Starting phenix.real_space_refine (version: dev) on Mon Dec 19 03:23:38 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl7_21816/12_2022/6wl7_21816.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl7_21816/12_2022/6wl7_21816.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl7_21816/12_2022/6wl7_21816.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl7_21816/12_2022/6wl7_21816.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl7_21816/12_2022/6wl7_21816.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl7_21816/12_2022/6wl7_21816.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 "A GLU 6": "OE1" <-> "OE2" Residue "Z GLU 117": "OE1" <-> "OE2" Residue "Z GLU 124": "OE1" <-> "OE2" Residue "a GLU 1017": "OE1" <-> "OE2" Residue "b GLU 1106": "OE1" <-> "OE2" Residue "b ASP 1108": "OD1" <-> "OD2" Residue "b GLU 1117": "OE1" <-> "OE2" Residue "d GLU 2117": "OE1" <-> "OE2" Residue "d GLU 2124": "OE1" <-> "OE2" Residue "B GLU 6": "OE1" <-> "OE2" Residue "e GLU 117": "OE1" <-> "OE2" Residue "e GLU 124": "OE1" <-> "OE2" Residue "f GLU 1017": "OE1" <-> "OE2" Residue "g GLU 1106": "OE1" <-> "OE2" Residue "g ASP 1108": "OD1" <-> "OD2" Residue "g GLU 1117": "OE1" <-> "OE2" Residue "i GLU 2117": "OE1" <-> "OE2" Residue "i GLU 2124": "OE1" <-> "OE2" Residue "C GLU 6": "OE1" <-> "OE2" Residue "j GLU 117": "OE1" <-> "OE2" Residue "j GLU 124": "OE1" <-> "OE2" Residue "k GLU 1017": "OE1" <-> "OE2" Residue "l GLU 1106": "OE1" <-> "OE2" Residue "l ASP 1108": "OD1" <-> "OD2" Residue "l GLU 1117": "OE1" <-> "OE2" Residue "n GLU 2117": "OE1" <-> "OE2" Residue "n GLU 2124": "OE1" <-> "OE2" Residue "D GLU 6": "OE1" <-> "OE2" Residue "o GLU 117": "OE1" <-> "OE2" Residue "o GLU 124": "OE1" <-> "OE2" Residue "p GLU 1017": "OE1" <-> "OE2" Residue "q GLU 1106": "OE1" <-> "OE2" Residue "q ASP 1108": "OD1" <-> "OD2" Residue "q GLU 1117": "OE1" <-> "OE2" Residue "s GLU 2117": "OE1" <-> "OE2" Residue "s GLU 2124": "OE1" <-> "OE2" Residue "E GLU 6": "OE1" <-> "OE2" Residue "t GLU 117": "OE1" <-> "OE2" Residue "t GLU 124": "OE1" <-> "OE2" Residue "u GLU 1017": "OE1" <-> "OE2" Residue "v GLU 1106": "OE1" <-> "OE2" Residue "v ASP 1108": "OD1" <-> "OD2" Residue "v GLU 1117": "OE1" <-> "OE2" Residue "x GLU 2117": "OE1" <-> "OE2" Residue "x GLU 2124": "OE1" <-> "OE2" Residue "F GLU 6": "OE1" <-> "OE2" Residue "y GLU 117": "OE1" <-> "OE2" Residue "y GLU 124": "OE1" <-> "OE2" Residue "z GLU 1017": "OE1" <-> "OE2" Residue "0 GLU 1106": "OE1" <-> "OE2" Residue "0 ASP 1108": "OD1" <-> "OD2" Residue "0 GLU 1117": "OE1" <-> "OE2" Residue "2 GLU 2117": "OE1" <-> "OE2" Residue "2 GLU 2124": "OE1" <-> "OE2" Residue "G GLU 6": "OE1" <-> "OE2" Residue "3 GLU 117": "OE1" <-> "OE2" Residue "3 GLU 124": "OE1" <-> "OE2" Residue "4 GLU 1017": "OE1" <-> "OE2" Residue "5 GLU 1106": "OE1" <-> "OE2" Residue "5 ASP 1108": "OD1" <-> "OD2" Residue "5 GLU 1117": "OE1" <-> "OE2" Residue "7 GLU 2117": "OE1" <-> "OE2" Residue "7 GLU 2124": "OE1" <-> "OE2" Residue "H GLU 6": "OE1" <-> "OE2" Residue "8 GLU 117": "OE1" <-> "OE2" Residue "8 GLU 124": "OE1" <-> "OE2" Residue "9 GLU 1017": "OE1" <-> "OE2" Residue "AA GLU 1106": "OE1" <-> "OE2" Residue "AA ASP 1108": "OD1" <-> "OD2" Residue "AA GLU 1117": "OE1" <-> "OE2" Residue "CA GLU 2117": "OE1" <-> "OE2" Residue "CA GLU 2124": "OE1" <-> "OE2" Residue "I GLU 6": "OE1" <-> "OE2" Residue "DA GLU 117": "OE1" <-> "OE2" Residue "DA GLU 124": "OE1" <-> "OE2" Residue "EA GLU 1017": "OE1" <-> "OE2" Residue "FA GLU 1106": "OE1" <-> "OE2" Residue "FA ASP 1108": "OD1" <-> "OD2" Residue "FA GLU 1117": "OE1" <-> "OE2" Residue "HA GLU 2117": "OE1" <-> "OE2" Residue "HA GLU 2124": "OE1" <-> "OE2" Residue "J GLU 6": "OE1" <-> "OE2" Residue "IA GLU 117": "OE1" <-> "OE2" Residue "IA GLU 124": "OE1" <-> "OE2" Residue "JA GLU 1017": "OE1" <-> "OE2" Residue "KA GLU 1106": "OE1" <-> "OE2" Residue "KA ASP 1108": "OD1" <-> "OD2" Residue "KA GLU 1117": "OE1" <-> "OE2" Residue "MA GLU 2117": "OE1" <-> "OE2" Residue "MA GLU 2124": "OE1" <-> "OE2" Residue "K GLU 6": "OE1" <-> "OE2" Residue "NA GLU 117": "OE1" <-> "OE2" Residue "NA GLU 124": "OE1" <-> "OE2" Residue "OA GLU 1017": "OE1" <-> "OE2" Residue "PA GLU 1106": "OE1" <-> "OE2" Residue "PA ASP 1108": "OD1" <-> "OD2" Residue "PA GLU 1117": "OE1" <-> "OE2" Residue "RA GLU 2117": "OE1" <-> "OE2" Residue "RA GLU 2124": "OE1" <-> "OE2" Residue "L GLU 6": "OE1" <-> "OE2" Residue "SA GLU 117": "OE1" <-> "OE2" Residue "SA GLU 124": "OE1" <-> "OE2" Residue "TA GLU 1017": "OE1" <-> "OE2" Residue "UA GLU 1106": "OE1" <-> "OE2" Residue "UA ASP 1108": "OD1" <-> "OD2" Residue "UA GLU 1117": "OE1" <-> "OE2" Residue "WA GLU 2117": "OE1" <-> "OE2" Residue "WA GLU 2124": "OE1" <-> "OE2" Residue "M GLU 6": "OE1" <-> "OE2" Residue "XA GLU 117": "OE1" <-> "OE2" Residue "XA GLU 124": "OE1" <-> "OE2" Residue "YA GLU 1017": "OE1" <-> "OE2" Residue "ZA GLU 1106": "OE1" <-> "OE2" Residue "ZA ASP 1108": "OD1" <-> "OD2" Residue "ZA GLU 1117": "OE1" <-> "OE2" Residue "bA GLU 2117": "OE1" <-> "OE2" Residue "bA GLU 2124": "OE1" <-> "OE2" Residue "N GLU 6": "OE1" <-> "OE2" Residue "cA GLU 117": "OE1" <-> "OE2" Residue "cA GLU 124": "OE1" <-> "OE2" Residue "dA GLU 1017": "OE1" <-> "OE2" Residue "eA GLU 1106": "OE1" <-> "OE2" Residue "eA ASP 1108": "OD1" <-> "OD2" Residue "eA GLU 1117": "OE1" <-> "OE2" Residue "gA GLU 2117": "OE1" <-> "OE2" Residue "gA GLU 2124": "OE1" <-> "OE2" Residue "O GLU 6": "OE1" <-> "OE2" Residue "hA GLU 117": "OE1" <-> "OE2" Residue "hA GLU 124": "OE1" <-> "OE2" Residue "iA GLU 1017": "OE1" <-> "OE2" Residue "jA GLU 1106": "OE1" <-> "OE2" Residue "jA ASP 1108": "OD1" <-> "OD2" Residue "jA GLU 1117": "OE1" <-> "OE2" Residue "lA GLU 2117": "OE1" <-> "OE2" Residue "lA GLU 2124": "OE1" <-> "OE2" Residue "P GLU 6": "OE1" <-> "OE2" Residue "mA GLU 117": "OE1" <-> "OE2" Residue "mA GLU 124": "OE1" <-> "OE2" Residue "nA GLU 1017": "OE1" <-> "OE2" Residue "oA GLU 1106": "OE1" <-> "OE2" Residue "oA ASP 1108": "OD1" <-> "OD2" Residue "oA GLU 1117": "OE1" <-> "OE2" Residue "qA GLU 2117": "OE1" <-> "OE2" Residue "qA GLU 2124": "OE1" <-> "OE2" Residue "Q GLU 6": "OE1" <-> "OE2" Residue "rA GLU 117": "OE1" <-> "OE2" Residue "rA GLU 124": "OE1" <-> "OE2" Residue "sA GLU 1017": "OE1" <-> "OE2" Residue "tA GLU 1106": "OE1" <-> "OE2" Residue "tA ASP 1108": "OD1" <-> "OD2" Residue "tA GLU 1117": "OE1" <-> "OE2" Residue "vA GLU 2117": "OE1" <-> "OE2" Residue "vA GLU 2124": "OE1" <-> "OE2" Residue "R GLU 6": "OE1" <-> "OE2" Residue "wA GLU 117": "OE1" <-> "OE2" Residue "wA GLU 124": "OE1" <-> "OE2" Residue "xA GLU 1017": "OE1" <-> "OE2" Residue "yA GLU 1106": "OE1" <-> "OE2" Residue "yA ASP 1108": "OD1" <-> "OD2" Residue "yA GLU 1117": "OE1" <-> "OE2" Residue "0A GLU 2117": "OE1" <-> "OE2" Residue "0A GLU 2124": "OE1" <-> "OE2" Residue "S GLU 6": "OE1" <-> "OE2" Residue "1A GLU 117": "OE1" <-> "OE2" Residue "1A GLU 124": "OE1" <-> "OE2" Residue "2A GLU 1017": "OE1" <-> "OE2" Residue "3A GLU 1106": "OE1" <-> "OE2" Residue "3A ASP 1108": "OD1" <-> "OD2" Residue "3A GLU 1117": "OE1" <-> "OE2" Residue "5A GLU 2117": "OE1" <-> "OE2" Residue "5A GLU 2124": "OE1" <-> "OE2" Residue "T GLU 6": "OE1" <-> "OE2" Residue "6A GLU 117": "OE1" <-> "OE2" Residue "6A GLU 124": "OE1" <-> "OE2" Residue "7A GLU 1017": "OE1" <-> "OE2" Residue "8A GLU 1106": "OE1" <-> "OE2" Residue "8A ASP 1108": "OD1" <-> "OD2" Residue "8A GLU 1117": "OE1" <-> "OE2" Residue "AB GLU 2117": "OE1" <-> "OE2" Residue "AB GLU 2124": "OE1" <-> "OE2" Residue "U GLU 6": "OE1" <-> "OE2" Residue "BB GLU 117": "OE1" <-> "OE2" Residue "BB GLU 124": "OE1" <-> "OE2" Residue "CB GLU 1017": "OE1" <-> "OE2" Residue "DB GLU 1106": "OE1" <-> "OE2" Residue "DB ASP 1108": "OD1" <-> "OD2" Residue "DB GLU 1117": "OE1" <-> "OE2" Residue "FB GLU 2117": "OE1" <-> "OE2" Residue "FB GLU 2124": "OE1" <-> "OE2" Residue "V GLU 6": "OE1" <-> "OE2" Residue "GB GLU 117": "OE1" <-> "OE2" Residue "GB GLU 124": "OE1" <-> "OE2" Residue "HB GLU 1017": "OE1" <-> "OE2" Residue "IB GLU 1106": "OE1" <-> "OE2" Residue "IB ASP 1108": "OD1" <-> "OD2" Residue "IB GLU 1117": "OE1" <-> "OE2" Residue "KB GLU 2117": "OE1" <-> "OE2" Residue "KB GLU 2124": "OE1" <-> "OE2" Residue "W GLU 6": "OE1" <-> "OE2" Residue "LB GLU 117": "OE1" <-> "OE2" Residue "LB GLU 124": "OE1" <-> "OE2" Residue "MB GLU 1017": "OE1" <-> "OE2" Residue "NB GLU 1106": "OE1" <-> "OE2" Residue "NB ASP 1108": "OD1" <-> "OD2" Residue "NB GLU 1117": "OE1" <-> "OE2" Residue "PB GLU 2117": "OE1" <-> "OE2" Residue "PB GLU 2124": "OE1" <-> "OE2" Residue "X GLU 6": "OE1" <-> "OE2" Residue "QB GLU 117": "OE1" <-> "OE2" Residue "QB GLU 124": "OE1" <-> "OE2" Residue "RB GLU 1017": "OE1" <-> "OE2" Residue "SB GLU 1106": "OE1" <-> "OE2" Residue "SB ASP 1108": "OD1" <-> "OD2" Residue "SB GLU 1117": "OE1" <-> "OE2" Residue "UB GLU 2117": "OE1" <-> "OE2" Residue "UB GLU 2124": "OE1" <-> "OE2" Residue "Y GLU 6": "OE1" <-> "OE2" Residue "VB GLU 117": "OE1" <-> "OE2" Residue "VB GLU 124": "OE1" <-> "OE2" Residue "WB GLU 1017": "OE1" <-> "OE2" Residue "XB GLU 1106": "OE1" <-> "OE2" Residue "XB ASP 1108": "OD1" <-> "OD2" Residue "XB GLU 1117": "OE1" <-> "OE2" Residue "ZB GLU 2117": "OE1" <-> "OE2" Residue "ZB GLU 2124": "OE1" <-> "OE2" Time to flip residues: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 34350 Number of models: 1 Model: "" Number of chains: 150 Chain: "A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "Z" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "a" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "b" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "c" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "d" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "B" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "e" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "f" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "g" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "h" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "i" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "C" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "j" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "k" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "l" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "m" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "n" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "D" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "o" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "p" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "q" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "r" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "s" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "E" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "t" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "u" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "v" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "w" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "x" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "F" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "y" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "z" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "0" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "1" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "2" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "G" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "3" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "4" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "5" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "6" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "7" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "H" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "8" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "9" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "AA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "BA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "CA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "I" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "DA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "EA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "FA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "GA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "HA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "J" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "IA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "JA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "KA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "LA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "MA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "K" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "NA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "OA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "PA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "QA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "RA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "L" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "SA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "TA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "UA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "VA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "WA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "M" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "XA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "YA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "ZA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "aA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "bA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "N" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "cA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "dA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "eA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "fA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "gA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "O" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "hA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "iA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "jA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "kA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "lA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "P" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "mA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "nA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "oA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "pA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "qA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "Q" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "rA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "sA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "tA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "uA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "vA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "R" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "wA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "xA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "yA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "zA" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "0A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "S" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "1A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "2A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "3A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "4A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "5A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "T" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "6A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "7A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "8A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "9A" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "AB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "U" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "BB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "CB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "DB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "EB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "FB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "V" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "GB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "HB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "IB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "JB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "KB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "W" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "LB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "MB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "NB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "OB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "PB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "X" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "QB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "RB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "SB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "TB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "UB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "Y" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "VB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "WB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "XB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "YB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Chain: "ZB" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 229 Classifications: {'peptide': 29} Modifications used: {'COO': 1} Link IDs: {'TRANS': 28} Time building chain proxies: 19.07, per 1000 atoms: 0.56 Number of scatterers: 34350 At special positions: 0 Unit cell: (121.68, 121.68, 173.68, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 6450 8.00 N 6150 7.00 C 21750 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 14.14 Conformation dependent library (CDL) restraints added in 4.7 seconds 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8700 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 0 sheets defined 96.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.75 Creating SS restraints... Processing helix chain 'A' and resid 1 through 29 Processing helix chain 'Z' and resid 102 through 129 Processing helix chain 'a' and resid 1002 through 1029 Processing helix chain 'b' and resid 1102 through 1129 Processing helix chain 'c' and resid 2002 through 2029 Processing helix chain 'd' and resid 2102 through 2129 Processing helix chain 'B' and resid 2 through 29 Processing helix chain 'e' and resid 102 through 129 Processing helix chain 'f' and resid 1002 through 1029 Processing helix chain 'g' and resid 1102 through 1129 Processing helix chain 'h' and resid 2002 through 2029 Processing helix chain 'i' and resid 2102 through 2129 Processing helix chain 'C' and resid 2 through 29 Processing helix chain 'j' and resid 102 through 129 Processing helix chain 'k' and resid 1002 through 1029 Processing helix chain 'l' and resid 1102 through 1129 Processing helix chain 'm' and resid 2002 through 2029 Processing helix chain 'n' and resid 2102 through 2129 Processing helix chain 'D' and resid 2 through 29 Processing helix chain 'o' and resid 102 through 129 Processing helix chain 'p' and resid 1002 through 1029 Processing helix chain 'q' and resid 1102 through 1129 Processing helix chain 'r' and resid 2002 through 2029 Processing helix chain 's' and resid 2102 through 2129 Processing helix chain 'E' and resid 2 through 29 Processing helix chain 't' and resid 102 through 129 Processing helix chain 'u' and resid 1002 through 1029 Processing helix chain 'v' and resid 1102 through 1129 Processing helix chain 'w' and resid 2002 through 2029 Processing helix chain 'x' and resid 2102 through 2129 Processing helix chain 'F' and resid 2 through 29 Processing helix chain 'y' and resid 102 through 129 Processing helix chain 'z' and resid 1002 through 1029 Processing helix chain '0' and resid 1102 through 1129 Processing helix chain '1' and resid 2002 through 2029 Processing helix chain '2' and resid 2102 through 2129 Processing helix chain 'G' and resid 2 through 29 Processing helix chain '3' and resid 102 through 129 Processing helix chain '4' and resid 1002 through 1029 Processing helix chain '5' and resid 1102 through 1129 Processing helix chain '6' and resid 2002 through 2029 Processing helix chain '7' and resid 2102 through 2129 Processing helix chain 'H' and resid 2 through 29 Processing helix chain '8' and resid 102 through 129 Processing helix chain '9' and resid 1002 through 1029 Processing helix chain 'AA' and resid 1102 through 1129 Processing helix chain 'BA' and resid 2002 through 2029 Processing helix chain 'CA' and resid 2102 through 2129 Processing helix chain 'I' and resid 2 through 29 Processing helix chain 'DA' and resid 102 through 129 Processing helix chain 'EA' and resid 1002 through 1029 Processing helix chain 'FA' and resid 1102 through 1129 Processing helix chain 'GA' and resid 2002 through 2029 Processing helix chain 'HA' and resid 2102 through 2129 Processing helix chain 'J' and resid 2 through 29 Processing helix chain 'IA' and resid 102 through 129 Processing helix chain 'JA' and resid 1002 through 1029 Processing helix chain 'KA' and resid 1102 through 1129 Processing helix chain 'LA' and resid 2002 through 2029 Processing helix chain 'MA' and resid 2102 through 2129 Processing helix chain 'K' and resid 2 through 29 Processing helix chain 'NA' and resid 102 through 129 Processing helix chain 'OA' and resid 1002 through 1029 Processing helix chain 'PA' and resid 1102 through 1129 Processing helix chain 'QA' and resid 2002 through 2029 Processing helix chain 'RA' and resid 2102 through 2129 Processing helix chain 'L' and resid 2 through 29 Processing helix chain 'SA' and resid 102 through 129 Processing helix chain 'TA' and resid 1002 through 1029 Processing helix chain 'UA' and resid 1102 through 1129 Processing helix chain 'VA' and resid 2002 through 2029 Processing helix chain 'WA' and resid 2102 through 2129 Processing helix chain 'M' and resid 2 through 29 Processing helix chain 'XA' and resid 102 through 129 Processing helix chain 'YA' and resid 1002 through 1029 Processing helix chain 'ZA' and resid 1102 through 1129 Processing helix chain 'aA' and resid 2002 through 2029 Processing helix chain 'bA' and resid 2102 through 2129 Processing helix chain 'N' and resid 2 through 29 Processing helix chain 'cA' and resid 102 through 129 Processing helix chain 'dA' and resid 1002 through 1029 Processing helix chain 'eA' and resid 1102 through 1129 Processing helix chain 'fA' and resid 2002 through 2029 Processing helix chain 'gA' and resid 2102 through 2129 Processing helix chain 'O' and resid 2 through 29 Processing helix chain 'hA' and resid 102 through 129 Processing helix chain 'iA' and resid 1002 through 1029 Processing helix chain 'jA' and resid 1102 through 1129 Processing helix chain 'kA' and resid 2002 through 2029 Processing helix chain 'lA' and resid 2102 through 2129 Processing helix chain 'P' and resid 2 through 29 Processing helix chain 'mA' and resid 102 through 129 Processing helix chain 'nA' and resid 1002 through 1029 Processing helix chain 'oA' and resid 1102 through 1129 Processing helix chain 'pA' and resid 2002 through 2029 Processing helix chain 'qA' and resid 2102 through 2129 Processing helix chain 'Q' and resid 2 through 29 Processing helix chain 'rA' and resid 102 through 129 Processing helix chain 'sA' and resid 1002 through 1029 Processing helix chain 'tA' and resid 1102 through 1129 Processing helix chain 'uA' and resid 2002 through 2029 Processing helix chain 'vA' and resid 2102 through 2129 Processing helix chain 'R' and resid 2 through 29 Processing helix chain 'wA' and resid 102 through 129 Processing helix chain 'xA' and resid 1002 through 1029 Processing helix chain 'yA' and resid 1102 through 1129 Processing helix chain 'zA' and resid 2002 through 2029 Processing helix chain '0A' and resid 2102 through 2129 Processing helix chain 'S' and resid 2 through 29 Processing helix chain '1A' and resid 102 through 129 Processing helix chain '2A' and resid 1002 through 1029 Processing helix chain '3A' and resid 1102 through 1129 Processing helix chain '4A' and resid 2002 through 2029 Processing helix chain '5A' and resid 2102 through 2129 Processing helix chain 'T' and resid 2 through 29 Processing helix chain '6A' and resid 102 through 129 Processing helix chain '7A' and resid 1002 through 1029 Processing helix chain '8A' and resid 1102 through 1129 Processing helix chain '9A' and resid 2002 through 2029 Processing helix chain 'AB' and resid 2102 through 2129 Processing helix chain 'U' and resid 2 through 29 Processing helix chain 'BB' and resid 102 through 129 Processing helix chain 'CB' and resid 1002 through 1029 Processing helix chain 'DB' and resid 1102 through 1129 Processing helix chain 'EB' and resid 2002 through 2029 Processing helix chain 'FB' and resid 2102 through 2129 Processing helix chain 'V' and resid 2 through 29 Processing helix chain 'GB' and resid 102 through 129 Processing helix chain 'HB' and resid 1002 through 1029 Processing helix chain 'IB' and resid 1102 through 1129 Processing helix chain 'JB' and resid 2002 through 2029 Processing helix chain 'KB' and resid 2102 through 2129 Processing helix chain 'W' and resid 2 through 29 Processing helix chain 'LB' and resid 102 through 129 Processing helix chain 'MB' and resid 1002 through 1029 Processing helix chain 'NB' and resid 1102 through 1129 Processing helix chain 'OB' and resid 2002 through 2029 Processing helix chain 'PB' and resid 2102 through 2129 Processing helix chain 'X' and resid 2 through 29 Processing helix chain 'QB' and resid 102 through 129 Processing helix chain 'RB' and resid 1002 through 1029 Processing helix chain 'SB' and resid 1102 through 1129 Processing helix chain 'TB' and resid 2002 through 2029 Processing helix chain 'UB' and resid 2102 through 2129 Processing helix chain 'Y' and resid 2 through 29 Processing helix chain 'VB' and resid 102 through 129 Processing helix chain 'WB' and resid 1002 through 1029 Processing helix chain 'XB' and resid 1102 through 1129 Processing helix chain 'YB' and resid 2002 through 2029 Processing helix chain 'ZB' and resid 2102 through 2129 3601 hydrogen bonds defined for protein. 10803 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: 13.04 Time building geometry restraints manager: 15.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 6300 1.29 - 1.35: 5700 1.35 - 1.41: 1500 1.41 - 1.48: 4650 1.48 - 1.54: 16350 Bond restraints: 34500 Sorted by residual: bond pdb=" CB LEU C 19 " pdb=" CG LEU C 19 " ideal model delta sigma weight residual 1.530 1.510 0.020 2.00e-02 2.50e+03 9.51e-01 bond pdb=" CB LEU X 19 " pdb=" CG LEU X 19 " ideal model delta sigma weight residual 1.530 1.511 0.019 2.00e-02 2.50e+03 9.40e-01 bond pdb=" CB LEU S 19 " pdb=" CG LEU S 19 " ideal model delta sigma weight residual 1.530 1.511 0.019 2.00e-02 2.50e+03 9.30e-01 bond pdb=" CB LEU D 19 " pdb=" CG LEU D 19 " ideal model delta sigma weight residual 1.530 1.511 0.019 2.00e-02 2.50e+03 9.16e-01 bond pdb=" CB LEU A 19 " pdb=" CG LEU A 19 " ideal model delta sigma weight residual 1.530 1.511 0.019 2.00e-02 2.50e+03 9.08e-01 ... (remaining 34495 not shown) Histogram of bond angle deviations from ideal: 106.10 - 111.16: 16460 111.16 - 116.21: 6796 116.21 - 121.27: 16576 121.27 - 126.33: 6368 126.33 - 131.38: 150 Bond angle restraints: 46350 Sorted by residual: angle pdb=" C ILE B 25 " pdb=" CA ILE B 25 " pdb=" CB ILE B 25 " ideal model delta sigma weight residual 111.70 109.58 2.12 1.28e+00 6.10e-01 2.75e+00 angle pdb=" C ILE G 25 " pdb=" CA ILE G 25 " pdb=" CB ILE G 25 " ideal model delta sigma weight residual 111.70 109.58 2.12 1.28e+00 6.10e-01 2.75e+00 angle pdb=" C ILE E 25 " pdb=" CA ILE E 25 " pdb=" CB ILE E 25 " ideal model delta sigma weight residual 111.70 109.59 2.11 1.28e+00 6.10e-01 2.72e+00 angle pdb=" C ILE K 25 " pdb=" CA ILE K 25 " pdb=" CB ILE K 25 " ideal model delta sigma weight residual 111.70 109.60 2.10 1.28e+00 6.10e-01 2.70e+00 angle pdb=" C ILEiA1025 " pdb=" CA ILEiA1025 " pdb=" CB ILEiA1025 " ideal model delta sigma weight residual 111.70 109.60 2.10 1.28e+00 6.10e-01 2.70e+00 ... (remaining 46345 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 19665 17.84 - 35.67: 1835 35.67 - 53.51: 250 53.51 - 71.35: 25 71.35 - 89.18: 125 Dihedral angle restraints: 21900 sinusoidal: 8850 harmonic: 13050 Sorted by residual: dihedral pdb=" CB GLUYB2024 " pdb=" CG GLUYB2024 " pdb=" CD GLUYB2024 " pdb=" OE1 GLUYB2024 " ideal model delta sinusoidal sigma weight residual 0.00 -89.18 89.18 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLUkA2024 " pdb=" CG GLUkA2024 " pdb=" CD GLUkA2024 " pdb=" OE1 GLUkA2024 " ideal model delta sinusoidal sigma weight residual 0.00 -89.17 89.17 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CB GLUOB2024 " pdb=" CG GLUOB2024 " pdb=" CD GLUOB2024 " pdb=" OE1 GLUOB2024 " ideal model delta sinusoidal sigma weight residual 0.00 -89.16 89.16 1 3.00e+01 1.11e-03 1.05e+01 ... (remaining 21897 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 3104 0.024 - 0.048: 1429 0.048 - 0.071: 390 0.071 - 0.095: 540 0.095 - 0.119: 87 Chirality restraints: 5550 Sorted by residual: chirality pdb=" CA ILE 41025 " pdb=" N ILE 41025 " pdb=" C ILE 41025 " pdb=" CB ILE 41025 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.55e-01 chirality pdb=" CA ILEiA1025 " pdb=" N ILEiA1025 " pdb=" C ILEiA1025 " pdb=" CB ILEiA1025 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.54e-01 chirality pdb=" CA ILEdA1025 " pdb=" N ILEdA1025 " pdb=" C ILEdA1025 " pdb=" CB ILEdA1025 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.53e-01 ... (remaining 5547 not shown) Planarity restraints: 6000 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA U 23 " -0.003 2.00e-02 2.50e+03 6.44e-03 4.15e-01 pdb=" C ALA U 23 " 0.011 2.00e-02 2.50e+03 pdb=" O ALA U 23 " -0.004 2.00e-02 2.50e+03 pdb=" N GLU U 24 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA m2023 " -0.003 2.00e-02 2.50e+03 6.44e-03 4.15e-01 pdb=" C ALA m2023 " 0.011 2.00e-02 2.50e+03 pdb=" O ALA m2023 " -0.004 2.00e-02 2.50e+03 pdb=" N GLU m2024 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALAQA2023 " -0.003 2.00e-02 2.50e+03 6.39e-03 4.08e-01 pdb=" C ALAQA2023 " 0.011 2.00e-02 2.50e+03 pdb=" O ALAQA2023 " -0.004 2.00e-02 2.50e+03 pdb=" N GLUQA2024 " -0.004 2.00e-02 2.50e+03 ... (remaining 5997 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 4785 2.74 - 3.28: 39858 3.28 - 3.82: 58585 3.82 - 4.36: 65856 4.36 - 4.90: 101051 Nonbonded interactions: 270135 Sorted by model distance: nonbonded pdb=" N GLN f1001 " pdb=" O GLN 62029 " model vdw 2.204 2.520 nonbonded pdb=" N GLNEA1001 " pdb=" O GLNuA2029 " model vdw 2.211 2.520 nonbonded pdb=" O GLN r2029 " pdb=" N GLNTA1001 " model vdw 2.218 2.520 nonbonded pdb=" O GLN m2029 " pdb=" N GLN z1001 " model vdw 2.219 2.520 nonbonded pdb=" N GLN B 1 " pdb=" O GLN 41029 " model vdw 2.224 2.520 ... (remaining 270130 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain '0' selection = chain '0A' selection = chain '1' selection = chain '1A' selection = chain '2' selection = chain '2A' selection = chain '3' selection = chain '3A' selection = chain '4' selection = chain '4A' selection = chain '5' selection = chain '5A' selection = chain '6' selection = chain '6A' selection = chain '7' selection = chain '7A' selection = chain '8' selection = chain '8A' selection = chain '9' selection = chain '9A' selection = chain 'A' selection = chain 'AA' selection = chain 'AB' selection = chain 'B' selection = chain 'BA' selection = chain 'BB' selection = chain 'C' selection = chain 'CA' selection = chain 'CB' selection = chain 'D' selection = chain 'DA' selection = chain 'DB' selection = chain 'E' selection = chain 'EA' selection = chain 'EB' selection = chain 'F' selection = chain 'FA' selection = chain 'FB' selection = chain 'G' selection = chain 'GA' selection = chain 'GB' selection = chain 'H' selection = chain 'HA' selection = chain 'HB' selection = chain 'I' selection = chain 'IA' selection = chain 'IB' selection = chain 'J' selection = chain 'JA' selection = chain 'JB' selection = chain 'K' selection = chain 'KA' selection = chain 'KB' selection = chain 'L' selection = chain 'LA' selection = chain 'LB' selection = chain 'M' selection = chain 'MA' selection = chain 'MB' selection = chain 'N' selection = chain 'NA' selection = chain 'NB' selection = chain 'O' selection = chain 'OA' selection = chain 'OB' selection = chain 'P' selection = chain 'PA' selection = chain 'PB' selection = chain 'Q' selection = chain 'QA' selection = chain 'QB' selection = chain 'R' selection = chain 'RA' selection = chain 'RB' selection = chain 'S' selection = chain 'SA' selection = chain 'SB' selection = chain 'T' selection = chain 'TA' selection = chain 'TB' selection = chain 'U' selection = chain 'UA' selection = chain 'UB' selection = chain 'V' selection = chain 'VA' selection = chain 'VB' selection = chain 'W' selection = chain 'WA' selection = chain 'WB' selection = chain 'X' selection = chain 'XA' selection = chain 'XB' selection = chain 'Y' selection = chain 'YA' selection = chain 'YB' selection = chain 'Z' selection = chain 'ZA' selection = chain 'ZB' selection = chain 'a' selection = chain 'aA' selection = chain 'b' selection = chain 'bA' selection = chain 'c' selection = chain 'cA' selection = chain 'd' selection = chain 'dA' selection = chain 'e' selection = chain 'eA' selection = chain 'f' selection = chain 'fA' selection = chain 'g' selection = chain 'gA' selection = chain 'h' selection = chain 'hA' selection = chain 'i' selection = chain 'iA' selection = chain 'j' selection = chain 'jA' selection = chain 'k' selection = chain 'kA' selection = chain 'l' selection = chain 'lA' selection = chain 'm' selection = chain 'mA' selection = chain 'n' selection = chain 'nA' selection = chain 'o' selection = chain 'oA' selection = chain 'p' selection = chain 'pA' selection = chain 'q' selection = chain 'qA' selection = chain 'r' selection = chain 'rA' selection = chain 's' selection = chain 'sA' selection = chain 't' selection = chain 'tA' selection = chain 'u' selection = chain 'uA' selection = chain 'v' selection = chain 'vA' selection = chain 'w' selection = chain 'wA' selection = chain 'x' selection = chain 'xA' selection = chain 'y' selection = chain 'yA' selection = chain 'z' selection = chain 'zA' } 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: 3 Type Number sf(0) Gaussians C 21750 2.51 5 N 6150 2.21 5 O 6450 1.98 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 9.850 Check model and map are aligned: 0.460 Convert atoms to be neutral: 0.270 Process input model: 84.790 Find NCS groups from input model: 3.210 Set up NCS constraints: 1.200 Set refine NCS operators: 0.000 Set scattering table: 0.020 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 104.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.025 34500 Z= 0.423 Angle : 0.580 4.525 46350 Z= 0.358 Chirality : 0.038 0.119 5550 Planarity : 0.002 0.006 6000 Dihedral : 14.928 89.184 13200 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.28 (0.11), residues: 4050 helix: 2.17 (0.07), residues: 4050 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1699 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1699 time to evaluate : 4.316 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: 0 outliers final: 0 residues processed: 1699 average time/residue: 0.5819 time to fit residues: 1441.8842 Evaluate side-chains 1030 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1030 time to evaluate : 4.202 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 253 optimal weight: 3.9990 chunk 227 optimal weight: 7.9990 chunk 126 optimal weight: 10.0000 chunk 77 optimal weight: 8.9990 chunk 153 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 chunk 235 optimal weight: 9.9990 chunk 90 optimal weight: 8.9990 chunk 142 optimal weight: 0.8980 chunk 175 optimal weight: 6.9990 chunk 272 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 101 GLN ** b1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 101 GLN l1101 GLN n2101 GLN x2101 GLN 01101 GLN 8 101 GLN AA1101 GLN CA2101 GLN HA2101 GLN ** IA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** KA1101 GLN MA2101 GLN ** PA1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** RA2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** SA 101 GLN UA1101 GLN WA2101 GLN ZA1101 GLN bA2101 GLN gA2101 GLN ** mA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** oA1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** rA 101 GLN ** 8A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** FB2101 GLN IB1101 GLN LB 101 GLN NB1101 GLN PB2101 GLN ** QB 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** SB1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** VB 101 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.3580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 34500 Z= 0.256 Angle : 0.575 5.491 46350 Z= 0.309 Chirality : 0.035 0.138 5550 Planarity : 0.003 0.024 6000 Dihedral : 3.394 15.607 4800 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.02 % Favored : 99.98 % Rotamer Outliers : 4.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.24 (0.10), residues: 4050 helix: 4.00 (0.06), residues: 4050 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1508 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1354 time to evaluate : 4.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 154 outliers final: 103 residues processed: 1405 average time/residue: 0.5099 time to fit residues: 1102.9397 Evaluate side-chains 1224 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1121 time to evaluate : 3.873 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 0 residues processed: 103 average time/residue: 0.3141 time to fit residues: 67.2548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 151 optimal weight: 7.9990 chunk 84 optimal weight: 10.0000 chunk 226 optimal weight: 2.9990 chunk 185 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 272 optimal weight: 6.9990 chunk 294 optimal weight: 10.0000 chunk 243 optimal weight: 0.7980 chunk 270 optimal weight: 0.0370 chunk 93 optimal weight: 9.9990 chunk 218 optimal weight: 6.9990 overall best weight: 3.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** b1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i2101 GLN n2101 GLN ** IA 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NA 101 GLN ** lA2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** oA1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** GB 101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.4218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 34500 Z= 0.242 Angle : 0.588 5.977 46350 Z= 0.312 Chirality : 0.035 0.203 5550 Planarity : 0.003 0.025 6000 Dihedral : 3.234 16.158 4800 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 12.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 3.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.88 (0.10), residues: 4050 helix: 4.39 (0.06), residues: 4050 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1458 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1335 time to evaluate : 4.190 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: 123 outliers final: 64 residues processed: 1392 average time/residue: 0.4928 time to fit residues: 1062.9037 Evaluate side-chains 1207 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1143 time to evaluate : 3.973 Switching outliers to nearest non-outliers outliers start: 64 outliers final: 0 residues processed: 64 average time/residue: 0.2996 time to fit residues: 41.5532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 269 optimal weight: 10.0000 chunk 205 optimal weight: 7.9990 chunk 141 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 130 optimal weight: 8.9990 chunk 183 optimal weight: 0.9980 chunk 273 optimal weight: 3.9990 chunk 289 optimal weight: 0.8980 chunk 143 optimal weight: 10.0000 chunk 259 optimal weight: 6.9990 chunk 78 optimal weight: 10.0000 overall best weight: 3.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** Z 101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b1101 GLN lA2101 GLN ** oA1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6A 101 GLN 8A1101 GLN ** AB2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** UB2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 34500 Z= 0.270 Angle : 0.638 6.438 46350 Z= 0.339 Chirality : 0.035 0.153 5550 Planarity : 0.003 0.023 6000 Dihedral : 3.162 15.258 4800 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 5.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.67 (0.10), residues: 4050 helix: 4.26 (0.06), residues: 4050 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1420 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 163 poor density : 1257 time to evaluate : 4.420 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: 163 outliers final: 86 residues processed: 1328 average time/residue: 0.5121 time to fit residues: 1056.4657 Evaluate side-chains 1209 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 1123 time to evaluate : 4.144 Switching outliers to nearest non-outliers outliers start: 86 outliers final: 0 residues processed: 86 average time/residue: 0.3162 time to fit residues: 57.5564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 241 optimal weight: 3.9990 chunk 164 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 247 optimal weight: 0.9980 chunk 200 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 148 optimal weight: 6.9990 chunk 260 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 101 GLN CA2101 GLN DA 101 GLN MA2122 HIS ** UA1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** XA 101 GLN ZA1101 GLN qA2101 GLN yA1122 HIS AB2101 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.4775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.047 34500 Z= 0.334 Angle : 0.705 6.989 46350 Z= 0.375 Chirality : 0.038 0.195 5550 Planarity : 0.003 0.026 6000 Dihedral : 3.186 16.693 4800 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 4.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.25 (0.10), residues: 4050 helix: 4.00 (0.06), residues: 4050 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1332 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 142 poor density : 1190 time to evaluate : 4.509 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: 142 outliers final: 71 residues processed: 1256 average time/residue: 0.5130 time to fit residues: 993.7304 Evaluate side-chains 1163 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1092 time to evaluate : 4.526 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 0.3052 time to fit residues: 46.9937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 97 optimal weight: 4.9990 chunk 261 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 170 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 290 optimal weight: 6.9990 chunk 240 optimal weight: 10.0000 chunk 134 optimal weight: 10.0000 chunk 24 optimal weight: 6.9990 chunk 96 optimal weight: 3.9990 chunk 152 optimal weight: 9.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: l1101 GLN MA2101 GLN ** UA1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** rA 101 GLN 0A2101 GLN VB 122 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.4967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.049 34500 Z= 0.296 Angle : 0.738 10.141 46350 Z= 0.393 Chirality : 0.037 0.200 5550 Planarity : 0.003 0.033 6000 Dihedral : 3.205 16.548 4800 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 13.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 4.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.12 (0.10), residues: 4050 helix: 3.93 (0.06), residues: 4050 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1361 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 138 poor density : 1223 time to evaluate : 4.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 138 outliers final: 80 residues processed: 1284 average time/residue: 0.5090 time to fit residues: 1010.9465 Evaluate side-chains 1190 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 1110 time to evaluate : 3.932 Switching outliers to nearest non-outliers outliers start: 80 outliers final: 0 residues processed: 80 average time/residue: 0.3008 time to fit residues: 50.9174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 279 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 165 optimal weight: 0.9980 chunk 211 optimal weight: 9.9990 chunk 164 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 162 optimal weight: 4.9990 chunk 289 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 176 optimal weight: 8.9990 chunk 133 optimal weight: 9.9990 overall best weight: 2.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: e 101 GLN y 101 GLN 8 101 GLN ** 3A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8A1101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 34500 Z= 0.274 Angle : 0.777 12.719 46350 Z= 0.415 Chirality : 0.038 0.271 5550 Planarity : 0.003 0.026 6000 Dihedral : 3.204 14.507 4800 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 13.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 3.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.95 (0.10), residues: 4050 helix: 3.82 (0.06), residues: 4050 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1375 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 1280 time to evaluate : 3.900 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 outliers start: 95 outliers final: 40 residues processed: 1317 average time/residue: 0.5188 time to fit residues: 1069.2533 Evaluate side-chains 1171 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 1131 time to evaluate : 4.396 Switching outliers to nearest non-outliers outliers start: 40 outliers final: 0 residues processed: 40 average time/residue: 0.3099 time to fit residues: 29.1586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 178 optimal weight: 8.9990 chunk 115 optimal weight: 5.9990 chunk 172 optimal weight: 0.0470 chunk 87 optimal weight: 5.9990 chunk 56 optimal weight: 5.9990 chunk 183 optimal weight: 10.0000 chunk 196 optimal weight: 9.9990 chunk 142 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 227 optimal weight: 4.9990 chunk 263 optimal weight: 9.9990 overall best weight: 4.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6A 101 GLN GB 101 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.5260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 34500 Z= 0.335 Angle : 0.846 12.076 46350 Z= 0.454 Chirality : 0.040 0.266 5550 Planarity : 0.003 0.034 6000 Dihedral : 3.219 16.112 4800 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 3.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.59 (0.11), residues: 4050 helix: 3.60 (0.07), residues: 4050 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1285 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1173 time to evaluate : 4.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 112 outliers final: 73 residues processed: 1208 average time/residue: 0.5094 time to fit residues: 948.5234 Evaluate side-chains 1165 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1092 time to evaluate : 3.979 Switching outliers to nearest non-outliers outliers start: 73 outliers final: 0 residues processed: 73 average time/residue: 0.3053 time to fit residues: 47.9279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 277 optimal weight: 0.9990 chunk 252 optimal weight: 3.9990 chunk 269 optimal weight: 10.0000 chunk 276 optimal weight: 5.9990 chunk 162 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 211 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 243 optimal weight: 2.9990 chunk 254 optimal weight: 9.9990 chunk 268 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 3A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.5376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.052 34500 Z= 0.316 Angle : 0.888 11.336 46350 Z= 0.475 Chirality : 0.040 0.275 5550 Planarity : 0.004 0.036 6000 Dihedral : 3.272 15.863 4800 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.44 (0.11), residues: 4050 helix: 3.51 (0.07), residues: 4050 sheet: None (None), residues: 0 loop : None (None), residues: 0 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1245 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1181 time to evaluate : 4.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 36 residues processed: 1206 average time/residue: 0.5207 time to fit residues: 976.7287 Evaluate side-chains 1158 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 1122 time to evaluate : 4.153 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.3078 time to fit residues: 26.5571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 176 optimal weight: 0.0970 chunk 284 optimal weight: 0.7980 chunk 173 optimal weight: 6.9990 chunk 135 optimal weight: 5.9990 chunk 198 optimal weight: 5.9990 chunk 298 optimal weight: 20.0000 chunk 275 optimal weight: 0.9990 chunk 237 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 chunk 145 optimal weight: 0.0470 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: gA2101 GLN lA2101 GLN 1A 101 GLN ** 3A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** AB2101 GLN NB1101 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.5654 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.048 34500 Z= 0.312 Angle : 0.959 12.080 46350 Z= 0.506 Chirality : 0.041 0.316 5550 Planarity : 0.003 0.041 6000 Dihedral : 3.372 16.080 4800 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.14 (0.11), residues: 4050 helix: 3.32 (0.07), residues: 4050 sheet: None (None), residues: 0 loop : None (None), residues: 0 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8100 Ramachandran restraints generated. 4050 Oldfield, 0 Emsley, 4050 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1358 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 1309 time to evaluate : 4.143 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 outliers start: 49 outliers final: 24 residues processed: 1327 average time/residue: 0.5045 time to fit residues: 1041.8182 Evaluate side-chains 1181 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1157 time to evaluate : 4.138 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.3120 time to fit residues: 19.3735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 189 optimal weight: 1.9990 chunk 253 optimal weight: 7.9990 chunk 72 optimal weight: 9.9990 chunk 219 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 238 optimal weight: 8.9990 chunk 99 optimal weight: 3.9990 chunk 244 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 3 122 HIS ** 3A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.060853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.049055 restraints weight = 134250.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.050790 restraints weight = 67419.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.052158 restraints weight = 41547.759| |-----------------------------------------------------------------------------| r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.5690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.054 34500 Z= 0.332 Angle : 0.973 11.945 46350 Z= 0.519 Chirality : 0.042 0.332 5550 Planarity : 0.004 0.038 6000 Dihedral : 3.339 17.132 4800 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.88 (0.11), residues: 4050 helix: 3.16 (0.07), residues: 4050 sheet: None (None), residues: 0 loop : None (None), residues: 0 =============================================================================== Job complete usr+sys time: 13490.31 seconds wall clock time: 237 minutes 19.93 seconds (14239.93 seconds total)