Starting phenix.real_space_refine (version: dev) on Fri Dec 16 21:44:03 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wjt_8847/12_2022/5wjt_8847_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wjt_8847/12_2022/5wjt_8847.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/5wjt_8847/12_2022/5wjt_8847.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wjt_8847/12_2022/5wjt_8847.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wjt_8847/12_2022/5wjt_8847_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5wjt_8847/12_2022/5wjt_8847_neut.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 35": "NH1" <-> "NH2" Residue "A ARG 53": "NH1" <-> "NH2" Residue "A ARG 129": "NH1" <-> "NH2" Residue "A ARG 264": "NH1" <-> "NH2" Residue "B ARG 15": "NH1" <-> "NH2" Residue "B ARG 35": "NH1" <-> "NH2" Residue "B ARG 53": "NH1" <-> "NH2" Residue "B ARG 129": "NH1" <-> "NH2" Residue "B ARG 264": "NH1" <-> "NH2" Residue "C ARG 15": "NH1" <-> "NH2" Residue "C ARG 35": "NH1" <-> "NH2" Residue "C ARG 53": "NH1" <-> "NH2" Residue "C ARG 129": "NH1" <-> "NH2" Residue "C ARG 264": "NH1" <-> "NH2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D ARG 35": "NH1" <-> "NH2" Residue "D ARG 53": "NH1" <-> "NH2" Residue "D ARG 129": "NH1" <-> "NH2" Residue "D ARG 264": "NH1" <-> "NH2" Residue "E ARG 15": "NH1" <-> "NH2" Residue "E ARG 35": "NH1" <-> "NH2" Residue "E ARG 53": "NH1" <-> "NH2" Residue "E ARG 129": "NH1" <-> "NH2" Residue "E ARG 264": "NH1" <-> "NH2" Residue "F ARG 15": "NH1" <-> "NH2" Residue "F ARG 35": "NH1" <-> "NH2" Residue "F ARG 53": "NH1" <-> "NH2" Residue "F ARG 129": "NH1" <-> "NH2" Residue "F ARG 264": "NH1" <-> "NH2" Residue "G ARG 15": "NH1" <-> "NH2" Residue "G ARG 35": "NH1" <-> "NH2" Residue "G ARG 53": "NH1" <-> "NH2" Residue "G ARG 129": "NH1" <-> "NH2" Residue "G ARG 264": "NH1" <-> "NH2" Residue "H ARG 15": "NH1" <-> "NH2" Residue "H ARG 35": "NH1" <-> "NH2" Residue "H ARG 53": "NH1" <-> "NH2" Residue "H ARG 129": "NH1" <-> "NH2" Residue "H ARG 264": "NH1" <-> "NH2" Residue "I ARG 15": "NH1" <-> "NH2" Residue "I ARG 35": "NH1" <-> "NH2" Residue "I ARG 53": "NH1" <-> "NH2" Residue "I ARG 129": "NH1" <-> "NH2" Residue "I ARG 264": "NH1" <-> "NH2" Residue "J ARG 15": "NH1" <-> "NH2" Residue "J ARG 35": "NH1" <-> "NH2" Residue "J ARG 53": "NH1" <-> "NH2" Residue "J ARG 129": "NH1" <-> "NH2" Residue "J ARG 264": "NH1" <-> "NH2" Residue "K ARG 15": "NH1" <-> "NH2" Residue "K ARG 35": "NH1" <-> "NH2" Residue "K ARG 53": "NH1" <-> "NH2" Residue "K ARG 129": "NH1" <-> "NH2" Residue "K ARG 264": "NH1" <-> "NH2" Residue "L ARG 15": "NH1" <-> "NH2" Residue "L ARG 35": "NH1" <-> "NH2" Residue "L ARG 53": "NH1" <-> "NH2" Residue "L ARG 129": "NH1" <-> "NH2" Residue "L ARG 264": "NH1" <-> "NH2" Residue "M ARG 15": "NH1" <-> "NH2" Residue "M ARG 35": "NH1" <-> "NH2" Residue "M ARG 53": "NH1" <-> "NH2" Residue "M ARG 129": "NH1" <-> "NH2" Residue "M ARG 264": "NH1" <-> "NH2" Residue "N ARG 15": "NH1" <-> "NH2" Residue "N ARG 35": "NH1" <-> "NH2" Residue "N ARG 53": "NH1" <-> "NH2" Residue "N ARG 129": "NH1" <-> "NH2" Residue "N ARG 264": "NH1" <-> "NH2" Residue "O ARG 15": "NH1" <-> "NH2" Residue "O ARG 35": "NH1" <-> "NH2" Residue "O ARG 53": "NH1" <-> "NH2" Residue "O ARG 129": "NH1" <-> "NH2" Residue "O ARG 264": "NH1" <-> "NH2" Residue "P ARG 15": "NH1" <-> "NH2" Residue "P ARG 35": "NH1" <-> "NH2" Residue "P ARG 53": "NH1" <-> "NH2" Residue "P ARG 129": "NH1" <-> "NH2" Residue "P ARG 264": "NH1" <-> "NH2" Residue "Q ARG 15": "NH1" <-> "NH2" Residue "Q ARG 35": "NH1" <-> "NH2" Residue "Q ARG 53": "NH1" <-> "NH2" Residue "Q ARG 129": "NH1" <-> "NH2" Residue "Q ARG 264": "NH1" <-> "NH2" Residue "R ARG 15": "NH1" <-> "NH2" Residue "R ARG 35": "NH1" <-> "NH2" Residue "R ARG 53": "NH1" <-> "NH2" Residue "R ARG 129": "NH1" <-> "NH2" Residue "R ARG 264": "NH1" <-> "NH2" Residue "S ARG 15": "NH1" <-> "NH2" Residue "S ARG 35": "NH1" <-> "NH2" Residue "S ARG 53": "NH1" <-> "NH2" Residue "S ARG 129": "NH1" <-> "NH2" Residue "S ARG 264": "NH1" <-> "NH2" Residue "T ARG 15": "NH1" <-> "NH2" Residue "T ARG 35": "NH1" <-> "NH2" Residue "T ARG 53": "NH1" <-> "NH2" Residue "T ARG 129": "NH1" <-> "NH2" Residue "T ARG 264": "NH1" <-> "NH2" Residue "U ARG 15": "NH1" <-> "NH2" Residue "U ARG 35": "NH1" <-> "NH2" Residue "U ARG 53": "NH1" <-> "NH2" Residue "U ARG 129": "NH1" <-> "NH2" Residue "U ARG 264": "NH1" <-> "NH2" Residue "V ARG 15": "NH1" <-> "NH2" Residue "V ARG 35": "NH1" <-> "NH2" Residue "V ARG 53": "NH1" <-> "NH2" Residue "V ARG 129": "NH1" <-> "NH2" Residue "V ARG 264": "NH1" <-> "NH2" Residue "W ARG 15": "NH1" <-> "NH2" Residue "W ARG 35": "NH1" <-> "NH2" Residue "W ARG 53": "NH1" <-> "NH2" Residue "W ARG 129": "NH1" <-> "NH2" Residue "W ARG 264": "NH1" <-> "NH2" Residue "X ARG 15": "NH1" <-> "NH2" Residue "X ARG 35": "NH1" <-> "NH2" Residue "X ARG 53": "NH1" <-> "NH2" Residue "X ARG 129": "NH1" <-> "NH2" Residue "X ARG 264": "NH1" <-> "NH2" Residue "Y ARG 15": "NH1" <-> "NH2" Residue "Y ARG 35": "NH1" <-> "NH2" Residue "Y ARG 53": "NH1" <-> "NH2" Residue "Y ARG 129": "NH1" <-> "NH2" Residue "Y ARG 264": "NH1" <-> "NH2" Residue "Z ARG 15": "NH1" <-> "NH2" Residue "Z ARG 35": "NH1" <-> "NH2" Residue "Z ARG 53": "NH1" <-> "NH2" Residue "Z ARG 129": "NH1" <-> "NH2" Residue "Z ARG 264": "NH1" <-> "NH2" Residue "a ARG 15": "NH1" <-> "NH2" Residue "a ARG 35": "NH1" <-> "NH2" Residue "a ARG 53": "NH1" <-> "NH2" Residue "a ARG 129": "NH1" <-> "NH2" Residue "a ARG 264": "NH1" <-> "NH2" Residue "b ARG 15": "NH1" <-> "NH2" Residue "b ARG 35": "NH1" <-> "NH2" Residue "b ARG 53": "NH1" <-> "NH2" Residue "b ARG 129": "NH1" <-> "NH2" Residue "b ARG 264": "NH1" <-> "NH2" Residue "c ARG 15": "NH1" <-> "NH2" Residue "c ARG 35": "NH1" <-> "NH2" Residue "c ARG 53": "NH1" <-> "NH2" Residue "c ARG 129": "NH1" <-> "NH2" Residue "c ARG 264": "NH1" <-> "NH2" Residue "d ARG 15": "NH1" <-> "NH2" Residue "d ARG 35": "NH1" <-> "NH2" Residue "d ARG 53": "NH1" <-> "NH2" Residue "d ARG 129": "NH1" <-> "NH2" Residue "d ARG 264": "NH1" <-> "NH2" Residue "e ARG 15": "NH1" <-> "NH2" Residue "e ARG 35": "NH1" <-> "NH2" Residue "e ARG 53": "NH1" <-> "NH2" Residue "e ARG 129": "NH1" <-> "NH2" Residue "e ARG 264": "NH1" <-> "NH2" Residue "f ARG 15": "NH1" <-> "NH2" Residue "f ARG 35": "NH1" <-> "NH2" Residue "f ARG 53": "NH1" <-> "NH2" Residue "f ARG 129": "NH1" <-> "NH2" Residue "f ARG 264": "NH1" <-> "NH2" Residue "g ARG 15": "NH1" <-> "NH2" Residue "g ARG 35": "NH1" <-> "NH2" Residue "g ARG 53": "NH1" <-> "NH2" Residue "g ARG 129": "NH1" <-> "NH2" Residue "g ARG 264": "NH1" <-> "NH2" Residue "h ARG 15": "NH1" <-> "NH2" Residue "h ARG 35": "NH1" <-> "NH2" Residue "h ARG 53": "NH1" <-> "NH2" Residue "h ARG 129": "NH1" <-> "NH2" Residue "h ARG 264": "NH1" <-> "NH2" Residue "i ARG 15": "NH1" <-> "NH2" Residue "i ARG 35": "NH1" <-> "NH2" Residue "i ARG 53": "NH1" <-> "NH2" Residue "i ARG 129": "NH1" <-> "NH2" Residue "i ARG 264": "NH1" <-> "NH2" Residue "j ARG 15": "NH1" <-> "NH2" Residue "j ARG 35": "NH1" <-> "NH2" Residue "j ARG 53": "NH1" <-> "NH2" Residue "j ARG 129": "NH1" <-> "NH2" Residue "j ARG 264": "NH1" <-> "NH2" Residue "k ARG 15": "NH1" <-> "NH2" Residue "k ARG 35": "NH1" <-> "NH2" Residue "k ARG 53": "NH1" <-> "NH2" Residue "k ARG 129": "NH1" <-> "NH2" Residue "k ARG 264": "NH1" <-> "NH2" Residue "l ARG 15": "NH1" <-> "NH2" Residue "l ARG 35": "NH1" <-> "NH2" Residue "l ARG 53": "NH1" <-> "NH2" Residue "l ARG 129": "NH1" <-> "NH2" Residue "l ARG 264": "NH1" <-> "NH2" Residue "m ARG 15": "NH1" <-> "NH2" Residue "m ARG 35": "NH1" <-> "NH2" Residue "m ARG 53": "NH1" <-> "NH2" Residue "m ARG 129": "NH1" <-> "NH2" Residue "m ARG 264": "NH1" <-> "NH2" Residue "n ARG 15": "NH1" <-> "NH2" Residue "n ARG 35": "NH1" <-> "NH2" Residue "n ARG 53": "NH1" <-> "NH2" Residue "n ARG 129": "NH1" <-> "NH2" Residue "n ARG 264": "NH1" <-> "NH2" Residue "o ARG 15": "NH1" <-> "NH2" Residue "o ARG 35": "NH1" <-> "NH2" Residue "o ARG 53": "NH1" <-> "NH2" Residue "o ARG 129": "NH1" <-> "NH2" Residue "o ARG 264": "NH1" <-> "NH2" Time to flip residues: 0.20s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/modules/chem_data/mon_lib" Total number of atoms: 92947 Number of models: 1 Model: "" Number of chains: 41 Chain: "A" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "B" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "C" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "D" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "E" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "F" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "G" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "H" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "I" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "J" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "K" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "L" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "M" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "N" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "O" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "P" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "Q" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "R" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "S" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "T" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "U" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "V" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "W" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "X" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "Y" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "Z" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "a" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "b" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "c" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "d" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "e" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "f" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "g" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "h" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "i" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "j" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "k" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "l" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "m" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "n" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Chain: "o" Number of atoms: 2267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2267 Classifications: {'peptide': 302} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 299} Time building chain proxies: 37.48, per 1000 atoms: 0.40 Number of scatterers: 92947 At special positions: 0 Unit cell: (154.35, 154.35, 340.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 328 16.00 O 19434 8.00 N 16974 7.00 C 56211 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: 29.57 Conformation dependent library (CDL) restraints added in 10.9 seconds 24600 Ramachandran restraints generated. 12300 Oldfield, 0 Emsley, 12300 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 23206 Finding SS restraints... Secondary structure from input PDB file: 328 helices and 82 sheets defined 67.2% alpha, 1.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.23 Creating SS restraints... Processing helix chain 'A' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER A 21 " --> pdb=" O SER A 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS A 25 " --> pdb=" O SER A 21 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE A 112 " --> pdb=" O ASP A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR A 142 " --> pdb=" O ASP A 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 143 " --> pdb=" O GLY A 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 139 through 143' Processing helix chain 'A' and resid 148 through 152 removed outlier: 3.666A pdb=" N GLN A 152 " --> pdb=" O PRO A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU A 235 " --> pdb=" O GLN A 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA A 237 " --> pdb=" O ALA A 233 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 293 Processing helix chain 'A' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL A 299 " --> pdb=" O GLN A 295 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER B 21 " --> pdb=" O SER B 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS B 25 " --> pdb=" O SER B 21 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE B 112 " --> pdb=" O ASP B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR B 142 " --> pdb=" O ASP B 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS B 143 " --> pdb=" O GLY B 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 139 through 143' Processing helix chain 'B' and resid 148 through 152 removed outlier: 3.666A pdb=" N GLN B 152 " --> pdb=" O PRO B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU B 235 " --> pdb=" O GLN B 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY B 236 " --> pdb=" O ARG B 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA B 237 " --> pdb=" O ALA B 233 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 293 Processing helix chain 'B' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL B 299 " --> pdb=" O GLN B 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER C 21 " --> pdb=" O SER C 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS C 25 " --> pdb=" O SER C 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 143 removed outlier: 3.674A pdb=" N TYR C 142 " --> pdb=" O ASP C 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS C 143 " --> pdb=" O GLY C 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 139 through 143' Processing helix chain 'C' and resid 148 through 152 removed outlier: 3.666A pdb=" N GLN C 152 " --> pdb=" O PRO C 149 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 264 removed outlier: 3.595A pdb=" N LEU C 235 " --> pdb=" O GLN C 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY C 236 " --> pdb=" O ARG C 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA C 237 " --> pdb=" O ALA C 233 " (cutoff:3.500A) Processing helix chain 'C' and resid 267 through 293 Processing helix chain 'C' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL C 299 " --> pdb=" O GLN C 295 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER D 21 " --> pdb=" O SER D 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS D 25 " --> pdb=" O SER D 21 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 98 removed outlier: 4.022A pdb=" N LYS D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE D 112 " --> pdb=" O ASP D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR D 142 " --> pdb=" O ASP D 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS D 143 " --> pdb=" O GLY D 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 139 through 143' Processing helix chain 'D' and resid 148 through 152 removed outlier: 3.666A pdb=" N GLN D 152 " --> pdb=" O PRO D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 264 removed outlier: 3.595A pdb=" N LEU D 235 " --> pdb=" O GLN D 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY D 236 " --> pdb=" O ARG D 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA D 237 " --> pdb=" O ALA D 233 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 293 Processing helix chain 'D' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL D 299 " --> pdb=" O GLN D 295 " (cutoff:3.500A) Processing helix chain 'E' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER E 21 " --> pdb=" O SER E 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS E 25 " --> pdb=" O SER E 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS E 51 " --> pdb=" O ALA E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE E 112 " --> pdb=" O ASP E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR E 142 " --> pdb=" O ASP E 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS E 143 " --> pdb=" O GLY E 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 139 through 143' Processing helix chain 'E' and resid 148 through 152 removed outlier: 3.666A pdb=" N GLN E 152 " --> pdb=" O PRO E 149 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU E 235 " --> pdb=" O GLN E 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY E 236 " --> pdb=" O ARG E 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA E 237 " --> pdb=" O ALA E 233 " (cutoff:3.500A) Processing helix chain 'E' and resid 267 through 293 Processing helix chain 'E' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL E 299 " --> pdb=" O GLN E 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER F 21 " --> pdb=" O SER F 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS F 25 " --> pdb=" O SER F 21 " (cutoff:3.500A) Processing helix chain 'F' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS F 51 " --> pdb=" O ALA F 47 " (cutoff:3.500A) Processing helix chain 'F' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE F 112 " --> pdb=" O ASP F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 143 removed outlier: 3.674A pdb=" N TYR F 142 " --> pdb=" O ASP F 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS F 143 " --> pdb=" O GLY F 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 139 through 143' Processing helix chain 'F' and resid 148 through 152 removed outlier: 3.667A pdb=" N GLN F 152 " --> pdb=" O PRO F 149 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU F 235 " --> pdb=" O GLN F 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY F 236 " --> pdb=" O ARG F 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 267 through 293 Processing helix chain 'F' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL F 299 " --> pdb=" O GLN F 295 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 31 removed outlier: 3.888A pdb=" N SER G 21 " --> pdb=" O SER G 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS G 25 " --> pdb=" O SER G 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS G 51 " --> pdb=" O ALA G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE G 112 " --> pdb=" O ASP G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 143 removed outlier: 3.674A pdb=" N TYR G 142 " --> pdb=" O ASP G 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS G 143 " --> pdb=" O GLY G 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 139 through 143' Processing helix chain 'G' and resid 148 through 152 removed outlier: 3.666A pdb=" N GLN G 152 " --> pdb=" O PRO G 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 264 removed outlier: 3.595A pdb=" N LEU G 235 " --> pdb=" O GLN G 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY G 236 " --> pdb=" O ARG G 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA G 237 " --> pdb=" O ALA G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 267 through 293 Processing helix chain 'G' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL G 299 " --> pdb=" O GLN G 295 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER H 21 " --> pdb=" O SER H 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS H 25 " --> pdb=" O SER H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS H 51 " --> pdb=" O ALA H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE H 112 " --> pdb=" O ASP H 108 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR H 142 " --> pdb=" O ASP H 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS H 143 " --> pdb=" O GLY H 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 139 through 143' Processing helix chain 'H' and resid 148 through 152 removed outlier: 3.667A pdb=" N GLN H 152 " --> pdb=" O PRO H 149 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU H 235 " --> pdb=" O GLN H 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY H 236 " --> pdb=" O ARG H 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA H 237 " --> pdb=" O ALA H 233 " (cutoff:3.500A) Processing helix chain 'H' and resid 267 through 293 Processing helix chain 'H' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL H 299 " --> pdb=" O GLN H 295 " (cutoff:3.500A) Processing helix chain 'I' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER I 21 " --> pdb=" O SER I 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS I 25 " --> pdb=" O SER I 21 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS I 51 " --> pdb=" O ALA I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE I 112 " --> pdb=" O ASP I 108 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR I 142 " --> pdb=" O ASP I 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS I 143 " --> pdb=" O GLY I 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 139 through 143' Processing helix chain 'I' and resid 148 through 152 removed outlier: 3.667A pdb=" N GLN I 152 " --> pdb=" O PRO I 149 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU I 235 " --> pdb=" O GLN I 231 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY I 236 " --> pdb=" O ARG I 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA I 237 " --> pdb=" O ALA I 233 " (cutoff:3.500A) Processing helix chain 'I' and resid 267 through 293 Processing helix chain 'I' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL I 299 " --> pdb=" O GLN I 295 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER J 21 " --> pdb=" O SER J 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS J 25 " --> pdb=" O SER J 21 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS J 51 " --> pdb=" O ALA J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE J 112 " --> pdb=" O ASP J 108 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR J 142 " --> pdb=" O ASP J 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS J 143 " --> pdb=" O GLY J 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 139 through 143' Processing helix chain 'J' and resid 148 through 152 removed outlier: 3.667A pdb=" N GLN J 152 " --> pdb=" O PRO J 149 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 264 removed outlier: 3.595A pdb=" N LEU J 235 " --> pdb=" O GLN J 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY J 236 " --> pdb=" O ARG J 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA J 237 " --> pdb=" O ALA J 233 " (cutoff:3.500A) Processing helix chain 'J' and resid 267 through 293 Processing helix chain 'J' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL J 299 " --> pdb=" O GLN J 295 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER K 21 " --> pdb=" O SER K 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS K 25 " --> pdb=" O SER K 21 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 98 removed outlier: 4.022A pdb=" N LYS K 51 " --> pdb=" O ALA K 47 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE K 112 " --> pdb=" O ASP K 108 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR K 142 " --> pdb=" O ASP K 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS K 143 " --> pdb=" O GLY K 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 139 through 143' Processing helix chain 'K' and resid 148 through 152 removed outlier: 3.666A pdb=" N GLN K 152 " --> pdb=" O PRO K 149 " (cutoff:3.500A) Processing helix chain 'K' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU K 235 " --> pdb=" O GLN K 231 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY K 236 " --> pdb=" O ARG K 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA K 237 " --> pdb=" O ALA K 233 " (cutoff:3.500A) Processing helix chain 'K' and resid 267 through 293 Processing helix chain 'K' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL K 299 " --> pdb=" O GLN K 295 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER L 21 " --> pdb=" O SER L 17 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS L 25 " --> pdb=" O SER L 21 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS L 51 " --> pdb=" O ALA L 47 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE L 112 " --> pdb=" O ASP L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 143 removed outlier: 3.674A pdb=" N TYR L 142 " --> pdb=" O ASP L 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS L 143 " --> pdb=" O GLY L 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 139 through 143' Processing helix chain 'L' and resid 148 through 152 removed outlier: 3.667A pdb=" N GLN L 152 " --> pdb=" O PRO L 149 " (cutoff:3.500A) Processing helix chain 'L' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU L 235 " --> pdb=" O GLN L 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY L 236 " --> pdb=" O ARG L 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA L 237 " --> pdb=" O ALA L 233 " (cutoff:3.500A) Processing helix chain 'L' and resid 267 through 293 Processing helix chain 'L' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL L 299 " --> pdb=" O GLN L 295 " (cutoff:3.500A) Processing helix chain 'M' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER M 21 " --> pdb=" O SER M 17 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS M 25 " --> pdb=" O SER M 21 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS M 51 " --> pdb=" O ALA M 47 " (cutoff:3.500A) Processing helix chain 'M' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE M 112 " --> pdb=" O ASP M 108 " (cutoff:3.500A) Processing helix chain 'M' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR M 142 " --> pdb=" O ASP M 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS M 143 " --> pdb=" O GLY M 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 139 through 143' Processing helix chain 'M' and resid 148 through 152 removed outlier: 3.667A pdb=" N GLN M 152 " --> pdb=" O PRO M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU M 235 " --> pdb=" O GLN M 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY M 236 " --> pdb=" O ARG M 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA M 237 " --> pdb=" O ALA M 233 " (cutoff:3.500A) Processing helix chain 'M' and resid 267 through 293 Processing helix chain 'M' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL M 299 " --> pdb=" O GLN M 295 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER N 21 " --> pdb=" O SER N 17 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS N 25 " --> pdb=" O SER N 21 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS N 51 " --> pdb=" O ALA N 47 " (cutoff:3.500A) Processing helix chain 'N' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE N 112 " --> pdb=" O ASP N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR N 142 " --> pdb=" O ASP N 139 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS N 143 " --> pdb=" O GLY N 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 139 through 143' Processing helix chain 'N' and resid 148 through 152 removed outlier: 3.666A pdb=" N GLN N 152 " --> pdb=" O PRO N 149 " (cutoff:3.500A) Processing helix chain 'N' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU N 235 " --> pdb=" O GLN N 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY N 236 " --> pdb=" O ARG N 232 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ALA N 237 " --> pdb=" O ALA N 233 " (cutoff:3.500A) Processing helix chain 'N' and resid 267 through 293 Processing helix chain 'N' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL N 299 " --> pdb=" O GLN N 295 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER O 21 " --> pdb=" O SER O 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS O 25 " --> pdb=" O SER O 21 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS O 51 " --> pdb=" O ALA O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE O 112 " --> pdb=" O ASP O 108 " (cutoff:3.500A) Processing helix chain 'O' and resid 139 through 143 removed outlier: 3.674A pdb=" N TYR O 142 " --> pdb=" O ASP O 139 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS O 143 " --> pdb=" O GLY O 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 139 through 143' Processing helix chain 'O' and resid 148 through 152 removed outlier: 3.667A pdb=" N GLN O 152 " --> pdb=" O PRO O 149 " (cutoff:3.500A) Processing helix chain 'O' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU O 235 " --> pdb=" O GLN O 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY O 236 " --> pdb=" O ARG O 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA O 237 " --> pdb=" O ALA O 233 " (cutoff:3.500A) Processing helix chain 'O' and resid 267 through 293 Processing helix chain 'O' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL O 299 " --> pdb=" O GLN O 295 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 31 removed outlier: 3.888A pdb=" N SER P 21 " --> pdb=" O SER P 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS P 25 " --> pdb=" O SER P 21 " (cutoff:3.500A) Processing helix chain 'P' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS P 51 " --> pdb=" O ALA P 47 " (cutoff:3.500A) Processing helix chain 'P' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE P 112 " --> pdb=" O ASP P 108 " (cutoff:3.500A) Processing helix chain 'P' and resid 139 through 143 removed outlier: 3.674A pdb=" N TYR P 142 " --> pdb=" O ASP P 139 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS P 143 " --> pdb=" O GLY P 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 139 through 143' Processing helix chain 'P' and resid 148 through 152 removed outlier: 3.667A pdb=" N GLN P 152 " --> pdb=" O PRO P 149 " (cutoff:3.500A) Processing helix chain 'P' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU P 235 " --> pdb=" O GLN P 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY P 236 " --> pdb=" O ARG P 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA P 237 " --> pdb=" O ALA P 233 " (cutoff:3.500A) Processing helix chain 'P' and resid 267 through 293 Processing helix chain 'P' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL P 299 " --> pdb=" O GLN P 295 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER Q 21 " --> pdb=" O SER Q 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS Q 25 " --> pdb=" O SER Q 21 " (cutoff:3.500A) Processing helix chain 'Q' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS Q 51 " --> pdb=" O ALA Q 47 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE Q 112 " --> pdb=" O ASP Q 108 " (cutoff:3.500A) Processing helix chain 'Q' and resid 139 through 143 removed outlier: 3.674A pdb=" N TYR Q 142 " --> pdb=" O ASP Q 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS Q 143 " --> pdb=" O GLY Q 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 139 through 143' Processing helix chain 'Q' and resid 148 through 152 removed outlier: 3.666A pdb=" N GLN Q 152 " --> pdb=" O PRO Q 149 " (cutoff:3.500A) Processing helix chain 'Q' and resid 213 through 264 removed outlier: 3.595A pdb=" N LEU Q 235 " --> pdb=" O GLN Q 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY Q 236 " --> pdb=" O ARG Q 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA Q 237 " --> pdb=" O ALA Q 233 " (cutoff:3.500A) Processing helix chain 'Q' and resid 267 through 293 Processing helix chain 'Q' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL Q 299 " --> pdb=" O GLN Q 295 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER R 21 " --> pdb=" O SER R 17 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS R 25 " --> pdb=" O SER R 21 " (cutoff:3.500A) Processing helix chain 'R' and resid 42 through 98 removed outlier: 4.022A pdb=" N LYS R 51 " --> pdb=" O ALA R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE R 112 " --> pdb=" O ASP R 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 143 removed outlier: 3.674A pdb=" N TYR R 142 " --> pdb=" O ASP R 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS R 143 " --> pdb=" O GLY R 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 139 through 143' Processing helix chain 'R' and resid 148 through 152 removed outlier: 3.667A pdb=" N GLN R 152 " --> pdb=" O PRO R 149 " (cutoff:3.500A) Processing helix chain 'R' and resid 213 through 264 removed outlier: 3.595A pdb=" N LEU R 235 " --> pdb=" O GLN R 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY R 236 " --> pdb=" O ARG R 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA R 237 " --> pdb=" O ALA R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 267 through 293 Processing helix chain 'R' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL R 299 " --> pdb=" O GLN R 295 " (cutoff:3.500A) Processing helix chain 'S' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER S 21 " --> pdb=" O SER S 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS S 25 " --> pdb=" O SER S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS S 51 " --> pdb=" O ALA S 47 " (cutoff:3.500A) Processing helix chain 'S' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE S 112 " --> pdb=" O ASP S 108 " (cutoff:3.500A) Processing helix chain 'S' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR S 142 " --> pdb=" O ASP S 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS S 143 " --> pdb=" O GLY S 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 139 through 143' Processing helix chain 'S' and resid 148 through 152 removed outlier: 3.666A pdb=" N GLN S 152 " --> pdb=" O PRO S 149 " (cutoff:3.500A) Processing helix chain 'S' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU S 235 " --> pdb=" O GLN S 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY S 236 " --> pdb=" O ARG S 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA S 237 " --> pdb=" O ALA S 233 " (cutoff:3.500A) Processing helix chain 'S' and resid 267 through 293 Processing helix chain 'S' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL S 299 " --> pdb=" O GLN S 295 " (cutoff:3.500A) Processing helix chain 'T' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER T 21 " --> pdb=" O SER T 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 42 through 98 removed outlier: 4.022A pdb=" N LYS T 51 " --> pdb=" O ALA T 47 " (cutoff:3.500A) Processing helix chain 'T' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE T 112 " --> pdb=" O ASP T 108 " (cutoff:3.500A) Processing helix chain 'T' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR T 142 " --> pdb=" O ASP T 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS T 143 " --> pdb=" O GLY T 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 139 through 143' Processing helix chain 'T' and resid 148 through 152 removed outlier: 3.666A pdb=" N GLN T 152 " --> pdb=" O PRO T 149 " (cutoff:3.500A) Processing helix chain 'T' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU T 235 " --> pdb=" O GLN T 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY T 236 " --> pdb=" O ARG T 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA T 237 " --> pdb=" O ALA T 233 " (cutoff:3.500A) Processing helix chain 'T' and resid 267 through 293 Processing helix chain 'T' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL T 299 " --> pdb=" O GLN T 295 " (cutoff:3.500A) Processing helix chain 'U' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER U 21 " --> pdb=" O SER U 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS U 25 " --> pdb=" O SER U 21 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS U 51 " --> pdb=" O ALA U 47 " (cutoff:3.500A) Processing helix chain 'U' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE U 112 " --> pdb=" O ASP U 108 " (cutoff:3.500A) Processing helix chain 'U' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR U 142 " --> pdb=" O ASP U 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS U 143 " --> pdb=" O GLY U 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 139 through 143' Processing helix chain 'U' and resid 148 through 152 removed outlier: 3.666A pdb=" N GLN U 152 " --> pdb=" O PRO U 149 " (cutoff:3.500A) Processing helix chain 'U' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU U 235 " --> pdb=" O GLN U 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY U 236 " --> pdb=" O ARG U 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA U 237 " --> pdb=" O ALA U 233 " (cutoff:3.500A) Processing helix chain 'U' and resid 267 through 293 Processing helix chain 'U' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL U 299 " --> pdb=" O GLN U 295 " (cutoff:3.500A) Processing helix chain 'V' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER V 21 " --> pdb=" O SER V 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS V 25 " --> pdb=" O SER V 21 " (cutoff:3.500A) Processing helix chain 'V' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS V 51 " --> pdb=" O ALA V 47 " (cutoff:3.500A) Processing helix chain 'V' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE V 112 " --> pdb=" O ASP V 108 " (cutoff:3.500A) Processing helix chain 'V' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR V 142 " --> pdb=" O ASP V 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS V 143 " --> pdb=" O GLY V 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 139 through 143' Processing helix chain 'V' and resid 148 through 152 removed outlier: 3.666A pdb=" N GLN V 152 " --> pdb=" O PRO V 149 " (cutoff:3.500A) Processing helix chain 'V' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU V 235 " --> pdb=" O GLN V 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY V 236 " --> pdb=" O ARG V 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA V 237 " --> pdb=" O ALA V 233 " (cutoff:3.500A) Processing helix chain 'V' and resid 267 through 293 Processing helix chain 'V' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL V 299 " --> pdb=" O GLN V 295 " (cutoff:3.500A) Processing helix chain 'W' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER W 21 " --> pdb=" O SER W 17 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS W 25 " --> pdb=" O SER W 21 " (cutoff:3.500A) Processing helix chain 'W' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS W 51 " --> pdb=" O ALA W 47 " (cutoff:3.500A) Processing helix chain 'W' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE W 112 " --> pdb=" O ASP W 108 " (cutoff:3.500A) Processing helix chain 'W' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR W 142 " --> pdb=" O ASP W 139 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS W 143 " --> pdb=" O GLY W 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 139 through 143' Processing helix chain 'W' and resid 148 through 152 removed outlier: 3.667A pdb=" N GLN W 152 " --> pdb=" O PRO W 149 " (cutoff:3.500A) Processing helix chain 'W' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU W 235 " --> pdb=" O GLN W 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY W 236 " --> pdb=" O ARG W 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA W 237 " --> pdb=" O ALA W 233 " (cutoff:3.500A) Processing helix chain 'W' and resid 267 through 293 Processing helix chain 'W' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL W 299 " --> pdb=" O GLN W 295 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER X 21 " --> pdb=" O SER X 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS X 25 " --> pdb=" O SER X 21 " (cutoff:3.500A) Processing helix chain 'X' and resid 42 through 98 removed outlier: 4.022A pdb=" N LYS X 51 " --> pdb=" O ALA X 47 " (cutoff:3.500A) Processing helix chain 'X' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE X 112 " --> pdb=" O ASP X 108 " (cutoff:3.500A) Processing helix chain 'X' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR X 142 " --> pdb=" O ASP X 139 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS X 143 " --> pdb=" O GLY X 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 139 through 143' Processing helix chain 'X' and resid 148 through 152 removed outlier: 3.666A pdb=" N GLN X 152 " --> pdb=" O PRO X 149 " (cutoff:3.500A) Processing helix chain 'X' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU X 235 " --> pdb=" O GLN X 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY X 236 " --> pdb=" O ARG X 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA X 237 " --> pdb=" O ALA X 233 " (cutoff:3.500A) Processing helix chain 'X' and resid 267 through 293 Processing helix chain 'X' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL X 299 " --> pdb=" O GLN X 295 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER Y 21 " --> pdb=" O SER Y 17 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS Y 25 " --> pdb=" O SER Y 21 " (cutoff:3.500A) Processing helix chain 'Y' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS Y 51 " --> pdb=" O ALA Y 47 " (cutoff:3.500A) Processing helix chain 'Y' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE Y 112 " --> pdb=" O ASP Y 108 " (cutoff:3.500A) Processing helix chain 'Y' and resid 139 through 143 removed outlier: 3.674A pdb=" N TYR Y 142 " --> pdb=" O ASP Y 139 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS Y 143 " --> pdb=" O GLY Y 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 139 through 143' Processing helix chain 'Y' and resid 148 through 152 removed outlier: 3.667A pdb=" N GLN Y 152 " --> pdb=" O PRO Y 149 " (cutoff:3.500A) Processing helix chain 'Y' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU Y 235 " --> pdb=" O GLN Y 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY Y 236 " --> pdb=" O ARG Y 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA Y 237 " --> pdb=" O ALA Y 233 " (cutoff:3.500A) Processing helix chain 'Y' and resid 267 through 293 Processing helix chain 'Y' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL Y 299 " --> pdb=" O GLN Y 295 " (cutoff:3.500A) Processing helix chain 'Z' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER Z 21 " --> pdb=" O SER Z 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS Z 25 " --> pdb=" O SER Z 21 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS Z 51 " --> pdb=" O ALA Z 47 " (cutoff:3.500A) Processing helix chain 'Z' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE Z 112 " --> pdb=" O ASP Z 108 " (cutoff:3.500A) Processing helix chain 'Z' and resid 139 through 143 removed outlier: 3.674A pdb=" N TYR Z 142 " --> pdb=" O ASP Z 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS Z 143 " --> pdb=" O GLY Z 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 139 through 143' Processing helix chain 'Z' and resid 148 through 152 removed outlier: 3.667A pdb=" N GLN Z 152 " --> pdb=" O PRO Z 149 " (cutoff:3.500A) Processing helix chain 'Z' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU Z 235 " --> pdb=" O GLN Z 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY Z 236 " --> pdb=" O ARG Z 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA Z 237 " --> pdb=" O ALA Z 233 " (cutoff:3.500A) Processing helix chain 'Z' and resid 267 through 293 Processing helix chain 'Z' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL Z 299 " --> pdb=" O GLN Z 295 " (cutoff:3.500A) Processing helix chain 'a' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER a 21 " --> pdb=" O SER a 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS a 25 " --> pdb=" O SER a 21 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS a 51 " --> pdb=" O ALA a 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE a 112 " --> pdb=" O ASP a 108 " (cutoff:3.500A) Processing helix chain 'a' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR a 142 " --> pdb=" O ASP a 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS a 143 " --> pdb=" O GLY a 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 139 through 143' Processing helix chain 'a' and resid 148 through 152 removed outlier: 3.667A pdb=" N GLN a 152 " --> pdb=" O PRO a 149 " (cutoff:3.500A) Processing helix chain 'a' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU a 235 " --> pdb=" O GLN a 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY a 236 " --> pdb=" O ARG a 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA a 237 " --> pdb=" O ALA a 233 " (cutoff:3.500A) Processing helix chain 'a' and resid 267 through 293 Processing helix chain 'a' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL a 299 " --> pdb=" O GLN a 295 " (cutoff:3.500A) Processing helix chain 'b' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER b 21 " --> pdb=" O SER b 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS b 25 " --> pdb=" O SER b 21 " (cutoff:3.500A) Processing helix chain 'b' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS b 51 " --> pdb=" O ALA b 47 " (cutoff:3.500A) Processing helix chain 'b' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE b 112 " --> pdb=" O ASP b 108 " (cutoff:3.500A) Processing helix chain 'b' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR b 142 " --> pdb=" O ASP b 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS b 143 " --> pdb=" O GLY b 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'b' and resid 139 through 143' Processing helix chain 'b' and resid 148 through 152 removed outlier: 3.667A pdb=" N GLN b 152 " --> pdb=" O PRO b 149 " (cutoff:3.500A) Processing helix chain 'b' and resid 213 through 264 removed outlier: 3.595A pdb=" N LEU b 235 " --> pdb=" O GLN b 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY b 236 " --> pdb=" O ARG b 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA b 237 " --> pdb=" O ALA b 233 " (cutoff:3.500A) Processing helix chain 'b' and resid 267 through 293 Processing helix chain 'b' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL b 299 " --> pdb=" O GLN b 295 " (cutoff:3.500A) Processing helix chain 'c' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER c 21 " --> pdb=" O SER c 17 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS c 25 " --> pdb=" O SER c 21 " (cutoff:3.500A) Processing helix chain 'c' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS c 51 " --> pdb=" O ALA c 47 " (cutoff:3.500A) Processing helix chain 'c' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE c 112 " --> pdb=" O ASP c 108 " (cutoff:3.500A) Processing helix chain 'c' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR c 142 " --> pdb=" O ASP c 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS c 143 " --> pdb=" O GLY c 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 139 through 143' Processing helix chain 'c' and resid 148 through 152 removed outlier: 3.666A pdb=" N GLN c 152 " --> pdb=" O PRO c 149 " (cutoff:3.500A) Processing helix chain 'c' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU c 235 " --> pdb=" O GLN c 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY c 236 " --> pdb=" O ARG c 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA c 237 " --> pdb=" O ALA c 233 " (cutoff:3.500A) Processing helix chain 'c' and resid 267 through 293 Processing helix chain 'c' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL c 299 " --> pdb=" O GLN c 295 " (cutoff:3.500A) Processing helix chain 'd' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER d 21 " --> pdb=" O SER d 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS d 25 " --> pdb=" O SER d 21 " (cutoff:3.500A) Processing helix chain 'd' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS d 51 " --> pdb=" O ALA d 47 " (cutoff:3.500A) Processing helix chain 'd' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE d 112 " --> pdb=" O ASP d 108 " (cutoff:3.500A) Processing helix chain 'd' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR d 142 " --> pdb=" O ASP d 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS d 143 " --> pdb=" O GLY d 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 139 through 143' Processing helix chain 'd' and resid 148 through 152 removed outlier: 3.666A pdb=" N GLN d 152 " --> pdb=" O PRO d 149 " (cutoff:3.500A) Processing helix chain 'd' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU d 235 " --> pdb=" O GLN d 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY d 236 " --> pdb=" O ARG d 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA d 237 " --> pdb=" O ALA d 233 " (cutoff:3.500A) Processing helix chain 'd' and resid 267 through 293 Processing helix chain 'd' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL d 299 " --> pdb=" O GLN d 295 " (cutoff:3.500A) Processing helix chain 'e' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER e 21 " --> pdb=" O SER e 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS e 25 " --> pdb=" O SER e 21 " (cutoff:3.500A) Processing helix chain 'e' and resid 42 through 98 removed outlier: 4.022A pdb=" N LYS e 51 " --> pdb=" O ALA e 47 " (cutoff:3.500A) Processing helix chain 'e' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE e 112 " --> pdb=" O ASP e 108 " (cutoff:3.500A) Processing helix chain 'e' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR e 142 " --> pdb=" O ASP e 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS e 143 " --> pdb=" O GLY e 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 139 through 143' Processing helix chain 'e' and resid 148 through 152 removed outlier: 3.667A pdb=" N GLN e 152 " --> pdb=" O PRO e 149 " (cutoff:3.500A) Processing helix chain 'e' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU e 235 " --> pdb=" O GLN e 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY e 236 " --> pdb=" O ARG e 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA e 237 " --> pdb=" O ALA e 233 " (cutoff:3.500A) Processing helix chain 'e' and resid 267 through 293 Processing helix chain 'e' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL e 299 " --> pdb=" O GLN e 295 " (cutoff:3.500A) Processing helix chain 'f' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER f 21 " --> pdb=" O SER f 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS f 25 " --> pdb=" O SER f 21 " (cutoff:3.500A) Processing helix chain 'f' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS f 51 " --> pdb=" O ALA f 47 " (cutoff:3.500A) Processing helix chain 'f' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE f 112 " --> pdb=" O ASP f 108 " (cutoff:3.500A) Processing helix chain 'f' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR f 142 " --> pdb=" O ASP f 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS f 143 " --> pdb=" O GLY f 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 139 through 143' Processing helix chain 'f' and resid 148 through 152 removed outlier: 3.667A pdb=" N GLN f 152 " --> pdb=" O PRO f 149 " (cutoff:3.500A) Processing helix chain 'f' and resid 213 through 264 removed outlier: 3.595A pdb=" N LEU f 235 " --> pdb=" O GLN f 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY f 236 " --> pdb=" O ARG f 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA f 237 " --> pdb=" O ALA f 233 " (cutoff:3.500A) Processing helix chain 'f' and resid 267 through 293 Processing helix chain 'f' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL f 299 " --> pdb=" O GLN f 295 " (cutoff:3.500A) Processing helix chain 'g' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER g 21 " --> pdb=" O SER g 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS g 25 " --> pdb=" O SER g 21 " (cutoff:3.500A) Processing helix chain 'g' and resid 42 through 98 removed outlier: 4.022A pdb=" N LYS g 51 " --> pdb=" O ALA g 47 " (cutoff:3.500A) Processing helix chain 'g' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE g 112 " --> pdb=" O ASP g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 139 through 143 removed outlier: 3.674A pdb=" N TYR g 142 " --> pdb=" O ASP g 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS g 143 " --> pdb=" O GLY g 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 139 through 143' Processing helix chain 'g' and resid 148 through 152 removed outlier: 3.667A pdb=" N GLN g 152 " --> pdb=" O PRO g 149 " (cutoff:3.500A) Processing helix chain 'g' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU g 235 " --> pdb=" O GLN g 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY g 236 " --> pdb=" O ARG g 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA g 237 " --> pdb=" O ALA g 233 " (cutoff:3.500A) Processing helix chain 'g' and resid 267 through 293 Processing helix chain 'g' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL g 299 " --> pdb=" O GLN g 295 " (cutoff:3.500A) Processing helix chain 'h' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER h 21 " --> pdb=" O SER h 17 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS h 25 " --> pdb=" O SER h 21 " (cutoff:3.500A) Processing helix chain 'h' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS h 51 " --> pdb=" O ALA h 47 " (cutoff:3.500A) Processing helix chain 'h' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE h 112 " --> pdb=" O ASP h 108 " (cutoff:3.500A) Processing helix chain 'h' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR h 142 " --> pdb=" O ASP h 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS h 143 " --> pdb=" O GLY h 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 139 through 143' Processing helix chain 'h' and resid 148 through 152 removed outlier: 3.667A pdb=" N GLN h 152 " --> pdb=" O PRO h 149 " (cutoff:3.500A) Processing helix chain 'h' and resid 213 through 264 removed outlier: 3.595A pdb=" N LEU h 235 " --> pdb=" O GLN h 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY h 236 " --> pdb=" O ARG h 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA h 237 " --> pdb=" O ALA h 233 " (cutoff:3.500A) Processing helix chain 'h' and resid 267 through 293 Processing helix chain 'h' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL h 299 " --> pdb=" O GLN h 295 " (cutoff:3.500A) Processing helix chain 'i' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER i 21 " --> pdb=" O SER i 17 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS i 25 " --> pdb=" O SER i 21 " (cutoff:3.500A) Processing helix chain 'i' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS i 51 " --> pdb=" O ALA i 47 " (cutoff:3.500A) Processing helix chain 'i' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE i 112 " --> pdb=" O ASP i 108 " (cutoff:3.500A) Processing helix chain 'i' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR i 142 " --> pdb=" O ASP i 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS i 143 " --> pdb=" O GLY i 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 139 through 143' Processing helix chain 'i' and resid 148 through 152 removed outlier: 3.666A pdb=" N GLN i 152 " --> pdb=" O PRO i 149 " (cutoff:3.500A) Processing helix chain 'i' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU i 235 " --> pdb=" O GLN i 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY i 236 " --> pdb=" O ARG i 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA i 237 " --> pdb=" O ALA i 233 " (cutoff:3.500A) Processing helix chain 'i' and resid 267 through 293 Processing helix chain 'i' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL i 299 " --> pdb=" O GLN i 295 " (cutoff:3.500A) Processing helix chain 'j' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER j 21 " --> pdb=" O SER j 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS j 25 " --> pdb=" O SER j 21 " (cutoff:3.500A) Processing helix chain 'j' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS j 51 " --> pdb=" O ALA j 47 " (cutoff:3.500A) Processing helix chain 'j' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE j 112 " --> pdb=" O ASP j 108 " (cutoff:3.500A) Processing helix chain 'j' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR j 142 " --> pdb=" O ASP j 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS j 143 " --> pdb=" O GLY j 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 139 through 143' Processing helix chain 'j' and resid 148 through 152 removed outlier: 3.667A pdb=" N GLN j 152 " --> pdb=" O PRO j 149 " (cutoff:3.500A) Processing helix chain 'j' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU j 235 " --> pdb=" O GLN j 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY j 236 " --> pdb=" O ARG j 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA j 237 " --> pdb=" O ALA j 233 " (cutoff:3.500A) Processing helix chain 'j' and resid 267 through 293 Processing helix chain 'j' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL j 299 " --> pdb=" O GLN j 295 " (cutoff:3.500A) Processing helix chain 'k' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER k 21 " --> pdb=" O SER k 17 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS k 25 " --> pdb=" O SER k 21 " (cutoff:3.500A) Processing helix chain 'k' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS k 51 " --> pdb=" O ALA k 47 " (cutoff:3.500A) Processing helix chain 'k' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE k 112 " --> pdb=" O ASP k 108 " (cutoff:3.500A) Processing helix chain 'k' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR k 142 " --> pdb=" O ASP k 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS k 143 " --> pdb=" O GLY k 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'k' and resid 139 through 143' Processing helix chain 'k' and resid 148 through 152 removed outlier: 3.666A pdb=" N GLN k 152 " --> pdb=" O PRO k 149 " (cutoff:3.500A) Processing helix chain 'k' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU k 235 " --> pdb=" O GLN k 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY k 236 " --> pdb=" O ARG k 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA k 237 " --> pdb=" O ALA k 233 " (cutoff:3.500A) Processing helix chain 'k' and resid 267 through 293 Processing helix chain 'k' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL k 299 " --> pdb=" O GLN k 295 " (cutoff:3.500A) Processing helix chain 'l' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER l 21 " --> pdb=" O SER l 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS l 25 " --> pdb=" O SER l 21 " (cutoff:3.500A) Processing helix chain 'l' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS l 51 " --> pdb=" O ALA l 47 " (cutoff:3.500A) Processing helix chain 'l' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE l 112 " --> pdb=" O ASP l 108 " (cutoff:3.500A) Processing helix chain 'l' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR l 142 " --> pdb=" O ASP l 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS l 143 " --> pdb=" O GLY l 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 139 through 143' Processing helix chain 'l' and resid 148 through 152 removed outlier: 3.667A pdb=" N GLN l 152 " --> pdb=" O PRO l 149 " (cutoff:3.500A) Processing helix chain 'l' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU l 235 " --> pdb=" O GLN l 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY l 236 " --> pdb=" O ARG l 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA l 237 " --> pdb=" O ALA l 233 " (cutoff:3.500A) Processing helix chain 'l' and resid 267 through 293 Processing helix chain 'l' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL l 299 " --> pdb=" O GLN l 295 " (cutoff:3.500A) Processing helix chain 'm' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER m 21 " --> pdb=" O SER m 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS m 25 " --> pdb=" O SER m 21 " (cutoff:3.500A) Processing helix chain 'm' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS m 51 " --> pdb=" O ALA m 47 " (cutoff:3.500A) Processing helix chain 'm' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE m 112 " --> pdb=" O ASP m 108 " (cutoff:3.500A) Processing helix chain 'm' and resid 139 through 143 removed outlier: 3.674A pdb=" N TYR m 142 " --> pdb=" O ASP m 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS m 143 " --> pdb=" O GLY m 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 139 through 143' Processing helix chain 'm' and resid 148 through 152 removed outlier: 3.666A pdb=" N GLN m 152 " --> pdb=" O PRO m 149 " (cutoff:3.500A) Processing helix chain 'm' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU m 235 " --> pdb=" O GLN m 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY m 236 " --> pdb=" O ARG m 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA m 237 " --> pdb=" O ALA m 233 " (cutoff:3.500A) Processing helix chain 'm' and resid 267 through 293 Processing helix chain 'm' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL m 299 " --> pdb=" O GLN m 295 " (cutoff:3.500A) Processing helix chain 'n' and resid 10 through 31 removed outlier: 3.889A pdb=" N SER n 21 " --> pdb=" O SER n 17 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS n 25 " --> pdb=" O SER n 21 " (cutoff:3.500A) Processing helix chain 'n' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS n 51 " --> pdb=" O ALA n 47 " (cutoff:3.500A) Processing helix chain 'n' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE n 112 " --> pdb=" O ASP n 108 " (cutoff:3.500A) Processing helix chain 'n' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR n 142 " --> pdb=" O ASP n 139 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS n 143 " --> pdb=" O GLY n 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 139 through 143' Processing helix chain 'n' and resid 148 through 152 removed outlier: 3.666A pdb=" N GLN n 152 " --> pdb=" O PRO n 149 " (cutoff:3.500A) Processing helix chain 'n' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU n 235 " --> pdb=" O GLN n 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY n 236 " --> pdb=" O ARG n 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA n 237 " --> pdb=" O ALA n 233 " (cutoff:3.500A) Processing helix chain 'n' and resid 267 through 293 Processing helix chain 'n' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL n 299 " --> pdb=" O GLN n 295 " (cutoff:3.500A) Processing helix chain 'o' and resid 10 through 31 removed outlier: 3.888A pdb=" N SER o 21 " --> pdb=" O SER o 17 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LYS o 25 " --> pdb=" O SER o 21 " (cutoff:3.500A) Processing helix chain 'o' and resid 42 through 98 removed outlier: 4.023A pdb=" N LYS o 51 " --> pdb=" O ALA o 47 " (cutoff:3.500A) Processing helix chain 'o' and resid 106 through 130 removed outlier: 4.347A pdb=" N ILE o 112 " --> pdb=" O ASP o 108 " (cutoff:3.500A) Processing helix chain 'o' and resid 139 through 143 removed outlier: 3.675A pdb=" N TYR o 142 " --> pdb=" O ASP o 139 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS o 143 " --> pdb=" O GLY o 140 " (cutoff:3.500A) No H-bonds generated for 'chain 'o' and resid 139 through 143' Processing helix chain 'o' and resid 148 through 152 removed outlier: 3.667A pdb=" N GLN o 152 " --> pdb=" O PRO o 149 " (cutoff:3.500A) Processing helix chain 'o' and resid 213 through 264 removed outlier: 3.594A pdb=" N LEU o 235 " --> pdb=" O GLN o 231 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY o 236 " --> pdb=" O ARG o 232 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ALA o 237 " --> pdb=" O ALA o 233 " (cutoff:3.500A) Processing helix chain 'o' and resid 267 through 293 Processing helix chain 'o' and resid 295 through 304 removed outlier: 3.540A pdb=" N VAL o 299 " --> pdb=" O GLN o 295 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 131 through 132 Processing sheet with id=AA2, first strand: chain 'A' and resid 157 through 158 Processing sheet with id=AA3, first strand: chain 'B' and resid 131 through 132 Processing sheet with id=AA4, first strand: chain 'B' and resid 157 through 158 Processing sheet with id=AA5, first strand: chain 'C' and resid 131 through 132 Processing sheet with id=AA6, first strand: chain 'C' and resid 157 through 158 Processing sheet with id=AA7, first strand: chain 'D' and resid 131 through 132 Processing sheet with id=AA8, first strand: chain 'D' and resid 157 through 158 Processing sheet with id=AA9, first strand: chain 'E' and resid 131 through 132 Processing sheet with id=AB1, first strand: chain 'E' and resid 157 through 158 Processing sheet with id=AB2, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AB3, first strand: chain 'F' and resid 157 through 158 Processing sheet with id=AB4, first strand: chain 'G' and resid 131 through 132 Processing sheet with id=AB5, first strand: chain 'G' and resid 157 through 158 Processing sheet with id=AB6, first strand: chain 'H' and resid 131 through 132 Processing sheet with id=AB7, first strand: chain 'H' and resid 157 through 158 Processing sheet with id=AB8, first strand: chain 'I' and resid 131 through 132 Processing sheet with id=AB9, first strand: chain 'I' and resid 157 through 158 Processing sheet with id=AC1, first strand: chain 'J' and resid 131 through 132 Processing sheet with id=AC2, first strand: chain 'J' and resid 157 through 158 Processing sheet with id=AC3, first strand: chain 'K' and resid 131 through 132 Processing sheet with id=AC4, first strand: chain 'K' and resid 157 through 158 Processing sheet with id=AC5, first strand: chain 'L' and resid 131 through 132 Processing sheet with id=AC6, first strand: chain 'L' and resid 157 through 158 Processing sheet with id=AC7, first strand: chain 'M' and resid 131 through 132 Processing sheet with id=AC8, first strand: chain 'M' and resid 157 through 158 Processing sheet with id=AC9, first strand: chain 'N' and resid 131 through 132 Processing sheet with id=AD1, first strand: chain 'N' and resid 157 through 158 Processing sheet with id=AD2, first strand: chain 'O' and resid 131 through 132 Processing sheet with id=AD3, first strand: chain 'O' and resid 157 through 158 Processing sheet with id=AD4, first strand: chain 'P' and resid 131 through 132 Processing sheet with id=AD5, first strand: chain 'P' and resid 157 through 158 Processing sheet with id=AD6, first strand: chain 'Q' and resid 131 through 132 Processing sheet with id=AD7, first strand: chain 'Q' and resid 157 through 158 Processing sheet with id=AD8, first strand: chain 'R' and resid 131 through 132 Processing sheet with id=AD9, first strand: chain 'R' and resid 157 through 158 Processing sheet with id=AE1, first strand: chain 'S' and resid 131 through 132 Processing sheet with id=AE2, first strand: chain 'S' and resid 157 through 158 Processing sheet with id=AE3, first strand: chain 'T' and resid 131 through 132 Processing sheet with id=AE4, first strand: chain 'T' and resid 157 through 158 Processing sheet with id=AE5, first strand: chain 'U' and resid 131 through 132 Processing sheet with id=AE6, first strand: chain 'U' and resid 157 through 158 Processing sheet with id=AE7, first strand: chain 'V' and resid 131 through 132 Processing sheet with id=AE8, first strand: chain 'V' and resid 157 through 158 Processing sheet with id=AE9, first strand: chain 'W' and resid 131 through 132 Processing sheet with id=AF1, first strand: chain 'W' and resid 157 through 158 Processing sheet with id=AF2, first strand: chain 'X' and resid 131 through 132 Processing sheet with id=AF3, first strand: chain 'X' and resid 157 through 158 Processing sheet with id=AF4, first strand: chain 'Y' and resid 131 through 132 Processing sheet with id=AF5, first strand: chain 'Y' and resid 157 through 158 Processing sheet with id=AF6, first strand: chain 'Z' and resid 131 through 132 Processing sheet with id=AF7, first strand: chain 'Z' and resid 157 through 158 Processing sheet with id=AF8, first strand: chain 'a' and resid 131 through 132 Processing sheet with id=AF9, first strand: chain 'a' and resid 157 through 158 Processing sheet with id=AG1, first strand: chain 'b' and resid 131 through 132 Processing sheet with id=AG2, first strand: chain 'b' and resid 157 through 158 Processing sheet with id=AG3, first strand: chain 'c' and resid 131 through 132 Processing sheet with id=AG4, first strand: chain 'c' and resid 157 through 158 Processing sheet with id=AG5, first strand: chain 'd' and resid 131 through 132 Processing sheet with id=AG6, first strand: chain 'd' and resid 157 through 158 Processing sheet with id=AG7, first strand: chain 'e' and resid 131 through 132 Processing sheet with id=AG8, first strand: chain 'e' and resid 157 through 158 Processing sheet with id=AG9, first strand: chain 'f' and resid 131 through 132 Processing sheet with id=AH1, first strand: chain 'f' and resid 157 through 158 Processing sheet with id=AH2, first strand: chain 'g' and resid 131 through 132 Processing sheet with id=AH3, first strand: chain 'g' and resid 157 through 158 Processing sheet with id=AH4, first strand: chain 'h' and resid 131 through 132 Processing sheet with id=AH5, first strand: chain 'h' and resid 157 through 158 Processing sheet with id=AH6, first strand: chain 'i' and resid 131 through 132 Processing sheet with id=AH7, first strand: chain 'i' and resid 157 through 158 Processing sheet with id=AH8, first strand: chain 'j' and resid 131 through 132 Processing sheet with id=AH9, first strand: chain 'j' and resid 157 through 158 Processing sheet with id=AI1, first strand: chain 'k' and resid 131 through 132 Processing sheet with id=AI2, first strand: chain 'k' and resid 157 through 158 Processing sheet with id=AI3, first strand: chain 'l' and resid 131 through 132 Processing sheet with id=AI4, first strand: chain 'l' and resid 157 through 158 Processing sheet with id=AI5, first strand: chain 'm' and resid 131 through 132 Processing sheet with id=AI6, first strand: chain 'm' and resid 157 through 158 Processing sheet with id=AI7, first strand: chain 'n' and resid 131 through 132 Processing sheet with id=AI8, first strand: chain 'n' and resid 157 through 158 Processing sheet with id=AI9, first strand: chain 'o' and resid 131 through 132 Processing sheet with id=AJ1, first strand: chain 'o' and resid 157 through 158 6806 hydrogen bonds defined for protein. 20049 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: 33.77 Time building geometry restraints manager: 32.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 32950 1.34 - 1.45: 8457 1.45 - 1.57: 51376 1.57 - 1.69: 41 1.69 - 1.80: 615 Bond restraints: 93439 Sorted by residual: bond pdb=" C ASP W 114 " pdb=" N GLU W 115 " ideal model delta sigma weight residual 1.334 1.384 -0.049 1.27e-02 6.20e+03 1.52e+01 bond pdb=" C ASP U 114 " pdb=" N GLU U 115 " ideal model delta sigma weight residual 1.334 1.384 -0.049 1.27e-02 6.20e+03 1.51e+01 bond pdb=" C ASP P 114 " pdb=" N GLU P 115 " ideal model delta sigma weight residual 1.334 1.384 -0.049 1.27e-02 6.20e+03 1.51e+01 bond pdb=" C ASP J 114 " pdb=" N GLU J 115 " ideal model delta sigma weight residual 1.334 1.384 -0.049 1.27e-02 6.20e+03 1.51e+01 bond pdb=" C ASP I 114 " pdb=" N GLU I 115 " ideal model delta sigma weight residual 1.334 1.384 -0.049 1.27e-02 6.20e+03 1.50e+01 ... (remaining 93434 not shown) Histogram of bond angle deviations from ideal: 97.94 - 104.69: 554 104.69 - 111.45: 40062 111.45 - 118.20: 32956 118.20 - 124.96: 51546 124.96 - 131.71: 957 Bond angle restraints: 126075 Sorted by residual: angle pdb=" N LEU E 197 " pdb=" CA LEU E 197 " pdb=" C LEU E 197 " ideal model delta sigma weight residual 110.80 121.80 -11.00 2.13e+00 2.20e-01 2.67e+01 angle pdb=" N LEU R 197 " pdb=" CA LEU R 197 " pdb=" C LEU R 197 " ideal model delta sigma weight residual 110.80 121.80 -11.00 2.13e+00 2.20e-01 2.66e+01 angle pdb=" N LEU C 197 " pdb=" CA LEU C 197 " pdb=" C LEU C 197 " ideal model delta sigma weight residual 110.80 121.79 -10.99 2.13e+00 2.20e-01 2.66e+01 angle pdb=" N LEU W 197 " pdb=" CA LEU W 197 " pdb=" C LEU W 197 " ideal model delta sigma weight residual 110.80 121.79 -10.99 2.13e+00 2.20e-01 2.66e+01 angle pdb=" N LEU m 197 " pdb=" CA LEU m 197 " pdb=" C LEU m 197 " ideal model delta sigma weight residual 110.80 121.79 -10.99 2.13e+00 2.20e-01 2.66e+01 ... (remaining 126070 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.15: 54901 14.15 - 28.29: 2050 28.29 - 42.44: 1064 42.44 - 56.59: 123 56.59 - 70.73: 123 Dihedral angle restraints: 58261 sinusoidal: 22632 harmonic: 35629 Sorted by residual: dihedral pdb=" CA THR K 200 " pdb=" C THR K 200 " pdb=" N LYS K 201 " pdb=" CA LYS K 201 " ideal model delta harmonic sigma weight residual 180.00 -143.64 -36.36 0 5.00e+00 4.00e-02 5.29e+01 dihedral pdb=" CA THR B 200 " pdb=" C THR B 200 " pdb=" N LYS B 201 " pdb=" CA LYS B 201 " ideal model delta harmonic sigma weight residual -180.00 -143.64 -36.36 0 5.00e+00 4.00e-02 5.29e+01 dihedral pdb=" CA THR M 200 " pdb=" C THR M 200 " pdb=" N LYS M 201 " pdb=" CA LYS M 201 " ideal model delta harmonic sigma weight residual -180.00 -143.64 -36.36 0 5.00e+00 4.00e-02 5.29e+01 ... (remaining 58258 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 8089 0.036 - 0.072: 4538 0.072 - 0.108: 1742 0.108 - 0.144: 391 0.144 - 0.180: 205 Chirality restraints: 14965 Sorted by residual: chirality pdb=" CB ILE E 36 " pdb=" CA ILE E 36 " pdb=" CG1 ILE E 36 " pdb=" CG2 ILE E 36 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" CB ILE b 36 " pdb=" CA ILE b 36 " pdb=" CG1 ILE b 36 " pdb=" CG2 ILE b 36 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.14e-01 chirality pdb=" CB ILE f 36 " pdb=" CA ILE f 36 " pdb=" CG1 ILE f 36 " pdb=" CG2 ILE f 36 " both_signs ideal model delta sigma weight residual False 2.64 2.83 -0.18 2.00e-01 2.50e+01 8.14e-01 ... (remaining 14962 not shown) Planarity restraints: 17097 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA H 106 " 0.015 2.00e-02 2.50e+03 2.97e-02 8.79e+00 pdb=" C ALA H 106 " -0.051 2.00e-02 2.50e+03 pdb=" O ALA H 106 " 0.019 2.00e-02 2.50e+03 pdb=" N THR H 107 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA m 106 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.77e+00 pdb=" C ALA m 106 " 0.051 2.00e-02 2.50e+03 pdb=" O ALA m 106 " -0.019 2.00e-02 2.50e+03 pdb=" N THR m 107 " -0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA o 106 " -0.015 2.00e-02 2.50e+03 2.96e-02 8.75e+00 pdb=" C ALA o 106 " 0.051 2.00e-02 2.50e+03 pdb=" O ALA o 106 " -0.019 2.00e-02 2.50e+03 pdb=" N THR o 107 " -0.017 2.00e-02 2.50e+03 ... (remaining 17094 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.28: 397 2.28 - 2.94: 46359 2.94 - 3.59: 150639 3.59 - 4.25: 229635 4.25 - 4.90: 384728 Nonbonded interactions: 811758 Sorted by model distance: nonbonded pdb=" OD1 ASP H 42 " pdb=" NH2 ARG n 89 " model vdw 1.626 2.520 nonbonded pdb=" OD1 ASP F 42 " pdb=" NH2 ARG l 89 " model vdw 1.627 2.520 nonbonded pdb=" NH2 ARG I 89 " pdb=" OD1 ASP o 42 " model vdw 1.627 2.520 nonbonded pdb=" OD1 ASP A 42 " pdb=" NH2 ARG f 89 " model vdw 1.627 2.520 nonbonded pdb=" NH2 ARG G 89 " pdb=" OD1 ASP m 42 " model vdw 1.627 2.520 ... (remaining 811753 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 328 5.16 5 C 56211 2.51 5 N 16974 2.21 5 O 19434 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 18.920 Check model and map are aligned: 1.030 Convert atoms to be neutral: 0.590 Process input model: 182.310 Find NCS groups from input model: 5.030 Set up NCS constraints: 0.890 Set refine NCS operators: 0.000 Set scattering table: 0.030 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 216.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 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 : 0.010 0.105 93439 Z= 0.674 Angle : 1.193 14.687 126075 Z= 0.659 Chirality : 0.052 0.180 14965 Planarity : 0.006 0.059 17097 Dihedral : 11.040 70.732 35055 Min Nonbonded Distance : 1.626 Molprobity Statistics. All-atom Clashscore : 13.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.00 % 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: -4.67 (0.06), residues: 12300 helix: -2.47 (0.04), residues: 8036 sheet: -2.86 (0.17), residues: 410 loop : -4.21 (0.09), residues: 3854 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24600 Ramachandran restraints generated. 12300 Oldfield, 0 Emsley, 12300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24600 Ramachandran restraints generated. 12300 Oldfield, 0 Emsley, 12300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2950 residues out of total 10004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 2909 time to evaluate : 8.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 26 residues processed: 2950 average time/residue: 0.8889 time to fit residues: 4352.9909 Evaluate side-chains 1294 residues out of total 10004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1268 time to evaluate : 8.213 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.7222 time to fit residues: 45.2550 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1230 random chunks: chunk 1038 optimal weight: 0.0970 chunk 932 optimal weight: 5.9990 chunk 517 optimal weight: 0.9990 chunk 318 optimal weight: 3.9990 chunk 628 optimal weight: 6.9990 chunk 498 optimal weight: 6.9990 chunk 964 optimal weight: 0.9990 chunk 373 optimal weight: 10.0000 chunk 586 optimal weight: 1.9990 chunk 717 optimal weight: 5.9990 chunk 1116 optimal weight: 5.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 ASN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 248 ASN A 298 ASN B 4 ASN B 26 ASN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN C 5 HIS C 26 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 248 ASN C 298 ASN D 4 ASN D 26 ASN D 37 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN D 248 ASN D 298 ASN E 4 ASN E 37 ASN E 67 GLN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 248 ASN F 5 HIS F 26 ASN F 151 ASN F 152 GLN F 248 ASN F 298 ASN G 26 ASN G 151 ASN ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 248 ASN G 298 ASN H 5 HIS H 26 ASN ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 248 ASN H 298 ASN I 26 ASN ** I 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 248 ASN I 298 ASN J 5 HIS J 26 ASN ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 248 ASN J 298 ASN ** K 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 248 ASN K 298 ASN L 4 ASN L 5 HIS L 26 ASN ** L 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 248 ASN L 298 ASN M 26 ASN ** M 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 248 ASN ** N 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 26 ASN ** N 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 248 ASN O 26 ASN ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 248 ASN O 298 ASN P 26 ASN ** P 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 248 ASN ** Q 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 26 ASN ** Q 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 248 ASN Q 298 ASN ** R 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 26 ASN R 37 ASN ** R 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 248 ASN R 298 ASN S 4 ASN S 5 HIS S 37 ASN S 151 ASN ** S 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 248 ASN T 5 HIS T 26 ASN ** T 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 248 ASN U 5 HIS U 26 ASN ** U 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 298 ASN V 5 HIS V 26 ASN V 74 GLN ** V 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 248 ASN V 298 ASN W 26 ASN ** W 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 248 ASN W 298 ASN X 5 HIS X 26 ASN X 67 GLN ** X 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 248 ASN X 298 ASN Y 26 ASN ** Y 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 248 ASN Y 298 ASN Z 5 HIS Z 26 ASN ** Z 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 248 ASN Z 298 ASN a 4 ASN a 55 GLN a 152 GLN a 162 ASN a 239 GLN a 248 ASN a 298 ASN b 5 HIS ** b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 298 ASN c 26 ASN c 37 ASN c 67 GLN c 151 ASN ** c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 248 ASN c 298 ASN d 26 ASN d 151 ASN ** d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 4 ASN e 5 HIS e 26 ASN ** e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 248 ASN f 26 ASN f 65 ASN ** f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 248 ASN g 4 ASN g 5 HIS g 26 ASN g 37 ASN ** g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 239 GLN g 248 ASN g 298 ASN h 5 HIS h 26 ASN h 65 ASN h 67 GLN h 151 ASN ** h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 248 ASN i 37 ASN ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 248 ASN i 298 ASN j 5 HIS j 26 ASN j 65 ASN j 248 ASN k 4 ASN k 5 HIS k 26 ASN k 37 ASN ** k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 244 HIS k 248 ASN k 298 ASN l 26 ASN ** l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 248 ASN m 37 ASN m 151 ASN ** m 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 248 ASN m 298 ASN n 26 ASN ** n 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 248 ASN o 26 ASN o 37 ASN o 151 ASN ** o 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 248 ASN Total number of N/Q/H flips: 158 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 93439 Z= 0.222 Angle : 0.760 11.158 126075 Z= 0.393 Chirality : 0.044 0.382 14965 Planarity : 0.005 0.066 17097 Dihedral : 7.241 61.884 12997 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.02 % Favored : 90.65 % Rotamer Outliers : 2.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.82 (0.07), residues: 12300 helix: 0.84 (0.05), residues: 8036 sheet: -2.64 (0.19), residues: 410 loop : -3.39 (0.11), residues: 3854 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24600 Ramachandran restraints generated. 12300 Oldfield, 0 Emsley, 12300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24600 Ramachandran restraints generated. 12300 Oldfield, 0 Emsley, 12300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2032 residues out of total 10004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 287 poor density : 1745 time to evaluate : 8.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 287 outliers final: 149 residues processed: 1949 average time/residue: 0.8175 time to fit residues: 2740.2840 Evaluate side-chains 1296 residues out of total 10004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 149 poor density : 1147 time to evaluate : 8.346 Switching outliers to nearest non-outliers outliers start: 149 outliers final: 0 residues processed: 149 average time/residue: 0.6391 time to fit residues: 193.8970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1230 random chunks: chunk 620 optimal weight: 5.9990 chunk 346 optimal weight: 1.9990 chunk 929 optimal weight: 3.9990 chunk 760 optimal weight: 0.4980 chunk 308 optimal weight: 7.9990 chunk 1118 optimal weight: 10.0000 chunk 1208 optimal weight: 0.8980 chunk 996 optimal weight: 3.9990 chunk 1109 optimal weight: 3.9990 chunk 381 optimal weight: 10.0000 chunk 897 optimal weight: 6.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 151 ASN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 298 ASN B 37 ASN B 96 GLN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 248 ASN ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 37 ASN C 96 GLN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 4 ASN ** D 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 14 ASN E 151 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN G 291 GLN G 298 ASN ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 5 HIS ** I 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 ASN J 96 GLN J 128 ASN ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 298 ASN ** L 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 5 HIS ** M 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 ASN N 151 ASN ** N 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 37 ASN ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 5 HIS P 37 ASN ** P 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 4 ASN ** Q 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 ASN Q 96 GLN ** Q 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 4 ASN ** R 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 298 ASN T 5 HIS ** T 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 5 HIS U 128 ASN ** U 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 162 ASN V 5 HIS V 65 ASN ** V 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 298 ASN ** W 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 84 HIS ** W 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 240 ASN X 5 HIS ** X 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 239 GLN Z 5 HIS ** Z 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 96 GLN a 162 ASN b 5 HIS ** b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 294 GLN c 4 ASN c 96 GLN ** c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 298 ASN d 37 ASN ** d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 248 ASN e 37 ASN ** e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 239 GLN e 240 ASN e 294 GLN f 37 ASN f 65 ASN f 96 GLN f 103 GLN ** f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 294 GLN ** g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 37 ASN h 96 GLN ** h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 96 GLN ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 37 ASN j 298 ASN k 37 ASN ** k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 37 ASN n 65 ASN ** n 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 294 GLN n 298 ASN ** o 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7846 moved from start: 0.4619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 93439 Z= 0.216 Angle : 0.694 12.285 126075 Z= 0.358 Chirality : 0.043 0.397 14965 Planarity : 0.003 0.035 17097 Dihedral : 6.851 65.337 12997 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.15 % Allowed : 8.75 % Favored : 91.11 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.31 (0.08), residues: 12300 helix: 1.96 (0.06), residues: 7913 sheet: -2.64 (0.20), residues: 410 loop : -3.36 (0.10), residues: 3977 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24600 Ramachandran restraints generated. 12300 Oldfield, 0 Emsley, 12300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24600 Ramachandran restraints generated. 12300 Oldfield, 0 Emsley, 12300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1467 residues out of total 10004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 123 poor density : 1344 time to evaluate : 8.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 123 outliers final: 45 residues processed: 1452 average time/residue: 0.7914 time to fit residues: 2009.7552 Evaluate side-chains 1140 residues out of total 10004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 1095 time to evaluate : 8.238 Switching outliers to nearest non-outliers outliers start: 45 outliers final: 0 residues processed: 45 average time/residue: 0.6815 time to fit residues: 67.9809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1230 random chunks: chunk 1105 optimal weight: 5.9990 chunk 841 optimal weight: 9.9990 chunk 580 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 534 optimal weight: 9.9990 chunk 751 optimal weight: 5.9990 chunk 1123 optimal weight: 7.9990 chunk 1188 optimal weight: 0.8980 chunk 586 optimal weight: 6.9990 chunk 1064 optimal weight: 0.0000 chunk 320 optimal weight: 4.9990 overall best weight: 3.5790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN A 291 GLN B 128 ASN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 291 GLN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 291 GLN ** D 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 291 GLN ** E 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 ASN E 291 GLN E 298 ASN F 37 ASN F 128 ASN F 151 ASN ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 291 GLN ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 291 GLN ** I 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 291 GLN ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 244 HIS J 291 GLN J 298 ASN K 128 ASN ** K 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 278 ASN K 291 GLN L 291 GLN L 298 ASN M 5 HIS M 37 ASN ** M 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 291 GLN M 294 GLN M 298 ASN ** N 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 162 ASN N 291 GLN N 295 GLN ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 291 GLN P 96 GLN ** P 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 283 GLN P 291 GLN ** Q 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 291 GLN ** R 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 291 GLN S 151 ASN ** S 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 291 GLN T 37 ASN ** T 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 291 GLN U 37 ASN ** U 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 291 GLN V 5 HIS V 37 ASN V 128 ASN ** V 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 291 GLN V 298 ASN ** W 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 37 ASN ** W 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 291 GLN X 5 HIS X 37 ASN X 65 ASN X 128 ASN ** X 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 291 GLN Y 37 ASN Y 151 ASN ** Y 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 298 ASN Z 5 HIS Z 37 ASN ** Z 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 291 GLN a 37 ASN a 278 ASN a 291 GLN a 294 GLN a 298 ASN b 5 HIS ** b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 248 ASN c 128 ASN c 151 ASN ** c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 239 GLN c 291 GLN d 65 ASN d 128 ASN d 151 ASN ** d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 291 GLN ** e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 294 GLN ** f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 291 GLN g 5 HIS ** g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 151 ASN ** h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 291 GLN ** i 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 294 GLN i 298 ASN j 5 HIS j 291 GLN ** k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 37 ASN ** l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 231 GLN l 291 GLN ** m 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 291 GLN ** o 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 89 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 93439 Z= 0.251 Angle : 0.682 11.387 126075 Z= 0.356 Chirality : 0.043 0.459 14965 Planarity : 0.003 0.043 17097 Dihedral : 6.558 62.105 12997 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.05 % Favored : 90.69 % Rotamer Outliers : 2.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.08), residues: 12300 helix: 2.26 (0.05), residues: 7913 sheet: -2.37 (0.21), residues: 410 loop : -3.36 (0.10), residues: 3977 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24600 Ramachandran restraints generated. 12300 Oldfield, 0 Emsley, 12300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24600 Ramachandran restraints generated. 12300 Oldfield, 0 Emsley, 12300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1467 residues out of total 10004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1241 time to evaluate : 8.554 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: 226 outliers final: 114 residues processed: 1416 average time/residue: 0.7817 time to fit residues: 1959.2809 Evaluate side-chains 1154 residues out of total 10004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 114 poor density : 1040 time to evaluate : 8.353 Switching outliers to nearest non-outliers outliers start: 114 outliers final: 0 residues processed: 114 average time/residue: 0.6488 time to fit residues: 151.5740 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1230 random chunks: chunk 990 optimal weight: 10.0000 chunk 674 optimal weight: 2.9990 chunk 17 optimal weight: 30.0000 chunk 885 optimal weight: 7.9990 chunk 490 optimal weight: 9.9990 chunk 1014 optimal weight: 5.9990 chunk 821 optimal weight: 5.9990 chunk 1 optimal weight: 10.0000 chunk 607 optimal weight: 5.9990 chunk 1067 optimal weight: 20.0000 chunk 300 optimal weight: 0.1980 overall best weight: 4.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 128 ASN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN E 4 ASN E 26 ASN E 128 ASN E 151 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 278 ASN E 298 ASN F 37 ASN ** F 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 96 GLN G 110 GLN ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN G 294 GLN G 298 ASN H 4 ASN H 128 ASN ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN ** I 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 283 GLN ** M 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 298 ASN N 151 ASN ** N 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 5 HIS P 128 ASN ** P 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 128 ASN ** Q 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 294 GLN R 128 ASN ** R 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 96 GLN ** S 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 96 GLN ** T 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 162 ASN U 248 ASN U 294 GLN U 298 ASN V 5 HIS ** V 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 128 ASN ** Y 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 5 HIS ** Z 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 294 GLN Z 298 ASN a 128 ASN b 5 HIS ** b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 294 GLN e 298 ASN f 110 GLN ** f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 55 GLN ** g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 162 ASN ** g 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 5 HIS h 128 ASN ** h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 4 ASN ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 298 ASN j 5 HIS j 67 GLN ** k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 128 ASN ** l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 151 ASN ** m 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 128 ASN ** n 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 5 HIS o 151 ASN ** o 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 55 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.5586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.058 93439 Z= 0.275 Angle : 0.687 13.708 126075 Z= 0.357 Chirality : 0.042 0.513 14965 Planarity : 0.003 0.036 17097 Dihedral : 6.457 61.940 12997 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 17.72 Ramachandran Plot: Outliers : 0.34 % Allowed : 9.05 % Favored : 90.61 % Rotamer Outliers : 2.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.08), residues: 12300 helix: 2.34 (0.05), residues: 7913 sheet: -2.34 (0.21), residues: 410 loop : -3.36 (0.10), residues: 3977 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24600 Ramachandran restraints generated. 12300 Oldfield, 0 Emsley, 12300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24600 Ramachandran restraints generated. 12300 Oldfield, 0 Emsley, 12300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1398 residues out of total 10004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1197 time to evaluate : 8.435 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: 201 outliers final: 59 residues processed: 1383 average time/residue: 0.7523 time to fit residues: 1851.8846 Evaluate side-chains 1148 residues out of total 10004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 1089 time to evaluate : 8.487 Switching outliers to nearest non-outliers outliers start: 59 outliers final: 0 residues processed: 59 average time/residue: 0.6605 time to fit residues: 84.4286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1230 random chunks: chunk 400 optimal weight: 3.9990 chunk 1070 optimal weight: 0.0870 chunk 235 optimal weight: 20.0000 chunk 698 optimal weight: 6.9990 chunk 293 optimal weight: 10.0000 chunk 1190 optimal weight: 2.9990 chunk 987 optimal weight: 5.9990 chunk 551 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 393 optimal weight: 0.9990 chunk 624 optimal weight: 5.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 294 GLN ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 128 ASN ** C 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 4 ASN H 37 ASN ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 26 ASN K 37 ASN ** K 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 278 ASN ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 128 ASN N 151 ASN ** N 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 128 ASN ** S 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 5 HIS ** V 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 298 ASN ** W 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 239 GLN Z 5 HIS ** Z 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 5 HIS b 37 ASN ** b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 248 ASN c 55 GLN ** c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 162 ASN c 239 GLN ** d 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 239 GLN ** f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 4 ASN ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 294 GLN i 298 ASN j 5 HIS j 67 GLN ** k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 93439 Z= 0.200 Angle : 0.658 11.906 126075 Z= 0.337 Chirality : 0.040 0.345 14965 Planarity : 0.003 0.028 17097 Dihedral : 6.341 65.604 12997 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 15.95 Ramachandran Plot: Outliers : 0.40 % Allowed : 8.81 % Favored : 90.79 % Rotamer Outliers : 1.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.12 (0.08), residues: 12300 helix: 2.69 (0.05), residues: 7913 sheet: -2.35 (0.22), residues: 410 loop : -3.29 (0.10), residues: 3977 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24600 Ramachandran restraints generated. 12300 Oldfield, 0 Emsley, 12300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24600 Ramachandran restraints generated. 12300 Oldfield, 0 Emsley, 12300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1444 residues out of total 10004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1273 time to evaluate : 8.297 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 outliers start: 171 outliers final: 74 residues processed: 1406 average time/residue: 0.8003 time to fit residues: 1961.5150 Evaluate side-chains 1173 residues out of total 10004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1099 time to evaluate : 8.253 Switching outliers to nearest non-outliers outliers start: 74 outliers final: 0 residues processed: 74 average time/residue: 0.6521 time to fit residues: 102.5554 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1230 random chunks: chunk 1147 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 678 optimal weight: 0.0470 chunk 869 optimal weight: 0.0470 chunk 673 optimal weight: 8.9990 chunk 1001 optimal weight: 5.9990 chunk 664 optimal weight: 6.9990 chunk 1185 optimal weight: 1.9990 chunk 741 optimal weight: 5.9990 chunk 722 optimal weight: 0.4980 chunk 547 optimal weight: 5.9990 overall best weight: 0.7178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 55 GLN C 152 GLN C 162 ASN ** D 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN F 55 GLN F 151 ASN F 162 ASN ** F 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 128 ASN ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 37 ASN K 152 GLN ** K 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 ASN ** M 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 ASN N 152 GLN O 128 ASN O 152 GLN ** O 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 96 GLN ** P 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 ASN ** Q 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 162 ASN Q 291 GLN ** R 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 162 ASN S 152 GLN ** S 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 162 ASN V 5 HIS ** V 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 162 ASN ** W 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 162 ASN ** Y 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 37 ASN ** Z 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 239 GLN b 5 HIS ** b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 152 GLN ** e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 294 GLN ** f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 96 GLN ** g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 5 HIS k 65 ASN ** k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 55 GLN ** m 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 162 ASN ** n 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.6173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 93439 Z= 0.164 Angle : 0.656 14.085 126075 Z= 0.329 Chirality : 0.039 0.319 14965 Planarity : 0.003 0.031 17097 Dihedral : 6.268 70.554 12997 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.38 % Allowed : 8.40 % Favored : 91.22 % Rotamer Outliers : 1.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.08), residues: 12300 helix: 2.72 (0.05), residues: 8200 sheet: -2.34 (0.23), residues: 410 loop : -3.04 (0.10), residues: 3690 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24600 Ramachandran restraints generated. 12300 Oldfield, 0 Emsley, 12300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24600 Ramachandran restraints generated. 12300 Oldfield, 0 Emsley, 12300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1436 residues out of total 10004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 1330 time to evaluate : 8.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 106 outliers final: 22 residues processed: 1422 average time/residue: 0.7832 time to fit residues: 1972.8924 Evaluate side-chains 1127 residues out of total 10004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 1105 time to evaluate : 8.247 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 0 residues processed: 22 average time/residue: 0.6326 time to fit residues: 38.0914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1230 random chunks: chunk 733 optimal weight: 7.9990 chunk 473 optimal weight: 6.9990 chunk 708 optimal weight: 8.9990 chunk 357 optimal weight: 4.9990 chunk 232 optimal weight: 0.9990 chunk 229 optimal weight: 10.0000 chunk 753 optimal weight: 0.7980 chunk 807 optimal weight: 7.9990 chunk 586 optimal weight: 5.9990 chunk 110 optimal weight: 9.9990 chunk 931 optimal weight: 0.8980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 294 GLN D 298 ASN E 4 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 298 ASN F 5 HIS ** F 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 298 ASN ** I 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 298 ASN K 152 GLN ** K 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 4 ASN ** O 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 162 ASN Q 291 GLN R 152 GLN ** S 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 294 GLN S 298 ASN ** T 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 151 ASN T 152 GLN ** U 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 283 GLN ** W 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 HIS ** X 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 162 ASN ** X 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 65 ASN ** Z 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 239 GLN b 5 HIS ** b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 294 GLN ** f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 55 GLN ** h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 162 ASN ** h 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 5 HIS ** k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 65 ASN ** l 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 294 GLN ** m 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 294 GLN o 298 ASN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.6276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 93439 Z= 0.220 Angle : 0.689 13.221 126075 Z= 0.346 Chirality : 0.040 0.335 14965 Planarity : 0.003 0.033 17097 Dihedral : 6.107 64.852 12997 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.39 % Allowed : 8.48 % Favored : 91.13 % Rotamer Outliers : 1.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.40 (0.08), residues: 12300 helix: 2.67 (0.05), residues: 8200 sheet: -2.26 (0.23), residues: 410 loop : -3.04 (0.10), residues: 3690 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24600 Ramachandran restraints generated. 12300 Oldfield, 0 Emsley, 12300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24600 Ramachandran restraints generated. 12300 Oldfield, 0 Emsley, 12300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1291 residues out of total 10004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 132 poor density : 1159 time to evaluate : 8.616 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: 132 outliers final: 78 residues processed: 1246 average time/residue: 0.7789 time to fit residues: 1743.0452 Evaluate side-chains 1157 residues out of total 10004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1079 time to evaluate : 8.255 Switching outliers to nearest non-outliers outliers start: 78 outliers final: 0 residues processed: 78 average time/residue: 0.6468 time to fit residues: 108.0097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1230 random chunks: chunk 1078 optimal weight: 7.9990 chunk 1135 optimal weight: 10.0000 chunk 1036 optimal weight: 10.0000 chunk 1104 optimal weight: 8.9990 chunk 664 optimal weight: 7.9990 chunk 481 optimal weight: 6.9990 chunk 867 optimal weight: 8.9990 chunk 339 optimal weight: 2.9990 chunk 998 optimal weight: 1.9990 chunk 1044 optimal weight: 7.9990 chunk 1100 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 ASN ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 162 ASN ** D 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 4 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 162 ASN ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 ASN ** I 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 298 ASN ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 162 ASN ** L 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 298 ASN O 4 ASN ** O 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 162 ASN Q 14 ASN ** Q 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 162 ASN ** S 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 128 ASN ** U 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 162 ASN ** U 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 162 ASN ** V 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 HIS ** X 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 298 ASN ** Z 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 5 HIS ** b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 248 ASN c 55 GLN ** c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 162 ASN ** d 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 294 GLN d 298 ASN ** e 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 37 ASN ** g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 4 ASN i 26 ASN ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 5 HIS ** j 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 37 ASN ** k 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 55 GLN ** m 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 162 ASN ** m 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7960 moved from start: 0.6351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.068 93439 Z= 0.342 Angle : 0.772 15.212 126075 Z= 0.395 Chirality : 0.045 0.437 14965 Planarity : 0.003 0.037 17097 Dihedral : 6.216 57.955 12997 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.40 % Allowed : 9.33 % Favored : 90.27 % Rotamer Outliers : 0.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.08), residues: 12300 helix: 2.30 (0.05), residues: 8159 sheet: -2.22 (0.22), residues: 410 loop : -3.18 (0.10), residues: 3731 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24600 Ramachandran restraints generated. 12300 Oldfield, 0 Emsley, 12300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24600 Ramachandran restraints generated. 12300 Oldfield, 0 Emsley, 12300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1190 residues out of total 10004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 1126 time to evaluate : 8.457 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 64 outliers final: 30 residues processed: 1179 average time/residue: 0.7594 time to fit residues: 1605.3173 Evaluate side-chains 1050 residues out of total 10004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1020 time to evaluate : 8.339 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 0 residues processed: 30 average time/residue: 0.6332 time to fit residues: 47.5378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1230 random chunks: chunk 725 optimal weight: 3.9990 chunk 1168 optimal weight: 7.9990 chunk 713 optimal weight: 3.9990 chunk 554 optimal weight: 10.0000 chunk 812 optimal weight: 4.9990 chunk 1225 optimal weight: 4.9990 chunk 1127 optimal weight: 5.9990 chunk 975 optimal weight: 8.9990 chunk 101 optimal weight: 3.9990 chunk 753 optimal weight: 9.9990 chunk 598 optimal weight: 8.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 GLN ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 151 ASN ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 298 ASN ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 ASN L 67 GLN ** L 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 217 GLN ** O 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** Q 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 162 ASN Q 294 GLN Q 298 ASN R 14 ASN ** S 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 294 GLN ** V 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 HIS ** X 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 4 ASN b 5 HIS ** b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 294 GLN ** f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 37 ASN ** g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 239 GLN g 294 GLN g 298 ASN ** h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 4 ASN ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 5 HIS ** j 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 278 ASN n 65 ASN ** n 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.6461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.076 93439 Z= 0.288 Angle : 0.749 13.412 126075 Z= 0.379 Chirality : 0.043 0.398 14965 Planarity : 0.003 0.030 17097 Dihedral : 6.225 61.303 12997 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.25 % Favored : 90.37 % Rotamer Outliers : 0.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.08), residues: 12300 helix: 2.37 (0.05), residues: 8159 sheet: -2.25 (0.22), residues: 410 loop : -3.19 (0.10), residues: 3731 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 24600 Ramachandran restraints generated. 12300 Oldfield, 0 Emsley, 12300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 24600 Ramachandran restraints generated. 12300 Oldfield, 0 Emsley, 12300 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1131 residues out of total 10004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 1087 time to evaluate : 8.462 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 26 residues processed: 1114 average time/residue: 0.7944 time to fit residues: 1584.9384 Evaluate side-chains 1060 residues out of total 10004 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 1034 time to evaluate : 8.256 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.6608 time to fit residues: 43.9297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1230 random chunks: chunk 775 optimal weight: 20.0000 chunk 1039 optimal weight: 0.0270 chunk 298 optimal weight: 3.9990 chunk 899 optimal weight: 4.9990 chunk 144 optimal weight: 8.9990 chunk 271 optimal weight: 3.9990 chunk 977 optimal weight: 20.0000 chunk 409 optimal weight: 0.9980 chunk 1003 optimal weight: 0.0050 chunk 123 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 overall best weight: 1.8056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 37 ASN ** F 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 217 GLN ** F 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 ASN ** I 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 294 GLN K 298 ASN ** L 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 291 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 4 ASN ** O 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 294 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 298 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 55 GLN ** Q 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 4 ASN ** S 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 294 GLN ** T 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 5 HIS ** X 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 162 ASN ** Z 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 239 GLN b 5 HIS ** b 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 248 ASN c 55 GLN ** c 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 162 ASN ** c 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 239 GLN ** h 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 4 ASN ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 192 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 5 HIS ** j 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 84 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 217 GLN ** l 227 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 65 ASN ** m 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.086440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.076022 restraints weight = 254129.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.078437 restraints weight = 130615.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.080043 restraints weight = 78511.845| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.6610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.052 93439 Z= 0.197 Angle : 0.703 13.617 126075 Z= 0.350 Chirality : 0.041 0.309 14965 Planarity : 0.003 0.035 17097 Dihedral : 6.151 70.871 12997 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 16.24 Ramachandran Plot: Outliers : 0.33 % Allowed : 9.18 % Favored : 90.49 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.08), residues: 12300 helix: 2.72 (0.05), residues: 8200 sheet: -2.31 (0.23), residues: 410 loop : -3.09 (0.10), residues: 3690 =============================================================================== Job complete usr+sys time: 27819.68 seconds wall clock time: 486 minutes 15.54 seconds (29175.54 seconds total)