Starting phenix.real_space_refine (version: dev) on Wed Apr 13 23:40:12 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yl3_10835/04_2022/6yl3_10835_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yl3_10835/04_2022/6yl3_10835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=1.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yl3_10835/04_2022/6yl3_10835.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yl3_10835/04_2022/6yl3_10835.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yl3_10835/04_2022/6yl3_10835_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6yl3_10835/04_2022/6yl3_10835_trim_updated.pdb" } resolution = 1.98 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= 0.007 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 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "E PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "H PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "K PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "N PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "Q PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "X PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "0 PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "3 PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "6 PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "9 PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.17s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 150156 Number of models: 1 Model: "" Number of chains: 84 Chain: "A" Number of atoms: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Conformer: "B" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} bond proxies already assigned to first conformer: 1497 Chain: "B" Number of atoms: 2061 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} bond proxies already assigned to first conformer: 2033 Chain: "C" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 535, 'PCIS': 3} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 535, 'PCIS': 3} Chain breaks: 1 bond proxies already assigned to first conformer: 8366 Chain: "D" Number of atoms: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Conformer: "B" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} bond proxies already assigned to first conformer: 1497 Chain: "E" Number of atoms: 2061 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} bond proxies already assigned to first conformer: 2033 Chain: "F" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 535, 'PCIS': 3} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 535, 'PCIS': 3} Chain breaks: 1 bond proxies already assigned to first conformer: 8366 Chain: "G" Number of atoms: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Conformer: "B" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} bond proxies already assigned to first conformer: 1497 Chain: "H" Number of atoms: 2061 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} bond proxies already assigned to first conformer: 2033 Chain: "I" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 535, 'PCIS': 3} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 535, 'PCIS': 3} Chain breaks: 1 bond proxies already assigned to first conformer: 8366 Chain: "J" Number of atoms: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Conformer: "B" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} bond proxies already assigned to first conformer: 1497 Chain: "K" Number of atoms: 2061 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} bond proxies already assigned to first conformer: 2033 Chain: "L" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 535, 'PCIS': 3} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 535, 'PCIS': 3} Chain breaks: 1 bond proxies already assigned to first conformer: 8366 Chain: "M" Number of atoms: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Conformer: "B" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} bond proxies already assigned to first conformer: 1497 Chain: "N" Number of atoms: 2061 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} bond proxies already assigned to first conformer: 2033 Chain: "O" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 535, 'PCIS': 3} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 535, 'PCIS': 3} Chain breaks: 1 bond proxies already assigned to first conformer: 8366 Chain: "P" Number of atoms: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Conformer: "B" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} bond proxies already assigned to first conformer: 1497 Chain: "Q" Number of atoms: 2061 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} bond proxies already assigned to first conformer: 2033 Chain: "R" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 535, 'PCIS': 3} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 535, 'PCIS': 3} Chain breaks: 1 bond proxies already assigned to first conformer: 8366 Chain: "S" Number of atoms: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Conformer: "B" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} bond proxies already assigned to first conformer: 1497 Chain: "T" Number of atoms: 2061 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} bond proxies already assigned to first conformer: 2033 Chain: "V" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 535, 'PCIS': 3} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 535, 'PCIS': 3} Chain breaks: 1 bond proxies already assigned to first conformer: 8366 Chain: "W" Number of atoms: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Conformer: "B" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} bond proxies already assigned to first conformer: 1497 Chain: "X" Number of atoms: 2061 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} bond proxies already assigned to first conformer: 2033 Chain: "Y" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 535, 'PCIS': 3} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 535, 'PCIS': 3} Chain breaks: 1 bond proxies already assigned to first conformer: 8366 Chain: "Z" Number of atoms: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Conformer: "B" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} bond proxies already assigned to first conformer: 1497 Chain: "0" Number of atoms: 2061 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} bond proxies already assigned to first conformer: 2033 Chain: "1" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 535, 'PCIS': 3} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 535, 'PCIS': 3} Chain breaks: 1 bond proxies already assigned to first conformer: 8366 Chain: "2" Number of atoms: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Conformer: "B" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} bond proxies already assigned to first conformer: 1497 Chain: "3" Number of atoms: 2061 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} bond proxies already assigned to first conformer: 2033 Chain: "4" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 535, 'PCIS': 3} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 535, 'PCIS': 3} Chain breaks: 1 bond proxies already assigned to first conformer: 8366 Chain: "5" Number of atoms: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Conformer: "B" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} bond proxies already assigned to first conformer: 1497 Chain: "6" Number of atoms: 2061 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} bond proxies already assigned to first conformer: 2033 Chain: "7" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 535, 'PCIS': 3} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 535, 'PCIS': 3} Chain breaks: 1 bond proxies already assigned to first conformer: 8366 Chain: "8" Number of atoms: 1661 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Conformer: "B" Number of residues, atoms: 100, 1577 Classifications: {'peptide': 100} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} bond proxies already assigned to first conformer: 1497 Chain: "9" Number of atoms: 2061 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} Conformer: "B" Number of residues, atoms: 132, 2036 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 9, 'TRANS': 122} bond proxies already assigned to first conformer: 2033 Chain: "U" Number of atoms: 8483 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 535, 'PCIS': 3} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 564, 8386 Classifications: {'peptide': 564} Link IDs: {'PTRANS': 25, 'TRANS': 535, 'PCIS': 3} Chain breaks: 1 bond proxies already assigned to first conformer: 8366 Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Y" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "1" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NI': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "B" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "C" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 224 Classifications: {'water': 224} Link IDs: {None: 223} Chain: "D" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "E" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "F" Number of atoms: 225 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 225 Classifications: {'water': 225} Link IDs: {None: 224} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 27 Classifications: {'water': 27} Link IDs: {None: 26} Chain: "H" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "I" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 227 Classifications: {'water': 227} Link IDs: {None: 226} Chain: "J" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "K" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "L" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 227 Classifications: {'water': 227} Link IDs: {None: 226} Chain: "M" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "N" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "O" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 222 Classifications: {'water': 222} Link IDs: {None: 221} Chain: "P" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "Q" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "R" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 216 Classifications: {'water': 216} Link IDs: {None: 215} Chain: "S" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "T" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "V" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 227, 227 Classifications: {'water': 227} Link IDs: {None: 226} Chain: "W" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "X" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "Y" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 226 Classifications: {'water': 226} Link IDs: {None: 225} Chain: "Z" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 26 Classifications: {'water': 26} Link IDs: {None: 25} Chain: "0" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "1" Number of atoms: 224 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 224 Classifications: {'water': 224} Link IDs: {None: 223} Chain: "2" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "3" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "4" Number of atoms: 216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 216 Classifications: {'water': 216} Link IDs: {None: 215} Chain: "5" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "6" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Classifications: {'water': 57} Link IDs: {None: 56} Chain: "7" Number of atoms: 220 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 220 Classifications: {'water': 220} Link IDs: {None: 219} Chain: "8" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "9" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 56 Classifications: {'water': 56} Link IDs: {None: 55} Chain: "U" Number of atoms: 223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 223 Classifications: {'water': 223} Link IDs: {None: 222} Residues with excluded nonbonded symmetry interactions: 132 residue: pdb=" N ALEU A 16 " occ=0.50 ... (36 atoms not shown) pdb="HD23BLEU A 16 " occ=0.50 residue: pdb=" N ALYS A 29 " occ=0.50 ... (42 atoms not shown) pdb=" HZ3BLYS A 29 " occ=0.50 residue: pdb=" N AMET A 57 " occ=0.50 ... (32 atoms not shown) pdb=" HE3BMET A 57 " occ=0.50 residue: pdb=" N ALYS A 66 " occ=0.50 ... (42 atoms not shown) pdb=" HZ3BLYS A 66 " occ=0.50 residue: pdb=" N AARG B 153 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG B 153 " occ=0.50 residue: pdb=" N ALYS C 20 " occ=0.50 ... (42 atoms not shown) pdb=" HZ3BLYS C 20 " occ=0.50 residue: pdb=" N AMET C 55 " occ=0.50 ... (32 atoms not shown) pdb=" HE3BMET C 55 " occ=0.50 residue: pdb=" N ALEU C 406 " occ=0.50 ... (36 atoms not shown) pdb="HD23BLEU C 406 " occ=0.50 residue: pdb=" N AMET C 434 " occ=0.50 ... (32 atoms not shown) pdb=" HE3BMET C 434 " occ=0.50 residue: pdb=" N AMET C 489 " occ=0.50 ... (32 atoms not shown) pdb=" HE3BMET C 489 " occ=0.50 residue: pdb=" N ALEU D 16 " occ=0.50 ... (36 atoms not shown) pdb="HD23BLEU D 16 " occ=0.50 residue: pdb=" N ALYS D 29 " occ=0.50 ... (42 atoms not shown) pdb=" HZ3BLYS D 29 " occ=0.50 ... (remaining 120 not shown) Time building chain proxies: 90.41, per 1000 atoms: 0.60 Number of scatterers: 150156 At special positions: 0 Unit cell: (169.335, 176.364, 169.974, 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) Ni 24 28.00 S 420 16.00 O 17700 8.00 N 12984 7.00 C 45984 6.00 H 73044 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 Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 103.34 Conformation dependent library (CDL) restraints added in 17.9 seconds 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17328 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: 276 helices and 132 sheets defined 35.4% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 10.32 Creating SS restraints... Processing helix chain 'A' and resid 4 through 27 removed outlier: 3.768A pdb=" N LEU A 11 " --> pdb=" O GLU A 7 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N MET A 12 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE A 13 " --> pdb=" O GLU A 9 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR A 14 " --> pdb=" O LYS A 10 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY A 27 " --> pdb=" O ARG A 23 " (cutoff:3.500A) Processing helix chain 'A' and resid 31 through 50 Processing helix chain 'A' and resid 52 through 70 removed outlier: 3.613A pdb=" N VAL A 63 " --> pdb=" O GLU A 59 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU A 64 " --> pdb=" O ALA A 60 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N ALYS A 66 " --> pdb=" O LYS A 62 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N ASP A 67 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL A 69 " --> pdb=" O THR A 65 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N MET A 70 " --> pdb=" O ALYS A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 78 removed outlier: 3.658A pdb=" N LEU A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) Proline residue: A 78 - end of helix Processing helix chain 'D' and resid 4 through 27 removed outlier: 3.768A pdb=" N LEU D 11 " --> pdb=" O GLU D 7 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE D 13 " --> pdb=" O GLU D 9 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR D 14 " --> pdb=" O LYS D 10 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY D 27 " --> pdb=" O ARG D 23 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 50 Processing helix chain 'D' and resid 52 through 70 removed outlier: 3.613A pdb=" N VAL D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU D 64 " --> pdb=" O ALA D 60 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR D 65 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ALYS D 66 " --> pdb=" O LYS D 62 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N ASP D 67 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP D 68 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 69 " --> pdb=" O THR D 65 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N MET D 70 " --> pdb=" O ALYS D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 72 through 78 removed outlier: 3.659A pdb=" N LEU D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Proline residue: D 78 - end of helix Processing helix chain 'G' and resid 4 through 27 removed outlier: 3.769A pdb=" N LEU G 11 " --> pdb=" O GLU G 7 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET G 12 " --> pdb=" O VAL G 8 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE G 13 " --> pdb=" O GLU G 9 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR G 14 " --> pdb=" O LYS G 10 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY G 27 " --> pdb=" O ARG G 23 " (cutoff:3.500A) Processing helix chain 'G' and resid 31 through 50 Processing helix chain 'G' and resid 52 through 70 removed outlier: 3.613A pdb=" N VAL G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR G 65 " --> pdb=" O SER G 61 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N ALYS G 66 " --> pdb=" O LYS G 62 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N ASP G 67 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP G 68 " --> pdb=" O LEU G 64 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL G 69 " --> pdb=" O THR G 65 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N MET G 70 " --> pdb=" O ALYS G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 72 through 78 removed outlier: 3.659A pdb=" N LEU G 76 " --> pdb=" O GLY G 72 " (cutoff:3.500A) Proline residue: G 78 - end of helix Processing helix chain 'J' and resid 4 through 27 removed outlier: 3.768A pdb=" N LEU J 11 " --> pdb=" O GLU J 7 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET J 12 " --> pdb=" O VAL J 8 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE J 13 " --> pdb=" O GLU J 9 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR J 14 " --> pdb=" O LYS J 10 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY J 27 " --> pdb=" O ARG J 23 " (cutoff:3.500A) Processing helix chain 'J' and resid 31 through 50 Processing helix chain 'J' and resid 52 through 70 removed outlier: 3.613A pdb=" N VAL J 63 " --> pdb=" O GLU J 59 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU J 64 " --> pdb=" O ALA J 60 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR J 65 " --> pdb=" O SER J 61 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N ALYS J 66 " --> pdb=" O LYS J 62 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N ASP J 67 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP J 68 " --> pdb=" O LEU J 64 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL J 69 " --> pdb=" O THR J 65 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N MET J 70 " --> pdb=" O ALYS J 66 " (cutoff:3.500A) Processing helix chain 'J' and resid 72 through 78 removed outlier: 3.659A pdb=" N LEU J 76 " --> pdb=" O GLY J 72 " (cutoff:3.500A) Proline residue: J 78 - end of helix Processing helix chain 'M' and resid 4 through 27 removed outlier: 3.768A pdb=" N LEU M 11 " --> pdb=" O GLU M 7 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET M 12 " --> pdb=" O VAL M 8 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE M 13 " --> pdb=" O GLU M 9 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR M 14 " --> pdb=" O LYS M 10 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY M 27 " --> pdb=" O ARG M 23 " (cutoff:3.500A) Processing helix chain 'M' and resid 31 through 50 Processing helix chain 'M' and resid 52 through 70 removed outlier: 3.613A pdb=" N VAL M 63 " --> pdb=" O GLU M 59 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU M 64 " --> pdb=" O ALA M 60 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR M 65 " --> pdb=" O SER M 61 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ALYS M 66 " --> pdb=" O LYS M 62 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N ASP M 67 " --> pdb=" O VAL M 63 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP M 68 " --> pdb=" O LEU M 64 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL M 69 " --> pdb=" O THR M 65 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N MET M 70 " --> pdb=" O ALYS M 66 " (cutoff:3.500A) Processing helix chain 'M' and resid 72 through 78 removed outlier: 3.658A pdb=" N LEU M 76 " --> pdb=" O GLY M 72 " (cutoff:3.500A) Proline residue: M 78 - end of helix Processing helix chain 'P' and resid 4 through 27 removed outlier: 3.769A pdb=" N LEU P 11 " --> pdb=" O GLU P 7 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N MET P 12 " --> pdb=" O VAL P 8 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE P 13 " --> pdb=" O GLU P 9 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR P 14 " --> pdb=" O LYS P 10 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY P 27 " --> pdb=" O ARG P 23 " (cutoff:3.500A) Processing helix chain 'P' and resid 31 through 50 Processing helix chain 'P' and resid 52 through 70 removed outlier: 3.613A pdb=" N VAL P 63 " --> pdb=" O GLU P 59 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU P 64 " --> pdb=" O ALA P 60 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR P 65 " --> pdb=" O SER P 61 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N ALYS P 66 " --> pdb=" O LYS P 62 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N ASP P 67 " --> pdb=" O VAL P 63 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP P 68 " --> pdb=" O LEU P 64 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N VAL P 69 " --> pdb=" O THR P 65 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N MET P 70 " --> pdb=" O ALYS P 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 72 through 78 removed outlier: 3.659A pdb=" N LEU P 76 " --> pdb=" O GLY P 72 " (cutoff:3.500A) Proline residue: P 78 - end of helix Processing helix chain 'S' and resid 4 through 27 removed outlier: 3.768A pdb=" N LEU S 11 " --> pdb=" O GLU S 7 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET S 12 " --> pdb=" O VAL S 8 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE S 13 " --> pdb=" O GLU S 9 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR S 14 " --> pdb=" O LYS S 10 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY S 27 " --> pdb=" O ARG S 23 " (cutoff:3.500A) Processing helix chain 'S' and resid 31 through 50 Processing helix chain 'S' and resid 52 through 70 removed outlier: 3.613A pdb=" N VAL S 63 " --> pdb=" O GLU S 59 " (cutoff:3.500A) removed outlier: 4.947A pdb=" N LEU S 64 " --> pdb=" O ALA S 60 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR S 65 " --> pdb=" O SER S 61 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ALYS S 66 " --> pdb=" O LYS S 62 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N ASP S 67 " --> pdb=" O VAL S 63 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N ASP S 68 " --> pdb=" O LEU S 64 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL S 69 " --> pdb=" O THR S 65 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N MET S 70 " --> pdb=" O ALYS S 66 " (cutoff:3.500A) Processing helix chain 'S' and resid 72 through 78 removed outlier: 3.658A pdb=" N LEU S 76 " --> pdb=" O GLY S 72 " (cutoff:3.500A) Proline residue: S 78 - end of helix Processing helix chain 'W' and resid 4 through 27 removed outlier: 3.769A pdb=" N LEU W 11 " --> pdb=" O GLU W 7 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N MET W 12 " --> pdb=" O VAL W 8 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE W 13 " --> pdb=" O GLU W 9 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR W 14 " --> pdb=" O LYS W 10 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY W 27 " --> pdb=" O ARG W 23 " (cutoff:3.500A) Processing helix chain 'W' and resid 31 through 50 Processing helix chain 'W' and resid 52 through 70 removed outlier: 3.612A pdb=" N VAL W 63 " --> pdb=" O GLU W 59 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU W 64 " --> pdb=" O ALA W 60 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N THR W 65 " --> pdb=" O SER W 61 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ALYS W 66 " --> pdb=" O LYS W 62 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N ASP W 67 " --> pdb=" O VAL W 63 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP W 68 " --> pdb=" O LEU W 64 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL W 69 " --> pdb=" O THR W 65 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N MET W 70 " --> pdb=" O ALYS W 66 " (cutoff:3.500A) Processing helix chain 'W' and resid 72 through 78 removed outlier: 3.659A pdb=" N LEU W 76 " --> pdb=" O GLY W 72 " (cutoff:3.500A) Proline residue: W 78 - end of helix Processing helix chain 'Z' and resid 4 through 27 removed outlier: 3.769A pdb=" N LEU Z 11 " --> pdb=" O GLU Z 7 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET Z 12 " --> pdb=" O VAL Z 8 " (cutoff:3.500A) removed outlier: 4.206A pdb=" N ILE Z 13 " --> pdb=" O GLU Z 9 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TYR Z 14 " --> pdb=" O LYS Z 10 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY Z 27 " --> pdb=" O ARG Z 23 " (cutoff:3.500A) Processing helix chain 'Z' and resid 31 through 50 Processing helix chain 'Z' and resid 52 through 70 removed outlier: 3.613A pdb=" N VAL Z 63 " --> pdb=" O GLU Z 59 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU Z 64 " --> pdb=" O ALA Z 60 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR Z 65 " --> pdb=" O SER Z 61 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ALYS Z 66 " --> pdb=" O LYS Z 62 " (cutoff:3.500A) removed outlier: 9.072A pdb=" N ASP Z 67 " --> pdb=" O VAL Z 63 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP Z 68 " --> pdb=" O LEU Z 64 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL Z 69 " --> pdb=" O THR Z 65 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N MET Z 70 " --> pdb=" O ALYS Z 66 " (cutoff:3.500A) Processing helix chain 'Z' and resid 72 through 78 removed outlier: 3.658A pdb=" N LEU Z 76 " --> pdb=" O GLY Z 72 " (cutoff:3.500A) Proline residue: Z 78 - end of helix Processing helix chain '2' and resid 4 through 27 removed outlier: 3.767A pdb=" N LEU 2 11 " --> pdb=" O GLU 2 7 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N MET 2 12 " --> pdb=" O VAL 2 8 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE 2 13 " --> pdb=" O GLU 2 9 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR 2 14 " --> pdb=" O LYS 2 10 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLY 2 27 " --> pdb=" O ARG 2 23 " (cutoff:3.500A) Processing helix chain '2' and resid 31 through 50 Processing helix chain '2' and resid 52 through 70 removed outlier: 3.612A pdb=" N VAL 2 63 " --> pdb=" O GLU 2 59 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU 2 64 " --> pdb=" O ALA 2 60 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N THR 2 65 " --> pdb=" O SER 2 61 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N ALYS 2 66 " --> pdb=" O LYS 2 62 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N ASP 2 67 " --> pdb=" O VAL 2 63 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP 2 68 " --> pdb=" O LEU 2 64 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL 2 69 " --> pdb=" O THR 2 65 " (cutoff:3.500A) removed outlier: 5.066A pdb=" N MET 2 70 " --> pdb=" O ALYS 2 66 " (cutoff:3.500A) Processing helix chain '2' and resid 72 through 78 removed outlier: 3.659A pdb=" N LEU 2 76 " --> pdb=" O GLY 2 72 " (cutoff:3.500A) Proline residue: 2 78 - end of helix Processing helix chain '5' and resid 4 through 27 removed outlier: 3.768A pdb=" N LEU 5 11 " --> pdb=" O GLU 5 7 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N MET 5 12 " --> pdb=" O VAL 5 8 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ILE 5 13 " --> pdb=" O GLU 5 9 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N TYR 5 14 " --> pdb=" O LYS 5 10 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY 5 27 " --> pdb=" O ARG 5 23 " (cutoff:3.500A) Processing helix chain '5' and resid 31 through 50 Processing helix chain '5' and resid 52 through 70 removed outlier: 3.613A pdb=" N VAL 5 63 " --> pdb=" O GLU 5 59 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N LEU 5 64 " --> pdb=" O ALA 5 60 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR 5 65 " --> pdb=" O SER 5 61 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N ALYS 5 66 " --> pdb=" O LYS 5 62 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N ASP 5 67 " --> pdb=" O VAL 5 63 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP 5 68 " --> pdb=" O LEU 5 64 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL 5 69 " --> pdb=" O THR 5 65 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N MET 5 70 " --> pdb=" O ALYS 5 66 " (cutoff:3.500A) Processing helix chain '5' and resid 72 through 78 removed outlier: 3.658A pdb=" N LEU 5 76 " --> pdb=" O GLY 5 72 " (cutoff:3.500A) Proline residue: 5 78 - end of helix Processing helix chain '8' and resid 4 through 27 removed outlier: 3.768A pdb=" N LEU 8 11 " --> pdb=" O GLU 8 7 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N MET 8 12 " --> pdb=" O VAL 8 8 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N ILE 8 13 " --> pdb=" O GLU 8 9 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR 8 14 " --> pdb=" O LYS 8 10 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY 8 27 " --> pdb=" O ARG 8 23 " (cutoff:3.500A) Processing helix chain '8' and resid 31 through 50 Processing helix chain '8' and resid 52 through 70 removed outlier: 3.613A pdb=" N VAL 8 63 " --> pdb=" O GLU 8 59 " (cutoff:3.500A) removed outlier: 4.946A pdb=" N LEU 8 64 " --> pdb=" O ALA 8 60 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR 8 65 " --> pdb=" O SER 8 61 " (cutoff:3.500A) removed outlier: 8.642A pdb=" N ALYS 8 66 " --> pdb=" O LYS 8 62 " (cutoff:3.500A) removed outlier: 9.071A pdb=" N ASP 8 67 " --> pdb=" O VAL 8 63 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASP 8 68 " --> pdb=" O LEU 8 64 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL 8 69 " --> pdb=" O THR 8 65 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N MET 8 70 " --> pdb=" O ALYS 8 66 " (cutoff:3.500A) Processing helix chain '8' and resid 72 through 78 removed outlier: 3.659A pdb=" N LEU 8 76 " --> pdb=" O GLY 8 72 " (cutoff:3.500A) Proline residue: 8 78 - end of helix Processing helix chain 'B' and resid 86 through 91 removed outlier: 3.650A pdb=" N ALA B 90 " --> pdb=" O ASP B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 145 through 159 removed outlier: 3.718A pdb=" N LEU B 149 " --> pdb=" O ARG B 145 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 91 removed outlier: 3.650A pdb=" N ALA E 90 " --> pdb=" O ASP E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 159 removed outlier: 3.717A pdb=" N LEU E 149 " --> pdb=" O ARG E 145 " (cutoff:3.500A) Processing helix chain 'H' and resid 86 through 91 removed outlier: 3.651A pdb=" N ALA H 90 " --> pdb=" O ASP H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 159 removed outlier: 3.718A pdb=" N LEU H 149 " --> pdb=" O ARG H 145 " (cutoff:3.500A) Processing helix chain 'K' and resid 86 through 91 removed outlier: 3.650A pdb=" N ALA K 90 " --> pdb=" O ASP K 86 " (cutoff:3.500A) Processing helix chain 'K' and resid 145 through 159 removed outlier: 3.718A pdb=" N LEU K 149 " --> pdb=" O ARG K 145 " (cutoff:3.500A) Processing helix chain 'N' and resid 86 through 91 removed outlier: 3.650A pdb=" N ALA N 90 " --> pdb=" O ASP N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 145 through 159 removed outlier: 3.718A pdb=" N LEU N 149 " --> pdb=" O ARG N 145 " (cutoff:3.500A) Processing helix chain 'Q' and resid 86 through 91 removed outlier: 3.649A pdb=" N ALA Q 90 " --> pdb=" O ASP Q 86 " (cutoff:3.500A) Processing helix chain 'Q' and resid 145 through 159 removed outlier: 3.718A pdb=" N LEU Q 149 " --> pdb=" O ARG Q 145 " (cutoff:3.500A) Processing helix chain 'T' and resid 86 through 91 removed outlier: 3.649A pdb=" N ALA T 90 " --> pdb=" O ASP T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 145 through 159 removed outlier: 3.718A pdb=" N LEU T 149 " --> pdb=" O ARG T 145 " (cutoff:3.500A) Processing helix chain 'X' and resid 86 through 91 removed outlier: 3.650A pdb=" N ALA X 90 " --> pdb=" O ASP X 86 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 159 removed outlier: 3.718A pdb=" N LEU X 149 " --> pdb=" O ARG X 145 " (cutoff:3.500A) Processing helix chain '0' and resid 86 through 91 removed outlier: 3.650A pdb=" N ALA 0 90 " --> pdb=" O ASP 0 86 " (cutoff:3.500A) Processing helix chain '0' and resid 145 through 159 removed outlier: 3.718A pdb=" N LEU 0 149 " --> pdb=" O ARG 0 145 " (cutoff:3.500A) Processing helix chain '3' and resid 86 through 91 removed outlier: 3.650A pdb=" N ALA 3 90 " --> pdb=" O ASP 3 86 " (cutoff:3.500A) Processing helix chain '3' and resid 145 through 159 removed outlier: 3.718A pdb=" N LEU 3 149 " --> pdb=" O ARG 3 145 " (cutoff:3.500A) Processing helix chain '6' and resid 86 through 91 removed outlier: 3.651A pdb=" N ALA 6 90 " --> pdb=" O ASP 6 86 " (cutoff:3.500A) Processing helix chain '6' and resid 145 through 159 removed outlier: 3.718A pdb=" N LEU 6 149 " --> pdb=" O ARG 6 145 " (cutoff:3.500A) Processing helix chain '9' and resid 86 through 91 removed outlier: 3.650A pdb=" N ALA 9 90 " --> pdb=" O ASP 9 86 " (cutoff:3.500A) Processing helix chain '9' and resid 145 through 159 removed outlier: 3.718A pdb=" N LEU 9 149 " --> pdb=" O ARG 9 145 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 13 Processing helix chain 'C' and resid 144 through 155 removed outlier: 4.987A pdb=" N ALA C 148 " --> pdb=" O SER C 144 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR C 149 " --> pdb=" O PRO C 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS C 150 " --> pdb=" O GLN C 146 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN C 154 " --> pdb=" O HIS C 150 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 173 Processing helix chain 'C' and resid 178 through 193 removed outlier: 3.680A pdb=" N GLU C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY C 191 " --> pdb=" O ARG C 187 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU C 192 " --> pdb=" O SER C 188 " (cutoff:3.500A) Proline residue: C 193 - end of helix Processing helix chain 'C' and resid 206 through 217 removed outlier: 4.757A pdb=" N LEU C 210 " --> pdb=" O GLY C 206 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN C 213 " --> pdb=" O PRO C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 230 through 245 Processing helix chain 'C' and resid 260 through 269 removed outlier: 3.639A pdb=" N GLU C 269 " --> pdb=" O ILE C 265 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 295 removed outlier: 4.906A pdb=" N SER C 294 " --> pdb=" O ILE C 290 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLN C 295 " --> pdb=" O ARG C 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 290 through 295' Processing helix chain 'C' and resid 312 through 326 removed outlier: 4.096A pdb=" N ASN C 326 " --> pdb=" O MET C 322 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 357 removed outlier: 3.933A pdb=" N SER C 340 " --> pdb=" O SER C 336 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG C 343 " --> pdb=" O GLU C 339 " (cutoff:3.500A) Proline residue: C 344 - end of helix Processing helix chain 'C' and resid 374 through 390 Processing helix chain 'C' and resid 401 through 413 removed outlier: 3.609A pdb=" N LYS C 411 " --> pdb=" O ARG C 407 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE C 412 " --> pdb=" O TYR C 408 " (cutoff:3.500A) Processing helix chain 'C' and resid 414 through 421 Processing helix chain 'C' and resid 481 through 486 removed outlier: 3.660A pdb=" N MET C 485 " --> pdb=" O MET C 481 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY C 486 " --> pdb=" O PHE C 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 481 through 486' Processing helix chain 'C' and resid 487 through 493 Processing helix chain 'C' and resid 498 through 505 Processing helix chain 'C' and resid 506 through 511 Processing helix chain 'F' and resid 5 through 13 Processing helix chain 'F' and resid 144 through 155 removed outlier: 4.987A pdb=" N ALA F 148 " --> pdb=" O SER F 144 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR F 149 " --> pdb=" O PRO F 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS F 150 " --> pdb=" O GLN F 146 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN F 154 " --> pdb=" O HIS F 150 " (cutoff:3.500A) Processing helix chain 'F' and resid 167 through 173 Processing helix chain 'F' and resid 178 through 193 removed outlier: 3.680A pdb=" N GLU F 190 " --> pdb=" O LEU F 186 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLY F 191 " --> pdb=" O ARG F 187 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU F 192 " --> pdb=" O SER F 188 " (cutoff:3.500A) Proline residue: F 193 - end of helix Processing helix chain 'F' and resid 206 through 217 removed outlier: 4.757A pdb=" N LEU F 210 " --> pdb=" O GLY F 206 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN F 213 " --> pdb=" O PRO F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 230 through 245 Processing helix chain 'F' and resid 260 through 269 removed outlier: 3.639A pdb=" N GLU F 269 " --> pdb=" O ILE F 265 " (cutoff:3.500A) Processing helix chain 'F' and resid 290 through 295 removed outlier: 4.906A pdb=" N SER F 294 " --> pdb=" O ILE F 290 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLN F 295 " --> pdb=" O ARG F 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 290 through 295' Processing helix chain 'F' and resid 312 through 326 removed outlier: 4.097A pdb=" N ASN F 326 " --> pdb=" O MET F 322 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 357 removed outlier: 3.932A pdb=" N SER F 340 " --> pdb=" O SER F 336 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG F 343 " --> pdb=" O GLU F 339 " (cutoff:3.500A) Proline residue: F 344 - end of helix Processing helix chain 'F' and resid 374 through 390 Processing helix chain 'F' and resid 401 through 413 removed outlier: 3.610A pdb=" N LYS F 411 " --> pdb=" O ARG F 407 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE F 412 " --> pdb=" O TYR F 408 " (cutoff:3.500A) Processing helix chain 'F' and resid 414 through 421 Processing helix chain 'F' and resid 481 through 486 removed outlier: 3.660A pdb=" N MET F 485 " --> pdb=" O MET F 481 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLY F 486 " --> pdb=" O PHE F 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 481 through 486' Processing helix chain 'F' and resid 487 through 493 Processing helix chain 'F' and resid 498 through 505 Processing helix chain 'F' and resid 506 through 511 Processing helix chain 'I' and resid 5 through 13 Processing helix chain 'I' and resid 144 through 155 removed outlier: 4.987A pdb=" N ALA I 148 " --> pdb=" O SER I 144 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR I 149 " --> pdb=" O PRO I 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS I 150 " --> pdb=" O GLN I 146 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN I 154 " --> pdb=" O HIS I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 173 Processing helix chain 'I' and resid 178 through 193 removed outlier: 3.680A pdb=" N GLU I 190 " --> pdb=" O LEU I 186 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY I 191 " --> pdb=" O ARG I 187 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU I 192 " --> pdb=" O SER I 188 " (cutoff:3.500A) Proline residue: I 193 - end of helix Processing helix chain 'I' and resid 206 through 217 removed outlier: 4.757A pdb=" N LEU I 210 " --> pdb=" O GLY I 206 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN I 213 " --> pdb=" O PRO I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 230 through 245 Processing helix chain 'I' and resid 260 through 269 removed outlier: 3.640A pdb=" N GLU I 269 " --> pdb=" O ILE I 265 " (cutoff:3.500A) Processing helix chain 'I' and resid 290 through 295 removed outlier: 4.905A pdb=" N SER I 294 " --> pdb=" O ILE I 290 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLN I 295 " --> pdb=" O ARG I 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 290 through 295' Processing helix chain 'I' and resid 312 through 326 removed outlier: 4.095A pdb=" N ASN I 326 " --> pdb=" O MET I 322 " (cutoff:3.500A) Processing helix chain 'I' and resid 335 through 357 removed outlier: 3.933A pdb=" N SER I 340 " --> pdb=" O SER I 336 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG I 343 " --> pdb=" O GLU I 339 " (cutoff:3.500A) Proline residue: I 344 - end of helix Processing helix chain 'I' and resid 374 through 390 Processing helix chain 'I' and resid 401 through 413 removed outlier: 3.610A pdb=" N LYS I 411 " --> pdb=" O ARG I 407 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE I 412 " --> pdb=" O TYR I 408 " (cutoff:3.500A) Processing helix chain 'I' and resid 414 through 421 Processing helix chain 'I' and resid 481 through 486 removed outlier: 3.660A pdb=" N MET I 485 " --> pdb=" O MET I 481 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY I 486 " --> pdb=" O PHE I 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 481 through 486' Processing helix chain 'I' and resid 487 through 493 Processing helix chain 'I' and resid 498 through 505 Processing helix chain 'I' and resid 506 through 511 Processing helix chain 'L' and resid 5 through 13 Processing helix chain 'L' and resid 144 through 155 removed outlier: 4.987A pdb=" N ALA L 148 " --> pdb=" O SER L 144 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR L 149 " --> pdb=" O PRO L 145 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N HIS L 150 " --> pdb=" O GLN L 146 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN L 154 " --> pdb=" O HIS L 150 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 173 Processing helix chain 'L' and resid 178 through 193 removed outlier: 3.680A pdb=" N GLU L 190 " --> pdb=" O LEU L 186 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY L 191 " --> pdb=" O ARG L 187 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU L 192 " --> pdb=" O SER L 188 " (cutoff:3.500A) Proline residue: L 193 - end of helix Processing helix chain 'L' and resid 206 through 217 removed outlier: 4.758A pdb=" N LEU L 210 " --> pdb=" O GLY L 206 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN L 213 " --> pdb=" O PRO L 209 " (cutoff:3.500A) Processing helix chain 'L' and resid 230 through 245 Processing helix chain 'L' and resid 260 through 269 removed outlier: 3.639A pdb=" N GLU L 269 " --> pdb=" O ILE L 265 " (cutoff:3.500A) Processing helix chain 'L' and resid 290 through 295 removed outlier: 4.906A pdb=" N SER L 294 " --> pdb=" O ILE L 290 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLN L 295 " --> pdb=" O ARG L 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 290 through 295' Processing helix chain 'L' and resid 312 through 326 removed outlier: 4.096A pdb=" N ASN L 326 " --> pdb=" O MET L 322 " (cutoff:3.500A) Processing helix chain 'L' and resid 335 through 357 removed outlier: 3.933A pdb=" N SER L 340 " --> pdb=" O SER L 336 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG L 343 " --> pdb=" O GLU L 339 " (cutoff:3.500A) Proline residue: L 344 - end of helix Processing helix chain 'L' and resid 374 through 390 Processing helix chain 'L' and resid 401 through 413 removed outlier: 3.609A pdb=" N LYS L 411 " --> pdb=" O ARG L 407 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ILE L 412 " --> pdb=" O TYR L 408 " (cutoff:3.500A) Processing helix chain 'L' and resid 414 through 421 Processing helix chain 'L' and resid 481 through 486 removed outlier: 3.660A pdb=" N MET L 485 " --> pdb=" O MET L 481 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N GLY L 486 " --> pdb=" O PHE L 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 481 through 486' Processing helix chain 'L' and resid 487 through 493 Processing helix chain 'L' and resid 498 through 505 Processing helix chain 'L' and resid 506 through 511 Processing helix chain 'O' and resid 5 through 13 Processing helix chain 'O' and resid 144 through 155 removed outlier: 4.988A pdb=" N ALA O 148 " --> pdb=" O SER O 144 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N TYR O 149 " --> pdb=" O PRO O 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS O 150 " --> pdb=" O GLN O 146 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN O 154 " --> pdb=" O HIS O 150 " (cutoff:3.500A) Processing helix chain 'O' and resid 167 through 173 Processing helix chain 'O' and resid 178 through 193 removed outlier: 3.680A pdb=" N GLU O 190 " --> pdb=" O LEU O 186 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY O 191 " --> pdb=" O ARG O 187 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU O 192 " --> pdb=" O SER O 188 " (cutoff:3.500A) Proline residue: O 193 - end of helix Processing helix chain 'O' and resid 206 through 217 removed outlier: 4.758A pdb=" N LEU O 210 " --> pdb=" O GLY O 206 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN O 213 " --> pdb=" O PRO O 209 " (cutoff:3.500A) Processing helix chain 'O' and resid 230 through 245 Processing helix chain 'O' and resid 260 through 269 removed outlier: 3.640A pdb=" N GLU O 269 " --> pdb=" O ILE O 265 " (cutoff:3.500A) Processing helix chain 'O' and resid 290 through 295 removed outlier: 4.906A pdb=" N SER O 294 " --> pdb=" O ILE O 290 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLN O 295 " --> pdb=" O ARG O 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 290 through 295' Processing helix chain 'O' and resid 312 through 326 removed outlier: 4.096A pdb=" N ASN O 326 " --> pdb=" O MET O 322 " (cutoff:3.500A) Processing helix chain 'O' and resid 335 through 357 removed outlier: 3.933A pdb=" N SER O 340 " --> pdb=" O SER O 336 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG O 343 " --> pdb=" O GLU O 339 " (cutoff:3.500A) Proline residue: O 344 - end of helix Processing helix chain 'O' and resid 374 through 390 Processing helix chain 'O' and resid 401 through 413 removed outlier: 3.609A pdb=" N LYS O 411 " --> pdb=" O ARG O 407 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE O 412 " --> pdb=" O TYR O 408 " (cutoff:3.500A) Processing helix chain 'O' and resid 414 through 421 Processing helix chain 'O' and resid 481 through 486 removed outlier: 3.660A pdb=" N MET O 485 " --> pdb=" O MET O 481 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY O 486 " --> pdb=" O PHE O 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 481 through 486' Processing helix chain 'O' and resid 487 through 493 Processing helix chain 'O' and resid 498 through 505 Processing helix chain 'O' and resid 506 through 511 Processing helix chain 'R' and resid 5 through 13 Processing helix chain 'R' and resid 144 through 155 removed outlier: 4.987A pdb=" N ALA R 148 " --> pdb=" O SER R 144 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR R 149 " --> pdb=" O PRO R 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS R 150 " --> pdb=" O GLN R 146 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN R 154 " --> pdb=" O HIS R 150 " (cutoff:3.500A) Processing helix chain 'R' and resid 167 through 173 Processing helix chain 'R' and resid 178 through 193 removed outlier: 3.680A pdb=" N GLU R 190 " --> pdb=" O LEU R 186 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLY R 191 " --> pdb=" O ARG R 187 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU R 192 " --> pdb=" O SER R 188 " (cutoff:3.500A) Proline residue: R 193 - end of helix Processing helix chain 'R' and resid 206 through 217 removed outlier: 4.757A pdb=" N LEU R 210 " --> pdb=" O GLY R 206 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN R 213 " --> pdb=" O PRO R 209 " (cutoff:3.500A) Processing helix chain 'R' and resid 230 through 245 Processing helix chain 'R' and resid 260 through 269 removed outlier: 3.639A pdb=" N GLU R 269 " --> pdb=" O ILE R 265 " (cutoff:3.500A) Processing helix chain 'R' and resid 290 through 295 removed outlier: 4.906A pdb=" N SER R 294 " --> pdb=" O ILE R 290 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLN R 295 " --> pdb=" O ARG R 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 290 through 295' Processing helix chain 'R' and resid 312 through 326 removed outlier: 4.095A pdb=" N ASN R 326 " --> pdb=" O MET R 322 " (cutoff:3.500A) Processing helix chain 'R' and resid 335 through 357 removed outlier: 3.932A pdb=" N SER R 340 " --> pdb=" O SER R 336 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ARG R 343 " --> pdb=" O GLU R 339 " (cutoff:3.500A) Proline residue: R 344 - end of helix Processing helix chain 'R' and resid 374 through 390 Processing helix chain 'R' and resid 401 through 413 removed outlier: 3.609A pdb=" N LYS R 411 " --> pdb=" O ARG R 407 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE R 412 " --> pdb=" O TYR R 408 " (cutoff:3.500A) Processing helix chain 'R' and resid 414 through 421 Processing helix chain 'R' and resid 481 through 486 removed outlier: 3.660A pdb=" N MET R 485 " --> pdb=" O MET R 481 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY R 486 " --> pdb=" O PHE R 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 481 through 486' Processing helix chain 'R' and resid 487 through 493 Processing helix chain 'R' and resid 498 through 505 Processing helix chain 'R' and resid 506 through 511 Processing helix chain 'V' and resid 5 through 13 Processing helix chain 'V' and resid 144 through 155 removed outlier: 4.987A pdb=" N ALA V 148 " --> pdb=" O SER V 144 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR V 149 " --> pdb=" O PRO V 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS V 150 " --> pdb=" O GLN V 146 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN V 154 " --> pdb=" O HIS V 150 " (cutoff:3.500A) Processing helix chain 'V' and resid 167 through 173 Processing helix chain 'V' and resid 178 through 193 removed outlier: 3.680A pdb=" N GLU V 190 " --> pdb=" O LEU V 186 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLY V 191 " --> pdb=" O ARG V 187 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU V 192 " --> pdb=" O SER V 188 " (cutoff:3.500A) Proline residue: V 193 - end of helix Processing helix chain 'V' and resid 206 through 217 removed outlier: 4.758A pdb=" N LEU V 210 " --> pdb=" O GLY V 206 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN V 213 " --> pdb=" O PRO V 209 " (cutoff:3.500A) Processing helix chain 'V' and resid 230 through 245 Processing helix chain 'V' and resid 260 through 269 removed outlier: 3.639A pdb=" N GLU V 269 " --> pdb=" O ILE V 265 " (cutoff:3.500A) Processing helix chain 'V' and resid 290 through 295 removed outlier: 4.906A pdb=" N SER V 294 " --> pdb=" O ILE V 290 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLN V 295 " --> pdb=" O ARG V 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 290 through 295' Processing helix chain 'V' and resid 312 through 326 removed outlier: 4.096A pdb=" N ASN V 326 " --> pdb=" O MET V 322 " (cutoff:3.500A) Processing helix chain 'V' and resid 335 through 357 removed outlier: 3.932A pdb=" N SER V 340 " --> pdb=" O SER V 336 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ARG V 343 " --> pdb=" O GLU V 339 " (cutoff:3.500A) Proline residue: V 344 - end of helix Processing helix chain 'V' and resid 374 through 390 Processing helix chain 'V' and resid 401 through 413 removed outlier: 3.610A pdb=" N LYS V 411 " --> pdb=" O ARG V 407 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE V 412 " --> pdb=" O TYR V 408 " (cutoff:3.500A) Processing helix chain 'V' and resid 414 through 421 Processing helix chain 'V' and resid 481 through 486 removed outlier: 3.660A pdb=" N MET V 485 " --> pdb=" O MET V 481 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY V 486 " --> pdb=" O PHE V 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 481 through 486' Processing helix chain 'V' and resid 487 through 493 Processing helix chain 'V' and resid 498 through 505 Processing helix chain 'V' and resid 506 through 511 Processing helix chain 'Y' and resid 5 through 13 Processing helix chain 'Y' and resid 144 through 155 removed outlier: 4.987A pdb=" N ALA Y 148 " --> pdb=" O SER Y 144 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR Y 149 " --> pdb=" O PRO Y 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS Y 150 " --> pdb=" O GLN Y 146 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN Y 154 " --> pdb=" O HIS Y 150 " (cutoff:3.500A) Processing helix chain 'Y' and resid 167 through 173 Processing helix chain 'Y' and resid 178 through 193 removed outlier: 3.680A pdb=" N GLU Y 190 " --> pdb=" O LEU Y 186 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY Y 191 " --> pdb=" O ARG Y 187 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU Y 192 " --> pdb=" O SER Y 188 " (cutoff:3.500A) Proline residue: Y 193 - end of helix Processing helix chain 'Y' and resid 206 through 217 removed outlier: 4.757A pdb=" N LEU Y 210 " --> pdb=" O GLY Y 206 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN Y 213 " --> pdb=" O PRO Y 209 " (cutoff:3.500A) Processing helix chain 'Y' and resid 230 through 245 Processing helix chain 'Y' and resid 260 through 269 removed outlier: 3.640A pdb=" N GLU Y 269 " --> pdb=" O ILE Y 265 " (cutoff:3.500A) Processing helix chain 'Y' and resid 290 through 295 removed outlier: 4.906A pdb=" N SER Y 294 " --> pdb=" O ILE Y 290 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLN Y 295 " --> pdb=" O ARG Y 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 290 through 295' Processing helix chain 'Y' and resid 312 through 326 removed outlier: 4.096A pdb=" N ASN Y 326 " --> pdb=" O MET Y 322 " (cutoff:3.500A) Processing helix chain 'Y' and resid 335 through 357 removed outlier: 3.933A pdb=" N SER Y 340 " --> pdb=" O SER Y 336 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG Y 343 " --> pdb=" O GLU Y 339 " (cutoff:3.500A) Proline residue: Y 344 - end of helix Processing helix chain 'Y' and resid 374 through 390 Processing helix chain 'Y' and resid 401 through 413 removed outlier: 3.609A pdb=" N LYS Y 411 " --> pdb=" O ARG Y 407 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE Y 412 " --> pdb=" O TYR Y 408 " (cutoff:3.500A) Processing helix chain 'Y' and resid 414 through 421 Processing helix chain 'Y' and resid 481 through 486 removed outlier: 3.660A pdb=" N MET Y 485 " --> pdb=" O MET Y 481 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY Y 486 " --> pdb=" O PHE Y 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 481 through 486' Processing helix chain 'Y' and resid 487 through 493 Processing helix chain 'Y' and resid 498 through 505 Processing helix chain 'Y' and resid 506 through 511 Processing helix chain '1' and resid 5 through 13 Processing helix chain '1' and resid 144 through 155 removed outlier: 4.987A pdb=" N ALA 1 148 " --> pdb=" O SER 1 144 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR 1 149 " --> pdb=" O PRO 1 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS 1 150 " --> pdb=" O GLN 1 146 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN 1 154 " --> pdb=" O HIS 1 150 " (cutoff:3.500A) Processing helix chain '1' and resid 167 through 173 Processing helix chain '1' and resid 178 through 193 removed outlier: 3.681A pdb=" N GLU 1 190 " --> pdb=" O LEU 1 186 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLY 1 191 " --> pdb=" O ARG 1 187 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU 1 192 " --> pdb=" O SER 1 188 " (cutoff:3.500A) Proline residue: 1 193 - end of helix Processing helix chain '1' and resid 206 through 217 removed outlier: 4.758A pdb=" N LEU 1 210 " --> pdb=" O GLY 1 206 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN 1 213 " --> pdb=" O PRO 1 209 " (cutoff:3.500A) Processing helix chain '1' and resid 230 through 245 Processing helix chain '1' and resid 260 through 269 removed outlier: 3.639A pdb=" N GLU 1 269 " --> pdb=" O ILE 1 265 " (cutoff:3.500A) Processing helix chain '1' and resid 290 through 295 removed outlier: 4.905A pdb=" N SER 1 294 " --> pdb=" O ILE 1 290 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLN 1 295 " --> pdb=" O ARG 1 291 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 290 through 295' Processing helix chain '1' and resid 312 through 326 removed outlier: 4.096A pdb=" N ASN 1 326 " --> pdb=" O MET 1 322 " (cutoff:3.500A) Processing helix chain '1' and resid 335 through 357 removed outlier: 3.933A pdb=" N SER 1 340 " --> pdb=" O SER 1 336 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ARG 1 343 " --> pdb=" O GLU 1 339 " (cutoff:3.500A) Proline residue: 1 344 - end of helix Processing helix chain '1' and resid 374 through 390 Processing helix chain '1' and resid 401 through 413 removed outlier: 3.609A pdb=" N LYS 1 411 " --> pdb=" O ARG 1 407 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ILE 1 412 " --> pdb=" O TYR 1 408 " (cutoff:3.500A) Processing helix chain '1' and resid 414 through 421 Processing helix chain '1' and resid 481 through 486 removed outlier: 3.661A pdb=" N MET 1 485 " --> pdb=" O MET 1 481 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N GLY 1 486 " --> pdb=" O PHE 1 482 " (cutoff:3.500A) No H-bonds generated for 'chain '1' and resid 481 through 486' Processing helix chain '1' and resid 487 through 493 Processing helix chain '1' and resid 498 through 505 Processing helix chain '1' and resid 506 through 511 Processing helix chain '4' and resid 5 through 13 Processing helix chain '4' and resid 144 through 155 removed outlier: 4.987A pdb=" N ALA 4 148 " --> pdb=" O SER 4 144 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR 4 149 " --> pdb=" O PRO 4 145 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N HIS 4 150 " --> pdb=" O GLN 4 146 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN 4 154 " --> pdb=" O HIS 4 150 " (cutoff:3.500A) Processing helix chain '4' and resid 167 through 173 Processing helix chain '4' and resid 178 through 193 removed outlier: 3.681A pdb=" N GLU 4 190 " --> pdb=" O LEU 4 186 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY 4 191 " --> pdb=" O ARG 4 187 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU 4 192 " --> pdb=" O SER 4 188 " (cutoff:3.500A) Proline residue: 4 193 - end of helix Processing helix chain '4' and resid 206 through 217 removed outlier: 4.757A pdb=" N LEU 4 210 " --> pdb=" O GLY 4 206 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN 4 213 " --> pdb=" O PRO 4 209 " (cutoff:3.500A) Processing helix chain '4' and resid 230 through 245 Processing helix chain '4' and resid 260 through 269 removed outlier: 3.639A pdb=" N GLU 4 269 " --> pdb=" O ILE 4 265 " (cutoff:3.500A) Processing helix chain '4' and resid 290 through 295 removed outlier: 4.906A pdb=" N SER 4 294 " --> pdb=" O ILE 4 290 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLN 4 295 " --> pdb=" O ARG 4 291 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 290 through 295' Processing helix chain '4' and resid 312 through 326 removed outlier: 4.096A pdb=" N ASN 4 326 " --> pdb=" O MET 4 322 " (cutoff:3.500A) Processing helix chain '4' and resid 335 through 357 removed outlier: 3.932A pdb=" N SER 4 340 " --> pdb=" O SER 4 336 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N ARG 4 343 " --> pdb=" O GLU 4 339 " (cutoff:3.500A) Proline residue: 4 344 - end of helix Processing helix chain '4' and resid 374 through 390 Processing helix chain '4' and resid 401 through 413 removed outlier: 3.609A pdb=" N LYS 4 411 " --> pdb=" O ARG 4 407 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE 4 412 " --> pdb=" O TYR 4 408 " (cutoff:3.500A) Processing helix chain '4' and resid 414 through 421 Processing helix chain '4' and resid 481 through 486 removed outlier: 3.660A pdb=" N MET 4 485 " --> pdb=" O MET 4 481 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY 4 486 " --> pdb=" O PHE 4 482 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 481 through 486' Processing helix chain '4' and resid 487 through 493 Processing helix chain '4' and resid 498 through 505 Processing helix chain '4' and resid 506 through 511 Processing helix chain '7' and resid 5 through 13 Processing helix chain '7' and resid 144 through 155 removed outlier: 4.988A pdb=" N ALA 7 148 " --> pdb=" O SER 7 144 " (cutoff:3.500A) removed outlier: 4.940A pdb=" N TYR 7 149 " --> pdb=" O PRO 7 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS 7 150 " --> pdb=" O GLN 7 146 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN 7 154 " --> pdb=" O HIS 7 150 " (cutoff:3.500A) Processing helix chain '7' and resid 167 through 173 Processing helix chain '7' and resid 178 through 193 removed outlier: 3.680A pdb=" N GLU 7 190 " --> pdb=" O LEU 7 186 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLY 7 191 " --> pdb=" O ARG 7 187 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N LEU 7 192 " --> pdb=" O SER 7 188 " (cutoff:3.500A) Proline residue: 7 193 - end of helix Processing helix chain '7' and resid 206 through 217 removed outlier: 4.757A pdb=" N LEU 7 210 " --> pdb=" O GLY 7 206 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN 7 213 " --> pdb=" O PRO 7 209 " (cutoff:3.500A) Processing helix chain '7' and resid 230 through 245 Processing helix chain '7' and resid 260 through 269 removed outlier: 3.639A pdb=" N GLU 7 269 " --> pdb=" O ILE 7 265 " (cutoff:3.500A) Processing helix chain '7' and resid 290 through 295 removed outlier: 4.905A pdb=" N SER 7 294 " --> pdb=" O ILE 7 290 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLN 7 295 " --> pdb=" O ARG 7 291 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 290 through 295' Processing helix chain '7' and resid 312 through 326 removed outlier: 4.096A pdb=" N ASN 7 326 " --> pdb=" O MET 7 322 " (cutoff:3.500A) Processing helix chain '7' and resid 335 through 357 removed outlier: 3.933A pdb=" N SER 7 340 " --> pdb=" O SER 7 336 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG 7 343 " --> pdb=" O GLU 7 339 " (cutoff:3.500A) Proline residue: 7 344 - end of helix Processing helix chain '7' and resid 374 through 390 Processing helix chain '7' and resid 401 through 413 removed outlier: 3.610A pdb=" N LYS 7 411 " --> pdb=" O ARG 7 407 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE 7 412 " --> pdb=" O TYR 7 408 " (cutoff:3.500A) Processing helix chain '7' and resid 414 through 421 Processing helix chain '7' and resid 481 through 486 removed outlier: 3.660A pdb=" N MET 7 485 " --> pdb=" O MET 7 481 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY 7 486 " --> pdb=" O PHE 7 482 " (cutoff:3.500A) No H-bonds generated for 'chain '7' and resid 481 through 486' Processing helix chain '7' and resid 487 through 493 Processing helix chain '7' and resid 498 through 505 Processing helix chain '7' and resid 506 through 511 Processing helix chain 'U' and resid 5 through 13 Processing helix chain 'U' and resid 144 through 155 removed outlier: 4.987A pdb=" N ALA U 148 " --> pdb=" O SER U 144 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR U 149 " --> pdb=" O PRO U 145 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N HIS U 150 " --> pdb=" O GLN U 146 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ASN U 154 " --> pdb=" O HIS U 150 " (cutoff:3.500A) Processing helix chain 'U' and resid 167 through 173 Processing helix chain 'U' and resid 178 through 193 removed outlier: 3.680A pdb=" N GLU U 190 " --> pdb=" O LEU U 186 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N GLY U 191 " --> pdb=" O ARG U 187 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N LEU U 192 " --> pdb=" O SER U 188 " (cutoff:3.500A) Proline residue: U 193 - end of helix Processing helix chain 'U' and resid 206 through 217 removed outlier: 4.758A pdb=" N LEU U 210 " --> pdb=" O GLY U 206 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N GLN U 213 " --> pdb=" O PRO U 209 " (cutoff:3.500A) Processing helix chain 'U' and resid 230 through 245 Processing helix chain 'U' and resid 260 through 269 removed outlier: 3.640A pdb=" N GLU U 269 " --> pdb=" O ILE U 265 " (cutoff:3.500A) Processing helix chain 'U' and resid 290 through 295 removed outlier: 4.907A pdb=" N SER U 294 " --> pdb=" O ILE U 290 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N GLN U 295 " --> pdb=" O ARG U 291 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 290 through 295' Processing helix chain 'U' and resid 312 through 326 removed outlier: 4.096A pdb=" N ASN U 326 " --> pdb=" O MET U 322 " (cutoff:3.500A) Processing helix chain 'U' and resid 335 through 357 removed outlier: 3.933A pdb=" N SER U 340 " --> pdb=" O SER U 336 " (cutoff:3.500A) removed outlier: 5.027A pdb=" N ARG U 343 " --> pdb=" O GLU U 339 " (cutoff:3.500A) Proline residue: U 344 - end of helix Processing helix chain 'U' and resid 374 through 390 Processing helix chain 'U' and resid 401 through 413 removed outlier: 3.610A pdb=" N LYS U 411 " --> pdb=" O ARG U 407 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ILE U 412 " --> pdb=" O TYR U 408 " (cutoff:3.500A) Processing helix chain 'U' and resid 414 through 421 Processing helix chain 'U' and resid 481 through 486 removed outlier: 3.660A pdb=" N MET U 485 " --> pdb=" O MET U 481 " (cutoff:3.500A) removed outlier: 5.083A pdb=" N GLY U 486 " --> pdb=" O PHE U 482 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 481 through 486' Processing helix chain 'U' and resid 487 through 493 Processing helix chain 'U' and resid 498 through 505 Processing helix chain 'U' and resid 506 through 511 Processing sheet with id= 1, first strand: chain 'A' and resid 79 through 85 Processing sheet with id= 2, first strand: chain 'D' and resid 79 through 85 Processing sheet with id= 3, first strand: chain 'G' and resid 79 through 85 Processing sheet with id= 4, first strand: chain 'J' and resid 79 through 85 Processing sheet with id= 5, first strand: chain 'M' and resid 79 through 85 Processing sheet with id= 6, first strand: chain 'P' and resid 79 through 85 Processing sheet with id= 7, first strand: chain 'S' and resid 79 through 85 Processing sheet with id= 8, first strand: chain 'W' and resid 79 through 85 Processing sheet with id= 9, first strand: chain 'Z' and resid 79 through 85 Processing sheet with id= 10, first strand: chain '2' and resid 79 through 85 Processing sheet with id= 11, first strand: chain '5' and resid 79 through 85 Processing sheet with id= 12, first strand: chain '8' and resid 79 through 85 Processing sheet with id= 13, first strand: chain 'B' and resid 55 through 62 removed outlier: 4.200A pdb=" N ASP B 109 " --> pdb=" O ASN B 62 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'B' and resid 68 through 72 removed outlier: 7.526A pdb=" N THR B 101 " --> pdb=" O SER B 72 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'E' and resid 55 through 62 removed outlier: 4.200A pdb=" N ASP E 109 " --> pdb=" O ASN E 62 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'E' and resid 68 through 72 removed outlier: 7.526A pdb=" N THR E 101 " --> pdb=" O SER E 72 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'H' and resid 55 through 62 removed outlier: 4.200A pdb=" N ASP H 109 " --> pdb=" O ASN H 62 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'H' and resid 68 through 72 removed outlier: 7.525A pdb=" N THR H 101 " --> pdb=" O SER H 72 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'K' and resid 55 through 62 removed outlier: 4.200A pdb=" N ASP K 109 " --> pdb=" O ASN K 62 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'K' and resid 68 through 72 removed outlier: 7.527A pdb=" N THR K 101 " --> pdb=" O SER K 72 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'N' and resid 55 through 62 removed outlier: 4.200A pdb=" N ASP N 109 " --> pdb=" O ASN N 62 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'N' and resid 68 through 72 removed outlier: 7.526A pdb=" N THR N 101 " --> pdb=" O SER N 72 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'Q' and resid 55 through 62 removed outlier: 4.200A pdb=" N ASP Q 109 " --> pdb=" O ASN Q 62 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'Q' and resid 68 through 72 removed outlier: 7.526A pdb=" N THR Q 101 " --> pdb=" O SER Q 72 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'T' and resid 55 through 62 removed outlier: 4.200A pdb=" N ASP T 109 " --> pdb=" O ASN T 62 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'T' and resid 68 through 72 removed outlier: 7.525A pdb=" N THR T 101 " --> pdb=" O SER T 72 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'X' and resid 55 through 62 removed outlier: 4.200A pdb=" N ASP X 109 " --> pdb=" O ASN X 62 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'X' and resid 68 through 72 removed outlier: 7.526A pdb=" N THR X 101 " --> pdb=" O SER X 72 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain '0' and resid 55 through 62 removed outlier: 4.200A pdb=" N ASP 0 109 " --> pdb=" O ASN 0 62 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain '0' and resid 68 through 72 removed outlier: 7.526A pdb=" N THR 0 101 " --> pdb=" O SER 0 72 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain '3' and resid 55 through 62 removed outlier: 4.200A pdb=" N ASP 3 109 " --> pdb=" O ASN 3 62 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain '3' and resid 68 through 72 removed outlier: 7.525A pdb=" N THR 3 101 " --> pdb=" O SER 3 72 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain '6' and resid 55 through 62 removed outlier: 4.199A pdb=" N ASP 6 109 " --> pdb=" O ASN 6 62 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain '6' and resid 68 through 72 removed outlier: 7.526A pdb=" N THR 6 101 " --> pdb=" O SER 6 72 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain '9' and resid 55 through 62 removed outlier: 4.200A pdb=" N ASP 9 109 " --> pdb=" O ASN 9 62 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain '9' and resid 68 through 72 removed outlier: 7.526A pdb=" N THR 9 101 " --> pdb=" O SER 9 72 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'C' and resid 19 through 23 removed outlier: 4.902A pdb=" N ASP C 19 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU C 28 " --> pdb=" O LEU C 23 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'C' and resid 97 through 100 removed outlier: 3.767A pdb=" N GLY C 98 " --> pdb=" O GLY C 90 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'C' and resid 129 through 132 Processing sheet with id= 40, first strand: chain 'C' and resid 157 through 161 removed outlier: 4.147A pdb=" N GLY C 220 " --> pdb=" O ILE C 198 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N HIS C 224 " --> pdb=" O GLY C 202 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'C' and resid 272 through 276 Processing sheet with id= 42, first strand: chain 'C' and resid 494 through 497 Processing sheet with id= 43, first strand: chain 'C' and resid 539 through 542 No H-bonds generated for sheet with id= 43 Processing sheet with id= 44, first strand: chain 'C' and resid 74 through 77 Processing sheet with id= 45, first strand: chain 'F' and resid 19 through 23 removed outlier: 4.901A pdb=" N ASP F 19 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 5.389A pdb=" N LEU F 28 " --> pdb=" O LEU F 23 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'F' and resid 97 through 100 removed outlier: 3.767A pdb=" N GLY F 98 " --> pdb=" O GLY F 90 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'F' and resid 129 through 132 Processing sheet with id= 48, first strand: chain 'F' and resid 157 through 161 removed outlier: 4.148A pdb=" N GLY F 220 " --> pdb=" O ILE F 198 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N HIS F 224 " --> pdb=" O GLY F 202 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'F' and resid 272 through 276 Processing sheet with id= 50, first strand: chain 'F' and resid 494 through 497 Processing sheet with id= 51, first strand: chain 'F' and resid 539 through 542 No H-bonds generated for sheet with id= 51 Processing sheet with id= 52, first strand: chain 'F' and resid 74 through 77 Processing sheet with id= 53, first strand: chain 'I' and resid 19 through 23 removed outlier: 4.902A pdb=" N ASP I 19 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU I 28 " --> pdb=" O LEU I 23 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'I' and resid 97 through 100 removed outlier: 3.767A pdb=" N GLY I 98 " --> pdb=" O GLY I 90 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'I' and resid 129 through 132 Processing sheet with id= 56, first strand: chain 'I' and resid 157 through 161 removed outlier: 4.147A pdb=" N GLY I 220 " --> pdb=" O ILE I 198 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N HIS I 224 " --> pdb=" O GLY I 202 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'I' and resid 272 through 276 Processing sheet with id= 58, first strand: chain 'I' and resid 494 through 497 Processing sheet with id= 59, first strand: chain 'I' and resid 539 through 542 No H-bonds generated for sheet with id= 59 Processing sheet with id= 60, first strand: chain 'I' and resid 74 through 77 Processing sheet with id= 61, first strand: chain 'L' and resid 19 through 23 removed outlier: 4.902A pdb=" N ASP L 19 " --> pdb=" O ILE L 32 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU L 28 " --> pdb=" O LEU L 23 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'L' and resid 97 through 100 removed outlier: 3.767A pdb=" N GLY L 98 " --> pdb=" O GLY L 90 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'L' and resid 129 through 132 Processing sheet with id= 64, first strand: chain 'L' and resid 157 through 161 removed outlier: 4.148A pdb=" N GLY L 220 " --> pdb=" O ILE L 198 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N HIS L 224 " --> pdb=" O GLY L 202 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'L' and resid 272 through 276 Processing sheet with id= 66, first strand: chain 'L' and resid 494 through 497 Processing sheet with id= 67, first strand: chain 'L' and resid 539 through 542 No H-bonds generated for sheet with id= 67 Processing sheet with id= 68, first strand: chain 'L' and resid 74 through 77 Processing sheet with id= 69, first strand: chain 'O' and resid 19 through 23 removed outlier: 4.902A pdb=" N ASP O 19 " --> pdb=" O ILE O 32 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU O 28 " --> pdb=" O LEU O 23 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'O' and resid 97 through 100 removed outlier: 3.767A pdb=" N GLY O 98 " --> pdb=" O GLY O 90 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'O' and resid 129 through 132 Processing sheet with id= 72, first strand: chain 'O' and resid 157 through 161 removed outlier: 4.147A pdb=" N GLY O 220 " --> pdb=" O ILE O 198 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N HIS O 224 " --> pdb=" O GLY O 202 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'O' and resid 272 through 276 Processing sheet with id= 74, first strand: chain 'O' and resid 494 through 497 Processing sheet with id= 75, first strand: chain 'O' and resid 539 through 542 No H-bonds generated for sheet with id= 75 Processing sheet with id= 76, first strand: chain 'O' and resid 74 through 77 Processing sheet with id= 77, first strand: chain 'R' and resid 19 through 23 removed outlier: 4.901A pdb=" N ASP R 19 " --> pdb=" O ILE R 32 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU R 28 " --> pdb=" O LEU R 23 " (cutoff:3.500A) Processing sheet with id= 78, first strand: chain 'R' and resid 97 through 100 removed outlier: 3.767A pdb=" N GLY R 98 " --> pdb=" O GLY R 90 " (cutoff:3.500A) Processing sheet with id= 79, first strand: chain 'R' and resid 129 through 132 Processing sheet with id= 80, first strand: chain 'R' and resid 157 through 161 removed outlier: 4.147A pdb=" N GLY R 220 " --> pdb=" O ILE R 198 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N HIS R 224 " --> pdb=" O GLY R 202 " (cutoff:3.500A) Processing sheet with id= 81, first strand: chain 'R' and resid 272 through 276 Processing sheet with id= 82, first strand: chain 'R' and resid 494 through 497 Processing sheet with id= 83, first strand: chain 'R' and resid 539 through 542 No H-bonds generated for sheet with id= 83 Processing sheet with id= 84, first strand: chain 'R' and resid 74 through 77 Processing sheet with id= 85, first strand: chain 'V' and resid 19 through 23 removed outlier: 4.901A pdb=" N ASP V 19 " --> pdb=" O ILE V 32 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU V 28 " --> pdb=" O LEU V 23 " (cutoff:3.500A) Processing sheet with id= 86, first strand: chain 'V' and resid 97 through 100 removed outlier: 3.767A pdb=" N GLY V 98 " --> pdb=" O GLY V 90 " (cutoff:3.500A) Processing sheet with id= 87, first strand: chain 'V' and resid 129 through 132 Processing sheet with id= 88, first strand: chain 'V' and resid 157 through 161 removed outlier: 4.147A pdb=" N GLY V 220 " --> pdb=" O ILE V 198 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N HIS V 224 " --> pdb=" O GLY V 202 " (cutoff:3.500A) Processing sheet with id= 89, first strand: chain 'V' and resid 272 through 276 Processing sheet with id= 90, first strand: chain 'V' and resid 494 through 497 Processing sheet with id= 91, first strand: chain 'V' and resid 539 through 542 No H-bonds generated for sheet with id= 91 Processing sheet with id= 92, first strand: chain 'V' and resid 74 through 77 Processing sheet with id= 93, first strand: chain 'Y' and resid 19 through 23 removed outlier: 4.901A pdb=" N ASP Y 19 " --> pdb=" O ILE Y 32 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU Y 28 " --> pdb=" O LEU Y 23 " (cutoff:3.500A) Processing sheet with id= 94, first strand: chain 'Y' and resid 97 through 100 removed outlier: 3.767A pdb=" N GLY Y 98 " --> pdb=" O GLY Y 90 " (cutoff:3.500A) Processing sheet with id= 95, first strand: chain 'Y' and resid 129 through 132 Processing sheet with id= 96, first strand: chain 'Y' and resid 157 through 161 removed outlier: 4.147A pdb=" N GLY Y 220 " --> pdb=" O ILE Y 198 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N HIS Y 224 " --> pdb=" O GLY Y 202 " (cutoff:3.500A) Processing sheet with id= 97, first strand: chain 'Y' and resid 272 through 276 Processing sheet with id= 98, first strand: chain 'Y' and resid 494 through 497 Processing sheet with id= 99, first strand: chain 'Y' and resid 539 through 542 No H-bonds generated for sheet with id= 99 Processing sheet with id=100, first strand: chain 'Y' and resid 74 through 77 Processing sheet with id=101, first strand: chain '1' and resid 19 through 23 removed outlier: 4.903A pdb=" N ASP 1 19 " --> pdb=" O ILE 1 32 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU 1 28 " --> pdb=" O LEU 1 23 " (cutoff:3.500A) Processing sheet with id=102, first strand: chain '1' and resid 97 through 100 removed outlier: 3.767A pdb=" N GLY 1 98 " --> pdb=" O GLY 1 90 " (cutoff:3.500A) Processing sheet with id=103, first strand: chain '1' and resid 129 through 132 Processing sheet with id=104, first strand: chain '1' and resid 157 through 161 removed outlier: 4.147A pdb=" N GLY 1 220 " --> pdb=" O ILE 1 198 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N HIS 1 224 " --> pdb=" O GLY 1 202 " (cutoff:3.500A) Processing sheet with id=105, first strand: chain '1' and resid 272 through 276 Processing sheet with id=106, first strand: chain '1' and resid 494 through 497 Processing sheet with id=107, first strand: chain '1' and resid 539 through 542 No H-bonds generated for sheet with id=107 Processing sheet with id=108, first strand: chain '1' and resid 74 through 77 Processing sheet with id=109, first strand: chain '4' and resid 19 through 23 removed outlier: 4.902A pdb=" N ASP 4 19 " --> pdb=" O ILE 4 32 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU 4 28 " --> pdb=" O LEU 4 23 " (cutoff:3.500A) Processing sheet with id=110, first strand: chain '4' and resid 97 through 100 removed outlier: 3.767A pdb=" N GLY 4 98 " --> pdb=" O GLY 4 90 " (cutoff:3.500A) Processing sheet with id=111, first strand: chain '4' and resid 129 through 132 Processing sheet with id=112, first strand: chain '4' and resid 157 through 161 removed outlier: 4.147A pdb=" N GLY 4 220 " --> pdb=" O ILE 4 198 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N HIS 4 224 " --> pdb=" O GLY 4 202 " (cutoff:3.500A) Processing sheet with id=113, first strand: chain '4' and resid 272 through 276 Processing sheet with id=114, first strand: chain '4' and resid 494 through 497 Processing sheet with id=115, first strand: chain '4' and resid 539 through 542 No H-bonds generated for sheet with id=115 Processing sheet with id=116, first strand: chain '4' and resid 74 through 77 Processing sheet with id=117, first strand: chain '7' and resid 19 through 23 removed outlier: 4.902A pdb=" N ASP 7 19 " --> pdb=" O ILE 7 32 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU 7 28 " --> pdb=" O LEU 7 23 " (cutoff:3.500A) Processing sheet with id=118, first strand: chain '7' and resid 97 through 100 removed outlier: 3.766A pdb=" N GLY 7 98 " --> pdb=" O GLY 7 90 " (cutoff:3.500A) Processing sheet with id=119, first strand: chain '7' and resid 129 through 132 Processing sheet with id=120, first strand: chain '7' and resid 157 through 161 removed outlier: 4.147A pdb=" N GLY 7 220 " --> pdb=" O ILE 7 198 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N HIS 7 224 " --> pdb=" O GLY 7 202 " (cutoff:3.500A) Processing sheet with id=121, first strand: chain '7' and resid 272 through 276 Processing sheet with id=122, first strand: chain '7' and resid 494 through 497 Processing sheet with id=123, first strand: chain '7' and resid 539 through 542 No H-bonds generated for sheet with id=123 Processing sheet with id=124, first strand: chain '7' and resid 74 through 77 Processing sheet with id=125, first strand: chain 'U' and resid 19 through 23 removed outlier: 4.901A pdb=" N ASP U 19 " --> pdb=" O ILE U 32 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LEU U 28 " --> pdb=" O LEU U 23 " (cutoff:3.500A) Processing sheet with id=126, first strand: chain 'U' and resid 97 through 100 removed outlier: 3.767A pdb=" N GLY U 98 " --> pdb=" O GLY U 90 " (cutoff:3.500A) Processing sheet with id=127, first strand: chain 'U' and resid 129 through 132 Processing sheet with id=128, first strand: chain 'U' and resid 157 through 161 removed outlier: 4.147A pdb=" N GLY U 220 " --> pdb=" O ILE U 198 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N HIS U 224 " --> pdb=" O GLY U 202 " (cutoff:3.500A) Processing sheet with id=129, first strand: chain 'U' and resid 272 through 276 Processing sheet with id=130, first strand: chain 'U' and resid 494 through 497 Processing sheet with id=131, first strand: chain 'U' and resid 539 through 542 No H-bonds generated for sheet with id=131 Processing sheet with id=132, first strand: chain 'U' and resid 74 through 77 2676 hydrogen bonds defined for protein. 7944 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: 70.11 Time building geometry restraints manager: 109.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.54 - 0.81: 14585 0.81 - 1.08: 58542 1.08 - 1.35: 30737 1.35 - 1.62: 43136 1.62 - 1.89: 936 Bond restraints: 147936 Sorted by residual: bond pdb=" N ALA O 435 " pdb=" H AALA O 435 " ideal model delta sigma weight residual 0.860 1.322 -0.462 2.00e-02 2.50e+03 5.33e+02 bond pdb=" N ALA L 435 " pdb=" H AALA L 435 " ideal model delta sigma weight residual 0.860 1.322 -0.462 2.00e-02 2.50e+03 5.33e+02 bond pdb=" N ALA 7 435 " pdb=" H AALA 7 435 " ideal model delta sigma weight residual 0.860 1.322 -0.462 2.00e-02 2.50e+03 5.33e+02 bond pdb=" N ALA V 435 " pdb=" H AALA V 435 " ideal model delta sigma weight residual 0.860 1.321 -0.461 2.00e-02 2.50e+03 5.32e+02 bond pdb=" N ALA C 435 " pdb=" H AALA C 435 " ideal model delta sigma weight residual 0.860 1.321 -0.461 2.00e-02 2.50e+03 5.32e+02 ... (remaining 147931 not shown) Histogram of bond angle deviations from ideal: 51.47 - 76.98: 168 76.98 - 102.49: 25160 102.49 - 128.00: 237116 128.00 - 153.51: 5432 153.51 - 179.01: 24 Bond angle restraints: 267900 Sorted by residual: angle pdb=" C AARG N 153 " pdb=" N ARG N 154 " pdb=" H AARG N 154 " ideal model delta sigma weight residual 124.93 57.56 67.37 3.00e+00 1.11e-01 5.04e+02 angle pdb=" C AARG X 153 " pdb=" N ARG X 154 " pdb=" H AARG X 154 " ideal model delta sigma weight residual 124.93 57.59 67.34 3.00e+00 1.11e-01 5.04e+02 angle pdb=" C AARG H 153 " pdb=" N ARG H 154 " pdb=" H AARG H 154 " ideal model delta sigma weight residual 124.93 57.61 67.32 3.00e+00 1.11e-01 5.04e+02 angle pdb=" C AARG B 153 " pdb=" N ARG B 154 " pdb=" H AARG B 154 " ideal model delta sigma weight residual 124.93 57.63 67.30 3.00e+00 1.11e-01 5.03e+02 angle pdb=" C AARG Q 153 " pdb=" N ARG Q 154 " pdb=" H AARG Q 154 " ideal model delta sigma weight residual 124.93 57.63 67.30 3.00e+00 1.11e-01 5.03e+02 ... (remaining 267895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 48845 17.94 - 35.88: 6339 35.88 - 53.82: 2237 53.82 - 71.76: 764 71.76 - 89.70: 171 Dihedral angle restraints: 58356 sinusoidal: 27528 harmonic: 30828 Sorted by residual: dihedral pdb=" CA PRO Y 287 " pdb=" C PRO Y 287 " pdb=" N ASP Y 288 " pdb=" CA ASP Y 288 " ideal model delta harmonic sigma weight residual -180.00 -149.08 -30.92 0 5.00e+00 4.00e-02 3.83e+01 dihedral pdb=" CA PRO R 287 " pdb=" C PRO R 287 " pdb=" N ASP R 288 " pdb=" CA ASP R 288 " ideal model delta harmonic sigma weight residual -180.00 -149.10 -30.90 0 5.00e+00 4.00e-02 3.82e+01 dihedral pdb=" CA PRO F 287 " pdb=" C PRO F 287 " pdb=" N ASP F 288 " pdb=" CA ASP F 288 " ideal model delta harmonic sigma weight residual -180.00 -149.11 -30.89 0 5.00e+00 4.00e-02 3.82e+01 ... (remaining 58353 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.322: 8404 0.322 - 0.644: 2108 0.644 - 0.966: 696 0.966 - 1.288: 192 1.288 - 1.610: 36 Chirality restraints: 11436 Sorted by residual: chirality pdb=" CG LEU F 299 " pdb=" CB LEU F 299 " pdb=" CD1 LEU F 299 " pdb=" CD2 LEU F 299 " both_signs ideal model delta sigma weight residual False -2.59 -0.98 -1.61 2.00e-01 2.50e+01 6.48e+01 chirality pdb=" CG LEU 4 299 " pdb=" CB LEU 4 299 " pdb=" CD1 LEU 4 299 " pdb=" CD2 LEU 4 299 " both_signs ideal model delta sigma weight residual False -2.59 -0.98 -1.61 2.00e-01 2.50e+01 6.47e+01 chirality pdb=" CG LEU U 299 " pdb=" CB LEU U 299 " pdb=" CD1 LEU U 299 " pdb=" CD2 LEU U 299 " both_signs ideal model delta sigma weight residual False -2.59 -0.98 -1.61 2.00e-01 2.50e+01 6.46e+01 ... (remaining 11433 not shown) Planarity restraints: 22704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN F 304 " -0.259 2.00e-02 2.50e+03 3.33e-01 1.66e+03 pdb=" CG ASN F 304 " 0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN F 304 " 0.243 2.00e-02 2.50e+03 pdb=" ND2 ASN F 304 " 0.002 2.00e-02 2.50e+03 pdb="HD21 ASN F 304 " -0.528 2.00e-02 2.50e+03 pdb="HD22 ASN F 304 " 0.507 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN R 304 " 0.259 2.00e-02 2.50e+03 3.32e-01 1.66e+03 pdb=" CG ASN R 304 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN R 304 " -0.243 2.00e-02 2.50e+03 pdb=" ND2 ASN R 304 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN R 304 " 0.528 2.00e-02 2.50e+03 pdb="HD22 ASN R 304 " -0.507 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN 4 304 " 0.258 2.00e-02 2.50e+03 3.32e-01 1.66e+03 pdb=" CG ASN 4 304 " -0.035 2.00e-02 2.50e+03 pdb=" OD1 ASN 4 304 " -0.242 2.00e-02 2.50e+03 pdb=" ND2 ASN 4 304 " -0.001 2.00e-02 2.50e+03 pdb="HD21 ASN 4 304 " 0.528 2.00e-02 2.50e+03 pdb="HD22 ASN 4 304 " -0.507 2.00e-02 2.50e+03 ... (remaining 22701 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.76: 2828 1.76 - 2.47: 110546 2.47 - 3.18: 488965 3.18 - 3.89: 699775 3.89 - 4.60: 1110811 Nonbonded interactions: 2412925 Sorted by model distance: nonbonded pdb=" HG1 THR L 167 " pdb=" OD2 ASP V 122 " model vdw 1.050 1.850 nonbonded pdb=" OD2 ASP F 122 " pdb=" HG1 THR Y 167 " model vdw 1.165 1.850 nonbonded pdb=" HG1 THR I 167 " pdb=" OD2 ASP U 122 " model vdw 1.244 1.850 nonbonded pdb=" OD2 ASP R 122 " pdb=" HG1 THR V 167 " model vdw 1.271 1.850 nonbonded pdb=" OD2 ASP 1 122 " pdb=" HG1 THR 7 167 " model vdw 1.308 1.850 ... (remaining 2412920 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain '0' and (resid 31 through 152 or resid 155 through 162)) selection = (chain '3' and (resid 31 through 152 or resid 155 through 162)) selection = (chain '6' and (resid 31 through 152 or resid 155 through 162)) selection = (chain '9' and (resid 31 through 152 or resid 155 through 162)) selection = (chain 'B' and (resid 31 through 152 or resid 155 through 162)) selection = (chain 'E' and (resid 31 through 152 or resid 155 through 162)) selection = (chain 'H' and (resid 31 through 152 or resid 155 through 162)) selection = (chain 'K' and (resid 31 through 152 or resid 155 through 162)) selection = (chain 'N' and (resid 31 through 152 or resid 155 through 162)) selection = (chain 'Q' and (resid 31 through 152 or resid 155 through 162)) selection = (chain 'T' and (resid 31 through 152 or resid 155 through 162)) selection = (chain 'X' and (resid 31 through 152 or resid 155 through 162)) } ncs_group { reference = (chain '1' and (resid 2 through 19 or resid 22 through 54 or resid 57 through 40 \ 5 or resid 408 through 433 or resid 436 through 488 or resid 491 through 572 or \ resid 601 through 602)) selection = (chain '4' and (resid 2 through 19 or resid 22 through 54 or resid 57 through 40 \ 5 or resid 408 through 433 or resid 436 through 488 or resid 491 through 572 or \ resid 601 through 602)) selection = (chain '7' and (resid 2 through 19 or resid 22 through 54 or resid 57 through 40 \ 5 or resid 408 through 433 or resid 436 through 488 or resid 491 through 572 or \ resid 601 through 602)) selection = (chain 'C' and (resid 2 through 19 or resid 22 through 54 or resid 57 through 40 \ 5 or resid 408 through 433 or resid 436 through 488 or resid 491 through 572 or \ resid 601 through 602)) selection = (chain 'F' and (resid 2 through 19 or resid 22 through 54 or resid 57 through 40 \ 5 or resid 408 through 433 or resid 436 through 488 or resid 491 through 572 or \ resid 601 through 602)) selection = (chain 'I' and (resid 2 through 19 or resid 22 through 54 or resid 57 through 40 \ 5 or resid 408 through 433 or resid 436 through 488 or resid 491 through 572 or \ resid 601 through 602)) selection = (chain 'L' and (resid 2 through 19 or resid 22 through 54 or resid 57 through 40 \ 5 or resid 408 through 433 or resid 436 through 488 or resid 491 through 572 or \ resid 601 through 602)) selection = (chain 'O' and (resid 2 through 19 or resid 22 through 54 or resid 57 through 40 \ 5 or resid 408 through 433 or resid 436 through 488 or resid 491 through 572 or \ resid 601 through 602)) selection = (chain 'R' and (resid 2 through 19 or resid 22 through 54 or resid 57 through 40 \ 5 or resid 408 through 433 or resid 436 through 488 or resid 491 through 572 or \ resid 601 through 602)) selection = (chain 'U' and (resid 2 through 19 or resid 22 through 54 or resid 57 through 40 \ 5 or resid 408 through 433 or resid 436 through 488 or resid 491 through 572 or \ resid 601 through 602)) selection = (chain 'V' and (resid 2 through 19 or resid 22 through 54 or resid 57 through 40 \ 5 or resid 408 through 433 or resid 436 through 488 or resid 491 through 572 or \ resid 601 through 602)) selection = (chain 'Y' and (resid 2 through 19 or resid 22 through 54 or resid 57 through 40 \ 5 or resid 408 through 433 or resid 436 through 488 or resid 491 through 572 or \ resid 601 through 602)) } ncs_group { reference = (chain '2' and (resid 1 through 15 or resid 18 through 28 or resid 31 through 56 \ or resid 59 through 65 or resid 68 through 100)) selection = (chain '5' and (resid 1 through 15 or resid 18 through 28 or resid 31 through 56 \ or resid 59 through 65 or resid 68 through 100)) selection = (chain '8' and (resid 1 through 15 or resid 18 through 28 or resid 31 through 56 \ or resid 59 through 65 or resid 68 through 100)) selection = (chain 'A' and (resid 1 through 15 or resid 18 through 28 or resid 31 through 56 \ or resid 59 through 65 or resid 68 through 100)) selection = (chain 'D' and (resid 1 through 15 or resid 18 through 28 or resid 31 through 56 \ or resid 59 through 65 or resid 68 through 100)) selection = (chain 'G' and (resid 1 through 15 or resid 18 through 28 or resid 31 through 56 \ or resid 59 through 65 or resid 68 through 100)) selection = (chain 'J' and (resid 1 through 15 or resid 18 through 28 or resid 31 through 56 \ or resid 59 through 65 or resid 68 through 100)) selection = (chain 'M' and (resid 1 through 15 or resid 18 through 28 or resid 31 through 56 \ or resid 59 through 65 or resid 68 through 100)) selection = (chain 'P' and (resid 1 through 15 or resid 18 through 28 or resid 31 through 56 \ or resid 59 through 65 or resid 68 through 100)) selection = (chain 'S' and (resid 1 through 15 or resid 18 through 28 or resid 31 through 56 \ or resid 59 through 65 or resid 68 through 100)) selection = (chain 'W' and (resid 1 through 15 or resid 18 through 28 or resid 31 through 56 \ or resid 59 through 65 or resid 68 through 100)) selection = (chain 'Z' and (resid 1 through 15 or resid 18 through 28 or resid 31 through 56 \ or resid 59 through 65 or resid 68 through 100)) } 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 Ni 24 6.56 5 S 420 5.16 5 C 45984 2.51 5 N 12984 2.21 5 O 17700 1.98 5 H 73044 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=0.50 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.370 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: 2.390 Extract box with map and model: 36.270 Check model and map are aligned: 1.630 Convert atoms to be neutral: 0.950 Process input model: 445.100 Find NCS groups from input model: 8.190 Set up NCS constraints: 0.640 Set refine NCS operators: 0.000 Set scattering table: 0.040 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.400 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 513.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 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 : 0.067 0.515 74892 Z= 4.443 Angle : 3.597 20.148 101616 Z= 2.117 Chirality : 0.358 1.610 11436 Planarity : 0.018 0.069 13488 Dihedral : 16.352 89.703 27804 Min Nonbonded Distance : 1.877 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.38 % Allowed : 5.25 % Favored : 94.36 % Rotamer Outliers : 2.74 % Cbeta Deviations : 2.84 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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: -2.46 (0.07), residues: 9780 helix: -2.65 (0.06), residues: 3060 sheet: 0.73 (0.15), residues: 1032 loop : -1.50 (0.07), residues: 5688 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1296 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1164 time to evaluate : 8.821 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 outliers start: 132 outliers final: 46 residues processed: 1250 average time/residue: 3.6364 time to fit residues: 6058.8239 Evaluate side-chains 1044 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 998 time to evaluate : 8.723 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 40 residues processed: 8 average time/residue: 1.6692 time to fit residues: 33.5628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 800 optimal weight: 5.9990 chunk 718 optimal weight: 5.9990 chunk 398 optimal weight: 5.9990 chunk 245 optimal weight: 5.9990 chunk 484 optimal weight: 5.9990 chunk 383 optimal weight: 5.9990 chunk 743 optimal weight: 2.9990 chunk 287 optimal weight: 5.9990 chunk 451 optimal weight: 5.9990 chunk 553 optimal weight: 5.9990 chunk 860 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN C 184 GLN ** C 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 528 HIS E 52 ASN F 184 GLN ** F 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 521 ASN F 528 HIS G 2 GLN H 52 ASN I 184 GLN ** I 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 52 ASN ** L 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 52 ASN O 184 GLN O 528 HIS P 2 GLN Q 52 ASN R 184 GLN R 521 ASN T 52 ASN V 184 GLN W 2 GLN X 52 ASN Y 184 GLN 0 52 ASN 1 184 GLN 3 52 ASN 4 150 HIS ** 4 325 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 4 528 HIS 4 538 ASN 6 52 ASN 7 184 GLN ** 9 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 52 ASN U 184 GLN U 521 ASN U 535 GLN U 538 ASN Total number of N/Q/H flips: 36 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.053 74892 Z= 0.385 Angle : 0.885 8.488 101616 Z= 0.483 Chirality : 0.053 0.260 11436 Planarity : 0.007 0.062 13488 Dihedral : 6.583 78.819 10500 Min Nonbonded Distance : 1.671 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.16 % Favored : 95.71 % Rotamer Outliers : 2.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.08), residues: 9780 helix: -1.03 (0.08), residues: 3144 sheet: 0.82 (0.14), residues: 1140 loop : -0.70 (0.08), residues: 5496 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1207 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 1092 time to evaluate : 8.839 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 outliers start: 115 outliers final: 36 residues processed: 1158 average time/residue: 3.6300 time to fit residues: 5610.9870 Evaluate side-chains 1105 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1069 time to evaluate : 8.704 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 29 residues processed: 7 average time/residue: 2.3354 time to fit residues: 35.6700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 478 optimal weight: 8.9990 chunk 267 optimal weight: 2.9990 chunk 716 optimal weight: 0.9990 chunk 586 optimal weight: 0.9980 chunk 237 optimal weight: 8.9990 chunk 862 optimal weight: 3.9990 chunk 931 optimal weight: 5.9990 chunk 768 optimal weight: 5.9990 chunk 855 optimal weight: 1.9990 chunk 294 optimal weight: 10.0000 chunk 691 optimal weight: 6.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 2 GLN B 34 ASN B 52 ASN C 521 ASN F 528 HIS H 52 ASN I 203 ASN J 2 GLN L 184 GLN M 2 GLN N 34 ASN O 203 ASN O 521 ASN O 528 HIS R 203 ASN R 528 HIS T 52 ASN V 351 ASN V 528 HIS V 538 ASN Z 2 GLN 0 52 ASN 2 2 GLN 3 34 ASN 4 528 HIS 7 528 HIS 7 538 ASN 9 34 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.3050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.065 74892 Z= 0.228 Angle : 0.693 7.931 101616 Z= 0.370 Chirality : 0.047 0.199 11436 Planarity : 0.005 0.050 13488 Dihedral : 6.092 80.157 10500 Min Nonbonded Distance : 1.796 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.43 % Favored : 96.44 % Rotamer Outliers : 1.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.36 (0.08), residues: 9780 helix: -0.25 (0.08), residues: 3168 sheet: 1.01 (0.14), residues: 1164 loop : -0.44 (0.08), residues: 5448 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1191 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1113 time to evaluate : 8.681 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 78 outliers final: 30 residues processed: 1151 average time/residue: 3.7321 time to fit residues: 5740.8753 Evaluate side-chains 1108 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1078 time to evaluate : 8.851 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 25 residues processed: 5 average time/residue: 2.3897 time to fit residues: 29.1119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 852 optimal weight: 3.9990 chunk 648 optimal weight: 4.9990 chunk 447 optimal weight: 4.9990 chunk 95 optimal weight: 7.9990 chunk 411 optimal weight: 4.9990 chunk 579 optimal weight: 7.9990 chunk 865 optimal weight: 5.9990 chunk 916 optimal weight: 3.9990 chunk 452 optimal weight: 10.0000 chunk 820 optimal weight: 5.9990 chunk 246 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 52 ASN C 521 ASN C 538 ASN F 528 HIS H 52 ASN I 203 ASN L 521 ASN O 203 ASN O 521 ASN Q 34 ASN R 203 ASN R 528 HIS T 34 ASN V 538 ASN Y 203 ASN 0 52 ASN 1 521 ASN 1 528 HIS 4 521 ASN 4 528 HIS 7 528 HIS 9 34 ASN U 203 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8346 moved from start: 0.3220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 74892 Z= 0.339 Angle : 0.774 7.655 101616 Z= 0.419 Chirality : 0.050 0.226 11436 Planarity : 0.006 0.053 13488 Dihedral : 6.190 77.956 10500 Min Nonbonded Distance : 1.557 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.10 % Favored : 95.77 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.44 (0.08), residues: 9780 helix: -0.29 (0.08), residues: 3156 sheet: 1.01 (0.14), residues: 1140 loop : -0.50 (0.08), residues: 5484 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1153 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 1077 time to evaluate : 8.684 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 76 outliers final: 34 residues processed: 1118 average time/residue: 3.6516 time to fit residues: 5449.7955 Evaluate side-chains 1115 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1081 time to evaluate : 8.088 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 28 residues processed: 6 average time/residue: 2.2117 time to fit residues: 30.9857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 763 optimal weight: 5.9990 chunk 520 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 682 optimal weight: 3.9990 chunk 378 optimal weight: 0.6980 chunk 781 optimal weight: 1.9990 chunk 633 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 467 optimal weight: 5.9990 chunk 822 optimal weight: 5.9990 chunk 231 optimal weight: 6.9990 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN B 52 ASN C 521 ASN C 538 ASN F 528 HIS F 538 ASN I 203 ASN I 312 ASN L 521 ASN N 34 ASN O 203 ASN O 521 ASN R 203 ASN R 312 ASN R 528 HIS T 34 ASN V 203 ASN Y 203 ASN 1 528 HIS 3 34 ASN 7 528 HIS 9 34 ASN U 203 ASN U 312 ASN U 528 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 74892 Z= 0.259 Angle : 0.705 7.733 101616 Z= 0.379 Chirality : 0.048 0.212 11436 Planarity : 0.005 0.048 13488 Dihedral : 6.037 78.760 10500 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.59 % Favored : 96.28 % Rotamer Outliers : 1.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.08), residues: 9780 helix: -0.10 (0.08), residues: 3168 sheet: 1.06 (0.14), residues: 1164 loop : -0.45 (0.08), residues: 5448 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 1095 time to evaluate : 8.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 65 outliers final: 32 residues processed: 1139 average time/residue: 3.6938 time to fit residues: 5613.5934 Evaluate side-chains 1107 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1075 time to evaluate : 8.670 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 29 residues processed: 3 average time/residue: 1.3914 time to fit residues: 18.4646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 308 optimal weight: 0.7980 chunk 825 optimal weight: 6.9990 chunk 181 optimal weight: 9.9990 chunk 538 optimal weight: 5.9990 chunk 226 optimal weight: 4.9990 chunk 917 optimal weight: 7.9990 chunk 761 optimal weight: 6.9990 chunk 424 optimal weight: 6.9990 chunk 76 optimal weight: 10.0000 chunk 303 optimal weight: 4.9990 chunk 481 optimal weight: 5.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN C 521 ASN C 538 ASN F 528 HIS I 203 ASN I 312 ASN I 521 ASN I 538 ASN L 521 ASN N 34 ASN O 203 ASN O 521 ASN Q 34 ASN R 203 ASN R 312 ASN R 528 HIS T 34 ASN V 203 ASN Y 203 ASN Y 521 ASN 1 528 HIS 3 34 ASN 7 528 HIS 9 34 ASN U 203 ASN U 312 ASN U 528 HIS U 538 ASN Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.051 74892 Z= 0.329 Angle : 0.754 7.692 101616 Z= 0.408 Chirality : 0.050 0.230 11436 Planarity : 0.006 0.050 13488 Dihedral : 6.122 78.313 10500 Min Nonbonded Distance : 1.643 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.09 % Favored : 95.79 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.08), residues: 9780 helix: -0.20 (0.08), residues: 3156 sheet: 1.03 (0.14), residues: 1164 loop : -0.45 (0.08), residues: 5460 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1155 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1081 time to evaluate : 8.888 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 outliers start: 74 outliers final: 41 residues processed: 1124 average time/residue: 3.6918 time to fit residues: 5567.1264 Evaluate side-chains 1111 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 1070 time to evaluate : 8.732 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 30 residues processed: 11 average time/residue: 2.9016 time to fit residues: 58.5642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 884 optimal weight: 6.9990 chunk 103 optimal weight: 4.9990 chunk 522 optimal weight: 6.9990 chunk 669 optimal weight: 5.9990 chunk 518 optimal weight: 2.9990 chunk 772 optimal weight: 3.9990 chunk 512 optimal weight: 4.9990 chunk 913 optimal weight: 0.9980 chunk 571 optimal weight: 0.8980 chunk 557 optimal weight: 10.0000 chunk 421 optimal weight: 6.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN C 521 ASN F 528 HIS I 203 ASN I 521 ASN L 521 ASN N 34 ASN O 203 ASN O 521 ASN Q 34 ASN R 203 ASN R 528 HIS T 34 ASN V 203 ASN V 538 ASN X 34 ASN Y 203 ASN Y 521 ASN 0 33 GLN 0 34 ASN 3 34 ASN 7 528 HIS 9 34 ASN U 203 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 74892 Z= 0.232 Angle : 0.681 7.575 101616 Z= 0.365 Chirality : 0.047 0.203 11436 Planarity : 0.005 0.047 13488 Dihedral : 5.967 78.855 10500 Min Nonbonded Distance : 1.791 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.48 % Favored : 96.39 % Rotamer Outliers : 1.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.08), residues: 9780 helix: 0.05 (0.08), residues: 3168 sheet: 1.10 (0.14), residues: 1164 loop : -0.38 (0.08), residues: 5448 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1153 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1094 time to evaluate : 8.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 59 outliers final: 35 residues processed: 1137 average time/residue: 3.6930 time to fit residues: 5605.0758 Evaluate side-chains 1100 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1065 time to evaluate : 8.356 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 30 residues processed: 6 average time/residue: 1.8980 time to fit residues: 29.3771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 565 optimal weight: 0.5980 chunk 364 optimal weight: 4.9990 chunk 545 optimal weight: 1.9990 chunk 275 optimal weight: 4.9990 chunk 179 optimal weight: 0.0570 chunk 177 optimal weight: 5.9990 chunk 580 optimal weight: 4.9990 chunk 622 optimal weight: 2.9990 chunk 451 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 718 optimal weight: 7.9990 overall best weight: 2.1304 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN C 521 ASN E 34 ASN F 528 HIS I 203 ASN I 521 ASN K 34 ASN L 521 ASN N 34 ASN O 203 ASN O 521 ASN Q 34 ASN R 203 ASN R 528 HIS T 34 ASN V 203 ASN X 34 ASN Y 203 ASN Y 521 ASN 0 34 ASN 3 34 ASN 7 528 HIS 9 34 ASN U 203 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 74892 Z= 0.204 Angle : 0.649 7.403 101616 Z= 0.346 Chirality : 0.046 0.181 11436 Planarity : 0.004 0.045 13488 Dihedral : 5.835 79.444 10500 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.51 % Favored : 96.36 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.08), residues: 9780 helix: 0.26 (0.08), residues: 3168 sheet: 1.15 (0.14), residues: 1164 loop : -0.31 (0.08), residues: 5448 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1134 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1085 time to evaluate : 8.662 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 outliers start: 49 outliers final: 30 residues processed: 1124 average time/residue: 3.6697 time to fit residues: 5525.9186 Evaluate side-chains 1107 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1077 time to evaluate : 8.053 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 30 residues processed: 0 time to fit residues: 10.5907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 831 optimal weight: 0.8980 chunk 875 optimal weight: 7.9990 chunk 798 optimal weight: 6.9990 chunk 851 optimal weight: 5.9990 chunk 512 optimal weight: 4.9990 chunk 370 optimal weight: 8.9990 chunk 668 optimal weight: 3.9990 chunk 261 optimal weight: 0.9980 chunk 769 optimal weight: 10.0000 chunk 805 optimal weight: 5.9990 chunk 848 optimal weight: 9.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN C 521 ASN E 34 ASN F 528 HIS H 34 ASN I 203 ASN I 521 ASN K 34 ASN L 521 ASN N 34 ASN O 203 ASN O 521 ASN Q 34 ASN R 203 ASN R 528 HIS T 34 ASN V 203 ASN X 34 ASN Y 203 ASN Y 521 ASN 0 34 ASN 3 34 ASN 7 528 HIS 9 34 ASN U 203 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.3504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 74892 Z= 0.265 Angle : 0.699 7.527 101616 Z= 0.376 Chirality : 0.048 0.202 11436 Planarity : 0.005 0.044 13488 Dihedral : 5.936 79.071 10500 Min Nonbonded Distance : 1.731 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.87 % Favored : 96.00 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.08), residues: 9780 helix: 0.10 (0.08), residues: 3168 sheet: 1.11 (0.14), residues: 1164 loop : -0.37 (0.08), residues: 5448 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1125 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 1077 time to evaluate : 8.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 48 outliers final: 32 residues processed: 1117 average time/residue: 3.6955 time to fit residues: 5563.8812 Evaluate side-chains 1116 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1084 time to evaluate : 8.498 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 31 residues processed: 1 average time/residue: 4.3846 time to fit residues: 16.4196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 559 optimal weight: 5.9990 chunk 900 optimal weight: 8.9990 chunk 549 optimal weight: 8.9990 chunk 427 optimal weight: 4.9990 chunk 625 optimal weight: 5.9990 chunk 944 optimal weight: 8.9990 chunk 869 optimal weight: 6.9990 chunk 752 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 580 optimal weight: 0.8980 chunk 461 optimal weight: 0.7980 overall best weight: 3.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN C 521 ASN C 538 ASN E 34 ASN F 528 HIS H 34 ASN I 203 ASN K 34 ASN L 521 ASN N 34 ASN O 203 ASN O 521 ASN Q 34 ASN R 203 ASN R 521 ASN R 528 HIS T 34 ASN V 203 ASN X 34 ASN Y 203 ASN Y 521 ASN 0 34 ASN 3 34 ASN 7 521 ASN 7 528 HIS 9 34 ASN U 203 ASN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.3529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 74892 Z= 0.247 Angle : 0.684 7.606 101616 Z= 0.366 Chirality : 0.047 0.203 11436 Planarity : 0.005 0.045 13488 Dihedral : 5.909 78.805 10500 Min Nonbonded Distance : 1.773 Molprobity Statistics. All-atom Clashscore : 4.94 Ramachandran Plot: Outliers : 0.13 % Allowed : 3.60 % Favored : 96.27 % Rotamer Outliers : 1.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.08), residues: 9780 helix: 0.15 (0.08), residues: 3168 sheet: 1.12 (0.14), residues: 1164 loop : -0.33 (0.08), residues: 5448 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 19560 Ramachandran restraints generated. 9780 Oldfield, 0 Emsley, 9780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1139 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1094 time to evaluate : 8.660 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 35 residues processed: 1128 average time/residue: 3.6503 time to fit residues: 5515.9432 Evaluate side-chains 1117 residues out of total 7548 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1082 time to evaluate : 8.710 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 32 residues processed: 3 average time/residue: 1.9281 time to fit residues: 20.0144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 948 random chunks: chunk 597 optimal weight: 5.9990 chunk 801 optimal weight: 6.9990 chunk 230 optimal weight: 5.9990 chunk 693 optimal weight: 7.9990 chunk 111 optimal weight: 3.9990 chunk 208 optimal weight: 4.9990 chunk 753 optimal weight: 5.9990 chunk 315 optimal weight: 0.3980 chunk 773 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 138 optimal weight: 6.9990 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 34 ASN C 521 ASN C 538 ASN E 34 ASN F 528 HIS H 34 ASN I 203 ASN K 34 ASN L 521 ASN N 34 ASN O 203 ASN O 521 ASN Q 34 ASN R 203 ASN R 528 HIS T 34 ASN V 203 ASN X 34 ASN Y 203 ASN Y 521 ASN 0 34 ASN 3 34 ASN 7 521 ASN 7 528 HIS 9 34 ASN U 203 ASN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.150024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.130294 restraints weight = 430051.819| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.51 r_work: 0.3305 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.3155 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3665 r_free = 0.3665 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3665 r_free = 0.3665 target_work(ls_wunit_k1) = 0.150 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.3507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.050 74892 Z= 0.309 Angle : 0.737 7.693 101616 Z= 0.398 Chirality : 0.049 0.222 11436 Planarity : 0.006 0.047 13488 Dihedral : 6.030 78.651 10500 Min Nonbonded Distance : 1.723 Molprobity Statistics. All-atom Clashscore : 5.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 4.04 % Favored : 95.83 % Rotamer Outliers : 1.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.32 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.08), residues: 9780 helix: -0.05 (0.08), residues: 3168 sheet: 1.08 (0.14), residues: 1164 loop : -0.41 (0.08), residues: 5448 =============================================================================== Job complete usr+sys time: 67237.28 seconds wall clock time: 1135 minutes 2.43 seconds (68102.43 seconds total)