Starting phenix.real_space_refine on Tue Feb 13 03:10:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0u_11971/02_2024/7b0u_11971_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0u_11971/02_2024/7b0u_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_11971/02_2024/7b0u_11971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0u_11971/02_2024/7b0u_11971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0u_11971/02_2024/7b0u_11971_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7b0u_11971/02_2024/7b0u_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: 0.25s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/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: 44.42, 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: 31.28 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: 23.48 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: 41.22 Time building geometry restraints manager: 34.42 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: 2.250 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: 15.700 Check model and map are aligned: 1.190 Set scattering table: 0.800 Process input model: 232.290 Find NCS groups from input model: 6.310 Set up NCS constraints: 0.730 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:2.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 261.580 ------------------------------------------------------------------------------- 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP f 20 HIS 0.005 0.001 HIS W 214 PHE 0.024 0.002 PHE M 8 TYR 0.040 0.002 TYR B 117 ARG 0.006 0.000 ARG 1 42 *********************** 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 : 8.838 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: B 1 MET cc_start: -0.0731 (ppp) cc_final: -0.1664 (ppp) REVERT: B 99 MET cc_start: 0.3399 (ptm) cc_final: 0.3010 (ptm) REVERT: C 213 HIS cc_start: 0.7966 (t-90) cc_final: 0.7637 (t70) REVERT: C 214 HIS cc_start: 0.6916 (m170) cc_final: 0.6552 (m-70) REVERT: D 21 MET cc_start: -0.1657 (ttt) cc_final: -0.1884 (ttt) REVERT: D 40 MET cc_start: 0.2672 (OUTLIER) cc_final: 0.2379 (ttm) REVERT: D 99 MET cc_start: -0.1062 (mtp) cc_final: -0.1262 (mtt) REVERT: D 127 MET cc_start: 0.1067 (ptm) cc_final: 0.0833 (mtt) REVERT: E 47 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.7731 (m-30) REVERT: F 91 GLU cc_start: 0.7936 (tp30) cc_final: 0.7724 (tp30) REVERT: G 1 MET cc_start: -0.0652 (tpp) cc_final: -0.0863 (tpp) REVERT: H 127 MET cc_start: -0.1440 (mtt) cc_final: -0.1655 (tmm) REVERT: I 21 ASP cc_start: 0.7903 (p0) cc_final: 0.7426 (t0) REVERT: I 55 ASP cc_start: 0.7493 (p0) cc_final: 0.7194 (p0) REVERT: I 114 GLN cc_start: 0.8252 (OUTLIER) cc_final: 0.7703 (pp30) REVERT: J 1 MET cc_start: -0.4285 (mmp) cc_final: -0.4676 (mmm) REVERT: M 1 MET cc_start: 0.0218 (ppp) cc_final: -0.0124 (ppp) REVERT: M 184 ASN cc_start: 0.9109 (t0) cc_final: 0.8894 (t0) REVERT: O 13 LEU cc_start: 0.8535 (mm) cc_final: 0.8268 (mm) REVERT: O 23 HIS cc_start: 0.6836 (t-170) cc_final: 0.6429 (t-170) REVERT: O 27 GLU cc_start: 0.8540 (pt0) cc_final: 0.7827 (pt0) REVERT: P 24 MET cc_start: 0.1820 (ptp) cc_final: 0.1367 (ptm) REVERT: Q 1 MET cc_start: -0.0498 (ptp) cc_final: -0.1003 (ptp) REVERT: Q 24 MET cc_start: 0.0869 (tmm) cc_final: 0.0279 (tmm) REVERT: Q 167 MET cc_start: 0.8460 (tmm) cc_final: 0.8013 (tmm) REVERT: L 1 MET cc_start: -0.0727 (ppp) cc_final: -0.1494 (ppp) REVERT: L 99 MET cc_start: 0.3262 (ptm) cc_final: 0.2840 (ptm) REVERT: R 213 HIS cc_start: 0.7968 (t-90) cc_final: 0.7643 (t70) REVERT: R 214 HIS cc_start: 0.6945 (m170) cc_final: 0.6589 (m-70) REVERT: S 21 MET cc_start: -0.1912 (ttt) cc_final: -0.2208 (ttt) REVERT: S 99 MET cc_start: -0.0794 (mtp) cc_final: -0.1008 (mtt) REVERT: S 127 MET cc_start: 0.1137 (ptm) cc_final: 0.0868 (mtt) REVERT: T 47 ASP cc_start: 0.8295 (OUTLIER) cc_final: 0.7724 (m-30) REVERT: U 91 GLU cc_start: 0.8011 (tp30) cc_final: 0.7649 (tp30) REVERT: V 1 MET cc_start: -0.0508 (tpp) cc_final: -0.0765 (tpp) REVERT: W 127 MET cc_start: -0.0950 (mtt) cc_final: -0.1516 (tmm) REVERT: X 21 ASP cc_start: 0.7671 (p0) cc_final: 0.7429 (p0) REVERT: X 114 GLN cc_start: 0.8280 (OUTLIER) cc_final: 0.7758 (pp30) REVERT: Y 1 MET cc_start: -0.4310 (mmp) cc_final: -0.4562 (mmm) REVERT: Z 1 MET cc_start: 0.0069 (ppp) cc_final: -0.0303 (ppp) REVERT: Z 40 MET cc_start: -0.0836 (ptm) cc_final: -0.1056 (ptm) REVERT: b 13 LEU cc_start: 0.8536 (mm) cc_final: 0.8335 (mm) REVERT: b 23 HIS cc_start: 0.7195 (t-170) cc_final: 0.6205 (t-170) REVERT: b 27 GLU cc_start: 0.8580 (pt0) cc_final: 0.7717 (pt0) REVERT: c 24 MET cc_start: 0.1807 (ptp) cc_final: 0.1340 (ptm) REVERT: d 1 MET cc_start: -0.0428 (ptp) cc_final: -0.0887 (ptp) REVERT: d 24 MET cc_start: 0.0923 (tmm) cc_final: 0.0376 (tmm) REVERT: d 167 MET cc_start: 0.8449 (tmm) cc_final: 0.8013 (tmm) REVERT: f 1 MET cc_start: -0.0607 (ppp) cc_final: -0.1441 (ppp) REVERT: f 99 MET cc_start: 0.3201 (ptm) cc_final: 0.2809 (ptm) REVERT: g 40 MET cc_start: -0.0332 (ttt) cc_final: -0.0599 (ttt) REVERT: g 213 HIS cc_start: 0.7988 (t-90) cc_final: 0.7665 (t70) REVERT: g 214 HIS cc_start: 0.6966 (m170) cc_final: 0.6613 (m-70) REVERT: h 21 MET cc_start: -0.1586 (ttt) cc_final: -0.2199 (ttt) REVERT: h 40 MET cc_start: 0.2829 (OUTLIER) cc_final: 0.2594 (ttm) REVERT: h 127 MET cc_start: 0.1203 (ptm) cc_final: 0.0890 (mtt) REVERT: i 47 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8010 (m-30) REVERT: j 91 GLU cc_start: 0.8001 (tp30) cc_final: 0.7748 (tp30) REVERT: l 127 MET cc_start: -0.0795 (mtt) cc_final: -0.1049 (tmm) REVERT: m 1 MET cc_start: 0.5307 (OUTLIER) cc_final: 0.5088 (ppp) REVERT: m 31 ASP cc_start: 0.8678 (t70) cc_final: 0.8338 (t0) REVERT: m 69 SER cc_start: 0.8712 (t) cc_final: 0.8473 (t) REVERT: m 114 GLN cc_start: 0.8405 (OUTLIER) cc_final: 0.7927 (pp30) REVERT: n 1 MET cc_start: -0.3599 (mmp) cc_final: -0.4225 (mmm) REVERT: o 1 MET cc_start: 0.0195 (ppp) cc_final: -0.0133 (ppp) REVERT: q 13 LEU cc_start: 0.8489 (mm) cc_final: 0.8253 (mm) REVERT: q 21 ASP cc_start: 0.7665 (m-30) cc_final: 0.6585 (t0) REVERT: r 24 MET cc_start: 0.1749 (ptp) cc_final: 0.1089 (ptm) REVERT: r 251 GLN cc_start: 0.5463 (pm20) cc_final: 0.4551 (pm20) REVERT: s 1 MET cc_start: -0.0557 (ptp) cc_final: -0.0810 (ptp) REVERT: s 167 MET cc_start: 0.8384 (tmm) cc_final: 0.7927 (tmm) REVERT: u 1 MET cc_start: -0.0641 (ppp) cc_final: -0.1401 (ppp) REVERT: u 99 MET cc_start: 0.3272 (ptm) cc_final: 0.2820 (ptm) REVERT: v 213 HIS cc_start: 0.7981 (t-90) cc_final: 0.7652 (t70) REVERT: v 214 HIS cc_start: 0.6931 (m170) cc_final: 0.6592 (m-70) REVERT: w 21 MET cc_start: -0.1865 (ttt) cc_final: -0.2278 (ttt) REVERT: w 40 MET cc_start: 0.2660 (OUTLIER) cc_final: 0.2386 (ttm) REVERT: w 127 MET cc_start: 0.1308 (ptm) cc_final: 0.1052 (mtt) REVERT: x 47 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.7997 (m-30) REVERT: y 91 GLU cc_start: 0.7956 (tp30) cc_final: 0.7634 (tp30) REVERT: 1 21 ASP cc_start: 0.7589 (p0) cc_final: 0.7152 (t0) REVERT: 1 31 ASP cc_start: 0.8636 (t70) cc_final: 0.8417 (t0) REVERT: 1 114 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.7718 (pp30) REVERT: 2 1 MET cc_start: -0.3942 (mmp) cc_final: -0.4305 (mmm) REVERT: 3 1 MET cc_start: 0.0289 (ppp) cc_final: 0.0002 (ppp) REVERT: 5 13 LEU cc_start: 0.8469 (mm) cc_final: 0.8236 (mm) REVERT: 5 21 ASP cc_start: 0.7665 (m-30) cc_final: 0.6594 (t0) REVERT: 6 24 MET cc_start: 0.1874 (ptp) cc_final: 0.1307 (ptm) REVERT: 7 1 MET cc_start: -0.0267 (ptp) cc_final: -0.0601 (ptp) REVERT: 7 21 MET cc_start: 0.3749 (ptp) cc_final: 0.3458 (ptp) REVERT: 7 24 MET cc_start: 0.0849 (tmm) cc_final: 0.0230 (tmm) REVERT: 7 167 MET cc_start: 0.8441 (tmm) cc_final: 0.8006 (tmm) outliers start: 64 outliers final: 23 residues processed: 1530 average time/residue: 0.8010 time to fit residues: 2190.2613 Evaluate side-chains 1270 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1235 time to evaluate : 8.667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain D residue 40 MET Chi-restraints excluded: chain E residue 47 ASP Chi-restraints excluded: chain F residue 13 LEU Chi-restraints excluded: chain I residue 114 GLN Chi-restraints excluded: chain I residue 115 GLU Chi-restraints excluded: chain J residue 231 LEU Chi-restraints excluded: chain M residue 99 MET Chi-restraints excluded: chain O residue 68 MET Chi-restraints excluded: chain L residue 175 THR Chi-restraints excluded: chain T residue 47 ASP Chi-restraints excluded: chain U residue 13 LEU Chi-restraints excluded: chain X residue 114 GLN Chi-restraints excluded: chain X residue 115 GLU Chi-restraints excluded: chain Y residue 231 LEU Chi-restraints excluded: chain Z residue 99 MET Chi-restraints excluded: chain f residue 175 THR Chi-restraints excluded: chain h residue 40 MET Chi-restraints excluded: chain i residue 47 ASP Chi-restraints excluded: chain j residue 13 LEU Chi-restraints excluded: chain m residue 1 MET Chi-restraints excluded: chain m residue 114 GLN Chi-restraints excluded: chain m residue 115 GLU Chi-restraints excluded: chain n residue 231 LEU Chi-restraints excluded: chain o residue 99 MET Chi-restraints excluded: chain q residue 68 MET Chi-restraints excluded: chain u residue 175 THR Chi-restraints excluded: chain w residue 40 MET Chi-restraints excluded: chain x residue 47 ASP Chi-restraints excluded: chain y residue 13 LEU Chi-restraints excluded: chain 1 residue 114 GLN Chi-restraints excluded: chain 1 residue 115 GLU Chi-restraints excluded: chain 2 residue 231 LEU Chi-restraints excluded: chain 3 residue 99 MET Chi-restraints excluded: chain 5 residue 68 MET 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 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1057 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= 0.189 Angle : 0.589 7.512 145156 Z= 0.308 Chirality : 0.043 0.206 17472 Planarity : 0.004 0.045 18240 Dihedral : 5.367 58.828 14153 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.24 % Allowed : 7.20 % Favored : 91.56 % 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: -0.09 (0.07), residues: 13128 helix: 1.22 (0.06), residues: 8424 sheet: -1.70 (0.18), residues: 752 loop : -2.61 (0.09), residues: 3952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP h 20 HIS 0.010 0.001 HIS 5 23 PHE 0.018 0.001 PHE q 57 TYR 0.024 0.002 TYR k 117 ARG 0.006 0.000 ARG z 235 *********************** 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 1459 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1313 time to evaluate : 8.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 GLU cc_start: 0.7108 (tm-30) cc_final: 0.6711 (tm-30) REVERT: B 29 ASP cc_start: -0.0466 (OUTLIER) cc_final: -0.0670 (p0) REVERT: D 258 MET cc_start: 0.8600 (OUTLIER) cc_final: 0.8231 (ttm) REVERT: G 1 MET cc_start: -0.0635 (tpp) cc_final: -0.1113 (tpp) REVERT: H 193 ARG cc_start: 0.7563 (mmm160) cc_final: 0.7355 (mmp80) REVERT: H 228 GLN cc_start: 0.8381 (mp10) cc_final: 0.8146 (mp10) REVERT: I 21 ASP cc_start: 0.8022 (p0) cc_final: 0.7753 (p0) REVERT: I 42 ARG cc_start: 0.8097 (mtm110) cc_final: 0.7515 (mtm110) REVERT: M 184 ASN cc_start: 0.9123 (t0) cc_final: 0.8892 (t0) REVERT: M 260 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8532 (ttmt) REVERT: O 13 LEU cc_start: 0.8595 (mm) cc_final: 0.8336 (mm) REVERT: O 23 HIS cc_start: 0.6843 (t-170) cc_final: 0.6418 (t-170) REVERT: O 27 GLU cc_start: 0.8470 (pt0) cc_final: 0.7524 (pt0) REVERT: P 21 MET cc_start: -0.1233 (pmm) cc_final: -0.1526 (pmm) REVERT: Q 167 MET cc_start: 0.8447 (tmm) cc_final: 0.7988 (tmm) REVERT: K 248 GLU cc_start: 0.7116 (tm-30) cc_final: 0.6799 (tm-30) REVERT: L 1 MET cc_start: -0.1603 (ppp) cc_final: -0.1943 (ppp) REVERT: S 258 MET cc_start: 0.8598 (ttm) cc_final: 0.8267 (ttm) REVERT: S 262 MET cc_start: 0.9081 (tpt) cc_final: 0.8877 (tpt) REVERT: T 35 LYS cc_start: 0.8343 (mmtt) cc_final: 0.8123 (mmtt) REVERT: W 1 MET cc_start: -0.4279 (mpp) cc_final: -0.4768 (ttt) REVERT: W 193 ARG cc_start: 0.7578 (mmm160) cc_final: 0.7364 (mmp80) REVERT: W 228 GLN cc_start: 0.8402 (mp10) cc_final: 0.8125 (mp10) REVERT: X 21 ASP cc_start: 0.7809 (p0) cc_final: 0.7312 (t0) REVERT: X 114 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7696 (pp30) REVERT: b 13 LEU cc_start: 0.8703 (mm) cc_final: 0.8456 (mm) REVERT: b 23 HIS cc_start: 0.7123 (t-170) cc_final: 0.6228 (t-170) REVERT: b 27 GLU cc_start: 0.8484 (pt0) cc_final: 0.7504 (pt0) REVERT: c 21 MET cc_start: -0.1229 (pmm) cc_final: -0.1550 (pmm) REVERT: d 24 MET cc_start: 0.0269 (tmm) cc_final: 0.0048 (tmm) REVERT: d 167 MET cc_start: 0.8419 (tmm) cc_final: 0.7963 (tmm) REVERT: e 248 GLU cc_start: 0.7125 (tm-30) cc_final: 0.6742 (tm-30) REVERT: h 258 MET cc_start: 0.8598 (ttm) cc_final: 0.8270 (ttm) REVERT: h 262 MET cc_start: 0.9089 (tpt) cc_final: 0.8877 (tpt) REVERT: i 20 LEU cc_start: 0.7718 (tt) cc_final: 0.7398 (tp) REVERT: k 1 MET cc_start: -0.0147 (tpp) cc_final: -0.0431 (ptt) REVERT: l 1 MET cc_start: -0.4029 (mpp) cc_final: -0.4617 (ttt) REVERT: l 193 ARG cc_start: 0.7595 (mmm160) cc_final: 0.7381 (mmp80) REVERT: l 228 GLN cc_start: 0.8385 (mp10) cc_final: 0.8103 (mp10) REVERT: m 114 GLN cc_start: 0.8270 (OUTLIER) cc_final: 0.7859 (pp30) REVERT: n 150 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.6286 (mp) REVERT: o 260 LYS cc_start: 0.8788 (ttmt) cc_final: 0.8583 (ttmt) REVERT: p 47 ASP cc_start: 0.7734 (t70) cc_final: 0.7329 (t0) REVERT: q 13 LEU cc_start: 0.8682 (mm) cc_final: 0.8428 (mm) REVERT: q 21 ASP cc_start: 0.7683 (m-30) cc_final: 0.6871 (t70) REVERT: q 68 MET cc_start: 0.8580 (mmt) cc_final: 0.8359 (mmt) REVERT: r 21 MET cc_start: -0.1353 (pmm) cc_final: -0.1649 (pmm) REVERT: s 167 MET cc_start: 0.8381 (tmm) cc_final: 0.7912 (tmm) REVERT: t 248 GLU cc_start: 0.7105 (tm-30) cc_final: 0.6794 (tm-30) REVERT: u 1 MET cc_start: -0.1432 (ppp) cc_final: -0.1640 (ppp) REVERT: w 258 MET cc_start: 0.8610 (ttm) cc_final: 0.8278 (ttm) REVERT: w 262 MET cc_start: 0.9094 (tpt) cc_final: 0.8889 (tpt) REVERT: 0 1 MET cc_start: -0.4058 (mpp) cc_final: -0.4631 (ttt) REVERT: 0 193 ARG cc_start: 0.7595 (mmm160) cc_final: 0.7375 (mmp80) REVERT: 0 228 GLN cc_start: 0.8388 (mp10) cc_final: 0.8108 (mp10) REVERT: 1 21 ASP cc_start: 0.7779 (p0) cc_final: 0.7281 (t0) REVERT: 3 260 LYS cc_start: 0.8759 (ttmt) cc_final: 0.8487 (ttmt) REVERT: 5 13 LEU cc_start: 0.8683 (mm) cc_final: 0.8384 (mm) REVERT: 5 21 ASP cc_start: 0.7679 (m-30) cc_final: 0.6873 (t70) REVERT: 6 21 MET cc_start: -0.1204 (pmm) cc_final: -0.1622 (pmm) REVERT: 7 167 MET cc_start: 0.8427 (tmm) cc_final: 0.7968 (tmm) outliers start: 146 outliers final: 98 residues processed: 1398 average time/residue: 0.8133 time to fit residues: 2028.8833 Evaluate side-chains 1308 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1205 time to evaluate : 8.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain C residue 249 LEU Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain G residue 21 MET Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain J residue 166 VAL Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain M residue 40 MET Chi-restraints excluded: chain M residue 99 MET Chi-restraints excluded: chain M residue 259 LYS Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 50 SER Chi-restraints excluded: chain P residue 166 VAL Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 254 THR Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain S residue 166 VAL Chi-restraints excluded: chain T residue 38 GLU Chi-restraints excluded: chain T residue 109 LEU Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 104 ASP Chi-restraints excluded: chain W residue 150 LEU Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 103 MET Chi-restraints excluded: chain X residue 114 GLN Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 257 THR Chi-restraints excluded: chain Z residue 99 MET Chi-restraints excluded: chain Z residue 157 LEU Chi-restraints excluded: chain Z residue 259 LYS Chi-restraints excluded: chain a residue 31 ASP Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 50 SER Chi-restraints excluded: chain c residue 166 VAL Chi-restraints excluded: chain c residue 196 VAL Chi-restraints excluded: chain c residue 254 THR Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain f residue 204 VAL Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 190 VAL Chi-restraints excluded: chain g residue 243 VAL Chi-restraints excluded: chain g residue 249 LEU Chi-restraints excluded: chain h residue 166 VAL Chi-restraints excluded: chain i residue 38 GLU Chi-restraints excluded: chain i residue 109 LEU Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 104 ASP Chi-restraints excluded: chain l residue 150 LEU Chi-restraints excluded: chain m residue 114 GLN Chi-restraints excluded: chain n residue 150 LEU Chi-restraints excluded: chain n residue 166 VAL Chi-restraints excluded: chain n residue 257 THR Chi-restraints excluded: chain o residue 40 MET Chi-restraints excluded: chain o residue 99 MET Chi-restraints excluded: chain o residue 157 LEU Chi-restraints excluded: chain o residue 259 LYS Chi-restraints excluded: chain p residue 31 ASP Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 50 SER Chi-restraints excluded: chain r residue 166 VAL Chi-restraints excluded: chain r residue 196 VAL Chi-restraints excluded: chain r residue 254 THR Chi-restraints excluded: chain r residue 257 THR Chi-restraints excluded: chain s residue 250 ASP Chi-restraints excluded: chain u residue 204 VAL Chi-restraints excluded: chain v residue 166 VAL Chi-restraints excluded: chain v residue 190 VAL Chi-restraints excluded: chain v residue 243 VAL Chi-restraints excluded: chain v residue 249 LEU Chi-restraints excluded: chain w residue 166 VAL Chi-restraints excluded: chain x residue 38 GLU Chi-restraints excluded: chain x residue 109 LEU Chi-restraints excluded: chain y residue 54 ILE Chi-restraints excluded: chain y residue 104 ASP Chi-restraints excluded: chain z residue 21 MET Chi-restraints excluded: chain 0 residue 150 LEU Chi-restraints excluded: chain 1 residue 103 MET Chi-restraints excluded: chain 2 residue 166 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 3 residue 40 MET Chi-restraints excluded: chain 3 residue 99 MET Chi-restraints excluded: chain 3 residue 157 LEU Chi-restraints excluded: chain 3 residue 259 LYS Chi-restraints excluded: chain 4 residue 31 ASP Chi-restraints excluded: chain 5 residue 39 THR Chi-restraints excluded: chain 5 residue 50 SER Chi-restraints excluded: chain 6 residue 166 VAL Chi-restraints excluded: chain 6 residue 196 VAL Chi-restraints excluded: chain 6 residue 254 THR Chi-restraints excluded: chain 6 residue 257 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1300 random chunks: chunk 656 optimal weight: 20.0000 chunk 366 optimal weight: 8.9990 chunk 982 optimal weight: 3.9990 chunk 803 optimal weight: 5.9990 chunk 325 optimal weight: 40.0000 chunk 1182 optimal weight: 5.9990 chunk 1277 optimal weight: 8.9990 chunk 1053 optimal weight: 5.9990 chunk 1172 optimal weight: 5.9990 chunk 403 optimal weight: 0.0020 chunk 948 optimal weight: 50.0000 overall best weight: 4.3996 ------------------------------------------------------------------------------- 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** ** D 213 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 228 GLN ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 214 HIS ** M 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 146 GLN ** 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 Z 217 GLN ** b 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 244 ASN ** 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 ** o 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 244 ASN ** 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 ** 3 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 107120 Z= 0.360 Angle : 0.687 8.364 145156 Z= 0.361 Chirality : 0.045 0.219 17472 Planarity : 0.004 0.049 18240 Dihedral : 5.580 61.521 14086 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.01 % Allowed : 6.84 % Favored : 93.15 % Rotamer: Outliers : 2.31 % Allowed : 11.07 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.07), residues: 13128 helix: 1.04 (0.06), residues: 8548 sheet: -1.82 (0.19), residues: 708 loop : -2.85 (0.09), residues: 3872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP 6 123 HIS 0.012 0.001 HIS E 23 PHE 0.025 0.002 PHE Z 161 TYR 0.020 0.002 TYR V 117 ARG 0.007 0.001 ARG Z 235 *********************** 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 1480 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 273 poor density : 1207 time to evaluate : 8.714 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: A 21 MET cc_start: 0.0447 (mmp) cc_final: 0.0180 (mmp) REVERT: B 99 MET cc_start: 0.2965 (ptm) cc_final: 0.2733 (ptm) REVERT: D 21 MET cc_start: -0.1877 (ttt) cc_final: -0.2169 (ttt) REVERT: I 1 MET cc_start: 0.4789 (ttp) cc_final: 0.4497 (ttp) REVERT: I 21 ASP cc_start: 0.7762 (p0) cc_final: 0.7513 (p0) REVERT: I 33 LEU cc_start: 0.8357 (mt) cc_final: 0.8097 (mt) REVERT: M 127 MET cc_start: -0.0620 (OUTLIER) cc_final: -0.1010 (ptt) REVERT: N 47 ASP cc_start: 0.8114 (t70) cc_final: 0.7502 (t0) REVERT: N 110 GLU cc_start: 0.8221 (pp20) cc_final: 0.7703 (pp20) REVERT: O 13 LEU cc_start: 0.8905 (mm) cc_final: 0.8625 (mm) REVERT: O 23 HIS cc_start: 0.7030 (t-170) cc_final: 0.6370 (t-170) REVERT: O 27 GLU cc_start: 0.8451 (pt0) cc_final: 0.7811 (pt0) REVERT: Q 24 MET cc_start: -0.0131 (tmm) cc_final: -0.0339 (tmm) REVERT: Q 154 SER cc_start: 0.6498 (t) cc_final: 0.6182 (m) REVERT: Q 167 MET cc_start: 0.8493 (tmm) cc_final: 0.8002 (tmm) REVERT: W 40 MET cc_start: -0.0766 (ppp) cc_final: -0.1052 (ppp) REVERT: X 20 LEU cc_start: 0.7761 (tp) cc_final: 0.7518 (tp) REVERT: X 21 ASP cc_start: 0.7691 (p0) cc_final: 0.7404 (p0) REVERT: X 114 GLN cc_start: 0.8240 (OUTLIER) cc_final: 0.7859 (pp30) REVERT: a 47 ASP cc_start: 0.8116 (t70) cc_final: 0.7503 (t0) REVERT: a 110 GLU cc_start: 0.8241 (pp20) cc_final: 0.7721 (pp20) REVERT: b 13 LEU cc_start: 0.8930 (mm) cc_final: 0.8653 (mm) REVERT: b 23 HIS cc_start: 0.7167 (t-170) cc_final: 0.6580 (t-170) REVERT: b 27 GLU cc_start: 0.8542 (pt0) cc_final: 0.7775 (pt0) REVERT: d 154 SER cc_start: 0.6498 (t) cc_final: 0.6205 (m) REVERT: d 167 MET cc_start: 0.8481 (tmm) cc_final: 0.7987 (tmm) REVERT: f 1 MET cc_start: -0.1248 (ppp) cc_final: -0.1758 (ppp) REVERT: m 114 GLN cc_start: 0.8238 (OUTLIER) cc_final: 0.7876 (pp30) REVERT: o 127 MET cc_start: -0.0814 (OUTLIER) cc_final: -0.1042 (ptt) REVERT: p 47 ASP cc_start: 0.7867 (t70) cc_final: 0.7412 (t0) REVERT: p 110 GLU cc_start: 0.8268 (pp20) cc_final: 0.7762 (pp20) REVERT: q 13 LEU cc_start: 0.8928 (mm) cc_final: 0.8640 (mm) REVERT: q 21 ASP cc_start: 0.7820 (m-30) cc_final: 0.6904 (t70) REVERT: q 28 PHE cc_start: 0.8603 (t80) cc_final: 0.8350 (t80) REVERT: q 68 MET cc_start: 0.8600 (mmt) cc_final: 0.8232 (mmt) REVERT: s 167 MET cc_start: 0.8495 (tmm) cc_final: 0.7999 (tmm) REVERT: u 1 MET cc_start: -0.1052 (ppp) cc_final: -0.1367 (ppp) REVERT: w 21 MET cc_start: -0.2068 (ttt) cc_final: -0.2290 (ttt) REVERT: 0 270 ASN cc_start: 0.6801 (p0) cc_final: 0.6597 (p0) REVERT: 1 1 MET cc_start: 0.4728 (ttp) cc_final: 0.4483 (ttp) REVERT: 1 21 ASP cc_start: 0.7755 (p0) cc_final: 0.7188 (t0) REVERT: 1 42 ARG cc_start: 0.8211 (mtm110) cc_final: 0.7953 (mtm-85) REVERT: 4 47 ASP cc_start: 0.8083 (t70) cc_final: 0.7453 (t0) REVERT: 4 110 GLU cc_start: 0.8234 (pp20) cc_final: 0.7747 (pp20) REVERT: 5 13 LEU cc_start: 0.8882 (mm) cc_final: 0.8592 (mm) REVERT: 5 21 ASP cc_start: 0.7805 (m-30) cc_final: 0.6901 (t70) REVERT: 5 28 PHE cc_start: 0.8561 (t80) cc_final: 0.8295 (t80) REVERT: 5 68 MET cc_start: 0.8733 (mmt) cc_final: 0.8371 (mmt) REVERT: 7 154 SER cc_start: 0.6475 (t) cc_final: 0.6179 (m) REVERT: 7 167 MET cc_start: 0.8475 (tmm) cc_final: 0.7981 (tmm) outliers start: 273 outliers final: 190 residues processed: 1375 average time/residue: 0.8031 time to fit residues: 1971.3305 Evaluate side-chains 1329 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 1135 time to evaluate : 8.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 91 GLU Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain J residue 29 ASP Chi-restraints excluded: chain J residue 166 VAL Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain M residue 40 MET Chi-restraints excluded: chain M residue 127 MET Chi-restraints excluded: chain M residue 209 THR Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 259 LYS Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 37 HIS Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 10 GLU Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 50 SER Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain P residue 166 VAL Chi-restraints excluded: chain P residue 182 ILE Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 254 THR Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain K residue 166 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 222 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain S residue 166 VAL Chi-restraints excluded: chain S residue 174 ASP Chi-restraints excluded: chain S residue 253 ILE Chi-restraints excluded: chain T residue 3 ILE Chi-restraints excluded: chain T residue 38 GLU Chi-restraints excluded: chain T residue 109 LEU Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 91 GLU Chi-restraints excluded: chain U residue 104 ASP Chi-restraints excluded: chain U residue 112 LEU Chi-restraints excluded: chain W residue 166 VAL Chi-restraints excluded: chain W residue 208 ASP Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 40 SER Chi-restraints excluded: chain X residue 55 ASP Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 103 MET Chi-restraints excluded: chain X residue 109 LEU Chi-restraints excluded: chain X residue 112 LEU Chi-restraints excluded: chain X residue 114 GLN Chi-restraints excluded: chain Y residue 29 ASP Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 257 THR Chi-restraints excluded: chain Z residue 40 MET Chi-restraints excluded: chain Z residue 222 VAL Chi-restraints excluded: chain Z residue 259 LYS Chi-restraints excluded: chain a residue 31 ASP Chi-restraints excluded: chain a residue 37 HIS Chi-restraints excluded: chain a residue 77 VAL Chi-restraints excluded: chain b residue 1 MET Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 50 SER Chi-restraints excluded: chain b residue 65 VAL Chi-restraints excluded: chain c residue 166 VAL Chi-restraints excluded: chain c residue 182 ILE Chi-restraints excluded: chain c residue 196 VAL Chi-restraints excluded: chain c residue 254 THR Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain e residue 166 VAL Chi-restraints excluded: chain e residue 196 VAL Chi-restraints excluded: chain e residue 234 ILE Chi-restraints excluded: chain f residue 166 VAL Chi-restraints excluded: chain f residue 204 VAL Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 190 VAL Chi-restraints excluded: chain g residue 243 VAL Chi-restraints excluded: chain h residue 166 VAL Chi-restraints excluded: chain h residue 174 ASP Chi-restraints excluded: chain h residue 253 ILE Chi-restraints excluded: chain i residue 3 ILE Chi-restraints excluded: chain i residue 38 GLU Chi-restraints excluded: chain i residue 109 LEU Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 78 VAL Chi-restraints excluded: chain j residue 91 GLU Chi-restraints excluded: chain j residue 104 ASP Chi-restraints excluded: chain j residue 112 LEU Chi-restraints excluded: chain l residue 166 VAL Chi-restraints excluded: chain l residue 208 ASP Chi-restraints excluded: chain m residue 13 LEU Chi-restraints excluded: chain m residue 55 ASP Chi-restraints excluded: chain m residue 81 ILE Chi-restraints excluded: chain m residue 103 MET Chi-restraints excluded: chain m residue 109 LEU Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain m residue 114 GLN Chi-restraints excluded: chain n residue 29 ASP Chi-restraints excluded: chain n residue 166 VAL Chi-restraints excluded: chain n residue 257 THR Chi-restraints excluded: chain o residue 40 MET Chi-restraints excluded: chain o residue 127 MET Chi-restraints excluded: chain o residue 209 THR Chi-restraints excluded: chain o residue 222 VAL Chi-restraints excluded: chain o residue 259 LYS Chi-restraints excluded: chain p residue 31 ASP Chi-restraints excluded: chain p residue 37 HIS Chi-restraints excluded: chain p residue 77 VAL Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 50 SER Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain r residue 166 VAL Chi-restraints excluded: chain r residue 182 ILE Chi-restraints excluded: chain r residue 196 VAL Chi-restraints excluded: chain r residue 209 THR Chi-restraints excluded: chain r residue 254 THR Chi-restraints excluded: chain r residue 257 THR Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 234 ILE Chi-restraints excluded: chain s residue 250 ASP Chi-restraints excluded: chain t residue 166 VAL Chi-restraints excluded: chain t residue 196 VAL Chi-restraints excluded: chain t residue 234 ILE Chi-restraints excluded: chain u residue 166 VAL Chi-restraints excluded: chain u residue 204 VAL Chi-restraints excluded: chain v residue 166 VAL Chi-restraints excluded: chain v residue 190 VAL Chi-restraints excluded: chain v residue 243 VAL Chi-restraints excluded: chain w residue 166 VAL Chi-restraints excluded: chain w residue 174 ASP Chi-restraints excluded: chain w residue 253 ILE Chi-restraints excluded: chain x residue 3 ILE Chi-restraints excluded: chain x residue 38 GLU Chi-restraints excluded: chain x residue 109 LEU Chi-restraints excluded: chain y residue 54 ILE Chi-restraints excluded: chain y residue 78 VAL Chi-restraints excluded: chain y residue 104 ASP Chi-restraints excluded: chain y residue 112 LEU Chi-restraints excluded: chain 0 residue 166 VAL Chi-restraints excluded: chain 0 residue 208 ASP Chi-restraints excluded: chain 1 residue 55 ASP Chi-restraints excluded: chain 1 residue 81 ILE Chi-restraints excluded: chain 1 residue 103 MET Chi-restraints excluded: chain 1 residue 109 LEU Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 2 residue 29 ASP Chi-restraints excluded: chain 2 residue 166 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 3 residue 40 MET Chi-restraints excluded: chain 3 residue 209 THR Chi-restraints excluded: chain 3 residue 222 VAL Chi-restraints excluded: chain 3 residue 259 LYS Chi-restraints excluded: chain 4 residue 31 ASP Chi-restraints excluded: chain 4 residue 37 HIS Chi-restraints excluded: chain 4 residue 77 VAL Chi-restraints excluded: chain 5 residue 39 THR Chi-restraints excluded: chain 5 residue 50 SER Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 6 residue 166 VAL Chi-restraints excluded: chain 6 residue 182 ILE Chi-restraints excluded: chain 6 residue 196 VAL Chi-restraints excluded: chain 6 residue 254 THR Chi-restraints excluded: chain 6 residue 257 THR Chi-restraints excluded: chain 7 residue 1 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1300 random chunks: chunk 1168 optimal weight: 6.9990 chunk 889 optimal weight: 5.9990 chunk 613 optimal weight: 5.9990 chunk 130 optimal weight: 50.0000 chunk 564 optimal weight: 5.9990 chunk 794 optimal weight: 7.9990 chunk 1186 optimal weight: 2.9990 chunk 1256 optimal weight: 30.0000 chunk 620 optimal weight: 8.9990 chunk 1124 optimal weight: 0.0670 chunk 338 optimal weight: 6.9990 overall best weight: 4.2126 ------------------------------------------------------------------------------- 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 146 GLN ** D 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 256 ASN ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 146 GLN ** R 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 146 GLN ** g 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 23 HIS s 256 ASN ** u 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 146 GLN ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 23 HIS 7 256 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.2382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 107120 Z= 0.341 Angle : 0.675 9.140 145156 Z= 0.355 Chirality : 0.045 0.187 17472 Planarity : 0.004 0.048 18240 Dihedral : 5.634 60.780 14074 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 2.82 % Allowed : 13.45 % Favored : 83.73 % 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: -0.51 (0.07), residues: 13128 helix: 0.91 (0.06), residues: 8552 sheet: -2.12 (0.17), residues: 784 loop : -2.89 (0.09), residues: 3792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP V 123 HIS 0.011 0.001 HIS E 23 PHE 0.021 0.002 PHE M 161 TYR 0.016 0.002 TYR k 118 ARG 0.005 0.001 ARG B 271 *********************** 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 1544 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 333 poor density : 1211 time to evaluate : 8.799 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: A 248 GLU cc_start: 0.7153 (tm-30) cc_final: 0.6871 (tm-30) REVERT: B 201 ILE cc_start: 0.9185 (mm) cc_final: 0.8867 (mt) REVERT: D 127 MET cc_start: 0.1265 (ptt) cc_final: 0.1011 (mtt) REVERT: F 68 MET cc_start: 0.8556 (tpp) cc_final: 0.8337 (tpp) REVERT: H 240 GLN cc_start: 0.8195 (tm-30) cc_final: 0.7868 (tm-30) REVERT: I 1 MET cc_start: 0.4544 (ttp) cc_final: 0.4287 (ttp) REVERT: I 7 LYS cc_start: 0.8261 (mtpt) cc_final: 0.7932 (mtmt) REVERT: I 21 ASP cc_start: 0.7816 (p0) cc_final: 0.7506 (p0) REVERT: I 33 LEU cc_start: 0.8293 (mt) cc_final: 0.8033 (mt) REVERT: I 105 LEU cc_start: 0.8210 (OUTLIER) cc_final: 0.7918 (tt) REVERT: I 114 GLN cc_start: 0.8223 (pp30) cc_final: 0.7990 (pp30) REVERT: N 47 ASP cc_start: 0.7889 (t70) cc_final: 0.7600 (t70) REVERT: N 110 GLU cc_start: 0.8176 (pp20) cc_final: 0.7713 (pp20) REVERT: O 13 LEU cc_start: 0.8931 (mm) cc_final: 0.8653 (mm) REVERT: O 23 HIS cc_start: 0.7546 (t-170) cc_final: 0.6607 (t-170) REVERT: O 27 GLU cc_start: 0.8678 (pt0) cc_final: 0.7417 (pt0) REVERT: P 186 LEU cc_start: 0.9027 (OUTLIER) cc_final: 0.8513 (mt) REVERT: Q 154 SER cc_start: 0.6500 (t) cc_final: 0.6229 (m) REVERT: Q 167 MET cc_start: 0.8508 (tmm) cc_final: 0.8065 (tmm) REVERT: K 248 GLU cc_start: 0.7197 (tm-30) cc_final: 0.6965 (tm-30) REVERT: L 201 ILE cc_start: 0.9206 (mm) cc_final: 0.8883 (mt) REVERT: S 21 MET cc_start: -0.1917 (ttt) cc_final: -0.2267 (ttt) REVERT: V 21 MET cc_start: -0.0316 (ttt) cc_final: -0.0589 (mtp) REVERT: X 105 LEU cc_start: 0.8241 (OUTLIER) cc_final: 0.7958 (tt) REVERT: X 114 GLN cc_start: 0.8290 (OUTLIER) cc_final: 0.8005 (pp30) REVERT: a 47 ASP cc_start: 0.7889 (t70) cc_final: 0.7602 (t70) REVERT: a 110 GLU cc_start: 0.8187 (pp20) cc_final: 0.7725 (pp20) REVERT: b 13 LEU cc_start: 0.8927 (mm) cc_final: 0.8632 (mm) REVERT: b 23 HIS cc_start: 0.7561 (t-170) cc_final: 0.6603 (t-170) REVERT: b 27 GLU cc_start: 0.8531 (pt0) cc_final: 0.7485 (pt0) REVERT: c 21 MET cc_start: -0.2110 (pmm) cc_final: -0.2319 (pmm) REVERT: c 186 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8506 (mt) REVERT: d 154 SER cc_start: 0.6503 (t) cc_final: 0.6243 (m) REVERT: d 167 MET cc_start: 0.8499 (tmm) cc_final: 0.8057 (tmm) REVERT: e 248 GLU cc_start: 0.7199 (tm-30) cc_final: 0.6935 (tm-30) REVERT: f 99 MET cc_start: 0.3517 (ptm) cc_final: 0.3212 (ptm) REVERT: f 201 ILE cc_start: 0.9187 (mm) cc_final: 0.8880 (mt) REVERT: l 240 GLN cc_start: 0.8171 (tm-30) cc_final: 0.7859 (tm-30) REVERT: m 42 ARG cc_start: 0.8102 (mtm110) cc_final: 0.7879 (mtm-85) REVERT: n 29 ASP cc_start: 0.0454 (OUTLIER) cc_final: 0.0239 (p0) REVERT: o 228 GLN cc_start: 0.8521 (mp10) cc_final: 0.8210 (mp10) REVERT: p 110 GLU cc_start: 0.8190 (pp20) cc_final: 0.7726 (pp20) REVERT: q 1 MET cc_start: 0.4314 (OUTLIER) cc_final: 0.3805 (ptm) REVERT: q 13 LEU cc_start: 0.8898 (mm) cc_final: 0.8621 (mm) REVERT: q 21 ASP cc_start: 0.8037 (m-30) cc_final: 0.6884 (t70) REVERT: q 23 HIS cc_start: 0.6853 (OUTLIER) cc_final: 0.5718 (t-170) REVERT: q 27 GLU cc_start: 0.8872 (pt0) cc_final: 0.7892 (pt0) REVERT: q 28 PHE cc_start: 0.8503 (t80) cc_final: 0.8238 (t80) REVERT: q 68 MET cc_start: 0.8631 (mmt) cc_final: 0.8220 (mmt) REVERT: r 21 MET cc_start: -0.2184 (pmm) cc_final: -0.2419 (pmm) REVERT: r 99 MET cc_start: 0.0079 (tpp) cc_final: -0.0305 (tpp) REVERT: r 186 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8511 (mt) REVERT: s 167 MET cc_start: 0.8514 (tmm) cc_final: 0.8074 (tmm) REVERT: t 248 GLU cc_start: 0.7170 (tm-30) cc_final: 0.6902 (tm-30) REVERT: u 99 MET cc_start: 0.3443 (ptm) cc_final: 0.3143 (ptm) REVERT: u 201 ILE cc_start: 0.9188 (mm) cc_final: 0.8877 (mt) REVERT: w 127 MET cc_start: 0.1478 (ptt) cc_final: 0.1274 (mtt) REVERT: 0 240 GLN cc_start: 0.8175 (tm-30) cc_final: 0.7851 (tm-30) REVERT: 1 1 MET cc_start: 0.4517 (ttp) cc_final: 0.4292 (ttp) REVERT: 1 7 LYS cc_start: 0.8107 (mtmt) cc_final: 0.7882 (mtmt) REVERT: 1 33 LEU cc_start: 0.8333 (mt) cc_final: 0.8077 (mt) REVERT: 1 42 ARG cc_start: 0.8100 (mtm110) cc_final: 0.7865 (mtm-85) REVERT: 1 114 GLN cc_start: 0.8196 (pp30) cc_final: 0.7963 (pp30) REVERT: 4 47 ASP cc_start: 0.7962 (t70) cc_final: 0.7708 (t70) REVERT: 4 110 GLU cc_start: 0.8202 (pp20) cc_final: 0.7731 (pp20) REVERT: 5 1 MET cc_start: 0.4176 (OUTLIER) cc_final: 0.3691 (ptm) REVERT: 5 13 LEU cc_start: 0.8901 (mm) cc_final: 0.8620 (mm) REVERT: 5 21 ASP cc_start: 0.8033 (m-30) cc_final: 0.6882 (t70) REVERT: 5 23 HIS cc_start: 0.6787 (OUTLIER) cc_final: 0.5662 (t-170) REVERT: 5 27 GLU cc_start: 0.8854 (pt0) cc_final: 0.7865 (pt0) REVERT: 5 28 PHE cc_start: 0.8460 (t80) cc_final: 0.8230 (t80) REVERT: 5 68 MET cc_start: 0.8804 (mmt) cc_final: 0.8468 (mmt) REVERT: 6 99 MET cc_start: 0.0278 (tpp) cc_final: -0.0021 (tpp) REVERT: 6 186 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8506 (mt) REVERT: 7 154 SER cc_start: 0.6483 (t) cc_final: 0.6225 (m) REVERT: 7 167 MET cc_start: 0.8495 (tmm) cc_final: 0.8052 (tmm) outliers start: 333 outliers final: 226 residues processed: 1440 average time/residue: 0.7933 time to fit residues: 2038.9937 Evaluate side-chains 1381 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 1143 time to evaluate : 8.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 217 GLN Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain C residue 243 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 227 CYS Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 38 GLU Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 39 THR Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 103 MET Chi-restraints excluded: chain I residue 105 LEU Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain J residue 29 ASP Chi-restraints excluded: chain J residue 166 VAL Chi-restraints excluded: chain J residue 208 ASP Chi-restraints excluded: chain J residue 215 ILE Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain M residue 40 MET Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 209 THR Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 252 ILE Chi-restraints excluded: chain M residue 259 LYS Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 37 HIS Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 50 SER Chi-restraints excluded: chain P residue 166 VAL Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 254 THR Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain K residue 166 VAL Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 217 GLN Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain R residue 243 VAL Chi-restraints excluded: chain S residue 166 VAL Chi-restraints excluded: chain S residue 227 CYS Chi-restraints excluded: chain S residue 253 ILE Chi-restraints excluded: chain T residue 3 ILE Chi-restraints excluded: chain T residue 38 GLU Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 109 LEU Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 99 VAL Chi-restraints excluded: chain U residue 104 ASP Chi-restraints excluded: chain U residue 112 LEU Chi-restraints excluded: chain V residue 166 VAL Chi-restraints excluded: chain W residue 150 LEU Chi-restraints excluded: chain W residue 166 VAL Chi-restraints excluded: chain X residue 13 LEU Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 55 ASP Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 100 LEU Chi-restraints excluded: chain X residue 103 MET Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 109 LEU Chi-restraints excluded: chain X residue 112 LEU Chi-restraints excluded: chain X residue 114 GLN Chi-restraints excluded: chain Y residue 29 ASP Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 204 VAL Chi-restraints excluded: chain Y residue 208 ASP Chi-restraints excluded: chain Y residue 215 ILE Chi-restraints excluded: chain Y residue 257 THR Chi-restraints excluded: chain Z residue 40 MET Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 222 VAL Chi-restraints excluded: chain Z residue 252 ILE Chi-restraints excluded: chain Z residue 259 LYS Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 31 ASP Chi-restraints excluded: chain a residue 37 HIS Chi-restraints excluded: chain a residue 77 VAL Chi-restraints excluded: chain a residue 95 THR Chi-restraints excluded: chain a residue 99 VAL Chi-restraints excluded: chain a residue 109 LEU Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 50 SER Chi-restraints excluded: chain c residue 166 VAL Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 196 VAL Chi-restraints excluded: chain c residue 254 THR Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain e residue 166 VAL Chi-restraints excluded: chain e residue 234 ILE Chi-restraints excluded: chain f residue 204 VAL Chi-restraints excluded: chain f residue 217 GLN Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 190 VAL Chi-restraints excluded: chain h residue 166 VAL Chi-restraints excluded: chain h residue 227 CYS Chi-restraints excluded: chain h residue 253 ILE Chi-restraints excluded: chain i residue 3 ILE Chi-restraints excluded: chain i residue 38 GLU Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 109 LEU Chi-restraints excluded: chain j residue 49 THR Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 78 VAL Chi-restraints excluded: chain j residue 99 VAL Chi-restraints excluded: chain j residue 104 ASP Chi-restraints excluded: chain j residue 112 LEU Chi-restraints excluded: chain k residue 166 VAL Chi-restraints excluded: chain l residue 150 LEU Chi-restraints excluded: chain l residue 166 VAL Chi-restraints excluded: chain m residue 13 LEU Chi-restraints excluded: chain m residue 55 ASP Chi-restraints excluded: chain m residue 81 ILE Chi-restraints excluded: chain m residue 100 LEU Chi-restraints excluded: chain m residue 103 MET Chi-restraints excluded: chain m residue 109 LEU Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain n residue 29 ASP Chi-restraints excluded: chain n residue 166 VAL Chi-restraints excluded: chain n residue 204 VAL Chi-restraints excluded: chain n residue 208 ASP Chi-restraints excluded: chain n residue 215 ILE Chi-restraints excluded: chain n residue 257 THR Chi-restraints excluded: chain o residue 40 MET Chi-restraints excluded: chain o residue 157 LEU Chi-restraints excluded: chain o residue 186 LEU Chi-restraints excluded: chain o residue 209 THR Chi-restraints excluded: chain o residue 222 VAL Chi-restraints excluded: chain o residue 252 ILE Chi-restraints excluded: chain o residue 259 LYS Chi-restraints excluded: chain p residue 8 LEU Chi-restraints excluded: chain p residue 31 ASP Chi-restraints excluded: chain p residue 37 HIS Chi-restraints excluded: chain p residue 77 VAL Chi-restraints excluded: chain p residue 95 THR Chi-restraints excluded: chain p residue 99 VAL Chi-restraints excluded: chain p residue 109 LEU Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 23 HIS Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 50 SER Chi-restraints excluded: chain r residue 166 VAL Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 196 VAL Chi-restraints excluded: chain r residue 209 THR Chi-restraints excluded: chain r residue 254 THR Chi-restraints excluded: chain r residue 257 THR Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 234 ILE Chi-restraints excluded: chain s residue 250 ASP Chi-restraints excluded: chain t residue 166 VAL Chi-restraints excluded: chain t residue 234 ILE Chi-restraints excluded: chain u residue 204 VAL Chi-restraints excluded: chain u residue 217 GLN Chi-restraints excluded: chain v residue 166 VAL Chi-restraints excluded: chain v residue 190 VAL Chi-restraints excluded: chain w residue 166 VAL Chi-restraints excluded: chain w residue 227 CYS Chi-restraints excluded: chain w residue 253 ILE Chi-restraints excluded: chain x residue 3 ILE Chi-restraints excluded: chain x residue 38 GLU Chi-restraints excluded: chain x residue 44 VAL Chi-restraints excluded: chain x residue 109 LEU Chi-restraints excluded: chain y residue 49 THR Chi-restraints excluded: chain y residue 54 ILE Chi-restraints excluded: chain y residue 78 VAL Chi-restraints excluded: chain y residue 99 VAL Chi-restraints excluded: chain y residue 104 ASP Chi-restraints excluded: chain y residue 112 LEU Chi-restraints excluded: chain z residue 166 VAL Chi-restraints excluded: chain 0 residue 150 LEU Chi-restraints excluded: chain 0 residue 166 VAL Chi-restraints excluded: chain 1 residue 55 ASP Chi-restraints excluded: chain 1 residue 81 ILE Chi-restraints excluded: chain 1 residue 100 LEU Chi-restraints excluded: chain 1 residue 103 MET Chi-restraints excluded: chain 1 residue 109 LEU Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 2 residue 29 ASP Chi-restraints excluded: chain 2 residue 166 VAL Chi-restraints excluded: chain 2 residue 204 VAL Chi-restraints excluded: chain 2 residue 208 ASP Chi-restraints excluded: chain 2 residue 215 ILE Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 3 residue 40 MET Chi-restraints excluded: chain 3 residue 157 LEU Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 3 residue 209 THR Chi-restraints excluded: chain 3 residue 222 VAL Chi-restraints excluded: chain 3 residue 252 ILE Chi-restraints excluded: chain 3 residue 259 LYS Chi-restraints excluded: chain 4 residue 8 LEU Chi-restraints excluded: chain 4 residue 31 ASP Chi-restraints excluded: chain 4 residue 37 HIS Chi-restraints excluded: chain 4 residue 77 VAL Chi-restraints excluded: chain 4 residue 95 THR Chi-restraints excluded: chain 4 residue 99 VAL Chi-restraints excluded: chain 4 residue 109 LEU Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 23 HIS Chi-restraints excluded: chain 5 residue 39 THR Chi-restraints excluded: chain 5 residue 50 SER Chi-restraints excluded: chain 6 residue 166 VAL Chi-restraints excluded: chain 6 residue 186 LEU Chi-restraints excluded: chain 6 residue 196 VAL Chi-restraints excluded: chain 6 residue 254 THR Chi-restraints excluded: chain 6 residue 257 THR Chi-restraints excluded: chain 7 residue 1 MET Chi-restraints excluded: chain 7 residue 250 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1300 random chunks: chunk 1046 optimal weight: 5.9990 chunk 713 optimal weight: 7.9990 chunk 18 optimal weight: 0.9980 chunk 935 optimal weight: 3.9990 chunk 518 optimal weight: 2.9990 chunk 1072 optimal weight: 0.9990 chunk 868 optimal weight: 0.7980 chunk 1 optimal weight: 20.0000 chunk 641 optimal weight: 0.2980 chunk 1127 optimal weight: 5.9990 chunk 317 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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** ** M 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 256 ASN b 29 GLN ** g 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 107120 Z= 0.168 Angle : 0.586 9.379 145156 Z= 0.305 Chirality : 0.043 0.176 17472 Planarity : 0.004 0.046 18240 Dihedral : 5.165 52.271 14071 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 1.94 % Allowed : 15.49 % Favored : 82.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.08 (0.07), residues: 13128 helix: 1.19 (0.06), residues: 8552 sheet: -1.70 (0.19), residues: 704 loop : -2.62 (0.09), residues: 3872 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 123 HIS 0.027 0.001 HIS 5 23 PHE 0.018 0.001 PHE O 28 TYR 0.018 0.002 TYR G 118 ARG 0.004 0.000 ARG Z 223 *********************** 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 1531 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 229 poor density : 1302 time to evaluate : 8.827 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: B 201 ILE cc_start: 0.9098 (mm) cc_final: 0.8804 (mt) REVERT: B 210 MET cc_start: 0.7502 (tpp) cc_final: 0.7147 (tpp) REVERT: B 214 HIS cc_start: 0.7447 (OUTLIER) cc_final: 0.7080 (m90) REVERT: G 21 MET cc_start: 0.0844 (mtp) cc_final: 0.0633 (ttt) REVERT: G 210 MET cc_start: 0.7853 (tmm) cc_final: 0.7637 (tmm) REVERT: H 240 GLN cc_start: 0.8134 (tm-30) cc_final: 0.7791 (tm-30) REVERT: I 1 MET cc_start: 0.4430 (ttp) cc_final: 0.4199 (ttp) REVERT: I 21 ASP cc_start: 0.7819 (p0) cc_final: 0.7501 (p0) REVERT: I 42 ARG cc_start: 0.8190 (mtm110) cc_final: 0.7876 (mtm-85) REVERT: N 110 GLU cc_start: 0.8229 (pp20) cc_final: 0.7684 (pp20) REVERT: O 13 LEU cc_start: 0.8728 (mm) cc_final: 0.8444 (mm) REVERT: O 23 HIS cc_start: 0.7425 (t-170) cc_final: 0.6503 (t-170) REVERT: O 27 GLU cc_start: 0.8382 (pt0) cc_final: 0.7684 (pt0) REVERT: Q 24 MET cc_start: 0.0302 (tmm) cc_final: -0.0104 (tmm) REVERT: Q 154 SER cc_start: 0.6378 (t) cc_final: 0.6066 (m) REVERT: Q 167 MET cc_start: 0.8456 (tmm) cc_final: 0.8030 (tmm) REVERT: L 201 ILE cc_start: 0.9109 (mm) cc_final: 0.8804 (mt) REVERT: L 210 MET cc_start: 0.7496 (tpp) cc_final: 0.7157 (tpp) REVERT: L 214 HIS cc_start: 0.7398 (OUTLIER) cc_final: 0.7056 (m90) REVERT: V 21 MET cc_start: -0.0234 (ttt) cc_final: -0.0510 (mtp) REVERT: V 210 MET cc_start: 0.7852 (tmm) cc_final: 0.7628 (tmm) REVERT: W 37 LYS cc_start: -0.0604 (OUTLIER) cc_final: -0.0838 (pttm) REVERT: X 114 GLN cc_start: 0.8155 (OUTLIER) cc_final: 0.7863 (pp30) REVERT: a 110 GLU cc_start: 0.8247 (pp20) cc_final: 0.7705 (pp20) REVERT: b 13 LEU cc_start: 0.8720 (mm) cc_final: 0.8430 (mm) REVERT: b 23 HIS cc_start: 0.7447 (t-170) cc_final: 0.6937 (t-170) REVERT: b 27 GLU cc_start: 0.8402 (pt0) cc_final: 0.7384 (pt0) REVERT: b 110 GLU cc_start: 0.8351 (pp20) cc_final: 0.8120 (pp20) REVERT: d 24 MET cc_start: 0.0351 (tmm) cc_final: 0.0091 (tmm) REVERT: d 154 SER cc_start: 0.6361 (t) cc_final: 0.6090 (m) REVERT: d 167 MET cc_start: 0.8458 (tmm) cc_final: 0.8036 (tmm) REVERT: f 201 ILE cc_start: 0.9103 (mm) cc_final: 0.8797 (mt) REVERT: f 210 MET cc_start: 0.7516 (tpp) cc_final: 0.7167 (tpp) REVERT: f 214 HIS cc_start: 0.7428 (OUTLIER) cc_final: 0.7076 (m90) REVERT: f 250 ASP cc_start: 0.7331 (t70) cc_final: 0.7042 (t0) REVERT: k 21 MET cc_start: -0.0166 (ttt) cc_final: -0.0476 (mtp) REVERT: k 210 MET cc_start: 0.7857 (tmm) cc_final: 0.7641 (tmm) REVERT: l 240 GLN cc_start: 0.8149 (tm-30) cc_final: 0.7818 (tm-30) REVERT: o 127 MET cc_start: 0.1127 (ptt) cc_final: 0.0578 (mmm) REVERT: p 110 GLU cc_start: 0.8244 (pp20) cc_final: 0.7699 (pp20) REVERT: q 13 LEU cc_start: 0.8733 (mm) cc_final: 0.8439 (mm) REVERT: q 21 ASP cc_start: 0.7826 (m-30) cc_final: 0.6938 (t70) REVERT: q 23 HIS cc_start: 0.7180 (t-170) cc_final: 0.6597 (t-170) REVERT: q 27 GLU cc_start: 0.8765 (pt0) cc_final: 0.8254 (pt0) REVERT: q 29 GLN cc_start: 0.9109 (tp40) cc_final: 0.8787 (tp40) REVERT: q 68 MET cc_start: 0.8459 (mmt) cc_final: 0.8067 (mmt) REVERT: q 110 GLU cc_start: 0.8425 (pp20) cc_final: 0.8174 (pp20) REVERT: r 21 MET cc_start: -0.2002 (pmm) cc_final: -0.2275 (pmm) REVERT: s 167 MET cc_start: 0.8431 (tmm) cc_final: 0.8017 (tmm) REVERT: u 201 ILE cc_start: 0.9097 (mm) cc_final: 0.8801 (mt) REVERT: u 210 MET cc_start: 0.7495 (tpp) cc_final: 0.7143 (tpp) REVERT: u 214 HIS cc_start: 0.7412 (OUTLIER) cc_final: 0.7055 (m90) REVERT: z 21 MET cc_start: -0.0015 (OUTLIER) cc_final: -0.0428 (mtp) REVERT: z 210 MET cc_start: 0.7833 (tmm) cc_final: 0.7611 (tmm) REVERT: 0 240 GLN cc_start: 0.8153 (tm-30) cc_final: 0.7805 (tm-30) REVERT: 1 1 MET cc_start: 0.4335 (ttp) cc_final: 0.4126 (ttp) REVERT: 4 110 GLU cc_start: 0.8228 (pp20) cc_final: 0.7671 (pp20) REVERT: 5 13 LEU cc_start: 0.8719 (mm) cc_final: 0.8444 (mm) REVERT: 5 21 ASP cc_start: 0.7863 (m-30) cc_final: 0.6906 (t70) REVERT: 5 23 HIS cc_start: 0.7160 (t-170) cc_final: 0.6631 (t-170) REVERT: 5 27 GLU cc_start: 0.8748 (pt0) cc_final: 0.8235 (pt0) REVERT: 5 29 GLN cc_start: 0.9073 (tp40) cc_final: 0.8731 (tp40) REVERT: 5 110 GLU cc_start: 0.8432 (pp20) cc_final: 0.8177 (pp20) REVERT: 7 24 MET cc_start: 0.0124 (tmm) cc_final: -0.0180 (tmm) REVERT: 7 154 SER cc_start: 0.6347 (t) cc_final: 0.6067 (m) REVERT: 7 167 MET cc_start: 0.8450 (tmm) cc_final: 0.8027 (tmm) outliers start: 229 outliers final: 160 residues processed: 1460 average time/residue: 0.7920 time to fit residues: 2064.5638 Evaluate side-chains 1354 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 1187 time to evaluate : 8.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 85 VAL Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain G residue 230 MET Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain J residue 29 ASP Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 166 VAL Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain M residue 40 MET Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 37 HIS Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 49 THR Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 50 SER Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain P residue 166 VAL Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 214 HIS Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain S residue 166 VAL Chi-restraints excluded: chain S residue 258 MET Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 109 LEU Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 104 ASP Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain U residue 112 LEU Chi-restraints excluded: chain V residue 166 VAL Chi-restraints excluded: chain V residue 230 MET Chi-restraints excluded: chain W residue 37 LYS Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 55 ASP Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 103 MET Chi-restraints excluded: chain X residue 114 GLN Chi-restraints excluded: chain Y residue 29 ASP Chi-restraints excluded: chain Y residue 88 LEU Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 257 THR Chi-restraints excluded: chain Z residue 40 MET Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 222 VAL Chi-restraints excluded: chain Z residue 256 ASN Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 31 ASP Chi-restraints excluded: chain a residue 37 HIS Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 49 THR Chi-restraints excluded: chain a residue 77 VAL Chi-restraints excluded: chain a residue 95 THR Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 50 SER Chi-restraints excluded: chain c residue 166 VAL Chi-restraints excluded: chain c residue 196 VAL Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain d residue 243 VAL Chi-restraints excluded: chain f residue 204 VAL Chi-restraints excluded: chain f residue 214 HIS Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain h residue 21 MET Chi-restraints excluded: chain h residue 166 VAL Chi-restraints excluded: chain h residue 258 MET Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 105 LEU Chi-restraints excluded: chain i residue 109 LEU Chi-restraints excluded: chain j residue 49 THR Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 75 LYS Chi-restraints excluded: chain j residue 104 ASP Chi-restraints excluded: chain j residue 105 LEU Chi-restraints excluded: chain j residue 112 LEU Chi-restraints excluded: chain k residue 166 VAL Chi-restraints excluded: chain k residue 230 MET Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 55 ASP Chi-restraints excluded: chain m residue 76 VAL Chi-restraints excluded: chain m residue 81 ILE Chi-restraints excluded: chain m residue 103 MET Chi-restraints excluded: chain n residue 29 ASP Chi-restraints excluded: chain n residue 88 LEU Chi-restraints excluded: chain n residue 166 VAL Chi-restraints excluded: chain n residue 257 THR Chi-restraints excluded: chain o residue 40 MET Chi-restraints excluded: chain o residue 57 THR Chi-restraints excluded: chain o residue 186 LEU Chi-restraints excluded: chain p residue 31 ASP Chi-restraints excluded: chain p residue 37 HIS Chi-restraints excluded: chain p residue 44 VAL Chi-restraints excluded: chain p residue 49 THR Chi-restraints excluded: chain p residue 77 VAL Chi-restraints excluded: chain p residue 95 THR Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 50 SER Chi-restraints excluded: chain r residue 166 VAL Chi-restraints excluded: chain r residue 196 VAL Chi-restraints excluded: chain r residue 209 THR Chi-restraints excluded: chain r residue 257 THR Chi-restraints excluded: chain s residue 234 ILE Chi-restraints excluded: chain u residue 204 VAL Chi-restraints excluded: chain u residue 214 HIS Chi-restraints excluded: chain v residue 166 VAL Chi-restraints excluded: chain w residue 166 VAL Chi-restraints excluded: chain w residue 258 MET Chi-restraints excluded: chain x residue 44 VAL Chi-restraints excluded: chain x residue 105 LEU Chi-restraints excluded: chain x residue 109 LEU Chi-restraints excluded: chain y residue 8 LEU Chi-restraints excluded: chain y residue 49 THR Chi-restraints excluded: chain y residue 54 ILE Chi-restraints excluded: chain y residue 85 VAL Chi-restraints excluded: chain y residue 104 ASP Chi-restraints excluded: chain y residue 105 LEU Chi-restraints excluded: chain y residue 112 LEU Chi-restraints excluded: chain z residue 21 MET Chi-restraints excluded: chain z residue 166 VAL Chi-restraints excluded: chain z residue 230 MET Chi-restraints excluded: chain 1 residue 55 ASP Chi-restraints excluded: chain 1 residue 81 ILE Chi-restraints excluded: chain 1 residue 103 MET Chi-restraints excluded: chain 2 residue 29 ASP Chi-restraints excluded: chain 2 residue 88 LEU Chi-restraints excluded: chain 2 residue 166 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 3 residue 40 MET Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 4 residue 31 ASP Chi-restraints excluded: chain 4 residue 37 HIS Chi-restraints excluded: chain 4 residue 49 THR Chi-restraints excluded: chain 4 residue 77 VAL Chi-restraints excluded: chain 4 residue 95 THR Chi-restraints excluded: chain 5 residue 39 THR Chi-restraints excluded: chain 5 residue 50 SER Chi-restraints excluded: chain 6 residue 166 VAL Chi-restraints excluded: chain 6 residue 196 VAL Chi-restraints excluded: chain 6 residue 257 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1300 random chunks: chunk 422 optimal weight: 4.9990 chunk 1131 optimal weight: 2.9990 chunk 248 optimal weight: 6.9990 chunk 737 optimal weight: 8.9990 chunk 310 optimal weight: 20.0000 chunk 1257 optimal weight: 5.9990 chunk 1044 optimal weight: 0.7980 chunk 582 optimal weight: 4.9990 chunk 104 optimal weight: 2.9990 chunk 416 optimal weight: 6.9990 chunk 660 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- 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 213 HIS ** M 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 213 HIS ** S 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 256 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** h 213 HIS ** h 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 217 GLN o 256 ASN ** u 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 213 HIS ** w 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 217 GLN ** 3 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 244 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.2633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 107120 Z= 0.291 Angle : 0.650 9.812 145156 Z= 0.339 Chirality : 0.044 0.203 17472 Planarity : 0.004 0.048 18240 Dihedral : 5.408 58.855 14071 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 19.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.20 % Favored : 92.80 % Rotamer: Outliers : 2.99 % Allowed : 15.74 % Favored : 81.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.19 (0.07), residues: 13128 helix: 1.12 (0.06), residues: 8548 sheet: -1.81 (0.19), residues: 704 loop : -2.70 (0.09), residues: 3876 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP z 123 HIS 0.006 0.001 HIS B 213 PHE 0.024 0.002 PHE p 57 TYR 0.017 0.002 TYR k 118 ARG 0.008 0.000 ARG O 42 *********************** 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 1549 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 353 poor density : 1196 time to evaluate : 8.912 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: B 201 ILE cc_start: 0.9176 (mm) cc_final: 0.8868 (mt) REVERT: F 12 LEU cc_start: 0.8524 (OUTLIER) cc_final: 0.8116 (tp) REVERT: F 68 MET cc_start: 0.8538 (tpp) cc_final: 0.8307 (tpp) REVERT: H 240 GLN cc_start: 0.8241 (tm-30) cc_final: 0.7856 (tm-30) REVERT: I 7 LYS cc_start: 0.8261 (mtpt) cc_final: 0.8023 (mtmt) REVERT: I 21 ASP cc_start: 0.7816 (p0) cc_final: 0.7472 (p0) REVERT: N 110 GLU cc_start: 0.8255 (pp20) cc_final: 0.7810 (pp20) REVERT: O 8 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8706 (pp) REVERT: O 13 LEU cc_start: 0.8867 (mm) cc_final: 0.8548 (mm) REVERT: O 23 HIS cc_start: 0.7529 (t-170) cc_final: 0.6638 (t-170) REVERT: O 27 GLU cc_start: 0.8665 (pt0) cc_final: 0.7447 (pt0) REVERT: O 42 ARG cc_start: 0.7472 (mtm-85) cc_final: 0.7195 (mtm-85) REVERT: P 186 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8568 (mt) REVERT: Q 154 SER cc_start: 0.6618 (t) cc_final: 0.6326 (m) REVERT: Q 167 MET cc_start: 0.8466 (tmm) cc_final: 0.8011 (tmm) REVERT: L 201 ILE cc_start: 0.9193 (mm) cc_final: 0.8879 (mt) REVERT: L 214 HIS cc_start: 0.7433 (OUTLIER) cc_final: 0.7175 (m90) REVERT: U 12 LEU cc_start: 0.8533 (OUTLIER) cc_final: 0.8116 (tp) REVERT: U 68 MET cc_start: 0.8493 (tpp) cc_final: 0.8257 (tpp) REVERT: V 21 MET cc_start: -0.0291 (ttt) cc_final: -0.0527 (mtp) REVERT: X 105 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7907 (tt) REVERT: X 114 GLN cc_start: 0.8237 (OUTLIER) cc_final: 0.7933 (pp30) REVERT: a 110 GLU cc_start: 0.8281 (pp20) cc_final: 0.7829 (pp20) REVERT: b 13 LEU cc_start: 0.8876 (mm) cc_final: 0.8573 (mm) REVERT: b 23 HIS cc_start: 0.7672 (t-170) cc_final: 0.6720 (t-170) REVERT: b 27 GLU cc_start: 0.8377 (pt0) cc_final: 0.7423 (pt0) REVERT: b 110 GLU cc_start: 0.8408 (pp20) cc_final: 0.8174 (pp20) REVERT: c 186 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8558 (mt) REVERT: d 154 SER cc_start: 0.6607 (t) cc_final: 0.6320 (m) REVERT: d 167 MET cc_start: 0.8455 (tmm) cc_final: 0.7999 (tmm) REVERT: f 201 ILE cc_start: 0.9177 (mm) cc_final: 0.8872 (mt) REVERT: f 214 HIS cc_start: 0.7465 (OUTLIER) cc_final: 0.7193 (m90) REVERT: j 12 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8252 (tp) REVERT: k 21 MET cc_start: -0.0242 (ttt) cc_final: -0.0500 (mtp) REVERT: l 240 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7877 (tm-30) REVERT: o 127 MET cc_start: 0.0759 (ptt) cc_final: 0.0417 (mmm) REVERT: p 79 THR cc_start: 0.8447 (t) cc_final: 0.8162 (t) REVERT: p 110 GLU cc_start: 0.8276 (pp20) cc_final: 0.7822 (pp20) REVERT: q 1 MET cc_start: 0.4323 (OUTLIER) cc_final: 0.3785 (ptm) REVERT: q 13 LEU cc_start: 0.8862 (mm) cc_final: 0.8525 (mm) REVERT: q 21 ASP cc_start: 0.7880 (m-30) cc_final: 0.6891 (t70) REVERT: q 23 HIS cc_start: 0.7605 (t-170) cc_final: 0.6542 (t-170) REVERT: q 27 GLU cc_start: 0.8991 (pt0) cc_final: 0.8080 (pt0) REVERT: q 68 MET cc_start: 0.8586 (mmt) cc_final: 0.8171 (mmt) REVERT: q 110 GLU cc_start: 0.8474 (pp20) cc_final: 0.8236 (pp20) REVERT: r 21 MET cc_start: -0.2777 (pmm) cc_final: -0.3014 (pmm) REVERT: r 186 LEU cc_start: 0.8902 (OUTLIER) cc_final: 0.8558 (mt) REVERT: s 167 MET cc_start: 0.8446 (tmm) cc_final: 0.8019 (tmm) REVERT: u 99 MET cc_start: 0.3683 (ptm) cc_final: 0.3432 (ptm) REVERT: u 201 ILE cc_start: 0.9182 (mm) cc_final: 0.8876 (mt) REVERT: u 214 HIS cc_start: 0.7447 (OUTLIER) cc_final: 0.7181 (m90) REVERT: w 127 MET cc_start: 0.0845 (mtt) cc_final: 0.0631 (ptt) REVERT: y 12 LEU cc_start: 0.8791 (OUTLIER) cc_final: 0.8394 (tp) REVERT: y 68 MET cc_start: 0.8491 (tpp) cc_final: 0.8278 (tpp) REVERT: z 21 MET cc_start: -0.0245 (ttt) cc_final: -0.0451 (mtp) REVERT: 0 40 MET cc_start: -0.0613 (ppp) cc_final: -0.0861 (ppp) REVERT: 0 240 GLN cc_start: 0.8254 (tm-30) cc_final: 0.7856 (tm-30) REVERT: 1 21 ASP cc_start: 0.7863 (p0) cc_final: 0.7425 (p0) REVERT: 1 33 LEU cc_start: 0.8107 (mt) cc_final: 0.7842 (mt) REVERT: 4 110 GLU cc_start: 0.8265 (pp20) cc_final: 0.7821 (pp20) REVERT: 5 1 MET cc_start: 0.4353 (OUTLIER) cc_final: 0.3862 (ptm) REVERT: 5 13 LEU cc_start: 0.8853 (mm) cc_final: 0.8508 (mm) REVERT: 5 21 ASP cc_start: 0.7860 (m-30) cc_final: 0.6859 (t70) REVERT: 5 23 HIS cc_start: 0.7570 (t-170) cc_final: 0.6532 (t-170) REVERT: 5 27 GLU cc_start: 0.8947 (pt0) cc_final: 0.7944 (pt0) REVERT: 5 68 MET cc_start: 0.8677 (mmt) cc_final: 0.8446 (mmt) REVERT: 5 103 MET cc_start: 0.7460 (OUTLIER) cc_final: 0.7183 (mtp) REVERT: 5 110 GLU cc_start: 0.8507 (pp20) cc_final: 0.8257 (pp20) REVERT: 6 186 LEU cc_start: 0.8904 (OUTLIER) cc_final: 0.8562 (mt) REVERT: 7 154 SER cc_start: 0.6590 (t) cc_final: 0.6309 (m) REVERT: 7 167 MET cc_start: 0.8448 (tmm) cc_final: 0.7998 (tmm) outliers start: 353 outliers final: 259 residues processed: 1454 average time/residue: 0.7776 time to fit residues: 2032.9547 Evaluate side-chains 1430 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 276 poor density : 1154 time to evaluate : 8.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain J residue 29 ASP Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 166 VAL Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain M residue 40 MET Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 209 THR Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 37 HIS Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain O residue 1 MET Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 50 SER Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain P residue 166 VAL Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 254 THR Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 166 VAL Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 214 HIS Chi-restraints excluded: chain L residue 271 ARG Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain S residue 21 MET Chi-restraints excluded: chain S residue 166 VAL Chi-restraints excluded: chain S residue 174 ASP Chi-restraints excluded: chain S residue 250 ASP Chi-restraints excluded: chain S residue 258 MET Chi-restraints excluded: chain T residue 3 ILE Chi-restraints excluded: chain T residue 61 ILE Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 109 LEU Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 62 LEU Chi-restraints excluded: chain U residue 75 LYS Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 104 ASP Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain U residue 112 LEU Chi-restraints excluded: chain V residue 166 VAL Chi-restraints excluded: chain W residue 150 LEU Chi-restraints excluded: chain W residue 166 VAL Chi-restraints excluded: chain W residue 208 ASP Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 55 ASP Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 103 MET Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 109 LEU Chi-restraints excluded: chain X residue 112 LEU Chi-restraints excluded: chain X residue 114 GLN Chi-restraints excluded: chain Y residue 29 ASP Chi-restraints excluded: chain Y residue 88 LEU Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 204 VAL Chi-restraints excluded: chain Y residue 257 THR Chi-restraints excluded: chain Z residue 40 MET Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 222 VAL Chi-restraints excluded: chain Z residue 252 ILE Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 31 ASP Chi-restraints excluded: chain a residue 37 HIS Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 77 VAL Chi-restraints excluded: chain a residue 99 VAL Chi-restraints excluded: chain a residue 109 LEU Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 50 SER Chi-restraints excluded: chain c residue 166 VAL Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 196 VAL Chi-restraints excluded: chain c residue 254 THR Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 242 ILE Chi-restraints excluded: chain e residue 150 LEU Chi-restraints excluded: chain e residue 166 VAL Chi-restraints excluded: chain e residue 196 VAL Chi-restraints excluded: chain e residue 234 ILE Chi-restraints excluded: chain f residue 166 VAL Chi-restraints excluded: chain f residue 170 ILE Chi-restraints excluded: chain f residue 204 VAL Chi-restraints excluded: chain f residue 214 HIS Chi-restraints excluded: chain f residue 271 ARG Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 190 VAL Chi-restraints excluded: chain h residue 21 MET Chi-restraints excluded: chain h residue 166 VAL Chi-restraints excluded: chain h residue 174 ASP Chi-restraints excluded: chain h residue 250 ASP Chi-restraints excluded: chain h residue 258 MET Chi-restraints excluded: chain i residue 3 ILE Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 61 ILE Chi-restraints excluded: chain i residue 105 LEU Chi-restraints excluded: chain i residue 109 LEU Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 12 LEU Chi-restraints excluded: chain j residue 39 THR Chi-restraints excluded: chain j residue 49 THR Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 62 LEU Chi-restraints excluded: chain j residue 75 LYS Chi-restraints excluded: chain j residue 104 ASP Chi-restraints excluded: chain j residue 105 LEU Chi-restraints excluded: chain j residue 112 LEU Chi-restraints excluded: chain k residue 166 VAL Chi-restraints excluded: chain l residue 150 LEU Chi-restraints excluded: chain l residue 166 VAL Chi-restraints excluded: chain l residue 208 ASP Chi-restraints excluded: chain m residue 13 LEU Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 55 ASP Chi-restraints excluded: chain m residue 62 LEU Chi-restraints excluded: chain m residue 76 VAL Chi-restraints excluded: chain m residue 81 ILE Chi-restraints excluded: chain m residue 103 MET Chi-restraints excluded: chain m residue 109 LEU Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain n residue 29 ASP Chi-restraints excluded: chain n residue 88 LEU Chi-restraints excluded: chain n residue 166 VAL Chi-restraints excluded: chain n residue 204 VAL Chi-restraints excluded: chain n residue 257 THR Chi-restraints excluded: chain o residue 40 MET Chi-restraints excluded: chain o residue 57 THR Chi-restraints excluded: chain o residue 157 LEU Chi-restraints excluded: chain o residue 186 LEU Chi-restraints excluded: chain o residue 256 ASN Chi-restraints excluded: chain p residue 8 LEU Chi-restraints excluded: chain p residue 31 ASP Chi-restraints excluded: chain p residue 37 HIS Chi-restraints excluded: chain p residue 44 VAL Chi-restraints excluded: chain p residue 77 VAL Chi-restraints excluded: chain p residue 95 THR Chi-restraints excluded: chain p residue 99 VAL Chi-restraints excluded: chain p residue 109 LEU Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 50 SER Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain r residue 166 VAL Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 196 VAL Chi-restraints excluded: chain r residue 254 THR Chi-restraints excluded: chain r residue 257 THR Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 234 ILE Chi-restraints excluded: chain s residue 250 ASP Chi-restraints excluded: chain t residue 150 LEU Chi-restraints excluded: chain t residue 166 VAL Chi-restraints excluded: chain t residue 196 VAL Chi-restraints excluded: chain t residue 234 ILE Chi-restraints excluded: chain u residue 166 VAL Chi-restraints excluded: chain u residue 204 VAL Chi-restraints excluded: chain u residue 214 HIS Chi-restraints excluded: chain v residue 166 VAL Chi-restraints excluded: chain v residue 190 VAL Chi-restraints excluded: chain w residue 166 VAL Chi-restraints excluded: chain w residue 174 ASP Chi-restraints excluded: chain w residue 250 ASP Chi-restraints excluded: chain w residue 258 MET Chi-restraints excluded: chain x residue 3 ILE Chi-restraints excluded: chain x residue 38 GLU Chi-restraints excluded: chain x residue 44 VAL Chi-restraints excluded: chain x residue 61 ILE Chi-restraints excluded: chain x residue 105 LEU Chi-restraints excluded: chain x residue 109 LEU Chi-restraints excluded: chain y residue 8 LEU Chi-restraints excluded: chain y residue 12 LEU Chi-restraints excluded: chain y residue 38 GLU Chi-restraints excluded: chain y residue 39 THR Chi-restraints excluded: chain y residue 49 THR Chi-restraints excluded: chain y residue 54 ILE Chi-restraints excluded: chain y residue 62 LEU Chi-restraints excluded: chain y residue 104 ASP Chi-restraints excluded: chain y residue 105 LEU Chi-restraints excluded: chain y residue 112 LEU Chi-restraints excluded: chain z residue 166 VAL Chi-restraints excluded: chain 0 residue 150 LEU Chi-restraints excluded: chain 0 residue 166 VAL Chi-restraints excluded: chain 0 residue 208 ASP Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 1 residue 55 ASP Chi-restraints excluded: chain 1 residue 62 LEU Chi-restraints excluded: chain 1 residue 81 ILE Chi-restraints excluded: chain 1 residue 103 MET Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 2 residue 29 ASP Chi-restraints excluded: chain 2 residue 88 LEU Chi-restraints excluded: chain 2 residue 166 VAL Chi-restraints excluded: chain 2 residue 204 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 3 residue 40 MET Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 157 LEU Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 3 residue 209 THR Chi-restraints excluded: chain 4 residue 8 LEU Chi-restraints excluded: chain 4 residue 31 ASP Chi-restraints excluded: chain 4 residue 37 HIS Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 4 residue 77 VAL Chi-restraints excluded: chain 4 residue 109 LEU Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 39 THR Chi-restraints excluded: chain 5 residue 50 SER Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 5 residue 103 MET Chi-restraints excluded: chain 6 residue 166 VAL Chi-restraints excluded: chain 6 residue 186 LEU Chi-restraints excluded: chain 6 residue 196 VAL Chi-restraints excluded: chain 6 residue 254 THR Chi-restraints excluded: chain 6 residue 257 THR Chi-restraints excluded: chain 7 residue 1 MET Chi-restraints excluded: chain 7 residue 250 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1300 random chunks: chunk 1212 optimal weight: 0.0030 chunk 141 optimal weight: 20.0000 chunk 716 optimal weight: 20.0000 chunk 918 optimal weight: 3.9990 chunk 711 optimal weight: 8.9990 chunk 1058 optimal weight: 20.0000 chunk 702 optimal weight: 7.9990 chunk 1252 optimal weight: 8.9990 chunk 784 optimal weight: 9.9990 chunk 763 optimal weight: 0.8980 chunk 578 optimal weight: 3.9990 overall best weight: 3.3796 ------------------------------------------------------------------------------- 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** ** G 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 17 GLN ** M 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 256 ASN ** d 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 256 ASN ** u 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 244 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2862 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= 0.288 Angle : 0.659 11.051 145156 Z= 0.343 Chirality : 0.044 0.197 17472 Planarity : 0.004 0.048 18240 Dihedral : 5.468 57.675 14071 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 19.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.88 % Favored : 93.12 % Rotamer: Outliers : 3.27 % Allowed : 16.24 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.07), residues: 13128 helix: 1.06 (0.06), residues: 8560 sheet: -1.88 (0.18), residues: 704 loop : -2.71 (0.09), residues: 3864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 123 HIS 0.005 0.001 HIS B 213 PHE 0.028 0.002 PHE N 57 TYR 0.018 0.002 TYR G 118 ARG 0.004 0.000 ARG s 235 *********************** 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 1586 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 386 poor density : 1200 time to evaluate : 8.905 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: B 201 ILE cc_start: 0.9187 (mm) cc_final: 0.8870 (mt) REVERT: B 214 HIS cc_start: 0.7496 (OUTLIER) cc_final: 0.7124 (m90) REVERT: F 12 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8055 (tp) REVERT: H 240 GLN cc_start: 0.8265 (tm-30) cc_final: 0.7868 (tm-30) REVERT: M 127 MET cc_start: 0.1314 (ptt) cc_final: 0.0908 (pmm) REVERT: N 75 LYS cc_start: 0.8599 (ptmm) cc_final: 0.8365 (ptmm) REVERT: N 110 GLU cc_start: 0.8195 (pp20) cc_final: 0.7751 (pp20) REVERT: O 8 LEU cc_start: 0.8959 (OUTLIER) cc_final: 0.8754 (pp) REVERT: O 13 LEU cc_start: 0.8884 (mm) cc_final: 0.8562 (mm) REVERT: O 23 HIS cc_start: 0.7584 (t-170) cc_final: 0.6665 (t-170) REVERT: O 27 GLU cc_start: 0.8369 (pt0) cc_final: 0.7615 (pt0) REVERT: O 42 ARG cc_start: 0.7693 (mtm-85) cc_final: 0.7333 (mtm-85) REVERT: P 186 LEU cc_start: 0.8926 (OUTLIER) cc_final: 0.8588 (mt) REVERT: Q 154 SER cc_start: 0.6580 (t) cc_final: 0.6326 (m) REVERT: Q 167 MET cc_start: 0.8400 (tmm) cc_final: 0.7963 (tmm) REVERT: L 201 ILE cc_start: 0.9210 (mm) cc_final: 0.8903 (mt) REVERT: L 214 HIS cc_start: 0.7479 (OUTLIER) cc_final: 0.7131 (m90) REVERT: L 230 MET cc_start: 0.7308 (mmm) cc_final: 0.6909 (tpp) REVERT: U 12 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8096 (tp) REVERT: V 21 MET cc_start: -0.0383 (ttt) cc_final: -0.0596 (mtp) REVERT: X 105 LEU cc_start: 0.8344 (OUTLIER) cc_final: 0.7956 (tt) REVERT: Z 127 MET cc_start: -0.0134 (mmm) cc_final: -0.0625 (pmm) REVERT: a 75 LYS cc_start: 0.8625 (ptmm) cc_final: 0.8396 (ptmm) REVERT: a 110 GLU cc_start: 0.8186 (pp20) cc_final: 0.7728 (pp20) REVERT: b 13 LEU cc_start: 0.8851 (mm) cc_final: 0.8477 (mm) REVERT: b 23 HIS cc_start: 0.7742 (t-170) cc_final: 0.6775 (t-170) REVERT: b 27 GLU cc_start: 0.8337 (pt0) cc_final: 0.7450 (pt0) REVERT: b 110 GLU cc_start: 0.8417 (pp20) cc_final: 0.8178 (pp20) REVERT: c 164 ILE cc_start: 0.8639 (OUTLIER) cc_final: 0.8406 (mp) REVERT: c 186 LEU cc_start: 0.8919 (OUTLIER) cc_final: 0.8577 (mt) REVERT: d 154 SER cc_start: 0.6553 (t) cc_final: 0.6285 (m) REVERT: d 167 MET cc_start: 0.8397 (tmm) cc_final: 0.7948 (tmm) REVERT: f 201 ILE cc_start: 0.9195 (mm) cc_final: 0.8880 (mt) REVERT: f 214 HIS cc_start: 0.7466 (OUTLIER) cc_final: 0.7097 (m90) REVERT: g 24 MET cc_start: 0.2816 (ptp) cc_final: 0.2586 (ptp) REVERT: j 12 LEU cc_start: 0.8610 (OUTLIER) cc_final: 0.8224 (tp) REVERT: k 21 MET cc_start: -0.0102 (ttt) cc_final: -0.0328 (mtp) REVERT: l 240 GLN cc_start: 0.8300 (tm-30) cc_final: 0.7897 (tm-30) REVERT: o 127 MET cc_start: 0.0584 (ptt) cc_final: 0.0239 (mmm) REVERT: p 110 GLU cc_start: 0.8204 (pp20) cc_final: 0.7778 (pp20) REVERT: q 1 MET cc_start: 0.4495 (OUTLIER) cc_final: 0.3977 (ptm) REVERT: q 13 LEU cc_start: 0.8836 (mm) cc_final: 0.8493 (mm) REVERT: q 21 ASP cc_start: 0.7758 (m-30) cc_final: 0.6821 (t70) REVERT: q 23 HIS cc_start: 0.7617 (t-170) cc_final: 0.6571 (t-170) REVERT: q 27 GLU cc_start: 0.8974 (pt0) cc_final: 0.8149 (pt0) REVERT: q 68 MET cc_start: 0.8599 (mmt) cc_final: 0.8151 (mmt) REVERT: q 110 GLU cc_start: 0.8455 (pp20) cc_final: 0.8203 (pp20) REVERT: r 164 ILE cc_start: 0.8651 (OUTLIER) cc_final: 0.8402 (mp) REVERT: r 186 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8576 (mt) REVERT: s 167 MET cc_start: 0.8369 (tmm) cc_final: 0.7961 (tmm) REVERT: u 99 MET cc_start: 0.3745 (ptm) cc_final: 0.3515 (ptm) REVERT: u 201 ILE cc_start: 0.9199 (mm) cc_final: 0.8897 (mt) REVERT: u 214 HIS cc_start: 0.7485 (OUTLIER) cc_final: 0.7126 (m90) REVERT: u 230 MET cc_start: 0.7339 (mmm) cc_final: 0.6915 (tpp) REVERT: w 99 MET cc_start: -0.0784 (OUTLIER) cc_final: -0.1036 (mtt) REVERT: y 12 LEU cc_start: 0.8789 (OUTLIER) cc_final: 0.8393 (tp) REVERT: 0 24 MET cc_start: -0.1867 (OUTLIER) cc_final: -0.2076 (ptt) REVERT: 0 240 GLN cc_start: 0.8300 (tm-30) cc_final: 0.7886 (tm-30) REVERT: 1 21 ASP cc_start: 0.7842 (p0) cc_final: 0.7457 (p0) REVERT: 1 30 GLU cc_start: 0.8498 (pp20) cc_final: 0.8251 (pp20) REVERT: 1 33 LEU cc_start: 0.8125 (mt) cc_final: 0.7824 (mt) REVERT: 3 127 MET cc_start: 0.0482 (pmm) cc_final: -0.0079 (mmm) REVERT: 4 110 GLU cc_start: 0.8194 (pp20) cc_final: 0.7770 (pp20) REVERT: 5 1 MET cc_start: 0.4551 (OUTLIER) cc_final: 0.4102 (ptm) REVERT: 5 13 LEU cc_start: 0.8860 (mm) cc_final: 0.8531 (mm) REVERT: 5 21 ASP cc_start: 0.7708 (m-30) cc_final: 0.6782 (t70) REVERT: 5 23 HIS cc_start: 0.7551 (t-170) cc_final: 0.6549 (t-170) REVERT: 5 27 GLU cc_start: 0.8760 (pt0) cc_final: 0.8062 (pt0) REVERT: 5 28 PHE cc_start: 0.8518 (t80) cc_final: 0.8303 (t80) REVERT: 5 68 MET cc_start: 0.8690 (mmt) cc_final: 0.8447 (mmt) REVERT: 5 110 GLU cc_start: 0.8471 (pp20) cc_final: 0.8215 (pp20) REVERT: 6 164 ILE cc_start: 0.8654 (OUTLIER) cc_final: 0.8416 (mp) REVERT: 6 186 LEU cc_start: 0.8924 (OUTLIER) cc_final: 0.8580 (mt) REVERT: 7 154 SER cc_start: 0.6560 (t) cc_final: 0.6294 (m) REVERT: 7 167 MET cc_start: 0.8386 (tmm) cc_final: 0.7943 (tmm) outliers start: 386 outliers final: 286 residues processed: 1472 average time/residue: 0.7933 time to fit residues: 2100.8079 Evaluate side-chains 1444 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 307 poor density : 1137 time to evaluate : 8.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain A residue 234 ILE Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain B residue 204 VAL Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain E residue 3 ILE Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 12 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 78 VAL Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 150 LEU Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain J residue 29 ASP Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 166 VAL Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain M residue 40 MET Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 209 THR Chi-restraints excluded: chain M residue 222 VAL Chi-restraints excluded: chain M residue 252 ILE Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 37 HIS Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 101 SER Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 50 SER Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain P residue 166 VAL Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 254 THR Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain Q residue 242 ILE Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain K residue 196 VAL Chi-restraints excluded: chain K residue 234 ILE Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 170 ILE Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 214 HIS Chi-restraints excluded: chain L residue 271 ARG Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain R residue 190 VAL Chi-restraints excluded: chain S residue 166 VAL Chi-restraints excluded: chain S residue 227 CYS Chi-restraints excluded: chain S residue 250 ASP Chi-restraints excluded: chain S residue 258 MET Chi-restraints excluded: chain T residue 3 ILE Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 61 ILE Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 109 LEU Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 39 THR Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 62 LEU Chi-restraints excluded: chain U residue 75 LYS Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 99 VAL Chi-restraints excluded: chain U residue 104 ASP Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain U residue 112 LEU Chi-restraints excluded: chain V residue 166 VAL Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain W residue 166 VAL Chi-restraints excluded: chain W residue 190 VAL Chi-restraints excluded: chain W residue 208 ASP Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 103 MET Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 109 LEU Chi-restraints excluded: chain X residue 112 LEU Chi-restraints excluded: chain Y residue 29 ASP Chi-restraints excluded: chain Y residue 88 LEU Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 204 VAL Chi-restraints excluded: chain Y residue 257 THR Chi-restraints excluded: chain Z residue 40 MET Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 222 VAL Chi-restraints excluded: chain Z residue 252 ILE Chi-restraints excluded: chain Z residue 256 ASN Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 31 ASP Chi-restraints excluded: chain a residue 37 HIS Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 77 VAL Chi-restraints excluded: chain a residue 99 VAL Chi-restraints excluded: chain a residue 101 SER Chi-restraints excluded: chain a residue 109 LEU Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 50 SER Chi-restraints excluded: chain c residue 164 ILE Chi-restraints excluded: chain c residue 166 VAL Chi-restraints excluded: chain c residue 186 LEU Chi-restraints excluded: chain c residue 196 VAL Chi-restraints excluded: chain c residue 254 THR Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain e residue 150 LEU Chi-restraints excluded: chain e residue 169 LEU Chi-restraints excluded: chain e residue 196 VAL Chi-restraints excluded: chain e residue 234 ILE Chi-restraints excluded: chain f residue 76 HIS Chi-restraints excluded: chain f residue 166 VAL Chi-restraints excluded: chain f residue 204 VAL Chi-restraints excluded: chain f residue 214 HIS Chi-restraints excluded: chain f residue 271 ARG Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 190 VAL Chi-restraints excluded: chain h residue 166 VAL Chi-restraints excluded: chain h residue 227 CYS Chi-restraints excluded: chain h residue 250 ASP Chi-restraints excluded: chain h residue 258 MET Chi-restraints excluded: chain i residue 3 ILE Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 61 ILE Chi-restraints excluded: chain i residue 105 LEU Chi-restraints excluded: chain i residue 109 LEU Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 12 LEU Chi-restraints excluded: chain j residue 39 THR Chi-restraints excluded: chain j residue 44 VAL Chi-restraints excluded: chain j residue 49 THR Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 62 LEU Chi-restraints excluded: chain j residue 75 LYS Chi-restraints excluded: chain j residue 78 VAL Chi-restraints excluded: chain j residue 99 VAL Chi-restraints excluded: chain j residue 104 ASP Chi-restraints excluded: chain j residue 105 LEU Chi-restraints excluded: chain j residue 112 LEU Chi-restraints excluded: chain k residue 166 VAL Chi-restraints excluded: chain k residue 173 ILE Chi-restraints excluded: chain l residue 150 LEU Chi-restraints excluded: chain l residue 166 VAL Chi-restraints excluded: chain l residue 190 VAL Chi-restraints excluded: chain l residue 208 ASP Chi-restraints excluded: chain l residue 232 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 44 VAL Chi-restraints excluded: chain m residue 55 ASP Chi-restraints excluded: chain m residue 62 LEU Chi-restraints excluded: chain m residue 76 VAL Chi-restraints excluded: chain m residue 81 ILE Chi-restraints excluded: chain m residue 103 MET Chi-restraints excluded: chain m residue 109 LEU Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain n residue 29 ASP Chi-restraints excluded: chain n residue 88 LEU Chi-restraints excluded: chain n residue 166 VAL Chi-restraints excluded: chain n residue 204 VAL Chi-restraints excluded: chain n residue 257 THR Chi-restraints excluded: chain o residue 40 MET Chi-restraints excluded: chain o residue 57 THR Chi-restraints excluded: chain o residue 186 LEU Chi-restraints excluded: chain o residue 252 ILE Chi-restraints excluded: chain p residue 8 LEU Chi-restraints excluded: chain p residue 31 ASP Chi-restraints excluded: chain p residue 37 HIS Chi-restraints excluded: chain p residue 44 VAL Chi-restraints excluded: chain p residue 77 VAL Chi-restraints excluded: chain p residue 99 VAL Chi-restraints excluded: chain p residue 101 SER Chi-restraints excluded: chain p residue 109 LEU Chi-restraints excluded: chain q residue 1 MET Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 50 SER Chi-restraints excluded: chain r residue 164 ILE Chi-restraints excluded: chain r residue 166 VAL Chi-restraints excluded: chain r residue 186 LEU Chi-restraints excluded: chain r residue 196 VAL Chi-restraints excluded: chain r residue 254 THR Chi-restraints excluded: chain r residue 257 THR Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 234 ILE Chi-restraints excluded: chain s residue 250 ASP Chi-restraints excluded: chain t residue 150 LEU Chi-restraints excluded: chain t residue 169 LEU Chi-restraints excluded: chain t residue 196 VAL Chi-restraints excluded: chain t residue 234 ILE Chi-restraints excluded: chain u residue 166 VAL Chi-restraints excluded: chain u residue 170 ILE Chi-restraints excluded: chain u residue 204 VAL Chi-restraints excluded: chain u residue 214 HIS Chi-restraints excluded: chain v residue 166 VAL Chi-restraints excluded: chain v residue 190 VAL Chi-restraints excluded: chain w residue 99 MET Chi-restraints excluded: chain w residue 166 VAL Chi-restraints excluded: chain w residue 227 CYS Chi-restraints excluded: chain w residue 250 ASP Chi-restraints excluded: chain w residue 258 MET Chi-restraints excluded: chain x residue 3 ILE Chi-restraints excluded: chain x residue 44 VAL Chi-restraints excluded: chain x residue 61 ILE Chi-restraints excluded: chain x residue 105 LEU Chi-restraints excluded: chain x residue 109 LEU Chi-restraints excluded: chain y residue 8 LEU Chi-restraints excluded: chain y residue 12 LEU Chi-restraints excluded: chain y residue 38 GLU Chi-restraints excluded: chain y residue 39 THR Chi-restraints excluded: chain y residue 49 THR Chi-restraints excluded: chain y residue 54 ILE Chi-restraints excluded: chain y residue 62 LEU Chi-restraints excluded: chain y residue 78 VAL Chi-restraints excluded: chain y residue 99 VAL Chi-restraints excluded: chain y residue 104 ASP Chi-restraints excluded: chain y residue 105 LEU Chi-restraints excluded: chain y residue 112 LEU Chi-restraints excluded: chain z residue 127 MET Chi-restraints excluded: chain z residue 166 VAL Chi-restraints excluded: chain z residue 173 ILE Chi-restraints excluded: chain 0 residue 24 MET Chi-restraints excluded: chain 0 residue 150 LEU Chi-restraints excluded: chain 0 residue 166 VAL Chi-restraints excluded: chain 0 residue 190 VAL Chi-restraints excluded: chain 0 residue 208 ASP Chi-restraints excluded: chain 0 residue 232 VAL Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 1 residue 62 LEU Chi-restraints excluded: chain 1 residue 81 ILE Chi-restraints excluded: chain 1 residue 99 VAL Chi-restraints excluded: chain 1 residue 103 MET Chi-restraints excluded: chain 1 residue 109 LEU Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 2 residue 29 ASP Chi-restraints excluded: chain 2 residue 88 LEU Chi-restraints excluded: chain 2 residue 166 VAL Chi-restraints excluded: chain 2 residue 204 VAL Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 3 residue 40 MET Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 3 residue 209 THR Chi-restraints excluded: chain 3 residue 222 VAL Chi-restraints excluded: chain 3 residue 252 ILE Chi-restraints excluded: chain 4 residue 8 LEU Chi-restraints excluded: chain 4 residue 31 ASP Chi-restraints excluded: chain 4 residue 37 HIS Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 4 residue 77 VAL Chi-restraints excluded: chain 4 residue 99 VAL Chi-restraints excluded: chain 4 residue 109 LEU Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 39 THR Chi-restraints excluded: chain 5 residue 50 SER Chi-restraints excluded: chain 5 residue 65 VAL Chi-restraints excluded: chain 6 residue 164 ILE Chi-restraints excluded: chain 6 residue 166 VAL Chi-restraints excluded: chain 6 residue 186 LEU Chi-restraints excluded: chain 6 residue 196 VAL Chi-restraints excluded: chain 6 residue 254 THR Chi-restraints excluded: chain 6 residue 257 THR Chi-restraints excluded: chain 7 residue 1 MET Chi-restraints excluded: chain 7 residue 250 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1300 random chunks: chunk 775 optimal weight: 6.9990 chunk 500 optimal weight: 0.7980 chunk 748 optimal weight: 8.9990 chunk 377 optimal weight: 0.8980 chunk 246 optimal weight: 5.9990 chunk 242 optimal weight: 2.9990 chunk 796 optimal weight: 2.9990 chunk 853 optimal weight: 4.9990 chunk 619 optimal weight: 0.9980 chunk 116 optimal weight: 0.0470 chunk 984 optimal weight: 10.0000 overall best weight: 1.1480 ------------------------------------------------------------------------------- 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** B 213 HIS ** C 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 213 HIS ** R 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 256 ASN f 213 HIS ** g 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 213 HIS ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7373 moved from start: 0.2843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 107120 Z= 0.181 Angle : 0.607 11.829 145156 Z= 0.313 Chirality : 0.043 0.215 17472 Planarity : 0.004 0.049 18240 Dihedral : 5.128 48.695 14068 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 2.54 % Allowed : 17.32 % Favored : 80.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.07), residues: 13128 helix: 1.22 (0.06), residues: 8560 sheet: -1.66 (0.18), residues: 704 loop : -2.58 (0.09), residues: 3864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP s 20 HIS 0.006 0.001 HIS G 214 PHE 0.024 0.001 PHE a 57 TYR 0.018 0.002 TYR f 117 ARG 0.008 0.000 ARG K 193 *********************** 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 1531 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 300 poor density : 1231 time to evaluate : 8.802 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: B 201 ILE cc_start: 0.9131 (mm) cc_final: 0.8849 (mt) REVERT: B 214 HIS cc_start: 0.7438 (OUTLIER) cc_final: 0.7124 (m90) REVERT: D 21 MET cc_start: -0.0038 (OUTLIER) cc_final: -0.0368 (mtt) REVERT: F 68 MET cc_start: 0.8345 (tpp) cc_final: 0.8114 (tpp) REVERT: H 240 GLN cc_start: 0.8250 (tm-30) cc_final: 0.7778 (tm-30) REVERT: J 24 MET cc_start: 0.1320 (ttp) cc_final: 0.1111 (tpp) REVERT: M 127 MET cc_start: 0.1215 (ptt) cc_final: 0.0787 (mmm) REVERT: N 110 GLU cc_start: 0.8208 (pp20) cc_final: 0.7739 (pp20) REVERT: O 8 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8640 (pp) REVERT: O 13 LEU cc_start: 0.8698 (mm) cc_final: 0.8391 (mm) REVERT: O 23 HIS cc_start: 0.7581 (t-170) cc_final: 0.6589 (t-170) REVERT: O 27 GLU cc_start: 0.8604 (pt0) cc_final: 0.7456 (pt0) REVERT: O 42 ARG cc_start: 0.7466 (mtm-85) cc_final: 0.7110 (mtm-85) REVERT: P 164 ILE cc_start: 0.8572 (OUTLIER) cc_final: 0.8332 (mp) REVERT: P 186 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8345 (mt) REVERT: Q 154 SER cc_start: 0.6511 (t) cc_final: 0.6225 (m) REVERT: Q 167 MET cc_start: 0.8372 (tmm) cc_final: 0.7962 (tmm) REVERT: L 201 ILE cc_start: 0.9147 (mm) cc_final: 0.8861 (mt) REVERT: L 214 HIS cc_start: 0.7386 (OUTLIER) cc_final: 0.7060 (m90) REVERT: S 21 MET cc_start: 0.0114 (OUTLIER) cc_final: -0.0296 (ttt) REVERT: U 12 LEU cc_start: 0.8517 (OUTLIER) cc_final: 0.8117 (tp) REVERT: X 30 GLU cc_start: 0.8405 (pp20) cc_final: 0.8158 (pp20) REVERT: X 105 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7890 (tt) REVERT: Z 217 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8394 (tp40) REVERT: a 110 GLU cc_start: 0.8233 (pp20) cc_final: 0.7746 (pp20) REVERT: b 13 LEU cc_start: 0.8658 (mm) cc_final: 0.8336 (mm) REVERT: b 23 HIS cc_start: 0.7582 (t-170) cc_final: 0.6653 (t-170) REVERT: b 27 GLU cc_start: 0.8351 (pt0) cc_final: 0.7641 (pt0) REVERT: b 110 GLU cc_start: 0.8383 (pp20) cc_final: 0.8115 (pp20) REVERT: c 53 VAL cc_start: 0.0471 (OUTLIER) cc_final: 0.0255 (t) REVERT: d 154 SER cc_start: 0.6385 (t) cc_final: 0.6154 (m) REVERT: d 167 MET cc_start: 0.8349 (tmm) cc_final: 0.7965 (tmm) REVERT: f 201 ILE cc_start: 0.9130 (mm) cc_final: 0.8843 (mt) REVERT: f 214 HIS cc_start: 0.7444 (OUTLIER) cc_final: 0.7108 (m90) REVERT: h 21 MET cc_start: -0.0119 (mtt) cc_final: -0.0676 (ttt) REVERT: j 12 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8176 (tp) REVERT: l 24 MET cc_start: -0.3202 (OUTLIER) cc_final: -0.3542 (mmt) REVERT: l 240 GLN cc_start: 0.8298 (tm-30) cc_final: 0.7828 (tm-30) REVERT: o 127 MET cc_start: 0.0645 (ptt) cc_final: 0.0436 (mmm) REVERT: p 110 GLU cc_start: 0.8252 (pp20) cc_final: 0.7805 (pp20) REVERT: q 13 LEU cc_start: 0.8698 (mm) cc_final: 0.8384 (mm) REVERT: q 21 ASP cc_start: 0.7576 (m-30) cc_final: 0.6732 (t70) REVERT: q 23 HIS cc_start: 0.7582 (t-170) cc_final: 0.6547 (t-170) REVERT: q 27 GLU cc_start: 0.8911 (pt0) cc_final: 0.8169 (pt0) REVERT: q 68 MET cc_start: 0.8487 (mmt) cc_final: 0.8104 (mmt) REVERT: q 110 GLU cc_start: 0.8423 (pp20) cc_final: 0.8165 (pp20) REVERT: s 167 MET cc_start: 0.8334 (tmm) cc_final: 0.7951 (tmm) REVERT: u 201 ILE cc_start: 0.9131 (mm) cc_final: 0.8846 (mt) REVERT: u 214 HIS cc_start: 0.7393 (OUTLIER) cc_final: 0.7074 (m90) REVERT: y 12 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8376 (tp) REVERT: 0 240 GLN cc_start: 0.8298 (tm-30) cc_final: 0.7812 (tm-30) REVERT: 4 110 GLU cc_start: 0.8244 (pp20) cc_final: 0.7796 (pp20) REVERT: 5 13 LEU cc_start: 0.8706 (mm) cc_final: 0.8402 (mm) REVERT: 5 21 ASP cc_start: 0.7569 (m-30) cc_final: 0.6675 (t70) REVERT: 5 23 HIS cc_start: 0.7763 (t-170) cc_final: 0.6737 (t-170) REVERT: 5 27 GLU cc_start: 0.8928 (pt0) cc_final: 0.8124 (pt0) REVERT: 5 103 MET cc_start: 0.7523 (mtt) cc_final: 0.7293 (mtp) REVERT: 5 110 GLU cc_start: 0.8446 (pp20) cc_final: 0.8205 (pp20) REVERT: 6 186 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8394 (mt) REVERT: 7 154 SER cc_start: 0.6423 (t) cc_final: 0.6180 (m) REVERT: 7 167 MET cc_start: 0.8341 (tmm) cc_final: 0.7959 (tmm) REVERT: 7 264 ARG cc_start: 0.8012 (ttm170) cc_final: 0.7781 (ttm-80) outliers start: 300 outliers final: 237 residues processed: 1447 average time/residue: 0.8030 time to fit residues: 2080.4812 Evaluate side-chains 1410 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 253 poor density : 1157 time to evaluate : 8.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 166 VAL Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain C residue 190 VAL Chi-restraints excluded: chain D residue 21 MET Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 54 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 112 LEU Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 232 VAL Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 62 LEU Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain J residue 29 ASP Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 166 VAL Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain M residue 40 MET Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 252 ILE Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 37 HIS Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 50 SER Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain P residue 164 ILE Chi-restraints excluded: chain P residue 166 VAL Chi-restraints excluded: chain P residue 186 LEU Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 254 THR Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 166 VAL Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain L residue 166 VAL Chi-restraints excluded: chain L residue 214 HIS Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain S residue 21 MET Chi-restraints excluded: chain S residue 166 VAL Chi-restraints excluded: chain S residue 253 ILE Chi-restraints excluded: chain S residue 258 MET Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 61 ILE Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 109 LEU Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 39 THR Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 62 LEU Chi-restraints excluded: chain U residue 75 LYS Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 99 VAL Chi-restraints excluded: chain U residue 104 ASP Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain U residue 112 LEU Chi-restraints excluded: chain V residue 166 VAL Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain W residue 190 VAL Chi-restraints excluded: chain W residue 208 ASP Chi-restraints excluded: chain W residue 232 VAL Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 76 VAL Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 103 MET Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 109 LEU Chi-restraints excluded: chain X residue 112 LEU Chi-restraints excluded: chain Y residue 29 ASP Chi-restraints excluded: chain Y residue 88 LEU Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 204 VAL Chi-restraints excluded: chain Y residue 208 ASP Chi-restraints excluded: chain Y residue 257 THR Chi-restraints excluded: chain Z residue 40 MET Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 222 VAL Chi-restraints excluded: chain Z residue 256 ASN Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 31 ASP Chi-restraints excluded: chain a residue 37 HIS Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 77 VAL Chi-restraints excluded: chain a residue 95 THR Chi-restraints excluded: chain a residue 99 VAL Chi-restraints excluded: chain a residue 109 LEU Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 50 SER Chi-restraints excluded: chain c residue 53 VAL Chi-restraints excluded: chain c residue 166 VAL Chi-restraints excluded: chain c residue 196 VAL Chi-restraints excluded: chain c residue 254 THR Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain d residue 250 ASP Chi-restraints excluded: chain e residue 150 LEU Chi-restraints excluded: chain e residue 166 VAL Chi-restraints excluded: chain f residue 76 HIS Chi-restraints excluded: chain f residue 214 HIS Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 190 VAL Chi-restraints excluded: chain h residue 166 VAL Chi-restraints excluded: chain h residue 253 ILE Chi-restraints excluded: chain h residue 258 MET Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 105 LEU Chi-restraints excluded: chain i residue 109 LEU Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 12 LEU Chi-restraints excluded: chain j residue 39 THR Chi-restraints excluded: chain j residue 44 VAL Chi-restraints excluded: chain j residue 49 THR Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 62 LEU Chi-restraints excluded: chain j residue 75 LYS Chi-restraints excluded: chain j residue 99 VAL Chi-restraints excluded: chain j residue 104 ASP Chi-restraints excluded: chain j residue 105 LEU Chi-restraints excluded: chain j residue 112 LEU Chi-restraints excluded: chain k residue 166 VAL Chi-restraints excluded: chain k residue 173 ILE Chi-restraints excluded: chain l residue 24 MET Chi-restraints excluded: chain l residue 190 VAL Chi-restraints excluded: chain l residue 201 ILE Chi-restraints excluded: chain l residue 232 VAL Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 55 ASP Chi-restraints excluded: chain m residue 62 LEU Chi-restraints excluded: chain m residue 76 VAL Chi-restraints excluded: chain m residue 81 ILE Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain n residue 29 ASP Chi-restraints excluded: chain n residue 88 LEU Chi-restraints excluded: chain n residue 166 VAL Chi-restraints excluded: chain n residue 204 VAL Chi-restraints excluded: chain n residue 257 THR Chi-restraints excluded: chain o residue 40 MET Chi-restraints excluded: chain o residue 57 THR Chi-restraints excluded: chain o residue 186 LEU Chi-restraints excluded: chain o residue 252 ILE Chi-restraints excluded: chain p residue 8 LEU Chi-restraints excluded: chain p residue 31 ASP Chi-restraints excluded: chain p residue 37 HIS Chi-restraints excluded: chain p residue 44 VAL Chi-restraints excluded: chain p residue 77 VAL Chi-restraints excluded: chain p residue 99 VAL Chi-restraints excluded: chain p residue 109 LEU Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 50 SER Chi-restraints excluded: chain r residue 166 VAL Chi-restraints excluded: chain r residue 196 VAL Chi-restraints excluded: chain r residue 254 THR Chi-restraints excluded: chain r residue 257 THR Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 234 ILE Chi-restraints excluded: chain t residue 166 VAL Chi-restraints excluded: chain u residue 76 HIS Chi-restraints excluded: chain u residue 166 VAL Chi-restraints excluded: chain u residue 214 HIS Chi-restraints excluded: chain v residue 166 VAL Chi-restraints excluded: chain v residue 190 VAL Chi-restraints excluded: chain w residue 166 VAL Chi-restraints excluded: chain w residue 258 MET Chi-restraints excluded: chain x residue 44 VAL Chi-restraints excluded: chain x residue 105 LEU Chi-restraints excluded: chain x residue 109 LEU Chi-restraints excluded: chain y residue 8 LEU Chi-restraints excluded: chain y residue 12 LEU Chi-restraints excluded: chain y residue 38 GLU Chi-restraints excluded: chain y residue 39 THR Chi-restraints excluded: chain y residue 49 THR Chi-restraints excluded: chain y residue 54 ILE Chi-restraints excluded: chain y residue 62 LEU Chi-restraints excluded: chain y residue 78 VAL Chi-restraints excluded: chain y residue 99 VAL Chi-restraints excluded: chain y residue 104 ASP Chi-restraints excluded: chain y residue 105 LEU Chi-restraints excluded: chain y residue 112 LEU Chi-restraints excluded: chain z residue 166 VAL Chi-restraints excluded: chain z residue 173 ILE Chi-restraints excluded: chain 0 residue 190 VAL Chi-restraints excluded: chain 0 residue 201 ILE Chi-restraints excluded: chain 0 residue 232 VAL Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 1 residue 62 LEU Chi-restraints excluded: chain 1 residue 81 ILE Chi-restraints excluded: chain 1 residue 103 MET Chi-restraints excluded: chain 1 residue 109 LEU Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 2 residue 29 ASP Chi-restraints excluded: chain 2 residue 88 LEU Chi-restraints excluded: chain 2 residue 166 VAL Chi-restraints excluded: chain 2 residue 204 VAL Chi-restraints excluded: chain 2 residue 208 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 3 residue 40 MET Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 3 residue 252 ILE Chi-restraints excluded: chain 4 residue 8 LEU Chi-restraints excluded: chain 4 residue 31 ASP Chi-restraints excluded: chain 4 residue 37 HIS Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 4 residue 77 VAL Chi-restraints excluded: chain 4 residue 109 LEU Chi-restraints excluded: chain 5 residue 39 THR Chi-restraints excluded: chain 5 residue 50 SER Chi-restraints excluded: chain 6 residue 166 VAL Chi-restraints excluded: chain 6 residue 186 LEU Chi-restraints excluded: chain 6 residue 196 VAL Chi-restraints excluded: chain 6 residue 254 THR Chi-restraints excluded: chain 6 residue 257 THR Chi-restraints excluded: chain 7 residue 1 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1300 random chunks: chunk 1139 optimal weight: 10.0000 chunk 1200 optimal weight: 9.9990 chunk 1095 optimal weight: 0.0570 chunk 1167 optimal weight: 0.2980 chunk 702 optimal weight: 3.9990 chunk 508 optimal weight: 0.9980 chunk 916 optimal weight: 0.8980 chunk 358 optimal weight: 0.9980 chunk 1055 optimal weight: 3.9990 chunk 1104 optimal weight: 10.0000 chunk 1163 optimal weight: 4.9990 overall best weight: 0.6498 ------------------------------------------------------------------------------- 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** ** H 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 217 GLN ** R 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7346 moved from start: 0.2881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 107120 Z= 0.170 Angle : 0.612 12.264 145156 Z= 0.313 Chirality : 0.043 0.217 17472 Planarity : 0.004 0.086 18240 Dihedral : 4.977 47.778 14068 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer: Outliers : 2.35 % Allowed : 17.81 % Favored : 79.83 % 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: 0.07 (0.07), residues: 13128 helix: 1.29 (0.06), residues: 8552 sheet: -1.49 (0.18), residues: 712 loop : -2.56 (0.09), residues: 3864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP r 20 HIS 0.007 0.001 HIS z 214 PHE 0.038 0.001 PHE r 91 TYR 0.017 0.001 TYR G 118 ARG 0.006 0.000 ARG A 193 *********************** 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 1499 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 1221 time to evaluate : 8.380 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: B 201 ILE cc_start: 0.9093 (mm) cc_final: 0.8822 (mt) REVERT: B 214 HIS cc_start: 0.7386 (OUTLIER) cc_final: 0.7117 (m90) REVERT: H 150 LEU cc_start: 0.8514 (mm) cc_final: 0.8096 (tp) REVERT: H 240 GLN cc_start: 0.8252 (tm-30) cc_final: 0.7733 (tm-30) REVERT: I 21 ASP cc_start: 0.7821 (p0) cc_final: 0.7029 (t0) REVERT: N 110 GLU cc_start: 0.8240 (pp20) cc_final: 0.7748 (pp20) REVERT: O 8 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8616 (pp) REVERT: O 13 LEU cc_start: 0.8638 (mm) cc_final: 0.8343 (mm) REVERT: O 23 HIS cc_start: 0.7464 (t-170) cc_final: 0.6537 (t-170) REVERT: O 27 GLU cc_start: 0.8467 (pt0) cc_final: 0.7489 (pt0) REVERT: Q 154 SER cc_start: 0.6412 (t) cc_final: 0.6083 (m) REVERT: Q 167 MET cc_start: 0.8374 (tmm) cc_final: 0.7913 (tmm) REVERT: L 201 ILE cc_start: 0.9114 (mm) cc_final: 0.8843 (mt) REVERT: L 214 HIS cc_start: 0.7406 (OUTLIER) cc_final: 0.7167 (m90) REVERT: L 230 MET cc_start: 0.7200 (mmm) cc_final: 0.6810 (tpp) REVERT: W 240 GLN cc_start: 0.8078 (tm-30) cc_final: 0.7827 (tm-30) REVERT: X 30 GLU cc_start: 0.8397 (pp20) cc_final: 0.8164 (pp20) REVERT: X 105 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7807 (tt) REVERT: Z 217 GLN cc_start: 0.8681 (mm-40) cc_final: 0.8306 (tp40) REVERT: a 110 GLU cc_start: 0.8261 (pp20) cc_final: 0.7773 (pp20) REVERT: b 13 LEU cc_start: 0.8664 (mm) cc_final: 0.8355 (mm) REVERT: b 23 HIS cc_start: 0.7582 (t-170) cc_final: 0.6594 (t-170) REVERT: b 27 GLU cc_start: 0.8616 (pt0) cc_final: 0.7523 (pt0) REVERT: b 68 MET cc_start: 0.8271 (mmt) cc_final: 0.7932 (mmt) REVERT: b 110 GLU cc_start: 0.8312 (pp20) cc_final: 0.8102 (pp20) REVERT: d 154 SER cc_start: 0.6379 (t) cc_final: 0.6071 (m) REVERT: d 167 MET cc_start: 0.8372 (tmm) cc_final: 0.7920 (tmm) REVERT: f 201 ILE cc_start: 0.9089 (mm) cc_final: 0.8820 (mt) REVERT: f 214 HIS cc_start: 0.7438 (OUTLIER) cc_final: 0.7197 (m90) REVERT: j 12 LEU cc_start: 0.8515 (OUTLIER) cc_final: 0.8123 (tp) REVERT: l 150 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8031 (tp) REVERT: l 240 GLN cc_start: 0.8305 (tm-30) cc_final: 0.7829 (tm-30) REVERT: p 110 GLU cc_start: 0.8258 (pp20) cc_final: 0.7764 (pp20) REVERT: q 13 LEU cc_start: 0.8685 (mm) cc_final: 0.8377 (mm) REVERT: q 21 ASP cc_start: 0.7469 (m-30) cc_final: 0.6597 (t0) REVERT: q 23 HIS cc_start: 0.7593 (t-170) cc_final: 0.6847 (t-170) REVERT: q 27 GLU cc_start: 0.8971 (pt0) cc_final: 0.8506 (pt0) REVERT: q 68 MET cc_start: 0.8429 (mmt) cc_final: 0.8034 (mmt) REVERT: s 167 MET cc_start: 0.8355 (tmm) cc_final: 0.7960 (tmm) REVERT: t 91 PHE cc_start: -0.1417 (OUTLIER) cc_final: -0.1645 (m-80) REVERT: u 93 LEU cc_start: -0.2322 (OUTLIER) cc_final: -0.2682 (mp) REVERT: u 201 ILE cc_start: 0.9097 (mm) cc_final: 0.8836 (mt) REVERT: u 214 HIS cc_start: 0.7398 (OUTLIER) cc_final: 0.7153 (m90) REVERT: u 230 MET cc_start: 0.7224 (mmm) cc_final: 0.6819 (tpp) REVERT: w 99 MET cc_start: -0.1048 (mtt) cc_final: -0.1362 (mpp) REVERT: 0 40 MET cc_start: -0.0625 (tmm) cc_final: -0.0973 (tpt) REVERT: 0 150 LEU cc_start: 0.8445 (mm) cc_final: 0.7997 (tp) REVERT: 0 240 GLN cc_start: 0.8310 (tm-30) cc_final: 0.7826 (tm-30) REVERT: 1 21 ASP cc_start: 0.7818 (p0) cc_final: 0.7330 (p0) REVERT: 4 110 GLU cc_start: 0.8240 (pp20) cc_final: 0.7752 (pp20) REVERT: 5 1 MET cc_start: 0.4146 (OUTLIER) cc_final: 0.3736 (ptm) REVERT: 5 13 LEU cc_start: 0.8705 (mm) cc_final: 0.8394 (mm) REVERT: 5 21 ASP cc_start: 0.7465 (m-30) cc_final: 0.6619 (t0) REVERT: 5 23 HIS cc_start: 0.7535 (t-170) cc_final: 0.6805 (t-170) REVERT: 5 27 GLU cc_start: 0.8742 (pt0) cc_final: 0.8368 (pt0) REVERT: 5 110 GLU cc_start: 0.8412 (pp20) cc_final: 0.8182 (pp20) REVERT: 7 154 SER cc_start: 0.6364 (t) cc_final: 0.6051 (m) REVERT: 7 167 MET cc_start: 0.8371 (tmm) cc_final: 0.7913 (tmm) outliers start: 278 outliers final: 225 residues processed: 1428 average time/residue: 0.8473 time to fit residues: 2177.2890 Evaluate side-chains 1397 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 1161 time to evaluate : 8.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain J residue 29 ASP Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 166 VAL Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain M residue 40 MET Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 37 HIS Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 50 SER Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 166 VAL Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain K residue 166 VAL Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain L residue 214 HIS Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain S residue 166 VAL Chi-restraints excluded: chain S residue 250 ASP Chi-restraints excluded: chain S residue 258 MET Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 109 LEU Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 38 GLU Chi-restraints excluded: chain U residue 39 THR Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 62 LEU Chi-restraints excluded: chain U residue 75 LYS Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 104 ASP Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain V residue 166 VAL Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain W residue 166 VAL Chi-restraints excluded: chain W residue 190 VAL Chi-restraints excluded: chain W residue 208 ASP Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 76 VAL Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 103 MET Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 112 LEU Chi-restraints excluded: chain Y residue 29 ASP Chi-restraints excluded: chain Y residue 88 LEU Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 204 VAL Chi-restraints excluded: chain Y residue 208 ASP Chi-restraints excluded: chain Y residue 257 THR Chi-restraints excluded: chain Z residue 40 MET Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 94 LEU Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 222 VAL Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 31 ASP Chi-restraints excluded: chain a residue 37 HIS Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 77 VAL Chi-restraints excluded: chain a residue 109 LEU Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 50 SER Chi-restraints excluded: chain c residue 57 THR Chi-restraints excluded: chain c residue 166 VAL Chi-restraints excluded: chain c residue 196 VAL Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain e residue 150 LEU Chi-restraints excluded: chain e residue 166 VAL Chi-restraints excluded: chain f residue 76 HIS Chi-restraints excluded: chain f residue 214 HIS Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain h residue 166 VAL Chi-restraints excluded: chain h residue 250 ASP Chi-restraints excluded: chain h residue 258 MET Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 105 LEU Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 12 LEU Chi-restraints excluded: chain j residue 39 THR Chi-restraints excluded: chain j residue 44 VAL Chi-restraints excluded: chain j residue 49 THR Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 62 LEU Chi-restraints excluded: chain j residue 75 LYS Chi-restraints excluded: chain j residue 78 VAL Chi-restraints excluded: chain j residue 104 ASP Chi-restraints excluded: chain j residue 105 LEU Chi-restraints excluded: chain j residue 112 LEU Chi-restraints excluded: chain k residue 166 VAL Chi-restraints excluded: chain k residue 173 ILE Chi-restraints excluded: chain l residue 150 LEU Chi-restraints excluded: chain l residue 166 VAL Chi-restraints excluded: chain l residue 190 VAL Chi-restraints excluded: chain l residue 201 ILE Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 44 VAL Chi-restraints excluded: chain m residue 55 ASP Chi-restraints excluded: chain m residue 76 VAL Chi-restraints excluded: chain m residue 81 ILE Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain n residue 29 ASP Chi-restraints excluded: chain n residue 88 LEU Chi-restraints excluded: chain n residue 150 LEU Chi-restraints excluded: chain n residue 166 VAL Chi-restraints excluded: chain n residue 204 VAL Chi-restraints excluded: chain n residue 208 ASP Chi-restraints excluded: chain n residue 257 THR Chi-restraints excluded: chain o residue 40 MET Chi-restraints excluded: chain o residue 57 THR Chi-restraints excluded: chain o residue 94 LEU Chi-restraints excluded: chain o residue 186 LEU Chi-restraints excluded: chain p residue 8 LEU Chi-restraints excluded: chain p residue 31 ASP Chi-restraints excluded: chain p residue 37 HIS Chi-restraints excluded: chain p residue 44 VAL Chi-restraints excluded: chain p residue 77 VAL Chi-restraints excluded: chain p residue 95 THR Chi-restraints excluded: chain p residue 109 LEU Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 50 SER Chi-restraints excluded: chain r residue 57 THR Chi-restraints excluded: chain r residue 114 ASP Chi-restraints excluded: chain r residue 166 VAL Chi-restraints excluded: chain r residue 196 VAL Chi-restraints excluded: chain r residue 254 THR Chi-restraints excluded: chain r residue 257 THR Chi-restraints excluded: chain s residue 250 ASP Chi-restraints excluded: chain t residue 91 PHE Chi-restraints excluded: chain t residue 150 LEU Chi-restraints excluded: chain t residue 166 VAL Chi-restraints excluded: chain u residue 93 LEU Chi-restraints excluded: chain u residue 214 HIS Chi-restraints excluded: chain v residue 166 VAL Chi-restraints excluded: chain v residue 190 VAL Chi-restraints excluded: chain w residue 166 VAL Chi-restraints excluded: chain w residue 250 ASP Chi-restraints excluded: chain w residue 258 MET Chi-restraints excluded: chain x residue 44 VAL Chi-restraints excluded: chain x residue 105 LEU Chi-restraints excluded: chain y residue 8 LEU Chi-restraints excluded: chain y residue 38 GLU Chi-restraints excluded: chain y residue 39 THR Chi-restraints excluded: chain y residue 49 THR Chi-restraints excluded: chain y residue 54 ILE Chi-restraints excluded: chain y residue 62 LEU Chi-restraints excluded: chain y residue 99 VAL Chi-restraints excluded: chain y residue 104 ASP Chi-restraints excluded: chain y residue 105 LEU Chi-restraints excluded: chain y residue 112 LEU Chi-restraints excluded: chain z residue 127 MET Chi-restraints excluded: chain z residue 166 VAL Chi-restraints excluded: chain z residue 173 ILE Chi-restraints excluded: chain 0 residue 166 VAL Chi-restraints excluded: chain 0 residue 190 VAL Chi-restraints excluded: chain 0 residue 201 ILE Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 1 residue 76 VAL Chi-restraints excluded: chain 1 residue 81 ILE Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 2 residue 29 ASP Chi-restraints excluded: chain 2 residue 88 LEU Chi-restraints excluded: chain 2 residue 166 VAL Chi-restraints excluded: chain 2 residue 204 VAL Chi-restraints excluded: chain 2 residue 208 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 3 residue 40 MET Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 3 residue 252 ILE Chi-restraints excluded: chain 4 residue 8 LEU Chi-restraints excluded: chain 4 residue 31 ASP Chi-restraints excluded: chain 4 residue 37 HIS Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 4 residue 61 ILE Chi-restraints excluded: chain 4 residue 77 VAL Chi-restraints excluded: chain 4 residue 109 LEU Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 39 THR Chi-restraints excluded: chain 5 residue 50 SER Chi-restraints excluded: chain 6 residue 57 THR Chi-restraints excluded: chain 6 residue 166 VAL Chi-restraints excluded: chain 6 residue 196 VAL Chi-restraints excluded: chain 6 residue 257 THR Chi-restraints excluded: chain 7 residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1300 random chunks: chunk 766 optimal weight: 4.9990 chunk 1234 optimal weight: 7.9990 chunk 753 optimal weight: 0.6980 chunk 585 optimal weight: 4.9990 chunk 858 optimal weight: 50.0000 chunk 1295 optimal weight: 6.9990 chunk 1192 optimal weight: 0.0670 chunk 1031 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 796 optimal weight: 2.9990 chunk 632 optimal weight: 5.9990 overall best weight: 1.9522 ------------------------------------------------------------------------------- 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** ** H 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 256 ASN ** R 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2967 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= 0.214 Angle : 0.630 12.876 145156 Z= 0.324 Chirality : 0.043 0.238 17472 Planarity : 0.004 0.048 18240 Dihedral : 5.029 48.717 14068 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.45 % Allowed : 17.76 % Favored : 79.78 % 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: 1.28 (0.06), residues: 8556 sheet: -1.48 (0.19), residues: 712 loop : -2.58 (0.09), residues: 3860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP 7 20 HIS 0.006 0.001 HIS V 214 PHE 0.037 0.001 PHE r 91 TYR 0.020 0.002 TYR u 117 ARG 0.007 0.000 ARG k 235 ********************** 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 1462 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 1172 time to evaluate : 7.874 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: B 93 LEU cc_start: -0.2841 (OUTLIER) cc_final: -0.3056 (mp) REVERT: B 201 ILE cc_start: 0.9106 (mm) cc_final: 0.8837 (mt) REVERT: B 214 HIS cc_start: 0.7447 (OUTLIER) cc_final: 0.7203 (m90) REVERT: D 99 MET cc_start: -0.0379 (mtt) cc_final: -0.0625 (mpp) REVERT: E 110 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7936 (pp20) REVERT: G 24 MET cc_start: 0.1321 (ptp) cc_final: 0.1104 (mpp) REVERT: H 127 MET cc_start: -0.1364 (tpp) cc_final: -0.1712 (tpp) REVERT: H 150 LEU cc_start: 0.8407 (mm) cc_final: 0.7952 (tp) REVERT: H 240 GLN cc_start: 0.8287 (tm-30) cc_final: 0.7794 (tm-30) REVERT: I 21 ASP cc_start: 0.7834 (p0) cc_final: 0.6999 (t0) REVERT: M 127 MET cc_start: 0.0997 (mmm) cc_final: 0.0785 (ptt) REVERT: O 8 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8710 (pp) REVERT: O 13 LEU cc_start: 0.8755 (mm) cc_final: 0.8440 (mm) REVERT: O 23 HIS cc_start: 0.7460 (t-170) cc_final: 0.6581 (t-170) REVERT: O 27 GLU cc_start: 0.8495 (pt0) cc_final: 0.7560 (pt0) REVERT: Q 24 MET cc_start: -0.1645 (ptm) cc_final: -0.1867 (tmm) REVERT: Q 154 SER cc_start: 0.6557 (t) cc_final: 0.6264 (m) REVERT: Q 167 MET cc_start: 0.8381 (tmm) cc_final: 0.7917 (tmm) REVERT: L 201 ILE cc_start: 0.9125 (mm) cc_final: 0.8841 (mt) REVERT: L 214 HIS cc_start: 0.7419 (OUTLIER) cc_final: 0.7169 (m90) REVERT: S 240 GLN cc_start: 0.8539 (tm-30) cc_final: 0.8335 (tm-30) REVERT: T 47 ASP cc_start: 0.8122 (t0) cc_final: 0.7659 (m-30) REVERT: X 105 LEU cc_start: 0.8227 (OUTLIER) cc_final: 0.7862 (tt) REVERT: Z 217 GLN cc_start: 0.8716 (mm-40) cc_final: 0.8332 (tp40) REVERT: a 110 GLU cc_start: 0.8278 (pp20) cc_final: 0.7791 (pp20) REVERT: b 13 LEU cc_start: 0.8702 (mm) cc_final: 0.8362 (mm) REVERT: b 23 HIS cc_start: 0.7547 (t-170) cc_final: 0.6646 (t-170) REVERT: b 27 GLU cc_start: 0.8382 (pt0) cc_final: 0.7525 (pt0) REVERT: d 154 SER cc_start: 0.6537 (t) cc_final: 0.6263 (m) REVERT: d 167 MET cc_start: 0.8395 (tmm) cc_final: 0.7957 (tmm) REVERT: f 201 ILE cc_start: 0.9106 (mm) cc_final: 0.8835 (mt) REVERT: f 214 HIS cc_start: 0.7449 (OUTLIER) cc_final: 0.7192 (m90) REVERT: h 240 GLN cc_start: 0.8531 (tm-30) cc_final: 0.8329 (tm-30) REVERT: j 12 LEU cc_start: 0.8601 (OUTLIER) cc_final: 0.8199 (tp) REVERT: l 240 GLN cc_start: 0.8325 (tm-30) cc_final: 0.7840 (tm-30) REVERT: p 110 GLU cc_start: 0.8277 (pp20) cc_final: 0.7796 (pp20) REVERT: q 13 LEU cc_start: 0.8725 (mm) cc_final: 0.8395 (mm) REVERT: q 21 ASP cc_start: 0.7519 (m-30) cc_final: 0.6771 (t70) REVERT: q 23 HIS cc_start: 0.7551 (t-170) cc_final: 0.6615 (t-170) REVERT: q 27 GLU cc_start: 0.8974 (pt0) cc_final: 0.8230 (pt0) REVERT: q 68 MET cc_start: 0.8502 (mmt) cc_final: 0.8071 (mmt) REVERT: s 167 MET cc_start: 0.8349 (tmm) cc_final: 0.7954 (tmm) REVERT: u 201 ILE cc_start: 0.9110 (mm) cc_final: 0.8835 (mt) REVERT: u 214 HIS cc_start: 0.7425 (OUTLIER) cc_final: 0.7181 (m90) REVERT: 0 240 GLN cc_start: 0.8342 (tm-30) cc_final: 0.7837 (tm-30) REVERT: 1 21 ASP cc_start: 0.7835 (p0) cc_final: 0.7337 (p0) REVERT: 5 1 MET cc_start: 0.4150 (OUTLIER) cc_final: 0.3735 (ptm) REVERT: 5 13 LEU cc_start: 0.8751 (mm) cc_final: 0.8424 (mm) REVERT: 5 21 ASP cc_start: 0.7451 (m-30) cc_final: 0.6756 (t70) REVERT: 5 23 HIS cc_start: 0.7710 (t-170) cc_final: 0.6949 (t-170) REVERT: 5 27 GLU cc_start: 0.8923 (pt0) cc_final: 0.8220 (pt0) REVERT: 5 110 GLU cc_start: 0.8503 (pp20) cc_final: 0.8279 (pp20) REVERT: 7 154 SER cc_start: 0.6524 (t) cc_final: 0.6245 (m) REVERT: 7 167 MET cc_start: 0.8380 (tmm) cc_final: 0.7934 (tmm) outliers start: 290 outliers final: 249 residues processed: 1396 average time/residue: 0.7692 time to fit residues: 1928.5124 Evaluate side-chains 1410 residues out of total 11808 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 258 poor density : 1152 time to evaluate : 7.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 LEU Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 196 VAL Chi-restraints excluded: chain B residue 76 HIS Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 214 HIS Chi-restraints excluded: chain C residue 166 VAL Chi-restraints excluded: chain D residue 166 VAL Chi-restraints excluded: chain D residue 250 ASP Chi-restraints excluded: chain D residue 253 ILE Chi-restraints excluded: chain D residue 258 MET Chi-restraints excluded: chain E residue 44 VAL Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 65 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain F residue 8 LEU Chi-restraints excluded: chain F residue 38 GLU Chi-restraints excluded: chain F residue 39 THR Chi-restraints excluded: chain F residue 49 THR Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 99 VAL Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 127 MET Chi-restraints excluded: chain G residue 166 VAL Chi-restraints excluded: chain G residue 173 ILE Chi-restraints excluded: chain G residue 196 VAL Chi-restraints excluded: chain H residue 166 VAL Chi-restraints excluded: chain H residue 190 VAL Chi-restraints excluded: chain H residue 208 ASP Chi-restraints excluded: chain I residue 24 THR Chi-restraints excluded: chain I residue 44 VAL Chi-restraints excluded: chain I residue 55 ASP Chi-restraints excluded: chain I residue 76 VAL Chi-restraints excluded: chain I residue 81 ILE Chi-restraints excluded: chain I residue 92 LEU Chi-restraints excluded: chain I residue 100 LEU Chi-restraints excluded: chain I residue 109 LEU Chi-restraints excluded: chain I residue 112 LEU Chi-restraints excluded: chain J residue 29 ASP Chi-restraints excluded: chain J residue 88 LEU Chi-restraints excluded: chain J residue 166 VAL Chi-restraints excluded: chain J residue 204 VAL Chi-restraints excluded: chain J residue 257 THR Chi-restraints excluded: chain M residue 40 MET Chi-restraints excluded: chain M residue 57 THR Chi-restraints excluded: chain M residue 94 LEU Chi-restraints excluded: chain M residue 166 VAL Chi-restraints excluded: chain M residue 186 LEU Chi-restraints excluded: chain M residue 252 ILE Chi-restraints excluded: chain M residue 256 ASN Chi-restraints excluded: chain N residue 8 LEU Chi-restraints excluded: chain N residue 31 ASP Chi-restraints excluded: chain N residue 37 HIS Chi-restraints excluded: chain N residue 44 VAL Chi-restraints excluded: chain N residue 77 VAL Chi-restraints excluded: chain N residue 99 VAL Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain O residue 8 LEU Chi-restraints excluded: chain O residue 39 THR Chi-restraints excluded: chain O residue 50 SER Chi-restraints excluded: chain O residue 65 VAL Chi-restraints excluded: chain P residue 57 THR Chi-restraints excluded: chain P residue 166 VAL Chi-restraints excluded: chain P residue 196 VAL Chi-restraints excluded: chain P residue 257 THR Chi-restraints excluded: chain Q residue 1 MET Chi-restraints excluded: chain K residue 150 LEU Chi-restraints excluded: chain K residue 166 VAL Chi-restraints excluded: chain K residue 169 LEU Chi-restraints excluded: chain L residue 76 HIS Chi-restraints excluded: chain L residue 204 VAL Chi-restraints excluded: chain L residue 214 HIS Chi-restraints excluded: chain R residue 166 VAL Chi-restraints excluded: chain S residue 166 VAL Chi-restraints excluded: chain S residue 250 ASP Chi-restraints excluded: chain S residue 253 ILE Chi-restraints excluded: chain S residue 258 MET Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 61 ILE Chi-restraints excluded: chain T residue 65 VAL Chi-restraints excluded: chain T residue 85 VAL Chi-restraints excluded: chain T residue 105 LEU Chi-restraints excluded: chain T residue 109 LEU Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 38 GLU Chi-restraints excluded: chain U residue 39 THR Chi-restraints excluded: chain U residue 49 THR Chi-restraints excluded: chain U residue 54 ILE Chi-restraints excluded: chain U residue 62 LEU Chi-restraints excluded: chain U residue 75 LYS Chi-restraints excluded: chain U residue 78 VAL Chi-restraints excluded: chain U residue 104 ASP Chi-restraints excluded: chain U residue 105 LEU Chi-restraints excluded: chain V residue 166 VAL Chi-restraints excluded: chain V residue 173 ILE Chi-restraints excluded: chain W residue 166 VAL Chi-restraints excluded: chain W residue 190 VAL Chi-restraints excluded: chain W residue 208 ASP Chi-restraints excluded: chain X residue 24 THR Chi-restraints excluded: chain X residue 62 LEU Chi-restraints excluded: chain X residue 76 VAL Chi-restraints excluded: chain X residue 81 ILE Chi-restraints excluded: chain X residue 105 LEU Chi-restraints excluded: chain X residue 109 LEU Chi-restraints excluded: chain X residue 112 LEU Chi-restraints excluded: chain Y residue 29 ASP Chi-restraints excluded: chain Y residue 88 LEU Chi-restraints excluded: chain Y residue 166 VAL Chi-restraints excluded: chain Y residue 204 VAL Chi-restraints excluded: chain Y residue 208 ASP Chi-restraints excluded: chain Y residue 257 THR Chi-restraints excluded: chain Z residue 40 MET Chi-restraints excluded: chain Z residue 57 THR Chi-restraints excluded: chain Z residue 94 LEU Chi-restraints excluded: chain Z residue 186 LEU Chi-restraints excluded: chain Z residue 222 VAL Chi-restraints excluded: chain a residue 8 LEU Chi-restraints excluded: chain a residue 31 ASP Chi-restraints excluded: chain a residue 37 HIS Chi-restraints excluded: chain a residue 44 VAL Chi-restraints excluded: chain a residue 77 VAL Chi-restraints excluded: chain a residue 95 THR Chi-restraints excluded: chain a residue 109 LEU Chi-restraints excluded: chain b residue 39 THR Chi-restraints excluded: chain b residue 50 SER Chi-restraints excluded: chain c residue 57 THR Chi-restraints excluded: chain c residue 166 VAL Chi-restraints excluded: chain c residue 196 VAL Chi-restraints excluded: chain c residue 254 THR Chi-restraints excluded: chain c residue 257 THR Chi-restraints excluded: chain d residue 1 MET Chi-restraints excluded: chain e residue 150 LEU Chi-restraints excluded: chain e residue 166 VAL Chi-restraints excluded: chain f residue 76 HIS Chi-restraints excluded: chain f residue 166 VAL Chi-restraints excluded: chain f residue 204 VAL Chi-restraints excluded: chain f residue 214 HIS Chi-restraints excluded: chain g residue 166 VAL Chi-restraints excluded: chain g residue 190 VAL Chi-restraints excluded: chain h residue 166 VAL Chi-restraints excluded: chain h residue 250 ASP Chi-restraints excluded: chain h residue 253 ILE Chi-restraints excluded: chain h residue 258 MET Chi-restraints excluded: chain i residue 44 VAL Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 105 LEU Chi-restraints excluded: chain j residue 8 LEU Chi-restraints excluded: chain j residue 12 LEU Chi-restraints excluded: chain j residue 39 THR Chi-restraints excluded: chain j residue 49 THR Chi-restraints excluded: chain j residue 54 ILE Chi-restraints excluded: chain j residue 62 LEU Chi-restraints excluded: chain j residue 75 LYS Chi-restraints excluded: chain j residue 78 VAL Chi-restraints excluded: chain j residue 104 ASP Chi-restraints excluded: chain j residue 105 LEU Chi-restraints excluded: chain j residue 112 LEU Chi-restraints excluded: chain k residue 166 VAL Chi-restraints excluded: chain k residue 173 ILE Chi-restraints excluded: chain l residue 150 LEU Chi-restraints excluded: chain l residue 166 VAL Chi-restraints excluded: chain l residue 190 VAL Chi-restraints excluded: chain l residue 201 ILE Chi-restraints excluded: chain l residue 208 ASP Chi-restraints excluded: chain m residue 24 THR Chi-restraints excluded: chain m residue 44 VAL Chi-restraints excluded: chain m residue 55 ASP Chi-restraints excluded: chain m residue 76 VAL Chi-restraints excluded: chain m residue 81 ILE Chi-restraints excluded: chain m residue 112 LEU Chi-restraints excluded: chain n residue 29 ASP Chi-restraints excluded: chain n residue 88 LEU Chi-restraints excluded: chain n residue 166 VAL Chi-restraints excluded: chain n residue 204 VAL Chi-restraints excluded: chain n residue 208 ASP Chi-restraints excluded: chain n residue 257 THR Chi-restraints excluded: chain o residue 40 MET Chi-restraints excluded: chain o residue 94 LEU Chi-restraints excluded: chain o residue 166 VAL Chi-restraints excluded: chain o residue 186 LEU Chi-restraints excluded: chain p residue 8 LEU Chi-restraints excluded: chain p residue 31 ASP Chi-restraints excluded: chain p residue 37 HIS Chi-restraints excluded: chain p residue 44 VAL Chi-restraints excluded: chain p residue 77 VAL Chi-restraints excluded: chain p residue 95 THR Chi-restraints excluded: chain p residue 109 LEU Chi-restraints excluded: chain q residue 39 THR Chi-restraints excluded: chain q residue 50 SER Chi-restraints excluded: chain r residue 57 THR Chi-restraints excluded: chain r residue 166 VAL Chi-restraints excluded: chain r residue 196 VAL Chi-restraints excluded: chain r residue 254 THR Chi-restraints excluded: chain r residue 257 THR Chi-restraints excluded: chain s residue 1 MET Chi-restraints excluded: chain s residue 234 ILE Chi-restraints excluded: chain s residue 250 ASP Chi-restraints excluded: chain t residue 150 LEU Chi-restraints excluded: chain t residue 166 VAL Chi-restraints excluded: chain u residue 214 HIS Chi-restraints excluded: chain v residue 166 VAL Chi-restraints excluded: chain v residue 190 VAL Chi-restraints excluded: chain w residue 166 VAL Chi-restraints excluded: chain w residue 250 ASP Chi-restraints excluded: chain w residue 253 ILE Chi-restraints excluded: chain w residue 258 MET Chi-restraints excluded: chain x residue 44 VAL Chi-restraints excluded: chain x residue 105 LEU Chi-restraints excluded: chain y residue 8 LEU Chi-restraints excluded: chain y residue 38 GLU Chi-restraints excluded: chain y residue 39 THR Chi-restraints excluded: chain y residue 49 THR Chi-restraints excluded: chain y residue 54 ILE Chi-restraints excluded: chain y residue 62 LEU Chi-restraints excluded: chain y residue 78 VAL Chi-restraints excluded: chain y residue 104 ASP Chi-restraints excluded: chain y residue 105 LEU Chi-restraints excluded: chain y residue 112 LEU Chi-restraints excluded: chain z residue 127 MET Chi-restraints excluded: chain z residue 166 VAL Chi-restraints excluded: chain z residue 173 ILE Chi-restraints excluded: chain 0 residue 166 VAL Chi-restraints excluded: chain 0 residue 190 VAL Chi-restraints excluded: chain 1 residue 24 THR Chi-restraints excluded: chain 1 residue 44 VAL Chi-restraints excluded: chain 1 residue 62 LEU Chi-restraints excluded: chain 1 residue 76 VAL Chi-restraints excluded: chain 1 residue 81 ILE Chi-restraints excluded: chain 1 residue 112 LEU Chi-restraints excluded: chain 2 residue 29 ASP Chi-restraints excluded: chain 2 residue 88 LEU Chi-restraints excluded: chain 2 residue 166 VAL Chi-restraints excluded: chain 2 residue 204 VAL Chi-restraints excluded: chain 2 residue 208 ASP Chi-restraints excluded: chain 2 residue 257 THR Chi-restraints excluded: chain 3 residue 40 MET Chi-restraints excluded: chain 3 residue 57 THR Chi-restraints excluded: chain 3 residue 94 LEU Chi-restraints excluded: chain 3 residue 166 VAL Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 3 residue 252 ILE Chi-restraints excluded: chain 4 residue 8 LEU Chi-restraints excluded: chain 4 residue 31 ASP Chi-restraints excluded: chain 4 residue 37 HIS Chi-restraints excluded: chain 4 residue 44 VAL Chi-restraints excluded: chain 4 residue 61 ILE Chi-restraints excluded: chain 4 residue 77 VAL Chi-restraints excluded: chain 4 residue 99 VAL Chi-restraints excluded: chain 4 residue 109 LEU Chi-restraints excluded: chain 5 residue 1 MET Chi-restraints excluded: chain 5 residue 39 THR Chi-restraints excluded: chain 5 residue 50 SER Chi-restraints excluded: chain 6 residue 57 THR Chi-restraints excluded: chain 6 residue 166 VAL Chi-restraints excluded: chain 6 residue 196 VAL Chi-restraints excluded: chain 6 residue 257 THR Chi-restraints excluded: chain 7 residue 1 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1300 random chunks: chunk 819 optimal weight: 30.0000 chunk 1098 optimal weight: 0.9990 chunk 315 optimal weight: 0.0370 chunk 950 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 chunk 286 optimal weight: 4.9990 chunk 1032 optimal weight: 10.0000 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: 3.4066 ------------------------------------------------------------------------------- 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** ** H 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 256 ASN ** g 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 244 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.147644 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.122913 restraints weight = 258470.064| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.128851 restraints weight = 131946.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.132523 restraints weight = 66268.341| |-----------------------------------------------------------------------------| r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3698 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3698 r_free = 0.3698 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48120 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3698 r_free = 0.3698 target_work(ls_wunit_k1) = 0.128 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 48120 | |-----------------------------------------------------------------------------| r_final: 0.3698 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.2978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.322 107120 Z= 0.307 Angle : 0.684 59.200 145156 Z= 0.360 Chirality : 0.045 0.832 17472 Planarity : 0.004 0.063 18240 Dihedral : 5.031 48.605 14068 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 2.46 % Allowed : 17.87 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.07), residues: 13128 helix: 1.27 (0.06), residues: 8556 sheet: -1.49 (0.18), residues: 712 loop : -2.58 (0.09), residues: 3860 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP 6 20 HIS 0.006 0.001 HIS x 23 PHE 0.074 0.002 PHE P 91 TYR 0.019 0.002 TYR u 117 ARG 0.009 0.000 ARG R 193 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 28915.09 seconds wall clock time: 497 minutes 49.78 seconds (29869.78 seconds total)