Starting phenix.real_space_refine (version: dev) on Mon Dec 19 18:09:06 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cb8_7449/12_2022/6cb8_7449_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cb8_7449/12_2022/6cb8_7449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cb8_7449/12_2022/6cb8_7449.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cb8_7449/12_2022/6cb8_7449.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cb8_7449/12_2022/6cb8_7449_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6cb8_7449/12_2022/6cb8_7449_neut_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "B PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "C TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "D TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "F TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "G TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "I TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "J TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "L TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "M TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "O TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "P TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "S TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "U TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "W TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Y TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Z TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "0 PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "0 TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "1 TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 103936 Number of models: 1 Model: "" Number of chains: 28 Chain: "B" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO B 233 " pdbres="CDL B 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "A" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO A 233 " pdbres="CDL A 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "C" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO C 233 " pdbres="CDL C 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "D" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO D 233 " pdbres="CDL D 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO E 233 " pdbres="CDL E 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "F" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO F 233 " pdbres="CDL F 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "G" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO G 233 " pdbres="CDL G 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "H" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO H 233 " pdbres="CDL H 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "I" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO I 233 " pdbres="CDL I 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "J" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO J 233 " pdbres="CDL J 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "K" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO K 233 " pdbres="CDL K 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "L" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO L 233 " pdbres="CDL L 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "M" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO M 233 " pdbres="CDL M 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "N" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO N 233 " pdbres="CDL N 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "O" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO O 233 " pdbres="CDL O 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "P" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO P 233 " pdbres="CDL P 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "Q" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO Q 233 " pdbres="CDL Q 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "R" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO R 233 " pdbres="CDL R 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "S" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO S 233 " pdbres="CDL S 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "T" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO T 233 " pdbres="CDL T 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "U" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO U 233 " pdbres="CDL U 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "V" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO V 233 " pdbres="CDL V 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "W" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO W 233 " pdbres="CDL W 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "X" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO X 233 " pdbres="CDL X 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "Y" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO Y 233 " pdbres="CDL Y 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "Z" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO Z 233 " pdbres="CDL Z 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "0" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO 0 233 " pdbres="CDL 0 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Chain: "1" Number of atoms: 3712 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3712 Unusual residues: {'CDL': 1} Classifications: {'peptide': 230, 'undetermined': 1} Modifications used: {'NH3': 1} Link IDs: {'CIS': 1, 'PTRANS': 11, 'TRANS': 217, None: 1} Not linked: pdbres="PRO 1 233 " pdbres="CDL 1 301 " Chain breaks: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 92 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'CDL:plan-3': 1, 'CDL:plan-2': 1, 'CDL:plan-1': 1, 'CDL:plan-4': 1} Unresolved non-hydrogen planarities: 16 Residues with excluded nonbonded symmetry interactions: 28 residue: pdb=" CB2 CDL B 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL B 301 " occ=0.00 residue: pdb=" CB2 CDL A 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL A 301 " occ=0.00 residue: pdb=" CB2 CDL C 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL C 301 " occ=0.00 residue: pdb=" CB2 CDL D 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL D 301 " occ=0.00 residue: pdb=" CB2 CDL E 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL E 301 " occ=0.00 residue: pdb=" CB2 CDL F 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL F 301 " occ=0.00 residue: pdb=" CB2 CDL G 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL G 301 " occ=0.00 residue: pdb=" CB2 CDL H 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL H 301 " occ=0.00 residue: pdb=" CB2 CDL I 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL I 301 " occ=0.00 residue: pdb=" CB2 CDL J 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL J 301 " occ=0.00 residue: pdb=" CB2 CDL K 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL K 301 " occ=0.00 residue: pdb=" CB2 CDL L 301 " occ=0.00 ... (12 atoms not shown) pdb=" PB2 CDL L 301 " occ=0.00 ... (remaining 16 not shown) Time building chain proxies: 35.66, per 1000 atoms: 0.34 Number of scatterers: 103936 At special positions: 0 Unit cell: (297, 295.68, 79.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 224 16.00 P 56 15.00 O 9688 8.00 N 8792 7.00 C 32872 6.00 H 52304 1.00 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 Atom "HETATM 3700 OB2 CDL B 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3700 OB2 CDL B 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3705 OA2 CDL B 301 .*. O " rejected from bonding due to valence issues. Atom "HETATM 3705 OA2 CDL B 301 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 72.01 Conformation dependent library (CDL) restraints added in 7.6 seconds 12656 Ramachandran restraints generated. 6328 Oldfield, 0 Emsley, 6328 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12320 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 140 helices and 84 sheets defined 22.2% alpha, 36.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.23 Creating SS restraints... Processing helix chain 'B' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP B 6 " --> pdb=" O PRO B 2 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU B 65 " --> pdb=" O LEU B 61 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 132 Processing helix chain 'B' and resid 138 through 148 Processing helix chain 'A' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP A 6 " --> pdb=" O PRO A 2 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 34 Processing helix chain 'A' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU A 65 " --> pdb=" O LEU A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 132 Processing helix chain 'A' and resid 138 through 148 Processing helix chain 'C' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP C 6 " --> pdb=" O PRO C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 34 Processing helix chain 'C' and resid 59 through 65 removed outlier: 5.387A pdb=" N GLU C 65 " --> pdb=" O LEU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 132 Processing helix chain 'C' and resid 138 through 148 Processing helix chain 'D' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP D 6 " --> pdb=" O PRO D 2 " (cutoff:3.500A) Processing helix chain 'D' and resid 29 through 34 Processing helix chain 'D' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU D 65 " --> pdb=" O LEU D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 132 Processing helix chain 'D' and resid 138 through 148 Processing helix chain 'E' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP E 6 " --> pdb=" O PRO E 2 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 34 Processing helix chain 'E' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU E 65 " --> pdb=" O LEU E 61 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 132 Processing helix chain 'E' and resid 138 through 148 Processing helix chain 'F' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP F 6 " --> pdb=" O PRO F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 34 Processing helix chain 'F' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU F 65 " --> pdb=" O LEU F 61 " (cutoff:3.500A) Processing helix chain 'F' and resid 121 through 132 Processing helix chain 'F' and resid 138 through 148 Processing helix chain 'G' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP G 6 " --> pdb=" O PRO G 2 " (cutoff:3.500A) Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU G 65 " --> pdb=" O LEU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 132 Processing helix chain 'G' and resid 138 through 148 Processing helix chain 'H' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP H 6 " --> pdb=" O PRO H 2 " (cutoff:3.500A) Processing helix chain 'H' and resid 29 through 34 Processing helix chain 'H' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU H 65 " --> pdb=" O LEU H 61 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 132 Processing helix chain 'H' and resid 138 through 148 Processing helix chain 'I' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP I 6 " --> pdb=" O PRO I 2 " (cutoff:3.500A) Processing helix chain 'I' and resid 29 through 34 Processing helix chain 'I' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU I 65 " --> pdb=" O LEU I 61 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 132 Processing helix chain 'I' and resid 138 through 148 Processing helix chain 'J' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP J 6 " --> pdb=" O PRO J 2 " (cutoff:3.500A) Processing helix chain 'J' and resid 29 through 34 Processing helix chain 'J' and resid 59 through 65 removed outlier: 3.500A pdb=" N LEU J 63 " --> pdb=" O THR J 59 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLU J 65 " --> pdb=" O LEU J 61 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 132 Processing helix chain 'J' and resid 138 through 148 Processing helix chain 'K' and resid 2 through 16 removed outlier: 3.624A pdb=" N ASP K 6 " --> pdb=" O PRO K 2 " (cutoff:3.500A) Processing helix chain 'K' and resid 29 through 34 Processing helix chain 'K' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU K 65 " --> pdb=" O LEU K 61 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 132 Processing helix chain 'K' and resid 138 through 148 Processing helix chain 'L' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP L 6 " --> pdb=" O PRO L 2 " (cutoff:3.500A) Processing helix chain 'L' and resid 29 through 34 Processing helix chain 'L' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU L 65 " --> pdb=" O LEU L 61 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 132 Processing helix chain 'L' and resid 138 through 148 Processing helix chain 'M' and resid 2 through 16 removed outlier: 3.624A pdb=" N ASP M 6 " --> pdb=" O PRO M 2 " (cutoff:3.500A) Processing helix chain 'M' and resid 29 through 34 Processing helix chain 'M' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU M 65 " --> pdb=" O LEU M 61 " (cutoff:3.500A) Processing helix chain 'M' and resid 121 through 132 Processing helix chain 'M' and resid 138 through 148 Processing helix chain 'N' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP N 6 " --> pdb=" O PRO N 2 " (cutoff:3.500A) Processing helix chain 'N' and resid 29 through 34 Processing helix chain 'N' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU N 65 " --> pdb=" O LEU N 61 " (cutoff:3.500A) Processing helix chain 'N' and resid 121 through 132 Processing helix chain 'N' and resid 138 through 148 Processing helix chain 'O' and resid 2 through 16 removed outlier: 3.624A pdb=" N ASP O 6 " --> pdb=" O PRO O 2 " (cutoff:3.500A) Processing helix chain 'O' and resid 29 through 34 Processing helix chain 'O' and resid 59 through 65 removed outlier: 3.500A pdb=" N LEU O 63 " --> pdb=" O THR O 59 " (cutoff:3.500A) removed outlier: 5.387A pdb=" N GLU O 65 " --> pdb=" O LEU O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 121 through 132 Processing helix chain 'O' and resid 138 through 148 Processing helix chain 'P' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP P 6 " --> pdb=" O PRO P 2 " (cutoff:3.500A) Processing helix chain 'P' and resid 29 through 34 Processing helix chain 'P' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU P 65 " --> pdb=" O LEU P 61 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 132 Processing helix chain 'P' and resid 138 through 148 Processing helix chain 'Q' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP Q 6 " --> pdb=" O PRO Q 2 " (cutoff:3.500A) Processing helix chain 'Q' and resid 29 through 34 Processing helix chain 'Q' and resid 59 through 65 removed outlier: 3.500A pdb=" N LEU Q 63 " --> pdb=" O THR Q 59 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLU Q 65 " --> pdb=" O LEU Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 121 through 132 Processing helix chain 'Q' and resid 138 through 148 Processing helix chain 'R' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP R 6 " --> pdb=" O PRO R 2 " (cutoff:3.500A) Processing helix chain 'R' and resid 29 through 34 Processing helix chain 'R' and resid 59 through 65 removed outlier: 3.500A pdb=" N LEU R 63 " --> pdb=" O THR R 59 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLU R 65 " --> pdb=" O LEU R 61 " (cutoff:3.500A) Processing helix chain 'R' and resid 121 through 132 Processing helix chain 'R' and resid 138 through 148 Processing helix chain 'S' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP S 6 " --> pdb=" O PRO S 2 " (cutoff:3.500A) Processing helix chain 'S' and resid 29 through 34 Processing helix chain 'S' and resid 59 through 65 removed outlier: 3.500A pdb=" N LEU S 63 " --> pdb=" O THR S 59 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N GLU S 65 " --> pdb=" O LEU S 61 " (cutoff:3.500A) Processing helix chain 'S' and resid 121 through 132 Processing helix chain 'S' and resid 138 through 148 Processing helix chain 'T' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP T 6 " --> pdb=" O PRO T 2 " (cutoff:3.500A) Processing helix chain 'T' and resid 29 through 34 Processing helix chain 'T' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU T 65 " --> pdb=" O LEU T 61 " (cutoff:3.500A) Processing helix chain 'T' and resid 121 through 132 Processing helix chain 'T' and resid 138 through 148 Processing helix chain 'U' and resid 2 through 16 removed outlier: 3.624A pdb=" N ASP U 6 " --> pdb=" O PRO U 2 " (cutoff:3.500A) Processing helix chain 'U' and resid 29 through 34 Processing helix chain 'U' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU U 65 " --> pdb=" O LEU U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 121 through 132 Processing helix chain 'U' and resid 138 through 148 Processing helix chain 'V' and resid 2 through 16 removed outlier: 3.624A pdb=" N ASP V 6 " --> pdb=" O PRO V 2 " (cutoff:3.500A) Processing helix chain 'V' and resid 29 through 34 Processing helix chain 'V' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU V 65 " --> pdb=" O LEU V 61 " (cutoff:3.500A) Processing helix chain 'V' and resid 121 through 132 Processing helix chain 'V' and resid 138 through 148 Processing helix chain 'W' and resid 2 through 16 removed outlier: 3.622A pdb=" N ASP W 6 " --> pdb=" O PRO W 2 " (cutoff:3.500A) Processing helix chain 'W' and resid 29 through 34 Processing helix chain 'W' and resid 59 through 65 removed outlier: 5.389A pdb=" N GLU W 65 " --> pdb=" O LEU W 61 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 132 Processing helix chain 'W' and resid 138 through 148 Processing helix chain 'X' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP X 6 " --> pdb=" O PRO X 2 " (cutoff:3.500A) Processing helix chain 'X' and resid 29 through 34 Processing helix chain 'X' and resid 59 through 65 removed outlier: 5.387A pdb=" N GLU X 65 " --> pdb=" O LEU X 61 " (cutoff:3.500A) Processing helix chain 'X' and resid 121 through 132 Processing helix chain 'X' and resid 138 through 148 Processing helix chain 'Y' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP Y 6 " --> pdb=" O PRO Y 2 " (cutoff:3.500A) Processing helix chain 'Y' and resid 29 through 34 Processing helix chain 'Y' and resid 59 through 65 removed outlier: 3.500A pdb=" N LEU Y 63 " --> pdb=" O THR Y 59 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N GLU Y 65 " --> pdb=" O LEU Y 61 " (cutoff:3.500A) Processing helix chain 'Y' and resid 121 through 132 Processing helix chain 'Y' and resid 138 through 148 Processing helix chain 'Z' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP Z 6 " --> pdb=" O PRO Z 2 " (cutoff:3.500A) Processing helix chain 'Z' and resid 29 through 34 Processing helix chain 'Z' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU Z 65 " --> pdb=" O LEU Z 61 " (cutoff:3.500A) Processing helix chain 'Z' and resid 121 through 132 Processing helix chain 'Z' and resid 138 through 148 Processing helix chain '0' and resid 2 through 16 removed outlier: 3.624A pdb=" N ASP 0 6 " --> pdb=" O PRO 0 2 " (cutoff:3.500A) Processing helix chain '0' and resid 29 through 34 Processing helix chain '0' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU 0 65 " --> pdb=" O LEU 0 61 " (cutoff:3.500A) Processing helix chain '0' and resid 121 through 132 Processing helix chain '0' and resid 138 through 148 Processing helix chain '1' and resid 2 through 16 removed outlier: 3.623A pdb=" N ASP 1 6 " --> pdb=" O PRO 1 2 " (cutoff:3.500A) Processing helix chain '1' and resid 29 through 34 Processing helix chain '1' and resid 59 through 65 removed outlier: 5.388A pdb=" N GLU 1 65 " --> pdb=" O LEU 1 61 " (cutoff:3.500A) Processing helix chain '1' and resid 121 through 132 Processing helix chain '1' and resid 138 through 148 Processing sheet with id= 1, first strand: chain 'B' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU B 204 " --> pdb=" O LEU B 24 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG B 207 " --> pdb=" O MET B 155 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET B 155 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS B 37 " --> pdb=" O VAL B 154 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'B' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL B 99 " --> pdb=" O VAL B 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR B 112 " --> pdb=" O THR B 165 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR B 165 " --> pdb=" O THR B 112 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 156 through 159 removed outlier: 4.621A pdb=" N GLU B 156 " --> pdb=" O ARG B 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA B 205 " --> pdb=" O VAL B 158 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU A 204 " --> pdb=" O LEU A 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG A 207 " --> pdb=" O MET A 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET A 155 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS A 37 " --> pdb=" O VAL A 154 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL A 99 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR A 112 " --> pdb=" O THR A 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR A 165 " --> pdb=" O THR A 112 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU A 156 " --> pdb=" O ARG A 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA A 205 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'C' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU C 204 " --> pdb=" O LEU C 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG C 207 " --> pdb=" O MET C 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET C 155 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N CYS C 37 " --> pdb=" O VAL C 154 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'C' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL C 99 " --> pdb=" O VAL C 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR C 112 " --> pdb=" O THR C 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR C 165 " --> pdb=" O THR C 112 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU C 156 " --> pdb=" O ARG C 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA C 205 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'D' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU D 204 " --> pdb=" O LEU D 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG D 207 " --> pdb=" O MET D 155 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET D 155 " --> pdb=" O ARG D 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS D 37 " --> pdb=" O VAL D 154 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'D' and resid 81 through 95 removed outlier: 3.728A pdb=" N VAL D 99 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR D 112 " --> pdb=" O THR D 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR D 165 " --> pdb=" O THR D 112 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'D' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU D 156 " --> pdb=" O ARG D 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA D 205 " --> pdb=" O VAL D 158 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'E' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU E 204 " --> pdb=" O LEU E 24 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG E 207 " --> pdb=" O MET E 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET E 155 " --> pdb=" O ARG E 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS E 37 " --> pdb=" O VAL E 154 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'E' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL E 99 " --> pdb=" O VAL E 95 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR E 112 " --> pdb=" O THR E 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR E 165 " --> pdb=" O THR E 112 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'E' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU E 156 " --> pdb=" O ARG E 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA E 205 " --> pdb=" O VAL E 158 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU F 204 " --> pdb=" O LEU F 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG F 207 " --> pdb=" O MET F 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET F 155 " --> pdb=" O ARG F 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS F 37 " --> pdb=" O VAL F 154 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL F 99 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR F 112 " --> pdb=" O THR F 165 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR F 165 " --> pdb=" O THR F 112 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'F' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU F 156 " --> pdb=" O ARG F 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA F 205 " --> pdb=" O VAL F 158 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU G 204 " --> pdb=" O LEU G 24 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG G 207 " --> pdb=" O MET G 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET G 155 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS G 37 " --> pdb=" O VAL G 154 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'G' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL G 99 " --> pdb=" O VAL G 95 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR G 112 " --> pdb=" O THR G 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR G 165 " --> pdb=" O THR G 112 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'G' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU G 156 " --> pdb=" O ARG G 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA G 205 " --> pdb=" O VAL G 158 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'H' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU H 204 " --> pdb=" O LEU H 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG H 207 " --> pdb=" O MET H 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET H 155 " --> pdb=" O ARG H 207 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS H 37 " --> pdb=" O VAL H 154 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'H' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL H 99 " --> pdb=" O VAL H 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR H 112 " --> pdb=" O THR H 165 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR H 165 " --> pdb=" O THR H 112 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'H' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU H 156 " --> pdb=" O ARG H 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA H 205 " --> pdb=" O VAL H 158 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'I' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU I 204 " --> pdb=" O LEU I 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG I 207 " --> pdb=" O MET I 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET I 155 " --> pdb=" O ARG I 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS I 37 " --> pdb=" O VAL I 154 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'I' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL I 99 " --> pdb=" O VAL I 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR I 112 " --> pdb=" O THR I 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR I 165 " --> pdb=" O THR I 112 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'I' and resid 156 through 159 removed outlier: 4.621A pdb=" N GLU I 156 " --> pdb=" O ARG I 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA I 205 " --> pdb=" O VAL I 158 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'J' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU J 204 " --> pdb=" O LEU J 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG J 207 " --> pdb=" O MET J 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET J 155 " --> pdb=" O ARG J 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS J 37 " --> pdb=" O VAL J 154 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'J' and resid 81 through 95 removed outlier: 3.728A pdb=" N VAL J 99 " --> pdb=" O VAL J 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR J 112 " --> pdb=" O THR J 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR J 165 " --> pdb=" O THR J 112 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'J' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU J 156 " --> pdb=" O ARG J 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA J 205 " --> pdb=" O VAL J 158 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'K' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU K 204 " --> pdb=" O LEU K 24 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG K 207 " --> pdb=" O MET K 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET K 155 " --> pdb=" O ARG K 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS K 37 " --> pdb=" O VAL K 154 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'K' and resid 81 through 95 removed outlier: 3.728A pdb=" N VAL K 99 " --> pdb=" O VAL K 95 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N THR K 112 " --> pdb=" O THR K 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR K 165 " --> pdb=" O THR K 112 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'K' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU K 156 " --> pdb=" O ARG K 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA K 205 " --> pdb=" O VAL K 158 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'L' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU L 204 " --> pdb=" O LEU L 24 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG L 207 " --> pdb=" O MET L 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET L 155 " --> pdb=" O ARG L 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS L 37 " --> pdb=" O VAL L 154 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'L' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL L 99 " --> pdb=" O VAL L 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR L 112 " --> pdb=" O THR L 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR L 165 " --> pdb=" O THR L 112 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'L' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU L 156 " --> pdb=" O ARG L 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA L 205 " --> pdb=" O VAL L 158 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'M' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU M 204 " --> pdb=" O LEU M 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG M 207 " --> pdb=" O MET M 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET M 155 " --> pdb=" O ARG M 207 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N CYS M 37 " --> pdb=" O VAL M 154 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'M' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL M 99 " --> pdb=" O VAL M 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR M 112 " --> pdb=" O THR M 165 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR M 165 " --> pdb=" O THR M 112 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'M' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU M 156 " --> pdb=" O ARG M 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA M 205 " --> pdb=" O VAL M 158 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'N' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU N 204 " --> pdb=" O LEU N 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG N 207 " --> pdb=" O MET N 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET N 155 " --> pdb=" O ARG N 207 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N CYS N 37 " --> pdb=" O VAL N 154 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'N' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL N 99 " --> pdb=" O VAL N 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR N 112 " --> pdb=" O THR N 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR N 165 " --> pdb=" O THR N 112 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'N' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU N 156 " --> pdb=" O ARG N 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA N 205 " --> pdb=" O VAL N 158 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'O' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU O 204 " --> pdb=" O LEU O 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG O 207 " --> pdb=" O MET O 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET O 155 " --> pdb=" O ARG O 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS O 37 " --> pdb=" O VAL O 154 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'O' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL O 99 " --> pdb=" O VAL O 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR O 112 " --> pdb=" O THR O 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR O 165 " --> pdb=" O THR O 112 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'O' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU O 156 " --> pdb=" O ARG O 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA O 205 " --> pdb=" O VAL O 158 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'P' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU P 204 " --> pdb=" O LEU P 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG P 207 " --> pdb=" O MET P 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET P 155 " --> pdb=" O ARG P 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS P 37 " --> pdb=" O VAL P 154 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'P' and resid 81 through 95 removed outlier: 3.726A pdb=" N VAL P 99 " --> pdb=" O VAL P 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR P 112 " --> pdb=" O THR P 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR P 165 " --> pdb=" O THR P 112 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'P' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU P 156 " --> pdb=" O ARG P 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA P 205 " --> pdb=" O VAL P 158 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'Q' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU Q 204 " --> pdb=" O LEU Q 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG Q 207 " --> pdb=" O MET Q 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET Q 155 " --> pdb=" O ARG Q 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS Q 37 " --> pdb=" O VAL Q 154 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'Q' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL Q 99 " --> pdb=" O VAL Q 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR Q 112 " --> pdb=" O THR Q 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR Q 165 " --> pdb=" O THR Q 112 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'Q' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU Q 156 " --> pdb=" O ARG Q 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA Q 205 " --> pdb=" O VAL Q 158 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'R' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU R 204 " --> pdb=" O LEU R 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG R 207 " --> pdb=" O MET R 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET R 155 " --> pdb=" O ARG R 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS R 37 " --> pdb=" O VAL R 154 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'R' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL R 99 " --> pdb=" O VAL R 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR R 112 " --> pdb=" O THR R 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR R 165 " --> pdb=" O THR R 112 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'R' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU R 156 " --> pdb=" O ARG R 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA R 205 " --> pdb=" O VAL R 158 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'S' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU S 204 " --> pdb=" O LEU S 24 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ARG S 207 " --> pdb=" O MET S 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET S 155 " --> pdb=" O ARG S 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS S 37 " --> pdb=" O VAL S 154 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'S' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL S 99 " --> pdb=" O VAL S 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR S 112 " --> pdb=" O THR S 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR S 165 " --> pdb=" O THR S 112 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'S' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU S 156 " --> pdb=" O ARG S 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA S 205 " --> pdb=" O VAL S 158 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'T' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU T 204 " --> pdb=" O LEU T 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG T 207 " --> pdb=" O MET T 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET T 155 " --> pdb=" O ARG T 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS T 37 " --> pdb=" O VAL T 154 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'T' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL T 99 " --> pdb=" O VAL T 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR T 112 " --> pdb=" O THR T 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR T 165 " --> pdb=" O THR T 112 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'T' and resid 156 through 159 removed outlier: 4.621A pdb=" N GLU T 156 " --> pdb=" O ARG T 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA T 205 " --> pdb=" O VAL T 158 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'U' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU U 204 " --> pdb=" O LEU U 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG U 207 " --> pdb=" O MET U 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET U 155 " --> pdb=" O ARG U 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS U 37 " --> pdb=" O VAL U 154 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'U' and resid 81 through 95 removed outlier: 3.726A pdb=" N VAL U 99 " --> pdb=" O VAL U 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR U 112 " --> pdb=" O THR U 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR U 165 " --> pdb=" O THR U 112 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'U' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU U 156 " --> pdb=" O ARG U 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA U 205 " --> pdb=" O VAL U 158 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'V' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU V 204 " --> pdb=" O LEU V 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG V 207 " --> pdb=" O MET V 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET V 155 " --> pdb=" O ARG V 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS V 37 " --> pdb=" O VAL V 154 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'V' and resid 81 through 95 removed outlier: 3.728A pdb=" N VAL V 99 " --> pdb=" O VAL V 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR V 112 " --> pdb=" O THR V 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR V 165 " --> pdb=" O THR V 112 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'V' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU V 156 " --> pdb=" O ARG V 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA V 205 " --> pdb=" O VAL V 158 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'W' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU W 204 " --> pdb=" O LEU W 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG W 207 " --> pdb=" O MET W 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET W 155 " --> pdb=" O ARG W 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS W 37 " --> pdb=" O VAL W 154 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'W' and resid 81 through 95 removed outlier: 3.728A pdb=" N VAL W 99 " --> pdb=" O VAL W 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR W 112 " --> pdb=" O THR W 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR W 165 " --> pdb=" O THR W 112 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'W' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU W 156 " --> pdb=" O ARG W 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA W 205 " --> pdb=" O VAL W 158 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'X' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU X 204 " --> pdb=" O LEU X 24 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG X 207 " --> pdb=" O MET X 155 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N MET X 155 " --> pdb=" O ARG X 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS X 37 " --> pdb=" O VAL X 154 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'X' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL X 99 " --> pdb=" O VAL X 95 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR X 112 " --> pdb=" O THR X 165 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR X 165 " --> pdb=" O THR X 112 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'X' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU X 156 " --> pdb=" O ARG X 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA X 205 " --> pdb=" O VAL X 158 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'Y' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU Y 204 " --> pdb=" O LEU Y 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG Y 207 " --> pdb=" O MET Y 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET Y 155 " --> pdb=" O ARG Y 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS Y 37 " --> pdb=" O VAL Y 154 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'Y' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL Y 99 " --> pdb=" O VAL Y 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR Y 112 " --> pdb=" O THR Y 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR Y 165 " --> pdb=" O THR Y 112 " (cutoff:3.500A) Processing sheet with id= 75, first strand: chain 'Y' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU Y 156 " --> pdb=" O ARG Y 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA Y 205 " --> pdb=" O VAL Y 158 " (cutoff:3.500A) Processing sheet with id= 76, first strand: chain 'Z' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU Z 204 " --> pdb=" O LEU Z 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG Z 207 " --> pdb=" O MET Z 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET Z 155 " --> pdb=" O ARG Z 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS Z 37 " --> pdb=" O VAL Z 154 " (cutoff:3.500A) Processing sheet with id= 77, first strand: chain 'Z' and resid 81 through 95 removed outlier: 3.728A pdb=" N VAL Z 99 " --> pdb=" O VAL Z 95 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N THR Z 112 " --> pdb=" O THR Z 165 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N THR Z 165 " --> pdb=" O THR Z 112 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'Z' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU Z 156 " --> pdb=" O ARG Z 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA Z 205 " --> pdb=" O VAL Z 158 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain '0' and resid 21 through 24 removed outlier: 7.147A pdb=" N LEU 0 204 " --> pdb=" O LEU 0 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG 0 207 " --> pdb=" O MET 0 155 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N MET 0 155 " --> pdb=" O ARG 0 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS 0 37 " --> pdb=" O VAL 0 154 " (cutoff:3.500A) Processing sheet with id= 80, first strand: chain '0' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL 0 99 " --> pdb=" O VAL 0 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR 0 112 " --> pdb=" O THR 0 165 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N THR 0 165 " --> pdb=" O THR 0 112 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain '0' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU 0 156 " --> pdb=" O ARG 0 207 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ALA 0 205 " --> pdb=" O VAL 0 158 " (cutoff:3.500A) Processing sheet with id= 82, first strand: chain '1' and resid 21 through 24 removed outlier: 7.148A pdb=" N LEU 1 204 " --> pdb=" O LEU 1 24 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG 1 207 " --> pdb=" O MET 1 155 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N MET 1 155 " --> pdb=" O ARG 1 207 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N CYS 1 37 " --> pdb=" O VAL 1 154 " (cutoff:3.500A) Processing sheet with id= 83, first strand: chain '1' and resid 81 through 95 removed outlier: 3.727A pdb=" N VAL 1 99 " --> pdb=" O VAL 1 95 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N THR 1 112 " --> pdb=" O THR 1 165 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N THR 1 165 " --> pdb=" O THR 1 112 " (cutoff:3.500A) Processing sheet with id= 84, first strand: chain '1' and resid 156 through 159 removed outlier: 4.620A pdb=" N GLU 1 156 " --> pdb=" O ARG 1 207 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA 1 205 " --> pdb=" O VAL 1 158 " (cutoff:3.500A) 2290 hydrogen bonds defined for protein. 6786 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: 44.74 Time building geometry restraints manager: 76.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 52220 1.03 - 1.23: 227 1.23 - 1.42: 21137 1.42 - 1.62: 30884 1.62 - 1.81: 420 Bond restraints: 104888 Sorted by residual: bond pdb=" OB2 CDL L 301 " pdb=" PB2 CDL L 301 " ideal model delta sigma weight residual 1.579 1.651 -0.072 1.50e-02 4.44e+03 2.27e+01 bond pdb=" OB2 CDL S 301 " pdb=" PB2 CDL S 301 " ideal model delta sigma weight residual 1.579 1.650 -0.071 1.50e-02 4.44e+03 2.23e+01 bond pdb=" OB2 CDL B 301 " pdb=" PB2 CDL B 301 " ideal model delta sigma weight residual 1.579 1.650 -0.071 1.50e-02 4.44e+03 2.23e+01 bond pdb=" OA2 CDL V 301 " pdb=" PA1 CDL V 301 " ideal model delta sigma weight residual 1.579 1.650 -0.071 1.50e-02 4.44e+03 2.23e+01 bond pdb=" OB2 CDL E 301 " pdb=" PB2 CDL E 301 " ideal model delta sigma weight residual 1.579 1.650 -0.071 1.50e-02 4.44e+03 2.22e+01 ... (remaining 104883 not shown) Histogram of bond angle deviations from ideal: 99.21 - 106.17: 1605 106.17 - 113.12: 125971 113.12 - 120.08: 29950 120.08 - 127.03: 32034 127.03 - 133.99: 476 Bond angle restraints: 190036 Sorted by residual: angle pdb=" CB2 CDL 0 301 " pdb=" OB2 CDL 0 301 " pdb=" PB2 CDL 0 301 " ideal model delta sigma weight residual 121.27 118.40 2.87 1.00e+00 1.00e+00 8.26e+00 angle pdb=" CB2 CDL J 301 " pdb=" OB2 CDL J 301 " pdb=" PB2 CDL J 301 " ideal model delta sigma weight residual 121.27 118.40 2.87 1.00e+00 1.00e+00 8.24e+00 angle pdb=" CB2 CDL X 301 " pdb=" OB2 CDL X 301 " pdb=" PB2 CDL X 301 " ideal model delta sigma weight residual 121.27 118.40 2.87 1.00e+00 1.00e+00 8.23e+00 angle pdb=" CB2 CDL T 301 " pdb=" OB2 CDL T 301 " pdb=" PB2 CDL T 301 " ideal model delta sigma weight residual 121.27 118.40 2.87 1.00e+00 1.00e+00 8.21e+00 angle pdb=" CB2 CDL D 301 " pdb=" OB2 CDL D 301 " pdb=" PB2 CDL D 301 " ideal model delta sigma weight residual 121.27 118.41 2.86 1.00e+00 1.00e+00 8.21e+00 ... (remaining 190031 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.26: 39068 14.26 - 28.52: 2288 28.52 - 42.78: 588 42.78 - 57.03: 84 57.03 - 71.29: 56 Dihedral angle restraints: 42084 sinusoidal: 20188 harmonic: 21896 Sorted by residual: dihedral pdb=" CA GLY Z 19 " pdb=" C GLY Z 19 " pdb=" N ASP Z 20 " pdb=" CA ASP Z 20 " ideal model delta harmonic sigma weight residual -180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA GLY D 19 " pdb=" C GLY D 19 " pdb=" N ASP D 20 " pdb=" CA ASP D 20 " ideal model delta harmonic sigma weight residual -180.00 -154.43 -25.57 0 5.00e+00 4.00e-02 2.61e+01 dihedral pdb=" CA GLY T 19 " pdb=" C GLY T 19 " pdb=" N ASP T 20 " pdb=" CA ASP T 20 " ideal model delta harmonic sigma weight residual -180.00 -154.44 -25.56 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 42081 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 4557 0.032 - 0.064: 2330 0.064 - 0.096: 976 0.096 - 0.129: 338 0.129 - 0.161: 59 Chirality restraints: 8260 Sorted by residual: chirality pdb=" CA VAL C 39 " pdb=" N VAL C 39 " pdb=" C VAL C 39 " pdb=" CB VAL C 39 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.45e-01 chirality pdb=" CA VAL N 39 " pdb=" N VAL N 39 " pdb=" C VAL N 39 " pdb=" CB VAL N 39 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.39e-01 chirality pdb=" CA VAL V 39 " pdb=" N VAL V 39 " pdb=" C VAL V 39 " pdb=" CB VAL V 39 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.38e-01 ... (remaining 8257 not shown) Planarity restraints: 15092 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU I 178 " 0.045 5.00e-02 4.00e+02 6.97e-02 7.78e+00 pdb=" N PRO I 179 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO I 179 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO I 179 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 178 " -0.045 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO D 179 " 0.121 5.00e-02 4.00e+02 pdb=" CA PRO D 179 " -0.037 5.00e-02 4.00e+02 pdb=" CD PRO D 179 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU M 178 " 0.045 5.00e-02 4.00e+02 6.97e-02 7.77e+00 pdb=" N PRO M 179 " -0.121 5.00e-02 4.00e+02 pdb=" CA PRO M 179 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO M 179 " 0.038 5.00e-02 4.00e+02 ... (remaining 15089 not shown) Histogram of nonbonded interaction distances: 0.07 - 0.98: 1274 0.98 - 1.88: 9173 1.88 - 2.79: 252777 2.79 - 3.69: 478912 3.69 - 4.60: 831360 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1573496 Sorted by model distance: nonbonded pdb="HD12 LEU B 125 " pdb=" HG LEU T 60 " model vdw 0.075 2.440 nonbonded pdb=" CA LEU B 47 " pdb=" HE3 TRP T 49 " model vdw 0.116 2.750 nonbonded pdb=" CG LEU B 183 " pdb=" HG2 GLU U 94 " model vdw 0.126 2.920 nonbonded pdb=" CB TYR B 223 " pdb=" O LEU T 210 " model vdw 0.173 3.100 nonbonded pdb=" CD ARG B 55 " pdb=" H GLU U 156 " model vdw 0.174 2.750 ... (remaining 1573491 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '1' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 56 5.49 5 S 224 5.16 5 C 32872 2.51 5 N 8792 2.21 5 O 9688 1.98 5 H 52304 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.400 Extract box with map and model: 17.760 Check model and map are aligned: 1.180 Convert atoms to be neutral: 0.670 Process input model: 274.620 Find NCS groups from input model: 4.300 Set up NCS constraints: 0.720 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 306.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.2633 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 : 0.006 0.072 52584 Z= 0.382 Angle : 0.841 8.453 71260 Z= 0.441 Chirality : 0.046 0.161 8260 Planarity : 0.006 0.070 8988 Dihedral : 11.534 71.294 19628 Min Nonbonded Distance : 0.173 Molprobity Statistics. All-atom Clashscore : 75.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.58 % Favored : 81.42 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.72 (0.08), residues: 6328 helix: -2.46 (0.12), residues: 1316 sheet: -3.41 (0.08), residues: 2688 loop : -4.85 (0.09), residues: 2324 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12656 Ramachandran restraints generated. 6328 Oldfield, 0 Emsley, 6328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12656 Ramachandran restraints generated. 6328 Oldfield, 0 Emsley, 6328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1427 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1427 time to evaluate : 6.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry 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revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1427 average time/residue: 1.3979 time to fit residues: 3159.1817 Evaluate side-chains 901 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 901 time to evaluate : 6.615 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 8.0812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 543 optimal weight: 5.9990 chunk 488 optimal weight: 1.9990 chunk 270 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 329 optimal weight: 0.3980 chunk 260 optimal weight: 4.9990 chunk 504 optimal weight: 0.9990 chunk 195 optimal weight: 0.6980 chunk 306 optimal weight: 3.9990 chunk 375 optimal weight: 5.9990 chunk 584 optimal weight: 0.8980 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 0 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN G 109 GLN L 116 GLN L 187 GLN L 191 ASN M 187 GLN N 187 GLN ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 187 GLN P 187 GLN Q 187 GLN R 187 GLN ** T 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 90 GLN ** T 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 83 ASN ** Y 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 217 ASN ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 217 ASN Z 230 GLN 0 173 ASN ** 1 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3413 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.013 1.471 52584 Z= 0.898 Angle : 1.461 35.956 71260 Z= 0.789 Chirality : 0.069 0.924 8260 Planarity : 0.010 0.248 8988 Dihedral : 8.774 59.149 7028 Min Nonbonded Distance : 1.414 Molprobity Statistics. All-atom Clashscore : 66.54 Ramachandran Plot: Outliers : 0.77 % Allowed : 14.93 % Favored : 84.29 % Rotamer Outliers : 3.09 % Cbeta Deviations : 0.94 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.36 % Twisted General : 0.80 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.84 (0.09), residues: 6328 helix: -1.39 (0.14), residues: 1273 sheet: -2.83 (0.10), residues: 2308 loop : -4.45 (0.09), residues: 2747 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12656 Ramachandran restraints generated. 6328 Oldfield, 0 Emsley, 6328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12656 Ramachandran restraints generated. 6328 Oldfield, 0 Emsley, 6328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1179 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1000 time to evaluate : 6.437 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 179 outliers final: 131 residues processed: 1129 average time/residue: 1.3019 time to fit residues: 2391.3263 Evaluate side-chains 932 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 131 poor density : 801 time to evaluate : 6.281 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 131 outliers final: 48 residues processed: 131 average time/residue: 1.0829 time to fit residues: 258.4505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 325 optimal weight: 0.0670 chunk 181 optimal weight: 0.5980 chunk 486 optimal weight: 4.9990 chunk 398 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 585 optimal weight: 2.9990 chunk 632 optimal weight: 0.9990 chunk 521 optimal weight: 6.9990 chunk 580 optimal weight: 0.7980 chunk 199 optimal weight: 3.9990 chunk 470 optimal weight: 0.6980 overall best weight: 0.6320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 88 GLN H 109 GLN ** H 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 78 ASN ** P 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 217 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3852 moved from start: 0.7014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.011 1.467 52584 Z= 0.751 Angle : 1.194 43.770 71260 Z= 0.651 Chirality : 0.058 0.811 8260 Planarity : 0.008 0.181 8988 Dihedral : 7.977 63.717 7028 Min Nonbonded Distance : 1.483 Molprobity Statistics. All-atom Clashscore : 52.86 Ramachandran Plot: Outliers : 0.24 % Allowed : 12.88 % Favored : 86.88 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.60 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.71 % Twisted General : 0.67 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.09 (0.10), residues: 6328 helix: -0.43 (0.16), residues: 1274 sheet: -2.57 (0.10), residues: 2386 loop : -3.98 (0.09), residues: 2668 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12656 Ramachandran restraints generated. 6328 Oldfield, 0 Emsley, 6328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12656 Ramachandran restraints generated. 6328 Oldfield, 0 Emsley, 6328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1092 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 165 poor density : 927 time to evaluate : 6.412 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 165 outliers final: 118 residues processed: 1058 average time/residue: 1.3272 time to fit residues: 2277.3923 Evaluate side-chains 910 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 118 poor density : 792 time to evaluate : 6.274 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 118 outliers final: 65 residues processed: 118 average time/residue: 1.1713 time to fit residues: 244.0979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 578 optimal weight: 0.6980 chunk 440 optimal weight: 1.9990 chunk 304 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 279 optimal weight: 4.9990 chunk 393 optimal weight: 2.9990 chunk 587 optimal weight: 2.9990 chunk 622 optimal weight: 0.0170 chunk 307 optimal weight: 3.9990 chunk 557 optimal weight: 4.9990 chunk 167 optimal weight: 6.9990 overall best weight: 1.7424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 230 GLN ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 230 GLN ** F 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 138 HIS M 78 ASN M 83 ASN ** N 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 83 ASN ** P 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 ASN ** S 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 116 GLN Y 32 HIS ** Z 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 217 ASN ** 0 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 78 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5227 moved from start: 1.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.012 1.478 52584 Z= 0.802 Angle : 1.293 42.989 71260 Z= 0.691 Chirality : 0.062 0.659 8260 Planarity : 0.009 0.189 8988 Dihedral : 8.398 73.474 7028 Min Nonbonded Distance : 1.511 Molprobity Statistics. All-atom Clashscore : 57.52 Ramachandran Plot: Outliers : 0.25 % Allowed : 15.41 % Favored : 84.34 % Rotamer Outliers : 5.47 % Cbeta Deviations : 0.49 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.71 % Twisted General : 0.70 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.15 (0.10), residues: 6328 helix: -0.72 (0.14), residues: 1306 sheet: -2.74 (0.10), residues: 2424 loop : -3.77 (0.10), residues: 2598 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12656 Ramachandran restraints generated. 6328 Oldfield, 0 Emsley, 6328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12656 Ramachandran restraints generated. 6328 Oldfield, 0 Emsley, 6328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1286 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 317 poor density : 969 time to evaluate : 6.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 317 outliers final: 191 residues processed: 1212 average time/residue: 1.2734 time to fit residues: 2504.7707 Evaluate side-chains 913 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 191 poor density : 722 time to evaluate : 6.444 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 191 outliers final: 67 residues processed: 191 average time/residue: 1.0973 time to fit residues: 372.8093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 644 random chunks: chunk 518 optimal weight: 3.9990 chunk 353 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 463 optimal weight: 0.9990 chunk 256 optimal weight: 3.9990 chunk 531 optimal weight: 1.9990 chunk 430 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 317 optimal weight: 4.9990 chunk 558 optimal weight: 4.9990 chunk 157 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 173 ASN C 32 HIS F 16 ASN G 78 ASN J 109 GLN L 109 GLN O 78 ASN P 78 ASN ** P 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 226 ASN ** S 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 147 HIS Z 217 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5376 moved from start: 1.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 1.471 52584 Z= 0.723 Angle : 1.085 42.340 71260 Z= 0.585 Chirality : 0.054 0.759 8260 Planarity : 0.007 0.181 8988 Dihedral : 7.610 69.438 7028 Min Nonbonded Distance : 1.447 Molprobity Statistics. All-atom Clashscore : 47.25 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.48 % Favored : 87.34 % Rotamer Outliers : 3.47 % Cbeta Deviations : 0.34 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.46 % Twisted Proline : 0.36 % Twisted General : 0.66 % 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: -3.68 (0.10), residues: 6328 helix: -0.15 (0.15), residues: 1305 sheet: -2.60 (0.10), residues: 2466 loop : -3.40 (0.11), residues: 2557 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12656 Ramachandran restraints generated. 6328 Oldfield, 0 Emsley, 6328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12656 Ramachandran restraints generated. 6328 Oldfield, 0 Emsley, 6328 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 999 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 798 time to evaluate : 6.563 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 201 outliers final: 147 residues processed: 963 average time/residue: 1.2515 time to fit residues: 1950.4048 Evaluate side-chains 827 residues out of total 5796 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 680 time to evaluate : 6.838 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 147 outliers final: 64 residues processed: 147 average time/residue: 1.1083 time to fit residues: 293.4152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/iotbx/cli_parser.py", line 864, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 736, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 50.2878 > 50: distance: 133 - 134: 4.520 distance: 134 - 139: 3.846 distance: 142 - 143: 3.358 distance: 144 - 145: 3.303 distance: 152 - 160: 3.249 distance: 153 - 154: 3.027 distance: 156 - 163: 3.290 distance: 171 - 172: 3.075 distance: 171 - 178: 4.363 distance: 171 - 442: 5.106 distance: 173 - 185: 3.706 distance: 174 - 439: 6.465 distance: 175 - 176: 4.382 distance: 175 - 177: 3.187 distance: 176 - 181: 5.581 distance: 177 - 182: 3.167 distance: 177 - 184: 3.052 distance: 185 - 186: 3.906 distance: 186 - 187: 3.778 distance: 186 - 189: 4.251 distance: 186 - 192: 3.012 distance: 190 - 191: 4.587 distance: 190 - 195: 3.755 distance: 191 - 198: 4.113 distance: 199 - 200: 3.265 distance: 199 - 207: 3.206 distance: 200 - 201: 5.474 distance: 200 - 208: 4.472 distance: 201 - 202: 7.932 distance: 201 - 218: 4.051 distance: 203 - 209: 4.278 distance: 203 - 210: 4.219 distance: 204 - 206: 4.235 distance: 205 - 214: 4.075 distance: 206 - 217: 4.087 distance: 218 - 226: 5.507 distance: 219 - 220: 3.764 distance: 219 - 222: 4.277 distance: 219 - 227: 4.565 distance: 220 - 221: 4.510 distance: 222 - 223: 4.845 distance: 222 - 228: 8.336 distance: 222 - 229: 3.612 distance: 223 - 224: 6.098 distance: 223 - 225: 6.450 distance: 230 - 231: 4.425 distance: 230 - 236: 6.651 distance: 231 - 232: 6.858 distance: 231 - 234: 6.379 distance: 231 - 237: 8.851 distance: 232 - 233: 25.622 distance: 232 - 241: 7.371 distance: 234 - 235: 3.733 distance: 234 - 238: 7.457 distance: 234 - 239: 4.580 distance: 235 - 240: 7.655 distance: 241 - 242: 4.852 distance: 241 - 249: 18.173 distance: 242 - 243: 7.966 distance: 242 - 245: 6.410 distance: 242 - 250: 4.088 distance: 243 - 244: 11.258 distance: 243 - 260: 8.532 distance: 245 - 246: 7.878 distance: 245 - 251: 6.962 distance: 245 - 252: 4.483 distance: 246 - 247: 5.282 distance: 246 - 248: 4.187 distance: 246 - 253: 5.099 distance: 247 - 256: 3.836 distance: 248 - 257: 3.201 distance: 260 - 261: 3.251 distance: 261 - 262: 4.140 distance: 261 - 269: 4.320 distance: 262 - 279: 3.974 distance: 264 - 265: 3.822 distance: 264 - 270: 3.681 distance: 266 - 273: 4.853 distance: 266 - 274: 4.872 distance: 266 - 275: 4.241