Starting phenix.real_space_refine on Sat Mar 2 21:03:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pj6_20353/03_2024/6pj6_20353_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pj6_20353/03_2024/6pj6_20353.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pj6_20353/03_2024/6pj6_20353_trim_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pj6_20353/03_2024/6pj6_20353_trim_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pj6_20353/03_2024/6pj6_20353_trim_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pj6_20353/03_2024/6pj6_20353.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pj6_20353/03_2024/6pj6_20353.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pj6_20353/03_2024/6pj6_20353_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pj6_20353/03_2024/6pj6_20353_trim_updated.pdb" } resolution = 2.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.035 sd= 2.434 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 9 Type Number sf(0) Gaussians Zn 1 6.06 5 P 3016 5.49 5 Mg 185 5.21 5 S 80 5.16 5 Na 1 4.78 5 C 45240 2.51 5 N 16917 2.21 5 O 29478 1.98 5 H 59624 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 167": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 177": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 182": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 189": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K GLU 194": "OE1" <-> "OE2" Residue "K ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 203": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "K ARG 212": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 64": "OE1" <-> "OE2" Residue "L ARG 77": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 83": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L GLU 89": "OE1" <-> "OE2" Residue "L ARG 169": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "L ARG 184": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M GLU 25": "OE1" <-> "OE2" Residue "M ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 49": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 61": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 102": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 162": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "M ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 71": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 80": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 92": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 102": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 112": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 115": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "N ARG 133": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 153": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 163": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "O ARG 170": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P ARG 27": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "P GLU 55": "OE1" <-> "OE2" Residue "P GLU 70": "OE1" <-> "OE2" Residue "Q GLU 37": "OE1" <-> "OE2" Residue "Q GLU 50": "OE1" <-> "OE2" Residue "R GLU 9": "OE1" <-> "OE2" Residue "R ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R PHE 89": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "R ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "R ARG 120": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "S GLU 106": "OE1" <-> "OE2" Residue "T ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 60": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "T GLU 86": "OE1" <-> "OE2" Residue "T ARG 126": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 55": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 59": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U ARG 114": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "U PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "V ARG 8": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 17": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 22": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 46": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 63": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 64": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 69": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 71": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V GLU 82": "OE1" <-> "OE2" Residue "V ARG 96": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "V ARG 118": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 25": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 81": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 102": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "W ARG 111": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ARG 39": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ARG 53": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ARG 62": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ARG 89": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ARG 101": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "X ARG 109": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ARG 48": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Y ARG 70": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z ARG 68": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z ARG 78": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z ARG 79": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "Z ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 84": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 88": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 95": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "a ARG 110": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b ARG 73": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "b TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "c ARG 6": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 7": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 82": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 86": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c ARG 94": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "c GLU 101": "OE1" <-> "OE2" Residue "d GLU 55": "OE1" <-> "OE2" Residue "d PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "e ARG 11": "NH1" <-> "NH2" Residue "f ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 11": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 18": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 37": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f GLU 43": "OE1" <-> "OE2" Residue "f ARG 50": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 57": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "f ARG 74": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g GLU 12": "OE1" <-> "OE2" Residue "g GLU 24": "OE1" <-> "OE2" Residue "g ARG 29": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 47": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "g ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h ARG 11": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "h GLU 37": "OE1" <-> "OE2" Residue "h ARG 45": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i ARG 10": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i ARG 16": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "i GLU 36": "OE1" <-> "OE2" Residue "i ARG 52": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "j ARG 44": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 3": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 12": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 14": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 19": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 21": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 33": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "k ARG 41": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ARG 13": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ARG 30": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ARG 40": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "l ARG 42": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "m ARG 24": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 154542 Number of models: 1 Model: "" Number of chains: 67 Chain: "I" Number of atoms: 93260 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2898, 93260 Classifications: {'RNA': 2898} Modifications used: {'3*END': 1, 'rna2p': 7, 'rna2p_pur': 275, 'rna2p_pyr': 145, 'rna3p': 17, 'rna3p_pur': 1389, 'rna3p_pyr': 1065} Link IDs: {'rna2p': 427, 'rna3p': 2470} Chain breaks: 1 Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 10 Chain: "J" Number of atoms: 3810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 3810 Classifications: {'RNA': 118} Modifications used: {'3*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 6, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 13, 'rna3p': 104} Chain: "K" Number of atoms: 4261 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 271, 4237 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} Conformer: "B" Number of residues, atoms: 271, 4237 Classifications: {'peptide': 271} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 17, 'TRANS': 253} bond proxies already assigned to first conformer: 4251 Chain: "L" Number of atoms: 3175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 3175 Classifications: {'peptide': 209} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain: "M" Number of atoms: 3171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 3171 Classifications: {'peptide': 201} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "N" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 2855 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "O" Number of atoms: 2694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 2694 Classifications: {'peptide': 176} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 167} Chain: "P" Number of atoms: 2258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 2258 Classifications: {'peptide': 149} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "Q" Number of atoms: 2007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 2007 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 9, 'TRANS': 124} Chain: "R" Number of atoms: 2291 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 2291 Classifications: {'peptide': 142} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "S" Number of atoms: 1950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1950 Classifications: {'peptide': 122} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 5, 'TRANS': 116} Chain: "T" Number of atoms: 2169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2169 Classifications: {'peptide': 144} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "U" Number of atoms: 2219 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2219 Classifications: {'peptide': 136} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "V" Number of atoms: 1960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 1960 Classifications: {'peptide': 120} Modifications used: {'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 115} Chain: "W" Number of atoms: 1815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 1815 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "X" Number of atoms: 1879 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 1879 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Y" Number of atoms: 1967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 1967 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "Z" Number of atoms: 1582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 1582 Classifications: {'peptide': 103} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 101} Chain: "a" Number of atoms: 1779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 1779 Classifications: {'peptide': 110} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "b" Number of atoms: 1546 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 1546 Classifications: {'peptide': 93} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 91} Chain: "c" Number of atoms: 1611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 1611 Classifications: {'peptide': 102} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "d" Number of atoms: 1533 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 1533 Classifications: {'peptide': 94} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "e" Number of atoms: 1156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1156 Classifications: {'peptide': 75} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 73} Chain: "f" Number of atoms: 1277 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1277 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "g" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 1032 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "h" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 937 Classifications: {'peptide': 58} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "i" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 902 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "j" Number of atoms: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 849 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "k" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 795 Classifications: {'peptide': 46} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "l" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 1076 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "m" Number of atoms: 642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 642 Classifications: {'peptide': 38} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "I" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 182 Unusual residues: {' MG': 182} Classifications: {'undetermined': 182} Link IDs: {None: 181} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' NA': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 3347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3347, 3347 Classifications: {'water': 3347} Link IDs: {None: 3346} Chain: "J" Number of atoms: 62 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 62 Classifications: {'water': 62} Link IDs: {None: 61} Chain: "K" Number of atoms: 59 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 59 Classifications: {'water': 59} Link IDs: {None: 58} Chain: "L" Number of atoms: 41 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 41 Classifications: {'water': 41} Link IDs: {None: 40} Chain: "M" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 42 Classifications: {'water': 42} Link IDs: {None: 41} Chain: "N" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "O" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "P" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "Q" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "R" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 17 Classifications: {'water': 17} Link IDs: {None: 16} Chain: "S" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "T" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "U" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "V" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 23 Classifications: {'water': 23} Link IDs: {None: 22} Chain: "W" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "X" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 14 Classifications: {'water': 14} Link IDs: {None: 13} Chain: "Y" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 33 Classifications: {'water': 33} Link IDs: {None: 32} Chain: "Z" Number of atoms: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 16, 16 Classifications: {'water': 16} Link IDs: {None: 15} Chain: "a" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 18 Classifications: {'water': 18} Link IDs: {None: 17} Chain: "b" Number of atoms: 15 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 15 Classifications: {'water': 15} Link IDs: {None: 14} Chain: "c" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Classifications: {'water': 7} Link IDs: {None: 6} Chain: "d" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "e" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "f" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "g" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "h" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "i" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "j" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "k" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "l" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "m" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A12KZ SG CYS m 11 73.983 171.248 50.600 1.00 53.85 S ATOM A12MB SG CYS m 14 76.756 170.164 53.407 1.00 50.82 S ATOM A12SL SG CYS m 27 74.801 173.710 52.884 1.00 49.16 S Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N AARG K 203 " occ=0.50 ... (46 atoms not shown) pdb="HH22BARG K 203 " occ=0.50 residue: pdb="MG MG I3123 " occ=0.50 residue: pdb="MG MG I3124 " occ=0.50 Time building chain proxies: 52.14, per 1000 atoms: 0.34 Number of scatterers: 154542 At special positions: 0 Unit cell: (186.594, 228.516, 226.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 9 Type Number sf(0) Zn 1 29.99 S 80 16.00 P 3016 15.00 Mg 185 11.99 Na 1 11.00 O 29478 8.00 N 16917 7.00 C 45240 6.00 H 59624 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 113.19 Conformation dependent library (CDL) restraints added in 5.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN m 101 " pdb="ZN ZN m 101 " - pdb=" ND1 HIS m 33 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 14 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 11 " pdb="ZN ZN m 101 " - pdb=" SG CYS m 27 " Number of angles added : 3 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6122 Finding SS restraints... Warning!!! ksdssp method is not applicable for structures that cannot fit in PDB format. Switching to from_ca. running find_ss_from_ca liberal... Secondary structure from input PDB file: 94 helices and 45 sheets defined 33.3% alpha, 19.0% beta 957 base pairs and 1553 stacking pairs defined. Time for finding SS restraints: 84.84 Creating SS restraints... Processing helix chain 'K' and resid 10 through 17 removed outlier: 7.610A pdb=" N HIS K 15 " --> pdb=" O PRO K 11 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N VAL K 16 " --> pdb=" O GLY K 12 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL K 17 " --> pdb=" O ARG K 13 " (cutoff:3.500A) Processing helix chain 'K' and resid 131 through 136 Proline residue: K 136 - end of helix Processing helix chain 'K' and resid 207 through 215 removed outlier: 4.166A pdb=" N ALA K 211 " --> pdb=" O LYS K 207 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG K 214 " --> pdb=" O ALA K 210 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY K 215 " --> pdb=" O ALA K 211 " (cutoff:3.500A) Processing helix chain 'K' and resid 221 through 226 removed outlier: 3.657A pdb=" N MET K 225 " --> pdb=" O ARG K 221 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N ASN K 226 " --> pdb=" O GLY K 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 221 through 226' Processing helix chain 'K' and resid 260 through 268 removed outlier: 6.556A pdb=" N ASP K 264 " --> pdb=" O ASN K 260 " (cutoff:3.500A) removed outlier: 5.515A pdb=" N LYS K 265 " --> pdb=" O LYS K 261 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N PHE K 266 " --> pdb=" O ARG K 262 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE K 267 " --> pdb=" O THR K 263 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N VAL K 268 " --> pdb=" O ASP K 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 260 through 268' Processing helix chain 'K' and resid 197 through 202 removed outlier: 4.011A pdb=" N MET K 201 " --> pdb=" O ALA K 198 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 61 removed outlier: 5.381A pdb=" N THR L 61 " --> pdb=" O ALA L 57 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 72 removed outlier: 3.590A pdb=" N ALA L 71 " --> pdb=" O HIS L 67 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 103 removed outlier: 4.140A pdb=" N ALA L 102 " --> pdb=" O VAL L 98 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N ASP L 103 " --> pdb=" O GLU L 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 98 through 103' Processing helix chain 'L' and resid 120 through 125 Processing helix chain 'L' and resid 39 through 44 Processing helix chain 'M' and resid 24 through 40 removed outlier: 3.566A pdb=" N ARG M 40 " --> pdb=" O ALA M 36 " (cutoff:3.500A) Processing helix chain 'M' and resid 48 through 53 removed outlier: 5.813A pdb=" N THR M 53 " --> pdb=" O ARG M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 97 through 116 Processing helix chain 'M' and resid 130 through 142 Processing helix chain 'M' and resid 154 through 163 removed outlier: 4.307A pdb=" N ASN M 163 " --> pdb=" O LEU M 159 " (cutoff:3.500A) Processing helix chain 'M' and resid 176 through 183 removed outlier: 3.524A pdb=" N PHE M 183 " --> pdb=" O SER M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 201 Processing helix chain 'M' and resid 16 through 21 Processing helix chain 'N' and resid 2 through 11 removed outlier: 3.610A pdb=" N ASP N 6 " --> pdb=" O ALA N 2 " (cutoff:3.500A) Processing helix chain 'N' and resid 12 through 21 removed outlier: 3.607A pdb=" N ASN N 21 " --> pdb=" O MET N 17 " (cutoff:3.500A) Processing helix chain 'N' and resid 46 through 62 removed outlier: 4.426A pdb=" N LEU N 50 " --> pdb=" O ASP N 46 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP N 51 " --> pdb=" O LYS N 47 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE N 60 " --> pdb=" O ASP N 56 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N GLY N 62 " --> pdb=" O ALA N 58 " (cutoff:3.500A) Processing helix chain 'N' and resid 93 through 111 removed outlier: 4.094A pdb=" N ILE N 106 " --> pdb=" O ARG N 102 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N VAL N 108 " --> pdb=" O ILE N 104 " (cutoff:3.500A) Proline residue: N 109 - end of helix Processing helix chain 'N' and resid 162 through 174 removed outlier: 3.552A pdb=" N LEU N 170 " --> pdb=" O GLY N 166 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N PHE N 173 " --> pdb=" O LEU N 169 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ASP N 174 " --> pdb=" O LEU N 170 " (cutoff:3.500A) Processing helix chain 'N' and resid 134 through 139 removed outlier: 3.659A pdb=" N ILE N 137 " --> pdb=" O GLU N 134 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE N 138 " --> pdb=" O GLN N 135 " (cutoff:3.500A) Proline residue: N 139 - end of helix No H-bonds generated for 'chain 'N' and resid 134 through 139' Processing helix chain 'O' and resid 2 through 8 Proline residue: O 8 - end of helix Processing helix chain 'O' and resid 60 through 81 removed outlier: 4.550A pdb=" N GLN O 64 " --> pdb=" O ASP O 60 " (cutoff:3.500A) Processing helix chain 'O' and resid 137 through 153 removed outlier: 3.851A pdb=" N ILE O 141 " --> pdb=" O ASP O 137 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR O 151 " --> pdb=" O ASP O 147 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ARG O 152 " --> pdb=" O LEU O 148 " (cutoff:3.500A) Processing helix chain 'P' and resid 22 through 28 Processing helix chain 'P' and resid 29 through 34 removed outlier: 4.287A pdb=" N GLY P 34 " --> pdb=" O LEU P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 40 through 76 removed outlier: 6.536A pdb=" N ILE P 44 " --> pdb=" O THR P 40 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N GLU P 45 " --> pdb=" O LYS P 41 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N PHE P 47 " --> pdb=" O ASN P 43 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N GLU P 48 " --> pdb=" O ILE P 44 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N ARG P 50 " --> pdb=" O PHE P 46 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N ARG P 51 " --> pdb=" O PHE P 47 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N LEU P 54 " --> pdb=" O ARG P 50 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N GLU P 55 " --> pdb=" O ARG P 51 " (cutoff:3.500A) removed outlier: 5.796A pdb=" N GLU P 60 " --> pdb=" O ALA P 56 " (cutoff:3.500A) removed outlier: 5.526A pdb=" N VAL P 61 " --> pdb=" O LYS P 57 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LEU P 62 " --> pdb=" O LEU P 58 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N ALA P 63 " --> pdb=" O ALA P 59 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N ALA P 64 " --> pdb=" O GLU P 60 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ASN P 66 " --> pdb=" O LEU P 62 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ALA P 67 " --> pdb=" O ALA P 63 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ALA P 69 " --> pdb=" O ALA P 65 " (cutoff:3.500A) removed outlier: 4.676A pdb=" N LYS P 71 " --> pdb=" O ALA P 67 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N ASN P 73 " --> pdb=" O ALA P 69 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N ALA P 74 " --> pdb=" O GLU P 70 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N LEU P 75 " --> pdb=" O LYS P 71 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU P 76 " --> pdb=" O ILE P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 95 through 105 removed outlier: 4.705A pdb=" N ILE P 99 " --> pdb=" O GLY P 95 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N VAL P 103 " --> pdb=" O ILE P 99 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N THR P 104 " --> pdb=" O ALA P 100 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N ALA P 105 " --> pdb=" O ASP P 101 " (cutoff:3.500A) Processing helix chain 'P' and resid 111 through 116 removed outlier: 3.560A pdb=" N VAL P 115 " --> pdb=" O ALA P 111 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N ARG P 116 " --> pdb=" O LYS P 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 111 through 116' Processing helix chain 'Q' and resid 22 through 28 Proline residue: Q 26 - end of helix No H-bonds generated for 'chain 'Q' and resid 22 through 28' Processing helix chain 'Q' and resid 34 through 47 removed outlier: 4.011A pdb=" N LYS Q 40 " --> pdb=" O MET Q 36 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N ASN Q 43 " --> pdb=" O CYS Q 39 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 81 removed outlier: 5.358A pdb=" N LEU Q 79 " --> pdb=" O PRO Q 75 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N LEU Q 80 " --> pdb=" O ALA Q 76 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LYS Q 81 " --> pdb=" O ALA Q 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 75 through 81' Processing helix chain 'Q' and resid 102 through 114 removed outlier: 4.657A pdb=" N THR Q 112 " --> pdb=" O GLU Q 108 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LYS Q 113 " --> pdb=" O ILE Q 109 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ALA Q 114 " --> pdb=" O ALA Q 110 " (cutoff:3.500A) Processing helix chain 'Q' and resid 125 through 137 removed outlier: 3.562A pdb=" N ILE Q 129 " --> pdb=" O MET Q 125 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N GLU Q 130 " --> pdb=" O THR Q 126 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N THR Q 132 " --> pdb=" O SER Q 128 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ALA Q 133 " --> pdb=" O ILE Q 129 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG Q 134 " --> pdb=" O GLU Q 130 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N SER Q 135 " --> pdb=" O GLY Q 131 " (cutoff:3.500A) Processing helix chain 'R' and resid 24 through 38 removed outlier: 3.705A pdb=" N GLU R 31 " --> pdb=" O ARG R 27 " (cutoff:3.500A) Processing helix chain 'R' and resid 88 through 96 Processing helix chain 'R' and resid 97 through 110 removed outlier: 4.340A pdb=" N ILE R 101 " --> pdb=" O PRO R 97 " (cutoff:3.500A) Proline residue: R 110 - end of helix Processing helix chain 'R' and resid 112 through 123 removed outlier: 3.566A pdb=" N ARG R 120 " --> pdb=" O ARG R 116 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LYS R 121 " --> pdb=" O ALA R 117 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N LEU R 122 " --> pdb=" O MET R 118 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N LYS R 123 " --> pdb=" O PHE R 119 " (cutoff:3.500A) Processing helix chain 'S' and resid 104 through 109 removed outlier: 4.666A pdb=" N ARG S 108 " --> pdb=" O THR S 104 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N SER S 109 " --> pdb=" O ARG S 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 104 through 109' Processing helix chain 'S' and resid 112 through 119 removed outlier: 3.625A pdb=" N ILE S 116 " --> pdb=" O PHE S 112 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N LEU S 118 " --> pdb=" O LYS S 114 " (cutoff:3.500A) Processing helix chain 'T' and resid 37 through 42 removed outlier: 5.538A pdb=" N SER T 42 " --> pdb=" O GLN T 38 " (cutoff:3.500A) Processing helix chain 'T' and resid 56 through 62 Proline residue: T 62 - end of helix Processing helix chain 'T' and resid 68 through 75 removed outlier: 4.295A pdb=" N ALA T 72 " --> pdb=" O SER T 68 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE T 73 " --> pdb=" O ARG T 69 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ALA T 75 " --> pdb=" O ALA T 71 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 85 removed outlier: 3.898A pdb=" N LEU T 82 " --> pdb=" O ARG T 78 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA T 83 " --> pdb=" O LEU T 79 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N LYS T 84 " --> pdb=" O SER T 80 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N VAL T 85 " --> pdb=" O ASP T 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 78 through 85' Processing helix chain 'T' and resid 91 through 99 Processing helix chain 'T' and resid 128 through 139 removed outlier: 3.865A pdb=" N ALA T 138 " --> pdb=" O ALA T 134 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLY T 139 " --> pdb=" O ILE T 135 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 58 removed outlier: 4.179A pdb=" N LYS U 58 " --> pdb=" O THR U 54 " (cutoff:3.500A) Processing helix chain 'U' and resid 109 through 125 removed outlier: 3.815A pdb=" N LYS U 123 " --> pdb=" O LEU U 119 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU U 124 " --> pdb=" O ALA U 120 " (cutoff:3.500A) Proline residue: U 125 - end of helix Processing helix chain 'V' and resid 13 through 32 Processing helix chain 'V' and resid 37 through 58 removed outlier: 4.044A pdb=" N ARG V 46 " --> pdb=" O LYS V 42 " (cutoff:3.500A) Proline residue: V 50 - end of helix removed outlier: 3.570A pdb=" N LYS V 56 " --> pdb=" O ILE V 52 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N THR V 57 " --> pdb=" O THR V 53 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ASP V 58 " --> pdb=" O LEU V 54 " (cutoff:3.500A) Processing helix chain 'V' and resid 59 through 71 Processing helix chain 'V' and resid 72 through 88 removed outlier: 4.860A pdb=" N GLY V 84 " --> pdb=" O PHE V 80 " (cutoff:3.500A) Proline residue: V 85 - end of helix Processing helix chain 'W' and resid 2 through 22 removed outlier: 3.577A pdb=" N ARG W 7 " --> pdb=" O LYS W 3 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N ARG W 13 " --> pdb=" O ARG W 9 " (cutoff:3.500A) removed outlier: 5.790A pdb=" N ALA W 14 " --> pdb=" O ARG W 10 " (cutoff:3.500A) Processing helix chain 'W' and resid 58 through 63 removed outlier: 6.427A pdb=" N LEU W 62 " --> pdb=" O ILE W 58 " (cutoff:3.500A) removed outlier: 5.528A pdb=" N LYS W 63 " --> pdb=" O ALA W 59 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 58 through 63' Processing helix chain 'W' and resid 67 through 86 Processing helix chain 'W' and resid 101 through 114 Processing helix chain 'X' and resid 2 through 13 removed outlier: 4.339A pdb=" N GLN X 12 " --> pdb=" O LEU X 8 " (cutoff:3.500A) Processing helix chain 'X' and resid 97 through 104 removed outlier: 4.648A pdb=" N ARG X 101 " --> pdb=" O LEU X 97 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLU X 102 " --> pdb=" O TYR X 98 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ARG X 103 " --> pdb=" O TYR X 99 " (cutoff:3.500A) removed outlier: 5.219A pdb=" N THR X 104 " --> pdb=" O LEU X 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 97 through 104' Processing helix chain 'Y' and resid 6 through 22 removed outlier: 3.645A pdb=" N ILE Y 17 " --> pdb=" O ARG Y 13 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS Y 22 " --> pdb=" O LEU Y 18 " (cutoff:3.500A) Processing helix chain 'Y' and resid 26 through 31 Processing helix chain 'Y' and resid 32 through 37 removed outlier: 3.855A pdb=" N GLN Y 37 " --> pdb=" O ARG Y 33 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 73 removed outlier: 3.765A pdb=" N ARG Y 51 " --> pdb=" O TYR Y 47 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N LYS Y 54 " --> pdb=" O ARG Y 50 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ARG Y 55 " --> pdb=" O ARG Y 51 " (cutoff:3.500A) Processing helix chain 'Y' and resid 75 through 87 Processing helix chain 'Y' and resid 91 through 102 Processing helix chain 'Y' and resid 103 through 118 Processing helix chain 'a' and resid 13 through 25 removed outlier: 3.569A pdb=" N LEU a 19 " --> pdb=" O GLN a 15 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL a 20 " --> pdb=" O LYS a 16 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N LEU a 23 " --> pdb=" O LEU a 19 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ILE a 24 " --> pdb=" O VAL a 20 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG a 25 " --> pdb=" O ALA a 21 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 39 removed outlier: 3.590A pdb=" N TYR a 38 " --> pdb=" O ASP a 34 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 61 removed outlier: 3.693A pdb=" N VAL a 45 " --> pdb=" O LYS a 41 " (cutoff:3.500A) Processing helix chain 'b' and resid 3 through 11 removed outlier: 3.861A pdb=" N LYS b 9 " --> pdb=" O GLU b 5 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL b 10 " --> pdb=" O ARG b 6 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N LEU b 11 " --> pdb=" O LEU b 7 " (cutoff:3.500A) Processing helix chain 'b' and resid 17 through 26 Processing helix chain 'b' and resid 39 through 51 Processing helix chain 'c' and resid 66 through 71 removed outlier: 3.946A pdb=" N VAL c 70 " --> pdb=" O GLN c 66 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N ALA c 71 " --> pdb=" O VAL c 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 66 through 71' Processing helix chain 'd' and resid 13 through 24 removed outlier: 3.525A pdb=" N ALA d 23 " --> pdb=" O ARG d 19 " (cutoff:3.500A) Processing helix chain 'd' and resid 43 through 53 removed outlier: 4.276A pdb=" N LYS d 53 " --> pdb=" O ASN d 49 " (cutoff:3.500A) Processing helix chain 'd' and resid 54 through 59 removed outlier: 4.277A pdb=" N SER d 58 " --> pdb=" O ALA d 54 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLU d 59 " --> pdb=" O GLU d 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 54 through 59' Processing helix chain 'f' and resid 52 through 63 Processing helix chain 'f' and resid 64 through 75 Processing helix chain 'g' and resid 2 through 10 removed outlier: 3.583A pdb=" N LEU g 6 " --> pdb=" O LYS g 2 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU g 8 " --> pdb=" O LYS g 4 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N LYS g 9 " --> pdb=" O GLU g 5 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N SER g 10 " --> pdb=" O LEU g 6 " (cutoff:3.500A) Processing helix chain 'g' and resid 11 through 35 removed outlier: 6.479A pdb=" N THR g 16 " --> pdb=" O GLU g 12 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU g 17 " --> pdb=" O GLU g 13 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N GLY g 35 " --> pdb=" O GLN g 31 " (cutoff:3.500A) Processing helix chain 'g' and resid 40 through 62 removed outlier: 4.589A pdb=" N LYS g 44 " --> pdb=" O SER g 40 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N GLY g 62 " --> pdb=" O ASN g 58 " (cutoff:3.500A) Processing helix chain 'h' and resid 17 through 28 Processing helix chain 'h' and resid 41 through 52 Processing helix chain 'i' and resid 9 through 19 removed outlier: 5.068A pdb=" N HIS i 19 " --> pdb=" O MET i 15 " (cutoff:3.500A) Processing helix chain 'k' and resid 8 through 16 Processing helix chain 'k' and resid 17 through 25 removed outlier: 4.159A pdb=" N THR k 24 " --> pdb=" O ALA k 20 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N LYS k 25 " --> pdb=" O ARG k 21 " (cutoff:3.500A) Processing helix chain 'k' and resid 26 through 38 Processing helix chain 'l' and resid 7 through 14 removed outlier: 4.001A pdb=" N ARG l 13 " --> pdb=" O GLY l 9 " (cutoff:3.500A) Processing helix chain 'l' and resid 32 through 37 removed outlier: 4.427A pdb=" N LYS l 36 " --> pdb=" O ILE l 32 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N ALA l 37 " --> pdb=" O LEU l 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 32 through 37' Processing helix chain 'l' and resid 38 through 46 Proline residue: l 46 - end of helix Processing helix chain 'l' and resid 51 through 63 removed outlier: 4.560A pdb=" N GLY l 56 " --> pdb=" O LYS l 52 " (cutoff:3.500A) removed outlier: 5.289A pdb=" N LEU l 57 " --> pdb=" O GLY l 53 " (cutoff:3.500A) Proline residue: l 63 - end of helix Processing sheet with id= 1, first strand: chain 'K' and resid 33 through 36 No H-bonds generated for sheet with id= 1 Processing sheet with id= 2, first strand: chain 'K' and resid 73 through 78 removed outlier: 4.913A pdb=" N ILE K 74 " --> pdb=" O SER K 118 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N SER K 118 " --> pdb=" O ILE K 74 " (cutoff:3.500A) removed outlier: 4.605A pdb=" N ASP K 114 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY K 127 " --> pdb=" O GLN K 115 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N GLN K 117 " --> pdb=" O GLY K 127 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'K' and resid 80 through 83 removed outlier: 5.543A pdb=" N ASN K 90 " --> pdb=" O ALA K 106 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'K' and resid 162 through 165 removed outlier: 6.711A pdb=" N THR K 173 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N GLU K 180 " --> pdb=" O LEU K 176 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'L' and resid 3 through 6 Processing sheet with id= 6, first strand: chain 'L' and resid 10 through 16 removed outlier: 3.747A pdb=" N GLY L 10 " --> pdb=" O VAL L 26 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL L 20 " --> pdb=" O THR L 16 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'L' and resid 79 through 84 removed outlier: 5.823A pdb=" N ARG L 46 " --> pdb=" O LEU L 84 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N GLN L 49 " --> pdb=" O THR L 35 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N GLN L 94 " --> pdb=" O VAL L 34 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'L' and resid 105 through 108 removed outlier: 6.191A pdb=" N LYS L 105 " --> pdb=" O VAL L 177 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'M' and resid 1 through 4 removed outlier: 4.637A pdb=" N MET M 1 " --> pdb=" O VAL M 14 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'M' and resid 117 through 120 removed outlier: 5.534A pdb=" N ARG M 117 " --> pdb=" O ASP M 184 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'N' and resid 65 through 69 removed outlier: 4.366A pdb=" N GLY N 86 " --> pdb=" O THR N 68 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N CYS N 87 " --> pdb=" O MET N 38 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N LYS N 33 " --> pdb=" O THR N 157 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N GLY N 39 " --> pdb=" O GLY N 151 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N GLY N 151 " --> pdb=" O GLY N 39 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'O' and resid 15 through 19 removed outlier: 3.549A pdb=" N ASP O 16 " --> pdb=" O LYS O 27 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N GLY O 28 " --> pdb=" O GLY O 31 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'O' and resid 41 through 45 removed outlier: 3.629A pdb=" N GLY O 53 " --> pdb=" O GLU O 42 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LYS O 44 " --> pdb=" O THR O 51 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N THR O 51 " --> pdb=" O LYS O 44 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'O' and resid 94 through 99 removed outlier: 5.546A pdb=" N VAL O 102 " --> pdb=" O LYS O 99 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ASN O 101 " --> pdb=" O LEU O 117 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'O' and resid 121 through 125 removed outlier: 5.774A pdb=" N THR O 129 " --> pdb=" O LEU O 89 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS O 85 " --> pdb=" O LEU O 133 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'P' and resid 2 through 5 removed outlier: 4.038A pdb=" N LEU P 5 " --> pdb=" O ASP P 17 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N ASP P 17 " --> pdb=" O LEU P 5 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'R' and resid 15 through 18 Processing sheet with id= 18, first strand: chain 'R' and resid 74 through 78 removed outlier: 7.954A pdb=" N GLY R 83 " --> pdb=" O THR R 78 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'S' and resid 18 through 21 removed outlier: 4.188A pdb=" N THR S 6 " --> pdb=" O CYS S 21 " (cutoff:3.500A) removed outlier: 5.686A pdb=" N ASN S 82 " --> pdb=" O MET S 7 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU S 86 " --> pdb=" O ALA S 11 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N ASP S 37 " --> pdb=" O VAL S 62 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'T' and resid 120 through 123 Processing sheet with id= 21, first strand: chain 'U' and resid 62 through 65 removed outlier: 3.635A pdb=" N TYR U 103 " --> pdb=" O LEU U 33 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N LEU U 33 " --> pdb=" O LEU U 102 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N LYS U 100 " --> pdb=" O ALA U 35 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'U' and resid 30 through 36 removed outlier: 7.903A pdb=" N SER U 30 " --> pdb=" O LYS U 133 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N LYS U 127 " --> pdb=" O VAL U 36 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'V' and resid 33 through 36 removed outlier: 5.945A pdb=" N ALA V 108 " --> pdb=" O PHE V 102 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N PHE V 102 " --> pdb=" O ALA V 108 " (cutoff:3.500A) removed outlier: 5.839A pdb=" N MET V 110 " --> pdb=" O CYS V 100 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'W' and resid 49 through 53 removed outlier: 3.704A pdb=" N VAL W 49 " --> pdb=" O VAL W 39 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ILE W 35 " --> pdb=" O THR W 53 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'X' and resid 38 through 45 removed outlier: 6.515A pdb=" N THR X 25 " --> pdb=" O LYS X 87 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER X 83 " --> pdb=" O LYS X 29 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'X' and resid 49 through 53 removed outlier: 3.704A pdb=" N ALA X 49 " --> pdb=" O THR X 60 " (cutoff:3.500A) removed outlier: 4.305A pdb=" N ARG X 53 " --> pdb=" O HIS X 56 " (cutoff:3.500A) removed outlier: 7.811A pdb=" N SER X 57 " --> pdb=" O THR X 76 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'Z' and resid 11 through 15 removed outlier: 3.557A pdb=" N MET Z 40 " --> pdb=" O VAL Z 4 " (cutoff:3.500A) removed outlier: 5.499A pdb=" N GLU Z 46 " --> pdb=" O ASN Z 43 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'Z' and resid 18 through 23 removed outlier: 4.320A pdb=" N GLN Z 18 " --> pdb=" O ILE Z 98 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ASP Z 95 " --> pdb=" O VAL Z 64 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LYS Z 60 " --> pdb=" O THR Z 99 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N GLU Z 31 " --> pdb=" O VAL Z 63 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'Z' and resid 57 through 60 Processing sheet with id= 30, first strand: chain 'Z' and resid 65 through 68 Processing sheet with id= 31, first strand: chain 'Z' and resid 69 through 78 removed outlier: 5.480A pdb=" N GLU Z 70 " --> pdb=" O GLN Z 91 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N GLN Z 91 " --> pdb=" O GLU Z 70 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR Z 83 " --> pdb=" O ARG Z 78 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'a' and resid 2 through 8 removed outlier: 4.856A pdb=" N THR a 100 " --> pdb=" O GLY a 79 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'a' and resid 81 through 88 removed outlier: 4.039A pdb=" N ARG a 92 " --> pdb=" O ARG a 88 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'b' and resid 12 through 15 removed outlier: 5.233A pdb=" N VAL b 31 " --> pdb=" O HIS b 15 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N ASN b 28 " --> pdb=" O LEU b 87 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N LYS b 81 " --> pdb=" O VAL b 34 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS b 66 " --> pdb=" O ARG b 77 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N ASP b 79 " --> pdb=" O LYS b 64 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N LYS b 64 " --> pdb=" O ASP b 79 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N LYS b 81 " --> pdb=" O VAL b 62 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N VAL b 62 " --> pdb=" O LYS b 81 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ALA b 83 " --> pdb=" O THR b 60 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N THR b 60 " --> pdb=" O ALA b 83 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N VAL b 85 " --> pdb=" O VAL b 58 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N VAL b 58 " --> pdb=" O VAL b 85 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'c' and resid 82 through 86 removed outlier: 7.503A pdb=" N ARG c 82 " --> pdb=" O LYS c 97 " (cutoff:3.500A) removed outlier: 5.507A pdb=" N ARG c 94 " --> pdb=" O ILE c 103 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU c 101 " --> pdb=" O PHE c 96 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'd' and resid 69 through 72 removed outlier: 6.474A pdb=" N ALA d 39 " --> pdb=" O ARG d 9 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ILE d 89 " --> pdb=" O PRO d 27 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'e' and resid 51 through 54 removed outlier: 4.124A pdb=" N THR e 58 " --> pdb=" O GLY e 54 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'e' and resid 65 through 71 Processing sheet with id= 39, first strand: chain 'f' and resid 12 through 19 removed outlier: 4.381A pdb=" N ASN f 23 " --> pdb=" O SER f 19 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'f' and resid 34 through 41 Processing sheet with id= 41, first strand: chain 'h' and resid 34 through 39 removed outlier: 4.245A pdb=" N HIS h 34 " --> pdb=" O GLN h 9 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N MET h 54 " --> pdb=" O THR h 10 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'j' and resid 8 through 13 removed outlier: 5.923A pdb=" N HIS j 19 " --> pdb=" O SER j 13 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'j' and resid 33 through 39 removed outlier: 4.365A pdb=" N LEU j 34 " --> pdb=" O GLU j 51 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N GLU j 51 " --> pdb=" O LEU j 34 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'l' and resid 22 through 25 removed outlier: 5.619A pdb=" N PHE l 22 " --> pdb=" O VAL l 50 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'm' and resid 14 through 19 removed outlier: 5.942A pdb=" N VAL m 22 " --> pdb=" O ARG m 19 " (cutoff:3.500A) 925 hydrogen bonds defined for protein. 2712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2399 hydrogen bonds 3798 hydrogen bond angles 0 basepair planarities 957 basepair parallelities 1553 stacking parallelities Total time for adding SS restraints: 353.42 Time building geometry restraints manager: 118.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.28: 66749 1.28 - 1.74: 91678 1.74 - 2.20: 146 2.20 - 2.66: 0 2.66 - 3.12: 2 Bond restraints: 158575 Sorted by residual: bond pdb=" C5' C I2606 " pdb=" H5' C I2606 " ideal model delta sigma weight residual 0.970 3.125 -2.155 2.00e-02 2.50e+03 1.16e+04 bond pdb=" C5' G I2607 " pdb=" H5' G I2607 " ideal model delta sigma weight residual 0.970 2.869 -1.899 2.00e-02 2.50e+03 9.02e+03 bond pdb=" C5 5MU I1939 " pdb=" C6 5MU I1939 " ideal model delta sigma weight residual 1.155 1.437 -0.282 2.00e-02 2.50e+03 1.99e+02 bond pdb=" C5 5MU I 747 " pdb=" C6 5MU I 747 " ideal model delta sigma weight residual 1.155 1.434 -0.279 2.00e-02 2.50e+03 1.94e+02 bond pdb=" C4 5MU I 747 " pdb=" C5 5MU I 747 " ideal model delta sigma weight residual 1.802 1.594 0.208 2.00e-02 2.50e+03 1.08e+02 ... (remaining 158570 not shown) Histogram of bond angle deviations from ideal: 62.62 - 78.67: 5 78.67 - 94.72: 3 94.72 - 110.77: 148750 110.77 - 126.83: 127613 126.83 - 142.88: 8450 Bond angle restraints: 284821 Sorted by residual: angle pdb=" H5' G I2607 " pdb=" C5' G I2607 " pdb="H5'' G I2607 " ideal model delta sigma weight residual 109.00 62.62 46.38 3.00e+00 1.11e-01 2.39e+02 angle pdb=" C5' A I 752 " pdb=" C4' A I 752 " pdb=" H4' A I 752 " ideal model delta sigma weight residual 109.00 70.66 38.34 3.00e+00 1.11e-01 1.63e+02 angle pdb=" C5' U I 138 " pdb=" C4' U I 138 " pdb=" H4' U I 138 " ideal model delta sigma weight residual 109.00 73.67 35.33 3.00e+00 1.11e-01 1.39e+02 angle pdb=" C4' C I2606 " pdb=" C3' C I2606 " pdb=" O3' C I2606 " ideal model delta sigma weight residual 113.00 129.12 -16.12 1.50e+00 4.44e-01 1.16e+02 angle pdb=" O4' U I 138 " pdb=" C4' U I 138 " pdb=" H4' U I 138 " ideal model delta sigma weight residual 109.00 78.34 30.66 3.00e+00 1.11e-01 1.04e+02 ... (remaining 284816 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.58: 66658 35.58 - 71.17: 10062 71.17 - 106.75: 1479 106.75 - 142.33: 12 142.33 - 177.91: 24 Dihedral angle restraints: 78235 sinusoidal: 67639 harmonic: 10596 Sorted by residual: dihedral pdb=" O4' U I 546 " pdb=" C1' U I 546 " pdb=" N1 U I 546 " pdb=" C2 U I 546 " ideal model delta sinusoidal sigma weight residual 200.00 26.73 173.27 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' U I 545 " pdb=" C1' U I 545 " pdb=" N1 U I 545 " pdb=" C2 U I 545 " ideal model delta sinusoidal sigma weight residual 200.00 29.81 170.19 1 1.50e+01 4.44e-03 8.47e+01 dihedral pdb=" O4' U I1174 " pdb=" C1' U I1174 " pdb=" N1 U I1174 " pdb=" C2 U I1174 " ideal model delta sinusoidal sigma weight residual 200.00 30.62 169.38 1 1.50e+01 4.44e-03 8.46e+01 ... (remaining 78232 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.160: 18757 0.160 - 0.321: 239 0.321 - 0.481: 10 0.481 - 0.641: 3 0.641 - 0.801: 2 Chirality restraints: 19011 Sorted by residual: chirality pdb=" CA ASP Y 49 " pdb=" N ASP Y 49 " pdb=" C ASP Y 49 " pdb=" CB ASP Y 49 " both_signs ideal model delta sigma weight residual False 2.51 1.71 0.80 2.00e-01 2.50e+01 1.61e+01 chirality pdb=" C4' U I 138 " pdb=" C5' U I 138 " pdb=" O4' U I 138 " pdb=" C3' U I 138 " both_signs ideal model delta sigma weight residual False -2.50 -1.75 -0.75 2.00e-01 2.50e+01 1.41e+01 chirality pdb=" C4' A I 752 " pdb=" C5' A I 752 " pdb=" O4' A I 752 " pdb=" C3' A I 752 " both_signs ideal model delta sigma weight residual False -2.50 -1.91 -0.60 2.00e-01 2.50e+01 8.85e+00 ... (remaining 19008 not shown) Planarity restraints: 13200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I1835 " -0.067 2.00e-02 2.50e+03 6.10e-01 8.37e+03 pdb=" C4' 2MG I1835 " -0.451 2.00e-02 2.50e+03 pdb=" O4' 2MG I1835 " -0.727 2.00e-02 2.50e+03 pdb=" C3' 2MG I1835 " 0.602 2.00e-02 2.50e+03 pdb=" O3' 2MG I1835 " 0.626 2.00e-02 2.50e+03 pdb=" C2' 2MG I1835 " 0.206 2.00e-02 2.50e+03 pdb=" O2' 2MG I1835 " -0.940 2.00e-02 2.50e+03 pdb=" C1' 2MG I1835 " -0.193 2.00e-02 2.50e+03 pdb=" N9 2MG I1835 " 0.945 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMC I2498 " 0.081 2.00e-02 2.50e+03 6.08e-01 8.33e+03 pdb=" C4' OMC I2498 " 0.446 2.00e-02 2.50e+03 pdb=" O4' OMC I2498 " 0.630 2.00e-02 2.50e+03 pdb=" C3' OMC I2498 " -0.592 2.00e-02 2.50e+03 pdb=" O3' OMC I2498 " -0.673 2.00e-02 2.50e+03 pdb=" C2' OMC I2498 " -0.168 2.00e-02 2.50e+03 pdb=" O2' OMC I2498 " 1.002 2.00e-02 2.50e+03 pdb=" C1' OMC I2498 " 0.198 2.00e-02 2.50e+03 pdb=" N1 OMC I2498 " -0.925 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG I2445 " -0.015 2.00e-02 2.50e+03 5.78e-01 7.51e+03 pdb=" C4' 2MG I2445 " -0.453 2.00e-02 2.50e+03 pdb=" O4' 2MG I2445 " -0.723 2.00e-02 2.50e+03 pdb=" C3' 2MG I2445 " 0.580 2.00e-02 2.50e+03 pdb=" O3' 2MG I2445 " 0.551 2.00e-02 2.50e+03 pdb=" C2' 2MG I2445 " 0.234 2.00e-02 2.50e+03 pdb=" O2' 2MG I2445 " -0.859 2.00e-02 2.50e+03 pdb=" C1' 2MG I2445 " -0.208 2.00e-02 2.50e+03 pdb=" N9 2MG I2445 " 0.895 2.00e-02 2.50e+03 ... (remaining 13197 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.85: 678 1.85 - 2.53: 103136 2.53 - 3.22: 427019 3.22 - 3.91: 667860 3.91 - 4.60: 985510 Nonbonded interactions: 2184203 Sorted by model distance: nonbonded pdb=" OD2 ASP S 80 " pdb=" HA3 GLY X 69 " model vdw 1.157 2.620 nonbonded pdb="HG22 THR O 25 " pdb="HG23 THR O 34 " model vdw 1.181 2.440 nonbonded pdb="MG MG I3123 " pdb="MG MG I3124 " model vdw 1.227 1.300 nonbonded pdb=" OP1 G I1266 " pdb=" HE ARG i 16 " model vdw 1.228 1.850 nonbonded pdb=" HZ3 LYS K 242 " pdb=" O HOH K 401 " model vdw 1.248 1.850 ... (remaining 2184198 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 7.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 1.740 Extract box with map and model: 32.420 Check model and map are aligned: 1.650 Set scattering table: 1.020 Process input model: 765.630 Find NCS groups from input model: 2.340 Set up NCS constraints: 0.340 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:12.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 825.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.282 98951 Z= 0.672 Angle : 1.069 24.182 148560 Z= 0.586 Chirality : 0.060 0.801 19011 Planarity : 0.020 0.610 7598 Dihedral : 23.521 177.915 57208 Min Nonbonded Distance : 1.227 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.58 % Favored : 94.36 % Rotamer: Outliers : 2.25 % Allowed : 7.01 % Favored : 90.74 % Cbeta Deviations : 0.46 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.65 (0.12), residues: 3298 helix: -2.22 (0.14), residues: 865 sheet: -1.14 (0.18), residues: 652 loop : -1.73 (0.13), residues: 1781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP L 80 HIS 0.018 0.003 HIS Z 89 PHE 0.037 0.004 PHE Y 57 TYR 0.046 0.004 TYR Y 32 ARG 0.066 0.002 ARG Y 48 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 837 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 777 time to evaluate : 4.941 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 114 ASP cc_start: 0.7762 (m-30) cc_final: 0.7507 (m-30) REVERT: K 125 LYS cc_start: 0.7032 (mttm) cc_final: 0.6795 (mmmt) REVERT: N 44 ILE cc_start: 0.7317 (pt) cc_final: 0.6998 (pp) REVERT: N 64 LYS cc_start: 0.5565 (pttm) cc_final: 0.4999 (mmtt) REVERT: N 102 ARG cc_start: 0.6043 (ttm110) cc_final: 0.5298 (ttm170) REVERT: O 3 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7810 (mtm180) REVERT: O 124 GLU cc_start: 0.7118 (mt-10) cc_final: 0.6572 (pp20) REVERT: P 8 LYS cc_start: 0.7445 (ttpt) cc_final: 0.7141 (ttpp) REVERT: Q 36 MET cc_start: 0.3040 (ttp) cc_final: 0.2471 (tpt) REVERT: Q 117 MET cc_start: -0.0940 (tpp) cc_final: -0.1486 (ttp) REVERT: R 81 ILE cc_start: 0.8867 (OUTLIER) cc_final: 0.8323 (pp) REVERT: R 98 GLU cc_start: 0.7489 (mp0) cc_final: 0.7049 (mp0) REVERT: R 138 GLN cc_start: 0.7689 (mt0) cc_final: 0.7172 (mm110) REVERT: S 114 LYS cc_start: 0.7341 (tttp) cc_final: 0.6921 (mmmt) REVERT: T 78 ARG cc_start: 0.7641 (mtp-110) cc_final: 0.6990 (mtt90) REVERT: T 91 ASP cc_start: 0.6724 (t0) cc_final: 0.6434 (t70) REVERT: U 59 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.6404 (mmt90) REVERT: W 13 ARG cc_start: 0.7455 (ttt90) cc_final: 0.7165 (ttt-90) REVERT: Z 60 LYS cc_start: 0.7634 (mtmm) cc_final: 0.7310 (mmmm) REVERT: c 86 ARG cc_start: 0.8339 (OUTLIER) cc_final: 0.6940 (ptp-170) REVERT: c 101 GLU cc_start: 0.7147 (mm-30) cc_final: 0.6828 (mm-30) REVERT: f 2 SER cc_start: 0.7960 (p) cc_final: 0.7742 (m) REVERT: g 11 VAL cc_start: 0.7886 (t) cc_final: 0.7444 (t) REVERT: i 12 LYS cc_start: 0.8304 (mmmt) cc_final: 0.8063 (mmtm) REVERT: k 1 MET cc_start: 0.7297 (mtp) cc_final: 0.7064 (mtp) REVERT: m 9 LYS cc_start: 0.8210 (mtpt) cc_final: 0.7924 (mttm) outliers start: 60 outliers final: 29 residues processed: 820 average time/residue: 3.8142 time to fit residues: 4052.3822 Evaluate side-chains 612 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 579 time to evaluate : 5.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain N residue 137 ILE Chi-restraints excluded: chain O residue 3 ARG Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 25 THR Chi-restraints excluded: chain O residue 35 ARG Chi-restraints excluded: chain O residue 152 ARG Chi-restraints excluded: chain P residue 48 GLU Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain S residue 28 SER Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 116 VAL Chi-restraints excluded: chain T residue 123 ARG Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 59 ARG Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 67 VAL Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 96 ARG Chi-restraints excluded: chain V residue 114 GLU Chi-restraints excluded: chain W residue 9 ARG Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain Y residue 52 GLN Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain b residue 12 ARG Chi-restraints excluded: chain c residue 86 ARG Chi-restraints excluded: chain h residue 10 THR Chi-restraints excluded: chain k residue 44 VAL Chi-restraints excluded: chain m residue 4 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 623 random chunks: chunk 526 optimal weight: 0.9980 chunk 472 optimal weight: 0.9980 chunk 262 optimal weight: 0.7980 chunk 161 optimal weight: 2.9990 chunk 318 optimal weight: 1.9990 chunk 252 optimal weight: 7.9990 chunk 488 optimal weight: 0.8980 chunk 188 optimal weight: 8.9990 chunk 296 optimal weight: 1.9990 chunk 363 optimal weight: 4.9990 chunk 565 optimal weight: 3.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 37 ASN K 60 GLN K 153 GLN L 32 ASN L 130 GLN M 115 GLN M 136 GLN P 66 ASN ** Q 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 43 ASN R 128 ASN T 35 HIS U 22 GLN V 11 ASN Y 44 GLN Y 52 GLN a 61 ASN g 27 ASN i 5 GLN i 6 ASN j 26 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.114 98951 Z= 0.150 Angle : 0.627 14.435 148560 Z= 0.344 Chirality : 0.036 0.775 19011 Planarity : 0.006 0.127 7598 Dihedral : 23.842 179.404 50759 Min Nonbonded Distance : 1.077 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.31 % Favored : 95.66 % Rotamer: Outliers : 2.95 % Allowed : 15.56 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.13), residues: 3298 helix: -0.60 (0.17), residues: 876 sheet: -0.78 (0.19), residues: 676 loop : -1.29 (0.14), residues: 1746 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 248 HIS 0.006 0.001 HIS l 31 PHE 0.014 0.001 PHE N 77 TYR 0.013 0.001 TYR W 36 ARG 0.010 0.001 ARG L 33 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 692 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 613 time to evaluate : 5.470 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: K 35 GLU cc_start: 0.8179 (mt-10) cc_final: 0.7939 (mt-10) REVERT: K 128 ASN cc_start: 0.8299 (m-40) cc_final: 0.7983 (m110) REVERT: K 183 LYS cc_start: 0.8080 (mttm) cc_final: 0.7820 (mtpm) REVERT: K 195 VAL cc_start: 0.7738 (OUTLIER) cc_final: 0.7320 (p) REVERT: L 128 ARG cc_start: 0.7765 (mtp180) cc_final: 0.7368 (mmt180) REVERT: M 69 ARG cc_start: 0.8750 (OUTLIER) cc_final: 0.7358 (ptp-170) REVERT: M 145 ASP cc_start: 0.7482 (t70) cc_final: 0.7117 (t0) REVERT: N 64 LYS cc_start: 0.5600 (pttm) cc_final: 0.5136 (mmtt) REVERT: N 102 ARG cc_start: 0.6129 (ttm110) cc_final: 0.5296 (ttm170) REVERT: O 85 LYS cc_start: 0.7236 (OUTLIER) cc_final: 0.7005 (tttp) REVERT: O 124 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6315 (pp20) REVERT: Q 36 MET cc_start: 0.3460 (ttp) cc_final: 0.2669 (tpt) REVERT: Q 117 MET cc_start: -0.0948 (tpp) cc_final: -0.1275 (ttp) REVERT: Q 125 MET cc_start: 0.2888 (ptt) cc_final: 0.2637 (ptp) REVERT: R 81 ILE cc_start: 0.8667 (OUTLIER) cc_final: 0.8117 (pp) REVERT: R 118 MET cc_start: 0.8503 (mtt) cc_final: 0.8269 (mtt) REVERT: T 78 ARG cc_start: 0.7457 (mtp-110) cc_final: 0.6984 (mtt90) REVERT: U 59 ARG cc_start: 0.6720 (OUTLIER) cc_final: 0.5936 (mmt90) REVERT: U 135 VAL cc_start: 0.7287 (OUTLIER) cc_final: 0.7027 (p) REVERT: V 49 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7597 (mt-10) REVERT: Z 1 MET cc_start: 0.7965 (tpt) cc_final: 0.7673 (tpt) REVERT: Z 45 GLU cc_start: 0.6572 (OUTLIER) cc_final: 0.6114 (mm-30) REVERT: Z 60 LYS cc_start: 0.7592 (mtmm) cc_final: 0.7379 (mttp) REVERT: b 74 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8045 (tp) REVERT: d 24 ASN cc_start: 0.7915 (m-40) cc_final: 0.7422 (t0) REVERT: d 53 LYS cc_start: 0.7782 (mttp) cc_final: 0.7493 (mmmt) REVERT: f 2 SER cc_start: 0.7875 (p) cc_final: 0.7665 (m) REVERT: h 58 GLU cc_start: 0.6690 (OUTLIER) cc_final: 0.6398 (tm-30) REVERT: i 10 ARG cc_start: 0.8230 (mtm-85) cc_final: 0.7991 (mtm-85) REVERT: j 45 GLN cc_start: 0.7816 (OUTLIER) cc_final: 0.7514 (mt0) REVERT: k 41 ARG cc_start: 0.7775 (mtm-85) cc_final: 0.7427 (mtm-85) REVERT: m 26 ILE cc_start: 0.8537 (pt) cc_final: 0.8290 (pp) outliers start: 79 outliers final: 31 residues processed: 655 average time/residue: 3.7250 time to fit residues: 3185.9340 Evaluate side-chains 600 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 559 time to evaluate : 5.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 37 ASN Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 85 LYS Chi-restraints excluded: chain O residue 152 ARG Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 131 ASN Chi-restraints excluded: chain S residue 28 SER Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 107 LEU Chi-restraints excluded: chain S residue 116 ILE Chi-restraints excluded: chain T residue 80 SER Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 59 ARG Chi-restraints excluded: chain U residue 65 ILE Chi-restraints excluded: chain U residue 135 VAL Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 27 SER Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain V residue 114 GLU Chi-restraints excluded: chain W residue 9 ARG Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain X residue 7 GLN Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain Y residue 87 SER Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain Z residue 45 GLU Chi-restraints excluded: chain Z residue 73 LYS Chi-restraints excluded: chain b residue 12 ARG Chi-restraints excluded: chain b residue 74 ILE Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain h residue 56 LYS Chi-restraints excluded: chain h residue 58 GLU Chi-restraints excluded: chain j residue 45 GLN Chi-restraints excluded: chain j residue 47 VAL Chi-restraints excluded: chain m residue 4 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 623 random chunks: chunk 314 optimal weight: 9.9990 chunk 175 optimal weight: 8.9990 chunk 470 optimal weight: 9.9990 chunk 385 optimal weight: 0.2980 chunk 156 optimal weight: 7.9990 chunk 566 optimal weight: 10.0000 chunk 612 optimal weight: 5.9990 chunk 504 optimal weight: 0.0980 chunk 562 optimal weight: 8.9990 chunk 193 optimal weight: 8.9990 chunk 454 optimal weight: 3.9990 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 ASN M 136 GLN N 27 GLN R 58 ASN R 128 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 45 GLN W 38 GLN X 10 GLN Y 44 GLN a 61 ASN d 49 ASN f 16 ASN g 27 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 98951 Z= 0.247 Angle : 0.645 13.445 148560 Z= 0.353 Chirality : 0.039 0.778 19011 Planarity : 0.006 0.136 7598 Dihedral : 23.752 179.339 50721 Min Nonbonded Distance : 0.978 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.89 % Favored : 95.08 % Rotamer: Outliers : 3.06 % Allowed : 17.18 % Favored : 79.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.85 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.14), residues: 3298 helix: -0.05 (0.17), residues: 878 sheet: -0.60 (0.19), residues: 656 loop : -1.16 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 248 HIS 0.006 0.001 HIS a 7 PHE 0.015 0.001 PHE N 77 TYR 0.014 0.002 TYR K 103 ARG 0.015 0.001 ARG Y 28 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 83 poor density : 580 time to evaluate : 5.603 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: K 130 LEU cc_start: 0.7869 (OUTLIER) cc_final: 0.7499 (pt) REVERT: L 128 ARG cc_start: 0.7800 (mtp180) cc_final: 0.7340 (mmt180) REVERT: M 40 ARG cc_start: 0.8559 (OUTLIER) cc_final: 0.7122 (mtt180) REVERT: M 69 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7301 (ptp-170) REVERT: M 145 ASP cc_start: 0.7520 (t70) cc_final: 0.7186 (t0) REVERT: N 64 LYS cc_start: 0.5614 (pttm) cc_final: 0.5106 (mmtt) REVERT: N 102 ARG cc_start: 0.6197 (ttm110) cc_final: 0.5262 (ttm170) REVERT: N 153 ASP cc_start: 0.6216 (m-30) cc_final: 0.5993 (m-30) REVERT: O 124 GLU cc_start: 0.6833 (mt-10) cc_final: 0.6281 (pp20) REVERT: P 9 VAL cc_start: 0.6928 (OUTLIER) cc_final: 0.6715 (t) REVERT: Q 36 MET cc_start: 0.3192 (ttp) cc_final: 0.2390 (tpt) REVERT: Q 117 MET cc_start: -0.1001 (tpp) cc_final: -0.1346 (ttp) REVERT: Q 125 MET cc_start: 0.2717 (ptp) cc_final: 0.2412 (ptp) REVERT: R 81 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8207 (pp) REVERT: R 118 MET cc_start: 0.8541 (mtt) cc_final: 0.8332 (mtt) REVERT: T 78 ARG cc_start: 0.7489 (mtp-110) cc_final: 0.6982 (mtt90) REVERT: U 59 ARG cc_start: 0.6846 (OUTLIER) cc_final: 0.6594 (mmt90) REVERT: Z 60 LYS cc_start: 0.7737 (mtmm) cc_final: 0.7491 (mttp) REVERT: c 12 ILE cc_start: 0.9013 (OUTLIER) cc_final: 0.8810 (tt) REVERT: d 24 ASN cc_start: 0.7854 (m-40) cc_final: 0.7484 (t0) REVERT: d 69 GLU cc_start: 0.7974 (OUTLIER) cc_final: 0.7426 (mp0) REVERT: h 58 GLU cc_start: 0.6715 (OUTLIER) cc_final: 0.6418 (tm-30) REVERT: i 10 ARG cc_start: 0.8280 (mtm-85) cc_final: 0.8070 (mtm-85) REVERT: j 45 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7613 (mt0) REVERT: m 4 ARG cc_start: 0.8227 (OUTLIER) cc_final: 0.7725 (ptt180) REVERT: m 26 ILE cc_start: 0.8608 (pt) cc_final: 0.8351 (pp) outliers start: 83 outliers final: 46 residues processed: 624 average time/residue: 3.7539 time to fit residues: 3061.3520 Evaluate side-chains 604 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 547 time to evaluate : 5.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 115 GLN Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain M residue 40 ARG Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 49 THR Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain O residue 152 ARG Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 131 ASN Chi-restraints excluded: chain S residue 28 SER Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 116 ILE Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 80 SER Chi-restraints excluded: chain T residue 117 THR Chi-restraints excluded: chain U residue 25 ASP Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 59 ARG Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 27 SER Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain W residue 9 ARG Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain W residue 89 ASP Chi-restraints excluded: chain W residue 91 SER Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain a residue 3 THR Chi-restraints excluded: chain a residue 108 SER Chi-restraints excluded: chain c residue 12 ILE Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 46 GLN Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain f residue 35 SER Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain h residue 52 SER Chi-restraints excluded: chain h residue 58 GLU Chi-restraints excluded: chain j residue 45 GLN Chi-restraints excluded: chain k residue 44 VAL Chi-restraints excluded: chain m residue 4 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 623 random chunks: chunk 559 optimal weight: 7.9990 chunk 426 optimal weight: 0.3980 chunk 294 optimal weight: 10.0000 chunk 62 optimal weight: 7.9990 chunk 270 optimal weight: 6.9990 chunk 380 optimal weight: 9.9990 chunk 568 optimal weight: 8.9990 chunk 602 optimal weight: 9.9990 chunk 297 optimal weight: 7.9990 chunk 539 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 37 ASN L 32 ASN P 20 ASN R 128 ASN T 99 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 44 GLN f 17 ASN g 27 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8342 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 98951 Z= 0.359 Angle : 0.724 13.368 148560 Z= 0.386 Chirality : 0.043 0.770 19011 Planarity : 0.007 0.138 7598 Dihedral : 23.836 179.408 50712 Min Nonbonded Distance : 0.912 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.58 % Favored : 94.39 % Rotamer: Outliers : 3.91 % Allowed : 17.92 % Favored : 78.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.12 (0.14), residues: 3298 helix: 0.04 (0.17), residues: 879 sheet: -0.66 (0.19), residues: 670 loop : -1.16 (0.14), residues: 1749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP U 92 HIS 0.007 0.002 HIS X 77 PHE 0.017 0.002 PHE N 77 TYR 0.017 0.002 TYR O 157 ARG 0.009 0.001 ARG a 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 106 poor density : 554 time to evaluate : 5.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 130 LEU cc_start: 0.7937 (OUTLIER) cc_final: 0.7534 (pt) REVERT: K 183 LYS cc_start: 0.8034 (mttm) cc_final: 0.7798 (mtpm) REVERT: L 89 GLU cc_start: 0.7124 (OUTLIER) cc_final: 0.6532 (mm-30) REVERT: L 128 ARG cc_start: 0.7837 (mtp180) cc_final: 0.7315 (mmt180) REVERT: M 69 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.7527 (ptp-170) REVERT: N 10 ASP cc_start: 0.5155 (OUTLIER) cc_final: 0.4904 (t0) REVERT: N 64 LYS cc_start: 0.5643 (pttm) cc_final: 0.5142 (mmtt) REVERT: N 94 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.6853 (mm-30) REVERT: N 102 ARG cc_start: 0.6545 (ttm110) cc_final: 0.5368 (ttm170) REVERT: N 142 ASP cc_start: 0.3228 (m-30) cc_final: 0.2948 (m-30) REVERT: N 153 ASP cc_start: 0.6303 (m-30) cc_final: 0.6016 (m-30) REVERT: O 45 HIS cc_start: 0.5688 (OUTLIER) cc_final: 0.5360 (m-70) REVERT: O 124 GLU cc_start: 0.6963 (mt-10) cc_final: 0.6351 (pp20) REVERT: P 9 VAL cc_start: 0.7516 (OUTLIER) cc_final: 0.7238 (t) REVERT: P 47 PHE cc_start: 0.4474 (OUTLIER) cc_final: 0.4206 (t80) REVERT: Q 36 MET cc_start: 0.2991 (ttp) cc_final: 0.2211 (tpt) REVERT: Q 117 MET cc_start: -0.0964 (tpp) cc_final: -0.1269 (ttp) REVERT: T 78 ARG cc_start: 0.7508 (mtp-110) cc_final: 0.6999 (mtt90) REVERT: T 141 LYS cc_start: 0.6883 (ttmm) cc_final: 0.6594 (ttmm) REVERT: W 93 ASP cc_start: 0.8768 (t0) cc_final: 0.8448 (t0) REVERT: Z 60 LYS cc_start: 0.7754 (mtmm) cc_final: 0.7520 (mttp) REVERT: c 7 ARG cc_start: 0.7227 (OUTLIER) cc_final: 0.5931 (tpt90) REVERT: c 12 ILE cc_start: 0.9064 (OUTLIER) cc_final: 0.8848 (tt) REVERT: d 24 ASN cc_start: 0.7857 (m-40) cc_final: 0.7615 (t0) REVERT: d 69 GLU cc_start: 0.7893 (OUTLIER) cc_final: 0.7334 (mp0) REVERT: h 58 GLU cc_start: 0.6801 (OUTLIER) cc_final: 0.6348 (mm-30) REVERT: j 45 GLN cc_start: 0.8033 (OUTLIER) cc_final: 0.7693 (mt0) REVERT: m 1 MET cc_start: 0.7926 (ptp) cc_final: 0.7574 (ptp) REVERT: m 4 ARG cc_start: 0.8223 (OUTLIER) cc_final: 0.7531 (ptt180) REVERT: m 13 ASN cc_start: 0.7915 (m110) cc_final: 0.7687 (m-40) outliers start: 106 outliers final: 56 residues processed: 615 average time/residue: 3.6644 time to fit residues: 2959.4147 Evaluate side-chains 606 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 536 time to evaluate : 7.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain M residue 40 ARG Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 10 ASP Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 94 GLU Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 45 HIS Chi-restraints excluded: chain O residue 49 THR Chi-restraints excluded: chain O residue 51 THR Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain O residue 114 ASP Chi-restraints excluded: chain O residue 152 ARG Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 47 PHE Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 131 ASN Chi-restraints excluded: chain S residue 28 SER Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 116 ILE Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 80 SER Chi-restraints excluded: chain T residue 117 THR Chi-restraints excluded: chain U residue 25 ASP Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain V residue 27 SER Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain W residue 9 ARG Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 40 ILE Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain a residue 3 THR Chi-restraints excluded: chain a residue 108 SER Chi-restraints excluded: chain c residue 7 ARG Chi-restraints excluded: chain c residue 12 ILE Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 46 GLN Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain f residue 35 SER Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain h residue 58 GLU Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain j residue 27 LYS Chi-restraints excluded: chain j residue 45 GLN Chi-restraints excluded: chain k residue 44 VAL Chi-restraints excluded: chain m residue 4 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 623 random chunks: chunk 501 optimal weight: 1.9990 chunk 341 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 448 optimal weight: 4.9990 chunk 248 optimal weight: 10.0000 chunk 513 optimal weight: 4.9990 chunk 416 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 307 optimal weight: 4.9990 chunk 540 optimal weight: 3.9990 chunk 151 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: ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 134 ASN L 32 ASN P 20 ASN R 128 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 45 GLN Y 44 GLN f 17 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8314 moved from start: 0.2841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 98951 Z= 0.271 Angle : 0.650 13.440 148560 Z= 0.354 Chirality : 0.039 0.782 19011 Planarity : 0.006 0.134 7598 Dihedral : 23.754 179.416 50707 Min Nonbonded Distance : 0.991 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.24 % Allowed : 19.40 % Favored : 77.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.14), residues: 3298 helix: 0.25 (0.18), residues: 881 sheet: -0.56 (0.19), residues: 674 loop : -1.09 (0.14), residues: 1743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 248 HIS 0.006 0.001 HIS d 44 PHE 0.013 0.001 PHE N 77 TYR 0.015 0.002 TYR O 157 ARG 0.009 0.001 ARG i 10 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 647 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 559 time to evaluate : 5.311 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 130 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7531 (pt) REVERT: K 183 LYS cc_start: 0.8028 (mttm) cc_final: 0.7780 (mtpm) REVERT: K 269 ARG cc_start: 0.7676 (OUTLIER) cc_final: 0.7213 (ttm-80) REVERT: L 89 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6525 (mm-30) REVERT: L 128 ARG cc_start: 0.7817 (mtp180) cc_final: 0.7315 (mmt180) REVERT: M 40 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.7302 (mtt180) REVERT: M 69 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7429 (ptp-170) REVERT: N 64 LYS cc_start: 0.5626 (pttm) cc_final: 0.5149 (mmtt) REVERT: N 102 ARG cc_start: 0.6531 (ttm110) cc_final: 0.5328 (ttm170) REVERT: N 153 ASP cc_start: 0.6283 (m-30) cc_final: 0.6031 (m-30) REVERT: O 124 GLU cc_start: 0.6960 (mt-10) cc_final: 0.6363 (pp20) REVERT: P 9 VAL cc_start: 0.7483 (OUTLIER) cc_final: 0.7205 (t) REVERT: P 47 PHE cc_start: 0.4272 (OUTLIER) cc_final: 0.4066 (t80) REVERT: Q 36 MET cc_start: 0.3085 (ttp) cc_final: 0.2106 (tpt) REVERT: Q 117 MET cc_start: -0.0970 (tpp) cc_final: -0.1219 (ttp) REVERT: T 78 ARG cc_start: 0.7527 (mtp-110) cc_final: 0.7043 (mtt90) REVERT: T 141 LYS cc_start: 0.6858 (ttmm) cc_final: 0.6607 (ttmm) REVERT: U 22 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.6286 (mp-120) REVERT: U 133 LYS cc_start: 0.8485 (OUTLIER) cc_final: 0.8162 (tttm) REVERT: V 32 GLU cc_start: 0.8325 (OUTLIER) cc_final: 0.7580 (mm-30) REVERT: W 69 ASP cc_start: 0.7242 (m-30) cc_final: 0.6788 (t0) REVERT: Z 60 LYS cc_start: 0.7753 (mtmm) cc_final: 0.7528 (mttp) REVERT: c 7 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.5971 (tpt90) REVERT: c 12 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8824 (tt) REVERT: g 8 GLU cc_start: 0.6488 (mm-30) cc_final: 0.6261 (mm-30) REVERT: h 58 GLU cc_start: 0.6793 (OUTLIER) cc_final: 0.6476 (tm-30) REVERT: j 45 GLN cc_start: 0.7982 (OUTLIER) cc_final: 0.7637 (mt0) REVERT: m 1 MET cc_start: 0.7938 (ptp) cc_final: 0.7506 (ptp) REVERT: m 13 ASN cc_start: 0.7978 (m110) cc_final: 0.7727 (m-40) outliers start: 88 outliers final: 57 residues processed: 603 average time/residue: 3.7271 time to fit residues: 2974.8269 Evaluate side-chains 616 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 545 time to evaluate : 5.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain L residue 1 MET Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain M residue 40 ARG Chi-restraints excluded: chain M residue 58 LYS Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 85 ILE Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 49 THR Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain O residue 114 ASP Chi-restraints excluded: chain O residue 152 ARG Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 47 PHE Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain Q residue 28 LEU Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 131 ASN Chi-restraints excluded: chain S residue 28 SER Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 116 ILE Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 80 SER Chi-restraints excluded: chain U residue 22 GLN Chi-restraints excluded: chain U residue 25 ASP Chi-restraints excluded: chain U residue 133 LYS Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 27 SER Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain W residue 9 ARG Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 40 ILE Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain a residue 3 THR Chi-restraints excluded: chain a residue 108 SER Chi-restraints excluded: chain c residue 7 ARG Chi-restraints excluded: chain c residue 12 ILE Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain f residue 35 SER Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain h residue 58 GLU Chi-restraints excluded: chain j residue 45 GLN Chi-restraints excluded: chain k residue 44 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 623 random chunks: chunk 202 optimal weight: 6.9990 chunk 542 optimal weight: 10.0000 chunk 119 optimal weight: 7.9990 chunk 353 optimal weight: 4.9990 chunk 148 optimal weight: 9.9990 chunk 602 optimal weight: 7.9990 chunk 500 optimal weight: 10.0000 chunk 279 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 199 optimal weight: 6.9990 chunk 316 optimal weight: 0.1980 overall best weight: 5.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 ASN P 18 GLN R 128 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 44 GLN d 24 ASN f 17 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.2914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.068 98951 Z= 0.344 Angle : 0.705 13.546 148560 Z= 0.377 Chirality : 0.042 0.777 19011 Planarity : 0.007 0.137 7598 Dihedral : 23.805 179.265 50702 Min Nonbonded Distance : 0.919 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.98 % Allowed : 19.51 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.14), residues: 3298 helix: 0.16 (0.17), residues: 888 sheet: -0.56 (0.19), residues: 671 loop : -1.12 (0.14), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP U 92 HIS 0.007 0.001 HIS X 77 PHE 0.014 0.002 PHE N 77 TYR 0.018 0.002 TYR O 157 ARG 0.007 0.001 ARG i 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 547 time to evaluate : 5.350 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: K 111 LYS cc_start: 0.8224 (OUTLIER) cc_final: 0.7796 (ptmt) REVERT: K 130 LEU cc_start: 0.7954 (OUTLIER) cc_final: 0.7543 (pt) REVERT: K 183 LYS cc_start: 0.8031 (mttm) cc_final: 0.7784 (mtpm) REVERT: K 269 ARG cc_start: 0.7707 (OUTLIER) cc_final: 0.7236 (ttm-80) REVERT: L 89 GLU cc_start: 0.7193 (OUTLIER) cc_final: 0.6628 (mm-30) REVERT: M 40 ARG cc_start: 0.8621 (OUTLIER) cc_final: 0.7318 (mtt180) REVERT: M 69 ARG cc_start: 0.8829 (OUTLIER) cc_final: 0.7475 (ptp-170) REVERT: N 64 LYS cc_start: 0.5602 (pttm) cc_final: 0.5142 (mmtt) REVERT: N 102 ARG cc_start: 0.6574 (ttm110) cc_final: 0.5328 (ttm170) REVERT: N 153 ASP cc_start: 0.6238 (m-30) cc_final: 0.5855 (m-30) REVERT: O 55 ARG cc_start: 0.7387 (mmm160) cc_final: 0.7094 (mtp85) REVERT: O 124 GLU cc_start: 0.7020 (mt-10) cc_final: 0.6417 (pp20) REVERT: O 163 ARG cc_start: 0.8076 (OUTLIER) cc_final: 0.7350 (ptm160) REVERT: P 9 VAL cc_start: 0.7634 (OUTLIER) cc_final: 0.7337 (t) REVERT: Q 36 MET cc_start: 0.2851 (ttp) cc_final: 0.1924 (tpt) REVERT: Q 117 MET cc_start: -0.0820 (tpp) cc_final: -0.1123 (ttp) REVERT: T 78 ARG cc_start: 0.7535 (mtp-110) cc_final: 0.7039 (mtt90) REVERT: T 141 LYS cc_start: 0.6887 (ttmm) cc_final: 0.6668 (ttmm) REVERT: U 22 GLN cc_start: 0.8207 (OUTLIER) cc_final: 0.6282 (mp-120) REVERT: U 133 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8297 (ttmm) REVERT: V 32 GLU cc_start: 0.8377 (OUTLIER) cc_final: 0.7546 (mm-30) REVERT: Y 93 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8487 (ttmt) REVERT: Z 60 LYS cc_start: 0.7747 (mtmm) cc_final: 0.7522 (mttp) REVERT: c 7 ARG cc_start: 0.7239 (OUTLIER) cc_final: 0.6002 (tpt90) REVERT: c 12 ILE cc_start: 0.9060 (OUTLIER) cc_final: 0.8838 (tt) REVERT: c 26 LYS cc_start: 0.8069 (OUTLIER) cc_final: 0.7787 (mmtp) REVERT: f 33 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8365 (mp) REVERT: g 8 GLU cc_start: 0.6509 (mm-30) cc_final: 0.6273 (mm-30) REVERT: h 58 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6397 (mm-30) REVERT: j 45 GLN cc_start: 0.8041 (OUTLIER) cc_final: 0.7665 (mt0) REVERT: m 1 MET cc_start: 0.7970 (ptp) cc_final: 0.7555 (ptp) REVERT: m 13 ASN cc_start: 0.7984 (m110) cc_final: 0.7698 (m-40) outliers start: 108 outliers final: 66 residues processed: 599 average time/residue: 3.6415 time to fit residues: 2872.8442 Evaluate side-chains 626 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 542 time to evaluate : 5.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 111 LYS Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain M residue 40 ARG Chi-restraints excluded: chain M residue 58 LYS Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 85 ILE Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 49 THR Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain O residue 114 ASP Chi-restraints excluded: chain O residue 152 ARG Chi-restraints excluded: chain O residue 163 ARG Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain Q residue 28 LEU Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 131 ASN Chi-restraints excluded: chain S residue 28 SER Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 116 ILE Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 80 SER Chi-restraints excluded: chain T residue 117 THR Chi-restraints excluded: chain U residue 22 GLN Chi-restraints excluded: chain U residue 25 ASP Chi-restraints excluded: chain U residue 133 LYS Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 27 SER Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain W residue 9 ARG Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 40 ILE Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain Y residue 93 LYS Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain a residue 3 THR Chi-restraints excluded: chain a residue 108 SER Chi-restraints excluded: chain c residue 7 ARG Chi-restraints excluded: chain c residue 12 ILE Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 26 LYS Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain e residue 72 LYS Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 35 SER Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 58 GLU Chi-restraints excluded: chain i residue 54 VAL Chi-restraints excluded: chain i residue 55 ILE Chi-restraints excluded: chain j residue 45 GLN Chi-restraints excluded: chain k residue 44 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 623 random chunks: chunk 581 optimal weight: 0.5980 chunk 67 optimal weight: 6.9990 chunk 343 optimal weight: 6.9990 chunk 440 optimal weight: 7.9990 chunk 341 optimal weight: 7.9990 chunk 507 optimal weight: 8.9990 chunk 336 optimal weight: 0.9980 chunk 600 optimal weight: 5.9990 chunk 375 optimal weight: 10.0000 chunk 366 optimal weight: 9.9990 chunk 277 optimal weight: 6.9990 overall best weight: 4.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 37 ASN K 46 ASN L 32 ASN P 18 GLN R 128 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 45 GLN Y 44 GLN d 24 ASN f 17 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 98951 Z= 0.278 Angle : 0.650 13.433 148560 Z= 0.353 Chirality : 0.039 0.784 19011 Planarity : 0.006 0.134 7598 Dihedral : 23.735 179.230 50702 Min Nonbonded Distance : 0.983 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 3.87 % Allowed : 19.80 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3298 helix: 0.32 (0.18), residues: 889 sheet: -0.53 (0.19), residues: 673 loop : -1.03 (0.14), residues: 1736 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 248 HIS 0.005 0.001 HIS d 44 PHE 0.011 0.002 PHE T 64 TYR 0.015 0.002 TYR O 157 ARG 0.009 0.001 ARG i 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 105 poor density : 561 time to evaluate : 5.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 130 LEU cc_start: 0.7940 (OUTLIER) cc_final: 0.7535 (pt) REVERT: K 183 LYS cc_start: 0.8027 (mttm) cc_final: 0.7781 (mtpm) REVERT: K 269 ARG cc_start: 0.7685 (OUTLIER) cc_final: 0.7248 (ttm-80) REVERT: L 89 GLU cc_start: 0.7127 (OUTLIER) cc_final: 0.6539 (mm-30) REVERT: L 128 ARG cc_start: 0.7898 (mtp180) cc_final: 0.7373 (mmt180) REVERT: M 40 ARG cc_start: 0.8556 (OUTLIER) cc_final: 0.7271 (mtt180) REVERT: M 69 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7425 (ptp-170) REVERT: N 10 ASP cc_start: 0.5466 (OUTLIER) cc_final: 0.5085 (t0) REVERT: N 64 LYS cc_start: 0.5567 (pttm) cc_final: 0.5126 (mmtt) REVERT: N 102 ARG cc_start: 0.6560 (ttm110) cc_final: 0.5293 (ttm170) REVERT: N 153 ASP cc_start: 0.6245 (m-30) cc_final: 0.5869 (m-30) REVERT: N 178 ARG cc_start: 0.4759 (ppp80) cc_final: 0.4416 (mtt180) REVERT: O 55 ARG cc_start: 0.7357 (mmm160) cc_final: 0.7061 (mtp85) REVERT: O 124 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6431 (pp20) REVERT: P 9 VAL cc_start: 0.7552 (OUTLIER) cc_final: 0.7264 (t) REVERT: Q 36 MET cc_start: 0.2813 (ttp) cc_final: 0.1859 (tpt) REVERT: Q 117 MET cc_start: -0.0704 (tpp) cc_final: -0.1090 (ttp) REVERT: T 78 ARG cc_start: 0.7531 (mtp-110) cc_final: 0.7057 (mtt90) REVERT: U 22 GLN cc_start: 0.8206 (OUTLIER) cc_final: 0.6287 (mp-120) REVERT: U 133 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8263 (ttmm) REVERT: V 32 GLU cc_start: 0.8359 (OUTLIER) cc_final: 0.7552 (mm-30) REVERT: W 69 ASP cc_start: 0.7241 (m-30) cc_final: 0.6802 (t0) REVERT: W 93 ASP cc_start: 0.8812 (t0) cc_final: 0.8517 (t0) REVERT: Z 60 LYS cc_start: 0.7746 (mtmm) cc_final: 0.7527 (mttp) REVERT: c 12 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8832 (tt) REVERT: d 2 PHE cc_start: 0.8006 (m-80) cc_final: 0.7747 (m-80) REVERT: d 46 LYS cc_start: 0.7641 (OUTLIER) cc_final: 0.6816 (mttp) REVERT: f 33 LEU cc_start: 0.8549 (OUTLIER) cc_final: 0.8348 (mp) REVERT: h 58 GLU cc_start: 0.6790 (OUTLIER) cc_final: 0.6477 (tm-30) REVERT: i 37 LYS cc_start: 0.7652 (mtpt) cc_final: 0.7337 (mtmt) REVERT: j 45 GLN cc_start: 0.8009 (OUTLIER) cc_final: 0.7672 (mt0) REVERT: m 1 MET cc_start: 0.7960 (ptp) cc_final: 0.7569 (ptp) REVERT: m 4 ARG cc_start: 0.8167 (OUTLIER) cc_final: 0.7485 (ptt180) REVERT: m 13 ASN cc_start: 0.7996 (m110) cc_final: 0.7699 (m-40) outliers start: 105 outliers final: 65 residues processed: 617 average time/residue: 3.5587 time to fit residues: 2898.0929 Evaluate side-chains 634 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 553 time to evaluate : 5.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain M residue 40 ARG Chi-restraints excluded: chain M residue 58 LYS Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 10 ASP Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 85 ILE Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 49 THR Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain O residue 114 ASP Chi-restraints excluded: chain O residue 152 ARG Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain Q residue 28 LEU Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 131 ASN Chi-restraints excluded: chain S residue 28 SER Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 116 ILE Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 80 SER Chi-restraints excluded: chain T residue 117 THR Chi-restraints excluded: chain U residue 22 GLN Chi-restraints excluded: chain U residue 25 ASP Chi-restraints excluded: chain U residue 133 LYS Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 27 SER Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain W residue 9 ARG Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 40 ILE Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain a residue 3 THR Chi-restraints excluded: chain b residue 74 ILE Chi-restraints excluded: chain c residue 12 ILE Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain d residue 46 LYS Chi-restraints excluded: chain e residue 72 LYS Chi-restraints excluded: chain f residue 33 LEU Chi-restraints excluded: chain f residue 35 SER Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain h residue 52 SER Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 58 GLU Chi-restraints excluded: chain i residue 55 ILE Chi-restraints excluded: chain j residue 45 GLN Chi-restraints excluded: chain k residue 44 VAL Chi-restraints excluded: chain m residue 4 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 623 random chunks: chunk 371 optimal weight: 0.8980 chunk 239 optimal weight: 8.9990 chunk 358 optimal weight: 8.9990 chunk 180 optimal weight: 6.9990 chunk 117 optimal weight: 10.0000 chunk 116 optimal weight: 9.9990 chunk 381 optimal weight: 0.4980 chunk 409 optimal weight: 20.0000 chunk 296 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 471 optimal weight: 5.9990 overall best weight: 4.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 37 ASN L 32 ASN P 18 GLN R 128 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 61 GLN Y 44 GLN d 24 ASN f 17 ASN g 36 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8327 moved from start: 0.3066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 98951 Z= 0.292 Angle : 0.667 13.448 148560 Z= 0.361 Chirality : 0.040 0.782 19011 Planarity : 0.007 0.135 7598 Dihedral : 23.746 179.246 50702 Min Nonbonded Distance : 0.950 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.80 % Allowed : 20.13 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3298 helix: 0.37 (0.18), residues: 880 sheet: -0.61 (0.19), residues: 673 loop : -1.02 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 248 HIS 0.006 0.001 HIS X 77 PHE 0.011 0.002 PHE T 64 TYR 0.016 0.002 TYR O 157 ARG 0.010 0.001 ARG i 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 103 poor density : 560 time to evaluate : 5.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 130 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7541 (pt) REVERT: K 183 LYS cc_start: 0.8028 (mttm) cc_final: 0.7777 (mtpm) REVERT: K 269 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7226 (ttm-80) REVERT: L 89 GLU cc_start: 0.7172 (OUTLIER) cc_final: 0.6609 (mm-30) REVERT: L 128 ARG cc_start: 0.7910 (mtp180) cc_final: 0.7382 (mmt180) REVERT: M 40 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.7266 (mtt180) REVERT: M 69 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.7409 (ptp-170) REVERT: N 10 ASP cc_start: 0.5564 (OUTLIER) cc_final: 0.5125 (t0) REVERT: N 32 GLU cc_start: 0.6577 (tt0) cc_final: 0.6267 (tt0) REVERT: N 64 LYS cc_start: 0.5558 (pttm) cc_final: 0.5116 (mmtt) REVERT: N 102 ARG cc_start: 0.6561 (ttm110) cc_final: 0.5329 (ttm170) REVERT: N 153 ASP cc_start: 0.6181 (m-30) cc_final: 0.5801 (m-30) REVERT: N 178 ARG cc_start: 0.4840 (ppp80) cc_final: 0.4527 (mtt180) REVERT: O 55 ARG cc_start: 0.7354 (mmm160) cc_final: 0.7060 (mtp85) REVERT: O 101 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7451 (p0) REVERT: O 124 GLU cc_start: 0.7027 (mt-10) cc_final: 0.6430 (pp20) REVERT: O 163 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7345 (ptm160) REVERT: P 9 VAL cc_start: 0.7609 (OUTLIER) cc_final: 0.7321 (t) REVERT: Q 36 MET cc_start: 0.2760 (ttp) cc_final: 0.1868 (tpt) REVERT: Q 117 MET cc_start: -0.0619 (tpp) cc_final: -0.1027 (ttp) REVERT: T 78 ARG cc_start: 0.7534 (mtp-110) cc_final: 0.7057 (mtt90) REVERT: T 141 LYS cc_start: 0.6886 (ttmm) cc_final: 0.6681 (ttmm) REVERT: U 22 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.6301 (mp-120) REVERT: U 133 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.8251 (ttmm) REVERT: V 32 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7532 (mm-30) REVERT: W 58 ILE cc_start: 0.7033 (OUTLIER) cc_final: 0.6637 (pp) REVERT: W 69 ASP cc_start: 0.7238 (m-30) cc_final: 0.6792 (t0) REVERT: W 93 ASP cc_start: 0.8824 (t0) cc_final: 0.8527 (t0) REVERT: Z 60 LYS cc_start: 0.7751 (mtmm) cc_final: 0.7532 (mttp) REVERT: a 92 ARG cc_start: 0.7562 (OUTLIER) cc_final: 0.6944 (ttm-80) REVERT: c 7 ARG cc_start: 0.7206 (OUTLIER) cc_final: 0.5968 (tpt90) REVERT: c 12 ILE cc_start: 0.9050 (OUTLIER) cc_final: 0.8840 (tt) REVERT: d 46 LYS cc_start: 0.7646 (OUTLIER) cc_final: 0.6839 (mttp) REVERT: h 58 GLU cc_start: 0.6821 (OUTLIER) cc_final: 0.6493 (tm-30) REVERT: i 37 LYS cc_start: 0.7677 (mtpt) cc_final: 0.7343 (mtmt) REVERT: j 45 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7684 (mt0) REVERT: m 1 MET cc_start: 0.7961 (ptp) cc_final: 0.7581 (ptp) REVERT: m 4 ARG cc_start: 0.8203 (OUTLIER) cc_final: 0.7510 (ptt180) REVERT: m 13 ASN cc_start: 0.7976 (m110) cc_final: 0.7668 (m-40) outliers start: 103 outliers final: 70 residues processed: 611 average time/residue: 3.6762 time to fit residues: 2955.1483 Evaluate side-chains 638 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 548 time to evaluate : 5.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 37 ASN Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain M residue 40 ARG Chi-restraints excluded: chain M residue 58 LYS Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 10 ASP Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 85 ILE Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 49 THR Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 101 ASN Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain O residue 114 ASP Chi-restraints excluded: chain O residue 152 ARG Chi-restraints excluded: chain O residue 163 ARG Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain P residue 4 ILE Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain Q residue 28 LEU Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 131 ASN Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 116 ILE Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 80 SER Chi-restraints excluded: chain U residue 22 GLN Chi-restraints excluded: chain U residue 25 ASP Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 133 LYS Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 27 SER Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain W residue 9 ARG Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 40 ILE Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain a residue 3 THR Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain b residue 74 ILE Chi-restraints excluded: chain c residue 7 ARG Chi-restraints excluded: chain c residue 12 ILE Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain d residue 11 GLU Chi-restraints excluded: chain d residue 46 LYS Chi-restraints excluded: chain e residue 72 LYS Chi-restraints excluded: chain f residue 35 SER Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain h residue 52 SER Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 58 GLU Chi-restraints excluded: chain i residue 55 ILE Chi-restraints excluded: chain j residue 45 GLN Chi-restraints excluded: chain k residue 44 VAL Chi-restraints excluded: chain m residue 4 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 623 random chunks: chunk 546 optimal weight: 9.9990 chunk 575 optimal weight: 0.9980 chunk 524 optimal weight: 6.9990 chunk 559 optimal weight: 8.9990 chunk 336 optimal weight: 6.9990 chunk 243 optimal weight: 6.9990 chunk 439 optimal weight: 3.9990 chunk 171 optimal weight: 10.0000 chunk 505 optimal weight: 7.9990 chunk 529 optimal weight: 9.9990 chunk 557 optimal weight: 0.9980 overall best weight: 3.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 ASN ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 18 GLN R 128 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 44 GLN ** d 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 36 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 98951 Z= 0.284 Angle : 0.691 59.158 148560 Z= 0.380 Chirality : 0.040 0.783 19011 Planarity : 0.007 0.135 7598 Dihedral : 23.746 179.238 50701 Min Nonbonded Distance : 0.951 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.58 % Allowed : 20.72 % Favored : 75.70 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3298 helix: 0.37 (0.18), residues: 880 sheet: -0.61 (0.19), residues: 673 loop : -1.02 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 248 HIS 0.006 0.001 HIS X 77 PHE 0.011 0.002 PHE T 64 TYR 0.025 0.002 TYR U 103 ARG 0.006 0.000 ARG i 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 549 time to evaluate : 5.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 130 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7539 (pt) REVERT: K 183 LYS cc_start: 0.8028 (mttm) cc_final: 0.7777 (mtpm) REVERT: K 269 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7226 (ttm-80) REVERT: L 89 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6597 (mm-30) REVERT: L 128 ARG cc_start: 0.7909 (mtp180) cc_final: 0.7382 (mmt180) REVERT: M 40 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7264 (mtt180) REVERT: M 69 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7406 (ptp-170) REVERT: N 10 ASP cc_start: 0.5565 (OUTLIER) cc_final: 0.5125 (t0) REVERT: N 26 MET cc_start: 0.8021 (mmm) cc_final: 0.7591 (mmm) REVERT: N 32 GLU cc_start: 0.6539 (tt0) cc_final: 0.6265 (tt0) REVERT: N 64 LYS cc_start: 0.5557 (pttm) cc_final: 0.5115 (mmtt) REVERT: N 102 ARG cc_start: 0.6561 (ttm110) cc_final: 0.5328 (ttm170) REVERT: N 153 ASP cc_start: 0.6185 (m-30) cc_final: 0.5804 (m-30) REVERT: N 178 ARG cc_start: 0.4840 (ppp80) cc_final: 0.4527 (mtt180) REVERT: O 55 ARG cc_start: 0.7353 (mmm160) cc_final: 0.7059 (mtp85) REVERT: O 101 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7459 (p0) REVERT: O 124 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6429 (pp20) REVERT: O 163 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7345 (ptm160) REVERT: P 9 VAL cc_start: 0.7608 (OUTLIER) cc_final: 0.7320 (t) REVERT: Q 36 MET cc_start: 0.2760 (ttp) cc_final: 0.1869 (tpt) REVERT: Q 117 MET cc_start: -0.0628 (tpp) cc_final: -0.1056 (ttp) REVERT: T 78 ARG cc_start: 0.7532 (mtp-110) cc_final: 0.7056 (mtt90) REVERT: U 22 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.6300 (mp-120) REVERT: U 133 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8250 (ttmm) REVERT: V 32 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7531 (mm-30) REVERT: W 58 ILE cc_start: 0.7057 (OUTLIER) cc_final: 0.6636 (pp) REVERT: W 69 ASP cc_start: 0.7237 (m-30) cc_final: 0.6792 (t0) REVERT: W 93 ASP cc_start: 0.8824 (t0) cc_final: 0.8526 (t0) REVERT: Z 60 LYS cc_start: 0.7749 (mtmm) cc_final: 0.7532 (mttp) REVERT: a 92 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.6944 (ttm-80) REVERT: c 7 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.5967 (tpt90) REVERT: c 12 ILE cc_start: 0.9048 (OUTLIER) cc_final: 0.8840 (tt) REVERT: d 2 PHE cc_start: 0.7995 (m-80) cc_final: 0.7755 (m-80) REVERT: d 46 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.6839 (mttp) REVERT: d 69 GLU cc_start: 0.8001 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: h 58 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6492 (tm-30) REVERT: i 37 LYS cc_start: 0.7676 (mtpt) cc_final: 0.7341 (mtmt) REVERT: j 45 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7682 (mt0) REVERT: m 1 MET cc_start: 0.7959 (ptp) cc_final: 0.7584 (ptp) REVERT: m 4 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7508 (ptt180) REVERT: m 13 ASN cc_start: 0.7975 (m110) cc_final: 0.7669 (m-40) outliers start: 97 outliers final: 71 residues processed: 597 average time/residue: 3.6687 time to fit residues: 2889.2208 Evaluate side-chains 641 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 549 time to evaluate : 5.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain M residue 40 ARG Chi-restraints excluded: chain M residue 58 LYS Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 10 ASP Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 85 ILE Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 49 THR Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 101 ASN Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain O residue 114 ASP Chi-restraints excluded: chain O residue 152 ARG Chi-restraints excluded: chain O residue 163 ARG Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain Q residue 28 LEU Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 131 ASN Chi-restraints excluded: chain S residue 28 SER Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 116 ILE Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 80 SER Chi-restraints excluded: chain U residue 22 GLN Chi-restraints excluded: chain U residue 25 ASP Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 133 LYS Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 27 SER Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain W residue 9 ARG Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 40 ILE Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain X residue 7 GLN Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain a residue 3 THR Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 108 SER Chi-restraints excluded: chain b residue 74 ILE Chi-restraints excluded: chain c residue 7 ARG Chi-restraints excluded: chain c residue 12 ILE Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain d residue 11 GLU Chi-restraints excluded: chain d residue 46 LYS Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain e residue 72 LYS Chi-restraints excluded: chain f residue 35 SER Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain h residue 52 SER Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 58 GLU Chi-restraints excluded: chain i residue 55 ILE Chi-restraints excluded: chain j residue 45 GLN Chi-restraints excluded: chain k residue 44 VAL Chi-restraints excluded: chain m residue 4 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 623 random chunks: chunk 367 optimal weight: 9.9990 chunk 591 optimal weight: 10.0000 chunk 361 optimal weight: 8.9990 chunk 280 optimal weight: 8.9990 chunk 411 optimal weight: 0.0970 chunk 620 optimal weight: 10.0000 chunk 571 optimal weight: 2.9990 chunk 494 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 381 optimal weight: 4.9990 chunk 303 optimal weight: 10.0000 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 ASN ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 18 GLN R 128 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 44 GLN ** d 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 36 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.3075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 98951 Z= 0.284 Angle : 0.691 59.158 148560 Z= 0.380 Chirality : 0.040 0.783 19011 Planarity : 0.007 0.135 7598 Dihedral : 23.746 179.238 50701 Min Nonbonded Distance : 0.951 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.43 % Allowed : 20.83 % Favored : 75.74 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3298 helix: 0.37 (0.18), residues: 880 sheet: -0.61 (0.19), residues: 673 loop : -1.02 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 248 HIS 0.006 0.001 HIS X 77 PHE 0.011 0.002 PHE T 64 TYR 0.025 0.002 TYR U 103 ARG 0.006 0.000 ARG i 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6596 Ramachandran restraints generated. 3298 Oldfield, 0 Emsley, 3298 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 549 time to evaluate : 5.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 130 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7539 (pt) REVERT: K 183 LYS cc_start: 0.8029 (mttm) cc_final: 0.7777 (mtpm) REVERT: K 269 ARG cc_start: 0.7690 (OUTLIER) cc_final: 0.7226 (ttm-80) REVERT: L 89 GLU cc_start: 0.7162 (OUTLIER) cc_final: 0.6597 (mm-30) REVERT: L 128 ARG cc_start: 0.7909 (mtp180) cc_final: 0.7382 (mmt180) REVERT: M 40 ARG cc_start: 0.8563 (OUTLIER) cc_final: 0.7264 (mtt180) REVERT: M 69 ARG cc_start: 0.8790 (OUTLIER) cc_final: 0.7406 (ptp-170) REVERT: N 10 ASP cc_start: 0.5565 (OUTLIER) cc_final: 0.5125 (t0) REVERT: N 26 MET cc_start: 0.8021 (mmm) cc_final: 0.7591 (mmm) REVERT: N 32 GLU cc_start: 0.6539 (tt0) cc_final: 0.6265 (tt0) REVERT: N 64 LYS cc_start: 0.5557 (pttm) cc_final: 0.5115 (mmtt) REVERT: N 102 ARG cc_start: 0.6561 (ttm110) cc_final: 0.5328 (ttm170) REVERT: N 153 ASP cc_start: 0.6181 (m-30) cc_final: 0.5804 (m-30) REVERT: N 178 ARG cc_start: 0.4840 (ppp80) cc_final: 0.4527 (mtt180) REVERT: O 55 ARG cc_start: 0.7353 (mmm160) cc_final: 0.7059 (mtp85) REVERT: O 101 ASN cc_start: 0.7677 (OUTLIER) cc_final: 0.7459 (p0) REVERT: O 124 GLU cc_start: 0.7026 (mt-10) cc_final: 0.6429 (pp20) REVERT: O 163 ARG cc_start: 0.8073 (OUTLIER) cc_final: 0.7345 (ptm160) REVERT: P 9 VAL cc_start: 0.7608 (OUTLIER) cc_final: 0.7320 (t) REVERT: Q 36 MET cc_start: 0.2760 (ttp) cc_final: 0.1869 (tpt) REVERT: Q 117 MET cc_start: -0.0628 (tpp) cc_final: -0.1055 (ttp) REVERT: T 78 ARG cc_start: 0.7532 (mtp-110) cc_final: 0.7056 (mtt90) REVERT: U 22 GLN cc_start: 0.8216 (OUTLIER) cc_final: 0.6300 (mp-120) REVERT: U 133 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8250 (ttmm) REVERT: V 32 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.7531 (mm-30) REVERT: W 58 ILE cc_start: 0.7057 (OUTLIER) cc_final: 0.6636 (pp) REVERT: W 69 ASP cc_start: 0.7238 (m-30) cc_final: 0.6792 (t0) REVERT: W 93 ASP cc_start: 0.8824 (t0) cc_final: 0.8526 (t0) REVERT: Z 60 LYS cc_start: 0.7749 (mtmm) cc_final: 0.7532 (mttp) REVERT: a 92 ARG cc_start: 0.7560 (OUTLIER) cc_final: 0.6944 (ttm-80) REVERT: c 7 ARG cc_start: 0.7205 (OUTLIER) cc_final: 0.5967 (tpt90) REVERT: c 12 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8840 (tt) REVERT: d 2 PHE cc_start: 0.7999 (m-80) cc_final: 0.7755 (m-80) REVERT: d 46 LYS cc_start: 0.7648 (OUTLIER) cc_final: 0.6839 (mttp) REVERT: d 69 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7384 (mp0) REVERT: h 58 GLU cc_start: 0.6820 (OUTLIER) cc_final: 0.6492 (tm-30) REVERT: i 37 LYS cc_start: 0.7676 (mtpt) cc_final: 0.7341 (mtmt) REVERT: j 45 GLN cc_start: 0.8015 (OUTLIER) cc_final: 0.7682 (mt0) REVERT: m 1 MET cc_start: 0.7959 (ptp) cc_final: 0.7584 (ptp) REVERT: m 4 ARG cc_start: 0.8201 (OUTLIER) cc_final: 0.7508 (ptt180) REVERT: m 13 ASN cc_start: 0.7975 (m110) cc_final: 0.7669 (m-40) outliers start: 93 outliers final: 71 residues processed: 595 average time/residue: 3.6119 time to fit residues: 2824.0626 Evaluate side-chains 640 residues out of total 2710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 548 time to evaluate : 5.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 3 VAL Chi-restraints excluded: chain K residue 71 LYS Chi-restraints excluded: chain K residue 130 LEU Chi-restraints excluded: chain K residue 141 VAL Chi-restraints excluded: chain K residue 195 VAL Chi-restraints excluded: chain K residue 204 VAL Chi-restraints excluded: chain K residue 269 ARG Chi-restraints excluded: chain L residue 13 ARG Chi-restraints excluded: chain L residue 58 ASN Chi-restraints excluded: chain L residue 89 GLU Chi-restraints excluded: chain L residue 91 THR Chi-restraints excluded: chain L residue 92 VAL Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain M residue 40 ARG Chi-restraints excluded: chain M residue 58 LYS Chi-restraints excluded: chain M residue 69 ARG Chi-restraints excluded: chain M residue 175 ILE Chi-restraints excluded: chain M residue 191 ASP Chi-restraints excluded: chain N residue 10 ASP Chi-restraints excluded: chain N residue 19 GLU Chi-restraints excluded: chain N residue 74 VAL Chi-restraints excluded: chain N residue 85 ILE Chi-restraints excluded: chain N residue 132 VAL Chi-restraints excluded: chain O residue 23 VAL Chi-restraints excluded: chain O residue 24 ILE Chi-restraints excluded: chain O residue 49 THR Chi-restraints excluded: chain O residue 72 LEU Chi-restraints excluded: chain O residue 74 SER Chi-restraints excluded: chain O residue 101 ASN Chi-restraints excluded: chain O residue 106 SER Chi-restraints excluded: chain O residue 114 ASP Chi-restraints excluded: chain O residue 152 ARG Chi-restraints excluded: chain O residue 163 ARG Chi-restraints excluded: chain O residue 171 THR Chi-restraints excluded: chain P residue 9 VAL Chi-restraints excluded: chain P residue 101 ASP Chi-restraints excluded: chain P residue 130 VAL Chi-restraints excluded: chain Q residue 28 LEU Chi-restraints excluded: chain Q residue 138 LEU Chi-restraints excluded: chain Q residue 139 VAL Chi-restraints excluded: chain R residue 81 ILE Chi-restraints excluded: chain R residue 131 ASN Chi-restraints excluded: chain S residue 28 SER Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 116 ILE Chi-restraints excluded: chain T residue 40 SER Chi-restraints excluded: chain T residue 80 SER Chi-restraints excluded: chain U residue 22 GLN Chi-restraints excluded: chain U residue 25 ASP Chi-restraints excluded: chain U residue 57 VAL Chi-restraints excluded: chain U residue 133 LYS Chi-restraints excluded: chain V residue 14 SER Chi-restraints excluded: chain V residue 27 SER Chi-restraints excluded: chain V residue 32 GLU Chi-restraints excluded: chain V residue 65 LEU Chi-restraints excluded: chain W residue 9 ARG Chi-restraints excluded: chain W residue 31 THR Chi-restraints excluded: chain W residue 40 ILE Chi-restraints excluded: chain W residue 49 VAL Chi-restraints excluded: chain W residue 58 ILE Chi-restraints excluded: chain W residue 78 VAL Chi-restraints excluded: chain X residue 7 GLN Chi-restraints excluded: chain X residue 32 VAL Chi-restraints excluded: chain X residue 66 ASN Chi-restraints excluded: chain X residue 83 SER Chi-restraints excluded: chain Z residue 22 LEU Chi-restraints excluded: chain Z residue 38 VAL Chi-restraints excluded: chain a residue 3 THR Chi-restraints excluded: chain a residue 92 ARG Chi-restraints excluded: chain a residue 108 SER Chi-restraints excluded: chain b residue 74 ILE Chi-restraints excluded: chain c residue 7 ARG Chi-restraints excluded: chain c residue 12 ILE Chi-restraints excluded: chain c residue 15 THR Chi-restraints excluded: chain c residue 21 LYS Chi-restraints excluded: chain c residue 72 ILE Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain d residue 11 GLU Chi-restraints excluded: chain d residue 46 LYS Chi-restraints excluded: chain d residue 69 GLU Chi-restraints excluded: chain e residue 72 LYS Chi-restraints excluded: chain f residue 35 SER Chi-restraints excluded: chain f residue 66 THR Chi-restraints excluded: chain g residue 58 ASN Chi-restraints excluded: chain h residue 52 SER Chi-restraints excluded: chain h residue 57 VAL Chi-restraints excluded: chain h residue 58 GLU Chi-restraints excluded: chain i residue 55 ILE Chi-restraints excluded: chain j residue 45 GLN Chi-restraints excluded: chain k residue 44 VAL Chi-restraints excluded: chain m residue 4 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 623 random chunks: chunk 392 optimal weight: 8.9990 chunk 526 optimal weight: 6.9990 chunk 151 optimal weight: 10.0000 chunk 455 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 137 optimal weight: 7.9990 chunk 495 optimal weight: 9.9990 chunk 207 optimal weight: 7.9990 chunk 508 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 32 ASN ** O 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 18 GLN R 128 ASN ** U 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 61 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 44 GLN ** d 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 36 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3919 r_free = 0.3919 target = 0.158052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.122084 restraints weight = 217002.414| |-----------------------------------------------------------------------------| r_work (start): 0.3476 rms_B_bonded: 0.66 r_work: 0.3351 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.3265 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.3265 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3272 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3272 r_free = 0.3272 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3272 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.3074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.201 98951 Z= 0.284 Angle : 0.691 59.200 148560 Z= 0.380 Chirality : 0.040 0.783 19011 Planarity : 0.007 0.135 7598 Dihedral : 23.746 179.238 50701 Min Nonbonded Distance : 0.951 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.43 % Allowed : 20.87 % Favored : 75.70 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.93 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.14), residues: 3298 helix: 0.37 (0.18), residues: 880 sheet: -0.61 (0.19), residues: 673 loop : -1.02 (0.14), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 248 HIS 0.006 0.001 HIS X 77 PHE 0.011 0.002 PHE T 64 TYR 0.025 0.002 TYR U 103 ARG 0.006 0.000 ARG i 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 61900.44 seconds wall clock time: 1062 minutes 15.60 seconds (63735.60 seconds total)