Starting phenix.real_space_refine (version: dev) on Tue May 24 21:29:25 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pj6_20353/05_2022/6pj6_20353_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pj6_20353/05_2022/6pj6_20353.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pj6_20353/05_2022/6pj6_20353_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pj6_20353/05_2022/6pj6_20353_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pj6_20353/05_2022/6pj6_20353_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pj6_20353/05_2022/6pj6_20353.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pj6_20353/05_2022/6pj6_20353.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pj6_20353/05_2022/6pj6_20353_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pj6_20353/05_2022/6pj6_20353_trim_updated.pdb" } resolution = 2.2 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= -0.035 sd= 2.434 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 "K ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 167": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 189": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 194": "OE1" <-> "OE2" Residue "K ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 64": "OE1" <-> "OE2" Residue "L ARG 77": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 89": "OE1" <-> "OE2" Residue "L ARG 169": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 184": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 25": "OE1" <-> "OE2" Residue "M ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 61": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 102": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 162": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 71": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 92": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 102": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 112": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 115": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 163": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P GLU 55": "OE1" <-> "OE2" Residue "P GLU 70": "OE1" <-> "OE2" Residue "Q GLU 37": "OE1" <-> "OE2" Residue "Q GLU 50": "OE1" <-> "OE2" Residue "R GLU 9": "OE1" <-> "OE2" Residue "R ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 120": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S GLU 106": "OE1" <-> "OE2" Residue "T ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 60": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T GLU 86": "OE1" <-> "OE2" Residue "T ARG 126": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 55": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 114": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 17": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 71": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V GLU 82": "OE1" <-> "OE2" Residue "V ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 25": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 81": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 102": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ARG 53": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ARG 89": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ARG 101": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ARG 109": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z ARG 68": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z ARG 79": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 86": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c GLU 101": "OE1" <-> "OE2" Residue "d GLU 55": "OE1" <-> "OE2" Residue "d PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e ARG 11": "NH1" <-> "NH2" Residue "f ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 11": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f GLU 43": "OE1" <-> "OE2" Residue "f ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g GLU 12": "OE1" <-> "OE2" Residue "g GLU 24": "OE1" <-> "OE2" Residue "g ARG 29": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h ARG 11": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h GLU 37": "OE1" <-> "OE2" Residue "h ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i ARG 10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i GLU 36": "OE1" <-> "OE2" Residue "i ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 14": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 154542 Number of models: 1 Model: "" Number of chains: 67 Chain: "I" Number of atoms: 93260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2898, 93260 Classifications: {'RNA': 2898} Modifications used: {'rna3p': 17, 'rna2p': 7, '3*END': 1, 'rna3p_pur': 1389, 'rna3p_pyr': 1065, 'rna2p_pur': 275, 'rna2p_pyr': 145} Link IDs: {'rna3p': 2470, 'rna2p': 427} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Chain: "J" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 3810 Classifications: {'RNA': 118} Modifications used: {'rna3p_pyr': 48, 'rna2p_pur': 7, 'rna3p_pur': 57, 'rna2p_pyr': 6, '3*END': 1} Link IDs: {'rna3p': 104, 'rna2p': 13} Chain: "K" Number of atoms: 4261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 271, 4237 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Conformer: "B" Number of residues, atoms: 271, 4237 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} bond proxies already assigned to first conformer: 4251 Chain: "L" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3175 Classifications: {'peptide': 209} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "M" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3171 Classifications: {'peptide': 201} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "N" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 2855 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "O" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 2694 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "P" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 2258 Classifications: {'peptide': 149} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "Q" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2007 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "R" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2291 Classifications: {'peptide': 142} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "S" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1950 Classifications: {'peptide': 122} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "T" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2169 Classifications: {'peptide': 144} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "U" Number of atoms: 2219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2219 Classifications: {'peptide': 136} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 1960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1960 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "W" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1815 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "X" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1879 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Y" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1967 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "Z" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1582 Classifications: {'peptide': 103} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "a" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1779 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "b" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1546 Classifications: {'peptide': 93} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "c" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 1611 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "d" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1533 Classifications: {'peptide': 94} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "e" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1156 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "f" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1277 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "g" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1032 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "h" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 937 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "i" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 902 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "j" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 849 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "k" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 795 Classifications: {'peptide': 46} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "l" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1076 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "m" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 642 Classifications: {'peptide': 38} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "I" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 182 Unusual residues: {' MG': 182} Classifications: {'undetermined': 182} Link IDs: {None: 181} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' NA': 1, ' MG': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 3347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3347, 3347 Classifications: {'water': 3347} Link IDs: {None: 3346} Chain: "J" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "K" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "L" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "M" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "N" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "O" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "P" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "Q" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "R" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "S" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "T" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "U" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "V" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "W" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "X" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "Y" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "Z" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "a" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "b" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "c" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "d" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "e" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "f" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "g" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "h" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "i" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "j" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "k" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "l" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "m" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A12KZ SG CYS m 11 73.983 171.248 50.600 1.00 53.85 S ATOM A12MB SG CYS m 14 76.756 170.164 53.407 1.00 50.82 S ATOM A12SL SG CYS m 27 74.801 173.710 52.884 1.00 49.16 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG K 203 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG K 203 " occ=0.50 residue: pdb="MG MG I3123 " occ=0.50 residue: pdb="MG MG I3124 " occ=0.50 Time building chain proxies: 55.93, per 1000 atoms: 0.36 Number of scatterers: 154542 At special positions: 0 Unit cell: (186.594, 228.516, 226.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 1 29.99 S 80 16.00 P 3016 15.00 Mg 185 11.99 Na 1 11.00 O 29478 8.00 N 16917 7.00 C 45240 6.00 H 59624 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 103.05 Conformation dependent library (CDL) restraints added in 5.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination Zn2+ tetrahedral coordination pdb=" ZN m 101 " pdb="ZN ZN m 101 " - pdb=" ND1 HIS m 33 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 14 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 11 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 27 " Number of angles added : 3 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6122 Finding SS restraints... Warning!!! ksdssp method is not applicable forstructures with more than 99999 atoms! Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 94 helices and 45 sheets defined 33.3% alpha, 19.0% beta 957 base pairs and 1553 stacking pairs defined. Time for finding SS restraints: 68.87 Creating SS restraints... Processing helix chain 'K' and resid 10 through 17 removed outlier: 7.610A pdb=" N HIS K 15 " --> pdb=" O PRO K 11 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL K 17 " --> pdb=" O ARG K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 136 Proline residue: K 136 - end of helix Processing helix chain 'K' and resid 207 through 215 removed outlier: 4.166A pdb=" N ALA K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG K 214 " --> pdb=" O ALA K 210 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY K 215 " --> pdb=" O ALA K 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 226 removed outlier: 3.657A pdb=" N MET K 225 " --> pdb=" O ARG K 221 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ASN K 226 " --> pdb=" O GLY K 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 221 through 226' Processing helix chain 'K' and resid 260 through 268 removed outlier: 6.556A pdb=" N ASP K 264 " --> pdb=" O ASN K 260 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LYS K 265 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PHE K 266 " --> pdb=" O ARG K 262 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE K 267 " --> pdb=" O THR K 263 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N VAL K 268 " --> pdb=" O ASP K 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 260 through 268' Processing helix chain 'K' and resid 197 through 202 removed outlier: 4.011A pdb=" N MET K 201 " --> pdb=" O ALA K 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 61 removed outlier: 5.381A pdb=" N THR L 61 " --> pdb=" O ALA L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 72 removed outlier: 3.590A pdb=" N ALA L 71 " --> pdb=" O HIS L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 103 removed outlier: 4.140A pdb=" N ALA L 102 " --> pdb=" O VAL L 98 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASP L 103 " --> pdb=" O GLU L 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 98 through 103' Processing helix chain 'L' and resid 120 through 125 Processing helix chain 'L' and resid 39 through 44 Processing helix chain 'M' and resid 24 through 40 removed outlier: 3.566A pdb=" N ARG M 40 " --> pdb=" O ALA M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 53 removed outlier: 5.813A pdb=" N THR M 53 " --> pdb=" O ARG M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 116 Processing helix chain 'M' and resid 130 through 142 Processing helix chain 'M' and resid 154 through 163 removed outlier: 4.307A pdb=" N ASN M 163 " --> pdb=" O LEU M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 183 removed outlier: 3.524A pdb=" N PHE M 183 " --> pdb=" O SER M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 201 Processing helix chain 'M' and resid 16 through 21 Processing helix chain 'N' and resid 2 through 11 removed outlier: 3.610A pdb=" N ASP N 6 " --> pdb=" O ALA N 2 " (cutoff:3.500A) Processing helix chain 'N' and resid 12 through 21 removed outlier: 3.607A pdb=" N ASN N 21 " --> pdb=" O MET N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 62 removed outlier: 4.426A pdb=" N LEU N 50 " --> pdb=" O ASP N 46 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP N 51 " --> pdb=" O LYS N 47 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE N 60 " --> pdb=" O ASP N 56 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLY N 62 " --> pdb=" O ALA N 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 111 removed outlier: 4.094A pdb=" N ILE N 106 " --> pdb=" O ARG N 102 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL N 108 " --> pdb=" O ILE N 104 " (cutoff:3.500A) Proline residue: N 109 - end of helix Processing helix chain 'N' and resid 162 through 174 removed outlier: 3.552A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE N 173 " --> pdb=" O LEU N 169 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP N 174 " --> pdb=" O LEU N 170 " (cutoff:3.500A) Processing helix chain 'N' and resid 134 through 139 removed outlier: 3.659A pdb=" N ILE N 137 " --> pdb=" O GLU N 134 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE N 138 " --> pdb=" O GLN N 135 " (cutoff:3.500A) Proline residue: N 139 - end of helix No H-bonds generated for 'chain 'N' and resid 134 through 139' Processing helix chain 'O' and resid 2 through 8 Proline residue: O 8 - end of helix Processing helix chain 'O' and resid 60 through 81 removed outlier: 4.550A pdb=" N GLN O 64 " --> pdb=" O ASP O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 153 removed outlier: 3.851A pdb=" N ILE O 141 " --> pdb=" O ASP O 137 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR O 151 " --> pdb=" O ASP O 147 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG O 152 " --> pdb=" O LEU O 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 28 Processing helix chain 'P' and resid 29 through 34 removed outlier: 4.287A pdb=" N GLY P 34 " --> pdb=" O LEU P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 76 removed outlier: 6.536A pdb=" N ILE P 44 " --> pdb=" O THR P 40 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N GLU P 45 " --> pdb=" O LYS P 41 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE P 47 " --> pdb=" O ASN P 43 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLU P 48 " --> pdb=" O ILE P 44 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG P 50 " --> pdb=" O PHE P 46 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG P 51 " --> pdb=" O PHE P 47 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU P 55 " --> pdb=" O ARG P 51 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLU P 60 " --> pdb=" O ALA P 56 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL P 61 " --> pdb=" O LYS P 57 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU P 62 " --> pdb=" O LEU P 58 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA P 63 " --> pdb=" O ALA P 59 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA P 64 " --> pdb=" O GLU P 60 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASN P 66 " --> pdb=" O LEU P 62 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA P 67 " --> pdb=" O ALA P 63 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA P 69 " --> pdb=" O ALA P 65 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LYS P 71 " --> pdb=" O ALA P 67 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ASN P 73 " --> pdb=" O ALA P 69 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ALA P 74 " --> pdb=" O GLU P 70 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU P 75 " --> pdb=" O LYS P 71 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU P 76 " --> pdb=" O ILE P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 105 removed outlier: 4.705A pdb=" N ILE P 99 " --> pdb=" O GLY P 95 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL P 103 " --> pdb=" O ILE P 99 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR P 104 " --> pdb=" O ALA P 100 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA P 105 " --> pdb=" O ASP P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 116 removed outlier: 3.560A pdb=" N VAL P 115 " --> pdb=" O ALA P 111 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ARG P 116 " --> pdb=" O LYS P 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 111 through 116' Processing helix chain 'Q' and resid 22 through 28 Proline residue: Q 26 - end of helix No H-bonds generated for 'chain 'Q' and resid 22 through 28' Processing helix chain 'Q' and resid 34 through 47 removed outlier: 4.011A pdb=" N LYS Q 40 " --> pdb=" O MET Q 36 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN Q 43 " --> pdb=" O CYS Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 81 removed outlier: 5.358A pdb=" N LEU Q 79 " --> pdb=" O PRO Q 75 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU Q 80 " --> pdb=" O ALA Q 76 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LYS Q 81 " --> pdb=" O ALA Q 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 75 through 81' Processing helix chain 'Q' and resid 102 through 114 removed outlier: 4.657A pdb=" N THR Q 112 " --> pdb=" O GLU Q 108 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS Q 113 " --> pdb=" O ILE Q 109 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA Q 114 " --> pdb=" O ALA Q 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 137 removed outlier: 3.562A pdb=" N ILE Q 129 " --> pdb=" O MET Q 125 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU Q 130 " --> pdb=" O THR Q 126 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR Q 132 " --> pdb=" O SER Q 128 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA Q 133 " --> pdb=" O ILE Q 129 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG Q 134 " --> pdb=" O GLU Q 130 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER Q 135 " --> pdb=" O GLY Q 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 38 removed outlier: 3.705A pdb=" N GLU R 31 " --> pdb=" O ARG R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 96 Processing helix chain 'R' and resid 97 through 110 removed outlier: 4.340A pdb=" N ILE R 101 " --> pdb=" O PRO R 97 " (cutoff:3.500A) Proline residue: R 110 - end of helix Processing helix chain 'R' and resid 112 through 123 removed outlier: 3.566A pdb=" N ARG R 120 " --> pdb=" O ARG R 116 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS R 121 " --> pdb=" O ALA R 117 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU R 122 " --> pdb=" O MET R 118 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LYS R 123 " --> pdb=" O PHE R 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 104 through 109 removed outlier: 4.666A pdb=" N ARG S 108 " --> pdb=" O THR S 104 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N SER S 109 " --> pdb=" O ARG S 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 104 through 109' Processing helix chain 'S' and resid 112 through 119 removed outlier: 3.625A pdb=" N ILE S 116 " --> pdb=" O PHE S 112 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU S 118 " --> pdb=" O LYS S 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 37 through 42 removed outlier: 5.538A pdb=" N SER T 42 " --> pdb=" O GLN T 38 " (cutoff:3.500A) Processing helix chain 'T' and resid 56 through 62 Proline residue: T 62 - end of helix Processing helix chain 'T' and resid 68 through 75 removed outlier: 4.295A pdb=" N ALA T 72 " --> pdb=" O SER T 68 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE T 73 " --> pdb=" O ARG T 69 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ALA T 75 " --> pdb=" O ALA T 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 85 removed outlier: 3.898A pdb=" N LEU T 82 " --> pdb=" O ARG T 78 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA T 83 " --> pdb=" O LEU T 79 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS T 84 " --> pdb=" O SER T 80 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL T 85 " --> pdb=" O ASP T 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 78 through 85' Processing helix chain 'T' and resid 91 through 99 Processing helix chain 'T' and resid 128 through 139 removed outlier: 3.865A pdb=" N ALA T 138 " --> pdb=" O ALA T 134 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY T 139 " --> pdb=" O ILE T 135 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 58 removed outlier: 4.179A pdb=" N LYS U 58 " --> pdb=" O THR U 54 " (cutoff:3.500A) Processing helix chain 'U' and resid 109 through 125 removed outlier: 3.815A pdb=" N LYS U 123 " --> pdb=" O LEU U 119 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU U 124 " --> pdb=" O ALA U 120 " (cutoff:3.500A) Proline residue: U 125 - end of helix Processing helix chain 'V' and resid 13 through 32 Processing helix chain 'V' and resid 37 through 58 removed outlier: 4.044A pdb=" N ARG V 46 " --> pdb=" O LYS V 42 " (cutoff:3.500A) Proline residue: V 50 - end of helix removed outlier: 3.570A pdb=" N LYS V 56 " --> pdb=" O ILE V 52 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR V 57 " --> pdb=" O THR V 53 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ASP V 58 " --> pdb=" O LEU V 54 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 71 Processing helix chain 'V' and resid 72 through 88 removed outlier: 4.860A pdb=" N GLY V 84 " --> pdb=" O PHE V 80 " (cutoff:3.500A) Proline residue: V 85 - end of helix Processing helix chain 'W' and resid 2 through 22 removed outlier: 3.577A pdb=" N ARG W 7 " --> pdb=" O LYS W 3 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ARG W 13 " --> pdb=" O ARG W 9 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ALA W 14 " --> pdb=" O ARG W 10 " (cutoff:3.500A) Processing helix chain 'W' and resid 58 through 63 removed outlier: 6.427A pdb=" N LEU W 62 " --> pdb=" O ILE W 58 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LYS W 63 " --> pdb=" O ALA W 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 58 through 63' Processing helix chain 'W' and resid 67 through 86 Processing helix chain 'W' and resid 101 through 114 Processing helix chain 'X' and resid 2 through 13 removed outlier: 4.339A pdb=" N GLN X 12 " --> pdb=" O LEU X 8 " (cutoff:3.500A) Processing helix chain 'X' and resid 97 through 104 removed outlier: 4.648A pdb=" N ARG X 101 " --> pdb=" O LEU X 97 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU X 102 " --> pdb=" O TYR X 98 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG X 103 " --> pdb=" O TYR X 99 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N THR X 104 " --> pdb=" O LEU X 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 97 through 104' Processing helix chain 'Y' and resid 6 through 22 removed outlier: 3.645A pdb=" N ILE Y 17 " --> pdb=" O ARG Y 13 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS Y 22 " --> pdb=" O LEU Y 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 31 Processing helix chain 'Y' and resid 32 through 37 removed outlier: 3.855A pdb=" N GLN Y 37 " --> pdb=" O ARG Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 73 removed outlier: 3.765A pdb=" N ARG Y 51 " --> pdb=" O TYR Y 47 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS Y 54 " --> pdb=" O ARG Y 50 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG Y 55 " --> pdb=" O ARG Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 75 through 87 Processing helix chain 'Y' and resid 91 through 102 Processing helix chain 'Y' and resid 103 through 118 Processing helix chain 'a' and resid 13 through 25 removed outlier: 3.569A pdb=" N LEU a 19 " --> pdb=" O GLN a 15 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL a 20 " --> pdb=" O LYS a 16 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU a 23 " --> pdb=" O LEU a 19 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE a 24 " --> pdb=" O VAL a 20 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG a 25 " --> pdb=" O ALA a 21 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 39 removed outlier: 3.590A pdb=" N TYR a 38 " --> pdb=" O ASP a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 61 removed outlier: 3.693A pdb=" N VAL a 45 " --> pdb=" O LYS a 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 3 through 11 removed outlier: 3.861A pdb=" N LYS b 9 " --> pdb=" O GLU b 5 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL b 10 " --> pdb=" O ARG b 6 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU b 11 " --> pdb=" O LEU b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 17 through 26 Processing helix chain 'b' and resid 39 through 51 Processing helix chain 'c' and resid 66 through 71 removed outlier: 3.946A pdb=" N VAL c 70 " --> pdb=" O GLN c 66 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ALA c 71 " --> pdb=" O VAL c 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 66 through 71' Processing helix chain 'd' and resid 13 through 24 removed outlier: 3.525A pdb=" N ALA d 23 " --> pdb=" O ARG d 19 " (cutoff:3.500A) Processing helix chain 'd' and resid 43 through 53 removed outlier: 4.276A pdb=" N LYS d 53 " --> pdb=" O ASN d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 54 through 59 removed outlier: 4.277A pdb=" N SER d 58 " --> pdb=" O ALA d 54 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU d 59 " --> pdb=" O GLU d 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 54 through 59' Processing helix chain 'f' and resid 52 through 63 Processing helix chain 'f' and resid 64 through 75 Processing helix chain 'g' and resid 2 through 10 removed outlier: 3.583A pdb=" N LEU g 6 " --> pdb=" O LYS g 2 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU g 8 " --> pdb=" O LYS g 4 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS g 9 " --> pdb=" O GLU g 5 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N SER g 10 " --> pdb=" O LEU g 6 " (cutoff:3.500A) Processing helix chain 'g' and resid 11 through 35 removed outlier: 6.479A pdb=" N THR g 16 " --> pdb=" O GLU g 12 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU g 17 " --> pdb=" O GLU g 13 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY g 35 " --> pdb=" O GLN g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 40 through 62 removed outlier: 4.589A pdb=" N LYS g 44 " --> pdb=" O SER g 40 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLY g 62 " --> pdb=" O ASN g 58 " (cutoff:3.500A) Processing helix chain 'h' and resid 17 through 28 Processing helix chain 'h' and resid 41 through 52 Processing helix chain 'i' and resid 9 through 19 removed outlier: 5.068A pdb=" N HIS i 19 " --> pdb=" O MET i 15 " (cutoff:3.500A) Processing helix chain 'k' and resid 8 through 16 Processing helix chain 'k' and resid 17 through 25 removed outlier: 4.159A pdb=" N THR k 24 " --> pdb=" O ALA k 20 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LYS k 25 " --> pdb=" O ARG k 21 " (cutoff:3.500A) Processing helix chain 'k' and resid 26 through 38 Processing helix chain 'l' and resid 7 through 14 removed outlier: 4.001A pdb=" N ARG l 13 " --> pdb=" O GLY l 9 " (cutoff:3.500A) Processing helix chain 'l' and resid 32 through 37 removed outlier: 4.427A pdb=" N LYS l 36 " --> pdb=" O ILE l 32 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ALA l 37 " --> pdb=" O LEU l 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 32 through 37' Processing helix chain 'l' and resid 38 through 46 Proline residue: l 46 - end of helix Processing helix chain 'l' and resid 51 through 63 removed outlier: 4.560A pdb=" N GLY l 56 " --> pdb=" O LYS l 52 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU l 57 " --> pdb=" O GLY l 53 " (cutoff:3.500A) Proline residue: l 63 - end of helix Processing sheet with id= 1, first strand: chain 'K' and resid 33 through 36 No H-bonds generated for sheet with id= 1 Processing sheet with id= 2, first strand: chain 'K' and resid 73 through 78 removed outlier: 4.913A pdb=" N ILE K 74 " --> pdb=" O SER K 118 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N SER K 118 " --> pdb=" O ILE K 74 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASP K 114 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY K 127 " --> pdb=" O GLN K 115 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLN K 117 " --> pdb=" O GLY K 127 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'K' and resid 80 through 83 removed outlier: 5.543A pdb=" N ASN K 90 " --> pdb=" O ALA K 106 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'K' and resid 162 through 165 removed outlier: 6.711A pdb=" N THR K 173 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU K 180 " --> pdb=" O LEU K 176 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'L' and resid 3 through 6 Processing sheet with id= 6, first strand: chain 'L' and resid 10 through 16 removed outlier: 3.747A pdb=" N GLY L 10 " --> pdb=" O VAL L 26 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL L 20 " --> pdb=" O THR L 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'L' and resid 79 through 84 removed outlier: 5.823A pdb=" N ARG L 46 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN L 49 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLN L 94 " --> pdb=" O VAL L 34 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'L' and resid 105 through 108 removed outlier: 6.191A pdb=" N LYS L 105 " --> pdb=" O VAL L 177 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'M' and resid 1 through 4 removed outlier: 4.637A pdb=" N MET M 1 " --> pdb=" O VAL M 14 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'M' and resid 117 through 120 removed outlier: 5.534A pdb=" N ARG M 117 " --> pdb=" O ASP M 184 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'N' and resid 65 through 69 removed outlier: 4.366A pdb=" N GLY N 86 " --> pdb=" O THR N 68 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS N 87 " --> pdb=" O MET N 38 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS N 33 " --> pdb=" O THR N 157 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLY N 39 " --> pdb=" O GLY N 151 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLY N 151 " --> pdb=" O GLY N 39 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'O' and resid 15 through 19 removed outlier: 3.549A pdb=" N ASP O 16 " --> pdb=" O LYS O 27 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY O 28 " --> pdb=" O GLY O 31 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'O' and resid 41 through 45 removed outlier: 3.629A pdb=" N GLY O 53 " --> pdb=" O GLU O 42 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS O 44 " --> pdb=" O THR O 51 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR O 51 " --> pdb=" O LYS O 44 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'O' and resid 94 through 99 removed outlier: 5.546A pdb=" N VAL O 102 " --> pdb=" O LYS O 99 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASN O 101 " --> pdb=" O LEU O 117 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'O' and resid 121 through 125 removed outlier: 5.774A pdb=" N THR O 129 " --> pdb=" O LEU O 89 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS O 85 " --> pdb=" O LEU O 133 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'P' and resid 2 through 5 removed outlier: 4.038A pdb=" N LEU P 5 " --> pdb=" O ASP P 17 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASP P 17 " --> pdb=" O LEU P 5 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'R' and resid 15 through 18 Processing sheet with id= 18, first strand: chain 'R' and resid 74 through 78 removed outlier: 7.954A pdb=" N GLY R 83 " --> pdb=" O THR R 78 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'S' and resid 18 through 21 removed outlier: 4.188A pdb=" N THR S 6 " --> pdb=" O CYS S 21 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ASN S 82 " --> pdb=" O MET S 7 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU S 86 " --> pdb=" O ALA S 11 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP S 37 " --> pdb=" O VAL S 62 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'T' and resid 120 through 123 Processing sheet with id= 21, first strand: chain 'U' and resid 62 through 65 removed outlier: 3.635A pdb=" N TYR U 103 " --> pdb=" O LEU U 33 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU U 33 " --> pdb=" O LEU U 102 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS U 100 " --> pdb=" O ALA U 35 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'U' and resid 30 through 36 removed outlier: 7.903A pdb=" N SER U 30 " --> pdb=" O LYS U 133 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS U 127 " --> pdb=" O VAL U 36 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'V' and resid 33 through 36 removed outlier: 5.945A pdb=" N ALA V 108 " --> pdb=" O PHE V 102 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE V 102 " --> pdb=" O ALA V 108 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N MET V 110 " --> pdb=" O CYS V 100 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'W' and resid 49 through 53 removed outlier: 3.704A pdb=" N VAL W 49 " --> pdb=" O VAL W 39 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE W 35 " --> pdb=" O THR W 53 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'X' and resid 38 through 45 removed outlier: 6.515A pdb=" N THR X 25 " --> pdb=" O LYS X 87 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER X 83 " --> pdb=" O LYS X 29 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'X' and resid 49 through 53 removed outlier: 3.704A pdb=" N ALA X 49 " --> pdb=" O THR X 60 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG X 53 " --> pdb=" O HIS X 56 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N SER X 57 " --> pdb=" O THR X 76 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'Z' and resid 11 through 15 removed outlier: 3.557A pdb=" N MET Z 40 " --> pdb=" O VAL Z 4 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU Z 46 " --> pdb=" O ASN Z 43 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'Z' and resid 18 through 23 removed outlier: 4.320A pdb=" N GLN Z 18 " --> pdb=" O ILE Z 98 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP Z 95 " --> pdb=" O VAL Z 64 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS Z 60 " --> pdb=" O THR Z 99 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLU Z 31 " --> pdb=" O VAL Z 63 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'Z' and resid 57 through 60 Processing sheet with id= 30, first strand: chain 'Z' and resid 65 through 68 Processing sheet with id= 31, first strand: chain 'Z' and resid 69 through 78 removed outlier: 5.480A pdb=" N GLU Z 70 " --> pdb=" O GLN Z 91 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLN Z 91 " --> pdb=" O GLU Z 70 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR Z 83 " --> pdb=" O ARG Z 78 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'a' and resid 2 through 8 removed outlier: 4.856A pdb=" N THR a 100 " --> pdb=" O GLY a 79 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'a' and resid 81 through 88 removed outlier: 4.039A pdb=" N ARG a 92 " --> pdb=" O ARG a 88 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'b' and resid 12 through 15 removed outlier: 5.233A pdb=" N VAL b 31 " --> pdb=" O HIS b 15 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASN b 28 " --> pdb=" O LEU b 87 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS b 81 " --> pdb=" O VAL b 34 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS b 66 " --> pdb=" O ARG b 77 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASP b 79 " --> pdb=" O LYS b 64 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LYS b 64 " --> pdb=" O ASP b 79 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS b 81 " --> pdb=" O VAL b 62 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL b 62 " --> pdb=" O LYS b 81 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA b 83 " --> pdb=" O THR b 60 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR b 60 " --> pdb=" O ALA b 83 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL b 85 " --> pdb=" O VAL b 58 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL b 58 " --> pdb=" O VAL b 85 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'c' and resid 82 through 86 removed outlier: 7.503A pdb=" N ARG c 82 " --> pdb=" O LYS c 97 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ARG c 94 " --> pdb=" O ILE c 103 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU c 101 " --> pdb=" O PHE c 96 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'd' and resid 69 through 72 removed outlier: 6.474A pdb=" N ALA d 39 " --> pdb=" O ARG d 9 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE d 89 " --> pdb=" O PRO d 27 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'e' and resid 51 through 54 removed outlier: 4.124A pdb=" N THR e 58 " --> pdb=" O GLY e 54 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'e' and resid 65 through 71 Processing sheet with id= 39, first strand: chain 'f' and resid 12 through 19 removed outlier: 4.381A pdb=" N ASN f 23 " --> pdb=" O SER f 19 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'f' and resid 34 through 41 Processing sheet with id= 41, first strand: chain 'h' and resid 34 through 39 removed outlier: 4.245A pdb=" N HIS h 34 " --> pdb=" O GLN h 9 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N MET h 54 " --> pdb=" O THR h 10 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'j' and resid 8 through 13 removed outlier: 5.923A pdb=" N HIS j 19 " --> pdb=" O SER j 13 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'j' and resid 33 through 39 removed outlier: 4.365A pdb=" N LEU j 34 " --> pdb=" O GLU j 51 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU j 51 " --> pdb=" O LEU j 34 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'l' and resid 22 through 25 removed outlier: 5.619A pdb=" N PHE l 22 " --> pdb=" O VAL l 50 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'm' and resid 14 through 19 removed outlier: 5.942A pdb=" N VAL m 22 " --> pdb=" O ARG m 19 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2399 hydrogen bonds 3798 hydrogen bond angles 0 basepair planarities 957 basepair parallelities 1553 stacking parallelities Total time for adding SS restraints: 464.35 Time building geometry restraints manager: 109.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.28: 66749 1.28 - 1.74: 91678 1.74 - 2.20: 146 2.20 - 2.66: 0 2.66 - 3.12: 2 Bond restraints: 158575 Sorted by residual: bond pdb=" C5' C I2606 " pdb=" H5' C I2606 " ideal model delta sigma weight residual 0.970 3.125 -2.155 2.00e-02 2.50e+03 1.16e+04 bond pdb=" C5' G I2607 " pdb=" H5' G I2607 " ideal model delta sigma weight residual 0.970 2.869 -1.899 2.00e-02 2.50e+03 9.02e+03 bond pdb=" C5 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.150 1.437 -0.287 2.00e-02 2.50e+03 2.07e+02 bond pdb=" C5 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.150 1.434 -0.284 2.00e-02 2.50e+03 2.01e+02 bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.805 1.594 0.211 2.00e-02 2.50e+03 1.11e+02 ... (remaining 158570 not shown) Histogram of bond angle deviations from ideal: 62.62 - 78.67: 5 78.67 - 94.72: 3 94.72 - 110.77: 148750 110.77 - 126.83: 127613 126.83 - 142.88: 8450 Bond angle restraints: 284821 Sorted by residual: angle pdb=" H5' G I2607 " pdb=" C5' G I2607 " pdb="H5'' G I2607 " ideal model delta sigma weight residual 109.00 62.62 46.38 3.00e+00 1.11e-01 2.39e+02 angle pdb=" C5' A I 752 " pdb=" C4' A I 752 " pdb=" H4' A I 752 " ideal model delta sigma weight residual 109.00 70.66 38.34 3.00e+00 1.11e-01 1.63e+02 angle pdb=" C5' U I 138 " pdb=" C4' U I 138 " pdb=" H4' U I 138 " ideal model delta sigma weight residual 109.00 73.67 35.33 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C4' C I2606 " pdb=" C3' C I2606 " pdb=" O3' C I2606 " ideal model delta sigma weight residual 113.00 129.12 -16.12 1.50e+00 4.44e-01 1.16e+02 angle pdb=" O4' U I 138 " pdb=" C4' U I 138 " pdb=" H4' U I 138 " ideal model delta sigma weight residual 109.00 78.34 30.66 3.00e+00 1.11e-01 1.04e+02 ... (remaining 284816 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 57825 35.58 - 71.17: 3929 71.17 - 106.75: 806 106.75 - 142.33: 12 142.33 - 177.91: 22 Dihedral angle restraints: 62594 sinusoidal: 51998 harmonic: 10596 Sorted by residual: dihedral pdb=" O4' U I 546 " pdb=" C1' U I 546 " pdb=" N1 U I 546 " pdb=" C2 U I 546 " ideal model delta sinusoidal sigma weight residual 200.00 26.73 173.27 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' U I 545 " pdb=" C1' U I 545 " pdb=" N1 U I 545 " pdb=" C2 U I 545 " ideal model delta sinusoidal sigma weight residual 200.00 29.81 170.19 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' U I1174 " pdb=" C1' U I1174 " pdb=" N1 U I1174 " pdb=" C2 U I1174 " ideal model delta sinusoidal sigma weight residual 200.00 30.62 169.38 1 1.50e+01 4.44e-03 8.46e+01 ... (remaining 62591 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 18757 0.160 - 0.321: 239 0.321 - 0.481: 10 0.481 - 0.641: 3 0.641 - 0.801: 2 Chirality restraints: 19011 Sorted by residual: chirality pdb=" CA ASP Y 49 " pdb=" N ASP Y 49 " pdb=" C ASP Y 49 " pdb=" CB ASP Y 49 " both_signs ideal model delta sigma weight residual False 2.51 1.71 0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" C4' U I 138 " pdb=" C5' U I 138 " pdb=" O4' U I 138 " pdb=" C3' U I 138 " both_signs ideal model delta sigma weight residual False -2.50 -1.75 -0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" C4' A I 752 " pdb=" C5' A I 752 " pdb=" O4' A I 752 " pdb=" C3' A I 752 " both_signs ideal model delta sigma weight residual False -2.50 -1.91 -0.60 2.00e-01 2.50e+01 8.85e+00 ... (remaining 19008 not shown) Planarity restraints: 13200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I1835 " -0.067 2.00e-02 2.50e+03 6.10e-01 8.37e+03 pdb=" C4' 2MG I1835 " -0.451 2.00e-02 2.50e+03 pdb=" O4' 2MG I1835 " -0.727 2.00e-02 2.50e+03 pdb=" C3' 2MG I1835 " 0.602 2.00e-02 2.50e+03 pdb=" O3' 2MG I1835 " 0.626 2.00e-02 2.50e+03 pdb=" C2' 2MG I1835 " 0.206 2.00e-02 2.50e+03 pdb=" O2' 2MG I1835 " -0.940 2.00e-02 2.50e+03 pdb=" C1' 2MG I1835 " -0.193 2.00e-02 2.50e+03 pdb=" N9 2MG I1835 " 0.945 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC I2498 " 0.081 2.00e-02 2.50e+03 6.08e-01 8.33e+03 pdb=" C4' OMC I2498 " 0.446 2.00e-02 2.50e+03 pdb=" O4' OMC I2498 " 0.630 2.00e-02 2.50e+03 pdb=" C3' OMC I2498 " -0.592 2.00e-02 2.50e+03 pdb=" O3' OMC I2498 " -0.673 2.00e-02 2.50e+03 pdb=" C2' OMC I2498 " -0.168 2.00e-02 2.50e+03 pdb=" O2' OMC I2498 " 1.002 2.00e-02 2.50e+03 pdb=" C1' OMC I2498 " 0.198 2.00e-02 2.50e+03 pdb=" N1 OMC I2498 " -0.925 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.015 2.00e-02 2.50e+03 5.78e-01 7.51e+03 pdb=" C4' 2MG I2445 " -0.453 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.723 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.580 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.551 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.234 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.859 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.208 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.895 2.00e-02 2.50e+03 ... (remaining 13197 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.85: 678 1.85 - 2.53: 103136 2.53 - 3.22: 427019 3.22 - 3.91: 667860 3.91 - 4.60: 985510 Nonbonded interactions: 2184203 Sorted by model distance: nonbonded pdb=" OD2 ASP S 80 " pdb=" HA3 GLY X 69 " model vdw 1.157 2.620 nonbonded pdb="HG22 THR O 25 " pdb="HG23 THR O 34 " model vdw 1.181 2.440 nonbonded pdb="MG MG I3123 " pdb="MG MG I3124 " model vdw 1.227 1.300 nonbonded pdb=" OP1 G I1266 " pdb=" HE ARG i 16 " model vdw 1.228 1.850 nonbonded pdb=" HZ3 LYS K 242 " pdb=" O HOH K 401 " model vdw 1.248 1.850 ... (remaining 2184198 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 9 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3016 5.49 5 Mg 185 5.21 5 S 80 5.16 5 Na 1 4.78 5 C 45240 2.51 5 N 16917 2.21 5 O 29478 1.98 5 H 59624 0.53 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.800 Extract box with map and model: 38.580 Check model and map are aligned: 1.750 Convert atoms to be neutral: 0.960 Process input model: 865.670 Find NCS groups from input model: 2.230 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Set scattering table: 0.050 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:12.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 932.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8450 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 : 0.011 0.287 98951 Z= 0.673 Angle : 1.067 23.968 148560 Z= 0.586 Chirality : 0.060 0.801 19011 Planarity : 0.020 0.610 7598 Dihedral : 15.160 177.915 46356 Min Nonbonded Distance : 1.227 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.58 % Favored : 94.36 % Rotamer Outliers : 2.25 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.12), residues: 3298 helix: -2.22 (0.14), residues: 865 sheet: -1.14 (0.18), residues: 652 loop : -1.73 (0.13), residues: 1781 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 777 time to evaluate : 5.544 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 outliers start: 60 outliers final: 29 residues processed: 820 average time/residue: 3.6118 time to fit residues: 3927.6248 Evaluate side-chains 607 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 578 time to evaluate : 5.535 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 29 outliers final: 25 residues processed: 6 average time/residue: 2.2433 time to fit residues: 25.7610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 623 random chunks: chunk 526 optimal weight: 0.9990 chunk 472 optimal weight: 0.8980 chunk 262 optimal weight: 0.6980 chunk 161 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 252 optimal weight: 7.9990 chunk 488 optimal weight: 0.8980 chunk 188 optimal weight: 8.9990 chunk 296 optimal weight: 1.9990 chunk 363 optimal weight: 4.9990 chunk 565 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 37 ASN K 60 GLN K 134 ASN K 153 GLN L 32 ASN L 130 GLN M 115 GLN M 136 GLN P 66 ASN Q 30 GLN Q 43 ASN R 128 ASN T 35 HIS U 22 GLN V 11 ASN Y 44 GLN Y 52 GLN a 61 ASN g 27 ASN i 5 GLN i 6 ASN j 26 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.086 98951 Z= 0.147 Angle : 0.626 15.264 148560 Z= 0.344 Chirality : 0.036 0.766 19011 Planarity : 0.006 0.132 7598 Dihedral : 14.328 179.316 39828 Min Nonbonded Distance : 1.081 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.22 % Favored : 95.75 % Rotamer Outliers : 2.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.13), residues: 3298 helix: -0.66 (0.16), residues: 877 sheet: -0.80 (0.19), residues: 678 loop : -1.31 (0.14), residues: 1743 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 618 time to evaluate : 5.605 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: 76 outliers final: 31 residues processed: 658 average time/residue: 3.5199 time to fit residues: 3092.9899 Evaluate side-chains 587 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 556 time to evaluate : 5.724 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 31 outliers final: 19 residues processed: 13 average time/residue: 2.0016 time to fit residues: 46.9311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 623 random chunks: chunk 314 optimal weight: 6.9990 chunk 175 optimal weight: 8.9990 chunk 470 optimal weight: 9.9990 chunk 385 optimal weight: 4.9990 chunk 156 optimal weight: 7.9990 chunk 566 optimal weight: 8.9990 chunk 612 optimal weight: 8.9990 chunk 504 optimal weight: 0.8980 chunk 562 optimal weight: 8.9990 chunk 193 optimal weight: 8.9990 chunk 454 optimal weight: 8.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 128 ASN L 32 ASN M 136 GLN N 27 GLN R 58 ASN R 128 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 45 GLN W 38 GLN ** W 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 10 GLN Y 44 GLN a 61 ASN d 24 ASN d 49 ASN f 6 GLN f 16 ASN g 27 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8455 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.072 98951 Z= 0.387 Angle : 0.751 13.575 148560 Z= 0.397 Chirality : 0.044 0.760 19011 Planarity : 0.007 0.142 7598 Dihedral : 14.508 179.838 39828 Min Nonbonded Distance : 0.885 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.31 % Favored : 94.66 % Rotamer Outliers : 3.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.14), residues: 3298 helix: -0.24 (0.17), residues: 884 sheet: -0.70 (0.19), residues: 662 loop : -1.27 (0.14), residues: 1752 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 661 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 562 time to evaluate : 5.617 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: 99 outliers final: 55 residues processed: 616 average time/residue: 3.4967 time to fit residues: 2885.6014 Evaluate side-chains 614 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 559 time to evaluate : 5.683 Switching outliers to nearest non-outliers outliers start: 55 outliers final: 34 residues processed: 21 average time/residue: 1.4446 time to fit residues: 61.1948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 623 random chunks: chunk 559 optimal weight: 4.9990 chunk 426 optimal weight: 10.0000 chunk 294 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 270 optimal weight: 6.9990 chunk 380 optimal weight: 6.9990 chunk 568 optimal weight: 4.9990 chunk 602 optimal weight: 6.9990 chunk 297 optimal weight: 7.9990 chunk 539 optimal weight: 4.9990 chunk 162 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 37 ASN L 32 ASN R 128 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 44 GLN Z 87 GLN d 24 ASN f 17 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.161 98951 Z= 0.358 Angle : 0.710 13.562 148560 Z= 0.379 Chirality : 0.043 0.768 19011 Planarity : 0.007 0.137 7598 Dihedral : 14.487 179.801 39828 Min Nonbonded Distance : 0.948 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.43 % Favored : 94.54 % Rotamer Outliers : 4.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -1.20 (0.14), residues: 3298 helix: -0.00 (0.17), residues: 885 sheet: -0.71 (0.19), residues: 661 loop : -1.21 (0.14), residues: 1752 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 681 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 111 poor density : 570 time to evaluate : 5.534 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 111 outliers final: 63 residues processed: 633 average time/residue: 3.4072 time to fit residues: 2901.5639 Evaluate side-chains 615 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 552 time to evaluate : 5.587 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 63 outliers final: 40 residues processed: 24 average time/residue: 1.5095 time to fit residues: 69.5855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 623 random chunks: chunk 501 optimal weight: 6.9990 chunk 341 optimal weight: 7.9990 chunk 8 optimal weight: 10.0000 chunk 448 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 513 optimal weight: 5.9990 chunk 416 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 307 optimal weight: 8.9990 chunk 540 optimal weight: 3.9990 chunk 151 optimal weight: 10.0000 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 37 ASN L 32 ASN R 128 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 45 GLN ** W 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 44 GLN d 24 ASN f 17 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8447 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.062 98951 Z= 0.327 Angle : 0.694 13.628 148560 Z= 0.373 Chirality : 0.042 0.773 19011 Planarity : 0.007 0.138 7598 Dihedral : 14.435 179.109 39828 Min Nonbonded Distance : 0.941 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.74 % Favored : 94.26 % Rotamer Outliers : 4.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.14), residues: 3298 helix: 0.13 (0.17), residues: 882 sheet: -0.62 (0.19), residues: 671 loop : -1.18 (0.14), residues: 1745 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 679 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 569 time to evaluate : 5.750 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: 110 outliers final: 75 residues processed: 624 average time/residue: 3.4415 time to fit residues: 2897.5057 Evaluate side-chains 627 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 552 time to evaluate : 5.613 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 75 outliers final: 44 residues processed: 32 average time/residue: 1.6387 time to fit residues: 95.7989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 623 random chunks: chunk 202 optimal weight: 6.9990 chunk 542 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 353 optimal weight: 1.9990 chunk 148 optimal weight: 9.9990 chunk 602 optimal weight: 0.9990 chunk 500 optimal weight: 9.9990 chunk 279 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 316 optimal weight: 1.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 37 ASN K 46 ASN L 32 ASN ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 18 GLN R 128 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 44 GLN d 24 ASN f 17 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 98951 Z= 0.253 Angle : 0.640 13.366 148560 Z= 0.350 Chirality : 0.039 0.783 19011 Planarity : 0.006 0.133 7598 Dihedral : 14.336 178.922 39828 Min Nonbonded Distance : 0.979 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer Outliers : 3.69 % 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: -0.90 (0.14), residues: 3298 helix: 0.36 (0.18), residues: 881 sheet: -0.60 (0.19), residues: 686 loop : -1.06 (0.14), residues: 1731 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 565 time to evaluate : 6.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 100 outliers final: 67 residues processed: 623 average time/residue: 3.4495 time to fit residues: 2918.2083 Evaluate side-chains 615 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 548 time to evaluate : 5.609 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 67 outliers final: 45 residues processed: 23 average time/residue: 1.5852 time to fit residues: 70.0492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 623 random chunks: chunk 581 optimal weight: 0.9980 chunk 67 optimal weight: 6.9990 chunk 343 optimal weight: 0.9980 chunk 440 optimal weight: 4.9990 chunk 341 optimal weight: 8.9990 chunk 507 optimal weight: 0.3980 chunk 336 optimal weight: 0.0980 chunk 600 optimal weight: 5.9990 chunk 375 optimal weight: 10.0000 chunk 366 optimal weight: 8.9990 chunk 277 optimal weight: 7.9990 overall best weight: 1.4982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 ASN P 18 GLN R 128 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 45 GLN W 61 GLN Y 44 GLN d 24 ASN f 17 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.046 98951 Z= 0.148 Angle : 0.594 13.251 148560 Z= 0.330 Chirality : 0.036 0.797 19011 Planarity : 0.006 0.127 7598 Dihedral : 14.311 179.081 39828 Min Nonbonded Distance : 1.094 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer Outliers : 2.91 % 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: -0.73 (0.14), residues: 3298 helix: 0.56 (0.18), residues: 881 sheet: -0.55 (0.19), residues: 679 loop : -0.97 (0.14), residues: 1738 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 561 time to evaluate : 5.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 79 outliers final: 61 residues processed: 615 average time/residue: 3.3994 time to fit residues: 2854.2622 Evaluate side-chains 611 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 550 time to evaluate : 5.594 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 61 outliers final: 45 residues processed: 17 average time/residue: 1.7398 time to fit residues: 55.2799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 623 random chunks: chunk 371 optimal weight: 2.9990 chunk 239 optimal weight: 8.9990 chunk 358 optimal weight: 9.9990 chunk 180 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 116 optimal weight: 10.0000 chunk 381 optimal weight: 9.9990 chunk 409 optimal weight: 20.0000 chunk 296 optimal weight: 8.9990 chunk 55 optimal weight: 8.9990 chunk 471 optimal weight: 10.0000 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 ASN P 18 GLN R 128 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 GLN Y 44 GLN f 17 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.089 98951 Z= 0.450 Angle : 0.776 13.815 148560 Z= 0.405 Chirality : 0.046 0.764 19011 Planarity : 0.008 0.142 7598 Dihedral : 14.509 179.500 39828 Min Nonbonded Distance : 0.892 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.92 % Favored : 94.05 % Rotamer Outliers : 3.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -0.99 (0.14), residues: 3298 helix: 0.25 (0.17), residues: 887 sheet: -0.68 (0.19), residues: 656 loop : -1.09 (0.14), residues: 1755 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 552 time to evaluate : 5.583 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: 95 outliers final: 73 residues processed: 607 average time/residue: 3.3851 time to fit residues: 2759.5031 Evaluate side-chains 628 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 555 time to evaluate : 5.610 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 73 outliers final: 47 residues processed: 27 average time/residue: 1.4779 time to fit residues: 76.5516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 623 random chunks: chunk 546 optimal weight: 7.9990 chunk 575 optimal weight: 6.9990 chunk 524 optimal weight: 3.9990 chunk 559 optimal weight: 7.9990 chunk 336 optimal weight: 6.9990 chunk 243 optimal weight: 5.9990 chunk 439 optimal weight: 0.9980 chunk 171 optimal weight: 10.0000 chunk 505 optimal weight: 7.9990 chunk 529 optimal weight: 7.9990 chunk 557 optimal weight: 0.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 37 ASN L 32 ASN P 18 GLN R 128 ASN R 136 GLN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 GLN Y 44 GLN d 24 ASN ** f 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.3104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.052 98951 Z= 0.261 Angle : 0.652 13.485 148560 Z= 0.355 Chirality : 0.039 0.778 19011 Planarity : 0.006 0.134 7598 Dihedral : 14.375 179.549 39828 Min Nonbonded Distance : 0.976 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -0.86 (0.14), residues: 3298 helix: 0.41 (0.18), residues: 886 sheet: -0.63 (0.19), residues: 666 loop : -1.03 (0.14), residues: 1746 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 564 time to evaluate : 5.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 71 outliers final: 57 residues processed: 612 average time/residue: 3.4129 time to fit residues: 2820.7236 Evaluate side-chains 614 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 557 time to evaluate : 5.483 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 57 outliers final: 44 residues processed: 14 average time/residue: 1.6562 time to fit residues: 44.9083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 623 random chunks: chunk 367 optimal weight: 9.9990 chunk 591 optimal weight: 8.9990 chunk 361 optimal weight: 7.9990 chunk 280 optimal weight: 8.9990 chunk 411 optimal weight: 6.9990 chunk 620 optimal weight: 8.9990 chunk 571 optimal weight: 0.9980 chunk 494 optimal weight: 7.9990 chunk 51 optimal weight: 7.9990 chunk 381 optimal weight: 8.9990 chunk 303 optimal weight: 6.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 ASN P 18 GLN R 128 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 GLN Y 44 GLN f 17 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 moved from start: 0.3109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.078 98951 Z= 0.381 Angle : 0.730 13.761 148560 Z= 0.387 Chirality : 0.043 0.768 19011 Planarity : 0.007 0.140 7598 Dihedral : 14.482 178.897 39828 Min Nonbonded Distance : 0.911 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.83 % Favored : 94.14 % Rotamer Outliers : 2.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -0.99 (0.14), residues: 3298 helix: 0.32 (0.18), residues: 879 sheet: -0.73 (0.19), residues: 665 loop : -1.10 (0.14), residues: 1754 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 555 time to evaluate : 5.569 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: 73 outliers final: 55 residues processed: 604 average time/residue: 3.4914 time to fit residues: 2830.8216 Evaluate side-chains 610 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 555 time to evaluate : 5.120 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 55 outliers final: 45 residues processed: 11 average time/residue: 1.4701 time to fit residues: 34.0333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 623 random chunks: chunk 392 optimal weight: 0.5980 chunk 526 optimal weight: 6.9990 chunk 151 optimal weight: 9.9990 chunk 455 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 137 optimal weight: 6.9990 chunk 495 optimal weight: 6.9990 chunk 207 optimal weight: 6.9990 chunk 508 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 overall best weight: 5.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 ASN P 18 GLN R 128 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 GLN Y 44 GLN d 24 ASN f 17 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.156802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.120257 restraints weight = 217046.073| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 0.65 r_work: 0.3422 rms_B_bonded: 0.76 restraints_weight: 0.5000 r_work: 0.3402 rms_B_bonded: 0.99 restraints_weight: 0.2500 r_work: 0.3378 rms_B_bonded: 1.33 restraints_weight: 0.1250 r_work: 0.3348 rms_B_bonded: 1.82 restraints_weight: 0.0625 r_work: 0.3309 rms_B_bonded: 2.53 restraints_weight: 0.0312 r_work: 0.3257 rms_B_bonded: 3.55 restraints_weight: 0.0156 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3905 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3905 r_free = 0.3905 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3905 r_free = 0.3905 target_work(ls_wunit_k1) = 0.157 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3905 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.071 98951 Z= 0.357 Angle : 0.712 13.624 148560 Z= 0.380 Chirality : 0.042 0.768 19011 Planarity : 0.007 0.138 7598 Dihedral : 14.470 178.886 39828 Min Nonbonded Distance : 0.931 Molprobity Statistics. All-atom Clashscore : 7.62 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.64 % Favored : 94.32 % Rotamer Outliers : 2.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % 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: -0.99 (0.14), residues: 3298 helix: 0.32 (0.17), residues: 880 sheet: -0.73 (0.18), residues: 679 loop : -1.10 (0.14), residues: 1739 =============================================================================== Job complete usr+sys time: 57491.16 seconds wall clock time: 974 minutes 39.33 seconds (58479.33 seconds total)