Starting phenix.real_space_refine (version: 1.21rc1) on Tue Oct 17 02:54:19 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl7_21816/10_2023/6wl7_21816.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl7_21816/10_2023/6wl7_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_21816/10_2023/6wl7_21816.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl7_21816/10_2023/6wl7_21816.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl7_21816/10_2023/6wl7_21816.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wl7_21816/10_2023/6wl7_21816.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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 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. 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/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: 16.61, per 1000 atoms: 0.48 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: 14.58 Conformation dependent library (CDL) restraints added in 4.5 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: 2.49 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: 11.56 Time building geometry restraints manager: 15.26 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 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: 2.520 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: 0.030 Extract box with map and model: 8.780 Check model and map are aligned: 0.500 Set scattering table: 0.300 Process input model: 82.250 Find NCS groups from input model: 2.820 Set up NCS constraints: 1.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 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 % Allowed : 7.14 % Favored : 92.86 % 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 : 3.979 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: 0.6277 time to fit residues: 1554.7070 Evaluate side-chains 1030 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1030 time to evaluate : 3.777 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.8833 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 moved from start: 0.3579 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 : 0.576 5.504 46350 Z= 0.309 Chirality : 0.035 0.138 5550 Planarity : 0.003 0.024 6000 Dihedral : 3.395 15.602 4800 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.02 % Favored : 99.98 % Rotamer: Outliers : 4.89 % Allowed : 24.19 % Favored : 70.92 % 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 1507 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1353 time to evaluate : 4.264 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: 1404 average time/residue: 0.5183 time to fit residues: 1115.4544 Evaluate side-chains 1223 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 1120 time to evaluate : 3.712 Switching outliers to nearest non-outliers outliers start: 103 outliers final: 0 residues processed: 103 average time/residue: 0.3111 time to fit residues: 66.0504 ------------------------------------------------------------------------------- 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: 3.9990 chunk 84 optimal weight: 9.9990 chunk 226 optimal weight: 9.9990 chunk 185 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 272 optimal weight: 8.9990 chunk 294 optimal weight: 9.9990 chunk 243 optimal weight: 3.9990 chunk 270 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 218 optimal weight: 10.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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** MA2101 GLN ** lA2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** oA1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 8A1101 GLN ** AB2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** GB 101 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.4157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 34500 Z= 0.287 Angle : 0.609 6.081 46350 Z= 0.324 Chirality : 0.036 0.224 5550 Planarity : 0.003 0.026 6000 Dihedral : 3.270 17.870 4800 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.25 % Allowed : 30.10 % Favored : 65.65 % 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: 6.69 (0.10), residues: 4050 helix: 4.28 (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 1376 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 134 poor density : 1242 time to evaluate : 4.498 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: 134 outliers final: 71 residues processed: 1306 average time/residue: 0.5111 time to fit residues: 1031.0794 Evaluate side-chains 1177 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1106 time to evaluate : 3.934 Switching outliers to nearest non-outliers outliers start: 71 outliers final: 0 residues processed: 71 average time/residue: 0.3039 time to fit residues: 46.1170 ------------------------------------------------------------------------------- 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: 2.9990 chunk 205 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 30 optimal weight: 0.4980 chunk 130 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 273 optimal weight: 7.9990 chunk 289 optimal weight: 2.9990 chunk 143 optimal weight: 7.9990 chunk 259 optimal weight: 0.9990 chunk 78 optimal weight: 0.8980 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b1101 GLN NA 101 GLN lA2101 GLN ** oA1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** AB2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** UB2101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.4639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 34500 Z= 0.216 Angle : 0.619 6.404 46350 Z= 0.325 Chirality : 0.034 0.153 5550 Planarity : 0.003 0.022 6000 Dihedral : 3.184 13.963 4800 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.71 % Allowed : 30.98 % Favored : 65.30 % 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: 6.89 (0.10), residues: 4050 helix: 4.40 (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 1538 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 1421 time to evaluate : 3.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 55 residues processed: 1478 average time/residue: 0.5018 time to fit residues: 1150.6029 Evaluate side-chains 1200 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1145 time to evaluate : 4.727 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 0 residues processed: 55 average time/residue: 0.3192 time to fit residues: 38.6746 ------------------------------------------------------------------------------- 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: 8.9990 chunk 164 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 215 optimal weight: 10.0000 chunk 119 optimal weight: 10.0000 chunk 247 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 148 optimal weight: 7.9990 chunk 260 optimal weight: 10.0000 chunk 73 optimal weight: 6.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Z 101 GLN j 101 GLN 3 122 HIS CA2101 GLN IA 122 HIS MA2122 HIS XA 101 GLN ZA1101 GLN qA2101 GLN yA1122 HIS 6A 101 GLN AB2101 GLN VB 122 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.4916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 34500 Z= 0.437 Angle : 0.764 6.994 46350 Z= 0.407 Chirality : 0.039 0.178 5550 Planarity : 0.003 0.031 6000 Dihedral : 3.241 18.194 4800 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 16.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 6.25 % Allowed : 35.78 % Favored : 57.97 % 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: 5.97 (0.10), residues: 4050 helix: 3.83 (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: 197 poor density : 1135 time to evaluate : 4.527 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: 197 outliers final: 124 residues processed: 1220 average time/residue: 0.5247 time to fit residues: 983.5779 Evaluate side-chains 1147 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 124 poor density : 1023 time to evaluate : 3.948 Switching outliers to nearest non-outliers outliers start: 124 outliers final: 0 residues processed: 124 average time/residue: 0.3028 time to fit residues: 76.9680 ------------------------------------------------------------------------------- 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: 0.7980 chunk 261 optimal weight: 3.9990 chunk 57 optimal weight: 8.9990 chunk 170 optimal weight: 4.9990 chunk 71 optimal weight: 10.0000 chunk 290 optimal weight: 2.9990 chunk 240 optimal weight: 9.9990 chunk 134 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 96 optimal weight: 8.9990 chunk 152 optimal weight: 7.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: DA 101 GLN MA2101 GLN rA 101 GLN 0A2101 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.5072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 34500 Z= 0.297 Angle : 0.735 9.996 46350 Z= 0.391 Chirality : 0.037 0.213 5550 Planarity : 0.003 0.034 6000 Dihedral : 3.240 17.883 4800 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.57 % Allowed : 37.30 % Favored : 58.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 6.11 (0.10), residues: 4050 helix: 3.92 (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 1357 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 144 poor density : 1213 time to evaluate : 3.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 144 outliers final: 75 residues processed: 1280 average time/residue: 0.4993 time to fit residues: 985.4395 Evaluate side-chains 1166 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1091 time to evaluate : 3.942 Switching outliers to nearest non-outliers outliers start: 75 outliers final: 0 residues processed: 75 average time/residue: 0.3106 time to fit residues: 49.6141 ------------------------------------------------------------------------------- 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: 3.9990 chunk 32 optimal weight: 8.9990 chunk 165 optimal weight: 1.9990 chunk 211 optimal weight: 4.9990 chunk 164 optimal weight: 7.9990 chunk 244 optimal weight: 8.9990 chunk 162 optimal weight: 9.9990 chunk 289 optimal weight: 4.9990 chunk 180 optimal weight: 6.9990 chunk 176 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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: 0.8582 moved from start: 0.5219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 34500 Z= 0.302 Angle : 0.772 11.587 46350 Z= 0.415 Chirality : 0.037 0.286 5550 Planarity : 0.003 0.027 6000 Dihedral : 3.220 16.831 4800 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.87 % Allowed : 39.37 % Favored : 56.76 % 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: 5.87 (0.10), residues: 4050 helix: 3.77 (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 1311 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1189 time to evaluate : 4.081 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 122 outliers final: 74 residues processed: 1241 average time/residue: 0.5124 time to fit residues: 979.1096 Evaluate side-chains 1164 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1090 time to evaluate : 3.681 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 0 residues processed: 74 average time/residue: 0.2952 time to fit residues: 46.6588 ------------------------------------------------------------------------------- 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: 8.9990 chunk 172 optimal weight: 4.9990 chunk 87 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 196 optimal weight: 5.9990 chunk 142 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 227 optimal weight: 0.8980 chunk 263 optimal weight: 10.0000 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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** GB 101 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.5316 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 34500 Z= 0.321 Angle : 0.834 11.846 46350 Z= 0.446 Chirality : 0.039 0.240 5550 Planarity : 0.003 0.029 6000 Dihedral : 3.222 16.947 4800 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.89 % Allowed : 41.33 % Favored : 55.78 % 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: 5.65 (0.10), residues: 4050 helix: 3.64 (0.06), 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 1245 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 1154 time to evaluate : 5.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 91 outliers final: 51 residues processed: 1189 average time/residue: 0.5214 time to fit residues: 958.2956 Evaluate side-chains 1132 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 1081 time to evaluate : 3.737 Switching outliers to nearest non-outliers outliers start: 51 outliers final: 0 residues processed: 51 average time/residue: 0.2955 time to fit residues: 33.7532 ------------------------------------------------------------------------------- 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: 0.9980 chunk 252 optimal weight: 0.9990 chunk 269 optimal weight: 1.9990 chunk 276 optimal weight: 3.9990 chunk 162 optimal weight: 5.9990 chunk 117 optimal weight: 10.0000 chunk 211 optimal weight: 1.9990 chunk 82 optimal weight: 10.0000 chunk 243 optimal weight: 6.9990 chunk 254 optimal weight: 10.0000 chunk 268 optimal weight: 5.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: lA2101 GLN ** 3A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6A 101 GLN AB2101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.5509 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= 0.300 Angle : 0.893 12.283 46350 Z= 0.474 Chirality : 0.039 0.243 5550 Planarity : 0.003 0.037 6000 Dihedral : 3.275 15.022 4800 Min Nonbonded Distance : 2.188 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.06 % Allowed : 42.89 % Favored : 55.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.50 (0.10), residues: 4050 helix: 3.54 (0.06), 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 1298 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 1233 time to evaluate : 4.291 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: 65 outliers final: 34 residues processed: 1256 average time/residue: 0.5080 time to fit residues: 983.2040 Evaluate side-chains 1146 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1112 time to evaluate : 4.174 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 0 residues processed: 34 average time/residue: 0.3063 time to fit residues: 24.9243 ------------------------------------------------------------------------------- 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: 0.8980 chunk 284 optimal weight: 0.0970 chunk 173 optimal weight: 0.0670 chunk 135 optimal weight: 7.9990 chunk 198 optimal weight: 6.9990 chunk 298 optimal weight: 5.9990 chunk 275 optimal weight: 5.9990 chunk 237 optimal weight: 0.9990 chunk 24 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 145 optimal weight: 1.9990 overall best weight: 0.8120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: gA2101 GLN 1A 101 GLN ** 3A1101 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** NB1101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.5744 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 : 0.965 12.607 46350 Z= 0.510 Chirality : 0.040 0.259 5550 Planarity : 0.003 0.039 6000 Dihedral : 3.353 14.849 4800 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.98 % Allowed : 45.78 % Favored : 53.24 % 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 1298 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 1267 time to evaluate : 3.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 15 residues processed: 1277 average time/residue: 0.5200 time to fit residues: 1027.5019 Evaluate side-chains 1147 residues out of total 3150 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 1132 time to evaluate : 4.203 Switching outliers to nearest non-outliers outliers start: 15 outliers final: 0 residues processed: 15 average time/residue: 0.3060 time to fit residues: 13.9305 ------------------------------------------------------------------------------- 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: 3.9990 chunk 253 optimal weight: 10.0000 chunk 72 optimal weight: 1.9990 chunk 219 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 66 optimal weight: 8.9990 chunk 238 optimal weight: 2.9990 chunk 99 optimal weight: 0.9990 chunk 244 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: XA 101 GLN qA2122 HIS 3A1101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.060841 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.048876 restraints weight = 131533.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.050724 restraints weight = 65850.951| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.051738 restraints weight = 40628.443| |-----------------------------------------------------------------------------| r_work (final): 0.3272 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.5796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 34500 Z= 0.322 Angle : 0.961 12.551 46350 Z= 0.512 Chirality : 0.041 0.318 5550 Planarity : 0.004 0.031 6000 Dihedral : 3.325 16.100 4800 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.13 % Allowed : 46.95 % Favored : 50.92 % 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: 4.93 (0.11), residues: 4050 helix: 3.19 (0.07), residues: 4050 sheet: None (None), residues: 0 loop : None (None), residues: 0 =============================================================================== Job complete usr+sys time: 13655.48 seconds wall clock time: 241 minutes 50.80 seconds (14510.80 seconds total)