 " model vdw 2.197 3.040 nonbonded pdb=" O VAL f 207 " pdb=" O2P TPO f 241 " model vdw 2.197 3.040 nonbonded pdb=" O VAL B 207 " pdb=" O1P TPO B 241 " model vdw 2.197 3.040 nonbonded pdb=" O VAL Z 204 " pdb=" NH1 ARG Z 235 " model vdw 2.199 2.520 ... (remaining 846411 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' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain '2' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain '3' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain '6' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain '7' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'A' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'B' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'C' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'D' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'G' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'H' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'J' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'K' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'L' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'M' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'P' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'Q' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'R' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'S' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'V' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'W' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'Y' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'Z' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'c' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'd' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'e' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'f' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'g' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'h' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'k' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'l' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'n' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'o' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'r' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 's' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 't' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'u' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'v' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'w' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) selection = (chain 'z' and (resid 1 through 174 or resid 176 through 236 or resid 238 throug \ h 240 or resid 242 through 274)) } ncs_group { reference = chain '1' selection = chain '4' selection = chain '5' selection = chain 'E' selection = chain 'F' selection = chain 'I' selection = chain 'N' selection = chain 'O' selection = chain 'T' selection = chain 'U' selection = chain 'X' selection = chain 'a' selection = chain 'b' selection = chain 'i' selection = chain 'j' selection = chain 'm' selection = chain 'p' selection = chain 'q' selection = chain 'x' selection = chain 'y' } 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=0.00 max=1.00 mean=0.54 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 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: 0.100 Extract box with map and model: 15.310 Check model and map are aligned: 1.010 Set scattering table: 0.640 Process input model: 229.830 Find NCS groups from input model: 6.220 Set up NCS constraints: 0.720 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 258.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7300 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 : 0.004 0.110 107120 Z= 0.281 Angle : 0.706 14.024 145156 Z= 0.352 Chirality : 0.045 0.569 17472 Planarity : 0.004 0.051 18240 Dihedral : 12.482 85.701 40072 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.54 % Allowed : 0.64 % Favored : 98.82 % Cbeta Deviations : 0.03 % 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: -0.21 (0.07), residues: 13128 helix: 1.12 (0.06), residues: 8328 sheet: -1.36 (0.20), residues: 636 loop : -2.60 (0.08), residues: 4164 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26256 Ramachandran restraints generated. 13128 Oldfield, 0 Emsley, 13128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26256 Ramachandran restraints generated. 13128 Oldfield, 0 Emsley, 13128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1567 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1503 time to evaluate : 8.576 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 23 residues processed: 1530 average time/residue: 0.8174 time to fit residues: 2241.0022 Evaluate side-chains 1247 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1224 time to evaluate : 8.376 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.7204 time to fit residues: 43.4291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1300 random chunks: chunk 1097 optimal weight: 2.9990 chunk 985 optimal weight: 5.9990 chunk 546 optimal weight: 2.9990 chunk 336 optimal weight: 30.0000 chunk 664 optimal weight: 6.9990 chunk 526 optimal weight: 10.0000 chunk 1018 optimal weight: 0.6980 chunk 394 optimal weight: 0.0980 chunk 619 optimal weight: 0.9990 chunk 758 optimal weight: 1.9990 chunk 1180 optimal weight: 8.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 146 GLN ** K 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 146 GLN b 23 HIS ** b 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 146 GLN ** t 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 146 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 107120 Z= 0.193 Angle : 0.596 7.580 145156 Z= 0.312 Chirality : 0.043 0.199 17472 Planarity : 0.004 0.045 18240 Dihedral : 5.007 50.061 14068 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 1.13 % Allowed : 7.20 % Favored : 91.67 % 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: -0.08 (0.07), residues: 13128 helix: 1.24 (0.06), residues: 8420 sheet: -1.69 (0.18), residues: 752 loop : -2.61 (0.09), residues: 3956 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26256 Ramachandran restraints generated. 13128 Oldfield, 0 Emsley, 13128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26256 Ramachandran restraints generated. 13128 Oldfield, 0 Emsley, 13128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1417 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1284 time to evaluate : 8.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 133 outliers final: 89 residues processed: 1366 average time/residue: 0.8378 time to fit residues: 2040.4072 Evaluate side-chains 1266 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1177 time to evaluate : 8.435 Switching outliers to nearest non-outliers outliers start: 89 outliers final: 0 residues processed: 89 average time/residue: 0.7255 time to fit residues: 134.4660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1300 random chunks: chunk 656 optimal weight: 6.9990 chunk 366 optimal weight: 8.9990 chunk 982 optimal weight: 6.9990 chunk 803 optimal weight: 5.9990 chunk 325 optimal weight: 40.0000 chunk 1182 optimal weight: 5.9990 chunk 1277 optimal weight: 7.9990 chunk 1053 optimal weight: 7.9990 chunk 1172 optimal weight: 8.9990 chunk 403 optimal weight: 4.9990 chunk 948 optimal weight: 50.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN ** G 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 HIS ** H 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 251 GLN M 217 GLN ** M 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 23 HIS ** K 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 146 GLN ** R 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 228 GLN ** S 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 214 HIS ** W 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 251 GLN Z 217 GLN b 23 HIS ** b 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 228 GLN ** k 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 214 HIS ** l 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 251 GLN ** o 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 217 GLN ** s 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 228 GLN ** z 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 214 HIS ** 0 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 251 GLN ** 3 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 217 GLN ** 3 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 256 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.087 107120 Z= 0.491 Angle : 0.798 8.506 145156 Z= 0.420 Chirality : 0.048 0.237 17472 Planarity : 0.005 0.051 18240 Dihedral : 5.913 59.500 14068 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 22.39 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.20 % Favored : 92.73 % Rotamer: Outliers : 1.87 % Allowed : 12.14 % Favored : 85.99 % 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: -0.68 (0.07), residues: 13128 helix: 0.77 (0.06), residues: 8528 sheet: -2.18 (0.18), residues: 708 loop : -2.90 (0.09), residues: 3892 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26256 Ramachandran restraints generated. 13128 Oldfield, 0 Emsley, 13128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26256 Ramachandran restraints generated. 13128 Oldfield, 0 Emsley, 13128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1393 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1172 time to evaluate : 8.588 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 221 outliers final: 133 residues processed: 1317 average time/residue: 0.8262 time to fit residues: 1942.0986 Evaluate side-chains 1224 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 133 poor density : 1091 time to evaluate : 8.460 Switching outliers to nearest non-outliers outliers start: 133 outliers final: 0 residues processed: 133 average time/residue: 0.7045 time to fit residues: 191.7765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1300 random chunks: chunk 1168 optimal weight: 0.0020 chunk 889 optimal weight: 4.9990 chunk 613 optimal weight: 4.9990 chunk 130 optimal weight: 40.0000 chunk 564 optimal weight: 1.9990 chunk 794 optimal weight: 7.9990 chunk 1186 optimal weight: 0.9990 chunk 1256 optimal weight: 30.0000 chunk 620 optimal weight: 8.9990 chunk 1124 optimal weight: 0.9980 chunk 338 optimal weight: 7.9990 overall best weight: 1.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN O 23 HIS S 228 GLN b 23 HIS b 29 GLN ** e 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 23 HIS ** t 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 23 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7397 moved from start: 0.2166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 107120 Z= 0.206 Angle : 0.601 10.022 145156 Z= 0.315 Chirality : 0.043 0.166 17472 Planarity : 0.004 0.046 18240 Dihedral : 5.342 52.324 14068 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 17.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % Rotamer: Outliers : 1.29 % Allowed : 14.11 % Favored : 84.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.07), residues: 13128 helix: 1.04 (0.06), residues: 8516 sheet: -1.84 (0.19), residues: 704 loop : -2.78 (0.09), residues: 3908 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26256 Ramachandran restraints generated. 13128 Oldfield, 0 Emsley, 13128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26256 Ramachandran restraints generated. 13128 Oldfield, 0 Emsley, 13128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1420 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 153 poor density : 1267 time to evaluate : 8.422 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 153 outliers final: 76 residues processed: 1382 average time/residue: 0.8357 time to fit residues: 2057.1953 Evaluate side-chains 1230 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1154 time to evaluate : 8.402 Switching outliers to nearest non-outliers outliers start: 76 outliers final: 0 residues processed: 76 average time/residue: 0.7079 time to fit residues: 116.0895 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1300 random chunks: chunk 1046 optimal weight: 9.9990 chunk 713 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 935 optimal weight: 9.9990 chunk 518 optimal weight: 0.6980 chunk 1072 optimal weight: 0.9990 chunk 868 optimal weight: 4.9990 chunk 1 optimal weight: 20.0000 chunk 641 optimal weight: 2.9990 chunk 1127 optimal weight: 1.9990 chunk 317 optimal weight: 0.7980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 256 ASN b 23 HIS ** g 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 256 ASN q 23 HIS ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 23 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7382 moved from start: 0.2256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 107120 Z= 0.193 Angle : 0.594 8.818 145156 Z= 0.309 Chirality : 0.043 0.198 17472 Planarity : 0.004 0.047 18240 Dihedral : 5.180 50.131 14068 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.47 % Favored : 93.53 % Rotamer: Outliers : 1.54 % Allowed : 15.64 % Favored : 82.82 % 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: -0.15 (0.07), residues: 13128 helix: 1.15 (0.06), residues: 8540 sheet: -1.63 (0.19), residues: 712 loop : -2.70 (0.09), residues: 3876 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26256 Ramachandran restraints generated. 13128 Oldfield, 0 Emsley, 13128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26256 Ramachandran restraints generated. 13128 Oldfield, 0 Emsley, 13128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1449 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 1267 time to evaluate : 8.514 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 182 outliers final: 117 residues processed: 1389 average time/residue: 0.8151 time to fit residues: 2010.5247 Evaluate side-chains 1291 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1174 time to evaluate : 8.483 Switching outliers to nearest non-outliers outliers start: 117 outliers final: 0 residues processed: 117 average time/residue: 0.7016 time to fit residues: 169.7725 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1300 random chunks: chunk 422 optimal weight: 3.9990 chunk 1131 optimal weight: 1.9990 chunk 248 optimal weight: 5.9990 chunk 737 optimal weight: 8.9990 chunk 310 optimal weight: 20.0000 chunk 1257 optimal weight: 5.9990 chunk 1044 optimal weight: 0.9990 chunk 582 optimal weight: 3.9990 chunk 104 optimal weight: 3.9990 chunk 416 optimal weight: 8.9990 chunk 660 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 151 GLN ** M 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 213 HIS ** S 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 146 GLN h 213 HIS ** h 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 23 HIS ** s 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 146 GLN w 213 HIS ** w 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 23 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7431 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 107120 Z= 0.269 Angle : 0.639 10.815 145156 Z= 0.332 Chirality : 0.044 0.212 17472 Planarity : 0.004 0.048 18240 Dihedral : 5.340 52.882 14068 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.92 % Favored : 93.08 % Rotamer: Outliers : 1.38 % Allowed : 16.98 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.07), residues: 13128 helix: 1.11 (0.06), residues: 8548 sheet: -1.74 (0.19), residues: 708 loop : -2.71 (0.09), residues: 3872 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26256 Ramachandran restraints generated. 13128 Oldfield, 0 Emsley, 13128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26256 Ramachandran restraints generated. 13128 Oldfield, 0 Emsley, 13128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1367 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1204 time to evaluate : 8.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 163 outliers final: 98 residues processed: 1318 average time/residue: 0.8451 time to fit residues: 1984.2526 Evaluate side-chains 1253 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 1155 time to evaluate : 8.472 Switching outliers to nearest non-outliers outliers start: 98 outliers final: 0 residues processed: 98 average time/residue: 0.7231 time to fit residues: 147.7231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1300 random chunks: chunk 1212 optimal weight: 0.8980 chunk 141 optimal weight: 6.9990 chunk 716 optimal weight: 20.0000 chunk 918 optimal weight: 3.9990 chunk 711 optimal weight: 4.9990 chunk 1058 optimal weight: 20.0000 chunk 702 optimal weight: 0.1980 chunk 1252 optimal weight: 10.0000 chunk 784 optimal weight: 10.0000 chunk 763 optimal weight: 8.9990 chunk 578 optimal weight: 0.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 213 HIS O 23 HIS ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 23 HIS ** f 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 23 HIS ** s 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 23 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 107120 Z= 0.226 Angle : 0.621 11.346 145156 Z= 0.322 Chirality : 0.043 0.233 17472 Planarity : 0.004 0.049 18240 Dihedral : 5.232 51.017 14068 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 17.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 1.17 % Allowed : 17.61 % Favored : 81.22 % 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: -0.12 (0.07), residues: 13128 helix: 1.16 (0.06), residues: 8552 sheet: -1.65 (0.19), residues: 708 loop : -2.66 (0.09), residues: 3868 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26256 Ramachandran restraints generated. 13128 Oldfield, 0 Emsley, 13128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26256 Ramachandran restraints generated. 13128 Oldfield, 0 Emsley, 13128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1364 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1226 time to evaluate : 8.488 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 138 outliers final: 71 residues processed: 1305 average time/residue: 0.8608 time to fit residues: 1993.4700 Evaluate side-chains 1229 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1158 time to evaluate : 8.498 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 0.7436 time to fit residues: 111.8051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1300 random chunks: chunk 775 optimal weight: 2.9990 chunk 500 optimal weight: 0.9990 chunk 748 optimal weight: 0.4980 chunk 377 optimal weight: 0.9980 chunk 246 optimal weight: 0.9980 chunk 242 optimal weight: 0.1980 chunk 796 optimal weight: 2.9990 chunk 853 optimal weight: 0.8980 chunk 619 optimal weight: 6.9990 chunk 116 optimal weight: 0.7980 chunk 984 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 213 HIS ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 23 HIS ** R 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 213 HIS ** g 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 213 HIS ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7344 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 107120 Z= 0.170 Angle : 0.610 13.424 145156 Z= 0.313 Chirality : 0.043 0.238 17472 Planarity : 0.003 0.059 18240 Dihedral : 5.005 47.034 14068 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 0.57 % Allowed : 18.27 % Favored : 81.16 % 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: 0.03 (0.07), residues: 13128 helix: 1.27 (0.06), residues: 8560 sheet: -1.51 (0.19), residues: 716 loop : -2.59 (0.09), residues: 3852 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26256 Ramachandran restraints generated. 13128 Oldfield, 0 Emsley, 13128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26256 Ramachandran restraints generated. 13128 Oldfield, 0 Emsley, 13128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1350 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 1283 time to evaluate : 8.562 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 67 outliers final: 23 residues processed: 1329 average time/residue: 0.8650 time to fit residues: 2039.5059 Evaluate side-chains 1204 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1181 time to evaluate : 8.488 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 0 residues processed: 23 average time/residue: 0.7157 time to fit residues: 43.7942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1300 random chunks: chunk 1139 optimal weight: 8.9990 chunk 1200 optimal weight: 3.9990 chunk 1095 optimal weight: 5.9990 chunk 1167 optimal weight: 0.9980 chunk 702 optimal weight: 7.9990 chunk 508 optimal weight: 2.9990 chunk 916 optimal weight: 5.9990 chunk 358 optimal weight: 0.2980 chunk 1055 optimal weight: 0.9980 chunk 1104 optimal weight: 1.9990 chunk 1163 optimal weight: 2.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 23 HIS ** R 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 23 HIS ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 23 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 107120 Z= 0.196 Angle : 0.628 12.199 145156 Z= 0.322 Chirality : 0.043 0.223 17472 Planarity : 0.004 0.099 18240 Dihedral : 5.005 46.891 14068 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.58 % Allowed : 18.97 % Favored : 80.46 % 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: 0.08 (0.07), residues: 13128 helix: 1.30 (0.06), residues: 8544 sheet: -1.47 (0.19), residues: 716 loop : -2.58 (0.09), residues: 3868 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26256 Ramachandran restraints generated. 13128 Oldfield, 0 Emsley, 13128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26256 Ramachandran restraints generated. 13128 Oldfield, 0 Emsley, 13128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1291 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 1223 time to evaluate : 7.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 68 outliers final: 31 residues processed: 1263 average time/residue: 0.8936 time to fit residues: 2035.2147 Evaluate side-chains 1195 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1164 time to evaluate : 8.473 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 0 residues processed: 31 average time/residue: 0.7336 time to fit residues: 55.2924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1300 random chunks: chunk 766 optimal weight: 2.9990 chunk 1234 optimal weight: 0.0040 chunk 753 optimal weight: 1.9990 chunk 585 optimal weight: 10.0000 chunk 858 optimal weight: 9.9990 chunk 1295 optimal weight: 0.9980 chunk 1192 optimal weight: 4.9990 chunk 1031 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 796 optimal weight: 2.9990 chunk 632 optimal weight: 20.0000 overall best weight: 1.5998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 23 HIS R 213 HIS ** R 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 23 HIS g 213 HIS ** g 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 23 HIS v 213 HIS ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 23 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 107120 Z= 0.203 Angle : 0.640 13.687 145156 Z= 0.327 Chirality : 0.043 0.257 17472 Planarity : 0.004 0.078 18240 Dihedral : 5.004 47.686 14068 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 17.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.40 % Favored : 93.60 % Rotamer: Outliers : 0.31 % Allowed : 19.36 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.07), residues: 13128 helix: 1.27 (0.06), residues: 8556 sheet: -1.47 (0.19), residues: 716 loop : -2.58 (0.09), residues: 3856 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 26256 Ramachandran restraints generated. 13128 Oldfield, 0 Emsley, 13128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 26256 Ramachandran restraints generated. 13128 Oldfield, 0 Emsley, 13128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1213 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1176 time to evaluate : 8.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 37 outliers final: 21 residues processed: 1194 average time/residue: 0.8638 time to fit residues: 1830.8765 Evaluate side-chains 1170 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 1149 time to evaluate : 8.452 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.7349 time to fit residues: 41.5431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1300 random chunks: chunk 819 optimal weight: 20.0000 chunk 1098 optimal weight: 0.9980 chunk 315 optimal weight: 1.9990 chunk 950 optimal weight: 20.0000 chunk 152 optimal weight: 5.9990 chunk 286 optimal weight: 0.0870 chunk 1032 optimal weight: 8.9990 chunk 432 optimal weight: 3.9990 chunk 1060 optimal weight: 6.9990 chunk 130 optimal weight: 50.0000 chunk 190 optimal weight: 6.9990 overall best weight: 2.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.145597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.120591 restraints weight = 248101.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.125044 restraints weight = 129316.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.129502 restraints weight = 75071.203| |-----------------------------------------------------------------------------| r_work (final): 0.3680 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3681 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3681 r_free = 0.3681 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48120 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3681 r_free = 0.3681 target_work(ls_wunit_k1) = 0.124 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48120 | |-----------------------------------------------------------------------------| r_final: 0.3681 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7436 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 107120 Z= 0.255 Angle : 0.662 13.299 145156 Z= 0.340 Chirality : 0.044 0.256 17472 Planarity : 0.004 0.066 18240 Dihedral : 5.142 49.484 14068 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 0.41 % Allowed : 19.37 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.07), residues: 13128 helix: 1.21 (0.06), residues: 8556 sheet: -1.58 (0.19), residues: 708 loop : -2.62 (0.09), residues: 3864 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28786.08 seconds wall clock time: 495 minutes 50.69 seconds (29750.69 seconds total)