Starting phenix.real_space_refine (version: dev) on Thu Apr 14 08:42:15 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvk_23539/04_2022/7lvk_23539_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvk_23539/04_2022/7lvk_23539.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvk_23539/04_2022/7lvk_23539_neut_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/7lvk_23539/04_2022/7lvk_23539_neut_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvk_23539/04_2022/7lvk_23539_neut_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvk_23539/04_2022/7lvk_23539.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvk_23539/04_2022/7lvk_23539.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvk_23539/04_2022/7lvk_23539_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lvk_23539/04_2022/7lvk_23539_neut_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= 0.000 sd= 0.004 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 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 23": "OE1" <-> "OE2" 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 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 GLU 17": "OE1" <-> "OE2" Residue "L ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 77": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 141": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 169": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 183": "OE1" <-> "OE2" 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 GLU 152": "OE1" <-> "OE2" Residue "M ARG 162": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N GLU 19": "OE1" <-> "OE2" 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 GLU 98": "OE1" <-> "OE2" 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 48": "OE1" <-> "OE2" Residue "R ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R LEU 36": "CD1" <-> "CD2" "HD11" <-> "HD21" "HD12" <-> "HD22" "HD13" <-> "HD23" Residue "R ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R GLU 43": "OE1" <-> "OE2" 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 "T ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 TYR 58": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T ARG 60": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T PHE 64": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "T ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 126": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 132": "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 GLU 27": "OE1" <-> "OE2" Residue "X ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X GLU 68": "OE1" <-> "OE2" 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 "Y ARG 92": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z GLU 37": "OE1" <-> "OE2" 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 GLU 25": "OE1" <-> "OE2" Residue "b GLU 56": "OE1" <-> "OE2" Residue "b ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 "d TYR 82": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 PHE 29": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" 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 GLU 70": "OE1" <-> "OE2" Residue "f ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" 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 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 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 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" Residue "m GLU 30": "OE1" <-> "OE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 151436 Number of models: 1 Model: "" Number of chains: 63 Chain: "I" Number of atoms: 93289 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2898, 93289 Classifications: {'RNA': 2898} Modifications used: {'rna3p': 16, 'rna2p': 6, '3*END': 1, 'rna3p_pur': 1389, 'rna3p_pyr': 1065, 'rna2p_pur': 275, 'rna2p_pyr': 147} Link IDs: {'rna3p': 2469, 'rna2p': 428} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 10 Chain: "J" Number of atoms: 3809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 3809 Classifications: {'RNA': 118} Modifications used: {'rna3p_pyr': 48, 'rna2p_pur': 7, 'rna3p_pur': 57, 'rna2p_pyr': 6} Link IDs: {'rna3p': 104, 'rna2p': 13} Chain: "K" Number of atoms: 4236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 4236 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "L" Number of atoms: 3182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3182 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: 2854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 2854 Classifications: {'peptide': 177} 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: "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: 2182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2182 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: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1655 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: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1545 Classifications: {'peptide': 93} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "c" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 1610 Classifications: {'peptide': 102} 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: 1150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1150 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 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: 1077 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1077 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: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 175 Unusual residues: {' MG': 175} Classifications: {'undetermined': 175} Link IDs: {None: 174} 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: "W" 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: 2340 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2340, 2340 Classifications: {'water': 2340} Link IDs: {None: 2339} Chain: "J" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 34 Classifications: {'water': 34} Link IDs: {None: 33} Chain: "K" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Chain: "L" Number of atoms: 44 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 44 Classifications: {'water': 44} Link IDs: {None: 43} Chain: "M" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 22 Classifications: {'water': 22} Link IDs: {None: 21} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "S" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 28 Classifications: {'water': 28} Link IDs: {None: 27} Chain: "U" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "V" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} 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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "Z" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "a" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "b" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Classifications: {'water': 3} Link IDs: {None: 2} 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: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "h" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Chain: "i" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "j" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} 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: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} 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 A113O SG CYS m 11 74.674 170.445 49.698 1.00 50.84 S ATOM A1150 SG CYS m 14 77.464 169.448 52.563 1.00 47.33 S ATOM A11BA SG CYS m 27 75.622 172.948 52.473 1.00 45.83 S Residues with excluded nonbonded symmetry interactions: 2 residue: pdb="MG MG I3124 " occ=0.50 residue: pdb="MG MG I3125 " occ=0.50 Time building chain proxies: 54.88, per 1000 atoms: 0.36 Number of scatterers: 151436 At special positions: 0 Unit cell: (184.128, 229.338, 242.49, 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 74 16.00 P 3016 15.00 Mg 179 11.99 Na 1 11.00 O 28107 8.00 N 16741 7.00 C 44613 6.00 H 58704 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: 99.00 Conformation dependent library (CDL) restraints added in 5.2 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 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5876 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: 87 helices and 44 sheets defined 32.6% alpha, 19.9% beta 979 base pairs and 1576 stacking pairs defined. Time for finding SS restraints: 68.77 Creating SS restraints... Processing helix chain 'K' and resid 10 through 16 removed outlier: 4.890A pdb=" N HIS K 15 " --> pdb=" O PRO K 11 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 30 through 35 removed outlier: 3.669A pdb=" N LEU K 34 " --> pdb=" O PHE K 30 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLU K 35 " --> pdb=" O ALA K 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 30 through 35' 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: 3.920A pdb=" N ALA K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG K 214 " --> pdb=" O ALA K 210 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 226 removed outlier: 3.677A pdb=" N MET K 225 " --> pdb=" O ARG K 221 " (cutoff:3.500A) removed outlier: 5.120A 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: 3.714A pdb=" N ASP K 264 " --> pdb=" O ASN K 260 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS K 265 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N PHE K 266 " --> pdb=" O ARG K 262 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N ILE K 267 " --> pdb=" O THR K 263 " (cutoff:3.500A) removed outlier: 5.313A 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 'L' and resid 56 through 61 removed outlier: 6.026A pdb=" N THR L 61 " --> pdb=" O ALA L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 72 removed outlier: 3.602A pdb=" N ALA L 71 " --> pdb=" O HIS L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 103 removed outlier: 4.255A pdb=" N ALA L 102 " --> pdb=" O VAL L 98 " (cutoff:3.500A) removed outlier: 5.114A 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 41 removed outlier: 5.731A pdb=" N GLN M 41 " --> pdb=" O ALA M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 53 removed outlier: 6.234A 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 removed outlier: 3.549A pdb=" N LEU M 134 " --> pdb=" O LYS M 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 154 through 163 removed outlier: 4.677A pdb=" N ASN M 163 " --> pdb=" O LEU M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 184 removed outlier: 5.927A pdb=" N ASP M 184 " --> pdb=" O LEU M 180 " (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 21 removed outlier: 4.464A pdb=" N VAL N 13 " --> pdb=" O LYS N 9 " (cutoff:3.500A) removed outlier: 5.566A pdb=" N LYS N 14 " --> pdb=" O ASP N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 42 through 47 removed outlier: 3.773A pdb=" N ASP N 46 " --> pdb=" O GLU N 42 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS N 47 " --> pdb=" O ALA N 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 42 through 47' Processing helix chain 'N' and resid 48 through 62 removed outlier: 3.619A pdb=" N GLY N 62 " --> pdb=" O ALA N 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 111 removed outlier: 3.781A pdb=" N ARG N 102 " --> pdb=" O GLU N 98 " (cutoff:3.500A) removed outlier: 5.170A 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: 3.699A pdb=" N PHE N 173 " --> pdb=" O LEU N 169 " (cutoff:3.500A) Processing helix chain 'N' and resid 134 through 139 removed outlier: 4.764A pdb=" N ILE N 137 " --> pdb=" O GLU N 134 " (cutoff:3.500A) Proline residue: N 139 - end of helix 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: 4.299A pdb=" N GLN O 64 " --> pdb=" O ASP O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 153 removed outlier: 4.238A pdb=" N ARG O 152 " --> pdb=" O LEU O 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 29 Processing helix chain 'P' and resid 40 through 71 removed outlier: 6.180A pdb=" N ILE P 44 " --> pdb=" O THR P 40 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N GLU P 45 " --> pdb=" O LYS P 41 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLU P 48 " --> pdb=" O ILE P 44 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N ARG P 50 " --> pdb=" O PHE P 46 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N ARG P 51 " --> pdb=" O PHE P 47 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LEU P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU P 55 " --> pdb=" O ARG P 51 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N LEU P 58 " --> pdb=" O LEU P 54 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA P 59 " --> pdb=" O GLU P 55 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N GLU P 60 " --> pdb=" O ALA P 56 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N VAL P 61 " --> pdb=" O LYS P 57 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASN P 66 " --> pdb=" O LEU P 62 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA P 67 " --> pdb=" O ALA P 63 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ARG P 68 " --> pdb=" O ALA P 64 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ALA P 69 " --> pdb=" O ALA P 65 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N GLU P 70 " --> pdb=" O ASN P 66 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N LYS P 71 " --> pdb=" O ALA P 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 38 removed outlier: 3.732A 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: 4.078A pdb=" N ILE R 101 " --> pdb=" O PRO R 97 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N MET R 108 " --> pdb=" O ALA R 104 " (cutoff:3.500A) Proline residue: R 110 - end of helix Processing helix chain 'R' and resid 112 through 123 removed outlier: 3.838A pdb=" N LYS R 121 " --> pdb=" O ALA R 117 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N LEU R 122 " --> pdb=" O MET R 118 " (cutoff:3.500A) removed outlier: 5.409A pdb=" N LYS R 123 " --> pdb=" O PHE R 119 " (cutoff:3.500A) Processing helix chain 'R' and resid 67 through 72 removed outlier: 4.342A pdb=" N LYS R 72 " --> pdb=" O ASN R 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 67 through 72' Processing helix chain 'S' and resid 104 through 109 removed outlier: 4.760A pdb=" N ARG S 108 " --> pdb=" O THR S 104 " (cutoff:3.500A) removed outlier: 5.514A 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 110 through 119 removed outlier: 7.239A pdb=" N LYS S 114 " --> pdb=" O GLU S 110 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE S 115 " --> pdb=" O LYS S 111 " (cutoff:3.500A) Processing helix chain 'T' and resid 37 through 42 removed outlier: 3.565A pdb=" N ARG T 41 " --> pdb=" O GLY T 37 " (cutoff:3.500A) removed outlier: 5.582A pdb=" N SER T 42 " --> pdb=" O GLN T 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 37 through 42' 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: 7.116A pdb=" N ALA T 72 " --> pdb=" O SER T 68 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ILE T 73 " --> pdb=" O ARG T 69 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N ALA T 75 " --> pdb=" O ALA T 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 85 removed outlier: 3.705A pdb=" N LEU T 82 " --> pdb=" O ARG T 78 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA T 83 " --> pdb=" O LEU T 79 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N LYS T 84 " --> pdb=" O SER T 80 " (cutoff:3.500A) removed outlier: 3.927A 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 Processing helix chain 'U' and resid 42 through 58 removed outlier: 4.564A pdb=" N LYS U 58 " --> pdb=" O THR U 54 " (cutoff:3.500A) Processing helix chain 'U' and resid 109 through 125 removed outlier: 3.931A pdb=" N LYS U 123 " --> pdb=" O LEU U 119 " (cutoff:3.500A) removed outlier: 3.659A 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 38 through 57 removed outlier: 4.191A pdb=" N ARG V 46 " --> pdb=" O LYS V 42 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL V 47 " --> pdb=" O GLU V 43 " (cutoff:3.500A) Proline residue: V 50 - end of helix removed outlier: 4.511A pdb=" N THR V 57 " --> pdb=" O THR V 53 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 71 Processing helix chain 'V' and resid 72 through 88 removed outlier: 4.968A 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: 3.592A pdb=" N ARG W 7 " --> pdb=" O LYS W 3 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N ARG W 13 " --> pdb=" O ARG W 9 " (cutoff:3.500A) removed outlier: 5.322A pdb=" N ALA W 14 " --> pdb=" O ARG W 10 " (cutoff:3.500A) Processing helix chain 'W' and resid 57 through 63 removed outlier: 5.292A pdb=" N GLN W 61 " --> pdb=" O ALA W 57 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N LEU W 62 " --> pdb=" O ILE W 58 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYS W 63 " --> pdb=" O ALA W 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 57 through 63' Processing helix chain 'W' and resid 67 through 86 Processing helix chain 'W' and resid 101 through 114 removed outlier: 5.403A pdb=" N ALA W 105 " --> pdb=" O GLY W 101 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 13 removed outlier: 4.457A pdb=" N GLN X 12 " --> pdb=" O LEU X 8 " (cutoff:3.500A) Processing helix chain 'X' and resid 97 through 104 removed outlier: 4.582A pdb=" N ARG X 101 " --> pdb=" O LEU X 97 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N GLU X 102 " --> pdb=" O TYR X 98 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG X 103 " --> pdb=" O TYR X 99 " (cutoff:3.500A) removed outlier: 5.146A 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: 3.552A pdb=" N ILE Y 17 " --> pdb=" O ARG Y 13 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 31 Processing helix chain 'Y' and resid 32 through 37 removed outlier: 3.771A pdb=" N GLN Y 37 " --> pdb=" O ARG Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 73 removed outlier: 3.810A pdb=" N ARG Y 51 " --> pdb=" O TYR Y 47 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LYS Y 54 " --> pdb=" O ARG Y 50 " (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: 3.849A pdb=" N VAL a 20 " --> pdb=" O LYS a 16 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N LEU a 23 " --> pdb=" O LEU a 19 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ILE a 24 " --> pdb=" O VAL a 20 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 39 Processing helix chain 'a' and resid 41 through 61 removed outlier: 3.676A pdb=" N VAL a 45 " --> pdb=" O LYS a 41 " (cutoff:3.500A) Processing helix chain 'a' and resid 65 through 70 removed outlier: 6.731A pdb=" N LEU a 69 " --> pdb=" O ASP a 65 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LYS a 70 " --> pdb=" O ILE a 66 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 65 through 70' Processing helix chain 'b' and resid 3 through 11 removed outlier: 3.809A pdb=" N LYS b 9 " --> pdb=" O GLU b 5 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N LEU b 11 " --> pdb=" O LEU b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 17 through 27 Processing helix chain 'b' and resid 39 through 51 Processing helix chain 'c' and resid 66 through 71 removed outlier: 3.861A pdb=" N VAL c 70 " --> pdb=" O GLN c 66 " (cutoff:3.500A) removed outlier: 5.073A 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 Processing helix chain 'd' and resid 43 through 54 removed outlier: 3.578A pdb=" N ALA d 52 " --> pdb=" O MET d 48 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N LYS d 53 " --> pdb=" O ASN d 49 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N ALA d 54 " --> pdb=" O MET d 50 " (cutoff:3.500A) 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: 3.844A pdb=" N GLU g 8 " --> pdb=" O LYS g 4 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LYS g 9 " --> pdb=" O GLU g 5 " (cutoff:3.500A) removed outlier: 5.529A pdb=" N SER g 10 " --> pdb=" O LEU g 6 " (cutoff:3.500A) Processing helix chain 'g' and resid 11 through 35 removed outlier: 6.358A pdb=" N THR g 16 " --> pdb=" O GLU g 12 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU g 17 " --> pdb=" O GLU g 13 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLY g 35 " --> pdb=" O GLN g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 40 through 62 removed outlier: 4.512A pdb=" N LYS g 44 " --> pdb=" O SER g 40 " (cutoff:3.500A) removed outlier: 4.406A 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: 4.695A 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: 4.082A pdb=" N THR k 24 " --> pdb=" O ALA k 20 " (cutoff:3.500A) removed outlier: 5.281A 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: 3.558A pdb=" N ARG l 13 " --> pdb=" O GLY l 9 " (cutoff:3.500A) Processing helix chain 'l' and resid 32 through 37 removed outlier: 4.568A pdb=" N LYS l 36 " --> pdb=" O ILE l 32 " (cutoff:3.500A) removed outlier: 5.359A 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: 4.570A pdb=" N GLY l 56 " --> pdb=" O LYS l 52 " (cutoff:3.500A) removed outlier: 5.107A 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 2 through 5 Processing sheet with id= 2, first strand: chain 'K' and resid 75 through 78 removed outlier: 4.677A pdb=" N ASP K 114 " --> pdb=" O VAL K 78 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'K' and resid 80 through 83 removed outlier: 3.658A pdb=" N ARG K 80 " --> pdb=" O LEU K 93 " (cutoff:3.500A) removed outlier: 5.472A 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: 6.696A pdb=" N THR K 173 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 3.863A 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 7 removed outlier: 6.990A pdb=" N ASP L 200 " --> pdb=" O THR L 112 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR L 112 " --> pdb=" O ASP L 200 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N GLU L 168 " --> pdb=" O SER L 113 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'L' and resid 10 through 16 removed outlier: 3.625A pdb=" N GLY L 10 " --> pdb=" O VAL L 26 " (cutoff:3.500A) removed outlier: 4.048A 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: 5.712A pdb=" N ARG L 46 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N GLN L 49 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 4.303A 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: 6.230A pdb=" N LYS L 105 " --> pdb=" O VAL L 177 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N VAL L 177 " --> pdb=" O LYS L 105 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'M' and resid 1 through 4 removed outlier: 3.851A 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 Processing sheet with id= 11, first strand: chain 'N' and resid 65 through 69 removed outlier: 8.421A pdb=" N ILE N 85 " --> pdb=" O VAL N 40 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL N 40 " --> pdb=" O ILE N 85 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLY N 39 " --> pdb=" O GLY N 151 " (cutoff:3.500A) removed outlier: 7.265A 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 20 removed outlier: 3.710A pdb=" N ASP O 16 " --> pdb=" O LYS O 27 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LYS O 27 " --> pdb=" O ASP O 16 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR O 25 " --> pdb=" O LYS O 18 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL O 23 " --> pdb=" O ASN O 20 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N GLN O 22 " --> pdb=" O LEU O 37 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'O' and resid 40 through 45 removed outlier: 7.202A pdb=" N ALA O 40 " --> pdb=" O ARG O 55 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'O' and resid 94 through 99 removed outlier: 5.437A pdb=" N VAL O 102 " --> pdb=" O LYS O 99 " (cutoff:3.500A) removed outlier: 6.726A 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: 5.572A pdb=" N THR O 129 " --> pdb=" O LEU O 89 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'P' and resid 2 through 5 removed outlier: 5.941A pdb=" N GLN P 2 " --> pdb=" O ALA P 39 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'P' and resid 105 through 108 removed outlier: 5.683A pdb=" N VAL P 108 " --> pdb=" O VAL P 138 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N VAL P 138 " --> pdb=" O VAL P 108 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'R' and resid 14 through 19 Processing sheet with id= 19, first strand: chain 'S' and resid 56 through 60 removed outlier: 4.408A pdb=" N ASP S 56 " --> pdb=" O ILE S 43 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LYS S 40 " --> pdb=" O ILE S 22 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N THR S 6 " --> pdb=" O CYS S 21 " (cutoff:3.500A) removed outlier: 5.841A pdb=" N ASN S 82 " --> pdb=" O MET S 7 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'S' and resid 68 through 71 removed outlier: 4.111A pdb=" N SER S 75 " --> pdb=" O ARG S 71 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'U' and resid 37 through 40 No H-bonds generated for sheet with id= 21 Processing sheet with id= 22, first strand: chain 'U' and resid 62 through 65 removed outlier: 3.614A pdb=" N TYR U 103 " --> pdb=" O LEU U 33 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LEU U 33 " --> pdb=" O LEU U 102 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N LYS U 100 " --> pdb=" O ALA U 35 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'U' and resid 30 through 36 removed outlier: 7.803A pdb=" N SER U 30 " --> pdb=" O LYS U 133 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS U 127 " --> pdb=" O VAL U 36 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'W' and resid 49 through 52 Processing sheet with id= 25, first strand: chain 'X' and resid 38 through 45 removed outlier: 6.577A pdb=" N THR X 25 " --> pdb=" O LYS X 87 " (cutoff:3.500A) removed outlier: 3.635A 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: 3.727A pdb=" N ALA X 49 " --> pdb=" O THR X 60 " (cutoff:3.500A) removed outlier: 4.569A pdb=" N ARG X 53 " --> pdb=" O HIS X 56 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'Z' and resid 11 through 15 removed outlier: 3.645A pdb=" N MET Z 40 " --> pdb=" O VAL Z 4 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N LEU Z 39 " --> pdb=" O LYS Z 48 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N LYS Z 48 " --> pdb=" O LEU Z 39 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N ILE Z 41 " --> pdb=" O GLU Z 46 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N GLU Z 46 " --> pdb=" O ILE Z 41 " (cutoff:3.500A) removed outlier: 5.457A pdb=" N ASN Z 43 " --> pdb=" O GLY Z 44 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'Z' and resid 18 through 23 removed outlier: 4.280A pdb=" N GLN Z 18 " --> pdb=" O ILE Z 98 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ASP Z 95 " --> pdb=" O VAL Z 64 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LYS Z 60 " --> pdb=" O THR Z 99 " (cutoff:3.500A) removed outlier: 4.650A 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 71 through 78 removed outlier: 4.177A 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 Processing sheet with id= 33, first strand: chain 'b' and resid 12 through 15 removed outlier: 5.289A pdb=" N VAL b 31 " --> pdb=" O HIS b 15 " (cutoff:3.500A) removed outlier: 6.098A pdb=" N ASN b 28 " --> pdb=" O LEU b 87 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS b 81 " --> pdb=" O VAL b 34 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG b 73 " --> pdb=" O HIS b 70 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N LYS b 66 " --> pdb=" O ARG b 77 " (cutoff:3.500A) removed outlier: 6.035A pdb=" N ASP b 79 " --> pdb=" O LYS b 64 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N LYS b 64 " --> pdb=" O ASP b 79 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LYS b 81 " --> pdb=" O VAL b 62 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL b 62 " --> pdb=" O LYS b 81 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N ALA b 83 " --> pdb=" O THR b 60 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N THR b 60 " --> pdb=" O ALA b 83 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL b 85 " --> pdb=" O VAL b 58 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL b 58 " --> pdb=" O VAL b 85 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'c' and resid 40 through 46 removed outlier: 4.801A pdb=" N ASN c 40 " --> pdb=" O ALA c 63 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N GLY c 57 " --> pdb=" O GLN c 46 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'c' and resid 82 through 87 removed outlier: 7.411A pdb=" N ARG c 82 " --> pdb=" O LYS c 97 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ARG c 94 " --> pdb=" O ILE c 103 " (cutoff:3.500A) removed outlier: 3.805A 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: 6.757A pdb=" N ALA d 39 " --> pdb=" O ARG d 9 " (cutoff:3.500A) removed outlier: 3.821A 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: 4.128A pdb=" N THR e 58 " --> pdb=" O GLY e 54 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'e' and resid 66 through 71 Processing sheet with id= 39, first strand: chain 'f' and resid 12 through 19 removed outlier: 4.527A pdb=" N ASN f 23 " --> pdb=" O SER f 19 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'f' and resid 35 through 41 Processing sheet with id= 41, first strand: chain 'h' and resid 33 through 39 removed outlier: 4.326A pdb=" N HIS h 34 " --> pdb=" O GLN h 9 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N MET h 54 " --> pdb=" O THR h 10 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'j' and resid 33 through 39 removed outlier: 5.101A pdb=" N LEU j 34 " --> pdb=" O GLU j 51 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLU j 51 " --> pdb=" O LEU j 34 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'l' and resid 22 through 25 removed outlier: 5.690A pdb=" N PHE l 22 " --> pdb=" O VAL l 50 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'm' and resid 1 through 5 removed outlier: 6.867A pdb=" N HIS m 33 " --> pdb=" O CYS m 27 " (cutoff:3.500A) removed outlier: 5.504A pdb=" N CYS m 27 " --> pdb=" O HIS m 33 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N ILE m 23 " --> pdb=" O GLN m 37 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N VAL m 22 " --> pdb=" O ARG m 19 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N SER m 28 " --> pdb=" O ASN m 13 " (cutoff:3.500A) removed outlier: 8.445A pdb=" N ASN m 13 " --> pdb=" O SER m 28 " (cutoff:3.500A) 918 hydrogen bonds defined for protein. 2694 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2465 hydrogen bonds 3880 hydrogen bond angles 0 basepair planarities 979 basepair parallelities 1576 stacking parallelities Total time for adding SS restraints: 422.90 Time building geometry restraints manager: 106.07 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 58694 1.03 - 1.23: 1795 1.23 - 1.42: 49987 1.42 - 1.62: 46020 1.62 - 1.81: 145 Bond restraints: 156641 Sorted by residual: bond pdb=" C THR L 151 " pdb=" O THR L 151 " ideal model delta sigma weight residual 1.244 1.079 0.165 1.00e-02 1.00e+04 2.72e+02 bond pdb=" C3' 8AH I2503 " pdb=" C4' 8AH I2503 " ideal model delta sigma weight residual 1.527 1.306 0.221 1.50e-02 4.44e+03 2.17e+02 bond pdb=" C5 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.150 1.435 -0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C5 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.150 1.435 -0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C GLY W 101 " pdb=" O GLY W 101 " ideal model delta sigma weight residual 1.235 1.073 0.162 1.35e-02 5.49e+03 1.44e+02 ... (remaining 156636 not shown) Histogram of bond angle deviations from ideal: 76.68 - 89.79: 3 89.79 - 102.90: 10045 102.90 - 116.01: 183003 116.01 - 129.12: 84327 129.12 - 142.23: 3970 Bond angle restraints: 281348 Sorted by residual: angle pdb=" C ASP Y 91 " pdb=" N ARG Y 92 " pdb=" CA ARG Y 92 " ideal model delta sigma weight residual 120.28 136.90 -16.62 1.34e+00 5.57e-01 1.54e+02 angle pdb=" C1' 8AH I2503 " pdb=" N9 8AH I2503 " pdb=" C4 8AH I2503 " ideal model delta sigma weight residual 90.55 127.74 -37.19 3.00e+00 1.11e-01 1.54e+02 angle pdb=" C1' 8AH I2503 " pdb=" N9 8AH I2503 " pdb=" C8 8AH I2503 " ideal model delta sigma weight residual 159.63 122.97 36.66 3.00e+00 1.11e-01 1.49e+02 angle pdb=" C ASP P 98 " pdb=" N ILE P 99 " pdb=" CA ILE P 99 " ideal model delta sigma weight residual 123.10 138.66 -15.56 1.33e+00 5.65e-01 1.37e+02 angle pdb=" O2' A I 6 " pdb=" C2' A I 6 " pdb=" C1' A I 6 " ideal model delta sigma weight residual 108.40 91.68 16.72 1.50e+00 4.44e-01 1.24e+02 ... (remaining 281343 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 56311 36.00 - 72.00: 3817 72.00 - 108.00: 697 108.00 - 144.00: 16 144.00 - 180.00: 965 Dihedral angle restraints: 61806 sinusoidal: 51620 harmonic: 10186 Sorted by residual: dihedral pdb=" CA ALA P 100 " pdb=" C ALA P 100 " pdb=" N ASP P 101 " pdb=" CA ASP P 101 " ideal model delta harmonic sigma weight residual 180.00 -128.83 -51.17 0 5.00e+00 4.00e-02 1.05e+02 dihedral pdb=" CA ARG P 116 " pdb=" C ARG P 116 " pdb=" N LEU P 117 " pdb=" CA LEU P 117 " ideal model delta harmonic sigma weight residual 180.00 -130.37 -49.63 0 5.00e+00 4.00e-02 9.85e+01 dihedral pdb=" O4' U I1584 " pdb=" C1' U I1584 " pdb=" N1 U I1584 " pdb=" C2 U I1584 " ideal model delta sinusoidal sigma weight residual 200.00 43.41 156.59 1 1.50e+01 4.44e-03 8.18e+01 ... (remaining 61803 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.609: 18850 0.609 - 1.217: 4 1.217 - 1.826: 0 1.826 - 2.435: 2 2.435 - 3.043: 1 Chirality restraints: 18857 Sorted by residual: chirality pdb=" CG LEU R 36 " pdb=" CB LEU R 36 " pdb=" CD1 LEU R 36 " pdb=" CD2 LEU R 36 " both_signs ideal model delta sigma weight residual False -2.59 0.45 -3.04 2.00e-01 2.50e+01 2.32e+02 chirality pdb=" CG LEU X 40 " pdb=" CB LEU X 40 " pdb=" CD1 LEU X 40 " pdb=" CD2 LEU X 40 " both_signs ideal model delta sigma weight residual False -2.59 -0.60 -1.99 2.00e-01 2.50e+01 9.87e+01 chirality pdb=" CG LEU L 79 " pdb=" CB LEU L 79 " pdb=" CD1 LEU L 79 " pdb=" CD2 LEU L 79 " both_signs ideal model delta sigma weight residual False -2.59 -0.68 -1.91 2.00e-01 2.50e+01 9.15e+01 ... (remaining 18854 not shown) Planarity restraints: 12908 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.052 2.00e-02 2.50e+03 6.01e-01 8.12e+03 pdb=" C4' 2MG I2445 " -0.454 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.749 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.595 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.591 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.223 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.898 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.194 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.938 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC I2498 " 0.058 2.00e-02 2.50e+03 5.96e-01 8.00e+03 pdb=" C4' OMC I2498 " 0.450 2.00e-02 2.50e+03 pdb=" O4' OMC I2498 " 0.638 2.00e-02 2.50e+03 pdb=" C3' OMC I2498 " -0.579 2.00e-02 2.50e+03 pdb=" O3' OMC I2498 " -0.634 2.00e-02 2.50e+03 pdb=" C2' OMC I2498 " -0.184 2.00e-02 2.50e+03 pdb=" O2' OMC I2498 " 0.966 2.00e-02 2.50e+03 pdb=" C1' OMC I2498 " 0.201 2.00e-02 2.50e+03 pdb=" N1 OMC I2498 " -0.916 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I1835 " -0.043 2.00e-02 2.50e+03 5.80e-01 7.56e+03 pdb=" C4' 2MG I1835 " -0.438 2.00e-02 2.50e+03 pdb=" O4' 2MG I1835 " -0.692 2.00e-02 2.50e+03 pdb=" C3' 2MG I1835 " 0.596 2.00e-02 2.50e+03 pdb=" O3' 2MG I1835 " 0.567 2.00e-02 2.50e+03 pdb=" C2' 2MG I1835 " 0.223 2.00e-02 2.50e+03 pdb=" O2' 2MG I1835 " -0.891 2.00e-02 2.50e+03 pdb=" C1' 2MG I1835 " -0.209 2.00e-02 2.50e+03 pdb=" N9 2MG I1835 " 0.887 2.00e-02 2.50e+03 ... (remaining 12905 not shown) Histogram of nonbonded interaction distances: 1.17 - 1.86: 953 1.86 - 2.54: 106054 2.54 - 3.23: 413768 3.23 - 3.91: 662929 3.91 - 4.60: 964501 Nonbonded interactions: 2148205 Sorted by model distance: nonbonded pdb="HO2' U I1078 " pdb=" OP1 A I1088 " model vdw 1.174 1.850 nonbonded pdb=" O LYS W 56 " pdb=" HG2 GLU W 60 " model vdw 1.198 2.620 nonbonded pdb=" HA ASN K 70 " pdb="HH12 ARG K 189 " model vdw 1.238 2.270 nonbonded pdb="HO2' A I 332 " pdb=" OP2 C I 334 " model vdw 1.280 1.850 nonbonded pdb="HO2' G I2318 " pdb=" O4 U I2321 " model vdw 1.293 1.850 ... (remaining 2148200 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 179 5.21 5 S 74 5.16 5 Na 1 4.78 5 C 44613 2.51 5 N 16741 2.21 5 O 28107 1.98 5 H 58704 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: 8.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 1.670 Extract box with map and model: 36.420 Check model and map are aligned: 1.670 Convert atoms to be neutral: 0.960 Process input model: 823.250 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.440 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: 0.040 Load rotamer database and sin/cos tables:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 887.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 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 : 0.009 0.285 97937 Z= 0.537 Angle : 0.930 37.189 147190 Z= 0.485 Chirality : 0.062 3.043 18857 Planarity : 0.018 0.601 7416 Dihedral : 14.606 179.582 45965 Min Nonbonded Distance : 1.324 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.06 % Favored : 94.78 % Rotamer Outliers : 0.81 % Cbeta Deviations : 0.27 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.23 % 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: -2.34 (0.13), residues: 3163 helix: -2.10 (0.14), residues: 841 sheet: -1.26 (0.18), residues: 653 loop : -1.28 (0.14), residues: 1669 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 784 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 763 time to evaluate : 5.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 7 residues processed: 777 average time/residue: 3.7035 time to fit residues: 3805.5909 Evaluate side-chains 613 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 606 time to evaluate : 5.293 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 3 average time/residue: 1.4101 time to fit residues: 12.8892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 515 optimal weight: 1.9990 chunk 462 optimal weight: 0.5980 chunk 256 optimal weight: 0.9980 chunk 157 optimal weight: 7.9990 chunk 311 optimal weight: 3.9990 chunk 247 optimal weight: 3.9990 chunk 478 optimal weight: 0.8980 chunk 185 optimal weight: 5.9990 chunk 290 optimal weight: 6.9990 chunk 355 optimal weight: 0.5980 chunk 553 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 60 GLN K 134 ASN ** K 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 195 GLN ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 80 HIS R 128 ASN U 60 GLN X 52 ASN Y 72 ASN g 39 GLN g 58 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.047 97937 Z= 0.158 Angle : 0.633 14.329 147190 Z= 0.343 Chirality : 0.038 1.907 18857 Planarity : 0.006 0.129 7416 Dihedral : 13.942 177.839 39683 Min Nonbonded Distance : 1.371 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.43 % Favored : 95.48 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -1.14 (0.14), residues: 3163 helix: -0.38 (0.17), residues: 857 sheet: -0.86 (0.18), residues: 661 loop : -0.83 (0.15), residues: 1645 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 650 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 610 time to evaluate : 5.456 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 16 residues processed: 626 average time/residue: 3.5129 time to fit residues: 2910.6764 Evaluate side-chains 591 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 575 time to evaluate : 5.236 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 7 residues processed: 9 average time/residue: 1.7461 time to fit residues: 30.9686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 307 optimal weight: 3.9990 chunk 171 optimal weight: 7.9990 chunk 461 optimal weight: 0.0970 chunk 377 optimal weight: 7.9990 chunk 152 optimal weight: 10.0000 chunk 554 optimal weight: 4.9990 chunk 599 optimal weight: 3.9990 chunk 494 optimal weight: 4.9990 chunk 550 optimal weight: 3.9990 chunk 189 optimal weight: 3.9990 chunk 445 optimal weight: 0.5980 overall best weight: 2.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 195 GLN ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 128 ASN U 60 GLN Y 72 ASN Z 86 GLN g 39 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.1990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.072 97937 Z= 0.288 Angle : 0.674 13.706 147190 Z= 0.363 Chirality : 0.041 1.612 18857 Planarity : 0.006 0.137 7416 Dihedral : 13.893 178.554 39683 Min Nonbonded Distance : 1.381 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.19 % Rotamer Outliers : 2.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.14), residues: 3163 helix: 0.22 (0.17), residues: 858 sheet: -0.70 (0.19), residues: 662 loop : -0.67 (0.15), residues: 1643 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 591 time to evaluate : 5.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 58 outliers final: 31 residues processed: 608 average time/residue: 3.5646 time to fit residues: 2883.5639 Evaluate side-chains 607 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 576 time to evaluate : 5.343 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 11 residues processed: 20 average time/residue: 1.8265 time to fit residues: 64.8326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 548 optimal weight: 6.9990 chunk 417 optimal weight: 4.9990 chunk 288 optimal weight: 4.9990 chunk 61 optimal weight: 4.9990 chunk 264 optimal weight: 4.9990 chunk 372 optimal weight: 10.0000 chunk 556 optimal weight: 2.9990 chunk 589 optimal weight: 6.9990 chunk 290 optimal weight: 6.9990 chunk 527 optimal weight: 2.9990 chunk 158 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 195 GLN ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 143 GLN R 128 ASN S 29 HIS U 60 GLN Z 18 GLN Z 86 GLN g 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.095 97937 Z= 0.451 Angle : 0.800 14.498 147190 Z= 0.415 Chirality : 0.047 1.661 18857 Planarity : 0.008 0.147 7416 Dihedral : 14.037 179.965 39683 Min Nonbonded Distance : 1.172 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.06 % Favored : 94.85 % Rotamer Outliers : 2.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.14), residues: 3163 helix: 0.22 (0.17), residues: 867 sheet: -0.62 (0.19), residues: 662 loop : -0.79 (0.15), residues: 1634 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 665 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 595 time to evaluate : 5.413 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 38 residues processed: 625 average time/residue: 3.5654 time to fit residues: 2954.6945 Evaluate side-chains 614 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 576 time to evaluate : 5.213 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 21 residues processed: 18 average time/residue: 1.8217 time to fit residues: 58.6556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 491 optimal weight: 3.9990 chunk 334 optimal weight: 5.9990 chunk 8 optimal weight: 5.9990 chunk 439 optimal weight: 5.9990 chunk 243 optimal weight: 2.9990 chunk 503 optimal weight: 3.9990 chunk 407 optimal weight: 50.0000 chunk 0 optimal weight: 5.9990 chunk 301 optimal weight: 3.9990 chunk 529 optimal weight: 0.0060 chunk 148 optimal weight: 8.9990 overall best weight: 3.0004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 134 ASN K 163 GLN M 136 GLN M 195 GLN ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 128 ASN S 29 HIS U 60 GLN W 98 GLN Y 72 ASN Z 18 GLN Z 86 GLN g 39 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.070 97937 Z= 0.321 Angle : 0.699 13.911 147190 Z= 0.373 Chirality : 0.043 1.637 18857 Planarity : 0.007 0.137 7416 Dihedral : 13.977 179.573 39683 Min Nonbonded Distance : 0.995 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.87 % Favored : 95.04 % Rotamer Outliers : 2.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -0.58 (0.14), residues: 3163 helix: 0.44 (0.18), residues: 869 sheet: -0.49 (0.19), residues: 652 loop : -0.73 (0.15), residues: 1642 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 578 time to evaluate : 5.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 62 outliers final: 42 residues processed: 608 average time/residue: 3.5076 time to fit residues: 2841.7312 Evaluate side-chains 614 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 572 time to evaluate : 5.340 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 25 residues processed: 18 average time/residue: 2.0316 time to fit residues: 63.1179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 198 optimal weight: 3.9990 chunk 530 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 346 optimal weight: 2.9990 chunk 145 optimal weight: 4.9990 chunk 590 optimal weight: 0.5980 chunk 489 optimal weight: 4.9990 chunk 273 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 309 optimal weight: 3.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 134 ASN M 136 GLN M 195 GLN ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 128 ASN U 60 GLN Z 18 GLN e 57 HIS g 39 GLN g 58 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.077 97937 Z= 0.348 Angle : 0.723 13.899 147190 Z= 0.382 Chirality : 0.044 1.653 18857 Planarity : 0.007 0.141 7416 Dihedral : 13.969 179.627 39683 Min Nonbonded Distance : 0.922 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.93 % Favored : 94.97 % Rotamer Outliers : 2.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.50 (0.14), residues: 3163 helix: 0.51 (0.18), residues: 868 sheet: -0.39 (0.19), residues: 647 loop : -0.71 (0.15), residues: 1648 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 578 time to evaluate : 5.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 70 outliers final: 42 residues processed: 612 average time/residue: 3.5675 time to fit residues: 2910.4299 Evaluate side-chains 620 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 578 time to evaluate : 5.441 Switching outliers to nearest non-outliers outliers start: 42 outliers final: 27 residues processed: 16 average time/residue: 2.0074 time to fit residues: 56.7248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 569 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 336 optimal weight: 4.9990 chunk 431 optimal weight: 3.9990 chunk 333 optimal weight: 0.9980 chunk 496 optimal weight: 1.9990 chunk 329 optimal weight: 2.9990 chunk 587 optimal weight: 2.9990 chunk 367 optimal weight: 9.9990 chunk 358 optimal weight: 4.9990 chunk 271 optimal weight: 2.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 134 ASN K 163 GLN M 136 GLN M 195 GLN ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 128 ASN U 60 GLN Z 18 GLN b 28 ASN d 12 GLN g 39 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.067 97937 Z= 0.281 Angle : 0.674 13.749 147190 Z= 0.363 Chirality : 0.041 1.655 18857 Planarity : 0.007 0.136 7416 Dihedral : 13.961 179.898 39683 Min Nonbonded Distance : 1.007 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.87 % Favored : 95.04 % Rotamer Outliers : 2.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % 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: -0.41 (0.14), residues: 3163 helix: 0.62 (0.18), residues: 868 sheet: -0.35 (0.19), residues: 644 loop : -0.65 (0.15), residues: 1651 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 575 time to evaluate : 5.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 53 outliers final: 41 residues processed: 608 average time/residue: 3.5422 time to fit residues: 2877.0469 Evaluate side-chains 610 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 569 time to evaluate : 5.294 Switching outliers to nearest non-outliers outliers start: 41 outliers final: 28 residues processed: 14 average time/residue: 1.7517 time to fit residues: 45.6000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 363 optimal weight: 4.9990 chunk 234 optimal weight: 4.9990 chunk 351 optimal weight: 3.9990 chunk 177 optimal weight: 3.9990 chunk 115 optimal weight: 3.9990 chunk 113 optimal weight: 3.9990 chunk 373 optimal weight: 6.9990 chunk 400 optimal weight: 5.9990 chunk 290 optimal weight: 6.9990 chunk 54 optimal weight: 5.9990 chunk 462 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 134 ASN K 163 GLN L 130 GLN M 136 GLN M 195 GLN ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 128 ASN U 60 GLN Z 18 GLN g 39 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.079 97937 Z= 0.363 Angle : 0.731 13.729 147190 Z= 0.386 Chirality : 0.044 1.656 18857 Planarity : 0.007 0.141 7416 Dihedral : 13.955 179.357 39683 Min Nonbonded Distance : 0.979 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.09 % Allowed : 5.03 % Favored : 94.88 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.46 (0.14), residues: 3163 helix: 0.57 (0.18), residues: 868 sheet: -0.34 (0.19), residues: 651 loop : -0.71 (0.15), residues: 1644 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 644 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 583 time to evaluate : 5.061 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 43 residues processed: 616 average time/residue: 3.4863 time to fit residues: 2851.5875 Evaluate side-chains 616 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 573 time to evaluate : 5.293 Switching outliers to nearest non-outliers outliers start: 43 outliers final: 29 residues processed: 16 average time/residue: 1.9103 time to fit residues: 54.1389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 534 optimal weight: 4.9990 chunk 563 optimal weight: 2.9990 chunk 513 optimal weight: 4.9990 chunk 547 optimal weight: 0.4980 chunk 329 optimal weight: 0.9980 chunk 238 optimal weight: 3.9990 chunk 430 optimal weight: 7.9990 chunk 168 optimal weight: 3.9990 chunk 495 optimal weight: 3.9990 chunk 518 optimal weight: 0.9990 chunk 545 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 134 ASN K 163 GLN M 136 GLN M 195 GLN ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 128 ASN S 29 HIS U 60 GLN ** W 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 18 GLN b 28 ASN d 12 GLN g 39 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.2695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.055 97937 Z= 0.227 Angle : 0.636 13.368 147190 Z= 0.346 Chirality : 0.039 1.651 18857 Planarity : 0.006 0.132 7416 Dihedral : 13.872 178.117 39683 Min Nonbonded Distance : 1.006 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.74 % Favored : 95.16 % Rotamer Outliers : 1.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.15), residues: 3163 helix: 0.72 (0.18), residues: 877 sheet: -0.30 (0.20), residues: 628 loop : -0.63 (0.15), residues: 1658 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 577 time to evaluate : 5.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 46 outliers final: 32 residues processed: 606 average time/residue: 3.5864 time to fit residues: 2890.2601 Evaluate side-chains 602 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 570 time to evaluate : 5.340 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 29 residues processed: 4 average time/residue: 1.8036 time to fit residues: 17.1211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 359 optimal weight: 0.7980 chunk 579 optimal weight: 7.9990 chunk 353 optimal weight: 3.9990 chunk 274 optimal weight: 5.9990 chunk 402 optimal weight: 5.9990 chunk 607 optimal weight: 4.9990 chunk 559 optimal weight: 4.9990 chunk 483 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 373 optimal weight: 0.8980 chunk 296 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 134 ASN M 136 GLN M 195 GLN ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 128 ASN U 60 GLN ** W 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 18 GLN b 28 ASN g 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.069 97937 Z= 0.304 Angle : 0.680 13.463 147190 Z= 0.365 Chirality : 0.042 1.656 18857 Planarity : 0.007 0.137 7416 Dihedral : 13.866 178.367 39683 Min Nonbonded Distance : 0.989 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.71 % Favored : 95.19 % Rotamer Outliers : 1.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.32 (0.14), residues: 3163 helix: 0.72 (0.18), residues: 871 sheet: -0.29 (0.19), residues: 654 loop : -0.62 (0.15), residues: 1638 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6326 Ramachandran restraints generated. 3163 Oldfield, 0 Emsley, 3163 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 581 time to evaluate : 5.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 36 residues processed: 610 average time/residue: 3.5536 time to fit residues: 2875.9391 Evaluate side-chains 616 residues out of total 2607 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 580 time to evaluate : 5.302 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 29 residues processed: 8 average time/residue: 1.7435 time to fit residues: 28.3594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 610 random chunks: chunk 384 optimal weight: 3.9990 chunk 515 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 446 optimal weight: 0.4980 chunk 71 optimal weight: 8.9990 chunk 134 optimal weight: 3.9990 chunk 484 optimal weight: 3.9990 chunk 202 optimal weight: 2.9990 chunk 497 optimal weight: 3.9990 chunk 61 optimal weight: 4.9990 chunk 89 optimal weight: 9.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 134 ASN M 136 GLN M 195 GLN ** O 101 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 128 ASN U 60 GLN b 28 ASN d 12 GLN g 39 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.143359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 83)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.098508 restraints weight = 175041.749| |-----------------------------------------------------------------------------| r_work (start): 0.3061 rms_B_bonded: 0.54 r_work: 0.3029 rms_B_bonded: 0.63 restraints_weight: 0.5000 r_work: 0.3010 rms_B_bonded: 0.81 restraints_weight: 0.2500 r_work: 0.2985 rms_B_bonded: 1.09 restraints_weight: 0.1250 r_work: 0.2949 rms_B_bonded: 1.53 restraints_weight: 0.0625 r_work: 0.2899 rms_B_bonded: 2.23 restraints_weight: 0.0312 r_work: 0.2826 rms_B_bonded: 3.34 restraints_weight: 0.0156 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3623 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3623 r_free = 0.3623 target_work(ls_wunit_k1) = 0.143 | | occupancies: max = 1.00 min = 0.69 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3623 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.2758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.072 97937 Z= 0.338 Angle : 0.706 13.595 147190 Z= 0.376 Chirality : 0.043 1.654 18857 Planarity : 0.007 0.140 7416 Dihedral : 13.900 179.540 39683 Min Nonbonded Distance : 0.971 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.74 % Favored : 95.16 % Rotamer Outliers : 1.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.37 (0.14), residues: 3163 helix: 0.64 (0.18), residues: 872 sheet: -0.27 (0.19), residues: 654 loop : -0.65 (0.15), residues: 1637 =============================================================================== Job complete usr+sys time: 56216.44 seconds wall clock time: 953 minutes 1.67 seconds (57181.67 seconds total)