Starting phenix.real_space_refine on Mon Mar 18 14:10:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z0u_11023/03_2024/6z0u_11023.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z0u_11023/03_2024/6z0u_11023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z0u_11023/03_2024/6z0u_11023.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z0u_11023/03_2024/6z0u_11023.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z0u_11023/03_2024/6z0u_11023.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6z0u_11023/03_2024/6z0u_11023.pdb" } resolution = 2.9 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= 0.001 sd= 0.006 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 Zn 24 6.06 5 S 720 5.16 5 C 54312 2.51 5 N 14904 2.21 5 O 17328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 56": "OD1" <-> "OD2" Residue "A ARG 71": "NH1" <-> "NH2" Residue "A GLU 129": "OE1" <-> "OE2" Residue "A GLU 234": "OE1" <-> "OE2" Residue "A GLU 250": "OE1" <-> "OE2" Residue "A ARG 252": "NH1" <-> "NH2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A ARG 289": "NH1" <-> "NH2" Residue "A GLU 349": "OE1" <-> "OE2" Residue "A PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 446": "OE1" <-> "OE2" Residue "C ARG 71": "NH1" <-> "NH2" Residue "C GLU 129": "OE1" <-> "OE2" Residue "C GLU 234": "OE1" <-> "OE2" Residue "C ARG 252": "NH1" <-> "NH2" Residue "C ARG 275": "NH1" <-> "NH2" Residue "C ASP 277": "OD1" <-> "OD2" Residue "C TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C ARG 289": "NH1" <-> "NH2" Residue "C GLU 403": "OE1" <-> "OE2" Residue "E ASP 56": "OD1" <-> "OD2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "E ASP 127": "OD1" <-> "OD2" Residue "E GLU 129": "OE1" <-> "OE2" Residue "E PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 234": "OE1" <-> "OE2" Residue "E GLU 250": "OE1" <-> "OE2" Residue "E ARG 252": "NH1" <-> "NH2" Residue "E ARG 275": "NH1" <-> "NH2" Residue "E TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 289": "NH1" <-> "NH2" Residue "E ARG 289": "NH1" <-> "NH2" Residue "E ASP 310": "OD1" <-> "OD2" Residue "E GLU 349": "OE1" <-> "OE2" Residue "E ASP 404": "OD1" <-> "OD2" Residue "E PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 56": "OD1" <-> "OD2" Residue "G ARG 71": "NH1" <-> "NH2" Residue "G GLU 129": "OE1" <-> "OE2" Residue "G GLU 234": "OE1" <-> "OE2" Residue "G GLU 250": "OE1" <-> "OE2" Residue "G ARG 252": "NH1" <-> "NH2" Residue "G ARG 275": "NH1" <-> "NH2" Residue "G TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 289": "NH1" <-> "NH2" Residue "G ARG 289": "NH1" <-> "NH2" Residue "G GLU 349": "OE1" <-> "OE2" Residue "G PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 446": "OE1" <-> "OE2" Residue "I ARG 71": "NH1" <-> "NH2" Residue "I GLU 129": "OE1" <-> "OE2" Residue "I GLU 234": "OE1" <-> "OE2" Residue "I ARG 252": "NH1" <-> "NH2" Residue "I ARG 275": "NH1" <-> "NH2" Residue "I ASP 277": "OD1" <-> "OD2" Residue "I TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 289": "NH1" <-> "NH2" Residue "I ARG 289": "NH1" <-> "NH2" Residue "I GLU 403": "OE1" <-> "OE2" Residue "K ASP 56": "OD1" <-> "OD2" Residue "K ARG 71": "NH1" <-> "NH2" Residue "K ASP 127": "OD1" <-> "OD2" Residue "K GLU 129": "OE1" <-> "OE2" Residue "K PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 234": "OE1" <-> "OE2" Residue "K GLU 250": "OE1" <-> "OE2" Residue "K ARG 252": "NH1" <-> "NH2" Residue "K ARG 275": "NH1" <-> "NH2" Residue "K TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 289": "NH1" <-> "NH2" Residue "K ARG 289": "NH1" <-> "NH2" Residue "K ASP 310": "OD1" <-> "OD2" Residue "K GLU 349": "OE1" <-> "OE2" Residue "K PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 56": "OD1" <-> "OD2" Residue "M ARG 71": "NH1" <-> "NH2" Residue "M GLU 129": "OE1" <-> "OE2" Residue "M GLU 234": "OE1" <-> "OE2" Residue "M GLU 250": "OE1" <-> "OE2" Residue "M ARG 252": "NH1" <-> "NH2" Residue "M ARG 275": "NH1" <-> "NH2" Residue "M TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 289": "NH1" <-> "NH2" Residue "M ARG 289": "NH1" <-> "NH2" Residue "M GLU 349": "OE1" <-> "OE2" Residue "M PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 446": "OE1" <-> "OE2" Residue "O ARG 71": "NH1" <-> "NH2" Residue "O GLU 129": "OE1" <-> "OE2" Residue "O GLU 234": "OE1" <-> "OE2" Residue "O ARG 252": "NH1" <-> "NH2" Residue "O ARG 275": "NH1" <-> "NH2" Residue "O ASP 277": "OD1" <-> "OD2" Residue "O TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 289": "NH1" <-> "NH2" Residue "O ARG 289": "NH1" <-> "NH2" Residue "O GLU 403": "OE1" <-> "OE2" Residue "Q ASP 56": "OD1" <-> "OD2" Residue "Q ARG 71": "NH1" <-> "NH2" Residue "Q ASP 127": "OD1" <-> "OD2" Residue "Q GLU 129": "OE1" <-> "OE2" Residue "Q PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 234": "OE1" <-> "OE2" Residue "Q GLU 250": "OE1" <-> "OE2" Residue "Q ARG 252": "NH1" <-> "NH2" Residue "Q ARG 275": "NH1" <-> "NH2" Residue "Q TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 289": "NH1" <-> "NH2" Residue "Q ARG 289": "NH1" <-> "NH2" Residue "Q ASP 310": "OD1" <-> "OD2" Residue "Q GLU 349": "OE1" <-> "OE2" Residue "Q PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ASP 56": "OD1" <-> "OD2" Residue "S ARG 71": "NH1" <-> "NH2" Residue "S GLU 129": "OE1" <-> "OE2" Residue "S GLU 234": "OE1" <-> "OE2" Residue "S GLU 250": "OE1" <-> "OE2" Residue "S ARG 252": "NH1" <-> "NH2" Residue "S ARG 275": "NH1" <-> "NH2" Residue "S TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 289": "NH1" <-> "NH2" Residue "S ARG 289": "NH1" <-> "NH2" Residue "S GLU 349": "OE1" <-> "OE2" Residue "S PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 446": "OE1" <-> "OE2" Residue "V ARG 71": "NH1" <-> "NH2" Residue "V GLU 129": "OE1" <-> "OE2" Residue "V GLU 234": "OE1" <-> "OE2" Residue "V ARG 252": "NH1" <-> "NH2" Residue "V ARG 275": "NH1" <-> "NH2" Residue "V ASP 277": "OD1" <-> "OD2" Residue "V TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V ARG 289": "NH1" <-> "NH2" Residue "V ARG 289": "NH1" <-> "NH2" Residue "V GLU 403": "OE1" <-> "OE2" Residue "X ASP 56": "OD1" <-> "OD2" Residue "X ARG 71": "NH1" <-> "NH2" Residue "X ASP 127": "OD1" <-> "OD2" Residue "X GLU 129": "OE1" <-> "OE2" Residue "X PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 234": "OE1" <-> "OE2" Residue "X GLU 250": "OE1" <-> "OE2" Residue "X ARG 252": "NH1" <-> "NH2" Residue "X ARG 275": "NH1" <-> "NH2" Residue "X TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 289": "NH1" <-> "NH2" Residue "X ARG 289": "NH1" <-> "NH2" Residue "X ASP 310": "OD1" <-> "OD2" Residue "X GLU 349": "OE1" <-> "OE2" Residue "X ASP 404": "OD1" <-> "OD2" Residue "X PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ASP 56": "OD1" <-> "OD2" Residue "Z ARG 71": "NH1" <-> "NH2" Residue "Z GLU 129": "OE1" <-> "OE2" Residue "Z GLU 234": "OE1" <-> "OE2" Residue "Z GLU 250": "OE1" <-> "OE2" Residue "Z ARG 252": "NH1" <-> "NH2" Residue "Z ARG 275": "NH1" <-> "NH2" Residue "Z TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z ARG 289": "NH1" <-> "NH2" Residue "Z ARG 289": "NH1" <-> "NH2" Residue "Z GLU 349": "OE1" <-> "OE2" Residue "Z PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 446": "OE1" <-> "OE2" Residue "BA ARG 71": "NH1" <-> "NH2" Residue "BA GLU 129": "OE1" <-> "OE2" Residue "BA GLU 234": "OE1" <-> "OE2" Residue "BA ARG 252": "NH1" <-> "NH2" Residue "BA ARG 275": "NH1" <-> "NH2" Residue "BA ASP 277": "OD1" <-> "OD2" Residue "BA TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "BA ARG 289": "NH1" <-> "NH2" Residue "BA ARG 289": "NH1" <-> "NH2" Residue "BA GLU 403": "OE1" <-> "OE2" Residue "DA ASP 56": "OD1" <-> "OD2" Residue "DA ARG 71": "NH1" <-> "NH2" Residue "DA ASP 127": "OD1" <-> "OD2" Residue "DA GLU 129": "OE1" <-> "OE2" Residue "DA PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA GLU 234": "OE1" <-> "OE2" Residue "DA GLU 250": "OE1" <-> "OE2" Residue "DA ARG 252": "NH1" <-> "NH2" Residue "DA ARG 275": "NH1" <-> "NH2" Residue "DA TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "DA ARG 289": "NH1" <-> "NH2" Residue "DA ARG 289": "NH1" <-> "NH2" Residue "DA ASP 310": "OD1" <-> "OD2" Residue "DA GLU 349": "OE1" <-> "OE2" Residue "DA ASP 404": "OD1" <-> "OD2" Residue "DA PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FA ASP 56": "OD1" <-> "OD2" Residue "FA ARG 71": "NH1" <-> "NH2" Residue "FA GLU 129": "OE1" <-> "OE2" Residue "FA GLU 234": "OE1" <-> "OE2" Residue "FA GLU 250": "OE1" <-> "OE2" Residue "FA ARG 252": "NH1" <-> "NH2" Residue "FA ARG 275": "NH1" <-> "NH2" Residue "FA TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FA ARG 289": "NH1" <-> "NH2" Residue "FA ARG 289": "NH1" <-> "NH2" Residue "FA GLU 349": "OE1" <-> "OE2" Residue "FA PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "FA GLU 446": "OE1" <-> "OE2" Residue "HA ARG 71": "NH1" <-> "NH2" Residue "HA GLU 129": "OE1" <-> "OE2" Residue "HA GLU 234": "OE1" <-> "OE2" Residue "HA ARG 252": "NH1" <-> "NH2" Residue "HA ARG 275": "NH1" <-> "NH2" Residue "HA ASP 277": "OD1" <-> "OD2" Residue "HA TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "HA ARG 289": "NH1" <-> "NH2" Residue "HA ARG 289": "NH1" <-> "NH2" Residue "HA GLU 403": "OE1" <-> "OE2" Residue "JA ASP 56": "OD1" <-> "OD2" Residue "JA ARG 71": "NH1" <-> "NH2" Residue "JA ASP 127": "OD1" <-> "OD2" Residue "JA GLU 129": "OE1" <-> "OE2" Residue "JA PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JA GLU 234": "OE1" <-> "OE2" Residue "JA GLU 250": "OE1" <-> "OE2" Residue "JA ARG 252": "NH1" <-> "NH2" Residue "JA ARG 275": "NH1" <-> "NH2" Residue "JA TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "JA ARG 289": "NH1" <-> "NH2" Residue "JA ARG 289": "NH1" <-> "NH2" Residue "JA ASP 310": "OD1" <-> "OD2" Residue "JA GLU 349": "OE1" <-> "OE2" Residue "JA PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA ASP 56": "OD1" <-> "OD2" Residue "LA ARG 71": "NH1" <-> "NH2" Residue "LA GLU 129": "OE1" <-> "OE2" Residue "LA GLU 234": "OE1" <-> "OE2" Residue "LA GLU 250": "OE1" <-> "OE2" Residue "LA ARG 252": "NH1" <-> "NH2" Residue "LA ARG 275": "NH1" <-> "NH2" Residue "LA TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA ARG 289": "NH1" <-> "NH2" Residue "LA ARG 289": "NH1" <-> "NH2" Residue "LA GLU 349": "OE1" <-> "OE2" Residue "LA PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "LA GLU 446": "OE1" <-> "OE2" Residue "NA ARG 71": "NH1" <-> "NH2" Residue "NA GLU 129": "OE1" <-> "OE2" Residue "NA GLU 234": "OE1" <-> "OE2" Residue "NA ARG 252": "NH1" <-> "NH2" Residue "NA ARG 275": "NH1" <-> "NH2" Residue "NA ASP 277": "OD1" <-> "OD2" Residue "NA TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "NA ARG 289": "NH1" <-> "NH2" Residue "NA ARG 289": "NH1" <-> "NH2" Residue "NA GLU 403": "OE1" <-> "OE2" Residue "PA ASP 56": "OD1" <-> "OD2" Residue "PA ARG 71": "NH1" <-> "NH2" Residue "PA ASP 127": "OD1" <-> "OD2" Residue "PA GLU 129": "OE1" <-> "OE2" Residue "PA PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "PA TYR 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "PA TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "PA GLU 234": "OE1" <-> "OE2" Residue "PA GLU 250": "OE1" <-> "OE2" Residue "PA ARG 252": "NH1" <-> "NH2" Residue "PA ARG 275": "NH1" <-> "NH2" Residue "PA TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "PA ARG 289": "NH1" <-> "NH2" Residue "PA ARG 289": "NH1" <-> "NH2" Residue "PA ASP 310": "OD1" <-> "OD2" Residue "PA GLU 349": "OE1" <-> "OE2" Residue "PA PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "RA ASP 56": "OD1" <-> "OD2" Residue "RA ARG 71": "NH1" <-> "NH2" Residue "RA GLU 129": "OE1" <-> "OE2" Residue "RA GLU 234": "OE1" <-> "OE2" Residue "RA GLU 250": "OE1" <-> "OE2" Residue "RA ARG 252": "NH1" <-> "NH2" Residue "RA ARG 275": "NH1" <-> "NH2" Residue "RA TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "RA ARG 289": "NH1" <-> "NH2" Residue "RA ARG 289": "NH1" <-> "NH2" Residue "RA GLU 349": "OE1" <-> "OE2" Residue "RA PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "RA GLU 446": "OE1" <-> "OE2" Residue "TA ARG 71": "NH1" <-> "NH2" Residue "TA GLU 129": "OE1" <-> "OE2" Residue "TA GLU 234": "OE1" <-> "OE2" Residue "TA ARG 252": "NH1" <-> "NH2" Residue "TA ARG 275": "NH1" <-> "NH2" Residue "TA ASP 277": "OD1" <-> "OD2" Residue "TA TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "TA ARG 289": "NH1" <-> "NH2" Residue "TA ARG 289": "NH1" <-> "NH2" Residue "TA GLU 403": "OE1" <-> "OE2" Residue "VA ASP 56": "OD1" <-> "OD2" Residue "VA ARG 71": "NH1" <-> "NH2" Residue "VA ASP 127": "OD1" <-> "OD2" Residue "VA GLU 129": "OE1" <-> "OE2" Residue "VA PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "VA TYR 192": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "VA GLU 234": "OE1" <-> "OE2" Residue "VA GLU 250": "OE1" <-> "OE2" Residue "VA ARG 252": "NH1" <-> "NH2" Residue "VA ARG 275": "NH1" <-> "NH2" Residue "VA TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "VA ARG 289": "NH1" <-> "NH2" Residue "VA ARG 289": "NH1" <-> "NH2" Residue "VA ASP 310": "OD1" <-> "OD2" Residue "VA GLU 349": "OE1" <-> "OE2" Residue "VA PHE 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 87288 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 3578 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3533 Chain: "C" Number of atoms: 3578 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3533 Chain: "E" Number of atoms: 3578 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3533 Chain: "G" Number of atoms: 3578 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3533 Chain: "I" Number of atoms: 3578 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3533 Chain: "K" Number of atoms: 3578 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3533 Chain: "M" Number of atoms: 3578 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3533 Chain: "O" Number of atoms: 3578 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3533 Chain: "Q" Number of atoms: 3578 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3533 Chain: "S" Number of atoms: 3578 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3533 Chain: "V" Number of atoms: 3578 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3533 Chain: "X" Number of atoms: 3578 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3533 Chain: "Z" Number of atoms: 3578 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3533 Chain: "BA" Number of atoms: 3578 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3533 Chain: "DA" Number of atoms: 3578 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3533 Chain: "FA" Number of atoms: 3578 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3533 Chain: "HA" Number of atoms: 3578 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3533 Chain: "JA" Number of atoms: 3578 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3533 Chain: "LA" Number of atoms: 3578 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3533 Chain: "NA" Number of atoms: 3578 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3533 Chain: "PA" Number of atoms: 3578 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3533 Chain: "RA" Number of atoms: 3578 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3533 Chain: "TA" Number of atoms: 3578 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3533 Chain: "VA" Number of atoms: 3578 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 Conformer: "B" Number of residues, atoms: 454, 3522 Classifications: {'peptide': 454} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 21, 'TRANS': 432} Chain breaks: 2 Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 52 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 22 bond proxies already assigned to first conformer: 3533 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "BA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "DA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "FA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "HA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "JA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "LA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "NA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "PA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "RA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "TA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "VA" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "E" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "G" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "I" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "K" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "M" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "O" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "Q" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "S" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "V" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "X" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "Z" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "BA" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "DA" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "FA" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "HA" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "JA" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "LA" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "NA" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "PA" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "RA" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "TA" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "VA" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1025 SG CYS A 134 16.062 99.592 29.589 1.00122.35 S ATOM 1077 SG CYS A 141 15.587 96.197 30.425 1.00108.59 S ATOM 4603 SG CYS C 134 27.010 57.929 29.575 1.00147.27 S ATOM 4655 SG CYS C 141 28.197 54.728 30.399 1.00123.49 S ATOM 8181 SG CYS E 134 57.412 27.436 29.549 1.00120.62 S ATOM 8233 SG CYS E 141 59.923 25.147 30.461 1.00118.91 S ATOM 11759 SG CYS G 134 98.887 16.062 29.590 1.00121.34 S ATOM 11811 SG CYS G 141 102.283 15.587 30.424 1.00107.45 S ATOM 15337 SG CYS I 134 140.552 27.011 29.571 1.00146.90 S ATOM 15389 SG CYS I 141 143.753 28.198 30.399 1.00121.05 S ATOM 18915 SG CYS K 134 171.043 57.412 29.550 1.00120.49 S ATOM 18967 SG CYS K 141 173.333 59.922 30.462 1.00119.72 S ATOM 22493 SG CYS M 134 182.418 98.888 29.589 1.00122.34 S ATOM 22545 SG CYS M 141 182.893 102.283 30.425 1.00106.74 S ATOM 26071 SG CYS O 134 171.468 140.552 29.576 1.00147.32 S ATOM 26123 SG CYS O 141 170.283 143.753 30.400 1.00122.09 S ATOM 29649 SG CYS Q 134 141.069 171.044 29.550 1.00120.65 S ATOM 29701 SG CYS Q 141 138.559 173.333 30.462 1.00116.38 S ATOM 33227 SG CYS S 134 99.592 182.418 29.589 1.00120.58 S ATOM 33279 SG CYS S 141 96.197 182.893 30.425 1.00109.00 S ATOM 36805 SG CYS V 134 57.931 171.469 29.570 1.00147.20 S ATOM 36857 SG CYS V 141 54.729 170.285 30.400 1.00123.16 S ATOM 40383 SG CYS X 134 27.436 141.069 29.549 1.00120.95 S ATOM 40435 SG CYS X 141 25.147 138.558 30.462 1.00118.07 S ATOM 43961 SG CYS Z 134 182.418 99.592 144.081 1.00122.90 S ATOM 44013 SG CYS Z 141 182.892 96.197 143.245 1.00110.31 S ATOM 47539 SG CYSBA 134 171.469 57.931 144.101 1.00146.90 S ATOM 47591 SG CYSBA 141 170.285 54.729 143.270 1.00123.17 S ATOM 51117 SG CYSDA 134 141.068 27.437 144.120 1.00121.37 S ATOM 51169 SG CYSDA 141 138.558 25.146 143.209 1.00117.42 S ATOM 54695 SG CYSFA 134 99.593 16.062 144.080 1.00122.63 S ATOM 54747 SG CYSFA 141 96.197 15.587 143.245 1.00111.87 S ATOM 58273 SG CYSHA 134 57.929 27.010 144.095 1.00147.74 S ATOM 58325 SG CYSHA 141 54.728 28.196 143.271 1.00120.90 S ATOM 61851 SG CYSJA 134 27.436 57.413 144.121 1.00121.99 S ATOM 61903 SG CYSJA 141 25.146 59.923 143.209 1.00119.41 S ATOM 65429 SG CYSLA 134 16.062 98.888 144.081 1.00120.89 S ATOM 65481 SG CYSLA 141 15.587 102.283 143.245 1.00108.66 S ATOM 69007 SG CYSNA 134 27.011 140.552 144.099 1.00148.23 S ATOM 69059 SG CYSNA 141 28.198 143.752 143.271 1.00121.70 S ATOM 72585 SG CYSPA 134 57.412 171.043 144.120 1.00120.31 S ATOM 72637 SG CYSPA 141 59.921 173.334 143.207 1.00118.74 S ATOM 76163 SG CYSRA 134 98.888 182.417 144.081 1.00121.27 S ATOM 76215 SG CYSRA 141 102.283 182.893 143.246 1.00107.59 S ATOM 79741 SG CYSTA 134 140.550 171.469 144.101 1.00146.76 S ATOM 79793 SG CYSTA 141 143.751 170.284 143.271 1.00123.05 S ATOM 83319 SG CYSVA 134 171.044 141.069 144.121 1.00121.70 S ATOM 83371 SG CYSVA 141 173.333 138.558 143.208 1.00117.63 S Residues with excluded nonbonded symmetry interactions: 48 residue: pdb=" N AARG A 41 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 41 " occ=0.50 residue: pdb=" N AASN A 186 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 186 " occ=0.50 residue: pdb=" N AARG C 41 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG C 41 " occ=0.50 residue: pdb=" N AASN C 186 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN C 186 " occ=0.50 residue: pdb=" N AARG E 41 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG E 41 " occ=0.50 residue: pdb=" N AASN E 186 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN E 186 " occ=0.50 residue: pdb=" N AARG G 41 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG G 41 " occ=0.50 residue: pdb=" N AASN G 186 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN G 186 " occ=0.50 residue: pdb=" N AARG I 41 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG I 41 " occ=0.50 residue: pdb=" N AASN I 186 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN I 186 " occ=0.50 residue: pdb=" N AARG K 41 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG K 41 " occ=0.50 residue: pdb=" N AASN K 186 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN K 186 " occ=0.50 ... (remaining 36 not shown) Time building chain proxies: 64.96, per 1000 atoms: 0.74 Number of scatterers: 87288 At special positions: 0 Unit cell: (199.307, 199.307, 174.497, 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) Zn 24 29.99 S 720 16.00 O 17328 8.00 N 14904 7.00 C 54312 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: 27.54 Conformation dependent library (CDL) restraints added in 22.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 134 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 141 " pdb="ZN ZN A1001 " - pdb=" NE2 HIS A 79 " pdb=" ZN C1001 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 134 " pdb="ZN ZN C1001 " - pdb=" SG CYS C 141 " pdb="ZN ZN C1001 " - pdb=" NE2 HIS C 79 " pdb=" ZN E1001 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 134 " pdb="ZN ZN E1001 " - pdb=" SG CYS E 141 " pdb="ZN ZN E1001 " - pdb=" NE2 HIS E 79 " pdb=" ZN G1001 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 134 " pdb="ZN ZN G1001 " - pdb=" SG CYS G 141 " pdb="ZN ZN G1001 " - pdb=" NE2 HIS G 79 " pdb=" ZN I1001 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 134 " pdb="ZN ZN I1001 " - pdb=" SG CYS I 141 " pdb="ZN ZN I1001 " - pdb=" NE2 HIS I 79 " pdb=" ZN K1001 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 134 " pdb="ZN ZN K1001 " - pdb=" SG CYS K 141 " pdb="ZN ZN K1001 " - pdb=" NE2 HIS K 79 " pdb=" ZN M1001 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 134 " pdb="ZN ZN M1001 " - pdb=" SG CYS M 141 " pdb="ZN ZN M1001 " - pdb=" NE2 HIS M 79 " pdb=" ZN O1001 " pdb="ZN ZN O1001 " - pdb=" SG CYS O 134 " pdb="ZN ZN O1001 " - pdb=" SG CYS O 141 " pdb="ZN ZN O1001 " - pdb=" NE2 HIS O 79 " pdb=" ZN Q1001 " pdb="ZN ZN Q1001 " - pdb=" SG CYS Q 134 " pdb="ZN ZN Q1001 " - pdb=" SG CYS Q 141 " pdb="ZN ZN Q1001 " - pdb=" NE2 HIS Q 79 " pdb=" ZN S1001 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 134 " pdb="ZN ZN S1001 " - pdb=" SG CYS S 141 " pdb="ZN ZN S1001 " - pdb=" NE2 HIS S 79 " pdb=" ZN V1001 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 134 " pdb="ZN ZN V1001 " - pdb=" SG CYS V 141 " pdb="ZN ZN V1001 " - pdb=" NE2 HIS V 79 " pdb=" ZN X1001 " pdb="ZN ZN X1001 " - pdb=" SG CYS X 134 " pdb="ZN ZN X1001 " - pdb=" SG CYS X 141 " pdb="ZN ZN X1001 " - pdb=" NE2 HIS X 79 " pdb=" ZN Z1001 " pdb="ZN ZN Z1001 " - pdb=" SG CYS Z 134 " pdb="ZN ZN Z1001 " - pdb=" SG CYS Z 141 " pdb="ZN ZN Z1001 " - pdb=" NE2 HIS Z 79 " pdb=" ZNBA1001 " pdb="ZN ZNBA1001 " - pdb=" SG CYSBA 134 " pdb="ZN ZNBA1001 " - pdb=" SG CYSBA 141 " pdb="ZN ZNBA1001 " - pdb=" NE2 HISBA 79 " pdb=" ZNDA1001 " pdb="ZN ZNDA1001 " - pdb=" SG CYSDA 134 " pdb="ZN ZNDA1001 " - pdb=" SG CYSDA 141 " pdb="ZN ZNDA1001 " - pdb=" NE2 HISDA 79 " pdb=" ZNFA1001 " pdb="ZN ZNFA1001 " - pdb=" SG CYSFA 134 " pdb="ZN ZNFA1001 " - pdb=" SG CYSFA 141 " pdb="ZN ZNFA1001 " - pdb=" NE2 HISFA 79 " pdb=" ZNHA1001 " pdb="ZN ZNHA1001 " - pdb=" SG CYSHA 134 " pdb="ZN ZNHA1001 " - pdb=" SG CYSHA 141 " pdb="ZN ZNHA1001 " - pdb=" NE2 HISHA 79 " pdb=" ZNJA1001 " pdb="ZN ZNJA1001 " - pdb=" SG CYSJA 134 " pdb="ZN ZNJA1001 " - pdb=" SG CYSJA 141 " pdb="ZN ZNJA1001 " - pdb=" NE2 HISJA 79 " pdb=" ZNLA1001 " pdb="ZN ZNLA1001 " - pdb=" SG CYSLA 134 " pdb="ZN ZNLA1001 " - pdb=" SG CYSLA 141 " pdb="ZN ZNLA1001 " - pdb=" NE2 HISLA 79 " pdb=" ZNNA1001 " pdb="ZN ZNNA1001 " - pdb=" SG CYSNA 134 " pdb="ZN ZNNA1001 " - pdb=" SG CYSNA 141 " pdb="ZN ZNNA1001 " - pdb=" NE2 HISNA 79 " pdb=" ZNPA1001 " pdb="ZN ZNPA1001 " - pdb=" SG CYSPA 134 " pdb="ZN ZNPA1001 " - pdb=" SG CYSPA 141 " pdb="ZN ZNPA1001 " - pdb=" NE2 HISPA 79 " pdb=" ZNRA1001 " pdb="ZN ZNRA1001 " - pdb=" SG CYSRA 134 " pdb="ZN ZNRA1001 " - pdb=" SG CYSRA 141 " pdb="ZN ZNRA1001 " - pdb=" NE2 HISRA 79 " pdb=" ZNTA1001 " pdb="ZN ZNTA1001 " - pdb=" SG CYSTA 134 " pdb="ZN ZNTA1001 " - pdb=" SG CYSTA 141 " pdb="ZN ZNTA1001 " - pdb=" NE2 HISTA 79 " pdb=" ZNVA1001 " pdb="ZN ZNVA1001 " - pdb=" SG CYSVA 134 " pdb="ZN ZNVA1001 " - pdb=" SG CYSVA 141 " pdb="ZN ZNVA1001 " - pdb=" NE2 HISVA 79 " 22032 Ramachandran restraints generated. 11016 Oldfield, 0 Emsley, 11016 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 21024 Finding SS restraints... Secondary structure from input PDB file: 360 helices and 122 sheets defined 33.9% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.39 Creating SS restraints... Processing helix chain 'A' and resid 13 through 22 removed outlier: 4.214A pdb=" N ALA A 17 " --> pdb=" O ALA A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 37 through 55 removed outlier: 3.613A pdb=" N AARG A 41 " --> pdb=" O HIS A 37 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU A 46 " --> pdb=" O ALA A 42 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 72 removed outlier: 4.007A pdb=" N ARG A 71 " --> pdb=" O ALA A 67 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET A 72 " --> pdb=" O PRO A 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 67 through 72' Processing helix chain 'A' and resid 87 through 102 removed outlier: 4.336A pdb=" N GLU A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER A 102 " --> pdb=" O ARG A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 125 removed outlier: 3.969A pdb=" N GLY A 117 " --> pdb=" O SER A 113 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 167 Processing helix chain 'A' and resid 193 through 195 No H-bonds generated for 'chain 'A' and resid 193 through 195' Processing helix chain 'A' and resid 203 through 205 No H-bonds generated for 'chain 'A' and resid 203 through 205' Processing helix chain 'A' and resid 252 through 257 Processing helix chain 'A' and resid 335 through 342 Processing helix chain 'A' and resid 343 through 348 removed outlier: 3.657A pdb=" N LEU A 346 " --> pdb=" O THR A 343 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA A 347 " --> pdb=" O GLY A 344 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR A 348 " --> pdb=" O ILE A 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 343 through 348' Processing helix chain 'A' and resid 351 through 365 Processing helix chain 'A' and resid 380 through 382 No H-bonds generated for 'chain 'A' and resid 380 through 382' Processing helix chain 'A' and resid 383 through 404 Processing helix chain 'A' and resid 461 through 471 removed outlier: 3.688A pdb=" N ARG A 467 " --> pdb=" O PRO A 463 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS A 469 " --> pdb=" O ARG A 465 " (cutoff:3.500A) Processing helix chain 'C' and resid 13 through 22 removed outlier: 4.164A pdb=" N ALA C 17 " --> pdb=" O ALA C 13 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 55 removed outlier: 3.664A pdb=" N AARG C 41 " --> pdb=" O HIS C 37 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU C 46 " --> pdb=" O ALA C 42 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 72 removed outlier: 3.980A pdb=" N ARG C 71 " --> pdb=" O ALA C 67 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET C 72 " --> pdb=" O PRO C 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 67 through 72' Processing helix chain 'C' and resid 87 through 102 removed outlier: 4.391A pdb=" N GLU C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER C 102 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 removed outlier: 3.902A pdb=" N GLY C 117 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 157 through 167 Processing helix chain 'C' and resid 193 through 195 No H-bonds generated for 'chain 'C' and resid 193 through 195' Processing helix chain 'C' and resid 203 through 205 No H-bonds generated for 'chain 'C' and resid 203 through 205' Processing helix chain 'C' and resid 252 through 257 Processing helix chain 'C' and resid 335 through 342 Processing helix chain 'C' and resid 343 through 348 removed outlier: 3.645A pdb=" N LEU C 346 " --> pdb=" O THR C 343 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALA C 347 " --> pdb=" O GLY C 344 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR C 348 " --> pdb=" O ILE C 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 343 through 348' Processing helix chain 'C' and resid 351 through 365 Processing helix chain 'C' and resid 380 through 382 No H-bonds generated for 'chain 'C' and resid 380 through 382' Processing helix chain 'C' and resid 383 through 404 Processing helix chain 'C' and resid 461 through 471 removed outlier: 3.595A pdb=" N ARG C 467 " --> pdb=" O PRO C 463 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS C 469 " --> pdb=" O ARG C 465 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 22 removed outlier: 4.147A pdb=" N ALA E 17 " --> pdb=" O ALA E 13 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 55 removed outlier: 3.618A pdb=" N AARG E 41 " --> pdb=" O HIS E 37 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU E 46 " --> pdb=" O ALA E 42 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 72 removed outlier: 4.010A pdb=" N ARG E 71 " --> pdb=" O ALA E 67 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET E 72 " --> pdb=" O PRO E 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 67 through 72' Processing helix chain 'E' and resid 87 through 102 removed outlier: 4.272A pdb=" N GLU E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER E 102 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 125 removed outlier: 4.008A pdb=" N GLY E 117 " --> pdb=" O SER E 113 " (cutoff:3.500A) Processing helix chain 'E' and resid 157 through 167 Processing helix chain 'E' and resid 193 through 195 No H-bonds generated for 'chain 'E' and resid 193 through 195' Processing helix chain 'E' and resid 203 through 205 No H-bonds generated for 'chain 'E' and resid 203 through 205' Processing helix chain 'E' and resid 252 through 257 Processing helix chain 'E' and resid 335 through 343 Processing helix chain 'E' and resid 344 through 348 removed outlier: 3.595A pdb=" N ALA E 347 " --> pdb=" O GLY E 344 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR E 348 " --> pdb=" O ILE E 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 344 through 348' Processing helix chain 'E' and resid 351 through 365 Processing helix chain 'E' and resid 380 through 382 No H-bonds generated for 'chain 'E' and resid 380 through 382' Processing helix chain 'E' and resid 383 through 404 removed outlier: 3.512A pdb=" N ARG E 399 " --> pdb=" O ALA E 395 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP E 401 " --> pdb=" O GLU E 397 " (cutoff:3.500A) Processing helix chain 'E' and resid 461 through 471 removed outlier: 3.560A pdb=" N ARG E 467 " --> pdb=" O PRO E 463 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYS E 469 " --> pdb=" O ARG E 465 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 22 removed outlier: 4.194A pdb=" N ALA G 17 " --> pdb=" O ALA G 13 " (cutoff:3.500A) Processing helix chain 'G' and resid 37 through 55 removed outlier: 3.612A pdb=" N AARG G 41 " --> pdb=" O HIS G 37 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU G 46 " --> pdb=" O ALA G 42 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 72 removed outlier: 4.008A pdb=" N ARG G 71 " --> pdb=" O ALA G 67 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET G 72 " --> pdb=" O PRO G 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 67 through 72' Processing helix chain 'G' and resid 87 through 102 removed outlier: 4.336A pdb=" N GLU G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER G 102 " --> pdb=" O ARG G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 125 removed outlier: 3.978A pdb=" N GLY G 117 " --> pdb=" O SER G 113 " (cutoff:3.500A) Processing helix chain 'G' and resid 157 through 167 Processing helix chain 'G' and resid 193 through 195 No H-bonds generated for 'chain 'G' and resid 193 through 195' Processing helix chain 'G' and resid 203 through 205 No H-bonds generated for 'chain 'G' and resid 203 through 205' Processing helix chain 'G' and resid 252 through 257 Processing helix chain 'G' and resid 335 through 342 Processing helix chain 'G' and resid 343 through 348 removed outlier: 3.657A pdb=" N LEU G 346 " --> pdb=" O THR G 343 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA G 347 " --> pdb=" O GLY G 344 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR G 348 " --> pdb=" O ILE G 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 343 through 348' Processing helix chain 'G' and resid 351 through 365 Processing helix chain 'G' and resid 380 through 382 No H-bonds generated for 'chain 'G' and resid 380 through 382' Processing helix chain 'G' and resid 383 through 404 Processing helix chain 'G' and resid 461 through 471 removed outlier: 3.684A pdb=" N ARG G 467 " --> pdb=" O PRO G 463 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS G 469 " --> pdb=" O ARG G 465 " (cutoff:3.500A) Processing helix chain 'I' and resid 13 through 22 removed outlier: 4.164A pdb=" N ALA I 17 " --> pdb=" O ALA I 13 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 55 removed outlier: 3.677A pdb=" N AARG I 41 " --> pdb=" O HIS I 37 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU I 46 " --> pdb=" O ALA I 42 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 72 removed outlier: 3.979A pdb=" N ARG I 71 " --> pdb=" O ALA I 67 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET I 72 " --> pdb=" O PRO I 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 67 through 72' Processing helix chain 'I' and resid 87 through 102 removed outlier: 4.391A pdb=" N GLU I 91 " --> pdb=" O ALA I 87 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SER I 102 " --> pdb=" O ARG I 98 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 125 removed outlier: 3.901A pdb=" N GLY I 117 " --> pdb=" O SER I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 157 through 167 Processing helix chain 'I' and resid 193 through 195 No H-bonds generated for 'chain 'I' and resid 193 through 195' Processing helix chain 'I' and resid 203 through 205 No H-bonds generated for 'chain 'I' and resid 203 through 205' Processing helix chain 'I' and resid 252 through 257 Processing helix chain 'I' and resid 335 through 342 Processing helix chain 'I' and resid 343 through 348 removed outlier: 3.645A pdb=" N LEU I 346 " --> pdb=" O THR I 343 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA I 347 " --> pdb=" O GLY I 344 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR I 348 " --> pdb=" O ILE I 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 343 through 348' Processing helix chain 'I' and resid 351 through 365 Processing helix chain 'I' and resid 380 through 382 No H-bonds generated for 'chain 'I' and resid 380 through 382' Processing helix chain 'I' and resid 383 through 404 Processing helix chain 'I' and resid 461 through 471 removed outlier: 3.596A pdb=" N ARG I 467 " --> pdb=" O PRO I 463 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS I 469 " --> pdb=" O ARG I 465 " (cutoff:3.500A) Processing helix chain 'K' and resid 13 through 22 removed outlier: 4.147A pdb=" N ALA K 17 " --> pdb=" O ALA K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 55 removed outlier: 3.619A pdb=" N AARG K 41 " --> pdb=" O HIS K 37 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEU K 46 " --> pdb=" O ALA K 42 " (cutoff:3.500A) Processing helix chain 'K' and resid 67 through 72 removed outlier: 4.010A pdb=" N ARG K 71 " --> pdb=" O ALA K 67 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET K 72 " --> pdb=" O PRO K 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 67 through 72' Processing helix chain 'K' and resid 87 through 102 removed outlier: 4.272A pdb=" N GLU K 91 " --> pdb=" O ALA K 87 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER K 102 " --> pdb=" O ARG K 98 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 125 removed outlier: 4.009A pdb=" N GLY K 117 " --> pdb=" O SER K 113 " (cutoff:3.500A) Processing helix chain 'K' and resid 157 through 167 Processing helix chain 'K' and resid 193 through 195 No H-bonds generated for 'chain 'K' and resid 193 through 195' Processing helix chain 'K' and resid 203 through 205 No H-bonds generated for 'chain 'K' and resid 203 through 205' Processing helix chain 'K' and resid 252 through 257 Processing helix chain 'K' and resid 335 through 343 Processing helix chain 'K' and resid 344 through 348 removed outlier: 3.578A pdb=" N ALA K 347 " --> pdb=" O GLY K 344 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR K 348 " --> pdb=" O ILE K 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 344 through 348' Processing helix chain 'K' and resid 351 through 365 Processing helix chain 'K' and resid 380 through 382 No H-bonds generated for 'chain 'K' and resid 380 through 382' Processing helix chain 'K' and resid 383 through 404 removed outlier: 3.512A pdb=" N ARG K 399 " --> pdb=" O ALA K 395 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASP K 401 " --> pdb=" O GLU K 397 " (cutoff:3.500A) Processing helix chain 'K' and resid 461 through 471 removed outlier: 3.558A pdb=" N ARG K 467 " --> pdb=" O PRO K 463 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS K 469 " --> pdb=" O ARG K 465 " (cutoff:3.500A) Processing helix chain 'M' and resid 13 through 22 removed outlier: 4.194A pdb=" N ALA M 17 " --> pdb=" O ALA M 13 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 55 removed outlier: 3.612A pdb=" N AARG M 41 " --> pdb=" O HIS M 37 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER M 44 " --> pdb=" O ALA M 40 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU M 46 " --> pdb=" O ALA M 42 " (cutoff:3.500A) Processing helix chain 'M' and resid 67 through 72 removed outlier: 4.007A pdb=" N ARG M 71 " --> pdb=" O ALA M 67 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET M 72 " --> pdb=" O PRO M 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 67 through 72' Processing helix chain 'M' and resid 87 through 102 removed outlier: 4.336A pdb=" N GLU M 91 " --> pdb=" O ALA M 87 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER M 102 " --> pdb=" O ARG M 98 " (cutoff:3.500A) Processing helix chain 'M' and resid 111 through 125 removed outlier: 3.969A pdb=" N GLY M 117 " --> pdb=" O SER M 113 " (cutoff:3.500A) Processing helix chain 'M' and resid 157 through 167 Processing helix chain 'M' and resid 193 through 195 No H-bonds generated for 'chain 'M' and resid 193 through 195' Processing helix chain 'M' and resid 203 through 205 No H-bonds generated for 'chain 'M' and resid 203 through 205' Processing helix chain 'M' and resid 252 through 257 Processing helix chain 'M' and resid 335 through 342 Processing helix chain 'M' and resid 343 through 348 removed outlier: 3.662A pdb=" N LEU M 346 " --> pdb=" O THR M 343 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA M 347 " --> pdb=" O GLY M 344 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N THR M 348 " --> pdb=" O ILE M 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 343 through 348' Processing helix chain 'M' and resid 351 through 365 Processing helix chain 'M' and resid 380 through 382 No H-bonds generated for 'chain 'M' and resid 380 through 382' Processing helix chain 'M' and resid 383 through 404 Processing helix chain 'M' and resid 461 through 471 removed outlier: 3.688A pdb=" N ARG M 467 " --> pdb=" O PRO M 463 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS M 469 " --> pdb=" O ARG M 465 " (cutoff:3.500A) Processing helix chain 'O' and resid 13 through 22 removed outlier: 4.163A pdb=" N ALA O 17 " --> pdb=" O ALA O 13 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 55 removed outlier: 3.676A pdb=" N AARG O 41 " --> pdb=" O HIS O 37 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER O 44 " --> pdb=" O ALA O 40 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU O 46 " --> pdb=" O ALA O 42 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 72 removed outlier: 3.979A pdb=" N ARG O 71 " --> pdb=" O ALA O 67 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET O 72 " --> pdb=" O PRO O 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 67 through 72' Processing helix chain 'O' and resid 87 through 102 removed outlier: 4.393A pdb=" N GLU O 91 " --> pdb=" O ALA O 87 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SER O 102 " --> pdb=" O ARG O 98 " (cutoff:3.500A) Processing helix chain 'O' and resid 111 through 125 removed outlier: 3.901A pdb=" N GLY O 117 " --> pdb=" O SER O 113 " (cutoff:3.500A) Processing helix chain 'O' and resid 157 through 167 Processing helix chain 'O' and resid 193 through 195 No H-bonds generated for 'chain 'O' and resid 193 through 195' Processing helix chain 'O' and resid 203 through 205 No H-bonds generated for 'chain 'O' and resid 203 through 205' Processing helix chain 'O' and resid 252 through 257 Processing helix chain 'O' and resid 335 through 342 Processing helix chain 'O' and resid 343 through 348 removed outlier: 3.645A pdb=" N LEU O 346 " --> pdb=" O THR O 343 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA O 347 " --> pdb=" O GLY O 344 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR O 348 " --> pdb=" O ILE O 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 343 through 348' Processing helix chain 'O' and resid 351 through 365 Processing helix chain 'O' and resid 380 through 382 No H-bonds generated for 'chain 'O' and resid 380 through 382' Processing helix chain 'O' and resid 383 through 404 Processing helix chain 'O' and resid 461 through 471 removed outlier: 3.595A pdb=" N ARG O 467 " --> pdb=" O PRO O 463 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYS O 469 " --> pdb=" O ARG O 465 " (cutoff:3.500A) Processing helix chain 'Q' and resid 13 through 22 removed outlier: 4.147A pdb=" N ALA Q 17 " --> pdb=" O ALA Q 13 " (cutoff:3.500A) Processing helix chain 'Q' and resid 37 through 55 removed outlier: 3.617A pdb=" N AARG Q 41 " --> pdb=" O HIS Q 37 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER Q 44 " --> pdb=" O ALA Q 40 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N LEU Q 46 " --> pdb=" O ALA Q 42 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 72 removed outlier: 4.010A pdb=" N ARG Q 71 " --> pdb=" O ALA Q 67 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET Q 72 " --> pdb=" O PRO Q 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 67 through 72' Processing helix chain 'Q' and resid 87 through 102 removed outlier: 4.277A pdb=" N GLU Q 91 " --> pdb=" O ALA Q 87 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER Q 102 " --> pdb=" O ARG Q 98 " (cutoff:3.500A) Processing helix chain 'Q' and resid 111 through 125 removed outlier: 4.041A pdb=" N GLY Q 117 " --> pdb=" O SER Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 157 through 167 Processing helix chain 'Q' and resid 193 through 195 No H-bonds generated for 'chain 'Q' and resid 193 through 195' Processing helix chain 'Q' and resid 203 through 205 No H-bonds generated for 'chain 'Q' and resid 203 through 205' Processing helix chain 'Q' and resid 252 through 257 Processing helix chain 'Q' and resid 335 through 343 Processing helix chain 'Q' and resid 344 through 348 removed outlier: 3.579A pdb=" N ALA Q 347 " --> pdb=" O GLY Q 344 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR Q 348 " --> pdb=" O ILE Q 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 344 through 348' Processing helix chain 'Q' and resid 351 through 365 Processing helix chain 'Q' and resid 380 through 382 No H-bonds generated for 'chain 'Q' and resid 380 through 382' Processing helix chain 'Q' and resid 383 through 404 removed outlier: 3.512A pdb=" N ARG Q 399 " --> pdb=" O ALA Q 395 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP Q 401 " --> pdb=" O GLU Q 397 " (cutoff:3.500A) Processing helix chain 'Q' and resid 461 through 471 removed outlier: 3.547A pdb=" N ARG Q 467 " --> pdb=" O PRO Q 463 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYS Q 469 " --> pdb=" O ARG Q 465 " (cutoff:3.500A) Processing helix chain 'S' and resid 13 through 22 removed outlier: 4.194A pdb=" N ALA S 17 " --> pdb=" O ALA S 13 " (cutoff:3.500A) Processing helix chain 'S' and resid 37 through 55 removed outlier: 3.612A pdb=" N AARG S 41 " --> pdb=" O HIS S 37 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER S 44 " --> pdb=" O ALA S 40 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU S 46 " --> pdb=" O ALA S 42 " (cutoff:3.500A) Processing helix chain 'S' and resid 67 through 72 removed outlier: 4.008A pdb=" N ARG S 71 " --> pdb=" O ALA S 67 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET S 72 " --> pdb=" O PRO S 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 67 through 72' Processing helix chain 'S' and resid 87 through 102 removed outlier: 4.336A pdb=" N GLU S 91 " --> pdb=" O ALA S 87 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER S 102 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing helix chain 'S' and resid 111 through 125 removed outlier: 3.969A pdb=" N GLY S 117 " --> pdb=" O SER S 113 " (cutoff:3.500A) Processing helix chain 'S' and resid 157 through 167 Processing helix chain 'S' and resid 193 through 195 No H-bonds generated for 'chain 'S' and resid 193 through 195' Processing helix chain 'S' and resid 203 through 205 No H-bonds generated for 'chain 'S' and resid 203 through 205' Processing helix chain 'S' and resid 252 through 257 Processing helix chain 'S' and resid 335 through 342 Processing helix chain 'S' and resid 343 through 348 removed outlier: 3.657A pdb=" N LEU S 346 " --> pdb=" O THR S 343 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA S 347 " --> pdb=" O GLY S 344 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR S 348 " --> pdb=" O ILE S 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 343 through 348' Processing helix chain 'S' and resid 351 through 365 Processing helix chain 'S' and resid 380 through 382 No H-bonds generated for 'chain 'S' and resid 380 through 382' Processing helix chain 'S' and resid 383 through 404 Processing helix chain 'S' and resid 461 through 471 removed outlier: 3.687A pdb=" N ARG S 467 " --> pdb=" O PRO S 463 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS S 469 " --> pdb=" O ARG S 465 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 22 removed outlier: 4.163A pdb=" N ALA V 17 " --> pdb=" O ALA V 13 " (cutoff:3.500A) Processing helix chain 'V' and resid 37 through 55 removed outlier: 3.664A pdb=" N AARG V 41 " --> pdb=" O HIS V 37 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER V 44 " --> pdb=" O ALA V 40 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEU V 46 " --> pdb=" O ALA V 42 " (cutoff:3.500A) Processing helix chain 'V' and resid 67 through 72 removed outlier: 3.979A pdb=" N ARG V 71 " --> pdb=" O ALA V 67 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N MET V 72 " --> pdb=" O PRO V 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 67 through 72' Processing helix chain 'V' and resid 87 through 102 removed outlier: 4.391A pdb=" N GLU V 91 " --> pdb=" O ALA V 87 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER V 102 " --> pdb=" O ARG V 98 " (cutoff:3.500A) Processing helix chain 'V' and resid 111 through 125 removed outlier: 3.903A pdb=" N GLY V 117 " --> pdb=" O SER V 113 " (cutoff:3.500A) Processing helix chain 'V' and resid 157 through 167 Processing helix chain 'V' and resid 193 through 195 No H-bonds generated for 'chain 'V' and resid 193 through 195' Processing helix chain 'V' and resid 203 through 205 No H-bonds generated for 'chain 'V' and resid 203 through 205' Processing helix chain 'V' and resid 252 through 257 Processing helix chain 'V' and resid 335 through 342 Processing helix chain 'V' and resid 343 through 348 removed outlier: 3.645A pdb=" N LEU V 346 " --> pdb=" O THR V 343 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA V 347 " --> pdb=" O GLY V 344 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THR V 348 " --> pdb=" O ILE V 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 343 through 348' Processing helix chain 'V' and resid 351 through 365 Processing helix chain 'V' and resid 380 through 382 No H-bonds generated for 'chain 'V' and resid 380 through 382' Processing helix chain 'V' and resid 383 through 404 Processing helix chain 'V' and resid 461 through 471 removed outlier: 3.595A pdb=" N ARG V 467 " --> pdb=" O PRO V 463 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYS V 469 " --> pdb=" O ARG V 465 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 22 removed outlier: 4.147A pdb=" N ALA X 17 " --> pdb=" O ALA X 13 " (cutoff:3.500A) Processing helix chain 'X' and resid 37 through 55 removed outlier: 3.620A pdb=" N AARG X 41 " --> pdb=" O HIS X 37 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER X 44 " --> pdb=" O ALA X 40 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU X 46 " --> pdb=" O ALA X 42 " (cutoff:3.500A) Processing helix chain 'X' and resid 67 through 72 removed outlier: 4.011A pdb=" N ARG X 71 " --> pdb=" O ALA X 67 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET X 72 " --> pdb=" O PRO X 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 67 through 72' Processing helix chain 'X' and resid 87 through 102 removed outlier: 4.273A pdb=" N GLU X 91 " --> pdb=" O ALA X 87 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SER X 102 " --> pdb=" O ARG X 98 " (cutoff:3.500A) Processing helix chain 'X' and resid 111 through 125 removed outlier: 4.008A pdb=" N GLY X 117 " --> pdb=" O SER X 113 " (cutoff:3.500A) Processing helix chain 'X' and resid 157 through 167 Processing helix chain 'X' and resid 193 through 195 No H-bonds generated for 'chain 'X' and resid 193 through 195' Processing helix chain 'X' and resid 203 through 205 No H-bonds generated for 'chain 'X' and resid 203 through 205' Processing helix chain 'X' and resid 252 through 257 Processing helix chain 'X' and resid 335 through 343 Processing helix chain 'X' and resid 344 through 348 removed outlier: 3.577A pdb=" N ALA X 347 " --> pdb=" O GLY X 344 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR X 348 " --> pdb=" O ILE X 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 344 through 348' Processing helix chain 'X' and resid 351 through 365 Processing helix chain 'X' and resid 380 through 382 No H-bonds generated for 'chain 'X' and resid 380 through 382' Processing helix chain 'X' and resid 383 through 404 removed outlier: 3.512A pdb=" N ARG X 399 " --> pdb=" O ALA X 395 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASP X 401 " --> pdb=" O GLU X 397 " (cutoff:3.500A) Processing helix chain 'X' and resid 461 through 471 removed outlier: 3.556A pdb=" N ARG X 467 " --> pdb=" O PRO X 463 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS X 469 " --> pdb=" O ARG X 465 " (cutoff:3.500A) Processing helix chain 'Z' and resid 13 through 22 removed outlier: 4.214A pdb=" N ALA Z 17 " --> pdb=" O ALA Z 13 " (cutoff:3.500A) Processing helix chain 'Z' and resid 37 through 55 removed outlier: 3.612A pdb=" N AARG Z 41 " --> pdb=" O HIS Z 37 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SER Z 44 " --> pdb=" O ALA Z 40 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEU Z 46 " --> pdb=" O ALA Z 42 " (cutoff:3.500A) Processing helix chain 'Z' and resid 67 through 72 removed outlier: 4.008A pdb=" N ARG Z 71 " --> pdb=" O ALA Z 67 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N MET Z 72 " --> pdb=" O PRO Z 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 67 through 72' Processing helix chain 'Z' and resid 87 through 102 removed outlier: 4.336A pdb=" N GLU Z 91 " --> pdb=" O ALA Z 87 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SER Z 102 " --> pdb=" O ARG Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 111 through 125 removed outlier: 3.969A pdb=" N GLY Z 117 " --> pdb=" O SER Z 113 " (cutoff:3.500A) Processing helix chain 'Z' and resid 157 through 167 Processing helix chain 'Z' and resid 193 through 195 No H-bonds generated for 'chain 'Z' and resid 193 through 195' Processing helix chain 'Z' and resid 203 through 205 No H-bonds generated for 'chain 'Z' and resid 203 through 205' Processing helix chain 'Z' and resid 252 through 257 Processing helix chain 'Z' and resid 335 through 342 Processing helix chain 'Z' and resid 343 through 348 removed outlier: 3.657A pdb=" N LEU Z 346 " --> pdb=" O THR Z 343 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA Z 347 " --> pdb=" O GLY Z 344 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR Z 348 " --> pdb=" O ILE Z 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 343 through 348' Processing helix chain 'Z' and resid 351 through 365 Processing helix chain 'Z' and resid 380 through 382 No H-bonds generated for 'chain 'Z' and resid 380 through 382' Processing helix chain 'Z' and resid 383 through 404 Processing helix chain 'Z' and resid 461 through 471 removed outlier: 3.688A pdb=" N ARG Z 467 " --> pdb=" O PRO Z 463 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYS Z 469 " --> pdb=" O ARG Z 465 " (cutoff:3.500A) Processing helix chain 'BA' and resid 13 through 22 removed outlier: 4.163A pdb=" N ALABA 17 " --> pdb=" O ALABA 13 " (cutoff:3.500A) Processing helix chain 'BA' and resid 37 through 55 removed outlier: 3.676A pdb=" N AARGBA 41 " --> pdb=" O HISBA 37 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SERBA 44 " --> pdb=" O ALABA 40 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEUBA 46 " --> pdb=" O ALABA 42 " (cutoff:3.500A) Processing helix chain 'BA' and resid 67 through 72 removed outlier: 3.979A pdb=" N ARGBA 71 " --> pdb=" O ALABA 67 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N METBA 72 " --> pdb=" O PROBA 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'BA' and resid 67 through 72' Processing helix chain 'BA' and resid 87 through 102 removed outlier: 4.390A pdb=" N GLUBA 91 " --> pdb=" O ALABA 87 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SERBA 102 " --> pdb=" O ARGBA 98 " (cutoff:3.500A) Processing helix chain 'BA' and resid 111 through 125 removed outlier: 3.902A pdb=" N GLYBA 117 " --> pdb=" O SERBA 113 " (cutoff:3.500A) Processing helix chain 'BA' and resid 157 through 167 Processing helix chain 'BA' and resid 193 through 195 No H-bonds generated for 'chain 'BA' and resid 193 through 195' Processing helix chain 'BA' and resid 203 through 205 No H-bonds generated for 'chain 'BA' and resid 203 through 205' Processing helix chain 'BA' and resid 252 through 257 Processing helix chain 'BA' and resid 335 through 342 Processing helix chain 'BA' and resid 343 through 348 removed outlier: 3.645A pdb=" N LEUBA 346 " --> pdb=" O THRBA 343 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALABA 347 " --> pdb=" O GLYBA 344 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THRBA 348 " --> pdb=" O ILEBA 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'BA' and resid 343 through 348' Processing helix chain 'BA' and resid 351 through 365 Processing helix chain 'BA' and resid 380 through 382 No H-bonds generated for 'chain 'BA' and resid 380 through 382' Processing helix chain 'BA' and resid 383 through 404 Processing helix chain 'BA' and resid 461 through 471 removed outlier: 3.595A pdb=" N ARGBA 467 " --> pdb=" O PROBA 463 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYSBA 469 " --> pdb=" O ARGBA 465 " (cutoff:3.500A) Processing helix chain 'DA' and resid 13 through 22 removed outlier: 4.147A pdb=" N ALADA 17 " --> pdb=" O ALADA 13 " (cutoff:3.500A) Processing helix chain 'DA' and resid 37 through 55 removed outlier: 3.620A pdb=" N AARGDA 41 " --> pdb=" O HISDA 37 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SERDA 44 " --> pdb=" O ALADA 40 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEUDA 46 " --> pdb=" O ALADA 42 " (cutoff:3.500A) Processing helix chain 'DA' and resid 67 through 72 removed outlier: 4.010A pdb=" N ARGDA 71 " --> pdb=" O ALADA 67 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N METDA 72 " --> pdb=" O PRODA 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'DA' and resid 67 through 72' Processing helix chain 'DA' and resid 87 through 102 removed outlier: 4.273A pdb=" N GLUDA 91 " --> pdb=" O ALADA 87 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SERDA 102 " --> pdb=" O ARGDA 98 " (cutoff:3.500A) Processing helix chain 'DA' and resid 111 through 125 removed outlier: 4.008A pdb=" N GLYDA 117 " --> pdb=" O SERDA 113 " (cutoff:3.500A) Processing helix chain 'DA' and resid 157 through 167 Processing helix chain 'DA' and resid 193 through 195 No H-bonds generated for 'chain 'DA' and resid 193 through 195' Processing helix chain 'DA' and resid 203 through 205 No H-bonds generated for 'chain 'DA' and resid 203 through 205' Processing helix chain 'DA' and resid 252 through 257 Processing helix chain 'DA' and resid 335 through 343 Processing helix chain 'DA' and resid 344 through 348 removed outlier: 3.595A pdb=" N ALADA 347 " --> pdb=" O GLYDA 344 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THRDA 348 " --> pdb=" O ILEDA 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'DA' and resid 344 through 348' Processing helix chain 'DA' and resid 351 through 365 Processing helix chain 'DA' and resid 380 through 382 No H-bonds generated for 'chain 'DA' and resid 380 through 382' Processing helix chain 'DA' and resid 383 through 404 removed outlier: 3.512A pdb=" N ARGDA 399 " --> pdb=" O ALADA 395 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASPDA 401 " --> pdb=" O GLUDA 397 " (cutoff:3.500A) Processing helix chain 'DA' and resid 461 through 471 removed outlier: 3.556A pdb=" N ARGDA 467 " --> pdb=" O PRODA 463 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N LYSDA 469 " --> pdb=" O ARGDA 465 " (cutoff:3.500A) Processing helix chain 'FA' and resid 13 through 22 removed outlier: 4.214A pdb=" N ALAFA 17 " --> pdb=" O ALAFA 13 " (cutoff:3.500A) Processing helix chain 'FA' and resid 37 through 55 removed outlier: 3.611A pdb=" N AARGFA 41 " --> pdb=" O HISFA 37 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SERFA 44 " --> pdb=" O ALAFA 40 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEUFA 46 " --> pdb=" O ALAFA 42 " (cutoff:3.500A) Processing helix chain 'FA' and resid 67 through 72 removed outlier: 4.008A pdb=" N ARGFA 71 " --> pdb=" O ALAFA 67 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N METFA 72 " --> pdb=" O PROFA 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'FA' and resid 67 through 72' Processing helix chain 'FA' and resid 87 through 102 removed outlier: 4.336A pdb=" N GLUFA 91 " --> pdb=" O ALAFA 87 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SERFA 102 " --> pdb=" O ARGFA 98 " (cutoff:3.500A) Processing helix chain 'FA' and resid 111 through 125 removed outlier: 3.978A pdb=" N GLYFA 117 " --> pdb=" O SERFA 113 " (cutoff:3.500A) Processing helix chain 'FA' and resid 157 through 167 Processing helix chain 'FA' and resid 193 through 195 No H-bonds generated for 'chain 'FA' and resid 193 through 195' Processing helix chain 'FA' and resid 203 through 205 No H-bonds generated for 'chain 'FA' and resid 203 through 205' Processing helix chain 'FA' and resid 252 through 257 Processing helix chain 'FA' and resid 335 through 342 Processing helix chain 'FA' and resid 343 through 348 removed outlier: 3.657A pdb=" N LEUFA 346 " --> pdb=" O THRFA 343 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALAFA 347 " --> pdb=" O GLYFA 344 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THRFA 348 " --> pdb=" O ILEFA 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'FA' and resid 343 through 348' Processing helix chain 'FA' and resid 351 through 365 Processing helix chain 'FA' and resid 380 through 382 No H-bonds generated for 'chain 'FA' and resid 380 through 382' Processing helix chain 'FA' and resid 383 through 404 Processing helix chain 'FA' and resid 461 through 471 removed outlier: 3.684A pdb=" N ARGFA 467 " --> pdb=" O PROFA 463 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N LYSFA 469 " --> pdb=" O ARGFA 465 " (cutoff:3.500A) Processing helix chain 'HA' and resid 13 through 22 removed outlier: 4.164A pdb=" N ALAHA 17 " --> pdb=" O ALAHA 13 " (cutoff:3.500A) Processing helix chain 'HA' and resid 37 through 55 removed outlier: 3.664A pdb=" N AARGHA 41 " --> pdb=" O HISHA 37 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SERHA 44 " --> pdb=" O ALAHA 40 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N LEUHA 46 " --> pdb=" O ALAHA 42 " (cutoff:3.500A) Processing helix chain 'HA' and resid 67 through 72 removed outlier: 3.979A pdb=" N ARGHA 71 " --> pdb=" O ALAHA 67 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N METHA 72 " --> pdb=" O PROHA 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'HA' and resid 67 through 72' Processing helix chain 'HA' and resid 87 through 102 removed outlier: 4.391A pdb=" N GLUHA 91 " --> pdb=" O ALAHA 87 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SERHA 102 " --> pdb=" O ARGHA 98 " (cutoff:3.500A) Processing helix chain 'HA' and resid 111 through 125 removed outlier: 3.903A pdb=" N GLYHA 117 " --> pdb=" O SERHA 113 " (cutoff:3.500A) Processing helix chain 'HA' and resid 157 through 167 Processing helix chain 'HA' and resid 193 through 195 No H-bonds generated for 'chain 'HA' and resid 193 through 195' Processing helix chain 'HA' and resid 203 through 205 No H-bonds generated for 'chain 'HA' and resid 203 through 205' Processing helix chain 'HA' and resid 252 through 257 Processing helix chain 'HA' and resid 335 through 342 Processing helix chain 'HA' and resid 343 through 348 removed outlier: 3.646A pdb=" N LEUHA 346 " --> pdb=" O THRHA 343 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ALAHA 347 " --> pdb=" O GLYHA 344 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THRHA 348 " --> pdb=" O ILEHA 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'HA' and resid 343 through 348' Processing helix chain 'HA' and resid 351 through 365 Processing helix chain 'HA' and resid 380 through 382 No H-bonds generated for 'chain 'HA' and resid 380 through 382' Processing helix chain 'HA' and resid 383 through 404 Processing helix chain 'HA' and resid 461 through 471 removed outlier: 3.596A pdb=" N ARGHA 467 " --> pdb=" O PROHA 463 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYSHA 469 " --> pdb=" O ARGHA 465 " (cutoff:3.500A) Processing helix chain 'JA' and resid 13 through 22 removed outlier: 4.146A pdb=" N ALAJA 17 " --> pdb=" O ALAJA 13 " (cutoff:3.500A) Processing helix chain 'JA' and resid 37 through 55 removed outlier: 3.620A pdb=" N AARGJA 41 " --> pdb=" O HISJA 37 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N SERJA 44 " --> pdb=" O ALAJA 40 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEUJA 46 " --> pdb=" O ALAJA 42 " (cutoff:3.500A) Processing helix chain 'JA' and resid 67 through 72 removed outlier: 4.005A pdb=" N ARGJA 71 " --> pdb=" O ALAJA 67 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N METJA 72 " --> pdb=" O PROJA 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'JA' and resid 67 through 72' Processing helix chain 'JA' and resid 87 through 102 removed outlier: 4.276A pdb=" N GLUJA 91 " --> pdb=" O ALAJA 87 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SERJA 102 " --> pdb=" O ARGJA 98 " (cutoff:3.500A) Processing helix chain 'JA' and resid 111 through 125 removed outlier: 4.020A pdb=" N GLYJA 117 " --> pdb=" O SERJA 113 " (cutoff:3.500A) Processing helix chain 'JA' and resid 157 through 167 Processing helix chain 'JA' and resid 193 through 195 No H-bonds generated for 'chain 'JA' and resid 193 through 195' Processing helix chain 'JA' and resid 203 through 205 No H-bonds generated for 'chain 'JA' and resid 203 through 205' Processing helix chain 'JA' and resid 252 through 257 Processing helix chain 'JA' and resid 335 through 343 Processing helix chain 'JA' and resid 344 through 348 removed outlier: 3.578A pdb=" N ALAJA 347 " --> pdb=" O GLYJA 344 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THRJA 348 " --> pdb=" O ILEJA 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'JA' and resid 344 through 348' Processing helix chain 'JA' and resid 351 through 365 Processing helix chain 'JA' and resid 380 through 382 No H-bonds generated for 'chain 'JA' and resid 380 through 382' Processing helix chain 'JA' and resid 383 through 404 removed outlier: 3.512A pdb=" N ARGJA 399 " --> pdb=" O ALAJA 395 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ASPJA 401 " --> pdb=" O GLUJA 397 " (cutoff:3.500A) Processing helix chain 'JA' and resid 461 through 471 removed outlier: 3.554A pdb=" N ARGJA 467 " --> pdb=" O PROJA 463 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N LYSJA 469 " --> pdb=" O ARGJA 465 " (cutoff:3.500A) Processing helix chain 'LA' and resid 13 through 22 removed outlier: 4.214A pdb=" N ALALA 17 " --> pdb=" O ALALA 13 " (cutoff:3.500A) Processing helix chain 'LA' and resid 37 through 55 removed outlier: 3.612A pdb=" N AARGLA 41 " --> pdb=" O HISLA 37 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SERLA 44 " --> pdb=" O ALALA 40 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEULA 46 " --> pdb=" O ALALA 42 " (cutoff:3.500A) Processing helix chain 'LA' and resid 67 through 72 removed outlier: 4.007A pdb=" N ARGLA 71 " --> pdb=" O ALALA 67 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N METLA 72 " --> pdb=" O PROLA 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'LA' and resid 67 through 72' Processing helix chain 'LA' and resid 87 through 102 removed outlier: 4.335A pdb=" N GLULA 91 " --> pdb=" O ALALA 87 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SERLA 102 " --> pdb=" O ARGLA 98 " (cutoff:3.500A) Processing helix chain 'LA' and resid 111 through 125 removed outlier: 3.969A pdb=" N GLYLA 117 " --> pdb=" O SERLA 113 " (cutoff:3.500A) Processing helix chain 'LA' and resid 157 through 167 Processing helix chain 'LA' and resid 193 through 195 No H-bonds generated for 'chain 'LA' and resid 193 through 195' Processing helix chain 'LA' and resid 203 through 205 No H-bonds generated for 'chain 'LA' and resid 203 through 205' Processing helix chain 'LA' and resid 252 through 257 Processing helix chain 'LA' and resid 335 through 342 Processing helix chain 'LA' and resid 343 through 348 removed outlier: 3.657A pdb=" N LEULA 346 " --> pdb=" O THRLA 343 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALALA 347 " --> pdb=" O GLYLA 344 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THRLA 348 " --> pdb=" O ILELA 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'LA' and resid 343 through 348' Processing helix chain 'LA' and resid 351 through 365 Processing helix chain 'LA' and resid 380 through 382 No H-bonds generated for 'chain 'LA' and resid 380 through 382' Processing helix chain 'LA' and resid 383 through 404 Processing helix chain 'LA' and resid 461 through 471 removed outlier: 3.688A pdb=" N ARGLA 467 " --> pdb=" O PROLA 463 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LYSLA 469 " --> pdb=" O ARGLA 465 " (cutoff:3.500A) Processing helix chain 'NA' and resid 13 through 22 removed outlier: 4.164A pdb=" N ALANA 17 " --> pdb=" O ALANA 13 " (cutoff:3.500A) Processing helix chain 'NA' and resid 37 through 55 removed outlier: 3.677A pdb=" N AARGNA 41 " --> pdb=" O HISNA 37 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SERNA 44 " --> pdb=" O ALANA 40 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEUNA 46 " --> pdb=" O ALANA 42 " (cutoff:3.500A) Processing helix chain 'NA' and resid 67 through 72 removed outlier: 3.980A pdb=" N ARGNA 71 " --> pdb=" O ALANA 67 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N METNA 72 " --> pdb=" O PRONA 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'NA' and resid 67 through 72' Processing helix chain 'NA' and resid 87 through 102 removed outlier: 4.390A pdb=" N GLUNA 91 " --> pdb=" O ALANA 87 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N SERNA 102 " --> pdb=" O ARGNA 98 " (cutoff:3.500A) Processing helix chain 'NA' and resid 111 through 125 removed outlier: 3.901A pdb=" N GLYNA 117 " --> pdb=" O SERNA 113 " (cutoff:3.500A) Processing helix chain 'NA' and resid 157 through 167 Processing helix chain 'NA' and resid 193 through 195 No H-bonds generated for 'chain 'NA' and resid 193 through 195' Processing helix chain 'NA' and resid 203 through 205 No H-bonds generated for 'chain 'NA' and resid 203 through 205' Processing helix chain 'NA' and resid 252 through 257 Processing helix chain 'NA' and resid 335 through 342 Processing helix chain 'NA' and resid 343 through 348 removed outlier: 3.645A pdb=" N LEUNA 346 " --> pdb=" O THRNA 343 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALANA 347 " --> pdb=" O GLYNA 344 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THRNA 348 " --> pdb=" O ILENA 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'NA' and resid 343 through 348' Processing helix chain 'NA' and resid 351 through 365 Processing helix chain 'NA' and resid 380 through 382 No H-bonds generated for 'chain 'NA' and resid 380 through 382' Processing helix chain 'NA' and resid 383 through 404 Processing helix chain 'NA' and resid 461 through 471 removed outlier: 3.596A pdb=" N ARGNA 467 " --> pdb=" O PRONA 463 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYSNA 469 " --> pdb=" O ARGNA 465 " (cutoff:3.500A) Processing helix chain 'PA' and resid 13 through 22 removed outlier: 4.148A pdb=" N ALAPA 17 " --> pdb=" O ALAPA 13 " (cutoff:3.500A) Processing helix chain 'PA' and resid 37 through 55 removed outlier: 3.619A pdb=" N AARGPA 41 " --> pdb=" O HISPA 37 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SERPA 44 " --> pdb=" O ALAPA 40 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N LEUPA 46 " --> pdb=" O ALAPA 42 " (cutoff:3.500A) Processing helix chain 'PA' and resid 67 through 72 removed outlier: 4.005A pdb=" N ARGPA 71 " --> pdb=" O ALAPA 67 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N METPA 72 " --> pdb=" O PROPA 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'PA' and resid 67 through 72' Processing helix chain 'PA' and resid 87 through 102 removed outlier: 4.272A pdb=" N GLUPA 91 " --> pdb=" O ALAPA 87 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N SERPA 102 " --> pdb=" O ARGPA 98 " (cutoff:3.500A) Processing helix chain 'PA' and resid 111 through 125 removed outlier: 4.009A pdb=" N GLYPA 117 " --> pdb=" O SERPA 113 " (cutoff:3.500A) Processing helix chain 'PA' and resid 157 through 167 Processing helix chain 'PA' and resid 193 through 195 No H-bonds generated for 'chain 'PA' and resid 193 through 195' Processing helix chain 'PA' and resid 203 through 205 No H-bonds generated for 'chain 'PA' and resid 203 through 205' Processing helix chain 'PA' and resid 252 through 257 Processing helix chain 'PA' and resid 335 through 343 Processing helix chain 'PA' and resid 344 through 348 removed outlier: 3.597A pdb=" N ALAPA 347 " --> pdb=" O GLYPA 344 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THRPA 348 " --> pdb=" O ILEPA 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'PA' and resid 344 through 348' Processing helix chain 'PA' and resid 351 through 365 Processing helix chain 'PA' and resid 380 through 382 No H-bonds generated for 'chain 'PA' and resid 380 through 382' Processing helix chain 'PA' and resid 383 through 404 removed outlier: 3.511A pdb=" N ARGPA 399 " --> pdb=" O ALAPA 395 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ASPPA 401 " --> pdb=" O GLUPA 397 " (cutoff:3.500A) Processing helix chain 'PA' and resid 461 through 471 removed outlier: 3.558A pdb=" N ARGPA 467 " --> pdb=" O PROPA 463 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYSPA 469 " --> pdb=" O ARGPA 465 " (cutoff:3.500A) Processing helix chain 'RA' and resid 13 through 22 removed outlier: 4.214A pdb=" N ALARA 17 " --> pdb=" O ALARA 13 " (cutoff:3.500A) Processing helix chain 'RA' and resid 37 through 55 removed outlier: 3.612A pdb=" N AARGRA 41 " --> pdb=" O HISRA 37 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N SERRA 44 " --> pdb=" O ALARA 40 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N LEURA 46 " --> pdb=" O ALARA 42 " (cutoff:3.500A) Processing helix chain 'RA' and resid 67 through 72 removed outlier: 4.006A pdb=" N ARGRA 71 " --> pdb=" O ALARA 67 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N METRA 72 " --> pdb=" O PRORA 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'RA' and resid 67 through 72' Processing helix chain 'RA' and resid 87 through 102 removed outlier: 4.337A pdb=" N GLURA 91 " --> pdb=" O ALARA 87 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N SERRA 102 " --> pdb=" O ARGRA 98 " (cutoff:3.500A) Processing helix chain 'RA' and resid 111 through 125 removed outlier: 3.970A pdb=" N GLYRA 117 " --> pdb=" O SERRA 113 " (cutoff:3.500A) Processing helix chain 'RA' and resid 157 through 167 Processing helix chain 'RA' and resid 193 through 195 No H-bonds generated for 'chain 'RA' and resid 193 through 195' Processing helix chain 'RA' and resid 203 through 205 No H-bonds generated for 'chain 'RA' and resid 203 through 205' Processing helix chain 'RA' and resid 252 through 257 Processing helix chain 'RA' and resid 335 through 342 Processing helix chain 'RA' and resid 343 through 348 removed outlier: 3.664A pdb=" N LEURA 346 " --> pdb=" O THRRA 343 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ALARA 347 " --> pdb=" O GLYRA 344 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N THRRA 348 " --> pdb=" O ILERA 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'RA' and resid 343 through 348' Processing helix chain 'RA' and resid 351 through 365 Processing helix chain 'RA' and resid 380 through 382 No H-bonds generated for 'chain 'RA' and resid 380 through 382' Processing helix chain 'RA' and resid 383 through 404 Processing helix chain 'RA' and resid 461 through 471 removed outlier: 3.707A pdb=" N ARGRA 467 " --> pdb=" O PRORA 463 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LYSRA 469 " --> pdb=" O ARGRA 465 " (cutoff:3.500A) Processing helix chain 'TA' and resid 13 through 22 removed outlier: 4.163A pdb=" N ALATA 17 " --> pdb=" O ALATA 13 " (cutoff:3.500A) Processing helix chain 'TA' and resid 37 through 55 removed outlier: 3.677A pdb=" N AARGTA 41 " --> pdb=" O HISTA 37 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SERTA 44 " --> pdb=" O ALATA 40 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEUTA 46 " --> pdb=" O ALATA 42 " (cutoff:3.500A) Processing helix chain 'TA' and resid 67 through 72 removed outlier: 3.979A pdb=" N ARGTA 71 " --> pdb=" O ALATA 67 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N METTA 72 " --> pdb=" O PROTA 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'TA' and resid 67 through 72' Processing helix chain 'TA' and resid 87 through 102 removed outlier: 4.389A pdb=" N GLUTA 91 " --> pdb=" O ALATA 87 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N SERTA 102 " --> pdb=" O ARGTA 98 " (cutoff:3.500A) Processing helix chain 'TA' and resid 111 through 125 removed outlier: 3.902A pdb=" N GLYTA 117 " --> pdb=" O SERTA 113 " (cutoff:3.500A) Processing helix chain 'TA' and resid 157 through 167 Processing helix chain 'TA' and resid 193 through 195 No H-bonds generated for 'chain 'TA' and resid 193 through 195' Processing helix chain 'TA' and resid 203 through 205 No H-bonds generated for 'chain 'TA' and resid 203 through 205' Processing helix chain 'TA' and resid 252 through 257 Processing helix chain 'TA' and resid 335 through 342 Processing helix chain 'TA' and resid 343 through 348 removed outlier: 3.645A pdb=" N LEUTA 346 " --> pdb=" O THRTA 343 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALATA 347 " --> pdb=" O GLYTA 344 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N THRTA 348 " --> pdb=" O ILETA 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'TA' and resid 343 through 348' Processing helix chain 'TA' and resid 351 through 365 Processing helix chain 'TA' and resid 380 through 382 No H-bonds generated for 'chain 'TA' and resid 380 through 382' Processing helix chain 'TA' and resid 383 through 404 Processing helix chain 'TA' and resid 461 through 471 removed outlier: 3.595A pdb=" N ARGTA 467 " --> pdb=" O PROTA 463 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LYSTA 469 " --> pdb=" O ARGTA 465 " (cutoff:3.500A) Processing helix chain 'VA' and resid 13 through 22 removed outlier: 4.146A pdb=" N ALAVA 17 " --> pdb=" O ALAVA 13 " (cutoff:3.500A) Processing helix chain 'VA' and resid 37 through 55 removed outlier: 3.618A pdb=" N AARGVA 41 " --> pdb=" O HISVA 37 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SERVA 44 " --> pdb=" O ALAVA 40 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LEUVA 46 " --> pdb=" O ALAVA 42 " (cutoff:3.500A) Processing helix chain 'VA' and resid 67 through 72 removed outlier: 4.005A pdb=" N ARGVA 71 " --> pdb=" O ALAVA 67 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N METVA 72 " --> pdb=" O PROVA 68 " (cutoff:3.500A) No H-bonds generated for 'chain 'VA' and resid 67 through 72' Processing helix chain 'VA' and resid 87 through 102 removed outlier: 4.277A pdb=" N GLUVA 91 " --> pdb=" O ALAVA 87 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N SERVA 102 " --> pdb=" O ARGVA 98 " (cutoff:3.500A) Processing helix chain 'VA' and resid 111 through 125 removed outlier: 4.045A pdb=" N GLYVA 117 " --> pdb=" O SERVA 113 " (cutoff:3.500A) Processing helix chain 'VA' and resid 157 through 167 Processing helix chain 'VA' and resid 193 through 195 No H-bonds generated for 'chain 'VA' and resid 193 through 195' Processing helix chain 'VA' and resid 203 through 205 No H-bonds generated for 'chain 'VA' and resid 203 through 205' Processing helix chain 'VA' and resid 252 through 257 Processing helix chain 'VA' and resid 335 through 343 Processing helix chain 'VA' and resid 344 through 348 removed outlier: 3.596A pdb=" N ALAVA 347 " --> pdb=" O GLYVA 344 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N THRVA 348 " --> pdb=" O ILEVA 345 " (cutoff:3.500A) No H-bonds generated for 'chain 'VA' and resid 344 through 348' Processing helix chain 'VA' and resid 351 through 365 Processing helix chain 'VA' and resid 380 through 382 No H-bonds generated for 'chain 'VA' and resid 380 through 382' Processing helix chain 'VA' and resid 383 through 404 removed outlier: 3.511A pdb=" N ARGVA 399 " --> pdb=" O ALAVA 395 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ASPVA 401 " --> pdb=" O GLUVA 397 " (cutoff:3.500A) Processing helix chain 'VA' and resid 461 through 471 removed outlier: 3.547A pdb=" N ARGVA 467 " --> pdb=" O PROVA 463 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N LYSVA 469 " --> pdb=" O ARGVA 465 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 6 removed outlier: 6.134A pdb=" N VAL A 4 " --> pdb=" O GLU A 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 134 removed outlier: 8.424A pdb=" N CYS A 134 " --> pdb=" O TYR A 78 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYS A 80 " --> pdb=" O CYS A 134 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE A 61 " --> pdb=" O HIS A 79 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL A 81 " --> pdb=" O ILE A 61 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASP A 63 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR A 60 " --> pdb=" O VAL A 147 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE A 149 " --> pdb=" O THR A 60 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU A 62 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLN A 151 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE A 64 " --> pdb=" O GLN A 151 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TYR A 285 " --> pdb=" O SER A 281 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER A 281 " --> pdb=" O TYR A 285 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL A 287 " --> pdb=" O VAL A 279 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 251 removed outlier: 4.192A pdb=" N TYR A 333 " --> pdb=" O ALA A 191 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 303 through 307 Processing sheet with id=AA5, first strand: chain 'A' and resid 414 through 415 Processing sheet with id=AA6, first strand: chain 'C' and resid 4 through 6 removed outlier: 6.103A pdb=" N VAL C 4 " --> pdb=" O GLU C 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 133 through 134 removed outlier: 8.381A pdb=" N CYS C 134 " --> pdb=" O TYR C 78 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N CYS C 80 " --> pdb=" O CYS C 134 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE C 61 " --> pdb=" O HIS C 79 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL C 81 " --> pdb=" O ILE C 61 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASP C 63 " --> pdb=" O VAL C 81 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR C 60 " --> pdb=" O VAL C 147 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE C 149 " --> pdb=" O THR C 60 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU C 62 " --> pdb=" O ILE C 149 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLN C 151 " --> pdb=" O LEU C 62 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE C 64 " --> pdb=" O GLN C 151 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR C 285 " --> pdb=" O SER C 281 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER C 281 " --> pdb=" O TYR C 285 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VAL C 287 " --> pdb=" O VAL C 279 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 246 through 251 removed outlier: 6.891A pdb=" N ALA C 189 " --> pdb=" O CYS C 331 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N TYR C 333 " --> pdb=" O ALA C 189 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ALA C 191 " --> pdb=" O TYR C 333 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 303 through 307 Processing sheet with id=AB1, first strand: chain 'C' and resid 414 through 415 Processing sheet with id=AB2, first strand: chain 'E' and resid 4 through 6 removed outlier: 6.141A pdb=" N VAL E 4 " --> pdb=" O GLU E 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 133 through 134 removed outlier: 8.295A pdb=" N CYS E 134 " --> pdb=" O TYR E 78 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N CYS E 80 " --> pdb=" O CYS E 134 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE E 61 " --> pdb=" O HIS E 79 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL E 81 " --> pdb=" O ILE E 61 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ASP E 63 " --> pdb=" O VAL E 81 " (cutoff:3.500A) removed outlier: 4.714A pdb=" N GLN E 151 " --> pdb=" O ILE E 64 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TYR E 285 " --> pdb=" O SER E 281 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N SER E 281 " --> pdb=" O TYR E 285 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL E 287 " --> pdb=" O VAL E 279 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 246 through 251 removed outlier: 4.108A pdb=" N TYR E 333 " --> pdb=" O ALA E 191 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 303 through 307 Processing sheet with id=AB6, first strand: chain 'E' and resid 414 through 415 Processing sheet with id=AB7, first strand: chain 'G' and resid 4 through 6 removed outlier: 6.136A pdb=" N VAL G 4 " --> pdb=" O GLU G 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'G' and resid 133 through 134 removed outlier: 8.424A pdb=" N CYS G 134 " --> pdb=" O TYR G 78 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYS G 80 " --> pdb=" O CYS G 134 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE G 61 " --> pdb=" O HIS G 79 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL G 81 " --> pdb=" O ILE G 61 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ASP G 63 " --> pdb=" O VAL G 81 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR G 60 " --> pdb=" O VAL G 147 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE G 149 " --> pdb=" O THR G 60 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU G 62 " --> pdb=" O ILE G 149 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLN G 151 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE G 64 " --> pdb=" O GLN G 151 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 246 through 251 removed outlier: 4.192A pdb=" N TYR G 333 " --> pdb=" O ALA G 191 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 263 through 267 Processing sheet with id=AC2, first strand: chain 'G' and resid 303 through 307 Processing sheet with id=AC3, first strand: chain 'G' and resid 414 through 415 Processing sheet with id=AC4, first strand: chain 'I' and resid 4 through 6 removed outlier: 6.103A pdb=" N VAL I 4 " --> pdb=" O GLU I 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'I' and resid 133 through 134 removed outlier: 8.382A pdb=" N CYS I 134 " --> pdb=" O TYR I 78 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N CYS I 80 " --> pdb=" O CYS I 134 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE I 61 " --> pdb=" O HIS I 79 " (cutoff:3.500A) removed outlier: 7.113A pdb=" N VAL I 81 " --> pdb=" O ILE I 61 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ASP I 63 " --> pdb=" O VAL I 81 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR I 60 " --> pdb=" O VAL I 147 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE I 149 " --> pdb=" O THR I 60 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU I 62 " --> pdb=" O ILE I 149 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLN I 151 " --> pdb=" O LEU I 62 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILE I 64 " --> pdb=" O GLN I 151 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N TYR I 285 " --> pdb=" O SER I 281 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER I 281 " --> pdb=" O TYR I 285 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL I 287 " --> pdb=" O VAL I 279 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 246 through 251 removed outlier: 6.891A pdb=" N ALA I 189 " --> pdb=" O CYS I 331 " (cutoff:3.500A) removed outlier: 9.223A pdb=" N TYR I 333 " --> pdb=" O ALA I 189 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ALA I 191 " --> pdb=" O TYR I 333 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 303 through 307 Processing sheet with id=AC8, first strand: chain 'I' and resid 414 through 415 Processing sheet with id=AC9, first strand: chain 'K' and resid 4 through 6 removed outlier: 6.137A pdb=" N VAL K 4 " --> pdb=" O GLU K 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'K' and resid 133 through 134 removed outlier: 8.293A pdb=" N CYS K 134 " --> pdb=" O TYR K 78 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N CYS K 80 " --> pdb=" O CYS K 134 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILE K 61 " --> pdb=" O HIS K 79 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL K 81 " --> pdb=" O ILE K 61 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ASP K 63 " --> pdb=" O VAL K 81 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLN K 151 " --> pdb=" O ILE K 64 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TYR K 285 " --> pdb=" O SER K 281 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER K 281 " --> pdb=" O TYR K 285 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL K 287 " --> pdb=" O VAL K 279 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'K' and resid 246 through 251 removed outlier: 4.112A pdb=" N TYR K 333 " --> pdb=" O ALA K 191 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'K' and resid 303 through 307 Processing sheet with id=AD4, first strand: chain 'K' and resid 414 through 415 Processing sheet with id=AD5, first strand: chain 'M' and resid 4 through 6 removed outlier: 6.135A pdb=" N VAL M 4 " --> pdb=" O GLU M 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'M' and resid 133 through 134 removed outlier: 8.424A pdb=" N CYS M 134 " --> pdb=" O TYR M 78 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYS M 80 " --> pdb=" O CYS M 134 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE M 61 " --> pdb=" O HIS M 79 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VAL M 81 " --> pdb=" O ILE M 61 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASP M 63 " --> pdb=" O VAL M 81 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THR M 60 " --> pdb=" O VAL M 147 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILE M 149 " --> pdb=" O THR M 60 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEU M 62 " --> pdb=" O ILE M 149 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLN M 151 " --> pdb=" O LEU M 62 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE M 64 " --> pdb=" O GLN M 151 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TYR M 285 " --> pdb=" O SER M 281 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER M 281 " --> pdb=" O TYR M 285 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VAL M 287 " --> pdb=" O VAL M 279 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'M' and resid 246 through 251 removed outlier: 4.194A pdb=" N TYR M 333 " --> pdb=" O ALA M 191 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 303 through 307 Processing sheet with id=AD9, first strand: chain 'M' and resid 414 through 415 Processing sheet with id=AE1, first strand: chain 'O' and resid 4 through 6 removed outlier: 6.103A pdb=" N VAL O 4 " --> pdb=" O GLU O 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'O' and resid 133 through 134 removed outlier: 8.383A pdb=" N CYS O 134 " --> pdb=" O TYR O 78 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N CYS O 80 " --> pdb=" O CYS O 134 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE O 61 " --> pdb=" O HIS O 79 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL O 81 " --> pdb=" O ILE O 61 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASP O 63 " --> pdb=" O VAL O 81 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR O 60 " --> pdb=" O VAL O 147 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILE O 149 " --> pdb=" O THR O 60 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEU O 62 " --> pdb=" O ILE O 149 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLN O 151 " --> pdb=" O LEU O 62 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE O 64 " --> pdb=" O GLN O 151 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR O 285 " --> pdb=" O SER O 281 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N SER O 281 " --> pdb=" O TYR O 285 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL O 287 " --> pdb=" O VAL O 279 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'O' and resid 246 through 251 removed outlier: 6.891A pdb=" N ALA O 189 " --> pdb=" O CYS O 331 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N TYR O 333 " --> pdb=" O ALA O 189 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ALA O 191 " --> pdb=" O TYR O 333 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'O' and resid 303 through 307 Processing sheet with id=AE5, first strand: chain 'O' and resid 414 through 415 Processing sheet with id=AE6, first strand: chain 'Q' and resid 4 through 6 removed outlier: 6.141A pdb=" N VAL Q 4 " --> pdb=" O GLU Q 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE6 Processing sheet with id=AE7, first strand: chain 'Q' and resid 133 through 134 removed outlier: 8.298A pdb=" N CYS Q 134 " --> pdb=" O TYR Q 78 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N CYS Q 80 " --> pdb=" O CYS Q 134 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILE Q 61 " --> pdb=" O HIS Q 79 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N VAL Q 81 " --> pdb=" O ILE Q 61 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ASP Q 63 " --> pdb=" O VAL Q 81 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THR Q 60 " --> pdb=" O VAL Q 147 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N ILE Q 149 " --> pdb=" O THR Q 60 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU Q 62 " --> pdb=" O ILE Q 149 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN Q 151 " --> pdb=" O LEU Q 62 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE Q 64 " --> pdb=" O GLN Q 151 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TYR Q 285 " --> pdb=" O SER Q 281 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SER Q 281 " --> pdb=" O TYR Q 285 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL Q 287 " --> pdb=" O VAL Q 279 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 246 through 251 removed outlier: 4.106A pdb=" N TYR Q 333 " --> pdb=" O ALA Q 191 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 303 through 307 Processing sheet with id=AF1, first strand: chain 'Q' and resid 414 through 415 Processing sheet with id=AF2, first strand: chain 'S' and resid 4 through 6 removed outlier: 6.135A pdb=" N VAL S 4 " --> pdb=" O GLU S 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'S' and resid 133 through 134 removed outlier: 8.423A pdb=" N CYS S 134 " --> pdb=" O TYR S 78 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYS S 80 " --> pdb=" O CYS S 134 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE S 61 " --> pdb=" O HIS S 79 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL S 81 " --> pdb=" O ILE S 61 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASP S 63 " --> pdb=" O VAL S 81 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR S 60 " --> pdb=" O VAL S 147 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ILE S 149 " --> pdb=" O THR S 60 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU S 62 " --> pdb=" O ILE S 149 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N GLN S 151 " --> pdb=" O LEU S 62 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N ILE S 64 " --> pdb=" O GLN S 151 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TYR S 285 " --> pdb=" O SER S 281 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER S 281 " --> pdb=" O TYR S 285 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL S 287 " --> pdb=" O VAL S 279 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'S' and resid 246 through 251 removed outlier: 4.194A pdb=" N TYR S 333 " --> pdb=" O ALA S 191 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'S' and resid 303 through 307 Processing sheet with id=AF6, first strand: chain 'S' and resid 414 through 415 Processing sheet with id=AF7, first strand: chain 'V' and resid 4 through 6 removed outlier: 6.103A pdb=" N VAL V 4 " --> pdb=" O GLU V 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF7 Processing sheet with id=AF8, first strand: chain 'V' and resid 133 through 134 removed outlier: 8.378A pdb=" N CYS V 134 " --> pdb=" O TYR V 78 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N CYS V 80 " --> pdb=" O CYS V 134 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILE V 61 " --> pdb=" O HIS V 79 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VAL V 81 " --> pdb=" O ILE V 61 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASP V 63 " --> pdb=" O VAL V 81 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR V 60 " --> pdb=" O VAL V 147 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILE V 149 " --> pdb=" O THR V 60 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU V 62 " --> pdb=" O ILE V 149 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLN V 151 " --> pdb=" O LEU V 62 " (cutoff:3.500A) removed outlier: 7.164A pdb=" N ILE V 64 " --> pdb=" O GLN V 151 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYR V 285 " --> pdb=" O SER V 281 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SER V 281 " --> pdb=" O TYR V 285 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VAL V 287 " --> pdb=" O VAL V 279 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'V' and resid 246 through 251 removed outlier: 6.891A pdb=" N ALA V 189 " --> pdb=" O CYS V 331 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N TYR V 333 " --> pdb=" O ALA V 189 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ALA V 191 " --> pdb=" O TYR V 333 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'V' and resid 303 through 307 Processing sheet with id=AG2, first strand: chain 'V' and resid 414 through 415 Processing sheet with id=AG3, first strand: chain 'X' and resid 4 through 6 removed outlier: 6.138A pdb=" N VAL X 4 " --> pdb=" O GLU X 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'X' and resid 133 through 134 removed outlier: 8.298A pdb=" N CYS X 134 " --> pdb=" O TYR X 78 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N CYS X 80 " --> pdb=" O CYS X 134 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ILE X 61 " --> pdb=" O HIS X 79 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N VAL X 81 " --> pdb=" O ILE X 61 " (cutoff:3.500A) removed outlier: 6.092A pdb=" N ASP X 63 " --> pdb=" O VAL X 81 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THR X 60 " --> pdb=" O VAL X 147 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N ILE X 149 " --> pdb=" O THR X 60 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N LEU X 62 " --> pdb=" O ILE X 149 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N GLN X 151 " --> pdb=" O LEU X 62 " (cutoff:3.500A) removed outlier: 7.221A pdb=" N ILE X 64 " --> pdb=" O GLN X 151 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N TYR X 285 " --> pdb=" O SER X 281 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SER X 281 " --> pdb=" O TYR X 285 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VAL X 287 " --> pdb=" O VAL X 279 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'X' and resid 246 through 251 removed outlier: 4.112A pdb=" N TYR X 333 " --> pdb=" O ALA X 191 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'X' and resid 303 through 307 Processing sheet with id=AG7, first strand: chain 'X' and resid 414 through 415 Processing sheet with id=AG8, first strand: chain 'Z' and resid 4 through 6 removed outlier: 6.135A pdb=" N VAL Z 4 " --> pdb=" O GLU Z 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG8 Processing sheet with id=AG9, first strand: chain 'Z' and resid 133 through 134 removed outlier: 8.424A pdb=" N CYS Z 134 " --> pdb=" O TYR Z 78 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYS Z 80 " --> pdb=" O CYS Z 134 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILE Z 61 " --> pdb=" O HIS Z 79 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VAL Z 81 " --> pdb=" O ILE Z 61 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASP Z 63 " --> pdb=" O VAL Z 81 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THR Z 60 " --> pdb=" O VAL Z 147 " (cutoff:3.500A) removed outlier: 7.855A pdb=" N ILE Z 149 " --> pdb=" O THR Z 60 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU Z 62 " --> pdb=" O ILE Z 149 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N GLN Z 151 " --> pdb=" O LEU Z 62 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILE Z 64 " --> pdb=" O GLN Z 151 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TYR Z 285 " --> pdb=" O SER Z 281 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SER Z 281 " --> pdb=" O TYR Z 285 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VAL Z 287 " --> pdb=" O VAL Z 279 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'Z' and resid 246 through 251 removed outlier: 4.193A pdb=" N TYR Z 333 " --> pdb=" O ALA Z 191 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'Z' and resid 303 through 307 Processing sheet with id=AH3, first strand: chain 'Z' and resid 414 through 415 Processing sheet with id=AH4, first strand: chain 'BA' and resid 4 through 6 removed outlier: 6.104A pdb=" N VALBA 4 " --> pdb=" O GLUBA 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'BA' and resid 133 through 134 removed outlier: 8.377A pdb=" N CYSBA 134 " --> pdb=" O TYRBA 78 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N CYSBA 80 " --> pdb=" O CYSBA 134 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N ILEBA 61 " --> pdb=" O HISBA 79 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VALBA 81 " --> pdb=" O ILEBA 61 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASPBA 63 " --> pdb=" O VALBA 81 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N THRBA 60 " --> pdb=" O VALBA 147 " (cutoff:3.500A) removed outlier: 7.887A pdb=" N ILEBA 149 " --> pdb=" O THRBA 60 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEUBA 62 " --> pdb=" O ILEBA 149 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLNBA 151 " --> pdb=" O LEUBA 62 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILEBA 64 " --> pdb=" O GLNBA 151 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYRBA 285 " --> pdb=" O SERBA 281 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SERBA 281 " --> pdb=" O TYRBA 285 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VALBA 287 " --> pdb=" O VALBA 279 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'BA' and resid 246 through 251 removed outlier: 6.891A pdb=" N ALABA 189 " --> pdb=" O CYSBA 331 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N TYRBA 333 " --> pdb=" O ALABA 189 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ALABA 191 " --> pdb=" O TYRBA 333 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'BA' and resid 303 through 307 Processing sheet with id=AH8, first strand: chain 'BA' and resid 414 through 415 Processing sheet with id=AH9, first strand: chain 'DA' and resid 4 through 6 removed outlier: 6.140A pdb=" N VALDA 4 " --> pdb=" O GLUDA 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH9 Processing sheet with id=AI1, first strand: chain 'DA' and resid 133 through 134 removed outlier: 8.295A pdb=" N CYSDA 134 " --> pdb=" O TYRDA 78 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N CYSDA 80 " --> pdb=" O CYSDA 134 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ILEDA 61 " --> pdb=" O HISDA 79 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VALDA 81 " --> pdb=" O ILEDA 61 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASPDA 63 " --> pdb=" O VALDA 81 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLNDA 151 " --> pdb=" O ILEDA 64 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TYRDA 285 " --> pdb=" O SERDA 281 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SERDA 281 " --> pdb=" O TYRDA 285 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VALDA 287 " --> pdb=" O VALDA 279 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'DA' and resid 246 through 251 removed outlier: 4.113A pdb=" N TYRDA 333 " --> pdb=" O ALADA 191 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'DA' and resid 303 through 307 Processing sheet with id=AI4, first strand: chain 'DA' and resid 414 through 415 Processing sheet with id=AI5, first strand: chain 'FA' and resid 4 through 6 removed outlier: 6.135A pdb=" N VALFA 4 " --> pdb=" O GLUFA 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI5 Processing sheet with id=AI6, first strand: chain 'FA' and resid 133 through 134 removed outlier: 8.424A pdb=" N CYSFA 134 " --> pdb=" O TYRFA 78 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYSFA 80 " --> pdb=" O CYSFA 134 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILEFA 61 " --> pdb=" O HISFA 79 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N VALFA 81 " --> pdb=" O ILEFA 61 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ASPFA 63 " --> pdb=" O VALFA 81 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N THRFA 60 " --> pdb=" O VALFA 147 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILEFA 149 " --> pdb=" O THRFA 60 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N LEUFA 62 " --> pdb=" O ILEFA 149 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLNFA 151 " --> pdb=" O LEUFA 62 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILEFA 64 " --> pdb=" O GLNFA 151 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TYRFA 285 " --> pdb=" O SERFA 281 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SERFA 281 " --> pdb=" O TYRFA 285 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N VALFA 287 " --> pdb=" O VALFA 279 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'FA' and resid 246 through 251 removed outlier: 4.193A pdb=" N TYRFA 333 " --> pdb=" O ALAFA 191 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'FA' and resid 303 through 307 Processing sheet with id=AI9, first strand: chain 'FA' and resid 414 through 415 Processing sheet with id=AJ1, first strand: chain 'HA' and resid 4 through 6 removed outlier: 6.103A pdb=" N VALHA 4 " --> pdb=" O GLUHA 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ1 Processing sheet with id=AJ2, first strand: chain 'HA' and resid 133 through 134 removed outlier: 8.381A pdb=" N CYSHA 134 " --> pdb=" O TYRHA 78 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N CYSHA 80 " --> pdb=" O CYSHA 134 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N ILEHA 61 " --> pdb=" O HISHA 79 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VALHA 81 " --> pdb=" O ILEHA 61 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N ASPHA 63 " --> pdb=" O VALHA 81 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THRHA 60 " --> pdb=" O VALHA 147 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILEHA 149 " --> pdb=" O THRHA 60 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEUHA 62 " --> pdb=" O ILEHA 149 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N GLNHA 151 " --> pdb=" O LEUHA 62 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N ILEHA 64 " --> pdb=" O GLNHA 151 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYRHA 285 " --> pdb=" O SERHA 281 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SERHA 281 " --> pdb=" O TYRHA 285 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N VALHA 287 " --> pdb=" O VALHA 279 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'HA' and resid 246 through 251 removed outlier: 6.890A pdb=" N ALAHA 189 " --> pdb=" O CYSHA 331 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N TYRHA 333 " --> pdb=" O ALAHA 189 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ALAHA 191 " --> pdb=" O TYRHA 333 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'HA' and resid 303 through 307 Processing sheet with id=AJ5, first strand: chain 'HA' and resid 414 through 415 Processing sheet with id=AJ6, first strand: chain 'JA' and resid 4 through 6 removed outlier: 6.139A pdb=" N VALJA 4 " --> pdb=" O GLUJA 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ6 Processing sheet with id=AJ7, first strand: chain 'JA' and resid 133 through 134 removed outlier: 8.294A pdb=" N CYSJA 134 " --> pdb=" O TYRJA 78 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N CYSJA 80 " --> pdb=" O CYSJA 134 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N ILEJA 61 " --> pdb=" O HISJA 79 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VALJA 81 " --> pdb=" O ILEJA 61 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ASPJA 63 " --> pdb=" O VALJA 81 " (cutoff:3.500A) removed outlier: 4.713A pdb=" N GLNJA 151 " --> pdb=" O ILEJA 64 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TYRJA 285 " --> pdb=" O SERJA 281 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SERJA 281 " --> pdb=" O TYRJA 285 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VALJA 287 " --> pdb=" O VALJA 279 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'JA' and resid 246 through 251 removed outlier: 4.112A pdb=" N TYRJA 333 " --> pdb=" O ALAJA 191 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'JA' and resid 303 through 307 Processing sheet with id=AK1, first strand: chain 'JA' and resid 414 through 415 Processing sheet with id=AK2, first strand: chain 'LA' and resid 4 through 6 removed outlier: 6.135A pdb=" N VALLA 4 " --> pdb=" O GLULA 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK2 Processing sheet with id=AK3, first strand: chain 'LA' and resid 133 through 134 removed outlier: 8.424A pdb=" N CYSLA 134 " --> pdb=" O TYRLA 78 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N CYSLA 80 " --> pdb=" O CYSLA 134 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ILELA 61 " --> pdb=" O HISLA 79 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VALLA 81 " --> pdb=" O ILELA 61 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N ASPLA 63 " --> pdb=" O VALLA 81 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N THRLA 60 " --> pdb=" O VALLA 147 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N ILELA 149 " --> pdb=" O THRLA 60 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEULA 62 " --> pdb=" O ILELA 149 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLNLA 151 " --> pdb=" O LEULA 62 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N ILELA 64 " --> pdb=" O GLNLA 151 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'LA' and resid 246 through 251 removed outlier: 4.192A pdb=" N TYRLA 333 " --> pdb=" O ALALA 191 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'LA' and resid 263 through 267 Processing sheet with id=AK6, first strand: chain 'LA' and resid 303 through 307 Processing sheet with id=AK7, first strand: chain 'LA' and resid 414 through 415 Processing sheet with id=AK8, first strand: chain 'NA' and resid 4 through 6 removed outlier: 6.103A pdb=" N VALNA 4 " --> pdb=" O GLUNA 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AK8 Processing sheet with id=AK9, first strand: chain 'NA' and resid 133 through 134 removed outlier: 8.383A pdb=" N CYSNA 134 " --> pdb=" O TYRNA 78 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N CYSNA 80 " --> pdb=" O CYSNA 134 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ILENA 61 " --> pdb=" O HISNA 79 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VALNA 81 " --> pdb=" O ILENA 61 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ASPNA 63 " --> pdb=" O VALNA 81 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N THRNA 60 " --> pdb=" O VALNA 147 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILENA 149 " --> pdb=" O THRNA 60 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEUNA 62 " --> pdb=" O ILENA 149 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N GLNNA 151 " --> pdb=" O LEUNA 62 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILENA 64 " --> pdb=" O GLNNA 151 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYRNA 285 " --> pdb=" O SERNA 281 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N SERNA 281 " --> pdb=" O TYRNA 285 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VALNA 287 " --> pdb=" O VALNA 279 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'NA' and resid 246 through 251 removed outlier: 6.891A pdb=" N ALANA 189 " --> pdb=" O CYSNA 331 " (cutoff:3.500A) removed outlier: 9.222A pdb=" N TYRNA 333 " --> pdb=" O ALANA 189 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ALANA 191 " --> pdb=" O TYRNA 333 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'NA' and resid 303 through 307 Processing sheet with id=AL3, first strand: chain 'NA' and resid 414 through 415 Processing sheet with id=AL4, first strand: chain 'PA' and resid 4 through 6 removed outlier: 6.137A pdb=" N VALPA 4 " --> pdb=" O GLUPA 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL4 Processing sheet with id=AL5, first strand: chain 'PA' and resid 133 through 134 removed outlier: 8.293A pdb=" N CYSPA 134 " --> pdb=" O TYRPA 78 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N CYSPA 80 " --> pdb=" O CYSPA 134 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ILEPA 61 " --> pdb=" O HISPA 79 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VALPA 81 " --> pdb=" O ILEPA 61 " (cutoff:3.500A) removed outlier: 6.091A pdb=" N ASPPA 63 " --> pdb=" O VALPA 81 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLNPA 151 " --> pdb=" O ILEPA 64 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TYRPA 285 " --> pdb=" O SERPA 281 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N SERPA 281 " --> pdb=" O TYRPA 285 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N VALPA 287 " --> pdb=" O VALPA 279 " (cutoff:3.500A) Processing sheet with id=AL6, first strand: chain 'PA' and resid 246 through 251 removed outlier: 4.112A pdb=" N TYRPA 333 " --> pdb=" O ALAPA 191 " (cutoff:3.500A) Processing sheet with id=AL7, first strand: chain 'PA' and resid 303 through 307 Processing sheet with id=AL8, first strand: chain 'PA' and resid 414 through 415 Processing sheet with id=AL9, first strand: chain 'RA' and resid 4 through 6 removed outlier: 6.135A pdb=" N VALRA 4 " --> pdb=" O GLURA 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AL9 Processing sheet with id=AM1, first strand: chain 'RA' and resid 133 through 134 removed outlier: 8.423A pdb=" N CYSRA 134 " --> pdb=" O TYRRA 78 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N CYSRA 80 " --> pdb=" O CYSRA 134 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ILERA 61 " --> pdb=" O HISRA 79 " (cutoff:3.500A) removed outlier: 7.073A pdb=" N VALRA 81 " --> pdb=" O ILERA 61 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ASPRA 63 " --> pdb=" O VALRA 81 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N THRRA 60 " --> pdb=" O VALRA 147 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N ILERA 149 " --> pdb=" O THRRA 60 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEURA 62 " --> pdb=" O ILERA 149 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N GLNRA 151 " --> pdb=" O LEURA 62 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N ILERA 64 " --> pdb=" O GLNRA 151 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TYRRA 285 " --> pdb=" O SERRA 281 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N SERRA 281 " --> pdb=" O TYRRA 285 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N VALRA 287 " --> pdb=" O VALRA 279 " (cutoff:3.500A) Processing sheet with id=AM2, first strand: chain 'RA' and resid 246 through 251 removed outlier: 4.193A pdb=" N TYRRA 333 " --> pdb=" O ALARA 191 " (cutoff:3.500A) Processing sheet with id=AM3, first strand: chain 'RA' and resid 303 through 307 Processing sheet with id=AM4, first strand: chain 'RA' and resid 414 through 415 Processing sheet with id=AM5, first strand: chain 'TA' and resid 4 through 6 removed outlier: 6.103A pdb=" N VALTA 4 " --> pdb=" O GLUTA 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AM5 Processing sheet with id=AM6, first strand: chain 'TA' and resid 133 through 134 removed outlier: 8.376A pdb=" N CYSTA 134 " --> pdb=" O TYRTA 78 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N CYSTA 80 " --> pdb=" O CYSTA 134 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N ILETA 61 " --> pdb=" O HISTA 79 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N VALTA 81 " --> pdb=" O ILETA 61 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ASPTA 63 " --> pdb=" O VALTA 81 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N THRTA 60 " --> pdb=" O VALTA 147 " (cutoff:3.500A) removed outlier: 7.888A pdb=" N ILETA 149 " --> pdb=" O THRTA 60 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N LEUTA 62 " --> pdb=" O ILETA 149 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N GLNTA 151 " --> pdb=" O LEUTA 62 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILETA 64 " --> pdb=" O GLNTA 151 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N TYRTA 285 " --> pdb=" O SERTA 281 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SERTA 281 " --> pdb=" O TYRTA 285 " (cutoff:3.500A) removed outlier: 6.443A pdb=" N VALTA 287 " --> pdb=" O VALTA 279 " (cutoff:3.500A) Processing sheet with id=AM7, first strand: chain 'TA' and resid 246 through 251 removed outlier: 6.890A pdb=" N ALATA 189 " --> pdb=" O CYSTA 331 " (cutoff:3.500A) removed outlier: 9.221A pdb=" N TYRTA 333 " --> pdb=" O ALATA 189 " (cutoff:3.500A) removed outlier: 8.121A pdb=" N ALATA 191 " --> pdb=" O TYRTA 333 " (cutoff:3.500A) Processing sheet with id=AM8, first strand: chain 'TA' and resid 303 through 307 Processing sheet with id=AM9, first strand: chain 'TA' and resid 414 through 415 Processing sheet with id=AN1, first strand: chain 'VA' and resid 4 through 6 removed outlier: 6.141A pdb=" N VALVA 4 " --> pdb=" O GLUVA 28 " (cutoff:3.500A) No H-bonds generated for sheet with id=AN1 Processing sheet with id=AN2, first strand: chain 'VA' and resid 133 through 134 removed outlier: 8.299A pdb=" N CYSVA 134 " --> pdb=" O TYRVA 78 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N CYSVA 80 " --> pdb=" O CYSVA 134 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILEVA 61 " --> pdb=" O HISVA 79 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VALVA 81 " --> pdb=" O ILEVA 61 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASPVA 63 " --> pdb=" O VALVA 81 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N GLNVA 151 " --> pdb=" O ILEVA 64 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N TYRVA 285 " --> pdb=" O SERVA 281 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N SERVA 281 " --> pdb=" O TYRVA 285 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VALVA 287 " --> pdb=" O VALVA 279 " (cutoff:3.500A) Processing sheet with id=AN3, first strand: chain 'VA' and resid 246 through 251 removed outlier: 4.108A pdb=" N TYRVA 333 " --> pdb=" O ALAVA 191 " (cutoff:3.500A) Processing sheet with id=AN4, first strand: chain 'VA' and resid 303 through 307 Processing sheet with id=AN5, first strand: chain 'VA' and resid 414 through 415 3458 hydrogen bonds defined for protein. 9886 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: 46.04 Time building geometry restraints manager: 30.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 27855 1.34 - 1.46: 14446 1.46 - 1.57: 44507 1.57 - 1.69: 0 1.69 - 1.81: 1056 Bond restraints: 87864 Sorted by residual: bond pdb=" N TYRVA 248 " pdb=" CA BTYRVA 248 " ideal model delta sigma weight residual 1.454 1.425 0.028 1.30e-02 5.92e+03 4.78e+00 bond pdb=" N TYR K 248 " pdb=" CA BTYR K 248 " ideal model delta sigma weight residual 1.454 1.425 0.028 1.30e-02 5.92e+03 4.75e+00 bond pdb=" N TYRPA 248 " pdb=" CA BTYRPA 248 " ideal model delta sigma weight residual 1.454 1.425 0.028 1.30e-02 5.92e+03 4.75e+00 bond pdb=" N TYRJA 248 " pdb=" CA BTYRJA 248 " ideal model delta sigma weight residual 1.454 1.426 0.028 1.30e-02 5.92e+03 4.71e+00 bond pdb=" N TYRBA 248 " pdb=" CA BTYRBA 248 " ideal model delta sigma weight residual 1.454 1.426 0.028 1.30e-02 5.92e+03 4.63e+00 ... (remaining 87859 not shown) Histogram of bond angle deviations from ideal: 99.22 - 106.19: 2570 106.19 - 113.15: 47857 113.15 - 120.11: 31177 120.11 - 127.08: 36733 127.08 - 134.04: 1063 Bond angle restraints: 119400 Sorted by residual: angle pdb=" N VALTA 122 " pdb=" CA VALTA 122 " pdb=" C VALTA 122 " ideal model delta sigma weight residual 113.39 108.24 5.15 1.47e+00 4.63e-01 1.23e+01 angle pdb=" N VAL O 122 " pdb=" CA VAL O 122 " pdb=" C VAL O 122 " ideal model delta sigma weight residual 113.39 108.25 5.14 1.47e+00 4.63e-01 1.22e+01 angle pdb=" N VALHA 122 " pdb=" CA VALHA 122 " pdb=" C VALHA 122 " ideal model delta sigma weight residual 113.39 108.26 5.13 1.47e+00 4.63e-01 1.22e+01 angle pdb=" N VAL C 122 " pdb=" CA VAL C 122 " pdb=" C VAL C 122 " ideal model delta sigma weight residual 113.39 108.27 5.12 1.47e+00 4.63e-01 1.21e+01 angle pdb=" N VALBA 122 " pdb=" CA VALBA 122 " pdb=" C VALBA 122 " ideal model delta sigma weight residual 113.39 108.27 5.12 1.47e+00 4.63e-01 1.21e+01 ... (remaining 119395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.09: 48789 16.09 - 32.19: 3583 32.19 - 48.28: 949 48.28 - 64.37: 135 64.37 - 80.46: 136 Dihedral angle restraints: 53592 sinusoidal: 20952 harmonic: 32640 Sorted by residual: dihedral pdb=" CA ASN V 209 " pdb=" C ASN V 209 " pdb=" N ILE V 210 " pdb=" CA ILE V 210 " ideal model delta harmonic sigma weight residual 180.00 158.38 21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA ASN O 209 " pdb=" C ASN O 209 " pdb=" N ILE O 210 " pdb=" CA ILE O 210 " ideal model delta harmonic sigma weight residual 180.00 158.40 21.60 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA ASNNA 209 " pdb=" C ASNNA 209 " pdb=" N ILENA 210 " pdb=" CA ILENA 210 " ideal model delta harmonic sigma weight residual 180.00 158.40 21.60 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 53589 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 10218 0.057 - 0.114: 2961 0.114 - 0.171: 309 0.171 - 0.227: 0 0.227 - 0.284: 24 Chirality restraints: 13512 Sorted by residual: chirality pdb=" CB ILERA 440 " pdb=" CA ILERA 440 " pdb=" CG1 ILERA 440 " pdb=" CG2 ILERA 440 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CB ILE G 440 " pdb=" CA ILE G 440 " pdb=" CG1 ILE G 440 " pdb=" CG2 ILE G 440 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" CB ILE S 440 " pdb=" CA ILE S 440 " pdb=" CG1 ILE S 440 " pdb=" CG2 ILE S 440 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 13509 not shown) Planarity restraints: 15288 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE V 391 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.67e+00 pdb=" C PHE V 391 " -0.028 2.00e-02 2.50e+03 pdb=" O PHE V 391 " 0.011 2.00e-02 2.50e+03 pdb=" N SER V 392 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE O 391 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.66e+00 pdb=" C PHE O 391 " -0.028 2.00e-02 2.50e+03 pdb=" O PHE O 391 " 0.011 2.00e-02 2.50e+03 pdb=" N SER O 392 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE C 391 " -0.008 2.00e-02 2.50e+03 1.63e-02 2.64e+00 pdb=" C PHE C 391 " 0.028 2.00e-02 2.50e+03 pdb=" O PHE C 391 " -0.011 2.00e-02 2.50e+03 pdb=" N SER C 392 " -0.009 2.00e-02 2.50e+03 ... (remaining 15285 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.61: 1233 2.61 - 3.18: 74792 3.18 - 3.76: 137813 3.76 - 4.33: 213443 4.33 - 4.90: 342719 Nonbonded interactions: 770000 Sorted by model distance: nonbonded pdb=" OE1 GLU Z 129 " pdb="ZN ZN Z1001 " model vdw 2.040 2.230 nonbonded pdb=" OE1 GLU M 129 " pdb="ZN ZN M1001 " model vdw 2.040 2.230 nonbonded pdb=" OE1 GLULA 129 " pdb="ZN ZNLA1001 " model vdw 2.041 2.230 nonbonded pdb=" OE1 GLU A 129 " pdb="ZN ZN A1001 " model vdw 2.041 2.230 nonbonded pdb=" OE1 GLU S 129 " pdb="ZN ZN S1001 " model vdw 2.041 2.230 ... (remaining 769995 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 'A' and (resid 3 through 40 or resid 42 through 185 or resid 187 through \ 218 or resid 220 through 247 or resid 249 through 288 or resid 290 through 388 o \ r resid 390 through 398 or resid 400 through 472 or resid 1001)) selection = (chain 'BA' and (resid 3 through 40 or resid 42 through 185 or resid 187 through \ 218 or resid 220 through 247 or resid 249 through 288 or resid 290 through 388 \ or resid 390 through 398 or resid 400 through 472 or resid 1001)) selection = (chain 'C' and (resid 3 through 40 or resid 42 through 185 or resid 187 through \ 218 or resid 220 through 247 or resid 249 through 288 or resid 290 through 388 o \ r resid 390 through 398 or resid 400 through 472 or resid 1001)) selection = (chain 'DA' and (resid 3 through 40 or resid 42 through 185 or resid 187 through \ 218 or resid 220 through 247 or resid 249 through 288 or resid 290 through 388 \ or resid 390 through 398 or resid 400 through 472 or resid 1001)) selection = (chain 'E' and (resid 3 through 40 or resid 42 through 185 or resid 187 through \ 218 or resid 220 through 247 or resid 249 through 288 or resid 290 through 388 o \ r resid 390 through 398 or resid 400 through 472 or resid 1001)) selection = (chain 'FA' and (resid 3 through 40 or resid 42 through 185 or resid 187 through \ 218 or resid 220 through 247 or resid 249 through 288 or resid 290 through 388 \ or resid 390 through 398 or resid 400 through 472 or resid 1001)) selection = (chain 'G' and (resid 3 through 40 or resid 42 through 185 or resid 187 through \ 218 or resid 220 through 247 or resid 249 through 288 or resid 290 through 388 o \ r resid 390 through 398 or resid 400 through 472 or resid 1001)) selection = (chain 'HA' and (resid 3 through 40 or resid 42 through 185 or resid 187 through \ 218 or resid 220 through 247 or resid 249 through 288 or resid 290 through 388 \ or resid 390 through 398 or resid 400 through 472 or resid 1001)) selection = (chain 'I' and (resid 3 through 40 or resid 42 through 185 or resid 187 through \ 218 or resid 220 through 247 or resid 249 through 288 or resid 290 through 388 o \ r resid 390 through 398 or resid 400 through 472 or resid 1001)) selection = (chain 'JA' and (resid 3 through 40 or resid 42 through 185 or resid 187 through \ 218 or resid 220 through 247 or resid 249 through 288 or resid 290 through 388 \ or resid 390 through 398 or resid 400 through 472 or resid 1001)) selection = (chain 'K' and (resid 3 through 40 or resid 42 through 185 or resid 187 through \ 218 or resid 220 through 247 or resid 249 through 288 or resid 290 through 388 o \ r resid 390 through 398 or resid 400 through 472 or resid 1001)) selection = (chain 'LA' and (resid 3 through 40 or resid 42 through 185 or resid 187 through \ 218 or resid 220 through 247 or resid 249 through 288 or resid 290 through 388 \ or resid 390 through 398 or resid 400 through 472 or resid 1001)) selection = (chain 'M' and (resid 3 through 40 or resid 42 through 185 or resid 187 through \ 218 or resid 220 through 247 or resid 249 through 288 or resid 290 through 388 o \ r resid 390 through 398 or resid 400 through 472 or resid 1001)) selection = (chain 'NA' and (resid 3 through 40 or resid 42 through 185 or resid 187 through \ 218 or resid 220 through 247 or resid 249 through 288 or resid 290 through 388 \ or resid 390 through 398 or resid 400 through 472 or resid 1001)) selection = (chain 'O' and (resid 3 through 40 or resid 42 through 185 or resid 187 through \ 218 or resid 220 through 247 or resid 249 through 288 or resid 290 through 388 o \ r resid 390 through 398 or resid 400 through 472 or resid 1001)) selection = (chain 'PA' and (resid 3 through 40 or resid 42 through 185 or resid 187 through \ 218 or resid 220 through 247 or resid 249 through 288 or resid 290 through 388 \ or resid 390 through 398 or resid 400 through 472 or resid 1001)) selection = (chain 'Q' and (resid 3 through 40 or resid 42 through 185 or resid 187 through \ 218 or resid 220 through 247 or resid 249 through 288 or resid 290 through 388 o \ r resid 390 through 398 or resid 400 through 472 or resid 1001)) selection = (chain 'RA' and (resid 3 through 40 or resid 42 through 185 or resid 187 through \ 218 or resid 220 through 247 or resid 249 through 288 or resid 290 through 388 \ or resid 390 through 398 or resid 400 through 472 or resid 1001)) selection = (chain 'S' and (resid 3 through 40 or resid 42 through 185 or resid 187 through \ 218 or resid 220 through 247 or resid 249 through 288 or resid 290 through 388 o \ r resid 390 through 398 or resid 400 through 472 or resid 1001)) selection = (chain 'TA' and (resid 3 through 40 or resid 42 through 185 or resid 187 through \ 218 or resid 220 through 247 or resid 249 through 288 or resid 290 through 388 \ or resid 390 through 398 or resid 400 through 472 or resid 1001)) selection = (chain 'V' and (resid 3 through 40 or resid 42 through 185 or resid 187 through \ 218 or resid 220 through 247 or resid 249 through 288 or resid 290 through 388 o \ r resid 390 through 398 or resid 400 through 472 or resid 1001)) selection = (chain 'VA' and (resid 3 through 40 or resid 42 through 185 or resid 187 through \ 218 or resid 220 through 247 or resid 249 through 288 or resid 290 through 388 \ or resid 390 through 398 or resid 400 through 472 or resid 1001)) selection = (chain 'X' and (resid 3 through 40 or resid 42 through 185 or resid 187 through \ 218 or resid 220 through 247 or resid 249 through 288 or resid 290 through 388 o \ r resid 390 through 398 or resid 400 through 472 or resid 1001)) selection = (chain 'Z' and (resid 3 through 40 or resid 42 through 185 or resid 187 through \ 218 or resid 220 through 247 or resid 249 through 288 or resid 290 through 388 o \ r resid 390 through 398 or resid 400 through 472 or resid 1001)) } 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=0.50 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.070 Extract box with map and model: 9.440 Check model and map are aligned: 0.960 Set scattering table: 0.600 Process input model: 255.350 Find NCS groups from input model: 5.190 Set up NCS constraints: 0.450 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: 0.020 Load rotamer database and sin/cos tables:11.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 285.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 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 : 0.007 0.050 87864 Z= 0.456 Angle : 0.735 10.930 119400 Z= 0.416 Chirality : 0.050 0.284 13512 Planarity : 0.005 0.039 15288 Dihedral : 13.189 80.465 32568 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 0.52 % Allowed : 3.98 % Favored : 95.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.59 (0.06), residues: 11016 helix: -2.77 (0.06), residues: 3504 sheet: -0.68 (0.10), residues: 2016 loop : -2.80 (0.07), residues: 5496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Z 421 HIS 0.004 0.001 HIS A 37 PHE 0.020 0.002 PHE C 183 TYR 0.021 0.002 TYR Q 382 ARG 0.005 0.001 ARGLA 171 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22032 Ramachandran restraints generated. 11016 Oldfield, 0 Emsley, 11016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22032 Ramachandran restraints generated. 11016 Oldfield, 0 Emsley, 11016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1159 residues out of total 9240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1159 time to evaluate : 7.488 Fit side-chains REVERT: A 59 SER cc_start: 0.7852 (m) cc_final: 0.7508 (p) REVERT: A 73 MET cc_start: 0.6383 (tpp) cc_final: 0.6112 (tpp) REVERT: A 228 MET cc_start: 0.7144 (ptt) cc_final: 0.6929 (pp-130) REVERT: A 342 MET cc_start: 0.8946 (mmm) cc_final: 0.8605 (mmp) REVERT: A 364 GLN cc_start: 0.7748 (pt0) cc_final: 0.7274 (mm-40) REVERT: C 228 MET cc_start: 0.7238 (ptt) cc_final: 0.6760 (pp-130) REVERT: C 250 GLU cc_start: 0.7057 (mm-30) cc_final: 0.6831 (mm-30) REVERT: E 59 SER cc_start: 0.7544 (m) cc_final: 0.7328 (p) REVERT: E 250 GLU cc_start: 0.7042 (mm-30) cc_final: 0.6736 (mm-30) REVERT: E 364 GLN cc_start: 0.7885 (pt0) cc_final: 0.7324 (mm-40) REVERT: G 59 SER cc_start: 0.7869 (m) cc_final: 0.7526 (p) REVERT: G 73 MET cc_start: 0.6399 (tpp) cc_final: 0.6123 (tpp) REVERT: G 227 ILE cc_start: 0.6608 (mt) cc_final: 0.6407 (pp) REVERT: G 228 MET cc_start: 0.7147 (ptt) cc_final: 0.6002 (tpt) REVERT: G 342 MET cc_start: 0.8946 (mmm) cc_final: 0.8610 (mmp) REVERT: G 364 GLN cc_start: 0.7755 (pt0) cc_final: 0.7270 (mm-40) REVERT: I 228 MET cc_start: 0.7243 (ptt) cc_final: 0.6767 (pp-130) REVERT: I 423 PHE cc_start: 0.8422 (p90) cc_final: 0.8136 (p90) REVERT: K 250 GLU cc_start: 0.7033 (mm-30) cc_final: 0.6722 (mm-30) REVERT: K 364 GLN cc_start: 0.7866 (pt0) cc_final: 0.7320 (mm-40) REVERT: M 59 SER cc_start: 0.7853 (m) cc_final: 0.7505 (p) REVERT: M 73 MET cc_start: 0.6377 (tpp) cc_final: 0.6106 (tpp) REVERT: M 228 MET cc_start: 0.7155 (ptt) cc_final: 0.6014 (tpt) REVERT: M 277 ASP cc_start: 0.7446 (t0) cc_final: 0.7221 (t70) REVERT: M 342 MET cc_start: 0.8941 (mmm) cc_final: 0.8601 (mmp) REVERT: M 364 GLN cc_start: 0.7718 (pt0) cc_final: 0.7255 (mm-40) REVERT: O 228 MET cc_start: 0.7234 (ptt) cc_final: 0.6760 (pp-130) REVERT: O 229 ARG cc_start: 0.6199 (ptm160) cc_final: 0.5993 (ptm160) REVERT: O 423 PHE cc_start: 0.8372 (p90) cc_final: 0.8091 (p90) REVERT: Q 59 SER cc_start: 0.7577 (m) cc_final: 0.7353 (p) REVERT: Q 250 GLU cc_start: 0.7069 (mm-30) cc_final: 0.6751 (mm-30) REVERT: Q 364 GLN cc_start: 0.7874 (pt0) cc_final: 0.7323 (mm-40) REVERT: S 59 SER cc_start: 0.7764 (m) cc_final: 0.7388 (p) REVERT: S 73 MET cc_start: 0.6386 (tpp) cc_final: 0.6116 (tpp) REVERT: S 228 MET cc_start: 0.7146 (ptt) cc_final: 0.5994 (tpt) REVERT: S 342 MET cc_start: 0.8944 (mmm) cc_final: 0.8606 (mmp) REVERT: S 364 GLN cc_start: 0.7747 (pt0) cc_final: 0.7274 (mm-40) REVERT: V 228 MET cc_start: 0.7244 (ptt) cc_final: 0.6765 (pp-130) REVERT: V 423 PHE cc_start: 0.8423 (p90) cc_final: 0.8133 (p90) REVERT: X 59 SER cc_start: 0.7564 (m) cc_final: 0.7296 (p) REVERT: X 250 GLU cc_start: 0.7083 (mm-30) cc_final: 0.6774 (mm-30) REVERT: X 364 GLN cc_start: 0.7869 (pt0) cc_final: 0.7319 (mm-40) REVERT: Z 59 SER cc_start: 0.7855 (m) cc_final: 0.7510 (p) REVERT: Z 73 MET cc_start: 0.6394 (tpp) cc_final: 0.6125 (tpp) REVERT: Z 228 MET cc_start: 0.7159 (ptt) cc_final: 0.6017 (tpt) REVERT: Z 342 MET cc_start: 0.8949 (mmm) cc_final: 0.8604 (mmp) REVERT: Z 364 GLN cc_start: 0.7763 (pt0) cc_final: 0.7264 (mm-40) REVERT: BA 228 MET cc_start: 0.7218 (ptt) cc_final: 0.6747 (pp-130) REVERT: BA 423 PHE cc_start: 0.8388 (p90) cc_final: 0.8106 (p90) REVERT: DA 59 SER cc_start: 0.7538 (m) cc_final: 0.7275 (p) REVERT: DA 250 GLU cc_start: 0.7045 (mm-30) cc_final: 0.6734 (mm-30) REVERT: DA 364 GLN cc_start: 0.7877 (pt0) cc_final: 0.7322 (mm-40) REVERT: FA 59 SER cc_start: 0.7862 (m) cc_final: 0.7518 (p) REVERT: FA 73 MET cc_start: 0.6371 (tpp) cc_final: 0.6101 (tpp) REVERT: FA 228 MET cc_start: 0.7163 (ptt) cc_final: 0.6015 (tpt) REVERT: FA 342 MET cc_start: 0.8937 (mmm) cc_final: 0.8593 (mmp) REVERT: FA 364 GLN cc_start: 0.7752 (pt0) cc_final: 0.7268 (mm-40) REVERT: HA 228 MET cc_start: 0.7217 (ptt) cc_final: 0.6744 (pp-130) REVERT: HA 423 PHE cc_start: 0.8365 (p90) cc_final: 0.8089 (p90) REVERT: JA 59 SER cc_start: 0.7544 (m) cc_final: 0.7330 (p) REVERT: JA 250 GLU cc_start: 0.7018 (mm-30) cc_final: 0.6719 (mm-30) REVERT: JA 364 GLN cc_start: 0.7878 (pt0) cc_final: 0.7323 (mm-40) REVERT: LA 59 SER cc_start: 0.7844 (m) cc_final: 0.7504 (p) REVERT: LA 73 MET cc_start: 0.6390 (tpp) cc_final: 0.6120 (tpp) REVERT: LA 227 ILE cc_start: 0.6612 (mt) cc_final: 0.6403 (pp) REVERT: LA 228 MET cc_start: 0.7172 (ptt) cc_final: 0.5986 (tpt) REVERT: LA 342 MET cc_start: 0.8947 (mmm) cc_final: 0.8611 (mmp) REVERT: LA 364 GLN cc_start: 0.7762 (pt0) cc_final: 0.7266 (mm-40) REVERT: NA 228 MET cc_start: 0.7240 (ptt) cc_final: 0.6763 (pp-130) REVERT: NA 423 PHE cc_start: 0.8381 (p90) cc_final: 0.8093 (p90) REVERT: PA 250 GLU cc_start: 0.7019 (mm-30) cc_final: 0.6715 (mm-30) REVERT: PA 364 GLN cc_start: 0.7869 (pt0) cc_final: 0.7323 (mm-40) REVERT: RA 59 SER cc_start: 0.7870 (m) cc_final: 0.7527 (p) REVERT: RA 73 MET cc_start: 0.6391 (tpp) cc_final: 0.6122 (tpp) REVERT: RA 228 MET cc_start: 0.7156 (ptt) cc_final: 0.6007 (tpt) REVERT: RA 342 MET cc_start: 0.8941 (mmm) cc_final: 0.8601 (mmp) REVERT: RA 364 GLN cc_start: 0.7749 (pt0) cc_final: 0.7268 (mm-40) REVERT: TA 228 MET cc_start: 0.7251 (ptt) cc_final: 0.6779 (pp-130) REVERT: TA 229 ARG cc_start: 0.6217 (ptm160) cc_final: 0.6015 (ptm160) REVERT: TA 423 PHE cc_start: 0.8394 (p90) cc_final: 0.8109 (p90) REVERT: VA 59 SER cc_start: 0.7554 (m) cc_final: 0.7281 (p) REVERT: VA 250 GLU cc_start: 0.7095 (mm-30) cc_final: 0.6784 (mm-30) REVERT: VA 364 GLN cc_start: 0.7876 (pt0) cc_final: 0.7328 (mm-40) outliers start: 0 outliers final: 0 residues processed: 1159 average time/residue: 1.6491 time to fit residues: 2569.5688 Evaluate side-chains 942 residues out of total 9240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 942 time to evaluate : 7.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 911 optimal weight: 5.9990 chunk 818 optimal weight: 5.9990 chunk 454 optimal weight: 1.9990 chunk 279 optimal weight: 5.9990 chunk 552 optimal weight: 0.0670 chunk 437 optimal weight: 5.9990 chunk 846 optimal weight: 3.9990 chunk 327 optimal weight: 0.0980 chunk 514 optimal weight: 1.9990 chunk 630 optimal weight: 10.0000 chunk 980 optimal weight: 5.9990 overall best weight: 1.6324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 ASN A 95 ASN A 157 HIS A 165 GLN A 186 ASN B A 203 GLN ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 389 GLN A A 441 GLN C 39 ASN C 157 HIS C 165 GLN C 186 ASN B C 203 GLN ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 389 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** C 441 GLN E 39 ASN E 157 HIS E 165 GLN E 186 ASN B E 203 GLN E 389 GLN A E 426 GLN G 39 ASN G 95 ASN G 157 HIS G 165 GLN G 186 ASN B G 203 GLN ** G 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 389 GLN A G 441 GLN I 39 ASN I 157 HIS I 165 GLN I 186 ASN B I 203 GLN ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 389 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** I 441 GLN K 39 ASN K 157 HIS K 165 GLN K 186 ASN B K 203 GLN K 389 GLN A K 426 GLN M 39 ASN M 95 ASN M 157 HIS M 165 GLN M 186 ASN B M 203 GLN ** M 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 389 GLN A M 441 GLN O 39 ASN O 157 HIS O 165 GLN O 186 ASN B O 203 GLN ** O 389 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** O 441 GLN Q 39 ASN Q 157 HIS Q 165 GLN Q 186 ASN B Q 203 GLN Q 389 GLN A Q 426 GLN S 39 ASN S 95 ASN S 157 HIS S 165 GLN S 186 ASN B S 203 GLN ** S 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 389 GLN A S 426 GLN S 441 GLN V 39 ASN V 157 HIS V 165 GLN V 186 ASN B V 203 GLN ** V 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 389 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** V 441 GLN X 39 ASN X 157 HIS X 165 GLN X 186 ASN B X 203 GLN X 389 GLN A X 426 GLN Z 39 ASN Z 95 ASN Z 157 HIS Z 165 GLN Z 186 ASN B Z 203 GLN ** Z 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 389 GLN A Z 441 GLN BA 39 ASN BA 157 HIS BA 165 GLN BA 186 ASN B BA 203 GLN ** BA 389 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** BA 441 GLN DA 39 ASN DA 157 HIS DA 165 GLN DA 186 ASN B DA 203 GLN DA 389 GLN A DA 426 GLN FA 39 ASN FA 95 ASN FA 157 HIS FA 165 GLN FA 186 ASN B FA 203 GLN ** FA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 389 GLN A FA 441 GLN HA 39 ASN HA 157 HIS HA 165 GLN HA 186 ASN B HA 203 GLN ** HA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 389 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** HA 441 GLN JA 39 ASN JA 157 HIS JA 165 GLN JA 186 ASN B JA 203 GLN JA 389 GLN A JA 426 GLN LA 39 ASN LA 95 ASN LA 157 HIS LA 165 GLN LA 186 ASN B LA 203 GLN ** LA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 389 GLN A LA 441 GLN NA 39 ASN NA 157 HIS NA 165 GLN NA 186 ASN B NA 203 GLN ** NA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NA 389 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** NA 441 GLN PA 39 ASN PA 157 HIS PA 165 GLN PA 186 ASN B PA 203 GLN PA 389 GLN A PA 426 GLN RA 39 ASN RA 95 ASN RA 157 HIS RA 165 GLN RA 186 ASN B RA 203 GLN ** RA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** RA 389 GLN A RA 441 GLN TA 39 ASN TA 157 HIS TA 165 GLN TA 186 ASN B TA 203 GLN ** TA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TA 389 GLN A ** both conformations clash, **PLEASE CHECK MANUALLY** TA 441 GLN VA 39 ASN VA 157 HIS VA 165 GLN VA 186 ASN B VA 203 GLN VA 389 GLN A VA 426 GLN Total number of N/Q/H flips: 169 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 87864 Z= 0.174 Angle : 0.569 8.922 119400 Z= 0.296 Chirality : 0.043 0.177 13512 Planarity : 0.005 0.039 15288 Dihedral : 4.555 18.880 12264 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.94 % Allowed : 9.01 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.07), residues: 11016 helix: -0.61 (0.08), residues: 3576 sheet: -0.22 (0.10), residues: 2184 loop : -2.29 (0.08), residues: 5256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 394 HIS 0.003 0.001 HIS C 308 PHE 0.024 0.002 PHE Z 423 TYR 0.013 0.001 TYR Q 382 ARG 0.003 0.001 ARG G 411 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22032 Ramachandran restraints generated. 11016 Oldfield, 0 Emsley, 11016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22032 Ramachandran restraints generated. 11016 Oldfield, 0 Emsley, 11016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1140 residues out of total 9240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1077 time to evaluate : 7.538 Fit side-chains REVERT: A 73 MET cc_start: 0.6421 (tpp) cc_final: 0.6157 (tpp) REVERT: A 228 MET cc_start: 0.7064 (ptt) cc_final: 0.6832 (pp-130) REVERT: A 342 MET cc_start: 0.8934 (mmm) cc_final: 0.8604 (mmp) REVERT: A 364 GLN cc_start: 0.7742 (pt0) cc_final: 0.7303 (mm-40) REVERT: C 133 PHE cc_start: 0.7328 (t80) cc_final: 0.6934 (t80) REVERT: C 228 MET cc_start: 0.7190 (ptt) cc_final: 0.6730 (pp-130) REVERT: E 250 GLU cc_start: 0.6800 (mm-30) cc_final: 0.6573 (mm-30) REVERT: E 364 GLN cc_start: 0.7825 (pt0) cc_final: 0.7323 (mm-40) REVERT: G 73 MET cc_start: 0.6434 (tpp) cc_final: 0.6173 (tpp) REVERT: G 228 MET cc_start: 0.7104 (ptt) cc_final: 0.6851 (pp-130) REVERT: G 342 MET cc_start: 0.8934 (mmm) cc_final: 0.8610 (mmp) REVERT: G 364 GLN cc_start: 0.7749 (pt0) cc_final: 0.7303 (mm-40) REVERT: I 228 MET cc_start: 0.7194 (ptt) cc_final: 0.6741 (pp-130) REVERT: I 423 PHE cc_start: 0.8423 (p90) cc_final: 0.8213 (p90) REVERT: K 250 GLU cc_start: 0.6779 (mm-30) cc_final: 0.6551 (mm-30) REVERT: K 364 GLN cc_start: 0.7801 (pt0) cc_final: 0.7317 (mm-40) REVERT: M 73 MET cc_start: 0.6416 (tpp) cc_final: 0.6150 (tpp) REVERT: M 228 MET cc_start: 0.7186 (ptt) cc_final: 0.6894 (pp-130) REVERT: M 277 ASP cc_start: 0.7587 (t0) cc_final: 0.7352 (t70) REVERT: M 342 MET cc_start: 0.8931 (mmm) cc_final: 0.8607 (mmp) REVERT: M 364 GLN cc_start: 0.7714 (pt0) cc_final: 0.7290 (mm-40) REVERT: O 133 PHE cc_start: 0.7305 (t80) cc_final: 0.6913 (t80) REVERT: O 228 MET cc_start: 0.7163 (ptt) cc_final: 0.6708 (pp-130) REVERT: O 423 PHE cc_start: 0.8376 (p90) cc_final: 0.8157 (p90) REVERT: Q 250 GLU cc_start: 0.6811 (mm-30) cc_final: 0.6575 (mm-30) REVERT: Q 364 GLN cc_start: 0.7810 (pt0) cc_final: 0.7326 (mm-40) REVERT: S 73 MET cc_start: 0.6421 (tpp) cc_final: 0.6160 (tpp) REVERT: S 228 MET cc_start: 0.7174 (ptt) cc_final: 0.6870 (pp-130) REVERT: S 342 MET cc_start: 0.8935 (mmm) cc_final: 0.8604 (mmp) REVERT: S 364 GLN cc_start: 0.7745 (pt0) cc_final: 0.7301 (mm-40) REVERT: V 228 MET cc_start: 0.7178 (ptt) cc_final: 0.6714 (pp-130) REVERT: V 423 PHE cc_start: 0.8422 (p90) cc_final: 0.8202 (p90) REVERT: X 250 GLU cc_start: 0.6835 (mm-30) cc_final: 0.6601 (mm-30) REVERT: X 364 GLN cc_start: 0.7816 (pt0) cc_final: 0.7316 (mm-40) REVERT: Z 73 MET cc_start: 0.6421 (tpp) cc_final: 0.6161 (tpp) REVERT: Z 228 MET cc_start: 0.7189 (ptt) cc_final: 0.6884 (pp-130) REVERT: Z 342 MET cc_start: 0.8936 (mmm) cc_final: 0.8608 (mmp) REVERT: Z 364 GLN cc_start: 0.7753 (pt0) cc_final: 0.7299 (mm-40) REVERT: BA 228 MET cc_start: 0.7153 (ptt) cc_final: 0.6693 (pp-130) REVERT: BA 423 PHE cc_start: 0.8392 (p90) cc_final: 0.8177 (p90) REVERT: DA 250 GLU cc_start: 0.6793 (mm-30) cc_final: 0.6562 (mm-30) REVERT: DA 364 GLN cc_start: 0.7820 (pt0) cc_final: 0.7322 (mm-40) REVERT: FA 73 MET cc_start: 0.6407 (tpp) cc_final: 0.6145 (tpp) REVERT: FA 228 MET cc_start: 0.7191 (ptt) cc_final: 0.6885 (pp-130) REVERT: FA 342 MET cc_start: 0.8918 (mmm) cc_final: 0.8597 (mmp) REVERT: FA 364 GLN cc_start: 0.7747 (pt0) cc_final: 0.7305 (mm-40) REVERT: HA 133 PHE cc_start: 0.7330 (t80) cc_final: 0.6937 (t80) REVERT: HA 228 MET cc_start: 0.7149 (ptt) cc_final: 0.6692 (pp-130) REVERT: HA 423 PHE cc_start: 0.8377 (p90) cc_final: 0.8164 (p90) REVERT: JA 250 GLU cc_start: 0.6767 (mm-30) cc_final: 0.6541 (mm-30) REVERT: JA 364 GLN cc_start: 0.7819 (pt0) cc_final: 0.7327 (mm-40) REVERT: LA 73 MET cc_start: 0.6434 (tpp) cc_final: 0.6165 (tpp) REVERT: LA 228 MET cc_start: 0.7063 (ptt) cc_final: 0.6815 (pp-130) REVERT: LA 342 MET cc_start: 0.8940 (mmm) cc_final: 0.8609 (mmp) REVERT: LA 364 GLN cc_start: 0.7760 (pt0) cc_final: 0.7301 (mm-40) REVERT: NA 228 MET cc_start: 0.7191 (ptt) cc_final: 0.6740 (pp-130) REVERT: NA 423 PHE cc_start: 0.8377 (p90) cc_final: 0.8160 (p90) REVERT: PA 250 GLU cc_start: 0.6767 (mm-30) cc_final: 0.6542 (mm-30) REVERT: PA 364 GLN cc_start: 0.7807 (pt0) cc_final: 0.7326 (mm-40) REVERT: RA 73 MET cc_start: 0.6433 (tpp) cc_final: 0.6169 (tpp) REVERT: RA 228 MET cc_start: 0.7176 (ptt) cc_final: 0.6869 (pp-130) REVERT: RA 342 MET cc_start: 0.8925 (mmm) cc_final: 0.8609 (mmp) REVERT: RA 364 GLN cc_start: 0.7740 (pt0) cc_final: 0.7304 (mm-40) REVERT: TA 228 MET cc_start: 0.7160 (ptt) cc_final: 0.6710 (pp-130) REVERT: TA 423 PHE cc_start: 0.8394 (p90) cc_final: 0.8177 (p90) REVERT: VA 250 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6612 (mm-30) REVERT: VA 364 GLN cc_start: 0.7815 (pt0) cc_final: 0.7326 (mm-40) outliers start: 63 outliers final: 24 residues processed: 1084 average time/residue: 1.5848 time to fit residues: 2345.0095 Evaluate side-chains 992 residues out of total 9240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 968 time to evaluate : 7.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain I residue 277 ASP Chi-restraints excluded: chain K residue 9 ASP Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain O residue 277 ASP Chi-restraints excluded: chain Q residue 9 ASP Chi-restraints excluded: chain Q residue 26 GLU Chi-restraints excluded: chain V residue 277 ASP Chi-restraints excluded: chain X residue 9 ASP Chi-restraints excluded: chain X residue 26 GLU Chi-restraints excluded: chain BA residue 277 ASP Chi-restraints excluded: chain DA residue 9 ASP Chi-restraints excluded: chain DA residue 26 GLU Chi-restraints excluded: chain HA residue 277 ASP Chi-restraints excluded: chain JA residue 9 ASP Chi-restraints excluded: chain JA residue 26 GLU Chi-restraints excluded: chain NA residue 277 ASP Chi-restraints excluded: chain PA residue 9 ASP Chi-restraints excluded: chain PA residue 26 GLU Chi-restraints excluded: chain TA residue 277 ASP Chi-restraints excluded: chain VA residue 9 ASP Chi-restraints excluded: chain VA residue 26 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 545 optimal weight: 30.0000 chunk 304 optimal weight: 9.9990 chunk 816 optimal weight: 2.9990 chunk 667 optimal weight: 0.8980 chunk 270 optimal weight: 20.0000 chunk 982 optimal weight: 6.9990 chunk 1061 optimal weight: 4.9990 chunk 875 optimal weight: 5.9990 chunk 974 optimal weight: 20.0000 chunk 334 optimal weight: 6.9990 chunk 788 optimal weight: 10.0000 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN A 259 HIS ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 441 GLN C 259 HIS ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN A E 53 GLN E 259 HIS G 53 GLN ** G 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 259 HIS G 441 GLN I 259 HIS ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 389 GLN A K 53 GLN K 259 HIS M 53 GLN M 259 HIS ** M 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 441 GLN O 259 HIS ** O 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 389 GLN A Q 53 GLN Q 259 HIS S 53 GLN ** S 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 259 HIS ** S 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 441 GLN V 259 HIS ** V 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 389 GLN A X 53 GLN X 259 HIS Z 53 GLN Z 259 HIS ** Z 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 441 GLN BA 259 HIS ** BA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 389 GLN A DA 53 GLN DA 259 HIS FA 53 GLN FA 259 HIS ** FA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FA 441 GLN HA 259 HIS ** HA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HA 389 GLN A JA 53 GLN JA 259 HIS LA 53 GLN LA 259 HIS ** LA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** LA 441 GLN NA 259 HIS ** NA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 389 GLN A PA 53 GLN PA 259 HIS RA 53 GLN ** RA 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** RA 259 HIS ** RA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** RA 441 GLN TA 259 HIS ** TA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TA 389 GLN A VA 53 GLN VA 259 HIS Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 87864 Z= 0.301 Angle : 0.612 8.861 119400 Z= 0.315 Chirality : 0.046 0.203 13512 Planarity : 0.005 0.040 15288 Dihedral : 4.688 21.342 12264 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.21 % Allowed : 10.14 % Favored : 88.66 % 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: -1.42 (0.08), residues: 11016 helix: 0.04 (0.09), residues: 3576 sheet: 0.12 (0.11), residues: 2136 loop : -2.14 (0.08), residues: 5304 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP I 394 HIS 0.003 0.001 HIS Z 164 PHE 0.028 0.002 PHE S 423 TYR 0.017 0.002 TYRJA 382 ARG 0.004 0.001 ARGFA 411 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22032 Ramachandran restraints generated. 11016 Oldfield, 0 Emsley, 11016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22032 Ramachandran restraints generated. 11016 Oldfield, 0 Emsley, 11016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1086 residues out of total 9240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 998 time to evaluate : 7.576 Fit side-chains REVERT: A 73 MET cc_start: 0.6405 (tpp) cc_final: 0.6157 (tpp) REVERT: A 342 MET cc_start: 0.8928 (mmm) cc_final: 0.8522 (mmp) REVERT: A 364 GLN cc_start: 0.7749 (pt0) cc_final: 0.7295 (mm-40) REVERT: C 133 PHE cc_start: 0.7346 (t80) cc_final: 0.7007 (t80) REVERT: C 228 MET cc_start: 0.7207 (ptt) cc_final: 0.6770 (pp-130) REVERT: E 250 GLU cc_start: 0.6927 (mm-30) cc_final: 0.6624 (mm-30) REVERT: E 364 GLN cc_start: 0.7810 (pt0) cc_final: 0.7330 (mm-40) REVERT: G 73 MET cc_start: 0.6431 (tpp) cc_final: 0.6168 (tpp) REVERT: G 228 MET cc_start: 0.7096 (ptt) cc_final: 0.6893 (pp-130) REVERT: G 342 MET cc_start: 0.8926 (mmm) cc_final: 0.8521 (mmp) REVERT: G 364 GLN cc_start: 0.7757 (pt0) cc_final: 0.7293 (mm-40) REVERT: I 133 PHE cc_start: 0.7307 (t80) cc_final: 0.6947 (t80) REVERT: I 228 MET cc_start: 0.7203 (ptt) cc_final: 0.6775 (pp-130) REVERT: K 250 GLU cc_start: 0.6930 (mm-30) cc_final: 0.6639 (mm-30) REVERT: K 364 GLN cc_start: 0.7786 (pt0) cc_final: 0.7325 (mm-40) REVERT: M 73 MET cc_start: 0.6396 (tpp) cc_final: 0.6144 (tpp) REVERT: M 228 MET cc_start: 0.7262 (ptt) cc_final: 0.6975 (pp-130) REVERT: M 277 ASP cc_start: 0.7575 (t0) cc_final: 0.7346 (t70) REVERT: M 342 MET cc_start: 0.8926 (mmm) cc_final: 0.8516 (mmp) REVERT: M 364 GLN cc_start: 0.7744 (pt0) cc_final: 0.7281 (mm-40) REVERT: O 133 PHE cc_start: 0.7328 (t80) cc_final: 0.6990 (t80) REVERT: O 228 MET cc_start: 0.7199 (ptt) cc_final: 0.6771 (pp-130) REVERT: Q 250 GLU cc_start: 0.6940 (mm-30) cc_final: 0.6645 (mm-30) REVERT: Q 364 GLN cc_start: 0.7805 (pt0) cc_final: 0.7327 (mm-40) REVERT: S 73 MET cc_start: 0.6424 (tpp) cc_final: 0.6163 (tpp) REVERT: S 228 MET cc_start: 0.7230 (ptt) cc_final: 0.6976 (pp-130) REVERT: S 342 MET cc_start: 0.8927 (mmm) cc_final: 0.8512 (mmp) REVERT: S 364 GLN cc_start: 0.7752 (pt0) cc_final: 0.7294 (mm-40) REVERT: V 133 PHE cc_start: 0.7348 (t80) cc_final: 0.6994 (t80) REVERT: V 228 MET cc_start: 0.7228 (ptt) cc_final: 0.6795 (pp-130) REVERT: X 250 GLU cc_start: 0.6967 (mm-30) cc_final: 0.6675 (mm-30) REVERT: X 364 GLN cc_start: 0.7801 (pt0) cc_final: 0.7324 (mm-40) REVERT: Z 73 MET cc_start: 0.6412 (tpp) cc_final: 0.6163 (tpp) REVERT: Z 228 MET cc_start: 0.7229 (ptt) cc_final: 0.6964 (pp-130) REVERT: Z 342 MET cc_start: 0.8932 (mmm) cc_final: 0.8521 (mmp) REVERT: Z 364 GLN cc_start: 0.7763 (pt0) cc_final: 0.7289 (mm-40) REVERT: BA 133 PHE cc_start: 0.7338 (t80) cc_final: 0.6983 (t80) REVERT: BA 228 MET cc_start: 0.7190 (ptt) cc_final: 0.6759 (pp-130) REVERT: DA 250 GLU cc_start: 0.6931 (mm-30) cc_final: 0.6636 (mm-30) REVERT: DA 364 GLN cc_start: 0.7804 (pt0) cc_final: 0.7330 (mm-40) REVERT: FA 73 MET cc_start: 0.6396 (tpp) cc_final: 0.6146 (tpp) REVERT: FA 228 MET cc_start: 0.7247 (ptt) cc_final: 0.6984 (pp-130) REVERT: FA 342 MET cc_start: 0.8918 (mmm) cc_final: 0.8517 (mmp) REVERT: FA 364 GLN cc_start: 0.7749 (pt0) cc_final: 0.7293 (mm-40) REVERT: HA 133 PHE cc_start: 0.7349 (t80) cc_final: 0.7012 (t80) REVERT: HA 228 MET cc_start: 0.7193 (ptt) cc_final: 0.6760 (pp-130) REVERT: JA 250 GLU cc_start: 0.6902 (mm-30) cc_final: 0.6619 (mm-30) REVERT: JA 364 GLN cc_start: 0.7812 (pt0) cc_final: 0.7327 (mm-40) REVERT: LA 73 MET cc_start: 0.6435 (tpp) cc_final: 0.6170 (tpp) REVERT: LA 342 MET cc_start: 0.8929 (mmm) cc_final: 0.8523 (mmp) REVERT: LA 364 GLN cc_start: 0.7766 (pt0) cc_final: 0.7294 (mm-40) REVERT: NA 228 MET cc_start: 0.7205 (ptt) cc_final: 0.6777 (pp-130) REVERT: PA 250 GLU cc_start: 0.6903 (mm-30) cc_final: 0.6614 (mm-30) REVERT: PA 364 GLN cc_start: 0.7801 (pt0) cc_final: 0.7326 (mm-40) REVERT: RA 73 MET cc_start: 0.6436 (tpp) cc_final: 0.6174 (tpp) REVERT: RA 228 MET cc_start: 0.7234 (ptt) cc_final: 0.6973 (pp-130) REVERT: RA 342 MET cc_start: 0.8926 (mmm) cc_final: 0.8524 (mmp) REVERT: RA 364 GLN cc_start: 0.7774 (pt0) cc_final: 0.7305 (mm-40) REVERT: TA 133 PHE cc_start: 0.7338 (t80) cc_final: 0.6983 (t80) REVERT: TA 228 MET cc_start: 0.7197 (ptt) cc_final: 0.6781 (pp-130) REVERT: VA 250 GLU cc_start: 0.6964 (mm-30) cc_final: 0.6674 (mm-30) REVERT: VA 364 GLN cc_start: 0.7803 (pt0) cc_final: 0.7334 (mm-40) outliers start: 88 outliers final: 62 residues processed: 1026 average time/residue: 1.6485 time to fit residues: 2279.6530 Evaluate side-chains 1045 residues out of total 9240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 983 time to evaluate : 7.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 277 ASP Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain K residue 9 ASP Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 277 ASP Chi-restraints excluded: chain K residue 348 THR Chi-restraints excluded: chain O residue 28 GLU Chi-restraints excluded: chain O residue 277 ASP Chi-restraints excluded: chain O residue 348 THR Chi-restraints excluded: chain Q residue 9 ASP Chi-restraints excluded: chain Q residue 26 GLU Chi-restraints excluded: chain Q residue 277 ASP Chi-restraints excluded: chain Q residue 348 THR Chi-restraints excluded: chain V residue 28 GLU Chi-restraints excluded: chain V residue 277 ASP Chi-restraints excluded: chain V residue 348 THR Chi-restraints excluded: chain X residue 9 ASP Chi-restraints excluded: chain X residue 26 GLU Chi-restraints excluded: chain X residue 277 ASP Chi-restraints excluded: chain X residue 348 THR Chi-restraints excluded: chain BA residue 28 GLU Chi-restraints excluded: chain BA residue 277 ASP Chi-restraints excluded: chain BA residue 348 THR Chi-restraints excluded: chain DA residue 9 ASP Chi-restraints excluded: chain DA residue 26 GLU Chi-restraints excluded: chain DA residue 81 VAL Chi-restraints excluded: chain DA residue 277 ASP Chi-restraints excluded: chain DA residue 348 THR Chi-restraints excluded: chain HA residue 28 GLU Chi-restraints excluded: chain HA residue 277 ASP Chi-restraints excluded: chain HA residue 348 THR Chi-restraints excluded: chain JA residue 9 ASP Chi-restraints excluded: chain JA residue 26 GLU Chi-restraints excluded: chain JA residue 81 VAL Chi-restraints excluded: chain JA residue 277 ASP Chi-restraints excluded: chain JA residue 348 THR Chi-restraints excluded: chain NA residue 28 GLU Chi-restraints excluded: chain NA residue 277 ASP Chi-restraints excluded: chain NA residue 348 THR Chi-restraints excluded: chain PA residue 9 ASP Chi-restraints excluded: chain PA residue 26 GLU Chi-restraints excluded: chain PA residue 81 VAL Chi-restraints excluded: chain PA residue 277 ASP Chi-restraints excluded: chain PA residue 348 THR Chi-restraints excluded: chain TA residue 28 GLU Chi-restraints excluded: chain TA residue 277 ASP Chi-restraints excluded: chain TA residue 348 THR Chi-restraints excluded: chain VA residue 9 ASP Chi-restraints excluded: chain VA residue 26 GLU Chi-restraints excluded: chain VA residue 81 VAL Chi-restraints excluded: chain VA residue 277 ASP Chi-restraints excluded: chain VA residue 348 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 970 optimal weight: 2.9990 chunk 738 optimal weight: 10.0000 chunk 509 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 468 optimal weight: 9.9990 chunk 659 optimal weight: 0.1980 chunk 986 optimal weight: 3.9990 chunk 1043 optimal weight: 8.9990 chunk 515 optimal weight: 1.9990 chunk 934 optimal weight: 10.0000 chunk 281 optimal weight: 8.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 53 GLN ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN A E 53 GLN G 53 GLN ** G 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 389 GLN A K 53 GLN M 53 GLN ** M 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 389 GLN A Q 53 GLN S 53 GLN ** S 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 389 GLN A X 53 GLN Z 53 GLN ** Z 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 389 GLN A DA 53 GLN FA 53 GLN ** FA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HA 389 GLN A JA 53 GLN LA 53 GLN ** LA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 389 GLN A PA 53 GLN RA 53 GLN ** RA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TA 389 GLN A VA 53 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 87864 Z= 0.156 Angle : 0.543 9.477 119400 Z= 0.278 Chirality : 0.042 0.159 13512 Planarity : 0.004 0.040 15288 Dihedral : 4.311 18.138 12264 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 1.22 % Allowed : 11.05 % Favored : 87.73 % 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: -0.95 (0.08), residues: 11016 helix: 0.61 (0.09), residues: 3600 sheet: 0.07 (0.11), residues: 2256 loop : -1.89 (0.08), residues: 5160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 394 HIS 0.003 0.001 HIS C 308 PHE 0.026 0.001 PHE M 423 TYR 0.011 0.001 TYR V 78 ARG 0.002 0.000 ARG S 411 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22032 Ramachandran restraints generated. 11016 Oldfield, 0 Emsley, 11016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22032 Ramachandran restraints generated. 11016 Oldfield, 0 Emsley, 11016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1148 residues out of total 9240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 89 poor density : 1059 time to evaluate : 7.432 Fit side-chains REVERT: A 73 MET cc_start: 0.6445 (tpp) cc_final: 0.6181 (tpp) REVERT: A 364 GLN cc_start: 0.7752 (pt0) cc_final: 0.7318 (mm-40) REVERT: C 133 PHE cc_start: 0.7308 (t80) cc_final: 0.6982 (t80) REVERT: C 228 MET cc_start: 0.7165 (ptt) cc_final: 0.6755 (pp-130) REVERT: C 277 ASP cc_start: 0.7831 (OUTLIER) cc_final: 0.7321 (t70) REVERT: E 228 MET cc_start: 0.7229 (OUTLIER) cc_final: 0.6517 (pp-130) REVERT: E 250 GLU cc_start: 0.6741 (mm-30) cc_final: 0.6525 (mm-30) REVERT: E 364 GLN cc_start: 0.7813 (pt0) cc_final: 0.7342 (mm-40) REVERT: G 73 MET cc_start: 0.6453 (tpp) cc_final: 0.6187 (tpp) REVERT: G 364 GLN cc_start: 0.7762 (pt0) cc_final: 0.7322 (mm-40) REVERT: I 133 PHE cc_start: 0.7283 (t80) cc_final: 0.6886 (t80) REVERT: I 228 MET cc_start: 0.7159 (ptt) cc_final: 0.6756 (pp-130) REVERT: I 277 ASP cc_start: 0.7848 (OUTLIER) cc_final: 0.7340 (t70) REVERT: K 228 MET cc_start: 0.7232 (OUTLIER) cc_final: 0.6530 (pp-130) REVERT: K 250 GLU cc_start: 0.6725 (mm-30) cc_final: 0.6498 (mm-30) REVERT: K 364 GLN cc_start: 0.7783 (pt0) cc_final: 0.7332 (mm-40) REVERT: M 73 MET cc_start: 0.6439 (tpp) cc_final: 0.6170 (tpp) REVERT: M 228 MET cc_start: 0.7185 (ptt) cc_final: 0.6904 (pp-130) REVERT: M 364 GLN cc_start: 0.7729 (pt0) cc_final: 0.7304 (mm-40) REVERT: O 133 PHE cc_start: 0.7281 (t80) cc_final: 0.6955 (t80) REVERT: O 228 MET cc_start: 0.7147 (ptt) cc_final: 0.6752 (pp-130) REVERT: O 277 ASP cc_start: 0.7760 (OUTLIER) cc_final: 0.7223 (t70) REVERT: Q 228 MET cc_start: 0.7223 (OUTLIER) cc_final: 0.6514 (pp-130) REVERT: Q 250 GLU cc_start: 0.6752 (mm-30) cc_final: 0.6527 (mm-30) REVERT: Q 364 GLN cc_start: 0.7779 (pt0) cc_final: 0.7327 (mm-40) REVERT: S 73 MET cc_start: 0.6444 (tpp) cc_final: 0.6178 (tpp) REVERT: S 228 MET cc_start: 0.7118 (ptt) cc_final: 0.6864 (pp-130) REVERT: S 364 GLN cc_start: 0.7762 (pt0) cc_final: 0.7316 (mm-40) REVERT: V 228 MET cc_start: 0.7206 (ptt) cc_final: 0.6773 (pp-130) REVERT: V 277 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7292 (t70) REVERT: X 228 MET cc_start: 0.7203 (OUTLIER) cc_final: 0.6498 (pp-130) REVERT: X 250 GLU cc_start: 0.6778 (mm-30) cc_final: 0.6549 (mm-30) REVERT: X 364 GLN cc_start: 0.7794 (pt0) cc_final: 0.7329 (mm-40) REVERT: Z 73 MET cc_start: 0.6450 (tpp) cc_final: 0.6188 (tpp) REVERT: Z 228 MET cc_start: 0.7130 (ptt) cc_final: 0.6874 (pp-130) REVERT: Z 364 GLN cc_start: 0.7766 (pt0) cc_final: 0.7311 (mm-40) REVERT: BA 228 MET cc_start: 0.7176 (ptt) cc_final: 0.6751 (pp-130) REVERT: BA 277 ASP cc_start: 0.7821 (OUTLIER) cc_final: 0.7323 (t70) REVERT: DA 228 MET cc_start: 0.7190 (OUTLIER) cc_final: 0.6495 (pp-130) REVERT: DA 250 GLU cc_start: 0.6737 (mm-30) cc_final: 0.6511 (mm-30) REVERT: DA 364 GLN cc_start: 0.7811 (pt0) cc_final: 0.7344 (mm-40) REVERT: FA 73 MET cc_start: 0.6432 (tpp) cc_final: 0.6168 (tpp) REVERT: FA 228 MET cc_start: 0.7125 (ptt) cc_final: 0.6874 (pp-130) REVERT: FA 364 GLN cc_start: 0.7752 (pt0) cc_final: 0.7318 (mm-40) REVERT: HA 133 PHE cc_start: 0.7310 (t80) cc_final: 0.6987 (t80) REVERT: HA 228 MET cc_start: 0.7144 (ptt) cc_final: 0.6739 (pp-130) REVERT: HA 277 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7290 (t70) REVERT: JA 228 MET cc_start: 0.7228 (OUTLIER) cc_final: 0.6526 (pp-130) REVERT: JA 250 GLU cc_start: 0.6712 (mm-30) cc_final: 0.6494 (mm-30) REVERT: JA 364 GLN cc_start: 0.7785 (pt0) cc_final: 0.7326 (mm-40) REVERT: LA 73 MET cc_start: 0.6454 (tpp) cc_final: 0.6183 (tpp) REVERT: LA 364 GLN cc_start: 0.7773 (pt0) cc_final: 0.7315 (mm-40) REVERT: NA 228 MET cc_start: 0.7156 (ptt) cc_final: 0.6756 (pp-130) REVERT: NA 277 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7284 (t70) REVERT: PA 228 MET cc_start: 0.7227 (OUTLIER) cc_final: 0.6522 (pp-130) REVERT: PA 250 GLU cc_start: 0.6708 (mm-30) cc_final: 0.6490 (mm-30) REVERT: PA 364 GLN cc_start: 0.7776 (pt0) cc_final: 0.7325 (mm-40) REVERT: RA 73 MET cc_start: 0.6458 (tpp) cc_final: 0.6190 (tpp) REVERT: RA 228 MET cc_start: 0.7111 (ptt) cc_final: 0.6857 (pp-130) REVERT: RA 364 GLN cc_start: 0.7757 (pt0) cc_final: 0.7319 (mm-40) REVERT: TA 133 PHE cc_start: 0.7319 (t80) cc_final: 0.6926 (t80) REVERT: TA 228 MET cc_start: 0.7159 (ptt) cc_final: 0.6761 (pp-130) REVERT: TA 277 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7310 (t70) REVERT: VA 228 MET cc_start: 0.7208 (OUTLIER) cc_final: 0.6502 (pp-130) REVERT: VA 250 GLU cc_start: 0.6783 (mm-30) cc_final: 0.6564 (mm-30) REVERT: VA 364 GLN cc_start: 0.7798 (pt0) cc_final: 0.7339 (mm-40) outliers start: 89 outliers final: 37 residues processed: 1093 average time/residue: 1.6723 time to fit residues: 2488.1982 Evaluate side-chains 1087 residues out of total 9240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1034 time to evaluate : 7.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 277 ASP Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain K residue 277 ASP Chi-restraints excluded: chain K residue 348 THR Chi-restraints excluded: chain O residue 28 GLU Chi-restraints excluded: chain O residue 277 ASP Chi-restraints excluded: chain Q residue 26 GLU Chi-restraints excluded: chain Q residue 228 MET Chi-restraints excluded: chain Q residue 277 ASP Chi-restraints excluded: chain Q residue 348 THR Chi-restraints excluded: chain V residue 28 GLU Chi-restraints excluded: chain V residue 277 ASP Chi-restraints excluded: chain X residue 26 GLU Chi-restraints excluded: chain X residue 228 MET Chi-restraints excluded: chain X residue 277 ASP Chi-restraints excluded: chain X residue 348 THR Chi-restraints excluded: chain BA residue 277 ASP Chi-restraints excluded: chain DA residue 26 GLU Chi-restraints excluded: chain DA residue 81 VAL Chi-restraints excluded: chain DA residue 228 MET Chi-restraints excluded: chain DA residue 277 ASP Chi-restraints excluded: chain DA residue 348 THR Chi-restraints excluded: chain HA residue 28 GLU Chi-restraints excluded: chain HA residue 277 ASP Chi-restraints excluded: chain JA residue 26 GLU Chi-restraints excluded: chain JA residue 81 VAL Chi-restraints excluded: chain JA residue 228 MET Chi-restraints excluded: chain JA residue 277 ASP Chi-restraints excluded: chain JA residue 348 THR Chi-restraints excluded: chain NA residue 28 GLU Chi-restraints excluded: chain NA residue 277 ASP Chi-restraints excluded: chain PA residue 26 GLU Chi-restraints excluded: chain PA residue 81 VAL Chi-restraints excluded: chain PA residue 228 MET Chi-restraints excluded: chain PA residue 277 ASP Chi-restraints excluded: chain PA residue 348 THR Chi-restraints excluded: chain TA residue 28 GLU Chi-restraints excluded: chain TA residue 277 ASP Chi-restraints excluded: chain VA residue 26 GLU Chi-restraints excluded: chain VA residue 81 VAL Chi-restraints excluded: chain VA residue 228 MET Chi-restraints excluded: chain VA residue 277 ASP Chi-restraints excluded: chain VA residue 348 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 869 optimal weight: 8.9990 chunk 592 optimal weight: 8.9990 chunk 15 optimal weight: 6.9990 chunk 777 optimal weight: 0.6980 chunk 430 optimal weight: 3.9990 chunk 890 optimal weight: 0.9990 chunk 721 optimal weight: 10.0000 chunk 1 optimal weight: 8.9990 chunk 533 optimal weight: 7.9990 chunk 937 optimal weight: 0.4980 chunk 263 optimal weight: 0.9980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 HIS C 389 GLN A E 53 GLN ** G 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 HIS ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 389 GLN A K 53 GLN ** M 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 136 HIS O 389 GLN A Q 53 GLN ** S 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 136 HIS ** V 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 389 GLN A X 53 GLN ** Z 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 136 HIS ** BA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 389 GLN A DA 53 GLN ** FA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HA 136 HIS ** HA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HA 389 GLN A JA 53 GLN ** LA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 136 HIS NA 389 GLN A PA 53 GLN ** RA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TA 136 HIS ** TA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TA 389 GLN A VA 53 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1736 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 87864 Z= 0.154 Angle : 0.536 10.040 119400 Z= 0.272 Chirality : 0.042 0.150 13512 Planarity : 0.004 0.036 15288 Dihedral : 4.168 17.917 12264 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 1.21 % Allowed : 12.21 % Favored : 86.58 % 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: -0.59 (0.08), residues: 11016 helix: 1.02 (0.09), residues: 3600 sheet: 0.21 (0.11), residues: 2304 loop : -1.77 (0.08), residues: 5112 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP M 394 HIS 0.003 0.001 HIS O 308 PHE 0.027 0.001 PHE Z 423 TYR 0.010 0.001 TYR C 78 ARG 0.002 0.000 ARG S 411 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22032 Ramachandran restraints generated. 11016 Oldfield, 0 Emsley, 11016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22032 Ramachandran restraints generated. 11016 Oldfield, 0 Emsley, 11016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1165 residues out of total 9240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 1077 time to evaluate : 7.800 Fit side-chains REVERT: A 73 MET cc_start: 0.6476 (tpp) cc_final: 0.6198 (tpp) REVERT: A 364 GLN cc_start: 0.7737 (pt0) cc_final: 0.7282 (mm-40) REVERT: C 133 PHE cc_start: 0.7242 (t80) cc_final: 0.6925 (t80) REVERT: C 228 MET cc_start: 0.7142 (ptt) cc_final: 0.6754 (pp-130) REVERT: C 277 ASP cc_start: 0.7785 (OUTLIER) cc_final: 0.7329 (t70) REVERT: E 228 MET cc_start: 0.7183 (OUTLIER) cc_final: 0.6444 (pp-130) REVERT: E 250 GLU cc_start: 0.6706 (mm-30) cc_final: 0.6494 (mm-30) REVERT: E 270 LEU cc_start: 0.7972 (mm) cc_final: 0.7755 (mp) REVERT: E 364 GLN cc_start: 0.7810 (pt0) cc_final: 0.7362 (mm-40) REVERT: G 63 ASP cc_start: 0.7985 (OUTLIER) cc_final: 0.7620 (m-30) REVERT: G 73 MET cc_start: 0.6490 (tpp) cc_final: 0.6221 (tpp) REVERT: G 364 GLN cc_start: 0.7751 (pt0) cc_final: 0.7316 (mm-40) REVERT: I 228 MET cc_start: 0.7135 (ptt) cc_final: 0.6757 (pp-130) REVERT: I 277 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7348 (t70) REVERT: K 228 MET cc_start: 0.7175 (OUTLIER) cc_final: 0.6447 (pp-130) REVERT: K 250 GLU cc_start: 0.6699 (mm-30) cc_final: 0.6479 (mm-30) REVERT: K 270 LEU cc_start: 0.7980 (mm) cc_final: 0.7761 (mp) REVERT: K 364 GLN cc_start: 0.7776 (pt0) cc_final: 0.7380 (mm-40) REVERT: M 63 ASP cc_start: 0.7955 (OUTLIER) cc_final: 0.7583 (m-30) REVERT: M 73 MET cc_start: 0.6467 (tpp) cc_final: 0.6188 (tpp) REVERT: M 228 MET cc_start: 0.7074 (ptt) cc_final: 0.6793 (pp-130) REVERT: M 364 GLN cc_start: 0.7713 (pt0) cc_final: 0.7268 (mm-40) REVERT: O 16 LYS cc_start: 0.8298 (mmpt) cc_final: 0.8089 (mmtm) REVERT: O 133 PHE cc_start: 0.7220 (t80) cc_final: 0.6901 (t80) REVERT: O 228 MET cc_start: 0.7123 (ptt) cc_final: 0.6778 (pp-130) REVERT: O 277 ASP cc_start: 0.7724 (OUTLIER) cc_final: 0.7236 (t70) REVERT: Q 228 MET cc_start: 0.7170 (OUTLIER) cc_final: 0.6441 (pp-130) REVERT: Q 250 GLU cc_start: 0.6713 (mm-30) cc_final: 0.6494 (mm-30) REVERT: Q 270 LEU cc_start: 0.7995 (mm) cc_final: 0.7776 (mp) REVERT: Q 364 GLN cc_start: 0.7801 (pt0) cc_final: 0.7358 (mm-40) REVERT: Q 472 LEU cc_start: 0.5492 (OUTLIER) cc_final: 0.5016 (pp) REVERT: S 63 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7610 (m-30) REVERT: S 73 MET cc_start: 0.6478 (tpp) cc_final: 0.6209 (tpp) REVERT: S 228 MET cc_start: 0.7034 (ptt) cc_final: 0.6752 (pp-130) REVERT: S 364 GLN cc_start: 0.7737 (pt0) cc_final: 0.7275 (mm-40) REVERT: V 16 LYS cc_start: 0.8308 (mmpt) cc_final: 0.8104 (mmtm) REVERT: V 133 PHE cc_start: 0.7218 (t80) cc_final: 0.6950 (t80) REVERT: V 228 MET cc_start: 0.7159 (ptt) cc_final: 0.6752 (pp-130) REVERT: V 277 ASP cc_start: 0.7759 (OUTLIER) cc_final: 0.7299 (t70) REVERT: X 228 MET cc_start: 0.7158 (OUTLIER) cc_final: 0.6422 (pp-130) REVERT: X 250 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6527 (mm-30) REVERT: X 270 LEU cc_start: 0.7971 (mm) cc_final: 0.7757 (mp) REVERT: X 364 GLN cc_start: 0.7793 (pt0) cc_final: 0.7366 (mm-40) REVERT: Z 63 ASP cc_start: 0.7977 (OUTLIER) cc_final: 0.7677 (m-30) REVERT: Z 73 MET cc_start: 0.6483 (tpp) cc_final: 0.6201 (tpp) REVERT: Z 228 MET cc_start: 0.7046 (ptt) cc_final: 0.6759 (pp-130) REVERT: Z 364 GLN cc_start: 0.7748 (pt0) cc_final: 0.7278 (mm-40) REVERT: BA 133 PHE cc_start: 0.7212 (t80) cc_final: 0.6947 (t80) REVERT: BA 228 MET cc_start: 0.7132 (ptt) cc_final: 0.6734 (pp-130) REVERT: BA 277 ASP cc_start: 0.7788 (OUTLIER) cc_final: 0.7342 (t70) REVERT: DA 228 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6422 (pp-130) REVERT: DA 250 GLU cc_start: 0.6714 (mm-30) cc_final: 0.6488 (mm-30) REVERT: DA 270 LEU cc_start: 0.7965 (mm) cc_final: 0.7751 (mp) REVERT: DA 364 GLN cc_start: 0.7810 (pt0) cc_final: 0.7367 (mm-40) REVERT: FA 73 MET cc_start: 0.6467 (tpp) cc_final: 0.6187 (tpp) REVERT: FA 228 MET cc_start: 0.7050 (ptt) cc_final: 0.6758 (pp-130) REVERT: FA 364 GLN cc_start: 0.7717 (pt0) cc_final: 0.7297 (mm-40) REVERT: HA 72 MET cc_start: 0.4888 (ptm) cc_final: 0.4682 (ptm) REVERT: HA 133 PHE cc_start: 0.7245 (t80) cc_final: 0.6931 (t80) REVERT: HA 228 MET cc_start: 0.7134 (ptt) cc_final: 0.6733 (pp-130) REVERT: HA 277 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7310 (t70) REVERT: JA 228 MET cc_start: 0.7178 (OUTLIER) cc_final: 0.6449 (pp-130) REVERT: JA 250 GLU cc_start: 0.6683 (mm-30) cc_final: 0.6472 (mm-30) REVERT: JA 270 LEU cc_start: 0.7957 (mm) cc_final: 0.7742 (mp) REVERT: JA 364 GLN cc_start: 0.7806 (pt0) cc_final: 0.7354 (mm-40) REVERT: LA 63 ASP cc_start: 0.7971 (OUTLIER) cc_final: 0.7615 (m-30) REVERT: LA 73 MET cc_start: 0.6489 (tpp) cc_final: 0.6219 (tpp) REVERT: LA 364 GLN cc_start: 0.7746 (pt0) cc_final: 0.7276 (mm-40) REVERT: NA 228 MET cc_start: 0.7133 (ptt) cc_final: 0.6756 (pp-130) REVERT: NA 277 ASP cc_start: 0.7753 (OUTLIER) cc_final: 0.7294 (t70) REVERT: PA 228 MET cc_start: 0.7169 (OUTLIER) cc_final: 0.6447 (pp-130) REVERT: PA 250 GLU cc_start: 0.6686 (mm-30) cc_final: 0.6472 (mm-30) REVERT: PA 270 LEU cc_start: 0.7954 (mm) cc_final: 0.7743 (mp) REVERT: PA 364 GLN cc_start: 0.7798 (pt0) cc_final: 0.7357 (mm-40) REVERT: RA 63 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7654 (m-30) REVERT: RA 73 MET cc_start: 0.6494 (tpp) cc_final: 0.6205 (tpp) REVERT: RA 228 MET cc_start: 0.7031 (ptt) cc_final: 0.6744 (pp-130) REVERT: RA 364 GLN cc_start: 0.7737 (pt0) cc_final: 0.7310 (mm-40) REVERT: TA 228 MET cc_start: 0.7130 (ptt) cc_final: 0.6783 (pp-130) REVERT: TA 277 ASP cc_start: 0.7772 (OUTLIER) cc_final: 0.7320 (t70) REVERT: VA 228 MET cc_start: 0.7161 (OUTLIER) cc_final: 0.6421 (pp-130) REVERT: VA 250 GLU cc_start: 0.6744 (mm-30) cc_final: 0.6528 (mm-30) REVERT: VA 270 LEU cc_start: 0.7992 (mm) cc_final: 0.7784 (mp) REVERT: VA 364 GLN cc_start: 0.7806 (pt0) cc_final: 0.7367 (mm-40) REVERT: VA 472 LEU cc_start: 0.5522 (OUTLIER) cc_final: 0.5042 (pp) outliers start: 88 outliers final: 40 residues processed: 1104 average time/residue: 1.6761 time to fit residues: 2507.0510 Evaluate side-chains 1117 residues out of total 9240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1053 time to evaluate : 7.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain G residue 63 ASP Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 277 ASP Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 123 MET Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain K residue 277 ASP Chi-restraints excluded: chain K residue 348 THR Chi-restraints excluded: chain M residue 63 ASP Chi-restraints excluded: chain O residue 28 GLU Chi-restraints excluded: chain O residue 277 ASP Chi-restraints excluded: chain Q residue 26 GLU Chi-restraints excluded: chain Q residue 228 MET Chi-restraints excluded: chain Q residue 277 ASP Chi-restraints excluded: chain Q residue 348 THR Chi-restraints excluded: chain Q residue 472 LEU Chi-restraints excluded: chain S residue 63 ASP Chi-restraints excluded: chain V residue 28 GLU Chi-restraints excluded: chain V residue 277 ASP Chi-restraints excluded: chain X residue 26 GLU Chi-restraints excluded: chain X residue 228 MET Chi-restraints excluded: chain X residue 277 ASP Chi-restraints excluded: chain X residue 348 THR Chi-restraints excluded: chain Z residue 63 ASP Chi-restraints excluded: chain BA residue 28 GLU Chi-restraints excluded: chain BA residue 277 ASP Chi-restraints excluded: chain DA residue 26 GLU Chi-restraints excluded: chain DA residue 81 VAL Chi-restraints excluded: chain DA residue 228 MET Chi-restraints excluded: chain DA residue 277 ASP Chi-restraints excluded: chain DA residue 348 THR Chi-restraints excluded: chain HA residue 28 GLU Chi-restraints excluded: chain HA residue 277 ASP Chi-restraints excluded: chain JA residue 26 GLU Chi-restraints excluded: chain JA residue 81 VAL Chi-restraints excluded: chain JA residue 228 MET Chi-restraints excluded: chain JA residue 277 ASP Chi-restraints excluded: chain JA residue 348 THR Chi-restraints excluded: chain LA residue 63 ASP Chi-restraints excluded: chain NA residue 28 GLU Chi-restraints excluded: chain NA residue 277 ASP Chi-restraints excluded: chain PA residue 26 GLU Chi-restraints excluded: chain PA residue 81 VAL Chi-restraints excluded: chain PA residue 123 MET Chi-restraints excluded: chain PA residue 228 MET Chi-restraints excluded: chain PA residue 277 ASP Chi-restraints excluded: chain PA residue 348 THR Chi-restraints excluded: chain RA residue 63 ASP Chi-restraints excluded: chain TA residue 28 GLU Chi-restraints excluded: chain TA residue 277 ASP Chi-restraints excluded: chain VA residue 26 GLU Chi-restraints excluded: chain VA residue 81 VAL Chi-restraints excluded: chain VA residue 228 MET Chi-restraints excluded: chain VA residue 277 ASP Chi-restraints excluded: chain VA residue 348 THR Chi-restraints excluded: chain VA residue 472 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 351 optimal weight: 10.0000 chunk 940 optimal weight: 6.9990 chunk 206 optimal weight: 10.0000 chunk 612 optimal weight: 20.0000 chunk 257 optimal weight: 0.7980 chunk 1044 optimal weight: 20.0000 chunk 867 optimal weight: 9.9990 chunk 483 optimal weight: 0.0770 chunk 86 optimal weight: 0.8980 chunk 345 optimal weight: 10.0000 chunk 548 optimal weight: 10.0000 overall best weight: 3.7542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 53 GLN C 136 HIS C 441 GLN ** G 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 53 GLN I 136 HIS ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 441 GLN ** M 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 53 GLN O 136 HIS O 441 GLN ** S 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 53 GLN V 136 HIS V 441 GLN ** Z 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 53 GLN BA 136 HIS ** BA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 441 GLN ** FA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HA 53 GLN HA 136 HIS HA 441 GLN ** LA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 53 GLN NA 136 HIS NA 441 GLN ** RA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TA 53 GLN TA 136 HIS ** TA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TA 441 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 87864 Z= 0.264 Angle : 0.581 9.581 119400 Z= 0.297 Chirality : 0.044 0.177 13512 Planarity : 0.005 0.040 15288 Dihedral : 4.436 20.689 12264 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.49 % Allowed : 12.20 % Favored : 86.31 % 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: -0.60 (0.08), residues: 11016 helix: 0.99 (0.09), residues: 3600 sheet: 0.31 (0.11), residues: 2256 loop : -1.80 (0.08), residues: 5160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPNA 394 HIS 0.003 0.001 HIS V 136 PHE 0.028 0.002 PHELA 423 TYR 0.013 0.002 TYRPA 382 ARG 0.003 0.000 ARG M 411 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22032 Ramachandran restraints generated. 11016 Oldfield, 0 Emsley, 11016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22032 Ramachandran restraints generated. 11016 Oldfield, 0 Emsley, 11016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1159 residues out of total 9240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1045 time to evaluate : 7.573 Fit side-chains REVERT: A 73 MET cc_start: 0.6496 (tpp) cc_final: 0.6213 (tpp) REVERT: A 364 GLN cc_start: 0.7741 (pt0) cc_final: 0.7258 (mm-40) REVERT: C 133 PHE cc_start: 0.7277 (t80) cc_final: 0.6965 (t80) REVERT: C 228 MET cc_start: 0.7184 (ptt) cc_final: 0.6794 (pp-130) REVERT: C 277 ASP cc_start: 0.7893 (OUTLIER) cc_final: 0.7341 (t70) REVERT: E 228 MET cc_start: 0.7106 (OUTLIER) cc_final: 0.6365 (pp-130) REVERT: E 250 GLU cc_start: 0.6884 (mm-30) cc_final: 0.6627 (mm-30) REVERT: E 270 LEU cc_start: 0.8021 (mm) cc_final: 0.7791 (mp) REVERT: E 364 GLN cc_start: 0.7772 (pt0) cc_final: 0.7324 (mm-40) REVERT: G 73 MET cc_start: 0.6432 (tpp) cc_final: 0.6150 (tpp) REVERT: G 364 GLN cc_start: 0.7762 (pt0) cc_final: 0.7303 (mm-40) REVERT: I 228 MET cc_start: 0.7173 (ptt) cc_final: 0.6796 (pp-130) REVERT: I 277 ASP cc_start: 0.7913 (OUTLIER) cc_final: 0.7344 (t70) REVERT: I 460 LEU cc_start: 0.4542 (OUTLIER) cc_final: 0.4219 (tt) REVERT: K 228 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6364 (pp-130) REVERT: K 250 GLU cc_start: 0.6895 (mm-30) cc_final: 0.6627 (mm-30) REVERT: K 270 LEU cc_start: 0.8030 (mm) cc_final: 0.7796 (mp) REVERT: K 364 GLN cc_start: 0.7769 (pt0) cc_final: 0.7341 (mm-40) REVERT: M 73 MET cc_start: 0.6489 (tpp) cc_final: 0.6207 (tpp) REVERT: M 228 MET cc_start: 0.7066 (ptt) cc_final: 0.6763 (pp-130) REVERT: M 364 GLN cc_start: 0.7719 (pt0) cc_final: 0.7245 (mm-40) REVERT: O 16 LYS cc_start: 0.8280 (mmpt) cc_final: 0.8075 (mmtm) REVERT: O 133 PHE cc_start: 0.7260 (t80) cc_final: 0.6949 (t80) REVERT: O 228 MET cc_start: 0.7168 (ptt) cc_final: 0.6778 (pp-130) REVERT: O 277 ASP cc_start: 0.7836 (OUTLIER) cc_final: 0.7246 (t70) REVERT: Q 228 MET cc_start: 0.7102 (OUTLIER) cc_final: 0.6365 (pp-130) REVERT: Q 250 GLU cc_start: 0.6907 (mm-30) cc_final: 0.6637 (mm-30) REVERT: Q 270 LEU cc_start: 0.8046 (mm) cc_final: 0.7813 (mp) REVERT: Q 364 GLN cc_start: 0.7775 (pt0) cc_final: 0.7329 (mm-40) REVERT: Q 472 LEU cc_start: 0.5456 (OUTLIER) cc_final: 0.4975 (pp) REVERT: S 73 MET cc_start: 0.6426 (tpp) cc_final: 0.6139 (tpp) REVERT: S 228 MET cc_start: 0.7055 (ptt) cc_final: 0.6758 (pp-130) REVERT: S 364 GLN cc_start: 0.7751 (pt0) cc_final: 0.7254 (mm-40) REVERT: V 16 LYS cc_start: 0.8295 (mmpt) cc_final: 0.8090 (mmtm) REVERT: V 228 MET cc_start: 0.7190 (ptt) cc_final: 0.6784 (pp-130) REVERT: V 277 ASP cc_start: 0.7868 (OUTLIER) cc_final: 0.7310 (t70) REVERT: X 228 MET cc_start: 0.7072 (OUTLIER) cc_final: 0.6339 (pp-130) REVERT: X 250 GLU cc_start: 0.6940 (mm-30) cc_final: 0.6673 (mm-30) REVERT: X 270 LEU cc_start: 0.8018 (mm) cc_final: 0.7791 (mp) REVERT: X 364 GLN cc_start: 0.7775 (pt0) cc_final: 0.7356 (mm-40) REVERT: Z 73 MET cc_start: 0.6431 (tpp) cc_final: 0.6148 (tpp) REVERT: Z 228 MET cc_start: 0.7064 (ptt) cc_final: 0.6764 (pp-130) REVERT: Z 364 GLN cc_start: 0.7767 (pt0) cc_final: 0.7253 (mm-40) REVERT: BA 228 MET cc_start: 0.7173 (ptt) cc_final: 0.6771 (pp-130) REVERT: BA 277 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7340 (t70) REVERT: DA 228 MET cc_start: 0.7064 (OUTLIER) cc_final: 0.6336 (pp-130) REVERT: DA 250 GLU cc_start: 0.6908 (mm-30) cc_final: 0.6639 (mm-30) REVERT: DA 270 LEU cc_start: 0.8011 (mm) cc_final: 0.7785 (mp) REVERT: DA 364 GLN cc_start: 0.7768 (pt0) cc_final: 0.7324 (mm-40) REVERT: FA 73 MET cc_start: 0.6483 (tpp) cc_final: 0.6202 (tpp) REVERT: FA 228 MET cc_start: 0.7069 (ptt) cc_final: 0.6761 (pp-130) REVERT: FA 364 GLN cc_start: 0.7755 (pt0) cc_final: 0.7270 (mm-40) REVERT: HA 133 PHE cc_start: 0.7273 (t80) cc_final: 0.6960 (t80) REVERT: HA 228 MET cc_start: 0.7173 (ptt) cc_final: 0.6772 (pp-130) REVERT: HA 277 ASP cc_start: 0.7854 (OUTLIER) cc_final: 0.7312 (t70) REVERT: JA 228 MET cc_start: 0.7093 (OUTLIER) cc_final: 0.6363 (pp-130) REVERT: JA 250 GLU cc_start: 0.6881 (mm-30) cc_final: 0.6624 (mm-30) REVERT: JA 270 LEU cc_start: 0.8008 (mm) cc_final: 0.7779 (mp) REVERT: JA 364 GLN cc_start: 0.7778 (pt0) cc_final: 0.7326 (mm-40) REVERT: LA 73 MET cc_start: 0.6437 (tpp) cc_final: 0.6151 (tpp) REVERT: LA 364 GLN cc_start: 0.7764 (pt0) cc_final: 0.7252 (mm-40) REVERT: NA 228 MET cc_start: 0.7178 (ptt) cc_final: 0.6797 (pp-130) REVERT: NA 277 ASP cc_start: 0.7858 (OUTLIER) cc_final: 0.7288 (t70) REVERT: PA 228 MET cc_start: 0.7097 (OUTLIER) cc_final: 0.6363 (pp-130) REVERT: PA 250 GLU cc_start: 0.6881 (mm-30) cc_final: 0.6621 (mm-30) REVERT: PA 270 LEU cc_start: 0.8005 (mm) cc_final: 0.7776 (mp) REVERT: PA 364 GLN cc_start: 0.7759 (pt0) cc_final: 0.7313 (mm-40) REVERT: RA 73 MET cc_start: 0.6441 (tpp) cc_final: 0.6156 (tpp) REVERT: RA 228 MET cc_start: 0.7051 (ptt) cc_final: 0.6744 (pp-130) REVERT: RA 364 GLN cc_start: 0.7753 (pt0) cc_final: 0.7275 (mm-40) REVERT: TA 228 MET cc_start: 0.7185 (ptt) cc_final: 0.6779 (pp-130) REVERT: TA 277 ASP cc_start: 0.7886 (OUTLIER) cc_final: 0.7331 (t70) REVERT: VA 228 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6342 (pp-130) REVERT: VA 250 GLU cc_start: 0.6937 (mm-30) cc_final: 0.6674 (mm-30) REVERT: VA 270 LEU cc_start: 0.8032 (mm) cc_final: 0.7804 (mp) REVERT: VA 364 GLN cc_start: 0.7759 (pt0) cc_final: 0.7320 (mm-40) REVERT: VA 472 LEU cc_start: 0.5484 (OUTLIER) cc_final: 0.5005 (pp) outliers start: 114 outliers final: 71 residues processed: 1080 average time/residue: 1.6314 time to fit residues: 2397.5461 Evaluate side-chains 1130 residues out of total 9240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1040 time to evaluate : 7.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 401 ASP Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 277 ASP Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 460 LEU Chi-restraints excluded: chain K residue 9 ASP Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 123 MET Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain K residue 277 ASP Chi-restraints excluded: chain K residue 348 THR Chi-restraints excluded: chain M residue 348 THR Chi-restraints excluded: chain M residue 401 ASP Chi-restraints excluded: chain O residue 28 GLU Chi-restraints excluded: chain O residue 277 ASP Chi-restraints excluded: chain O residue 348 THR Chi-restraints excluded: chain Q residue 9 ASP Chi-restraints excluded: chain Q residue 26 GLU Chi-restraints excluded: chain Q residue 228 MET Chi-restraints excluded: chain Q residue 277 ASP Chi-restraints excluded: chain Q residue 348 THR Chi-restraints excluded: chain Q residue 472 LEU Chi-restraints excluded: chain S residue 401 ASP Chi-restraints excluded: chain V residue 28 GLU Chi-restraints excluded: chain V residue 277 ASP Chi-restraints excluded: chain V residue 348 THR Chi-restraints excluded: chain X residue 9 ASP Chi-restraints excluded: chain X residue 26 GLU Chi-restraints excluded: chain X residue 228 MET Chi-restraints excluded: chain X residue 277 ASP Chi-restraints excluded: chain X residue 348 THR Chi-restraints excluded: chain Z residue 348 THR Chi-restraints excluded: chain Z residue 401 ASP Chi-restraints excluded: chain BA residue 28 GLU Chi-restraints excluded: chain BA residue 277 ASP Chi-restraints excluded: chain BA residue 348 THR Chi-restraints excluded: chain DA residue 9 ASP Chi-restraints excluded: chain DA residue 26 GLU Chi-restraints excluded: chain DA residue 81 VAL Chi-restraints excluded: chain DA residue 228 MET Chi-restraints excluded: chain DA residue 277 ASP Chi-restraints excluded: chain DA residue 348 THR Chi-restraints excluded: chain FA residue 348 THR Chi-restraints excluded: chain FA residue 401 ASP Chi-restraints excluded: chain HA residue 28 GLU Chi-restraints excluded: chain HA residue 277 ASP Chi-restraints excluded: chain HA residue 348 THR Chi-restraints excluded: chain JA residue 9 ASP Chi-restraints excluded: chain JA residue 26 GLU Chi-restraints excluded: chain JA residue 81 VAL Chi-restraints excluded: chain JA residue 228 MET Chi-restraints excluded: chain JA residue 277 ASP Chi-restraints excluded: chain JA residue 348 THR Chi-restraints excluded: chain LA residue 348 THR Chi-restraints excluded: chain LA residue 401 ASP Chi-restraints excluded: chain NA residue 28 GLU Chi-restraints excluded: chain NA residue 277 ASP Chi-restraints excluded: chain NA residue 348 THR Chi-restraints excluded: chain PA residue 9 ASP Chi-restraints excluded: chain PA residue 26 GLU Chi-restraints excluded: chain PA residue 81 VAL Chi-restraints excluded: chain PA residue 123 MET Chi-restraints excluded: chain PA residue 228 MET Chi-restraints excluded: chain PA residue 277 ASP Chi-restraints excluded: chain PA residue 348 THR Chi-restraints excluded: chain RA residue 348 THR Chi-restraints excluded: chain RA residue 401 ASP Chi-restraints excluded: chain TA residue 28 GLU Chi-restraints excluded: chain TA residue 277 ASP Chi-restraints excluded: chain TA residue 348 THR Chi-restraints excluded: chain VA residue 9 ASP Chi-restraints excluded: chain VA residue 26 GLU Chi-restraints excluded: chain VA residue 81 VAL Chi-restraints excluded: chain VA residue 228 MET Chi-restraints excluded: chain VA residue 277 ASP Chi-restraints excluded: chain VA residue 348 THR Chi-restraints excluded: chain VA residue 472 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 1007 optimal weight: 9.9990 chunk 117 optimal weight: 5.9990 chunk 595 optimal weight: 0.0030 chunk 763 optimal weight: 4.9990 chunk 591 optimal weight: 9.9990 chunk 879 optimal weight: 8.9990 chunk 583 optimal weight: 9.9990 chunk 1040 optimal weight: 20.0000 chunk 651 optimal weight: 7.9990 chunk 634 optimal weight: 9.9990 chunk 480 optimal weight: 7.9990 overall best weight: 5.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 136 HIS ** NA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 87864 Z= 0.356 Angle : 0.620 8.537 119400 Z= 0.320 Chirality : 0.046 0.192 13512 Planarity : 0.005 0.049 15288 Dihedral : 4.698 21.560 12264 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 1.75 % Allowed : 12.12 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.08), residues: 11016 helix: 0.81 (0.09), residues: 3600 sheet: 0.30 (0.11), residues: 2256 loop : -1.82 (0.08), residues: 5160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRPJA 421 HIS 0.004 0.001 HISNA 136 PHE 0.025 0.002 PHE S 423 TYR 0.019 0.002 TYR O 382 ARG 0.004 0.001 ARG S 411 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22032 Ramachandran restraints generated. 11016 Oldfield, 0 Emsley, 11016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22032 Ramachandran restraints generated. 11016 Oldfield, 0 Emsley, 11016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1134 residues out of total 9240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 996 time to evaluate : 7.547 Fit side-chains REVERT: A 364 GLN cc_start: 0.7744 (pt0) cc_final: 0.7245 (mm-40) REVERT: C 133 PHE cc_start: 0.7275 (t80) cc_final: 0.7021 (t80) REVERT: C 228 MET cc_start: 0.7039 (ptt) cc_final: 0.6700 (pp-130) REVERT: C 460 LEU cc_start: 0.4491 (OUTLIER) cc_final: 0.4138 (tt) REVERT: E 250 GLU cc_start: 0.6971 (mm-30) cc_final: 0.6648 (mm-30) REVERT: E 270 LEU cc_start: 0.8019 (mm) cc_final: 0.7789 (mp) REVERT: E 364 GLN cc_start: 0.7815 (pt0) cc_final: 0.7361 (mm-40) REVERT: G 73 MET cc_start: 0.6647 (tpp) cc_final: 0.6361 (tpp) REVERT: G 364 GLN cc_start: 0.7764 (pt0) cc_final: 0.7265 (mm-40) REVERT: I 228 MET cc_start: 0.7045 (ptt) cc_final: 0.6721 (pp-130) REVERT: I 460 LEU cc_start: 0.4562 (OUTLIER) cc_final: 0.4233 (tt) REVERT: K 250 GLU cc_start: 0.6943 (mm-30) cc_final: 0.6621 (mm-30) REVERT: K 270 LEU cc_start: 0.8024 (mm) cc_final: 0.7792 (mp) REVERT: K 364 GLN cc_start: 0.7800 (pt0) cc_final: 0.7382 (mm-40) REVERT: M 228 MET cc_start: 0.7011 (ptt) cc_final: 0.6766 (pp-130) REVERT: M 364 GLN cc_start: 0.7723 (pt0) cc_final: 0.7219 (mm-40) REVERT: O 16 LYS cc_start: 0.8268 (mmpt) cc_final: 0.8053 (mmtm) REVERT: O 133 PHE cc_start: 0.7289 (t80) cc_final: 0.7043 (t80) REVERT: O 228 MET cc_start: 0.6988 (ptt) cc_final: 0.6663 (pp-130) REVERT: O 460 LEU cc_start: 0.4522 (OUTLIER) cc_final: 0.4163 (tt) REVERT: Q 250 GLU cc_start: 0.6984 (mm-30) cc_final: 0.6651 (mm-30) REVERT: Q 270 LEU cc_start: 0.8044 (mm) cc_final: 0.7811 (mp) REVERT: Q 364 GLN cc_start: 0.7814 (pt0) cc_final: 0.7398 (mm-40) REVERT: Q 472 LEU cc_start: 0.5462 (OUTLIER) cc_final: 0.4960 (pp) REVERT: S 73 MET cc_start: 0.6633 (tpp) cc_final: 0.6349 (tpp) REVERT: S 228 MET cc_start: 0.7002 (ptt) cc_final: 0.6754 (pp-130) REVERT: S 364 GLN cc_start: 0.7754 (pt0) cc_final: 0.7228 (mm-40) REVERT: V 16 LYS cc_start: 0.8278 (mmpt) cc_final: 0.8067 (mmtm) REVERT: V 133 PHE cc_start: 0.7351 (t80) cc_final: 0.7048 (t80) REVERT: V 228 MET cc_start: 0.7077 (ptt) cc_final: 0.6747 (pp-130) REVERT: V 460 LEU cc_start: 0.4492 (OUTLIER) cc_final: 0.4178 (tt) REVERT: X 250 GLU cc_start: 0.6998 (mm-30) cc_final: 0.6677 (mm-30) REVERT: X 270 LEU cc_start: 0.8015 (mm) cc_final: 0.7789 (mp) REVERT: X 364 GLN cc_start: 0.7767 (pt0) cc_final: 0.7361 (mm-40) REVERT: Z 228 MET cc_start: 0.7012 (ptt) cc_final: 0.6761 (pp-130) REVERT: Z 364 GLN cc_start: 0.7767 (pt0) cc_final: 0.7230 (mm-40) REVERT: BA 133 PHE cc_start: 0.7343 (t80) cc_final: 0.7042 (t80) REVERT: BA 228 MET cc_start: 0.7034 (ptt) cc_final: 0.6710 (pp-130) REVERT: BA 460 LEU cc_start: 0.4537 (OUTLIER) cc_final: 0.4218 (tt) REVERT: DA 250 GLU cc_start: 0.6975 (mm-30) cc_final: 0.6644 (mm-30) REVERT: DA 270 LEU cc_start: 0.8010 (mm) cc_final: 0.7782 (mp) REVERT: DA 364 GLN cc_start: 0.7810 (pt0) cc_final: 0.7367 (mm-40) REVERT: FA 228 MET cc_start: 0.7013 (ptt) cc_final: 0.6762 (pp-130) REVERT: FA 364 GLN cc_start: 0.7757 (pt0) cc_final: 0.7262 (mm-40) REVERT: HA 133 PHE cc_start: 0.7278 (t80) cc_final: 0.7027 (t80) REVERT: HA 228 MET cc_start: 0.7030 (ptt) cc_final: 0.6705 (pp-130) REVERT: HA 460 LEU cc_start: 0.4554 (OUTLIER) cc_final: 0.4204 (tt) REVERT: JA 250 GLU cc_start: 0.6949 (mm-30) cc_final: 0.6633 (mm-30) REVERT: JA 270 LEU cc_start: 0.8002 (mm) cc_final: 0.7775 (mp) REVERT: JA 364 GLN cc_start: 0.7817 (pt0) cc_final: 0.7409 (mm-40) REVERT: LA 73 MET cc_start: 0.6653 (tpp) cc_final: 0.6367 (tpp) REVERT: LA 364 GLN cc_start: 0.7765 (pt0) cc_final: 0.7223 (mm-40) REVERT: NA 228 MET cc_start: 0.7046 (ptt) cc_final: 0.6723 (pp-130) REVERT: PA 250 GLU cc_start: 0.6928 (mm-30) cc_final: 0.6616 (mm-30) REVERT: PA 270 LEU cc_start: 0.8003 (mm) cc_final: 0.7773 (mp) REVERT: PA 364 GLN cc_start: 0.7804 (pt0) cc_final: 0.7391 (mm-40) REVERT: RA 73 MET cc_start: 0.6632 (tpp) cc_final: 0.6361 (tpp) REVERT: RA 228 MET cc_start: 0.7001 (ptt) cc_final: 0.6745 (pp-130) REVERT: RA 364 GLN cc_start: 0.7781 (pt0) cc_final: 0.7290 (mm-40) REVERT: TA 228 MET cc_start: 0.7050 (ptt) cc_final: 0.6722 (pp-130) REVERT: VA 250 GLU cc_start: 0.7008 (mm-30) cc_final: 0.6680 (mm-30) REVERT: VA 270 LEU cc_start: 0.8029 (mm) cc_final: 0.7796 (mp) REVERT: VA 364 GLN cc_start: 0.7803 (pt0) cc_final: 0.7359 (mm-40) REVERT: VA 472 LEU cc_start: 0.5494 (OUTLIER) cc_final: 0.4989 (pp) outliers start: 138 outliers final: 86 residues processed: 1055 average time/residue: 1.6482 time to fit residues: 2365.8300 Evaluate side-chains 1094 residues out of total 9240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 94 poor density : 1000 time to evaluate : 7.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain C residue 16 LYS Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 401 ASP Chi-restraints excluded: chain I residue 16 LYS Chi-restraints excluded: chain I residue 28 GLU Chi-restraints excluded: chain I residue 277 ASP Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 460 LEU Chi-restraints excluded: chain K residue 9 ASP Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 232 LYS Chi-restraints excluded: chain K residue 277 ASP Chi-restraints excluded: chain K residue 348 THR Chi-restraints excluded: chain M residue 348 THR Chi-restraints excluded: chain M residue 401 ASP Chi-restraints excluded: chain O residue 28 GLU Chi-restraints excluded: chain O residue 277 ASP Chi-restraints excluded: chain O residue 348 THR Chi-restraints excluded: chain O residue 460 LEU Chi-restraints excluded: chain Q residue 9 ASP Chi-restraints excluded: chain Q residue 26 GLU Chi-restraints excluded: chain Q residue 277 ASP Chi-restraints excluded: chain Q residue 348 THR Chi-restraints excluded: chain Q residue 472 LEU Chi-restraints excluded: chain S residue 348 THR Chi-restraints excluded: chain S residue 401 ASP Chi-restraints excluded: chain V residue 28 GLU Chi-restraints excluded: chain V residue 277 ASP Chi-restraints excluded: chain V residue 348 THR Chi-restraints excluded: chain V residue 460 LEU Chi-restraints excluded: chain X residue 9 ASP Chi-restraints excluded: chain X residue 26 GLU Chi-restraints excluded: chain X residue 277 ASP Chi-restraints excluded: chain X residue 348 THR Chi-restraints excluded: chain Z residue 348 THR Chi-restraints excluded: chain Z residue 401 ASP Chi-restraints excluded: chain BA residue 16 LYS Chi-restraints excluded: chain BA residue 28 GLU Chi-restraints excluded: chain BA residue 277 ASP Chi-restraints excluded: chain BA residue 348 THR Chi-restraints excluded: chain BA residue 460 LEU Chi-restraints excluded: chain DA residue 9 ASP Chi-restraints excluded: chain DA residue 26 GLU Chi-restraints excluded: chain DA residue 81 VAL Chi-restraints excluded: chain DA residue 277 ASP Chi-restraints excluded: chain DA residue 348 THR Chi-restraints excluded: chain FA residue 348 THR Chi-restraints excluded: chain FA residue 401 ASP Chi-restraints excluded: chain HA residue 16 LYS Chi-restraints excluded: chain HA residue 28 GLU Chi-restraints excluded: chain HA residue 277 ASP Chi-restraints excluded: chain HA residue 348 THR Chi-restraints excluded: chain HA residue 460 LEU Chi-restraints excluded: chain JA residue 9 ASP Chi-restraints excluded: chain JA residue 26 GLU Chi-restraints excluded: chain JA residue 81 VAL Chi-restraints excluded: chain JA residue 277 ASP Chi-restraints excluded: chain JA residue 348 THR Chi-restraints excluded: chain LA residue 348 THR Chi-restraints excluded: chain LA residue 401 ASP Chi-restraints excluded: chain NA residue 16 LYS Chi-restraints excluded: chain NA residue 28 GLU Chi-restraints excluded: chain NA residue 81 VAL Chi-restraints excluded: chain NA residue 277 ASP Chi-restraints excluded: chain NA residue 348 THR Chi-restraints excluded: chain PA residue 9 ASP Chi-restraints excluded: chain PA residue 26 GLU Chi-restraints excluded: chain PA residue 81 VAL Chi-restraints excluded: chain PA residue 277 ASP Chi-restraints excluded: chain PA residue 348 THR Chi-restraints excluded: chain RA residue 348 THR Chi-restraints excluded: chain RA residue 401 ASP Chi-restraints excluded: chain TA residue 16 LYS Chi-restraints excluded: chain TA residue 28 GLU Chi-restraints excluded: chain TA residue 277 ASP Chi-restraints excluded: chain TA residue 348 THR Chi-restraints excluded: chain VA residue 9 ASP Chi-restraints excluded: chain VA residue 26 GLU Chi-restraints excluded: chain VA residue 81 VAL Chi-restraints excluded: chain VA residue 277 ASP Chi-restraints excluded: chain VA residue 348 THR Chi-restraints excluded: chain VA residue 472 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 643 optimal weight: 30.0000 chunk 415 optimal weight: 9.9990 chunk 621 optimal weight: 6.9990 chunk 313 optimal weight: 10.0000 chunk 204 optimal weight: 1.9990 chunk 201 optimal weight: 2.9990 chunk 661 optimal weight: 0.9980 chunk 709 optimal weight: 3.9990 chunk 514 optimal weight: 0.9990 chunk 97 optimal weight: 0.5980 chunk 818 optimal weight: 20.0000 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN A ** G 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 HIS ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 389 GLN A ** S 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 389 GLN A ** Z 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 389 GLN A ** FA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** HA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HA 389 GLN A ** LA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 389 GLN A ** RA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TA 136 HIS ** TA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TA 389 GLN A Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 87864 Z= 0.160 Angle : 0.539 7.501 119400 Z= 0.276 Chirality : 0.042 0.153 13512 Planarity : 0.004 0.035 15288 Dihedral : 4.240 18.223 12264 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.42 % Allowed : 12.56 % Favored : 86.01 % 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: -0.37 (0.08), residues: 11016 helix: 1.25 (0.09), residues: 3600 sheet: 0.41 (0.11), residues: 2256 loop : -1.69 (0.08), residues: 5160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 394 HIS 0.004 0.001 HISLA 308 PHE 0.025 0.001 PHENA 133 TYR 0.011 0.001 TYRHA 78 ARG 0.002 0.000 ARG M 411 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22032 Ramachandran restraints generated. 11016 Oldfield, 0 Emsley, 11016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22032 Ramachandran restraints generated. 11016 Oldfield, 0 Emsley, 11016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1174 residues out of total 9240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1066 time to evaluate : 7.621 Fit side-chains REVERT: A 73 MET cc_start: 0.6427 (tpp) cc_final: 0.6135 (tpp) REVERT: A 364 GLN cc_start: 0.7733 (pt0) cc_final: 0.7285 (mm-40) REVERT: A 472 LEU cc_start: 0.5419 (OUTLIER) cc_final: 0.4922 (pp) REVERT: C 133 PHE cc_start: 0.7275 (t80) cc_final: 0.6977 (t80) REVERT: C 228 MET cc_start: 0.7035 (ptt) cc_final: 0.6714 (pp-130) REVERT: C 277 ASP cc_start: 0.7837 (OUTLIER) cc_final: 0.7332 (t70) REVERT: E 228 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6257 (pp-130) REVERT: E 250 GLU cc_start: 0.6751 (mm-30) cc_final: 0.6508 (mm-30) REVERT: E 270 LEU cc_start: 0.7964 (mm) cc_final: 0.7735 (mp) REVERT: E 364 GLN cc_start: 0.7801 (pt0) cc_final: 0.7392 (mm-40) REVERT: G 73 MET cc_start: 0.6443 (tpp) cc_final: 0.6145 (tpp) REVERT: G 364 GLN cc_start: 0.7764 (pt0) cc_final: 0.7288 (mm-40) REVERT: G 472 LEU cc_start: 0.5427 (OUTLIER) cc_final: 0.4927 (pp) REVERT: I 228 MET cc_start: 0.7027 (ptt) cc_final: 0.6719 (pp-130) REVERT: I 277 ASP cc_start: 0.7862 (OUTLIER) cc_final: 0.7353 (t70) REVERT: K 95 ASN cc_start: 0.6693 (t0) cc_final: 0.6487 (t0) REVERT: K 228 MET cc_start: 0.6999 (OUTLIER) cc_final: 0.6257 (pp-130) REVERT: K 250 GLU cc_start: 0.6720 (mm-30) cc_final: 0.6470 (mm-30) REVERT: K 270 LEU cc_start: 0.7969 (mm) cc_final: 0.7739 (mp) REVERT: K 364 GLN cc_start: 0.7782 (pt0) cc_final: 0.7416 (mm-40) REVERT: M 73 MET cc_start: 0.6424 (tpp) cc_final: 0.6130 (tpp) REVERT: M 364 GLN cc_start: 0.7711 (pt0) cc_final: 0.7273 (mm-40) REVERT: M 472 LEU cc_start: 0.5432 (OUTLIER) cc_final: 0.4921 (pp) REVERT: O 16 LYS cc_start: 0.8297 (mmpt) cc_final: 0.8079 (mmtm) REVERT: O 133 PHE cc_start: 0.7255 (t80) cc_final: 0.6955 (t80) REVERT: O 228 MET cc_start: 0.7018 (ptt) cc_final: 0.6714 (pp-130) REVERT: O 277 ASP cc_start: 0.7781 (OUTLIER) cc_final: 0.7241 (t70) REVERT: Q 228 MET cc_start: 0.7014 (OUTLIER) cc_final: 0.6265 (pp-130) REVERT: Q 250 GLU cc_start: 0.6762 (mm-30) cc_final: 0.6510 (mm-30) REVERT: Q 270 LEU cc_start: 0.7989 (mm) cc_final: 0.7761 (mp) REVERT: Q 364 GLN cc_start: 0.7811 (pt0) cc_final: 0.7409 (mm-40) REVERT: Q 472 LEU cc_start: 0.5441 (OUTLIER) cc_final: 0.4965 (pp) REVERT: S 73 MET cc_start: 0.6426 (tpp) cc_final: 0.6130 (tpp) REVERT: S 364 GLN cc_start: 0.7731 (pt0) cc_final: 0.7280 (mm-40) REVERT: S 472 LEU cc_start: 0.5430 (OUTLIER) cc_final: 0.4930 (pp) REVERT: V 16 LYS cc_start: 0.8309 (mmpt) cc_final: 0.8093 (mmtm) REVERT: V 228 MET cc_start: 0.7096 (ptt) cc_final: 0.6779 (pp-130) REVERT: V 277 ASP cc_start: 0.7811 (OUTLIER) cc_final: 0.7307 (t70) REVERT: X 95 ASN cc_start: 0.6693 (t0) cc_final: 0.6485 (t0) REVERT: X 228 MET cc_start: 0.6974 (OUTLIER) cc_final: 0.6228 (pp-130) REVERT: X 250 GLU cc_start: 0.6775 (mm-30) cc_final: 0.6527 (mm-30) REVERT: X 270 LEU cc_start: 0.7960 (mm) cc_final: 0.7735 (mp) REVERT: X 364 GLN cc_start: 0.7791 (pt0) cc_final: 0.7432 (mm-40) REVERT: Z 73 MET cc_start: 0.6434 (tpp) cc_final: 0.6138 (tpp) REVERT: Z 228 MET cc_start: 0.6902 (ptt) cc_final: 0.6694 (pp-130) REVERT: Z 364 GLN cc_start: 0.7755 (pt0) cc_final: 0.7275 (mm-40) REVERT: Z 472 LEU cc_start: 0.5401 (OUTLIER) cc_final: 0.4907 (pp) REVERT: BA 228 MET cc_start: 0.7075 (ptt) cc_final: 0.6743 (pp-130) REVERT: BA 277 ASP cc_start: 0.7826 (OUTLIER) cc_final: 0.7337 (t70) REVERT: DA 228 MET cc_start: 0.6968 (OUTLIER) cc_final: 0.6223 (pp-130) REVERT: DA 250 GLU cc_start: 0.6731 (mm-30) cc_final: 0.6481 (mm-30) REVERT: DA 270 LEU cc_start: 0.7954 (mm) cc_final: 0.7728 (mp) REVERT: DA 364 GLN cc_start: 0.7797 (pt0) cc_final: 0.7393 (mm-40) REVERT: FA 73 MET cc_start: 0.6411 (tpp) cc_final: 0.6116 (tpp) REVERT: FA 228 MET cc_start: 0.6915 (ptt) cc_final: 0.6708 (pp-130) REVERT: FA 364 GLN cc_start: 0.7757 (pt0) cc_final: 0.7288 (mm-40) REVERT: FA 472 LEU cc_start: 0.5369 (OUTLIER) cc_final: 0.4885 (pp) REVERT: HA 133 PHE cc_start: 0.7278 (t80) cc_final: 0.6984 (t80) REVERT: HA 228 MET cc_start: 0.7069 (ptt) cc_final: 0.6740 (pp-130) REVERT: HA 277 ASP cc_start: 0.7800 (OUTLIER) cc_final: 0.7306 (t70) REVERT: JA 228 MET cc_start: 0.6996 (OUTLIER) cc_final: 0.6257 (pp-130) REVERT: JA 250 GLU cc_start: 0.6711 (mm-30) cc_final: 0.6471 (mm-30) REVERT: JA 270 LEU cc_start: 0.7951 (mm) cc_final: 0.7724 (mp) REVERT: JA 364 GLN cc_start: 0.7812 (pt0) cc_final: 0.7404 (mm-40) REVERT: LA 73 MET cc_start: 0.6445 (tpp) cc_final: 0.6146 (tpp) REVERT: LA 364 GLN cc_start: 0.7742 (pt0) cc_final: 0.7276 (mm-40) REVERT: LA 472 LEU cc_start: 0.5420 (OUTLIER) cc_final: 0.4919 (pp) REVERT: NA 228 MET cc_start: 0.7031 (ptt) cc_final: 0.6717 (pp-130) REVERT: NA 277 ASP cc_start: 0.7806 (OUTLIER) cc_final: 0.7299 (t70) REVERT: NA 460 LEU cc_start: 0.4416 (OUTLIER) cc_final: 0.4109 (tt) REVERT: PA 228 MET cc_start: 0.6997 (OUTLIER) cc_final: 0.6254 (pp-130) REVERT: PA 250 GLU cc_start: 0.6704 (mm-30) cc_final: 0.6461 (mm-30) REVERT: PA 270 LEU cc_start: 0.7946 (mm) cc_final: 0.7720 (mp) REVERT: PA 364 GLN cc_start: 0.7804 (pt0) cc_final: 0.7402 (mm-40) REVERT: RA 73 MET cc_start: 0.6445 (tpp) cc_final: 0.6148 (tpp) REVERT: RA 228 MET cc_start: 0.6888 (ptt) cc_final: 0.6688 (pp-130) REVERT: RA 364 GLN cc_start: 0.7745 (pt0) cc_final: 0.7287 (mm-40) REVERT: RA 472 LEU cc_start: 0.5419 (OUTLIER) cc_final: 0.4924 (pp) REVERT: TA 228 MET cc_start: 0.7040 (ptt) cc_final: 0.6727 (pp-130) REVERT: TA 277 ASP cc_start: 0.7825 (OUTLIER) cc_final: 0.7324 (t70) REVERT: TA 460 LEU cc_start: 0.4373 (OUTLIER) cc_final: 0.4055 (tt) REVERT: VA 228 MET cc_start: 0.6955 (OUTLIER) cc_final: 0.6212 (pp-130) REVERT: VA 250 GLU cc_start: 0.6791 (mm-30) cc_final: 0.6545 (mm-30) REVERT: VA 270 LEU cc_start: 0.7969 (mm) cc_final: 0.7745 (mp) REVERT: VA 364 GLN cc_start: 0.7789 (pt0) cc_final: 0.7391 (mm-40) REVERT: VA 472 LEU cc_start: 0.5478 (OUTLIER) cc_final: 0.5000 (pp) outliers start: 108 outliers final: 48 residues processed: 1107 average time/residue: 1.5731 time to fit residues: 2382.7359 Evaluate side-chains 1118 residues out of total 9240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1042 time to evaluate : 7.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 228 MET Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain G residue 401 ASP Chi-restraints excluded: chain G residue 472 LEU Chi-restraints excluded: chain I residue 277 ASP Chi-restraints excluded: chain K residue 9 ASP Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 228 MET Chi-restraints excluded: chain K residue 277 ASP Chi-restraints excluded: chain K residue 348 THR Chi-restraints excluded: chain M residue 401 ASP Chi-restraints excluded: chain M residue 472 LEU Chi-restraints excluded: chain O residue 277 ASP Chi-restraints excluded: chain Q residue 9 ASP Chi-restraints excluded: chain Q residue 26 GLU Chi-restraints excluded: chain Q residue 228 MET Chi-restraints excluded: chain Q residue 277 ASP Chi-restraints excluded: chain Q residue 348 THR Chi-restraints excluded: chain Q residue 472 LEU Chi-restraints excluded: chain S residue 401 ASP Chi-restraints excluded: chain S residue 472 LEU Chi-restraints excluded: chain V residue 277 ASP Chi-restraints excluded: chain X residue 9 ASP Chi-restraints excluded: chain X residue 26 GLU Chi-restraints excluded: chain X residue 228 MET Chi-restraints excluded: chain X residue 277 ASP Chi-restraints excluded: chain X residue 348 THR Chi-restraints excluded: chain Z residue 401 ASP Chi-restraints excluded: chain Z residue 472 LEU Chi-restraints excluded: chain BA residue 277 ASP Chi-restraints excluded: chain DA residue 9 ASP Chi-restraints excluded: chain DA residue 26 GLU Chi-restraints excluded: chain DA residue 81 VAL Chi-restraints excluded: chain DA residue 228 MET Chi-restraints excluded: chain DA residue 277 ASP Chi-restraints excluded: chain DA residue 348 THR Chi-restraints excluded: chain FA residue 401 ASP Chi-restraints excluded: chain FA residue 472 LEU Chi-restraints excluded: chain HA residue 277 ASP Chi-restraints excluded: chain JA residue 9 ASP Chi-restraints excluded: chain JA residue 26 GLU Chi-restraints excluded: chain JA residue 81 VAL Chi-restraints excluded: chain JA residue 228 MET Chi-restraints excluded: chain JA residue 277 ASP Chi-restraints excluded: chain JA residue 348 THR Chi-restraints excluded: chain LA residue 401 ASP Chi-restraints excluded: chain LA residue 472 LEU Chi-restraints excluded: chain NA residue 277 ASP Chi-restraints excluded: chain NA residue 348 THR Chi-restraints excluded: chain NA residue 460 LEU Chi-restraints excluded: chain PA residue 9 ASP Chi-restraints excluded: chain PA residue 26 GLU Chi-restraints excluded: chain PA residue 81 VAL Chi-restraints excluded: chain PA residue 228 MET Chi-restraints excluded: chain PA residue 277 ASP Chi-restraints excluded: chain PA residue 348 THR Chi-restraints excluded: chain RA residue 401 ASP Chi-restraints excluded: chain RA residue 472 LEU Chi-restraints excluded: chain TA residue 81 VAL Chi-restraints excluded: chain TA residue 277 ASP Chi-restraints excluded: chain TA residue 460 LEU Chi-restraints excluded: chain VA residue 9 ASP Chi-restraints excluded: chain VA residue 26 GLU Chi-restraints excluded: chain VA residue 81 VAL Chi-restraints excluded: chain VA residue 228 MET Chi-restraints excluded: chain VA residue 277 ASP Chi-restraints excluded: chain VA residue 348 THR Chi-restraints excluded: chain VA residue 472 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 946 optimal weight: 8.9990 chunk 997 optimal weight: 30.0000 chunk 909 optimal weight: 20.0000 chunk 970 optimal weight: 8.9990 chunk 996 optimal weight: 6.9990 chunk 583 optimal weight: 5.9990 chunk 422 optimal weight: 20.0000 chunk 761 optimal weight: 9.9990 chunk 297 optimal weight: 9.9990 chunk 876 optimal weight: 5.9990 chunk 917 optimal weight: 20.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 HIS ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 389 GLN A ** G 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 HIS ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 136 HIS ** O 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 389 GLN A ** S 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 136 HIS ** V 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 389 GLN A ** Z 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 136 HIS ** BA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 389 GLN A ** FA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HA 136 HIS ** HA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HA 389 GLN A ** LA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 136 HIS ** NA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 389 GLN A ** RA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TA 136 HIS ** TA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TA 389 GLN A Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 87864 Z= 0.466 Angle : 0.670 9.411 119400 Z= 0.346 Chirality : 0.049 0.200 13512 Planarity : 0.006 0.058 15288 Dihedral : 4.850 22.456 12264 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 1.55 % Allowed : 12.62 % Favored : 85.83 % 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: -0.69 (0.08), residues: 11016 helix: 0.74 (0.09), residues: 3600 sheet: 0.66 (0.11), residues: 2136 loop : -1.87 (0.08), residues: 5280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP X 421 HIS 0.007 0.001 HIS V 136 PHE 0.034 0.002 PHE A 423 TYR 0.020 0.002 TYR Q 382 ARG 0.004 0.001 ARG M 411 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22032 Ramachandran restraints generated. 11016 Oldfield, 0 Emsley, 11016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22032 Ramachandran restraints generated. 11016 Oldfield, 0 Emsley, 11016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1113 residues out of total 9240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 120 poor density : 993 time to evaluate : 7.646 Fit side-chains REVERT: A 364 GLN cc_start: 0.7775 (pt0) cc_final: 0.7268 (mm-40) REVERT: A 472 LEU cc_start: 0.5585 (OUTLIER) cc_final: 0.5203 (pp) REVERT: C 133 PHE cc_start: 0.7276 (t80) cc_final: 0.7019 (t80) REVERT: C 228 MET cc_start: 0.7005 (ptt) cc_final: 0.6720 (pp-130) REVERT: C 460 LEU cc_start: 0.4552 (OUTLIER) cc_final: 0.4238 (tt) REVERT: E 250 GLU cc_start: 0.7013 (mm-30) cc_final: 0.6690 (mm-30) REVERT: E 270 LEU cc_start: 0.8000 (mm) cc_final: 0.7758 (mp) REVERT: E 364 GLN cc_start: 0.7845 (pt0) cc_final: 0.7401 (mm-40) REVERT: E 446 GLU cc_start: 0.6952 (mm-30) cc_final: 0.6633 (mp0) REVERT: E 472 LEU cc_start: 0.5428 (OUTLIER) cc_final: 0.4967 (pp) REVERT: G 364 GLN cc_start: 0.7806 (pt0) cc_final: 0.7308 (mm-40) REVERT: G 472 LEU cc_start: 0.5587 (OUTLIER) cc_final: 0.5203 (pp) REVERT: I 228 MET cc_start: 0.7044 (ptt) cc_final: 0.6763 (pp-130) REVERT: I 460 LEU cc_start: 0.4570 (OUTLIER) cc_final: 0.4255 (tt) REVERT: K 250 GLU cc_start: 0.7031 (mm-30) cc_final: 0.6698 (mm-30) REVERT: K 270 LEU cc_start: 0.8006 (mm) cc_final: 0.7761 (mp) REVERT: K 364 GLN cc_start: 0.7790 (pt0) cc_final: 0.7392 (mm-40) REVERT: K 446 GLU cc_start: 0.6954 (mm-30) cc_final: 0.6638 (mp0) REVERT: K 472 LEU cc_start: 0.5416 (OUTLIER) cc_final: 0.4962 (pp) REVERT: M 364 GLN cc_start: 0.7753 (pt0) cc_final: 0.7254 (mm-40) REVERT: M 472 LEU cc_start: 0.5599 (OUTLIER) cc_final: 0.5202 (pp) REVERT: O 16 LYS cc_start: 0.8263 (mmpt) cc_final: 0.8048 (mmtm) REVERT: O 133 PHE cc_start: 0.7257 (t80) cc_final: 0.6999 (t80) REVERT: O 228 MET cc_start: 0.7022 (ptt) cc_final: 0.6747 (pp-130) REVERT: O 460 LEU cc_start: 0.4583 (OUTLIER) cc_final: 0.4261 (tt) REVERT: Q 250 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6689 (mm-30) REVERT: Q 270 LEU cc_start: 0.8029 (mm) cc_final: 0.7783 (mp) REVERT: Q 364 GLN cc_start: 0.7802 (pt0) cc_final: 0.7397 (mm-40) REVERT: Q 446 GLU cc_start: 0.6932 (mm-30) cc_final: 0.6621 (mp0) REVERT: Q 472 LEU cc_start: 0.5456 (OUTLIER) cc_final: 0.4956 (pp) REVERT: S 364 GLN cc_start: 0.7782 (pt0) cc_final: 0.7271 (mm-40) REVERT: S 472 LEU cc_start: 0.5597 (OUTLIER) cc_final: 0.5211 (pp) REVERT: V 16 LYS cc_start: 0.8275 (mmpt) cc_final: 0.8065 (mmtm) REVERT: V 228 MET cc_start: 0.7026 (ptt) cc_final: 0.6720 (pp-130) REVERT: X 250 GLU cc_start: 0.7078 (mm-30) cc_final: 0.6747 (mm-30) REVERT: X 270 LEU cc_start: 0.7999 (mm) cc_final: 0.7756 (mp) REVERT: X 364 GLN cc_start: 0.7782 (pt0) cc_final: 0.7362 (mm-40) REVERT: X 446 GLU cc_start: 0.6961 (mm-30) cc_final: 0.6651 (mp0) REVERT: X 472 LEU cc_start: 0.5413 (OUTLIER) cc_final: 0.4937 (pp) REVERT: Z 364 GLN cc_start: 0.7798 (pt0) cc_final: 0.7258 (mm-40) REVERT: Z 472 LEU cc_start: 0.5567 (OUTLIER) cc_final: 0.5185 (pp) REVERT: BA 228 MET cc_start: 0.6963 (ptt) cc_final: 0.6673 (pp-130) REVERT: DA 250 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6712 (mm-30) REVERT: DA 270 LEU cc_start: 0.7992 (mm) cc_final: 0.7753 (mp) REVERT: DA 364 GLN cc_start: 0.7838 (pt0) cc_final: 0.7399 (mm-40) REVERT: DA 446 GLU cc_start: 0.6939 (mm-30) cc_final: 0.6619 (mp0) REVERT: DA 472 LEU cc_start: 0.5407 (OUTLIER) cc_final: 0.4949 (pp) REVERT: FA 364 GLN cc_start: 0.7797 (pt0) cc_final: 0.7305 (mm-40) REVERT: FA 472 LEU cc_start: 0.5546 (OUTLIER) cc_final: 0.5169 (pp) REVERT: HA 133 PHE cc_start: 0.7279 (t80) cc_final: 0.7028 (t80) REVERT: HA 228 MET cc_start: 0.6952 (ptt) cc_final: 0.6666 (pp-130) REVERT: HA 460 LEU cc_start: 0.4543 (OUTLIER) cc_final: 0.4239 (tt) REVERT: JA 250 GLU cc_start: 0.7016 (mm-30) cc_final: 0.6696 (mm-30) REVERT: JA 270 LEU cc_start: 0.7986 (mm) cc_final: 0.7745 (mp) REVERT: JA 364 GLN cc_start: 0.7806 (pt0) cc_final: 0.7394 (mm-40) REVERT: JA 446 GLU cc_start: 0.6921 (mm-30) cc_final: 0.6609 (mp0) REVERT: LA 364 GLN cc_start: 0.7792 (pt0) cc_final: 0.7263 (mm-40) REVERT: LA 472 LEU cc_start: 0.5588 (OUTLIER) cc_final: 0.5200 (pp) REVERT: NA 228 MET cc_start: 0.7051 (ptt) cc_final: 0.6765 (pp-130) REVERT: NA 460 LEU cc_start: 0.4549 (OUTLIER) cc_final: 0.4241 (tt) REVERT: PA 250 GLU cc_start: 0.7014 (mm-30) cc_final: 0.6691 (mm-30) REVERT: PA 270 LEU cc_start: 0.7986 (mm) cc_final: 0.7744 (mp) REVERT: PA 364 GLN cc_start: 0.7799 (pt0) cc_final: 0.7392 (mm-40) REVERT: PA 446 GLU cc_start: 0.7006 (mm-30) cc_final: 0.6679 (mp0) REVERT: PA 472 LEU cc_start: 0.5438 (OUTLIER) cc_final: 0.4972 (pp) REVERT: RA 364 GLN cc_start: 0.7783 (pt0) cc_final: 0.7266 (mm-40) REVERT: RA 472 LEU cc_start: 0.5564 (OUTLIER) cc_final: 0.5167 (pp) REVERT: TA 228 MET cc_start: 0.7045 (ptt) cc_final: 0.6750 (pp-130) REVERT: VA 250 GLU cc_start: 0.7044 (mm-30) cc_final: 0.6721 (mm-30) REVERT: VA 270 LEU cc_start: 0.8006 (mm) cc_final: 0.7770 (mp) REVERT: VA 364 GLN cc_start: 0.7835 (pt0) cc_final: 0.7400 (mm-40) REVERT: VA 446 GLU cc_start: 0.6993 (mm-30) cc_final: 0.6665 (mp0) REVERT: VA 472 LEU cc_start: 0.5487 (OUTLIER) cc_final: 0.4978 (pp) outliers start: 120 outliers final: 77 residues processed: 1044 average time/residue: 1.6573 time to fit residues: 2356.6708 Evaluate side-chains 1075 residues out of total 9240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 978 time to evaluate : 7.532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 THR Chi-restraints excluded: chain A residue 379 MET Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain C residue 28 GLU Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 202 GLU Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain G residue 348 THR Chi-restraints excluded: chain G residue 379 MET Chi-restraints excluded: chain G residue 401 ASP Chi-restraints excluded: chain G residue 472 LEU Chi-restraints excluded: chain I residue 277 ASP Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain I residue 460 LEU Chi-restraints excluded: chain K residue 9 ASP Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 277 ASP Chi-restraints excluded: chain K residue 348 THR Chi-restraints excluded: chain K residue 472 LEU Chi-restraints excluded: chain M residue 348 THR Chi-restraints excluded: chain M residue 401 ASP Chi-restraints excluded: chain M residue 472 LEU Chi-restraints excluded: chain O residue 277 ASP Chi-restraints excluded: chain O residue 348 THR Chi-restraints excluded: chain O residue 460 LEU Chi-restraints excluded: chain Q residue 9 ASP Chi-restraints excluded: chain Q residue 26 GLU Chi-restraints excluded: chain Q residue 277 ASP Chi-restraints excluded: chain Q residue 348 THR Chi-restraints excluded: chain Q residue 472 LEU Chi-restraints excluded: chain S residue 401 ASP Chi-restraints excluded: chain S residue 472 LEU Chi-restraints excluded: chain V residue 28 GLU Chi-restraints excluded: chain V residue 277 ASP Chi-restraints excluded: chain V residue 348 THR Chi-restraints excluded: chain X residue 9 ASP Chi-restraints excluded: chain X residue 26 GLU Chi-restraints excluded: chain X residue 277 ASP Chi-restraints excluded: chain X residue 348 THR Chi-restraints excluded: chain X residue 472 LEU Chi-restraints excluded: chain Z residue 348 THR Chi-restraints excluded: chain Z residue 401 ASP Chi-restraints excluded: chain Z residue 472 LEU Chi-restraints excluded: chain BA residue 277 ASP Chi-restraints excluded: chain BA residue 348 THR Chi-restraints excluded: chain DA residue 9 ASP Chi-restraints excluded: chain DA residue 26 GLU Chi-restraints excluded: chain DA residue 81 VAL Chi-restraints excluded: chain DA residue 277 ASP Chi-restraints excluded: chain DA residue 348 THR Chi-restraints excluded: chain DA residue 472 LEU Chi-restraints excluded: chain FA residue 348 THR Chi-restraints excluded: chain FA residue 401 ASP Chi-restraints excluded: chain FA residue 472 LEU Chi-restraints excluded: chain HA residue 28 GLU Chi-restraints excluded: chain HA residue 277 ASP Chi-restraints excluded: chain HA residue 348 THR Chi-restraints excluded: chain HA residue 460 LEU Chi-restraints excluded: chain JA residue 9 ASP Chi-restraints excluded: chain JA residue 26 GLU Chi-restraints excluded: chain JA residue 81 VAL Chi-restraints excluded: chain JA residue 277 ASP Chi-restraints excluded: chain JA residue 348 THR Chi-restraints excluded: chain LA residue 348 THR Chi-restraints excluded: chain LA residue 401 ASP Chi-restraints excluded: chain LA residue 472 LEU Chi-restraints excluded: chain NA residue 277 ASP Chi-restraints excluded: chain NA residue 348 THR Chi-restraints excluded: chain NA residue 460 LEU Chi-restraints excluded: chain PA residue 9 ASP Chi-restraints excluded: chain PA residue 26 GLU Chi-restraints excluded: chain PA residue 81 VAL Chi-restraints excluded: chain PA residue 277 ASP Chi-restraints excluded: chain PA residue 348 THR Chi-restraints excluded: chain PA residue 472 LEU Chi-restraints excluded: chain RA residue 348 THR Chi-restraints excluded: chain RA residue 401 ASP Chi-restraints excluded: chain RA residue 472 LEU Chi-restraints excluded: chain TA residue 16 LYS Chi-restraints excluded: chain TA residue 81 VAL Chi-restraints excluded: chain TA residue 277 ASP Chi-restraints excluded: chain TA residue 348 THR Chi-restraints excluded: chain VA residue 9 ASP Chi-restraints excluded: chain VA residue 26 GLU Chi-restraints excluded: chain VA residue 81 VAL Chi-restraints excluded: chain VA residue 277 ASP Chi-restraints excluded: chain VA residue 348 THR Chi-restraints excluded: chain VA residue 472 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 966 optimal weight: 5.9990 chunk 636 optimal weight: 0.2980 chunk 1025 optimal weight: 3.9990 chunk 626 optimal weight: 7.9990 chunk 486 optimal weight: 3.9990 chunk 713 optimal weight: 1.9990 chunk 1075 optimal weight: 20.0000 chunk 990 optimal weight: 10.0000 chunk 856 optimal weight: 3.9990 chunk 88 optimal weight: 9.9990 chunk 661 optimal weight: 5.9990 overall best weight: 2.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 209 ASN ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 209 ASN ** V 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** BA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HA 209 ASN ** HA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** NA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** TA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 87864 Z= 0.225 Angle : 0.580 9.975 119400 Z= 0.297 Chirality : 0.044 0.162 13512 Planarity : 0.005 0.037 15288 Dihedral : 4.486 20.166 12264 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.24 % Allowed : 13.20 % Favored : 85.56 % 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: -0.49 (0.08), residues: 11016 helix: 1.08 (0.09), residues: 3600 sheet: 0.39 (0.11), residues: 2256 loop : -1.74 (0.08), residues: 5160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 394 HIS 0.003 0.001 HISHA 308 PHE 0.027 0.002 PHE I 423 TYR 0.013 0.001 TYRBA 78 ARG 0.003 0.000 ARGDA 411 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 22032 Ramachandran restraints generated. 11016 Oldfield, 0 Emsley, 11016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 22032 Ramachandran restraints generated. 11016 Oldfield, 0 Emsley, 11016 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1127 residues out of total 9240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1036 time to evaluate : 7.518 Fit side-chains REVERT: A 364 GLN cc_start: 0.7748 (pt0) cc_final: 0.7265 (mm-40) REVERT: A 472 LEU cc_start: 0.5506 (OUTLIER) cc_final: 0.5043 (pp) REVERT: C 133 PHE cc_start: 0.7299 (t80) cc_final: 0.7033 (t80) REVERT: C 228 MET cc_start: 0.6960 (ptt) cc_final: 0.6679 (pp-130) REVERT: C 277 ASP cc_start: 0.7907 (OUTLIER) cc_final: 0.7321 (t70) REVERT: C 460 LEU cc_start: 0.4493 (OUTLIER) cc_final: 0.4202 (tt) REVERT: E 250 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6554 (mm-30) REVERT: E 270 LEU cc_start: 0.7977 (mm) cc_final: 0.7747 (mp) REVERT: E 364 GLN cc_start: 0.7807 (pt0) cc_final: 0.7423 (mm-40) REVERT: E 472 LEU cc_start: 0.5385 (OUTLIER) cc_final: 0.4861 (pp) REVERT: G 364 GLN cc_start: 0.7804 (pt0) cc_final: 0.7313 (mm-40) REVERT: G 472 LEU cc_start: 0.5551 (OUTLIER) cc_final: 0.5098 (pp) REVERT: I 228 MET cc_start: 0.6984 (ptt) cc_final: 0.6705 (pp-130) REVERT: I 277 ASP cc_start: 0.7929 (OUTLIER) cc_final: 0.7337 (t70) REVERT: K 250 GLU cc_start: 0.6828 (mm-30) cc_final: 0.6535 (mm-30) REVERT: K 270 LEU cc_start: 0.8004 (mm) cc_final: 0.7778 (mp) REVERT: K 364 GLN cc_start: 0.7777 (pt0) cc_final: 0.7397 (mm-40) REVERT: K 472 LEU cc_start: 0.5372 (OUTLIER) cc_final: 0.4858 (pp) REVERT: M 364 GLN cc_start: 0.7738 (pt0) cc_final: 0.7263 (mm-40) REVERT: M 472 LEU cc_start: 0.5521 (OUTLIER) cc_final: 0.5043 (pp) REVERT: O 16 LYS cc_start: 0.8267 (mmpt) cc_final: 0.8046 (mmtm) REVERT: O 133 PHE cc_start: 0.7281 (t80) cc_final: 0.7014 (t80) REVERT: O 228 MET cc_start: 0.6952 (ptt) cc_final: 0.6683 (pp-130) REVERT: O 277 ASP cc_start: 0.7851 (OUTLIER) cc_final: 0.7231 (t70) REVERT: Q 250 GLU cc_start: 0.6840 (mm-30) cc_final: 0.6547 (mm-30) REVERT: Q 270 LEU cc_start: 0.8025 (mm) cc_final: 0.7797 (mp) REVERT: Q 364 GLN cc_start: 0.7793 (pt0) cc_final: 0.7406 (mm-40) REVERT: Q 472 LEU cc_start: 0.5461 (OUTLIER) cc_final: 0.4948 (pp) REVERT: S 364 GLN cc_start: 0.7765 (pt0) cc_final: 0.7275 (mm-40) REVERT: S 472 LEU cc_start: 0.5517 (OUTLIER) cc_final: 0.5053 (pp) REVERT: V 16 LYS cc_start: 0.8276 (mmpt) cc_final: 0.8059 (mmtm) REVERT: V 228 MET cc_start: 0.7033 (ptt) cc_final: 0.6715 (pp-130) REVERT: V 277 ASP cc_start: 0.7881 (OUTLIER) cc_final: 0.7290 (t70) REVERT: X 250 GLU cc_start: 0.6867 (mm-30) cc_final: 0.6576 (mm-30) REVERT: X 270 LEU cc_start: 0.7995 (mm) cc_final: 0.7775 (mp) REVERT: X 364 GLN cc_start: 0.7783 (pt0) cc_final: 0.7397 (mm-40) REVERT: X 472 LEU cc_start: 0.5369 (OUTLIER) cc_final: 0.4852 (pp) REVERT: Z 364 GLN cc_start: 0.7766 (pt0) cc_final: 0.7265 (mm-40) REVERT: Z 472 LEU cc_start: 0.5489 (OUTLIER) cc_final: 0.5028 (pp) REVERT: BA 228 MET cc_start: 0.7013 (ptt) cc_final: 0.6696 (pp-130) REVERT: BA 277 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7322 (t70) REVERT: DA 250 GLU cc_start: 0.6846 (mm-30) cc_final: 0.6551 (mm-30) REVERT: DA 270 LEU cc_start: 0.7993 (mm) cc_final: 0.7772 (mp) REVERT: DA 364 GLN cc_start: 0.7818 (pt0) cc_final: 0.7439 (mm-40) REVERT: DA 472 LEU cc_start: 0.5367 (OUTLIER) cc_final: 0.4840 (pp) REVERT: FA 364 GLN cc_start: 0.7794 (pt0) cc_final: 0.7307 (mm-40) REVERT: FA 472 LEU cc_start: 0.5503 (OUTLIER) cc_final: 0.5064 (pp) REVERT: HA 133 PHE cc_start: 0.7304 (t80) cc_final: 0.7038 (t80) REVERT: HA 228 MET cc_start: 0.6961 (ptt) cc_final: 0.6664 (pp-130) REVERT: HA 277 ASP cc_start: 0.7869 (OUTLIER) cc_final: 0.7292 (t70) REVERT: JA 250 GLU cc_start: 0.6821 (mm-30) cc_final: 0.6533 (mm-30) REVERT: JA 270 LEU cc_start: 0.7987 (mm) cc_final: 0.7762 (mp) REVERT: JA 364 GLN cc_start: 0.7795 (pt0) cc_final: 0.7405 (mm-40) REVERT: LA 364 GLN cc_start: 0.7772 (pt0) cc_final: 0.7268 (mm-40) REVERT: LA 472 LEU cc_start: 0.5516 (OUTLIER) cc_final: 0.5048 (pp) REVERT: NA 228 MET cc_start: 0.6987 (ptt) cc_final: 0.6702 (pp-130) REVERT: NA 277 ASP cc_start: 0.7876 (OUTLIER) cc_final: 0.7283 (t70) REVERT: PA 250 GLU cc_start: 0.6818 (mm-30) cc_final: 0.6527 (mm-30) REVERT: PA 270 LEU cc_start: 0.7983 (mm) cc_final: 0.7763 (mp) REVERT: PA 364 GLN cc_start: 0.7785 (pt0) cc_final: 0.7401 (mm-40) REVERT: PA 472 LEU cc_start: 0.5389 (OUTLIER) cc_final: 0.4865 (pp) REVERT: RA 364 GLN cc_start: 0.7787 (pt0) cc_final: 0.7313 (mm-40) REVERT: RA 472 LEU cc_start: 0.5517 (OUTLIER) cc_final: 0.5069 (pp) REVERT: TA 84 MET cc_start: 0.6269 (mtt) cc_final: 0.5924 (mtt) REVERT: TA 228 MET cc_start: 0.6977 (ptt) cc_final: 0.6685 (pp-130) REVERT: TA 277 ASP cc_start: 0.7899 (OUTLIER) cc_final: 0.7313 (t70) REVERT: VA 250 GLU cc_start: 0.6865 (mm-30) cc_final: 0.6582 (mm-30) REVERT: VA 270 LEU cc_start: 0.7996 (mm) cc_final: 0.7770 (mp) REVERT: VA 364 GLN cc_start: 0.7815 (pt0) cc_final: 0.7440 (mm-40) REVERT: VA 472 LEU cc_start: 0.5489 (OUTLIER) cc_final: 0.4973 (pp) outliers start: 91 outliers final: 57 residues processed: 1061 average time/residue: 1.6039 time to fit residues: 2328.8932 Evaluate side-chains 1101 residues out of total 9240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1020 time to evaluate : 8.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 ASP Chi-restraints excluded: chain A residue 472 LEU Chi-restraints excluded: chain C residue 209 ASN Chi-restraints excluded: chain C residue 277 ASP Chi-restraints excluded: chain C residue 348 THR Chi-restraints excluded: chain C residue 460 LEU Chi-restraints excluded: chain E residue 9 ASP Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 348 THR Chi-restraints excluded: chain E residue 472 LEU Chi-restraints excluded: chain G residue 379 MET Chi-restraints excluded: chain G residue 401 ASP Chi-restraints excluded: chain G residue 472 LEU Chi-restraints excluded: chain I residue 277 ASP Chi-restraints excluded: chain I residue 348 THR Chi-restraints excluded: chain K residue 9 ASP Chi-restraints excluded: chain K residue 26 GLU Chi-restraints excluded: chain K residue 81 VAL Chi-restraints excluded: chain K residue 277 ASP Chi-restraints excluded: chain K residue 348 THR Chi-restraints excluded: chain K residue 472 LEU Chi-restraints excluded: chain M residue 401 ASP Chi-restraints excluded: chain M residue 472 LEU Chi-restraints excluded: chain O residue 277 ASP Chi-restraints excluded: chain O residue 348 THR Chi-restraints excluded: chain Q residue 9 ASP Chi-restraints excluded: chain Q residue 26 GLU Chi-restraints excluded: chain Q residue 277 ASP Chi-restraints excluded: chain Q residue 348 THR Chi-restraints excluded: chain Q residue 472 LEU Chi-restraints excluded: chain S residue 401 ASP Chi-restraints excluded: chain S residue 472 LEU Chi-restraints excluded: chain V residue 209 ASN Chi-restraints excluded: chain V residue 277 ASP Chi-restraints excluded: chain V residue 348 THR Chi-restraints excluded: chain X residue 9 ASP Chi-restraints excluded: chain X residue 26 GLU Chi-restraints excluded: chain X residue 277 ASP Chi-restraints excluded: chain X residue 348 THR Chi-restraints excluded: chain X residue 472 LEU Chi-restraints excluded: chain Z residue 401 ASP Chi-restraints excluded: chain Z residue 472 LEU Chi-restraints excluded: chain BA residue 277 ASP Chi-restraints excluded: chain BA residue 348 THR Chi-restraints excluded: chain DA residue 9 ASP Chi-restraints excluded: chain DA residue 26 GLU Chi-restraints excluded: chain DA residue 81 VAL Chi-restraints excluded: chain DA residue 277 ASP Chi-restraints excluded: chain DA residue 348 THR Chi-restraints excluded: chain DA residue 472 LEU Chi-restraints excluded: chain FA residue 401 ASP Chi-restraints excluded: chain FA residue 472 LEU Chi-restraints excluded: chain HA residue 209 ASN Chi-restraints excluded: chain HA residue 277 ASP Chi-restraints excluded: chain JA residue 9 ASP Chi-restraints excluded: chain JA residue 26 GLU Chi-restraints excluded: chain JA residue 81 VAL Chi-restraints excluded: chain JA residue 277 ASP Chi-restraints excluded: chain JA residue 348 THR Chi-restraints excluded: chain LA residue 401 ASP Chi-restraints excluded: chain LA residue 472 LEU Chi-restraints excluded: chain NA residue 277 ASP Chi-restraints excluded: chain NA residue 348 THR Chi-restraints excluded: chain PA residue 9 ASP Chi-restraints excluded: chain PA residue 26 GLU Chi-restraints excluded: chain PA residue 81 VAL Chi-restraints excluded: chain PA residue 277 ASP Chi-restraints excluded: chain PA residue 348 THR Chi-restraints excluded: chain PA residue 472 LEU Chi-restraints excluded: chain RA residue 401 ASP Chi-restraints excluded: chain RA residue 472 LEU Chi-restraints excluded: chain TA residue 277 ASP Chi-restraints excluded: chain TA residue 348 THR Chi-restraints excluded: chain VA residue 9 ASP Chi-restraints excluded: chain VA residue 26 GLU Chi-restraints excluded: chain VA residue 81 VAL Chi-restraints excluded: chain VA residue 277 ASP Chi-restraints excluded: chain VA residue 348 THR Chi-restraints excluded: chain VA residue 472 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 525 optimal weight: 4.9990 chunk 680 optimal weight: 3.9990 chunk 912 optimal weight: 10.0000 chunk 262 optimal weight: 0.9990 chunk 790 optimal weight: 5.9990 chunk 126 optimal weight: 2.9990 chunk 238 optimal weight: 8.9990 chunk 858 optimal weight: 2.9990 chunk 359 optimal weight: 0.1980 chunk 881 optimal weight: 9.9990 chunk 108 optimal weight: 0.7980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 136 HIS C 209 ASN ** C 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 136 HIS ** I 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 136 HIS ** O 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 136 HIS V 209 ASN ** V 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** BA 136 HIS ** BA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** FA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** HA 136 HIS HA 209 ASN ** HA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** LA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 136 HIS ** NA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** TA 136 HIS ** TA 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.167155 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.126600 restraints weight = 469482.496| |-----------------------------------------------------------------------------| r_work (start): 0.3325 rms_B_bonded: 6.13 r_work: 0.2804 rms_B_bonded: 6.04 restraints_weight: 2.0000 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2785 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2785 r_free = 0.2785 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2784 r_free = 0.2784 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.13 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2784 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8775 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 87864 Z= 0.170 Angle : 0.558 14.194 119400 Z= 0.282 Chirality : 0.042 0.151 13512 Planarity : 0.004 0.034 15288 Dihedral : 4.258 18.551 12264 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 1.23 % Allowed : 13.39 % Favored : 85.38 % 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: -0.22 (0.08), residues: 11016 helix: 1.45 (0.09), residues: 3600 sheet: 0.47 (0.11), residues: 2256 loop : -1.65 (0.08), residues: 5160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Z 394 HIS 0.003 0.001 HISNA 308 PHE 0.025 0.002 PHETA 423 TYR 0.011 0.001 TYRTA 78 ARG 0.002 0.000 ARG M 411 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33634.85 seconds wall clock time: 588 minutes 31.66 seconds (35311.66 seconds total)