Starting phenix.real_space_refine on Sat Mar 2 08:50:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q98_4477/03_2024/6q98_4477_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q98_4477/03_2024/6q98_4477.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q98_4477/03_2024/6q98_4477_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q98_4477/03_2024/6q98_4477_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q98_4477/03_2024/6q98_4477_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q98_4477/03_2024/6q98_4477.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q98_4477/03_2024/6q98_4477.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q98_4477/03_2024/6q98_4477_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6q98_4477/03_2024/6q98_4477_updated.pdb" } resolution = 4.3 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= 0.002 sd= 0.018 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: 7 Type Number sf(0) Gaussians Zn 2 6.06 5 P 4920 5.49 5 Mg 429 5.21 5 S 162 5.16 5 C 77098 2.51 5 N 28565 2.21 5 O 42702 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "5 ARG 19": "NH1" <-> "NH2" Residue "5 GLU 107": "OE1" <-> "OE2" Residue "5 ARG 145": "NH1" <-> "NH2" Residue "5 ARG 153": "NH1" <-> "NH2" Residue "B GLU 23": "OE1" <-> "OE2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B GLU 180": "OE1" <-> "OE2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B GLU 199": "OE1" <-> "OE2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "C ARG 13": "NH1" <-> "NH2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "C ARG 77": "NH1" <-> "NH2" Residue "C ARG 83": "NH1" <-> "NH2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F ARG 152": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F ARG 170": "NH1" <-> "NH2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "H GLU 47": "OE1" <-> "OE2" Residue "H ARG 62": "NH1" <-> "NH2" Residue "I TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 34": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K ARG 17": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K GLU 110": "OE1" <-> "OE2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 123": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "L GLU 136": "OE1" <-> "OE2" Residue "M ARG 10": "NH1" <-> "NH2" Residue "M ARG 18": "NH1" <-> "NH2" Residue "M ARG 40": "NH1" <-> "NH2" Residue "M ARG 50": "NH1" <-> "NH2" Residue "M ARG 55": "NH1" <-> "NH2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N GLU 43": "OE1" <-> "OE2" Residue "N ARG 46": "NH1" <-> "NH2" Residue "N GLU 49": "OE1" <-> "OE2" Residue "N ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N GLU 74": "OE1" <-> "OE2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 118": "NH1" <-> "NH2" Residue "O ARG 10": "NH1" <-> "NH2" Residue "O ARG 13": "NH1" <-> "NH2" Residue "O ARG 16": "NH1" <-> "NH2" Residue "O GLU 20": "OE1" <-> "OE2" Residue "O ARG 25": "NH1" <-> "NH2" Residue "O ARG 81": "NH1" <-> "NH2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "O PHE 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 21": "NH1" <-> "NH2" Residue "P GLU 27": "OE1" <-> "OE2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P GLU 68": "OE1" <-> "OE2" Residue "P ARG 89": "NH1" <-> "NH2" Residue "P ARG 101": "NH1" <-> "NH2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R ARG 68": "NH1" <-> "NH2" Residue "R ARG 78": "NH1" <-> "NH2" Residue "R ARG 79": "NH1" <-> "NH2" Residue "R ARG 84": "NH1" <-> "NH2" Residue "S ARG 84": "NH1" <-> "NH2" Residue "S ARG 88": "NH1" <-> "NH2" Residue "S ARG 92": "NH1" <-> "NH2" Residue "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 3": "NH1" <-> "NH2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "T GLU 25": "OE1" <-> "OE2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U ARG 94": "NH1" <-> "NH2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ARG 18": "NH1" <-> "NH2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "X ARG 45": "NH1" <-> "NH2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "Y GLU 13": "OE1" <-> "OE2" Residue "Y GLU 24": "OE1" <-> "OE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 11": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z ARG 45": "NH1" <-> "NH2" Residue "a ARG 56": "NH1" <-> "NH2" Residue "a ARG 63": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c ARG 28": "NH1" <-> "NH2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 41": "NH1" <-> "NH2" Residue "e ARG 13": "NH1" <-> "NH2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ARG 42": "NH1" <-> "NH2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "g ARG 63": "NH1" <-> "NH2" Residue "g ARG 74": "NH1" <-> "NH2" Residue "g ARG 208": "NH1" <-> "NH2" Residue "g GLU 223": "OE1" <-> "OE2" Residue "g ARG 225": "NH1" <-> "NH2" Residue "h GLU 28": "OE1" <-> "OE2" Residue "h ARG 54": "NH1" <-> "NH2" Residue "h ARG 72": "NH1" <-> "NH2" Residue "h ARG 88": "NH1" <-> "NH2" Residue "h GLU 105": "OE1" <-> "OE2" Residue "h GLU 125": "OE1" <-> "OE2" Residue "h ARG 127": "NH1" <-> "NH2" Residue "h ARG 131": "NH1" <-> "NH2" Residue "h ARG 132": "NH1" <-> "NH2" Residue "h ARG 164": "NH1" <-> "NH2" Residue "i TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "i GLU 69": "OE1" <-> "OE2" Residue "i ARG 73": "NH1" <-> "NH2" Residue "i ARG 81": "NH1" <-> "NH2" Residue "i GLU 95": "OE1" <-> "OE2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j ARG 68": "NH1" <-> "NH2" Residue "j ARG 69": "NH1" <-> "NH2" Residue "j ARG 93": "NH1" <-> "NH2" Residue "j ARG 157": "NH1" <-> "NH2" Residue "k PHE 8": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "k ARG 45": "NH1" <-> "NH2" Residue "k GLU 73": "OE1" <-> "OE2" Residue "k GLU 75": "OE1" <-> "OE2" Residue "k ARG 79": "NH1" <-> "NH2" Residue "l ARG 4": "NH1" <-> "NH2" Residue "l ARG 53": "NH1" <-> "NH2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ARG 79": "NH1" <-> "NH2" Residue "l ARG 92": "NH1" <-> "NH2" Residue "m GLU 42": "OE1" <-> "OE2" Residue "m GLU 58": "OE1" <-> "OE2" Residue "n ARG 11": "NH1" <-> "NH2" Residue "n ARG 41": "NH1" <-> "NH2" Residue "n ARG 130": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o ARG 45": "NH1" <-> "NH2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "p ARG 37": "NH1" <-> "NH2" Residue "p ARG 69": "NH1" <-> "NH2" Residue "p ARG 93": "NH1" <-> "NH2" Residue "p ARG 106": "NH1" <-> "NH2" Residue "q ARG 9": "NH1" <-> "NH2" Residue "q ARG 14": "NH1" <-> "NH2" Residue "q ARG 50": "NH1" <-> "NH2" Residue "q ARG 83": "NH1" <-> "NH2" Residue "r ARG 29": "NH1" <-> "NH2" Residue "r ARG 70": "NH1" <-> "NH2" Residue "r ARG 87": "NH1" <-> "NH2" Residue "r ARG 109": "NH1" <-> "NH2" Residue "s ARG 59": "NH1" <-> "NH2" Residue "s ARG 63": "NH1" <-> "NH2" Residue "s ARG 65": "NH1" <-> "NH2" Residue "s ARG 69": "NH1" <-> "NH2" Residue "s ARG 85": "NH1" <-> "NH2" Residue "t ARG 72": "NH1" <-> "NH2" Residue "t ARG 89": "NH1" <-> "NH2" Residue "u ARG 28": "NH1" <-> "NH2" Residue "u PHE 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "u ARG 51": "NH1" <-> "NH2" Residue "v ARG 11": "NH1" <-> "NH2" Residue "v ARG 27": "NH1" <-> "NH2" Residue "v ARG 65": "NH1" <-> "NH2" Residue "v ARG 77": "NH1" <-> "NH2" Residue "w PHE 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 61": "NH1" <-> "NH2" Residue "x ARG 32": "NH1" <-> "NH2" Residue "y ARG 60": "NH1" <-> "NH2" Residue "y ARG 74": "NH1" <-> "NH2" Residue "z ARG 33": "NH1" <-> "NH2" Residue "z ARG 45": "NH1" <-> "NH2" Residue "z ARG 55": "NH1" <-> "NH2" Residue "z ARG 62": "NH1" <-> "NH2" Residue "z ARG 67": "NH1" <-> "NH2" Residue "z ARG 69": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 153878 Number of models: 1 Model: "" Number of chains: 71 Chain: "1" Number of atoms: 62336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62336 Classifications: {'RNA': 2903} Modifications used: {'rna2p': 5, 'rna2p_pur': 289, 'rna2p_pyr': 167, 'rna3p': 17, 'rna3p_pur': 1378, 'rna3p_pyr': 1047} Link IDs: {'rna2p': 460, 'rna3p': 2442} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "2" Number of atoms: 32929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32929 Classifications: {'RNA': 1534} Modifications used: {'rna2p': 1, 'rna2p_pur': 117, 'rna2p_pyr': 89, 'rna3p': 10, 'rna3p_pur': 752, 'rna3p_pyr': 564} Link IDs: {'rna2p': 206, 'rna3p': 1327} Chain breaks: 3 Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 7, 'rna2p_pyr': 8, 'rna3p_pur': 57, 'rna3p_pyr': 48} Link IDs: {'rna2p': 14, 'rna3p': 105} Chain: "5" Number of atoms: 1209 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1209 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 2, 'TRANS': 147} Chain: "6" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 110 Classifications: {'peptide': 22} Link IDs: {'TRANS': 21} Chain: "B" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "C" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Chain: "D" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "E" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "F" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1313 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "G" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 980 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "I" Number of atoms: 984 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 984 Classifications: {'peptide': 135} Link IDs: {'PTRANS': 9, 'TRANS': 125} Chain: "J" Number of atoms: 1129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 142, 1129 Classifications: {'peptide': 142} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 135} Chain: "K" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 946 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 5, 'TRANS': 117} Chain: "L" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 1053 Classifications: {'peptide': 144} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 139} Chain: "M" Number of atoms: 1074 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1074 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Chain: "N" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 951 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "O" Number of atoms: 892 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 892 Classifications: {'peptide': 116} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 113} Chain: "P" Number of atoms: 917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 917 Classifications: {'peptide': 114} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 110} Chain: "Q" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'TRANS': 116} Chain: "R" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 816 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'TRANS': 101} Chain: "S" Number of atoms: 857 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 857 Classifications: {'peptide': 110} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 107} Chain: "T" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 746 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "U" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 788 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "V" Number of atoms: 753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 753 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 89} Chain: "W" Number of atoms: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 582 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "X" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 625 Classifications: {'peptide': 77} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "Y" Number of atoms: 501 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 501 Classifications: {'peptide': 62} Modifications used: {'COO': 1} Link IDs: {'TRANS': 61} Chain: "Z" Number of atoms: 448 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 448 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 2, 'TRANS': 55} Chain: "a" Number of atoms: 472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 472 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain breaks: 1 Chain: "b" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 444 Classifications: {'peptide': 56} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 54} Chain: "c" Number of atoms: 426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 426 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "d" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 377 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "e" Number of atoms: 504 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 504 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "f" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 38, 302 Classifications: {'peptide': 38} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 36} Chain: "g" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "h" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1636 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "i" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "j" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "k" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "l" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "m" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "n" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "o" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 790 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "p" Number of atoms: 877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 877 Classifications: {'peptide': 117} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 109} Chain: "q" Number of atoms: 951 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 951 Classifications: {'peptide': 122} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 114} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'0TD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 867 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "s" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "t" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "u" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "v" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "w" Number of atoms: 544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 544 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "x" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "y" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 669 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "z" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "4" Number of atoms: 7758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 7758 Classifications: {'RNA': 363} Modifications used: {'rna2p_pur': 34, 'rna2p_pyr': 22, 'rna3p_pur': 164, 'rna3p_pyr': 143} Link IDs: {'rna2p': 55, 'rna3p': 307} Chain breaks: 1 Chain: "1" Number of atoms: 283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 283 Unusual residues: {' MG': 283} Classifications: {'undetermined': 283} Link IDs: {None: 282} Chain: "2" Number of atoms: 126 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 126 Unusual residues: {' MG': 126} Classifications: {'undetermined': 126} Link IDs: {None: 125} Chain: "3" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Unusual residues: {' MG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0IW0 SG CYS a 40 133.004 198.614 46.805 1.00104.36 S ATOM A0KFN SG CYS f 11 180.957 132.614 118.166 1.00 52.90 S ATOM A0KGC SG CYS f 14 181.373 128.801 116.305 1.00 53.79 S ATOM A0KJ7 SG CYS f 27 183.048 130.126 119.562 1.00 51.89 S Time building chain proxies: 58.40, per 1000 atoms: 0.38 Number of scatterers: 153878 At special positions: 0 Unit cell: (244.95, 308.2, 276, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 2 29.99 S 162 16.00 P 4920 15.00 Mg 429 11.99 O 42702 8.00 N 28565 7.00 C 77098 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS a 18 " - pdb=" SG CYS a 37 " distance=2.03 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: 68.82 Conformation dependent library (CDL) restraints added in 7.3 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 101 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 40 " pdb=" ZN f 102 " pdb="ZN ZN f 102 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 102 " - pdb=" SG CYS f 27 " pdb="ZN ZN f 102 " - pdb=" SG CYS f 14 " 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11278 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: 178 helices and 64 sheets defined 37.5% alpha, 15.5% beta 1040 base pairs and 2079 stacking pairs defined. Time for finding SS restraints: 72.07 Creating SS restraints... Processing helix chain '5' and resid 19 through 24 removed outlier: 6.510A pdb=" N GLU 5 23 " --> pdb=" O ARG 5 19 " (cutoff:3.500A) Processing helix chain '5' and resid 41 through 47 removed outlier: 3.518A pdb=" N ARG 5 45 " --> pdb=" O VAL 5 41 " (cutoff:3.500A) Processing helix chain '5' and resid 93 through 105 removed outlier: 5.286A pdb=" N SER 5 99 " --> pdb=" O ARG 5 95 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU 5 100 " --> pdb=" O GLU 5 96 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N TYR 5 101 " --> pdb=" O LEU 5 97 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N GLY 5 102 " --> pdb=" O ASP 5 98 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ARG 5 103 " --> pdb=" O SER 5 99 " (cutoff:3.500A) Processing helix chain '5' and resid 138 through 160 removed outlier: 4.367A pdb=" N GLU 5 144 " --> pdb=" O SER 5 140 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N ARG 5 145 " --> pdb=" O ASP 5 141 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N VAL 5 149 " --> pdb=" O ARG 5 145 " (cutoff:3.500A) removed outlier: 4.904A pdb=" N ASP 5 150 " --> pdb=" O GLU 5 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 136 removed outlier: 3.947A pdb=" N ILE B 135 " --> pdb=" O PRO B 131 " (cutoff:3.500A) Proline residue: B 136 - end of helix No H-bonds generated for 'chain 'B' and resid 131 through 136' Processing helix chain 'B' and resid 199 through 204 removed outlier: 3.785A pdb=" N ARG B 203 " --> pdb=" O GLU B 199 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N VAL B 204 " --> pdb=" O HIS B 200 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 199 through 204' Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.789A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 268 removed outlier: 3.682A pdb=" N ILE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.405A pdb=" N VAL B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 263 through 268' Processing helix chain 'C' and resid 61 through 72 Processing helix chain 'C' and resid 97 through 102 removed outlier: 4.630A pdb=" N PHE C 101 " --> pdb=" O SER C 97 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N ALA C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 102' Processing helix chain 'C' and resid 121 through 126 removed outlier: 3.640A pdb=" N ASN C 126 " --> pdb=" O THR C 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 121 through 126' Processing helix chain 'D' and resid 15 through 21 removed outlier: 3.642A pdb=" N ARG D 21 " --> pdb=" O THR D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 40 removed outlier: 4.869A pdb=" N VAL D 28 " --> pdb=" O ASN D 24 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N ARG D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 removed outlier: 3.561A pdb=" N LEU D 105 " --> pdb=" O TYR D 101 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU D 109 " --> pdb=" O LEU D 105 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N SER D 110 " --> pdb=" O LYS D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 142 removed outlier: 3.865A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN D 136 " --> pdb=" O LYS D 132 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N LYS D 139 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASP D 140 " --> pdb=" O GLN D 136 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 165 removed outlier: 4.436A pdb=" N PHE D 158 " --> pdb=" O ASP D 154 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ASN D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N LEU D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N HIS D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 183 removed outlier: 4.465A pdb=" N PHE D 183 " --> pdb=" O SER D 179 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 201 removed outlier: 4.574A pdb=" N LYS D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N GLN D 195 " --> pdb=" O ASP D 191 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ALA D 201 " --> pdb=" O GLU D 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 21 removed outlier: 5.332A pdb=" N VAL E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N LYS E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) removed outlier: 4.846A pdb=" N MET E 17 " --> pdb=" O VAL E 13 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N THR E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N GLU E 19 " --> pdb=" O LYS E 15 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N PHE E 20 " --> pdb=" O LEU E 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 62 removed outlier: 3.781A pdb=" N LEU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASP E 51 " --> pdb=" O LYS E 47 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ASN E 52 " --> pdb=" O LYS E 48 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N ALA E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA E 54 " --> pdb=" O LEU E 50 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LEU E 57 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N ALA E 58 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE E 60 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLY E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 removed outlier: 4.409A pdb=" N TRP E 97 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE E 106 " --> pdb=" O ARG E 102 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA E 107 " --> pdb=" O LEU E 103 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N VAL E 108 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Proline residue: E 109 - end of helix Processing helix chain 'E' and resid 134 through 139 removed outlier: 5.294A pdb=" N PHE E 138 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Proline residue: E 139 - end of helix No H-bonds generated for 'chain 'E' and resid 134 through 139' Processing helix chain 'E' and resid 162 through 174 removed outlier: 4.388A pdb=" N ALA E 172 " --> pdb=" O ALA E 168 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N PHE E 173 " --> pdb=" O LEU E 169 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N ASP E 174 " --> pdb=" O LEU E 170 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 8 removed outlier: 3.927A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) Proline residue: F 8 - end of helix Processing helix chain 'F' and resid 60 through 81 removed outlier: 3.760A pdb=" N GLY F 66 " --> pdb=" O TRP F 62 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N THR F 67 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU F 81 " --> pdb=" O ILE F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.611A pdb=" N GLN F 143 " --> pdb=" O GLN F 139 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG F 149 " --> pdb=" O ALA F 145 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N TYR F 151 " --> pdb=" O ASP F 147 " (cutoff:3.500A) removed outlier: 5.369A pdb=" N ARG F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ARG F 153 " --> pdb=" O ARG F 149 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 28 Processing helix chain 'G' and resid 29 through 34 removed outlier: 4.723A pdb=" N GLN G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) Processing helix chain 'G' and resid 42 through 49 removed outlier: 4.055A pdb=" N ALA G 49 " --> pdb=" O GLU G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 53 through 73 removed outlier: 3.651A pdb=" N ALA G 65 " --> pdb=" O VAL G 61 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N ASN G 66 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ARG G 68 " --> pdb=" O ALA G 64 " (cutoff:3.500A) removed outlier: 4.732A pdb=" N ALA G 69 " --> pdb=" O ALA G 65 " (cutoff:3.500A) removed outlier: 4.894A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 removed outlier: 5.738A pdb=" N ILE G 99 " --> pdb=" O GLY G 95 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA G 102 " --> pdb=" O ASP G 98 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR G 104 " --> pdb=" O ALA G 100 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 21 removed outlier: 4.000A pdb=" N VAL H 18 " --> pdb=" O GLU H 14 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LYS H 20 " --> pdb=" O SER H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 48 removed outlier: 3.942A pdb=" N THR H 39 " --> pdb=" O VAL H 35 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLY H 45 " --> pdb=" O LEU H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 64 removed outlier: 4.041A pdb=" N VAL H 64 " --> pdb=" O LEU H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 79 Proline residue: H 79 - end of helix Processing helix chain 'H' and resid 95 through 106 removed outlier: 5.304A pdb=" N PHE H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ALA H 100 " --> pdb=" O PHE H 96 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LYS H 101 " --> pdb=" O LYS H 97 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 31 removed outlier: 3.937A pdb=" N GLY I 28 " --> pdb=" O GLY I 24 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N GLN I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) removed outlier: 5.109A pdb=" N GLY I 31 " --> pdb=" O LEU I 27 " (cutoff:3.500A) Processing helix chain 'I' and resid 33 through 48 Processing helix chain 'I' and resid 74 through 84 Processing helix chain 'I' and resid 102 through 111 removed outlier: 4.141A pdb=" N GLU I 107 " --> pdb=" O ALA I 103 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE I 108 " --> pdb=" O GLN I 104 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N ALA I 109 " --> pdb=" O LEU I 105 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN I 110 " --> pdb=" O GLN I 106 " (cutoff:3.500A) Processing helix chain 'I' and resid 123 through 135 removed outlier: 5.012A pdb=" N SER I 127 " --> pdb=" O ALA I 123 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLY I 130 " --> pdb=" O ARG I 126 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N THR I 131 " --> pdb=" O SER I 127 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ALA I 132 " --> pdb=" O ILE I 128 " (cutoff:3.500A) removed outlier: 5.102A pdb=" N ARG I 133 " --> pdb=" O GLU I 129 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N SER I 134 " --> pdb=" O GLY I 130 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.761A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 removed outlier: 3.559A pdb=" N ASP J 71 " --> pdb=" O ASN J 67 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 98 through 110 removed outlier: 3.549A pdb=" N GLU J 102 " --> pdb=" O GLU J 98 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 123 removed outlier: 4.406A pdb=" N ARG J 120 " --> pdb=" O ARG J 116 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N LYS J 123 " --> pdb=" O PHE J 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 119 removed outlier: 3.841A pdb=" N ILE K 116 " --> pdb=" O PHE K 112 " (cutoff:3.500A) Processing helix chain 'L' and resid 56 through 62 Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 74 removed outlier: 4.397A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.990A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 85' Processing helix chain 'L' and resid 91 through 99 removed outlier: 4.210A pdb=" N LYS L 96 " --> pdb=" O LEU L 92 " (cutoff:3.500A) removed outlier: 4.701A pdb=" N ALA L 97 " --> pdb=" O ASN L 93 " (cutoff:3.500A) removed outlier: 4.601A pdb=" N ALA L 98 " --> pdb=" O THR L 94 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ASN L 99 " --> pdb=" O LEU L 95 " (cutoff:3.500A) Processing helix chain 'L' and resid 128 through 139 removed outlier: 4.180A pdb=" N ALA L 133 " --> pdb=" O LYS L 129 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ALA L 134 " --> pdb=" O GLY L 130 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA L 138 " --> pdb=" O ALA L 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 removed outlier: 4.180A pdb=" N ILE M 46 " --> pdb=" O THR M 42 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N GLU M 47 " --> pdb=" O ALA M 43 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N VAL M 57 " --> pdb=" O MET M 53 " (cutoff:3.500A) Processing helix chain 'M' and resid 110 through 125 removed outlier: 4.435A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ALA M 116 " --> pdb=" O LEU M 112 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N PHE M 117 " --> pdb=" O ALA M 113 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LEU M 124 " --> pdb=" O ALA M 120 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.937A pdb=" N GLN N 18 " --> pdb=" O SER N 14 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N ARG N 22 " --> pdb=" O GLN N 18 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N ASN N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ARG N 30 " --> pdb=" O GLY N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 39 through 58 removed outlier: 4.769A pdb=" N GLU N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.425A pdb=" N ALA N 55 " --> pdb=" O LEU N 51 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS N 56 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 4.825A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) removed outlier: 5.084A pdb=" N ASP N 58 " --> pdb=" O LEU N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 Processing helix chain 'N' and resid 72 through 88 removed outlier: 4.555A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLU N 82 " --> pdb=" O LYS N 78 " (cutoff:3.500A) removed outlier: 4.899A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix removed outlier: 4.556A pdb=" N ALA N 88 " --> pdb=" O GLY N 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 22 removed outlier: 4.193A pdb=" N ALA O 6 " --> pdb=" O ASP O 2 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N ARG O 10 " --> pdb=" O ALA O 6 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N ALA O 11 " --> pdb=" O ARG O 7 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N THR O 12 " --> pdb=" O ILE O 8 " (cutoff:3.500A) removed outlier: 7.281A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N LYS O 17 " --> pdb=" O ARG O 13 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N LEU O 21 " --> pdb=" O LYS O 17 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 4.148A pdb=" N ALA O 73 " --> pdb=" O ASP O 69 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL O 74 " --> pdb=" O ALA O 70 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ALA O 79 " --> pdb=" O GLY O 75 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLU O 80 " --> pdb=" O LYS O 76 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N LYS O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.986A pdb=" N GLU O 112 " --> pdb=" O ASP O 108 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA O 113 " --> pdb=" O ALA O 109 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N GLY O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 14 removed outlier: 3.812A pdb=" N LEU P 8 " --> pdb=" O ILE P 4 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N GLU P 9 " --> pdb=" O ILE P 5 " (cutoff:3.500A) removed outlier: 4.607A pdb=" N GLN P 10 " --> pdb=" O LYS P 6 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N GLU P 11 " --> pdb=" O GLN P 7 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N MET P 13 " --> pdb=" O GLU P 9 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N LYS P 14 " --> pdb=" O GLN P 10 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 103 removed outlier: 3.642A pdb=" N LEU P 100 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ARG P 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG P 103 " --> pdb=" O LEU P 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.587A pdb=" N ARG Q 11 " --> pdb=" O GLY Q 7 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ALA Q 12 " --> pdb=" O VAL Q 8 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N LYS Q 16 " --> pdb=" O ALA Q 12 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ILE Q 17 " --> pdb=" O ARG Q 13 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N LYS Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 4.610A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 36 through 56 removed outlier: 3.579A pdb=" N ARG Q 50 " --> pdb=" O ALA Q 46 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG Q 55 " --> pdb=" O ARG Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 59 through 73 removed outlier: 4.720A pdb=" N ALA Q 63 " --> pdb=" O GLN Q 59 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG Q 64 " --> pdb=" O LEU Q 60 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 removed outlier: 3.610A pdb=" N ALA Q 86 " --> pdb=" O GLY Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 91 through 101 removed outlier: 3.729A pdb=" N LEU Q 95 " --> pdb=" O ASP Q 91 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ALA Q 96 " --> pdb=" O ARG Q 92 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N VAL Q 100 " --> pdb=" O ALA Q 96 " (cutoff:3.500A) Processing helix chain 'Q' and resid 102 through 118 Processing helix chain 'S' and resid 13 through 25 removed outlier: 4.796A pdb=" N VAL S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 5.074A pdb=" N ARG S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 5.028A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 5.867A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.913A pdb=" N LEU S 36 " --> pdb=" O ALA S 32 " (cutoff:3.500A) removed outlier: 4.743A pdb=" N TYR S 38 " --> pdb=" O ASP S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 4.389A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS S 48 " --> pdb=" O ALA S 44 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 11 removed outlier: 3.917A pdb=" N LYS T 9 " --> pdb=" O GLU T 5 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N VAL T 10 " --> pdb=" O ARG T 6 " (cutoff:3.500A) removed outlier: 5.150A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 26 removed outlier: 5.248A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 50 removed outlier: 4.546A pdb=" N ALA T 46 " --> pdb=" O GLU T 42 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N GLN T 48 " --> pdb=" O LYS T 44 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LYS T 49 " --> pdb=" O ALA T 45 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU T 50 " --> pdb=" O ALA T 46 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.854A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N ALA U 71 " --> pdb=" O VAL U 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 66 through 71' Processing helix chain 'V' and resid 13 through 24 Processing helix chain 'V' and resid 43 through 53 removed outlier: 3.929A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 3.699A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 62 removed outlier: 3.859A pdb=" N ARG X 57 " --> pdb=" O ALA X 53 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ASP X 60 " --> pdb=" O MET X 56 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS X 61 " --> pdb=" O ARG X 57 " (cutoff:3.500A) Processing helix chain 'X' and resid 63 through 75 removed outlier: 3.624A pdb=" N VAL X 67 " --> pdb=" O GLY X 63 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ARG X 72 " --> pdb=" O LEU X 68 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA X 73 " --> pdb=" O ALA X 69 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N GLY X 75 " --> pdb=" O LEU X 71 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 9 removed outlier: 5.567A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) removed outlier: 5.088A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 35 removed outlier: 4.785A pdb=" N LEU Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASN Y 15 " --> pdb=" O VAL Y 11 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR Y 16 " --> pdb=" O GLU Y 12 " (cutoff:3.500A) removed outlier: 5.041A pdb=" N LEU Y 19 " --> pdb=" O ASN Y 15 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA Y 33 " --> pdb=" O ARG Y 29 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 61 removed outlier: 5.100A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N VAL Y 53 " --> pdb=" O ASP Y 49 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN Y 58 " --> pdb=" O LYS Y 54 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 removed outlier: 4.284A pdb=" N GLY Z 28 " --> pdb=" O LEU Z 24 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 52 removed outlier: 4.183A pdb=" N ASN Z 49 " --> pdb=" O ARG Z 45 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA Z 50 " --> pdb=" O GLY Z 46 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N VAL Z 51 " --> pdb=" O MET Z 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 43 through 48 removed outlier: 4.487A pdb=" N LYS a 47 " --> pdb=" O PHE a 43 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N GLN a 48 " --> pdb=" O PHE a 44 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 43 through 48' Processing helix chain 'a' and resid 56 through 64 removed outlier: 3.616A pdb=" N PHE a 64 " --> pdb=" O PHE a 60 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 21 removed outlier: 4.646A pdb=" N ARG b 17 " --> pdb=" O ARG b 13 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER b 18 " --> pdb=" O GLY b 14 " (cutoff:3.500A) removed outlier: 4.919A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ASP b 20 " --> pdb=" O ARG b 16 " (cutoff:3.500A) Processing helix chain 'c' and resid 26 through 31 Proline residue: c 31 - end of helix No H-bonds generated for 'chain 'c' and resid 26 through 31' Processing helix chain 'd' and resid 8 through 16 removed outlier: 4.694A pdb=" N ARG d 14 " --> pdb=" O LEU d 10 " (cutoff:3.500A) Processing helix chain 'd' and resid 17 through 25 removed outlier: 3.780A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) removed outlier: 6.272A pdb=" N LYS d 25 " --> pdb=" O ARG d 21 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 38 removed outlier: 3.935A pdb=" N ALA d 32 " --> pdb=" O ARG d 28 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ARG d 33 " --> pdb=" O GLN d 29 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ARG d 35 " --> pdb=" O LEU d 31 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N ALA d 36 " --> pdb=" O ALA d 32 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LYS d 37 " --> pdb=" O ARG d 33 " (cutoff:3.500A) Processing helix chain 'e' and resid 7 through 14 removed outlier: 4.320A pdb=" N ALA e 11 " --> pdb=" O VAL e 7 " (cutoff:3.500A) removed outlier: 4.280A pdb=" N LYS e 12 " --> pdb=" O ARG e 8 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ARG e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 46 removed outlier: 4.101A pdb=" N LYS e 41 " --> pdb=" O ALA e 37 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N HIS e 43 " --> pdb=" O LYS e 39 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU e 44 " --> pdb=" O ARG e 40 " (cutoff:3.500A) Proline residue: e 46 - end of helix Processing helix chain 'e' and resid 51 through 63 removed outlier: 4.270A pdb=" N LEU e 55 " --> pdb=" O SER e 51 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N GLY e 56 " --> pdb=" O LYS e 52 " (cutoff:3.500A) removed outlier: 5.728A pdb=" N LEU e 57 " --> pdb=" O GLY e 53 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N ALA e 60 " --> pdb=" O GLY e 56 " (cutoff:3.500A) Proline residue: e 63 - end of helix Processing helix chain 'g' and resid 5 through 13 removed outlier: 3.641A pdb=" N MET g 9 " --> pdb=" O SER g 5 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LYS g 11 " --> pdb=" O ARG g 7 " (cutoff:3.500A) Processing helix chain 'g' and resid 27 through 32 removed outlier: 4.111A pdb=" N ILE g 31 " --> pdb=" O MET g 27 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N PHE g 32 " --> pdb=" O LYS g 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 27 through 32' Processing helix chain 'g' and resid 44 through 64 Proline residue: g 48 - end of helix removed outlier: 4.769A pdb=" N ALA g 53 " --> pdb=" O MET g 49 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU g 54 " --> pdb=" O PHE g 50 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ALA g 55 " --> pdb=" O ASN g 51 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN g 58 " --> pdb=" O LEU g 54 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N LYS g 64 " --> pdb=" O ILE g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 74 through 88 removed outlier: 5.913A pdb=" N GLU g 78 " --> pdb=" O ARG g 74 " (cutoff:3.500A) removed outlier: 5.704A pdb=" N ALA g 79 " --> pdb=" O ALA g 75 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N LYS g 81 " --> pdb=" O SER g 77 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N ASP g 82 " --> pdb=" O GLU g 78 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N CYS g 87 " --> pdb=" O ALA g 83 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 123 removed outlier: 5.044A pdb=" N GLN g 109 " --> pdb=" O LYS g 105 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLN g 122 " --> pdb=" O GLU g 118 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ASP g 123 " --> pdb=" O THR g 119 " (cutoff:3.500A) Processing helix chain 'g' and resid 130 through 148 removed outlier: 4.187A pdb=" N MET g 136 " --> pdb=" O LYS g 132 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N GLU g 140 " --> pdb=" O MET g 136 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N LEU g 141 " --> pdb=" O ARG g 137 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASN g 146 " --> pdb=" O GLU g 142 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU g 148 " --> pdb=" O LEU g 144 " (cutoff:3.500A) Processing helix chain 'g' and resid 150 through 155 removed outlier: 5.502A pdb=" N MET g 154 " --> pdb=" O GLY g 150 " (cutoff:3.500A) Processing helix chain 'g' and resid 169 through 180 removed outlier: 4.191A pdb=" N ILE g 173 " --> pdb=" O GLU g 169 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LYS g 174 " --> pdb=" O HIS g 170 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU g 175 " --> pdb=" O ILE g 171 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N ALA g 176 " --> pdb=" O ALA g 172 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N ASN g 177 " --> pdb=" O ILE g 173 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLY g 180 " --> pdb=" O ALA g 176 " (cutoff:3.500A) Processing helix chain 'g' and resid 206 through 227 removed outlier: 4.220A pdb=" N THR g 220 " --> pdb=" O ALA g 216 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N VAL g 221 " --> pdb=" O VAL g 217 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N SER g 226 " --> pdb=" O ARG g 222 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 12 removed outlier: 4.044A pdb=" N ILE h 10 " --> pdb=" O HIS h 6 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N ARG h 11 " --> pdb=" O PRO h 7 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LEU h 12 " --> pdb=" O ASN h 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 6 through 12' Processing helix chain 'h' and resid 26 through 48 removed outlier: 4.953A pdb=" N ALA h 30 " --> pdb=" O THR h 26 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ASP h 31 " --> pdb=" O LYS h 27 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASN h 32 " --> pdb=" O GLU h 28 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU h 33 " --> pdb=" O PHE h 29 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N SER h 35 " --> pdb=" O ASP h 31 " (cutoff:3.500A) removed outlier: 5.539A pdb=" N ARG h 40 " --> pdb=" O ASP h 36 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N GLN h 41 " --> pdb=" O PHE h 37 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N TYR h 42 " --> pdb=" O LYS h 38 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N LYS h 45 " --> pdb=" O GLN h 41 " (cutoff:3.500A) Processing helix chain 'h' and resid 73 through 78 Processing helix chain 'h' and resid 83 through 96 removed outlier: 4.636A pdb=" N LYS h 89 " --> pdb=" O GLU h 85 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL h 91 " --> pdb=" O LEU h 87 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA h 92 " --> pdb=" O ARG h 88 " (cutoff:3.500A) Processing helix chain 'h' and resid 112 through 127 removed outlier: 3.971A pdb=" N ILE h 120 " --> pdb=" O VAL h 116 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N THR h 121 " --> pdb=" O ALA h 117 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG h 126 " --> pdb=" O SER h 122 " (cutoff:3.500A) Processing helix chain 'h' and resid 129 through 145 Processing helix chain 'i' and resid 7 through 16 removed outlier: 3.830A pdb=" N LEU i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N GLU i 15 " --> pdb=" O LEU i 11 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N GLY i 16 " --> pdb=" O SER i 12 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 66 removed outlier: 3.513A pdb=" N VAL i 53 " --> pdb=" O SER i 49 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS i 58 " --> pdb=" O GLN i 54 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ARG i 63 " --> pdb=" O GLN i 59 " (cutoff:3.500A) Processing helix chain 'i' and resid 68 through 82 removed outlier: 3.533A pdb=" N ASN i 74 " --> pdb=" O ARG i 70 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA i 80 " --> pdb=" O TYR i 76 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N ARG i 81 " --> pdb=" O LYS i 77 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU i 82 " --> pdb=" O GLU i 78 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 removed outlier: 4.215A pdb=" N GLU i 95 " --> pdb=" O LEU i 91 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG i 97 " --> pdb=" O LEU i 93 " (cutoff:3.500A) Processing helix chain 'i' and resid 98 through 106 Processing helix chain 'i' and resid 110 through 121 removed outlier: 3.922A pdb=" N LYS i 121 " --> pdb=" O LEU i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 146 through 151 removed outlier: 5.012A pdb=" N LYS i 151 " --> pdb=" O GLU i 147 " (cutoff:3.500A) Processing helix chain 'i' and resid 152 through 166 removed outlier: 3.899A pdb=" N LYS i 156 " --> pdb=" O GLN i 152 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N ALA i 158 " --> pdb=" O ARG i 154 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N GLU i 160 " --> pdb=" O LYS i 156 " (cutoff:3.500A) removed outlier: 4.796A pdb=" N LEU i 161 " --> pdb=" O ALA i 157 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ALA i 162 " --> pdb=" O ALA i 158 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N GLU i 163 " --> pdb=" O LEU i 159 " (cutoff:3.500A) removed outlier: 4.533A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 4.503A pdb=" N LEU i 191 " --> pdb=" O GLU i 187 " (cutoff:3.500A) removed outlier: 5.034A pdb=" N SER i 192 " --> pdb=" O ARG i 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 187 through 192' Processing helix chain 'i' and resid 196 through 205 removed outlier: 4.103A pdb=" N ILE i 200 " --> pdb=" O ASN i 196 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL i 201 " --> pdb=" O GLU i 197 " (cutoff:3.500A) removed outlier: 5.199A pdb=" N GLU i 202 " --> pdb=" O HIS i 198 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU i 203 " --> pdb=" O LEU i 199 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N TYR i 204 " --> pdb=" O ILE i 200 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N SER i 205 " --> pdb=" O VAL i 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 196 through 205' Processing helix chain 'j' and resid 55 through 69 removed outlier: 3.773A pdb=" N GLN j 61 " --> pdb=" O PRO j 57 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N LYS j 62 " --> pdb=" O ALA j 58 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ARG j 68 " --> pdb=" O MET j 64 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N ARG j 69 " --> pdb=" O GLU j 65 " (cutoff:3.500A) Processing helix chain 'j' and resid 109 through 119 removed outlier: 4.496A pdb=" N ALA j 113 " --> pdb=" O GLY j 109 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL j 114 " --> pdb=" O ALA j 110 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N VAL j 117 " --> pdb=" O ALA j 113 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N ALA j 118 " --> pdb=" O VAL j 114 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLY j 119 " --> pdb=" O LEU j 115 " (cutoff:3.500A) Processing helix chain 'j' and resid 133 through 147 removed outlier: 3.974A pdb=" N VAL j 137 " --> pdb=" O PRO j 133 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N ARG j 138 " --> pdb=" O ILE j 134 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA j 139 " --> pdb=" O ASN j 135 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N MET j 147 " --> pdb=" O GLY j 143 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 158 Processing helix chain 'j' and resid 160 through 165 removed outlier: 4.787A pdb=" N ILE j 164 " --> pdb=" O SER j 160 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU j 165 " --> pdb=" O VAL j 161 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 160 through 165' Processing helix chain 'k' and resid 16 through 33 removed outlier: 5.072A pdb=" N GLY k 20 " --> pdb=" O GLU k 16 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLU k 23 " --> pdb=" O PRO k 19 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N ILE k 29 " --> pdb=" O TYR k 25 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA k 32 " --> pdb=" O ALA k 28 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N GLU k 33 " --> pdb=" O ILE k 29 " (cutoff:3.500A) Processing helix chain 'k' and resid 67 through 81 removed outlier: 4.064A pdb=" N ILE k 71 " --> pdb=" O PRO k 67 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ASP k 72 " --> pdb=" O GLN k 68 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N GLU k 73 " --> pdb=" O GLU k 69 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N ASN k 81 " --> pdb=" O THR k 77 " (cutoff:3.500A) Processing helix chain 'l' and resid 20 through 31 removed outlier: 3.637A pdb=" N LYS l 25 " --> pdb=" O GLU l 21 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ASN l 28 " --> pdb=" O ALA l 24 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ILE l 29 " --> pdb=" O LYS l 25 " (cutoff:3.500A) Processing helix chain 'l' and resid 36 through 55 removed outlier: 3.865A pdb=" N SER l 41 " --> pdb=" O SER l 37 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ALA l 51 " --> pdb=" O LEU l 47 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLN l 52 " --> pdb=" O GLU l 48 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N GLY l 55 " --> pdb=" O ALA l 51 " (cutoff:3.500A) Processing helix chain 'l' and resid 58 through 70 removed outlier: 5.524A pdb=" N GLU l 63 " --> pdb=" O LEU l 59 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N VAL l 64 " --> pdb=" O GLU l 60 " (cutoff:3.500A) removed outlier: 5.343A pdb=" N ALA l 65 " --> pdb=" O ALA l 61 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N LEU l 66 " --> pdb=" O PHE l 62 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ARG l 70 " --> pdb=" O LEU l 66 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 111 removed outlier: 3.721A pdb=" N ASN l 97 " --> pdb=" O PRO l 93 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N ARG l 102 " --> pdb=" O ALA l 98 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ILE l 104 " --> pdb=" O ALA l 100 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ALA l 107 " --> pdb=" O TRP l 103 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS l 110 " --> pdb=" O GLU l 106 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ARG l 111 " --> pdb=" O ALA l 107 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 130 removed outlier: 3.782A pdb=" N LEU l 120 " --> pdb=" O MET l 116 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N ALA l 121 " --> pdb=" O ALA l 117 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N ASN l 122 " --> pdb=" O LEU l 118 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLU l 123 " --> pdb=" O ARG l 119 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LEU l 124 " --> pdb=" O LEU l 120 " (cutoff:3.500A) removed outlier: 5.453A pdb=" N SER l 125 " --> pdb=" O ALA l 121 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU l 129 " --> pdb=" O SER l 125 " (cutoff:3.500A) Processing helix chain 'l' and resid 132 through 149 removed outlier: 4.881A pdb=" N LYS l 136 " --> pdb=" O GLY l 132 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N LYS l 149 " --> pdb=" O ALA l 145 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 21 removed outlier: 3.917A pdb=" N ASP m 9 " --> pdb=" O ASP m 5 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N ARG m 15 " --> pdb=" O LEU m 11 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY m 17 " --> pdb=" O ARG m 13 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN m 21 " --> pdb=" O GLY m 17 " (cutoff:3.500A) Processing helix chain 'm' and resid 30 through 44 removed outlier: 4.136A pdb=" N VAL m 34 " --> pdb=" O SER m 30 " (cutoff:3.500A) Processing helix chain 'm' and resid 112 through 120 removed outlier: 3.829A pdb=" N GLN m 118 " --> pdb=" O ARG m 114 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ALA m 119 " --> pdb=" O ALA m 115 " (cutoff:3.500A) Processing helix chain 'n' and resid 34 through 39 removed outlier: 3.779A pdb=" N TYR n 38 " --> pdb=" O SER n 34 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 54 removed outlier: 5.124A pdb=" N VAL n 48 " --> pdb=" O ALA n 44 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ARG n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 51 - end of helix Processing helix chain 'n' and resid 57 through 62 removed outlier: 5.434A pdb=" N LEU n 61 " --> pdb=" O MET n 57 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N ASP n 62 " --> pdb=" O VAL n 58 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 57 through 62' Processing helix chain 'n' and resid 75 through 92 removed outlier: 3.871A pdb=" N ASP n 91 " --> pdb=" O LEU n 87 " (cutoff:3.500A) Processing helix chain 'n' and resid 94 through 102 removed outlier: 3.744A pdb=" N LEU n 98 " --> pdb=" O LEU n 94 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ALA n 101 " --> pdb=" O GLU n 97 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLY n 102 " --> pdb=" O LEU n 98 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 33 removed outlier: 4.150A pdb=" N ILE o 18 " --> pdb=" O ASP o 14 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ASP o 19 " --> pdb=" O HIS o 15 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLU o 24 " --> pdb=" O GLN o 20 " (cutoff:3.500A) Processing helix chain 'o' and resid 84 through 90 removed outlier: 5.164A pdb=" N MET o 88 " --> pdb=" O VAL o 84 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 4.609A pdb=" N SER p 50 " --> pdb=" O THR p 46 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N GLY p 51 " --> pdb=" O ALA p 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 46 through 51' Processing helix chain 'p' and resid 61 through 78 removed outlier: 3.615A pdb=" N VAL p 65 " --> pdb=" O PHE p 61 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG p 69 " --> pdb=" O VAL p 65 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ASP p 72 " --> pdb=" O GLU p 68 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ALA p 73 " --> pdb=" O ARG p 69 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N VAL p 74 " --> pdb=" O CYS p 70 " (cutoff:3.500A) removed outlier: 5.025A pdb=" N GLU p 76 " --> pdb=" O ASP p 72 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N TYR p 77 " --> pdb=" O ALA p 73 " (cutoff:3.500A) Processing helix chain 'p' and resid 94 through 104 removed outlier: 4.511A pdb=" N ARG p 98 " --> pdb=" O GLU p 94 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ALA p 99 " --> pdb=" O SER p 95 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA p 102 " --> pdb=" O ARG p 98 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N GLY p 104 " --> pdb=" O LEU p 100 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 11 Proline residue: q 11 - end of helix Processing helix chain 'q' and resid 113 through 118 removed outlier: 4.485A pdb=" N TYR q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 21 removed outlier: 5.072A pdb=" N THR r 20 " --> pdb=" O VAL r 16 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N SER r 21 " --> pdb=" O ILE r 17 " (cutoff:3.500A) Processing helix chain 'r' and resid 27 through 38 removed outlier: 5.096A pdb=" N LYS r 31 " --> pdb=" O LYS r 27 " (cutoff:3.500A) removed outlier: 3.998A pdb=" N ALA r 32 " --> pdb=" O THR r 28 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ALA r 35 " --> pdb=" O LYS r 31 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ALA r 37 " --> pdb=" O ILE r 33 " (cutoff:3.500A) Processing helix chain 'r' and resid 49 through 64 removed outlier: 5.635A pdb=" N LEU r 56 " --> pdb=" O GLN r 52 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ARG r 57 " --> pdb=" O ILE r 53 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ASP r 58 " --> pdb=" O ASP r 54 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N GLU r 59 " --> pdb=" O THR r 55 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N ALA r 61 " --> pdb=" O ARG r 57 " (cutoff:3.500A) removed outlier: 4.048A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N VAL r 64 " --> pdb=" O VAL r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 65 through 83 removed outlier: 4.296A pdb=" N ARG r 70 " --> pdb=" O GLU r 66 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N ARG r 71 " --> pdb=" O GLY r 67 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ASP r 82 " --> pdb=" O LYS r 78 " (cutoff:3.500A) removed outlier: 5.061A pdb=" N LEU r 83 " --> pdb=" O ARG r 79 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 94 removed outlier: 4.679A pdb=" N HIS r 91 " --> pdb=" O ARG r 87 " (cutoff:3.500A) removed outlier: 5.001A pdb=" N ARG r 92 " --> pdb=" O GLY r 88 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLY r 94 " --> pdb=" O ARG r 90 " (cutoff:3.500A) Processing helix chain 'r' and resid 106 through 111 Processing helix chain 's' and resid 3 through 21 removed outlier: 4.245A pdb=" N LYS s 7 " --> pdb=" O LYS s 3 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N ALA s 8 " --> pdb=" O GLN s 4 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N ARG s 9 " --> pdb=" O SER s 5 " (cutoff:3.500A) removed outlier: 4.060A pdb=" N LYS s 12 " --> pdb=" O ALA s 8 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N VAL s 14 " --> pdb=" O GLU s 10 " (cutoff:3.500A) Processing helix chain 's' and resid 22 through 34 removed outlier: 4.159A pdb=" N GLU s 26 " --> pdb=" O ALA s 22 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA s 29 " --> pdb=" O ALA s 25 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N VAL s 34 " --> pdb=" O ILE s 30 " (cutoff:3.500A) Processing helix chain 's' and resid 37 through 52 removed outlier: 4.677A pdb=" N ARG s 41 " --> pdb=" O SER s 37 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N TRP s 42 " --> pdb=" O ASP s 38 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA s 44 " --> pdb=" O ASP s 40 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N LEU s 48 " --> pdb=" O ALA s 44 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N GLN s 49 " --> pdb=" O VAL s 45 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU s 51 " --> pdb=" O LYS s 47 " (cutoff:3.500A) Proline residue: s 52 - end of helix Processing helix chain 's' and resid 80 through 91 removed outlier: 4.441A pdb=" N VAL s 84 " --> pdb=" O SER s 80 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET s 89 " --> pdb=" O ARG s 85 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 16 removed outlier: 3.678A pdb=" N ILE t 11 " --> pdb=" O ALA t 7 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N SER t 13 " --> pdb=" O ALA t 9 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N GLU t 14 " --> pdb=" O LYS t 10 " (cutoff:3.500A) Processing helix chain 't' and resid 24 through 43 removed outlier: 4.045A pdb=" N GLN t 28 " --> pdb=" O SER t 24 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL t 29 " --> pdb=" O THR t 25 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 4.708A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N PHE t 43 " --> pdb=" O LEU t 39 " (cutoff:3.500A) Processing helix chain 't' and resid 49 through 74 removed outlier: 4.933A pdb=" N ARG t 53 " --> pdb=" O ASP t 49 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ARG t 54 " --> pdb=" O HIS t 50 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N GLY t 55 " --> pdb=" O HIS t 51 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N LYS t 71 " --> pdb=" O LEU t 67 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 86 removed outlier: 4.968A pdb=" N GLU t 83 " --> pdb=" O THR t 79 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ARG t 84 " --> pdb=" O GLN t 80 " (cutoff:3.500A) Processing helix chain 'u' and resid 53 through 64 removed outlier: 3.931A pdb=" N HIS u 59 " --> pdb=" O ASP u 55 " (cutoff:3.500A) Processing helix chain 'u' and resid 68 through 82 removed outlier: 4.199A pdb=" N LYS u 76 " --> pdb=" O ALA u 72 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N ASN u 79 " --> pdb=" O ILE u 75 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N LYS u 80 " --> pdb=" O LYS u 76 " (cutoff:3.500A) removed outlier: 5.452A pdb=" N ALA u 81 " --> pdb=" O GLU u 77 " (cutoff:3.500A) Processing helix chain 'w' and resid 11 through 17 removed outlier: 5.089A pdb=" N ALA w 15 " --> pdb=" O CYS w 11 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLU w 16 " --> pdb=" O ARG w 12 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N GLY w 17 " --> pdb=" O PHE w 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 11 through 17' Processing helix chain 'w' and resid 25 through 34 removed outlier: 5.091A pdb=" N LEU w 29 " --> pdb=" O ASP w 25 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N ASN w 31 " --> pdb=" O ALA w 27 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N THR w 34 " --> pdb=" O LYS w 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 41 through 46 removed outlier: 3.734A pdb=" N THR w 45 " --> pdb=" O PRO w 41 " (cutoff:3.500A) Processing helix chain 'w' and resid 48 through 66 removed outlier: 3.987A pdb=" N LEU w 65 " --> pdb=" O ARG w 61 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 26 Processing helix chain 'x' and resid 71 through 76 removed outlier: 5.637A pdb=" N ALA x 75 " --> pdb=" O LEU x 71 " (cutoff:3.500A) Proline residue: x 76 - end of helix No H-bonds generated for 'chain 'x' and resid 71 through 76' Processing helix chain 'y' and resid 4 through 41 removed outlier: 4.211A pdb=" N ARG y 10 " --> pdb=" O SER y 6 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ILE y 12 " --> pdb=" O LYS y 8 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N GLN y 13 " --> pdb=" O LYS y 9 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N SER y 14 " --> pdb=" O ARG y 10 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N GLU y 15 " --> pdb=" O ALA y 11 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N LYS y 16 " --> pdb=" O ILE y 12 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N ALA y 17 " --> pdb=" O GLN y 13 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA y 22 " --> pdb=" O ARG y 18 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N MET y 27 " --> pdb=" O SER y 23 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N VAL y 35 " --> pdb=" O PHE y 31 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA y 37 " --> pdb=" O LYS y 33 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA y 38 " --> pdb=" O LYS y 34 " (cutoff:3.500A) Processing helix chain 'y' and resid 43 through 65 removed outlier: 3.810A pdb=" N LYS y 49 " --> pdb=" O ALA y 45 " (cutoff:3.500A) Proline residue: y 56 - end of helix removed outlier: 4.467A pdb=" N ARG y 60 " --> pdb=" O PRO y 56 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA y 63 " --> pdb=" O ASP y 59 " (cutoff:3.500A) Processing helix chain 'y' and resid 68 through 87 removed outlier: 4.097A pdb=" N ALA y 72 " --> pdb=" O HIS y 68 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ALA y 81 " --> pdb=" O ALA y 77 " (cutoff:3.500A) removed outlier: 4.758A pdb=" N ALA y 87 " --> pdb=" O ILE y 83 " (cutoff:3.500A) Processing helix chain 'z' and resid 11 through 27 removed outlier: 4.334A pdb=" N ARG z 17 " --> pdb=" O ASP z 13 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG z 21 " --> pdb=" O ARG z 17 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ALA z 26 " --> pdb=" O SER z 22 " (cutoff:3.500A) Processing helix chain 'z' and resid 28 through 38 removed outlier: 4.770A pdb=" N PHE z 37 " --> pdb=" O ARG z 33 " (cutoff:3.500A) removed outlier: 5.344A pdb=" N TYR z 38 " --> pdb=" O ARG z 34 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 69 removed outlier: 5.002A pdb=" N ARG z 45 " --> pdb=" O PRO z 41 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA z 48 " --> pdb=" O GLU z 44 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N ARG z 55 " --> pdb=" O SER z 51 " (cutoff:3.500A) removed outlier: 5.390A pdb=" N ARG z 62 " --> pdb=" O LYS z 58 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLU z 63 " --> pdb=" O LYS z 59 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ASN z 64 " --> pdb=" O LEU z 60 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ALA z 65 " --> pdb=" O ALA z 61 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR z 68 " --> pdb=" O ASN z 64 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ARG z 69 " --> pdb=" O ALA z 65 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '5' and resid 29 through 33 removed outlier: 4.092A pdb=" N VAL 5 125 " --> pdb=" O ALA 5 32 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TYR 5 117 " --> pdb=" O LYS 5 124 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '5' and resid 63 through 66 removed outlier: 4.039A pdb=" N ALA 5 63 " --> pdb=" O LEU 5 90 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'B' and resid 2 through 5 Processing sheet with id= 4, first strand: chain 'B' and resid 33 through 36 No H-bonds generated for sheet with id= 4 Processing sheet with id= 5, first strand: chain 'B' and resid 80 through 83 removed outlier: 6.718A pdb=" N LEU B 93 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ILE B 74 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N SER B 118 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 5.073A pdb=" N ASP B 114 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 138 through 142 removed outlier: 4.154A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE B 164 " --> pdb=" O SER B 139 " (cutoff:3.500A) removed outlier: 7.027A pdb=" N THR B 173 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N LEU B 176 " --> pdb=" O GLU B 180 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N GLU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 143 through 146 removed outlier: 6.652A pdb=" N ASN B 143 " --> pdb=" O THR B 191 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N THR B 191 " --> pdb=" O ASN B 143 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ARG B 189 " --> pdb=" O GLU B 145 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 91 through 96 removed outlier: 3.569A pdb=" N ARG B 102 " --> pdb=" O VAL B 94 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 3 through 7 removed outlier: 6.696A pdb=" N ASP C 200 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N THR C 112 " --> pdb=" O ASP C 200 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 10 through 16 removed outlier: 4.010A pdb=" N GLY C 10 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ILE C 27 " --> pdb=" O LEU C 187 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 32 through 35 removed outlier: 6.705A pdb=" N GLN C 49 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLN C 36 " --> pdb=" O GLN C 49 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 47 through 51 removed outlier: 3.837A pdb=" N ILE C 48 " --> pdb=" O PHE C 82 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N PHE C 82 " --> pdb=" O ILE C 48 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 105 through 108 removed outlier: 6.562A pdb=" N LYS C 105 " --> pdb=" O VAL C 177 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL C 107 " --> pdb=" O LEU C 175 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'D' and resid 117 through 120 removed outlier: 4.027A pdb=" N LYS D 185 " --> pdb=" O ASP D 145 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N LEU D 147 " --> pdb=" O LYS D 185 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ILE D 149 " --> pdb=" O VAL D 187 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N VAL D 146 " --> pdb=" O LYS D 166 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP D 168 " --> pdb=" O VAL D 146 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR D 150 " --> pdb=" O ARG D 170 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'E' and resid 65 through 68 removed outlier: 4.397A pdb=" N GLY E 86 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N VAL E 89 " --> pdb=" O LEU E 36 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N GLY E 39 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N GLY E 151 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LEU E 152 " --> pdb=" O VAL E 132 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE E 154 " --> pdb=" O MET E 130 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 23 through 27 removed outlier: 4.495A pdb=" N ILE F 24 " --> pdb=" O ARG F 35 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N ARG F 35 " --> pdb=" O ILE F 24 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 94 through 98 Processing sheet with id= 18, first strand: chain 'F' and resid 121 through 125 removed outlier: 7.032A pdb=" N THR F 129 " --> pdb=" O LEU F 89 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'G' and resid 3 through 6 No H-bonds generated for sheet with id= 19 Processing sheet with id= 20, first strand: chain 'G' and resid 76 through 81 removed outlier: 6.615A pdb=" N GLU G 76 " --> pdb=" O LYS G 141 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE G 143 " --> pdb=" O GLU G 76 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL G 78 " --> pdb=" O ILE G 143 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ILE G 80 " --> pdb=" O ASN G 145 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'H' and resid 23 through 28 removed outlier: 3.875A pdb=" N LEU H 23 " --> pdb=" O GLU H 87 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU H 87 " --> pdb=" O LEU H 23 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'J' and resid 14 through 19 removed outlier: 3.652A pdb=" N TYR J 53 " --> pdb=" O ASP J 14 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU J 57 " --> pdb=" O VAL J 18 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'J' and resid 74 through 77 Processing sheet with id= 24, first strand: chain 'K' and resid 18 through 21 removed outlier: 4.238A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'K' and resid 68 through 71 removed outlier: 3.879A pdb=" N SER K 75 " --> pdb=" O ARG K 71 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'M' and resid 103 through 106 removed outlier: 3.501A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LYS M 34 " --> pdb=" O THR M 129 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.734A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLU N 114 " --> pdb=" O ARG N 96 " (cutoff:3.500A) removed outlier: 9.021A pdb=" N TYR N 94 " --> pdb=" O VAL N 116 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'O' and resid 35 through 41 removed outlier: 3.509A pdb=" N ASP O 93 " --> pdb=" O LEU O 26 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'P' and resid 49 through 53 removed outlier: 4.686A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 4.678A pdb=" N ARG P 53 " --> pdb=" O HIS P 56 " (cutoff:3.500A) removed outlier: 5.035A pdb=" N HIS P 56 " --> pdb=" O ARG P 53 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N THR P 60 " --> pdb=" O ILE P 48 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ILE P 48 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER P 83 " --> pdb=" O LYS P 29 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'P' and resid 57 through 64 removed outlier: 6.754A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N PHE P 59 " --> pdb=" O PHE P 74 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'R' and resid 11 through 15 removed outlier: 3.852A pdb=" N PHE R 5 " --> pdb=" O HIS R 12 " (cutoff:3.500A) removed outlier: 5.636A pdb=" N LEU R 39 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE R 41 " --> pdb=" O LYS R 48 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ASN R 43 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N GLU R 46 " --> pdb=" O ASN R 43 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'R' and resid 19 through 23 removed outlier: 3.980A pdb=" N VAL R 20 " --> pdb=" O VAL R 96 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL R 96 " --> pdb=" O VAL R 20 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N PHE R 35 " --> pdb=" O ILE R 59 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'R' and resid 57 through 60 Processing sheet with id= 34, first strand: chain 'R' and resid 65 through 73 removed outlier: 3.692A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N GLN R 91 " --> pdb=" O GLY R 69 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N LYS R 71 " --> pdb=" O HIS R 89 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N HIS R 89 " --> pdb=" O LYS R 71 " (cutoff:3.500A) removed outlier: 4.645A pdb=" N LYS R 73 " --> pdb=" O GLN R 87 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N GLN R 87 " --> pdb=" O LYS R 73 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'S' and resid 2 through 8 Processing sheet with id= 36, first strand: chain 'T' and resid 12 through 15 removed outlier: 3.779A pdb=" N ALA T 13 " --> pdb=" O LYS T 33 " (cutoff:3.500A) removed outlier: 5.594A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ALA T 83 " --> pdb=" O LEU T 32 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N TRP T 80 " --> pdb=" O VAL T 63 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N VAL T 63 " --> pdb=" O TRP T 80 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'U' and resid 40 through 44 removed outlier: 5.118A pdb=" N ASN U 40 " --> pdb=" O ALA U 63 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL U 42 " --> pdb=" O LYS U 61 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS U 61 " --> pdb=" O VAL U 42 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'U' and resid 83 through 87 removed outlier: 3.557A pdb=" N ARG U 86 " --> pdb=" O VAL U 93 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'V' and resid 2 through 5 removed outlier: 5.790A pdb=" N PHE V 2 " --> pdb=" O VAL V 60 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE V 4 " --> pdb=" O THR V 62 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'V' and resid 37 through 42 removed outlier: 3.651A pdb=" N LEU V 38 " --> pdb=" O ILE V 30 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA V 28 " --> pdb=" O ILE V 40 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N PHE V 26 " --> pdb=" O LEU V 42 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ILE V 29 " --> pdb=" O ILE V 89 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N ARG V 93 " --> pdb=" O TYR V 31 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N HIS V 88 " --> pdb=" O GLN V 78 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'W' and resid 66 through 71 removed outlier: 3.562A pdb=" N GLU W 70 " --> pdb=" O PHE W 79 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'X' and resid 12 through 18 removed outlier: 3.716A pdb=" N VAL X 13 " --> pdb=" O PHE X 29 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY X 15 " --> pdb=" O ARG X 27 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N ASN X 17 " --> pdb=" O THR X 25 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N THR X 25 " --> pdb=" O ASN X 17 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'Z' and resid 35 through 39 removed outlier: 3.511A pdb=" N ARG Z 38 " --> pdb=" O ILE Z 5 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N LYS Z 6 " --> pdb=" O GLU Z 58 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'a' and resid 21 through 24 removed outlier: 4.100A pdb=" N SER a 15 " --> pdb=" O LEU a 32 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'c' and resid 20 through 24 Processing sheet with id= 46, first strand: chain 'f' and resid 1 through 4 removed outlier: 5.649A pdb=" N ILE f 23 " --> pdb=" O GLN f 37 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL f 22 " --> pdb=" O ARG f 19 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N LYS f 15 " --> pdb=" O ILE f 26 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'g' and resid 89 through 92 removed outlier: 3.805A pdb=" N ALA g 185 " --> pdb=" O PHE g 198 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE g 200 " --> pdb=" O ALA g 185 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'h' and resid 19 through 22 removed outlier: 3.576A pdb=" N ARG h 54 " --> pdb=" O HIS h 69 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE h 64 " --> pdb=" O PRO h 98 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N VAL h 66 " --> pdb=" O GLN h 100 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'h' and resid 164 through 170 removed outlier: 6.164A pdb=" N ARG h 164 " --> pdb=" O GLY h 155 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N VAL h 151 " --> pdb=" O TYR h 168 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLY h 194 " --> pdb=" O THR h 191 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE h 196 " --> pdb=" O ALA h 189 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ALA h 189 " --> pdb=" O ILE h 196 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N SER h 187 " --> pdb=" O VAL h 198 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N VAL h 200 " --> pdb=" O ASN h 185 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N ASN h 185 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LYS h 204 " --> pdb=" O ASP h 181 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N ASP h 181 " --> pdb=" O LYS h 204 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'i' and resid 140 through 144 removed outlier: 3.682A pdb=" N ASP i 141 " --> pdb=" O PHE i 182 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU i 179 " --> pdb=" O ASP i 174 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'j' and resid 11 through 15 Processing sheet with id= 52, first strand: chain 'j' and resid 84 through 88 removed outlier: 3.762A pdb=" N VAL j 94 " --> pdb=" O GLY j 87 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ARG j 93 " --> pdb=" O TYR j 128 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ALA j 99 " --> pdb=" O ASN j 122 " (cutoff:3.500A) removed outlier: 5.833A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'k' and resid 38 through 43 removed outlier: 3.792A pdb=" N ARG k 38 " --> pdb=" O ASN k 63 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N GLU k 40 " --> pdb=" O LEU k 61 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N LEU k 61 " --> pdb=" O GLU k 40 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N TRP k 42 " --> pdb=" O TYR k 59 " (cutoff:3.500A) removed outlier: 5.829A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N HIS k 58 " --> pdb=" O VAL k 10 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL k 60 " --> pdb=" O PHE k 8 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE k 8 " --> pdb=" O VAL k 60 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE k 6 " --> pdb=" O MET k 62 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'l' and resid 73 through 77 Processing sheet with id= 55, first strand: chain 'm' and resid 23 through 28 removed outlier: 6.368A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N VAL m 25 " --> pdb=" O LEU m 61 " (cutoff:3.500A) removed outlier: 4.043A pdb=" N MET m 27 " --> pdb=" O LEU m 59 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'm' and resid 103 through 106 removed outlier: 7.013A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'n' and resid 5 through 11 removed outlier: 4.056A pdb=" N ALA n 16 " --> pdb=" O LYS n 68 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS n 68 " --> pdb=" O ALA n 16 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'p' and resid 42 through 45 removed outlier: 4.545A pdb=" N GLY p 19 " --> pdb=" O ASN p 81 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N ASN p 109 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLY p 88 " --> pdb=" O VAL p 113 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'q' and resid 36 through 41 removed outlier: 3.593A pdb=" N ARG q 36 " --> pdb=" O ARG q 54 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL q 52 " --> pdb=" O TYR q 38 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N ARG q 54 " --> pdb=" O THR q 35 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS q 30 " --> pdb=" O ILE q 82 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N CYS q 34 " --> pdb=" O SER q 78 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N SER q 78 " --> pdb=" O CYS q 34 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) removed outlier: 5.449A pdb=" N HIS q 96 " --> pdb=" O ARG q 83 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'q' and resid 51 through 57 removed outlier: 4.876A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N PHE q 61 " --> pdb=" O LEU q 57 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'u' and resid 4 through 10 removed outlier: 3.977A pdb=" N PHE u 16 " --> pdb=" O HIS u 9 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N TYR u 17 " --> pdb=" O PHE u 38 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N PHE u 38 " --> pdb=" O TYR u 17 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N VAL u 19 " --> pdb=" O VAL u 36 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N VAL u 21 " --> pdb=" O GLU u 34 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N GLU u 34 " --> pdb=" O VAL u 21 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'v' and resid 7 through 11 Processing sheet with id= 63, first strand: chain 'v' and resid 20 through 26 No H-bonds generated for sheet with id= 63 Processing sheet with id= 64, first strand: chain 'x' and resid 48 through 52 removed outlier: 4.087A pdb=" N ILE x 49 " --> pdb=" O VAL x 60 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N VAL x 60 " --> pdb=" O ILE x 49 " (cutoff:3.500A) 1464 hydrogen bonds defined for protein. 4353 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 2637 hydrogen bonds 4220 hydrogen bond angles 0 basepair planarities 1040 basepair parallelities 2079 stacking parallelities Total time for adding SS restraints: 212.61 Time building geometry restraints manager: 73.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 12452 1.27 - 1.41: 58651 1.41 - 1.55: 85512 1.55 - 1.70: 9851 1.70 - 1.84: 288 Bond restraints: 166754 Sorted by residual: bond pdb=" C4 5MU 11939 " pdb=" C5 5MU 11939 " ideal model delta sigma weight residual 1.802 1.474 0.328 2.00e-02 2.50e+03 2.69e+02 bond pdb=" C4 5MU 1 747 " pdb=" C5 5MU 1 747 " ideal model delta sigma weight residual 1.802 1.482 0.320 2.00e-02 2.50e+03 2.56e+02 bond pdb=" N1 5MU 11939 " pdb=" C6 5MU 11939 " ideal model delta sigma weight residual 1.635 1.331 0.304 2.00e-02 2.50e+03 2.30e+02 bond pdb=" N1 5MU 1 747 " pdb=" C6 5MU 1 747 " ideal model delta sigma weight residual 1.635 1.338 0.297 2.00e-02 2.50e+03 2.20e+02 bond pdb=" C4 3TD 11915 " pdb=" O4 3TD 11915 " ideal model delta sigma weight residual 1.163 1.399 -0.236 2.00e-02 2.50e+03 1.39e+02 ... (remaining 166749 not shown) Histogram of bond angle deviations from ideal: 92.79 - 101.93: 4099 101.93 - 111.06: 94244 111.06 - 120.19: 89828 120.19 - 129.33: 57371 129.33 - 138.46: 3958 Bond angle restraints: 249500 Sorted by residual: angle pdb=" O3' C 4 48 " pdb=" P C 4 49 " pdb=" O5' C 4 49 " ideal model delta sigma weight residual 104.00 119.69 -15.69 1.50e+00 4.44e-01 1.09e+02 angle pdb=" C1' G7M 12069 " pdb=" N9 G7M 12069 " pdb=" C8 G7M 12069 " ideal model delta sigma weight residual 94.96 124.31 -29.35 3.00e+00 1.11e-01 9.57e+01 angle pdb=" O3' C 4 266 " pdb=" P G 4 267 " pdb=" O5' G 4 267 " ideal model delta sigma weight residual 104.00 118.41 -14.41 1.50e+00 4.44e-01 9.23e+01 angle pdb=" O3' U 4 161 " pdb=" P A 4 162 " pdb=" O5' A 4 162 " ideal model delta sigma weight residual 104.00 118.38 -14.38 1.50e+00 4.44e-01 9.20e+01 angle pdb=" O3' G 4 163 " pdb=" P G 4 164 " pdb=" O5' G 4 164 " ideal model delta sigma weight residual 104.00 117.89 -13.89 1.50e+00 4.44e-01 8.58e+01 ... (remaining 249495 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 92101 35.91 - 71.83: 12988 71.83 - 107.74: 1460 107.74 - 143.66: 51 143.66 - 179.57: 63 Dihedral angle restraints: 106663 sinusoidal: 89188 harmonic: 17475 Sorted by residual: dihedral pdb=" C5* PSU 11917 " pdb=" C4* PSU 11917 " pdb=" C3* PSU 11917 " pdb=" O3* PSU 11917 " ideal model delta sinusoidal sigma weight residual 82.00 -81.12 163.12 1 8.00e+00 1.56e-02 2.94e+02 dihedral pdb=" C5* PSU 12605 " pdb=" C4* PSU 12605 " pdb=" C3* PSU 12605 " pdb=" O3* PSU 12605 " ideal model delta sinusoidal sigma weight residual 82.00 -77.30 159.30 1 8.00e+00 1.56e-02 2.90e+02 dihedral pdb=" C5* PSU 11911 " pdb=" C4* PSU 11911 " pdb=" C3* PSU 11911 " pdb=" O3* PSU 11911 " ideal model delta sinusoidal sigma weight residual 82.00 -75.96 157.96 1 8.00e+00 1.56e-02 2.89e+02 ... (remaining 106660 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.098: 31796 1.098 - 2.196: 0 2.196 - 3.295: 0 3.295 - 4.393: 0 4.393 - 5.491: 24 Chirality restraints: 31820 Sorted by residual: chirality pdb=" C2' 6MZ 12030 " pdb=" C3' 6MZ 12030 " pdb=" O2' 6MZ 12030 " pdb=" C1' 6MZ 12030 " both_signs ideal model delta sigma weight residual False -2.75 2.74 -5.49 2.00e-01 2.50e+01 7.54e+02 chirality pdb=" C3' 6MZ 11618 " pdb=" C4' 6MZ 11618 " pdb=" O3' 6MZ 11618 " pdb=" C2' 6MZ 11618 " both_signs ideal model delta sigma weight residual False -2.74 2.70 -5.44 2.00e-01 2.50e+01 7.41e+02 chirality pdb=" C2' OMU 12552 " pdb=" C3' OMU 12552 " pdb=" O2' OMU 12552 " pdb=" C1' OMU 12552 " both_signs ideal model delta sigma weight residual False -2.75 2.67 -5.42 2.00e-01 2.50e+01 7.34e+02 ... (remaining 31817 not shown) Planarity restraints: 13336 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 7MG 2 527 " -0.013 2.00e-02 2.50e+03 6.57e-01 9.72e+03 pdb=" C4' 7MG 2 527 " 0.551 2.00e-02 2.50e+03 pdb=" O4' 7MG 2 527 " 0.806 2.00e-02 2.50e+03 pdb=" C3' 7MG 2 527 " -0.502 2.00e-02 2.50e+03 pdb=" O3' 7MG 2 527 " -0.651 2.00e-02 2.50e+03 pdb=" C2' 7MG 2 527 " -0.167 2.00e-02 2.50e+03 pdb=" O2' 7MG 2 527 " 0.929 2.00e-02 2.50e+03 pdb=" C1' 7MG 2 527 " 0.199 2.00e-02 2.50e+03 pdb=" N9 7MG 2 527 " -1.152 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 11835 " 0.053 2.00e-02 2.50e+03 5.98e-01 8.04e+03 pdb=" C4' 2MG 11835 " 0.441 2.00e-02 2.50e+03 pdb=" O4' 2MG 11835 " 0.672 2.00e-02 2.50e+03 pdb=" C3' 2MG 11835 " -0.601 2.00e-02 2.50e+03 pdb=" O3' 2MG 11835 " -0.613 2.00e-02 2.50e+03 pdb=" C2' 2MG 11835 " -0.198 2.00e-02 2.50e+03 pdb=" O2' 2MG 11835 " 0.947 2.00e-02 2.50e+03 pdb=" C1' 2MG 11835 " 0.217 2.00e-02 2.50e+03 pdb=" N9 2MG 11835 " -0.920 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MU 1 747 " 0.059 2.00e-02 2.50e+03 5.89e-01 7.79e+03 pdb=" C4' 5MU 1 747 " -0.438 2.00e-02 2.50e+03 pdb=" O4' 5MU 1 747 " -0.809 2.00e-02 2.50e+03 pdb=" C3' 5MU 1 747 " 0.604 2.00e-02 2.50e+03 pdb=" O3' 5MU 1 747 " 0.487 2.00e-02 2.50e+03 pdb=" C2' 5MU 1 747 " 0.246 2.00e-02 2.50e+03 pdb=" O2' 5MU 1 747 " -0.823 2.00e-02 2.50e+03 pdb=" C1' 5MU 1 747 " -0.254 2.00e-02 2.50e+03 pdb=" N1 5MU 1 747 " 0.928 2.00e-02 2.50e+03 ... (remaining 13333 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 3009 2.54 - 3.13: 105786 3.13 - 3.72: 311748 3.72 - 4.31: 387378 4.31 - 4.90: 538105 Nonbonded interactions: 1346026 Sorted by model distance: nonbonded pdb="MG MG 13029 " pdb="MG MG 13250 " model vdw 1.954 1.300 nonbonded pdb=" OP2 C 12499 " pdb="MG MG 13083 " model vdw 1.993 2.170 nonbonded pdb=" O4 U 11263 " pdb="MG MG 13262 " model vdw 1.999 2.170 nonbonded pdb=" OP1 C 12573 " pdb="MG MG 13089 " model vdw 2.000 2.170 nonbonded pdb=" OP2 C 1 198 " pdb="MG MG 13094 " model vdw 2.014 2.170 ... (remaining 1346021 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.150 Extract box with map and model: 17.550 Check model and map are aligned: 1.780 Set scattering table: 1.110 Process input model: 542.610 Find NCS groups from input model: 3.160 Set up NCS constraints: 0.350 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:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 572.000 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 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 : 0.008 0.328 166754 Z= 0.508 Angle : 1.202 29.348 249500 Z= 0.602 Chirality : 0.150 5.491 31820 Planarity : 0.019 0.657 13336 Dihedral : 25.151 179.574 95382 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.01 % Favored : 87.94 % Rotamer: Outliers : 0.48 % Allowed : 11.15 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.86 (0.08), residues: 6021 helix: -3.52 (0.08), residues: 1636 sheet: -2.89 (0.15), residues: 936 loop : -3.28 (0.09), residues: 3449 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP 5 118 HIS 0.018 0.002 HIS J 47 PHE 0.033 0.003 PHE E 100 TYR 0.031 0.003 TYR O 64 ARG 0.015 0.001 ARG M 18 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1645 residues out of total 4987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1621 time to evaluate : 6.800 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 33 LEU cc_start: 0.8323 (mt) cc_final: 0.8043 (tp) REVERT: B 60 GLN cc_start: 0.8292 (mt0) cc_final: 0.8015 (mt0) REVERT: B 67 PHE cc_start: 0.8637 (m-80) cc_final: 0.8351 (m-10) REVERT: B 111 LYS cc_start: 0.8974 (pttm) cc_final: 0.8772 (tttm) REVERT: B 142 HIS cc_start: 0.8725 (p-80) cc_final: 0.8348 (p90) REVERT: B 180 GLU cc_start: 0.8500 (mp0) cc_final: 0.7783 (mp0) REVERT: B 201 MET cc_start: 0.8918 (ptt) cc_final: 0.7321 (tpp) REVERT: B 229 ASP cc_start: 0.7717 (m-30) cc_final: 0.7433 (m-30) REVERT: C 11 MET cc_start: 0.8077 (tpp) cc_final: 0.7758 (mmm) REVERT: C 14 ILE cc_start: 0.9201 (mm) cc_final: 0.8966 (mm) REVERT: C 28 GLU cc_start: 0.7685 (tm-30) cc_final: 0.7212 (tm-30) REVERT: C 149 ASN cc_start: 0.8120 (t0) cc_final: 0.7881 (t0) REVERT: D 1 MET cc_start: 0.4394 (tpt) cc_final: 0.3694 (ttm) REVERT: E 5 HIS cc_start: 0.8022 (t70) cc_final: 0.7676 (t70) REVERT: E 38 MET cc_start: 0.7642 (tpt) cc_final: 0.7329 (tpt) REVERT: E 96 MET cc_start: 0.7971 (ttp) cc_final: 0.7526 (ttt) REVERT: E 165 GLU cc_start: 0.7656 (tt0) cc_final: 0.7270 (tt0) REVERT: F 107 LEU cc_start: 0.8736 (mt) cc_final: 0.7872 (mp) REVERT: G 47 PHE cc_start: 0.7503 (t80) cc_final: 0.7046 (t80) REVERT: H 38 MET cc_start: 0.0210 (mtt) cc_final: -0.0514 (tpp) REVERT: H 52 MET cc_start: 0.3243 (tmm) cc_final: 0.2984 (tpt) REVERT: H 65 GLU cc_start: 0.8614 (tm-30) cc_final: 0.8139 (tm-30) REVERT: H 86 MET cc_start: 0.7502 (mpp) cc_final: 0.7079 (mpp) REVERT: I 116 MET cc_start: 0.3920 (mtp) cc_final: 0.3173 (mtp) REVERT: I 133 ARG cc_start: 0.7902 (ttm170) cc_final: 0.7514 (ttp-170) REVERT: J 43 GLU cc_start: 0.7853 (pm20) cc_final: 0.7450 (pt0) REVERT: J 132 HIS cc_start: 0.8136 (m-70) cc_final: 0.7923 (m-70) REVERT: J 136 GLN cc_start: 0.8926 (mt0) cc_final: 0.8063 (pm20) REVERT: K 21 CYS cc_start: 0.9218 (t) cc_final: 0.8451 (t) REVERT: K 39 ILE cc_start: 0.9006 (pt) cc_final: 0.8710 (pt) REVERT: K 41 ILE cc_start: 0.8929 (pt) cc_final: 0.8196 (pt) REVERT: K 44 LYS cc_start: 0.8577 (mmtt) cc_final: 0.8345 (mmmm) REVERT: K 70 ARG cc_start: 0.8469 (mtp85) cc_final: 0.7937 (tpt-90) REVERT: K 108 ARG cc_start: 0.6759 (ptm160) cc_final: 0.4780 (ppt170) REVERT: L 70 LYS cc_start: 0.8494 (ttmm) cc_final: 0.7986 (ttmm) REVERT: M 10 ARG cc_start: 0.7923 (ttm-80) cc_final: 0.7370 (mtm-85) REVERT: M 17 ASN cc_start: 0.9020 (t0) cc_final: 0.8631 (t0) REVERT: M 22 GLN cc_start: 0.7398 (mm-40) cc_final: 0.7129 (tp40) REVERT: M 103 TYR cc_start: 0.7248 (m-80) cc_final: 0.6825 (m-80) REVERT: M 108 VAL cc_start: 0.8824 (t) cc_final: 0.8574 (t) REVERT: M 136 MET cc_start: 0.7053 (ttm) cc_final: 0.6804 (ttt) REVERT: N 18 GLN cc_start: 0.8465 (tt0) cc_final: 0.8058 (mt0) REVERT: N 62 ASN cc_start: 0.8275 (m110) cc_final: 0.7803 (m-40) REVERT: N 74 GLU cc_start: 0.8142 (tp30) cc_final: 0.7911 (tp30) REVERT: N 110 MET cc_start: 0.7248 (mtp) cc_final: 0.6685 (mtp) REVERT: N 114 GLU cc_start: 0.7590 (tt0) cc_final: 0.7331 (tt0) REVERT: O 9 ARG cc_start: 0.8043 (ttp80) cc_final: 0.7113 (ttp80) REVERT: P 13 MET cc_start: 0.7591 (mtt) cc_final: 0.6928 (mtt) REVERT: Q 37 GLN cc_start: 0.8633 (tt0) cc_final: 0.8245 (tm-30) REVERT: Q 52 GLN cc_start: 0.8364 (mt0) cc_final: 0.8151 (mt0) REVERT: Q 66 ASN cc_start: 0.7927 (t0) cc_final: 0.7512 (t0) REVERT: Q 106 PHE cc_start: 0.9151 (t80) cc_final: 0.8711 (t80) REVERT: S 40 ASN cc_start: 0.8669 (m-40) cc_final: 0.7850 (p0) REVERT: S 97 LEU cc_start: 0.9122 (mt) cc_final: 0.8849 (mp) REVERT: S 99 ARG cc_start: 0.8494 (mtt90) cc_final: 0.8214 (mtm-85) REVERT: S 110 ARG cc_start: 0.7711 (mpt90) cc_final: 0.6936 (ptm160) REVERT: U 22 ARG cc_start: 0.6300 (ptp-110) cc_final: 0.5904 (ppt170) REVERT: V 76 ASP cc_start: 0.7861 (t70) cc_final: 0.7182 (t0) REVERT: W 29 GLU cc_start: 0.7655 (pt0) cc_final: 0.7272 (pt0) REVERT: W 70 GLU cc_start: 0.8108 (pt0) cc_final: 0.7366 (pt0) REVERT: W 75 LYS cc_start: 0.8156 (mtmt) cc_final: 0.7903 (mmmt) REVERT: X 23 ASN cc_start: 0.8905 (t0) cc_final: 0.8679 (t0) REVERT: Y 8 GLU cc_start: 0.8465 (tm-30) cc_final: 0.8200 (tm-30) REVERT: Z 12 SER cc_start: 0.8545 (t) cc_final: 0.8219 (p) REVERT: d 31 LEU cc_start: 0.9016 (mt) cc_final: 0.8770 (mm) REVERT: d 35 ARG cc_start: 0.8341 (mtt90) cc_final: 0.7978 (mtt90) REVERT: f 19 ARG cc_start: 0.8257 (mtt180) cc_final: 0.7877 (mtt180) REVERT: g 49 MET cc_start: 0.7184 (mtp) cc_final: 0.6956 (mtt) REVERT: g 60 ILE cc_start: 0.8339 (mt) cc_final: 0.8024 (mm) REVERT: g 120 GLN cc_start: 0.7672 (tm-30) cc_final: 0.7403 (tm-30) REVERT: g 168 HIS cc_start: 0.8242 (t70) cc_final: 0.7982 (t70) REVERT: g 208 ARG cc_start: 0.7445 (mtm180) cc_final: 0.7160 (mtm180) REVERT: h 18 TRP cc_start: 0.8050 (m-90) cc_final: 0.7790 (m-90) REVERT: h 59 ARG cc_start: 0.6221 (ptp-170) cc_final: 0.5725 (tmm-80) REVERT: h 93 ASP cc_start: 0.6894 (p0) cc_final: 0.6666 (p0) REVERT: h 110 GLU cc_start: 0.5705 (mp0) cc_final: 0.5135 (mp0) REVERT: h 123 GLN cc_start: 0.7370 (mm110) cc_final: 0.6957 (mm-40) REVERT: i 55 LEU cc_start: 0.8285 (tt) cc_final: 0.7960 (tt) REVERT: i 139 PRO cc_start: 0.6224 (Cg_exo) cc_final: 0.5335 (Cg_endo) REVERT: i 186 PRO cc_start: 0.9172 (Cg_endo) cc_final: 0.8704 (Cg_exo) REVERT: j 23 LYS cc_start: 0.8562 (tmmt) cc_final: 0.8163 (ttpp) REVERT: j 61 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8125 (tm-30) REVERT: j 95 PHE cc_start: 0.8443 (t80) cc_final: 0.7777 (t80) REVERT: j 112 ARG cc_start: 0.8441 (ttm-80) cc_final: 0.7768 (mtp85) REVERT: j 156 LYS cc_start: 0.9154 (mmmt) cc_final: 0.8918 (mmmt) REVERT: k 64 VAL cc_start: 0.8687 (p) cc_final: 0.8280 (p) REVERT: k 80 PHE cc_start: 0.8464 (m-10) cc_final: 0.8232 (m-10) REVERT: l 11 LYS cc_start: 0.6850 (mmtt) cc_final: 0.6595 (mmmt) REVERT: l 102 ARG cc_start: 0.8063 (ttm110) cc_final: 0.7639 (mtt-85) REVERT: m 18 GLN cc_start: 0.9331 (mm-40) cc_final: 0.9039 (mm-40) REVERT: m 48 ASP cc_start: 0.8207 (t0) cc_final: 0.7994 (t0) REVERT: m 52 GLU cc_start: 0.8435 (pp20) cc_final: 0.8136 (pp20) REVERT: m 59 LEU cc_start: 0.8063 (tp) cc_final: 0.7678 (tp) REVERT: m 73 GLU cc_start: 0.6923 (tt0) cc_final: 0.6483 (mp0) REVERT: m 77 ARG cc_start: 0.8456 (tpt-90) cc_final: 0.8056 (ttt-90) REVERT: m 95 VAL cc_start: 0.9266 (t) cc_final: 0.8726 (t) REVERT: m 124 GLU cc_start: 0.7749 (tt0) cc_final: 0.7184 (mt-10) REVERT: n 22 LYS cc_start: 0.6825 (ttmm) cc_final: 0.6476 (pttm) REVERT: n 35 LEU cc_start: 0.8915 (tp) cc_final: 0.8650 (tp) REVERT: o 64 GLN cc_start: 0.6747 (tp40) cc_final: 0.6258 (mm-40) REVERT: p 100 LEU cc_start: 0.9295 (tp) cc_final: 0.8927 (tt) REVERT: p 116 ILE cc_start: 0.9043 (mm) cc_final: 0.8780 (mm) REVERT: q 81 LEU cc_start: 0.8991 (tp) cc_final: 0.8597 (tp) REVERT: q 83 ARG cc_start: 0.7537 (OUTLIER) cc_final: 0.6377 (ttp-110) REVERT: r 44 LYS cc_start: 0.6078 (mtmt) cc_final: 0.5843 (mptt) REVERT: r 66 GLU cc_start: 0.7407 (tp30) cc_final: 0.7196 (tp30) REVERT: r 75 MET cc_start: 0.6684 (ptp) cc_final: 0.5730 (mmt) REVERT: r 81 MET cc_start: 0.7510 (mmm) cc_final: 0.6764 (mmm) REVERT: r 101 ARG cc_start: 0.6681 (mtp180) cc_final: 0.6102 (mpt180) REVERT: s 6 MET cc_start: 0.7982 (mmm) cc_final: 0.7646 (mmm) REVERT: s 76 LYS cc_start: 0.8917 (tttp) cc_final: 0.8347 (mptt) REVERT: s 83 LYS cc_start: 0.8063 (ptpp) cc_final: 0.6876 (ptpp) REVERT: t 37 ASN cc_start: 0.8278 (m-40) cc_final: 0.8072 (m110) REVERT: t 59 MET cc_start: 0.8401 (mtt) cc_final: 0.8183 (mtm) REVERT: t 64 ARG cc_start: 0.8210 (tpm170) cc_final: 0.7737 (tpp80) REVERT: t 65 LYS cc_start: 0.7812 (tppt) cc_final: 0.7296 (tppt) REVERT: u 54 LEU cc_start: 0.8227 (mt) cc_final: 0.7791 (tt) REVERT: u 71 VAL cc_start: 0.8736 (t) cc_final: 0.8433 (t) REVERT: v 17 MET cc_start: 0.7228 (ptt) cc_final: 0.6942 (ptt) REVERT: v 19 LYS cc_start: 0.9129 (mtpp) cc_final: 0.8914 (tttm) REVERT: v 25 ILE cc_start: 0.7853 (mp) cc_final: 0.7584 (mt) REVERT: v 27 ARG cc_start: 0.6910 (tpt170) cc_final: 0.6215 (mmt180) REVERT: v 43 LYS cc_start: 0.8410 (mmmt) cc_final: 0.8166 (mtpt) REVERT: w 12 ARG cc_start: 0.5903 (mmt-90) cc_final: 0.5695 (mmt-90) REVERT: w 19 GLN cc_start: 0.7065 (pt0) cc_final: 0.6712 (mt0) REVERT: w 23 TYR cc_start: 0.8080 (p90) cc_final: 0.7835 (p90) REVERT: w 50 LYS cc_start: 0.8448 (tttt) cc_final: 0.8159 (ttpt) REVERT: w 68 LEU cc_start: 0.8314 (mt) cc_final: 0.8104 (mp) REVERT: x 10 PHE cc_start: 0.5981 (t80) cc_final: 0.5355 (t80) REVERT: x 40 ILE cc_start: 0.7055 (mp) cc_final: 0.6849 (mm) REVERT: z 5 LYS cc_start: 0.7551 (pttm) cc_final: 0.6665 (pttp) REVERT: z 39 GLU cc_start: 0.7684 (tp30) cc_final: 0.6730 (tm-30) REVERT: z 40 LYS cc_start: 0.6309 (tttp) cc_final: 0.6098 (mtpp) REVERT: z 42 THR cc_start: 0.8823 (t) cc_final: 0.8505 (m) REVERT: z 63 GLU cc_start: 0.6626 (pm20) cc_final: 0.6339 (tm-30) outliers start: 24 outliers final: 8 residues processed: 1638 average time/residue: 1.5511 time to fit residues: 4337.0884 Evaluate side-chains 1208 residues out of total 4987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 1199 time to evaluate : 6.890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 911 optimal weight: 20.0000 chunk 818 optimal weight: 4.9990 chunk 454 optimal weight: 10.0000 chunk 279 optimal weight: 20.0000 chunk 552 optimal weight: 7.9990 chunk 437 optimal weight: 10.0000 chunk 846 optimal weight: 8.9990 chunk 327 optimal weight: 10.0000 chunk 514 optimal weight: 2.9990 chunk 630 optimal weight: 2.9990 chunk 980 optimal weight: 8.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 93 ASN 5 105 ASN 5 120 ASN 5 148 GLN ** B 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN ** C 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 GLN D 29 HIS D 115 GLN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 63 GLN ** F 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 GLN G 11 ASN I 30 GLN J 86 GLN K 82 ASN K 93 GLN L 35 HIS L 104 GLN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 GLN N 81 ASN O 38 GLN O 61 GLN P 12 GLN P 15 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 66 ASN R 12 HIS ** R 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN S 40 ASN S 60 HIS S 61 ASN ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 59 ASN T 91 GLN U 45 HIS U 69 ASN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 76 ASN ** a 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 19 HIS ** d 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 29 GLN e 26 HIS e 43 HIS g 19 GLN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 42 ASN g 109 GLN ** h 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 69 HIS ** h 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 185 ASN i 54 GLN ** i 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 71 GLN ** i 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 131 ASN ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 82 GLN k 46 GLN k 63 ASN l 68 ASN m 16 ASN n 31 ASN o 15 HIS ** r 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 71 HIS u 18 GLN ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** w 54 GLN ** x 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 83 HIS y 3 ASN y 55 GLN y 68 HIS Total number of N/Q/H flips: 61 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.174 166754 Z= 0.318 Angle : 0.837 17.880 249500 Z= 0.431 Chirality : 0.043 0.402 31820 Planarity : 0.007 0.175 13336 Dihedral : 25.429 179.259 83395 Min Nonbonded Distance : 1.762 Molprobity Statistics. All-atom Clashscore : 21.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.54 % Favored : 88.44 % Rotamer: Outliers : 0.20 % Allowed : 8.10 % Favored : 91.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.13 (0.09), residues: 6021 helix: -2.50 (0.10), residues: 1685 sheet: -2.64 (0.16), residues: 917 loop : -2.98 (0.09), residues: 3419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP 5 118 HIS 0.010 0.002 HIS J 77 PHE 0.022 0.002 PHE I 41 TYR 0.024 0.002 TYR g 213 ARG 0.009 0.001 ARG Q 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1451 residues out of total 4987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1441 time to evaluate : 6.878 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 65 LEU cc_start: 0.8849 (mt) cc_final: 0.8428 (mp) REVERT: 5 142 ILE cc_start: 0.9036 (OUTLIER) cc_final: 0.8691 (mm) REVERT: B 33 LEU cc_start: 0.8370 (mt) cc_final: 0.8117 (tp) REVERT: B 34 LEU cc_start: 0.8162 (mt) cc_final: 0.7961 (mt) REVERT: B 60 GLN cc_start: 0.8403 (mt0) cc_final: 0.8094 (mt0) REVERT: B 100 GLU cc_start: 0.7482 (mt-10) cc_final: 0.7189 (mt-10) REVERT: B 124 ILE cc_start: 0.7192 (mt) cc_final: 0.6978 (mt) REVERT: B 180 GLU cc_start: 0.8558 (mp0) cc_final: 0.7989 (mp0) REVERT: B 201 MET cc_start: 0.8781 (ptt) cc_final: 0.7162 (tpp) REVERT: B 229 ASP cc_start: 0.7536 (m-30) cc_final: 0.7312 (m-30) REVERT: C 21 SER cc_start: 0.9340 (t) cc_final: 0.8796 (p) REVERT: C 149 ASN cc_start: 0.8230 (t0) cc_final: 0.7906 (t0) REVERT: E 5 HIS cc_start: 0.8003 (t70) cc_final: 0.7553 (t70) REVERT: E 33 LYS cc_start: 0.8344 (pttm) cc_final: 0.7963 (pttm) REVERT: E 38 MET cc_start: 0.7790 (tpt) cc_final: 0.7356 (tpt) REVERT: E 90 THR cc_start: 0.8241 (p) cc_final: 0.7113 (p) REVERT: E 96 MET cc_start: 0.8018 (ttp) cc_final: 0.7631 (ttt) REVERT: F 139 GLN cc_start: 0.8017 (OUTLIER) cc_final: 0.7421 (tm-30) REVERT: G 11 ASN cc_start: 0.4500 (OUTLIER) cc_final: 0.4272 (t0) REVERT: G 47 PHE cc_start: 0.7612 (t80) cc_final: 0.7245 (t80) REVERT: H 38 MET cc_start: 0.0821 (mtt) cc_final: -0.0186 (tpp) REVERT: H 52 MET cc_start: 0.4010 (tmm) cc_final: 0.2987 (tmm) REVERT: I 116 MET cc_start: 0.4184 (mtp) cc_final: 0.3907 (mtp) REVERT: I 133 ARG cc_start: 0.7769 (ttm170) cc_final: 0.7515 (ttp-170) REVERT: J 43 GLU cc_start: 0.8001 (pm20) cc_final: 0.7605 (pt0) REVERT: J 136 GLN cc_start: 0.8996 (mt0) cc_final: 0.8246 (pm20) REVERT: K 82 ASN cc_start: 0.8674 (m-40) cc_final: 0.8432 (p0) REVERT: K 108 ARG cc_start: 0.6832 (ptm160) cc_final: 0.5108 (ppt170) REVERT: M 10 ARG cc_start: 0.7981 (ttm-80) cc_final: 0.7540 (mtm-85) REVERT: M 17 ASN cc_start: 0.9125 (t0) cc_final: 0.8717 (t0) REVERT: M 103 TYR cc_start: 0.7236 (m-80) cc_final: 0.6697 (m-80) REVERT: M 115 GLU cc_start: 0.8584 (mp0) cc_final: 0.8298 (mt-10) REVERT: N 4 ARG cc_start: 0.7926 (mmm160) cc_final: 0.7642 (tpt90) REVERT: N 46 ARG cc_start: 0.8520 (mtp180) cc_final: 0.8300 (ttm170) REVERT: O 9 ARG cc_start: 0.8179 (ttp80) cc_final: 0.7069 (ttp80) REVERT: O 17 LYS cc_start: 0.7924 (tptt) cc_final: 0.7558 (tttt) REVERT: O 64 TYR cc_start: 0.7295 (t80) cc_final: 0.7074 (t80) REVERT: P 34 GLU cc_start: 0.6562 (pt0) cc_final: 0.5852 (pt0) REVERT: Q 37 GLN cc_start: 0.8309 (tt0) cc_final: 0.7810 (tt0) REVERT: Q 66 ASN cc_start: 0.8186 (t0) cc_final: 0.7694 (t0) REVERT: Q 106 PHE cc_start: 0.9216 (t80) cc_final: 0.8979 (t80) REVERT: S 94 ASP cc_start: 0.7771 (t0) cc_final: 0.7377 (t0) REVERT: S 110 ARG cc_start: 0.7746 (mpt90) cc_final: 0.6938 (ptm160) REVERT: T 40 LYS cc_start: 0.7197 (ptmt) cc_final: 0.6756 (ptpt) REVERT: U 6 ARG cc_start: 0.8720 (mmt180) cc_final: 0.8489 (tpp-160) REVERT: U 22 ARG cc_start: 0.6209 (ptp-110) cc_final: 0.5705 (ppt170) REVERT: V 51 GLN cc_start: 0.7818 (pp30) cc_final: 0.7453 (tm-30) REVERT: W 37 ILE cc_start: 0.9419 (mp) cc_final: 0.9186 (mp) REVERT: W 70 GLU cc_start: 0.7999 (pt0) cc_final: 0.7137 (pt0) REVERT: W 72 LYS cc_start: 0.8897 (mtpt) cc_final: 0.8572 (mtmt) REVERT: c 32 GLU cc_start: 0.5527 (tp30) cc_final: 0.5242 (tp30) REVERT: d 31 LEU cc_start: 0.9019 (mt) cc_final: 0.8731 (mm) REVERT: e 22 PHE cc_start: 0.8442 (m-80) cc_final: 0.8237 (m-80) REVERT: f 19 ARG cc_start: 0.8053 (mtt180) cc_final: 0.7127 (mtt180) REVERT: g 49 MET cc_start: 0.7448 (mtp) cc_final: 0.7175 (mtt) REVERT: g 120 GLN cc_start: 0.7725 (tm-30) cc_final: 0.7433 (tm-30) REVERT: g 168 HIS cc_start: 0.8268 (t70) cc_final: 0.7945 (t70) REVERT: g 208 ARG cc_start: 0.7302 (mtm180) cc_final: 0.6950 (mtm110) REVERT: h 23 PHE cc_start: 0.7667 (t80) cc_final: 0.7410 (t80) REVERT: h 59 ARG cc_start: 0.6182 (ptp-170) cc_final: 0.5411 (tmm-80) REVERT: h 91 VAL cc_start: 0.7561 (m) cc_final: 0.7319 (m) REVERT: j 23 LYS cc_start: 0.8507 (tmmt) cc_final: 0.8106 (ttpp) REVERT: j 29 ARG cc_start: 0.8321 (mtm-85) cc_final: 0.8007 (mtm-85) REVERT: j 61 GLN cc_start: 0.8286 (tm-30) cc_final: 0.8024 (tm-30) REVERT: j 95 PHE cc_start: 0.8491 (t80) cc_final: 0.7833 (t80) REVERT: j 112 ARG cc_start: 0.8483 (ttm-80) cc_final: 0.7648 (mtp85) REVERT: l 11 LYS cc_start: 0.7048 (mmtt) cc_final: 0.6812 (mmmt) REVERT: l 52 GLN cc_start: 0.8563 (tp40) cc_final: 0.8346 (tp-100) REVERT: l 102 ARG cc_start: 0.7958 (ttm110) cc_final: 0.7629 (mtp85) REVERT: m 83 LEU cc_start: 0.8379 (tp) cc_final: 0.8138 (tp) REVERT: m 124 GLU cc_start: 0.7670 (tt0) cc_final: 0.7420 (mt-10) REVERT: n 22 LYS cc_start: 0.6801 (ttmm) cc_final: 0.6383 (pttm) REVERT: n 57 MET cc_start: 0.3578 (mtp) cc_final: 0.2936 (ttm) REVERT: n 114 LYS cc_start: 0.5478 (tttm) cc_final: 0.4959 (ttpt) REVERT: n 122 ARG cc_start: 0.4349 (mtp180) cc_final: 0.3905 (mtm180) REVERT: o 64 GLN cc_start: 0.6866 (tp40) cc_final: 0.6298 (mm-40) REVERT: o 71 LEU cc_start: 0.8855 (mm) cc_final: 0.8526 (mm) REVERT: p 68 GLU cc_start: 0.7853 (mp0) cc_final: 0.7539 (mp0) REVERT: p 116 ILE cc_start: 0.9037 (mm) cc_final: 0.8747 (mm) REVERT: q 34 CYS cc_start: 0.7477 (m) cc_final: 0.6632 (m) REVERT: q 39 THR cc_start: 0.8961 (m) cc_final: 0.8472 (p) REVERT: q 49 LEU cc_start: 0.8984 (mp) cc_final: 0.8646 (mp) REVERT: q 53 CYS cc_start: 0.8047 (t) cc_final: 0.7272 (t) REVERT: r 69 LEU cc_start: 0.7619 (tp) cc_final: 0.6861 (tt) REVERT: r 81 MET cc_start: 0.7388 (mmm) cc_final: 0.6978 (mmt) REVERT: r 101 ARG cc_start: 0.6769 (mtp180) cc_final: 0.6309 (mpt180) REVERT: s 76 LYS cc_start: 0.8857 (tttp) cc_final: 0.8254 (mptt) REVERT: s 83 LYS cc_start: 0.8198 (ptpp) cc_final: 0.7228 (ptpp) REVERT: s 96 LEU cc_start: 0.8064 (mt) cc_final: 0.7556 (mt) REVERT: t 37 ASN cc_start: 0.8593 (m-40) cc_final: 0.8234 (m110) REVERT: t 45 GLU cc_start: 0.6776 (tp30) cc_final: 0.6547 (tp30) REVERT: t 65 LYS cc_start: 0.7826 (tppt) cc_final: 0.7190 (tppt) REVERT: u 39 PHE cc_start: 0.8353 (t80) cc_final: 0.8012 (t80) REVERT: u 54 LEU cc_start: 0.8124 (mt) cc_final: 0.7852 (tt) REVERT: u 69 ASP cc_start: 0.8243 (m-30) cc_final: 0.7591 (t70) REVERT: u 71 VAL cc_start: 0.8761 (t) cc_final: 0.8510 (t) REVERT: v 27 ARG cc_start: 0.6962 (tpt170) cc_final: 0.6162 (mmt180) REVERT: w 50 LYS cc_start: 0.8485 (tttt) cc_final: 0.8177 (ttpt) REVERT: w 68 LEU cc_start: 0.8029 (mt) cc_final: 0.7814 (mp) REVERT: z 5 LYS cc_start: 0.7763 (pttm) cc_final: 0.6998 (pttp) REVERT: z 39 GLU cc_start: 0.7851 (tp30) cc_final: 0.7349 (tm-30) REVERT: z 63 GLU cc_start: 0.6491 (pm20) cc_final: 0.6042 (tm-30) outliers start: 10 outliers final: 2 residues processed: 1444 average time/residue: 1.3708 time to fit residues: 3402.5386 Evaluate side-chains 1158 residues out of total 4987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 1153 time to evaluate : 6.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 545 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 chunk 816 optimal weight: 0.0370 chunk 667 optimal weight: 6.9990 chunk 270 optimal weight: 10.0000 chunk 982 optimal weight: 0.7980 chunk 1061 optimal weight: 40.0000 chunk 875 optimal weight: 7.9990 chunk 974 optimal weight: 7.9990 chunk 334 optimal weight: 20.0000 chunk 788 optimal weight: 2.9990 overall best weight: 3.7664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 70 ASN C 49 GLN D 9 GLN D 41 GLN ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN F 139 GLN ** G 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 GLN N 81 ASN O 38 GLN P 15 GLN P 56 HIS S 15 GLN ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN ** a 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 61 ASN a 65 ASN b 19 HIS d 6 GLN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 41 GLN h 69 HIS ** h 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 54 GLN ** i 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 152 GLN ** k 11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** m 16 ASN ** r 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** t 40 GLN ** u 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 55 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7798 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.106 166754 Z= 0.232 Angle : 0.726 14.182 249500 Z= 0.380 Chirality : 0.038 0.383 31820 Planarity : 0.006 0.130 13336 Dihedral : 25.179 179.418 83395 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 18.70 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.13 % Favored : 89.85 % Rotamer: Outliers : 0.08 % Allowed : 6.06 % Favored : 93.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.10), residues: 6021 helix: -1.87 (0.11), residues: 1705 sheet: -2.41 (0.16), residues: 913 loop : -2.83 (0.10), residues: 3403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP P 31 HIS 0.011 0.001 HIS r 14 PHE 0.017 0.002 PHE h 23 TYR 0.027 0.002 TYR J 75 ARG 0.023 0.001 ARG l 119 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1473 residues out of total 4987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1469 time to evaluate : 6.849 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 65 LEU cc_start: 0.8882 (mt) cc_final: 0.8588 (mp) REVERT: 5 142 ILE cc_start: 0.8968 (mp) cc_final: 0.8574 (mm) REVERT: B 33 LEU cc_start: 0.8026 (mt) cc_final: 0.7823 (tp) REVERT: B 60 GLN cc_start: 0.8379 (mt0) cc_final: 0.8122 (mt0) REVERT: B 124 ILE cc_start: 0.7252 (mt) cc_final: 0.6996 (mt) REVERT: B 180 GLU cc_start: 0.8630 (mp0) cc_final: 0.7955 (mp0) REVERT: B 201 MET cc_start: 0.8895 (ptt) cc_final: 0.7259 (tpp) REVERT: C 21 SER cc_start: 0.9302 (t) cc_final: 0.8975 (p) REVERT: C 80 TRP cc_start: 0.8493 (m-90) cc_final: 0.8093 (m-90) REVERT: C 149 ASN cc_start: 0.8151 (t0) cc_final: 0.7796 (t0) REVERT: D 88 ARG cc_start: 0.7889 (mmp80) cc_final: 0.7548 (mmt180) REVERT: E 5 HIS cc_start: 0.7864 (t70) cc_final: 0.7459 (t70) REVERT: E 19 GLU cc_start: 0.8712 (tm-30) cc_final: 0.8200 (tm-30) REVERT: E 33 LYS cc_start: 0.8264 (pttm) cc_final: 0.7834 (pttm) REVERT: E 38 MET cc_start: 0.7703 (tpt) cc_final: 0.7288 (tpt) REVERT: E 90 THR cc_start: 0.8103 (p) cc_final: 0.7140 (p) REVERT: E 96 MET cc_start: 0.8058 (ttp) cc_final: 0.7568 (ttt) REVERT: E 165 GLU cc_start: 0.7301 (tt0) cc_final: 0.6829 (tt0) REVERT: F 71 LEU cc_start: 0.9254 (mt) cc_final: 0.8911 (mt) REVERT: F 107 LEU cc_start: 0.8755 (tp) cc_final: 0.8301 (mm) REVERT: G 46 PHE cc_start: 0.8037 (t80) cc_final: 0.7750 (t80) REVERT: G 47 PHE cc_start: 0.7697 (t80) cc_final: 0.7289 (t80) REVERT: H 38 MET cc_start: 0.0719 (mtt) cc_final: -0.0041 (tpp) REVERT: H 52 MET cc_start: 0.4197 (tmm) cc_final: 0.3139 (tmm) REVERT: I 116 MET cc_start: 0.4303 (mtp) cc_final: 0.4028 (mtp) REVERT: I 133 ARG cc_start: 0.7789 (ttm170) cc_final: 0.7458 (ttp-170) REVERT: J 43 GLU cc_start: 0.7861 (pm20) cc_final: 0.7492 (pt0) REVERT: J 136 GLN cc_start: 0.8968 (mt0) cc_final: 0.8129 (pm20) REVERT: K 82 ASN cc_start: 0.8667 (m-40) cc_final: 0.8334 (p0) REVERT: K 108 ARG cc_start: 0.7134 (ptm160) cc_final: 0.5091 (ppt170) REVERT: L 23 ILE cc_start: 0.9318 (tt) cc_final: 0.9079 (tt) REVERT: L 29 LYS cc_start: 0.8241 (pttt) cc_final: 0.7911 (pttt) REVERT: L 57 LEU cc_start: 0.8588 (tp) cc_final: 0.8043 (tt) REVERT: L 70 LYS cc_start: 0.8447 (ttmm) cc_final: 0.8155 (ttpt) REVERT: M 10 ARG cc_start: 0.7956 (ttm-80) cc_final: 0.7381 (mtm-85) REVERT: M 17 ASN cc_start: 0.9172 (t0) cc_final: 0.8778 (t0) REVERT: M 103 TYR cc_start: 0.7222 (m-80) cc_final: 0.6583 (m-80) REVERT: N 71 ARG cc_start: 0.8671 (mmm-85) cc_final: 0.8142 (tpp80) REVERT: O 9 ARG cc_start: 0.8260 (ttp80) cc_final: 0.7239 (ttp80) REVERT: O 17 LYS cc_start: 0.7740 (tptt) cc_final: 0.7409 (tttt) REVERT: O 67 ASN cc_start: 0.8041 (p0) cc_final: 0.7312 (p0) REVERT: P 34 GLU cc_start: 0.5990 (pt0) cc_final: 0.5362 (pt0) REVERT: Q 37 GLN cc_start: 0.8323 (tt0) cc_final: 0.7735 (tt0) REVERT: Q 66 ASN cc_start: 0.8101 (t0) cc_final: 0.7554 (t0) REVERT: S 15 GLN cc_start: 0.7760 (mt0) cc_final: 0.7461 (mt0) REVERT: S 52 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7854 (mm-30) REVERT: S 94 ASP cc_start: 0.7605 (t0) cc_final: 0.7165 (t0) REVERT: S 110 ARG cc_start: 0.7597 (mpt90) cc_final: 0.6807 (ptm160) REVERT: U 6 ARG cc_start: 0.8744 (mmt180) cc_final: 0.8414 (tpp-160) REVERT: U 22 ARG cc_start: 0.5869 (ptp-110) cc_final: 0.5588 (ppt170) REVERT: V 51 GLN cc_start: 0.7454 (pp30) cc_final: 0.7220 (tm-30) REVERT: W 37 ILE cc_start: 0.9332 (mp) cc_final: 0.9121 (mp) REVERT: W 56 ASP cc_start: 0.7909 (p0) cc_final: 0.7615 (p0) REVERT: W 70 GLU cc_start: 0.7903 (pt0) cc_final: 0.7133 (pt0) REVERT: W 72 LYS cc_start: 0.8798 (mtpt) cc_final: 0.8521 (mtmt) REVERT: X 30 LEU cc_start: 0.9592 (mm) cc_final: 0.9379 (mt) REVERT: d 31 LEU cc_start: 0.9027 (mt) cc_final: 0.8744 (mm) REVERT: e 22 PHE cc_start: 0.8548 (m-80) cc_final: 0.8296 (m-80) REVERT: f 19 ARG cc_start: 0.8169 (mtt180) cc_final: 0.7773 (mtt180) REVERT: g 9 MET cc_start: 0.5415 (tpp) cc_final: 0.4955 (tpp) REVERT: g 49 MET cc_start: 0.7439 (mtp) cc_final: 0.7195 (mtt) REVERT: g 120 GLN cc_start: 0.7796 (tm-30) cc_final: 0.7495 (tm-30) REVERT: g 168 HIS cc_start: 0.8256 (t70) cc_final: 0.7890 (t70) REVERT: j 23 LYS cc_start: 0.8478 (tmmt) cc_final: 0.8248 (ptmm) REVERT: j 61 GLN cc_start: 0.8163 (tm-30) cc_final: 0.7834 (tm-30) REVERT: j 95 PHE cc_start: 0.8458 (t80) cc_final: 0.7766 (t80) REVERT: j 112 ARG cc_start: 0.8427 (ttm-80) cc_final: 0.8137 (mtp85) REVERT: j 156 LYS cc_start: 0.9021 (tptt) cc_final: 0.8815 (mmmt) REVERT: k 13 ASP cc_start: 0.7661 (m-30) cc_final: 0.7287 (m-30) REVERT: l 11 LYS cc_start: 0.6924 (mmtt) cc_final: 0.6656 (mmmt) REVERT: l 102 ARG cc_start: 0.7927 (ttm110) cc_final: 0.7620 (mtt-85) REVERT: m 67 GLN cc_start: 0.7145 (tt0) cc_final: 0.6928 (tt0) REVERT: n 22 LYS cc_start: 0.6570 (ttmm) cc_final: 0.6279 (pttm) REVERT: o 64 GLN cc_start: 0.6687 (tp40) cc_final: 0.6116 (mm-40) REVERT: p 116 ILE cc_start: 0.9042 (mm) cc_final: 0.8738 (mm) REVERT: q 34 CYS cc_start: 0.7484 (m) cc_final: 0.6822 (m) REVERT: q 49 LEU cc_start: 0.8608 (mp) cc_final: 0.8387 (mp) REVERT: q 53 CYS cc_start: 0.7929 (t) cc_final: 0.7177 (t) REVERT: q 115 SER cc_start: 0.9266 (t) cc_final: 0.8634 (m) REVERT: r 69 LEU cc_start: 0.7812 (tp) cc_final: 0.7580 (tt) REVERT: r 75 MET cc_start: 0.6424 (ptp) cc_final: 0.5788 (mmt) REVERT: r 81 MET cc_start: 0.7358 (mmm) cc_final: 0.6895 (mmm) REVERT: r 101 ARG cc_start: 0.6608 (mtp180) cc_final: 0.6164 (mpt180) REVERT: r 109 ARG cc_start: 0.7464 (tpt-90) cc_final: 0.6408 (ttt-90) REVERT: s 6 MET cc_start: 0.8077 (mmm) cc_final: 0.7699 (mmt) REVERT: s 76 LYS cc_start: 0.8952 (tttp) cc_final: 0.8339 (mptt) REVERT: s 83 LYS cc_start: 0.8190 (ptpp) cc_final: 0.7119 (ptpp) REVERT: t 37 ASN cc_start: 0.8564 (m-40) cc_final: 0.8259 (m110) REVERT: t 59 MET cc_start: 0.8372 (mtm) cc_final: 0.8075 (mtm) REVERT: t 64 ARG cc_start: 0.7989 (tpp80) cc_final: 0.7618 (tpp80) REVERT: t 65 LYS cc_start: 0.7683 (tppt) cc_final: 0.7186 (tppt) REVERT: u 39 PHE cc_start: 0.8232 (t80) cc_final: 0.7933 (t80) REVERT: u 69 ASP cc_start: 0.8103 (m-30) cc_final: 0.7496 (t70) REVERT: u 71 VAL cc_start: 0.8619 (t) cc_final: 0.8399 (t) REVERT: v 43 LYS cc_start: 0.7748 (mtpp) cc_final: 0.7313 (mtpp) REVERT: v 80 GLU cc_start: 0.7611 (tm-30) cc_final: 0.7030 (tm-30) REVERT: w 50 LYS cc_start: 0.8525 (tttt) cc_final: 0.8207 (ttpt) REVERT: x 71 LEU cc_start: 0.6169 (mt) cc_final: 0.5925 (mt) REVERT: y 76 LYS cc_start: 0.7532 (mttt) cc_final: 0.7173 (mptt) REVERT: z 5 LYS cc_start: 0.7732 (pttm) cc_final: 0.6891 (pttp) REVERT: z 63 GLU cc_start: 0.6420 (pm20) cc_final: 0.6022 (tm-30) outliers start: 4 outliers final: 1 residues processed: 1472 average time/residue: 1.3615 time to fit residues: 3441.5253 Evaluate side-chains 1159 residues out of total 4987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1158 time to evaluate : 6.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 970 optimal weight: 6.9990 chunk 738 optimal weight: 20.0000 chunk 509 optimal weight: 7.9990 chunk 108 optimal weight: 30.0000 chunk 468 optimal weight: 0.9980 chunk 659 optimal weight: 0.6980 chunk 986 optimal weight: 7.9990 chunk 1043 optimal weight: 10.0000 chunk 515 optimal weight: 9.9990 chunk 934 optimal weight: 6.9990 chunk 281 optimal weight: 10.0000 overall best weight: 4.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 GLN D 115 GLN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 GLN ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 9 GLN N 81 ASN O 38 GLN P 56 HIS ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 40 ASN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 5 ASN ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN ** a 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 61 ASN ** b 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 6 GLN ** g 19 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 58 ASN g 168 HIS h 69 HIS ** h 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 54 GLN ** i 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 152 GLN ** k 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 16 ASN ** r 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 62 ASN ** s 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 54 GLN ** x 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 20 HIS y 68 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.134 166754 Z= 0.277 Angle : 0.755 13.816 249500 Z= 0.392 Chirality : 0.039 0.385 31820 Planarity : 0.006 0.128 13336 Dihedral : 25.161 179.933 83395 Min Nonbonded Distance : 1.748 Molprobity Statistics. All-atom Clashscore : 21.28 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.76 % Favored : 88.22 % Rotamer: Outliers : 0.04 % Allowed : 5.01 % Favored : 94.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.10), residues: 6021 helix: -1.60 (0.12), residues: 1715 sheet: -2.27 (0.16), residues: 904 loop : -2.75 (0.10), residues: 3402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP p 44 HIS 0.011 0.002 HIS r 91 PHE 0.031 0.002 PHE d 18 TYR 0.035 0.002 TYR J 75 ARG 0.011 0.001 ARG m 88 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1424 residues out of total 4987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1422 time to evaluate : 6.927 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 65 LEU cc_start: 0.8897 (mt) cc_final: 0.8602 (mp) REVERT: 5 151 LYS cc_start: 0.7409 (mmpt) cc_final: 0.6960 (tppt) REVERT: B 60 GLN cc_start: 0.8428 (mt0) cc_final: 0.8115 (mt0) REVERT: B 145 GLU cc_start: 0.8355 (mt-10) cc_final: 0.7928 (mt-10) REVERT: B 180 GLU cc_start: 0.8629 (mp0) cc_final: 0.7949 (mp0) REVERT: B 201 MET cc_start: 0.8938 (ptt) cc_final: 0.7272 (tpp) REVERT: C 21 SER cc_start: 0.9243 (t) cc_final: 0.8918 (p) REVERT: C 38 LYS cc_start: 0.8275 (mttp) cc_final: 0.7405 (mttt) REVERT: C 49 GLN cc_start: 0.8668 (pt0) cc_final: 0.8384 (pt0) REVERT: C 149 ASN cc_start: 0.8391 (t0) cc_final: 0.8091 (t0) REVERT: D 1 MET cc_start: 0.4360 (tpt) cc_final: 0.3372 (ttm) REVERT: D 72 SER cc_start: 0.9252 (t) cc_final: 0.8679 (m) REVERT: D 88 ARG cc_start: 0.7853 (mmp80) cc_final: 0.7530 (mmt180) REVERT: D 97 ASN cc_start: 0.8143 (m-40) cc_final: 0.7540 (m-40) REVERT: D 141 MET cc_start: 0.5552 (mtt) cc_final: 0.5347 (mtt) REVERT: E 5 HIS cc_start: 0.7981 (t70) cc_final: 0.7567 (t70) REVERT: E 19 GLU cc_start: 0.9011 (tm-30) cc_final: 0.8240 (tm-30) REVERT: E 26 MET cc_start: 0.8554 (mtp) cc_final: 0.8308 (mtp) REVERT: E 33 LYS cc_start: 0.8293 (pttm) cc_final: 0.7766 (pttm) REVERT: E 38 MET cc_start: 0.7620 (tpt) cc_final: 0.7206 (tpt) REVERT: E 96 MET cc_start: 0.8131 (ttp) cc_final: 0.7805 (tpp) REVERT: E 165 GLU cc_start: 0.7326 (tt0) cc_final: 0.6929 (tt0) REVERT: G 46 PHE cc_start: 0.8107 (t80) cc_final: 0.7816 (t80) REVERT: H 38 MET cc_start: -0.0030 (mtt) cc_final: -0.0479 (tpp) REVERT: H 52 MET cc_start: 0.3960 (tmm) cc_final: 0.2864 (tmm) REVERT: H 65 GLU cc_start: 0.8221 (tm-30) cc_final: 0.7724 (tm-30) REVERT: I 116 MET cc_start: 0.4131 (mtp) cc_final: 0.3357 (mtp) REVERT: I 133 ARG cc_start: 0.7766 (ttm170) cc_final: 0.7460 (ttp-170) REVERT: J 136 GLN cc_start: 0.8995 (mt0) cc_final: 0.8220 (pm20) REVERT: K 82 ASN cc_start: 0.8731 (m-40) cc_final: 0.8463 (p0) REVERT: K 108 ARG cc_start: 0.7084 (ptm160) cc_final: 0.4525 (ppt170) REVERT: L 7 SER cc_start: 0.9284 (t) cc_final: 0.8975 (p) REVERT: L 29 LYS cc_start: 0.8268 (pttt) cc_final: 0.7899 (pttt) REVERT: L 50 PHE cc_start: 0.8669 (t80) cc_final: 0.8331 (t80) REVERT: M 10 ARG cc_start: 0.7975 (ttm-80) cc_final: 0.7364 (mtm-85) REVERT: M 17 ASN cc_start: 0.9193 (t0) cc_final: 0.8776 (t0) REVERT: M 47 GLU cc_start: 0.7718 (tp30) cc_final: 0.7500 (tp30) REVERT: M 103 TYR cc_start: 0.7345 (m-80) cc_final: 0.6392 (m-80) REVERT: N 71 ARG cc_start: 0.8662 (mmm-85) cc_final: 0.8137 (tpp80) REVERT: N 114 GLU cc_start: 0.7168 (tt0) cc_final: 0.6904 (tt0) REVERT: O 9 ARG cc_start: 0.8252 (ttp80) cc_final: 0.7072 (ttp80) REVERT: O 17 LYS cc_start: 0.7767 (tptt) cc_final: 0.7505 (tttt) REVERT: O 67 ASN cc_start: 0.8452 (p0) cc_final: 0.6836 (p0) REVERT: P 34 GLU cc_start: 0.5960 (pt0) cc_final: 0.5027 (pt0) REVERT: P 56 HIS cc_start: 0.7929 (m-70) cc_final: 0.7646 (m90) REVERT: P 87 LYS cc_start: 0.7457 (mmtt) cc_final: 0.7207 (mmtt) REVERT: P 98 TYR cc_start: 0.7379 (m-80) cc_final: 0.7177 (m-80) REVERT: Q 37 GLN cc_start: 0.8357 (tt0) cc_final: 0.7779 (tt0) REVERT: Q 66 ASN cc_start: 0.8158 (t0) cc_final: 0.7642 (t0) REVERT: Q 83 LEU cc_start: 0.9001 (mm) cc_final: 0.8788 (mm) REVERT: R 77 PHE cc_start: 0.8699 (t80) cc_final: 0.8482 (t80) REVERT: R 82 HIS cc_start: 0.9339 (t70) cc_final: 0.9096 (t70) REVERT: R 97 LYS cc_start: 0.5874 (tttt) cc_final: 0.5057 (mttt) REVERT: R 98 ILE cc_start: 0.8468 (mm) cc_final: 0.8200 (mm) REVERT: S 52 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7828 (mm-30) REVERT: S 94 ASP cc_start: 0.7559 (t0) cc_final: 0.7342 (t0) REVERT: S 110 ARG cc_start: 0.7437 (mpt90) cc_final: 0.6576 (ptm160) REVERT: T 40 LYS cc_start: 0.6781 (ptmt) cc_final: 0.6495 (ptpt) REVERT: U 6 ARG cc_start: 0.8734 (mmt180) cc_final: 0.8321 (tpp-160) REVERT: U 22 ARG cc_start: 0.6053 (ptp-110) cc_final: 0.5638 (ppt170) REVERT: W 37 ILE cc_start: 0.9368 (mp) cc_final: 0.9163 (mp) REVERT: W 56 ASP cc_start: 0.7890 (p0) cc_final: 0.7480 (p0) REVERT: W 70 GLU cc_start: 0.7958 (pt0) cc_final: 0.7581 (pt0) REVERT: X 30 LEU cc_start: 0.9553 (mm) cc_final: 0.9349 (mt) REVERT: Z 4 THR cc_start: 0.6886 (t) cc_final: 0.6264 (p) REVERT: e 16 LYS cc_start: 0.8459 (ttpt) cc_final: 0.8160 (tttt) REVERT: e 22 PHE cc_start: 0.8546 (m-80) cc_final: 0.8337 (m-80) REVERT: f 19 ARG cc_start: 0.8151 (mtt180) cc_final: 0.7733 (mtt180) REVERT: g 49 MET cc_start: 0.7434 (mtp) cc_final: 0.7227 (mtt) REVERT: h 93 ASP cc_start: 0.6879 (p0) cc_final: 0.6675 (p0) REVERT: j 29 ARG cc_start: 0.8259 (mtm-85) cc_final: 0.7910 (mtm-85) REVERT: j 52 LYS cc_start: 0.9116 (tptm) cc_final: 0.8706 (tppt) REVERT: j 61 GLN cc_start: 0.8188 (tm-30) cc_final: 0.7889 (tm-30) REVERT: j 69 ARG cc_start: 0.7169 (mtm110) cc_final: 0.6502 (ttp-170) REVERT: j 112 ARG cc_start: 0.8455 (ttm-80) cc_final: 0.8253 (mtp-110) REVERT: j 147 MET cc_start: 0.7243 (ttt) cc_final: 0.6956 (ttt) REVERT: j 156 LYS cc_start: 0.9052 (tptt) cc_final: 0.8791 (mmmt) REVERT: k 13 ASP cc_start: 0.7834 (m-30) cc_final: 0.7407 (m-30) REVERT: l 11 LYS cc_start: 0.6971 (mmtt) cc_final: 0.6706 (mmmt) REVERT: l 102 ARG cc_start: 0.8118 (ttm110) cc_final: 0.7723 (mtp85) REVERT: m 27 MET cc_start: 0.8862 (ppp) cc_final: 0.8392 (ppp) REVERT: m 32 LEU cc_start: 0.9036 (pp) cc_final: 0.8805 (pp) REVERT: m 83 LEU cc_start: 0.8372 (tp) cc_final: 0.8141 (tp) REVERT: n 115 LYS cc_start: 0.8031 (mttt) cc_final: 0.7496 (mttm) REVERT: o 64 GLN cc_start: 0.6662 (tp40) cc_final: 0.6402 (mm-40) REVERT: p 68 GLU cc_start: 0.7901 (mt-10) cc_final: 0.7347 (mp0) REVERT: p 116 ILE cc_start: 0.8987 (mm) cc_final: 0.8688 (mm) REVERT: q 6 GLN cc_start: 0.8045 (tp40) cc_final: 0.7693 (tp-100) REVERT: q 34 CYS cc_start: 0.7663 (m) cc_final: 0.7166 (m) REVERT: q 49 LEU cc_start: 0.8466 (mp) cc_final: 0.8177 (mp) REVERT: q 53 CYS cc_start: 0.8063 (t) cc_final: 0.7317 (t) REVERT: r 81 MET cc_start: 0.8099 (mmm) cc_final: 0.6838 (mmm) REVERT: r 101 ARG cc_start: 0.6752 (mtp180) cc_final: 0.6401 (mpt180) REVERT: r 109 ARG cc_start: 0.7475 (tpt170) cc_final: 0.5719 (ttt-90) REVERT: s 6 MET cc_start: 0.8045 (mmm) cc_final: 0.7667 (mmt) REVERT: s 76 LYS cc_start: 0.8942 (tttp) cc_final: 0.8339 (mptt) REVERT: s 83 LYS cc_start: 0.8135 (ptpp) cc_final: 0.7083 (ptpp) REVERT: t 45 GLU cc_start: 0.6708 (tp30) cc_final: 0.6318 (tp30) REVERT: t 65 LYS cc_start: 0.8040 (tppt) cc_final: 0.7499 (tppt) REVERT: u 16 PHE cc_start: 0.9097 (t80) cc_final: 0.8805 (t80) REVERT: u 35 ARG cc_start: 0.8617 (ptp-110) cc_final: 0.7873 (ptp-110) REVERT: u 69 ASP cc_start: 0.8067 (m-30) cc_final: 0.7504 (t70) REVERT: u 71 VAL cc_start: 0.8677 (t) cc_final: 0.8450 (t) REVERT: v 27 ARG cc_start: 0.6415 (mmt180) cc_final: 0.6113 (mmt180) REVERT: v 38 ILE cc_start: 0.6649 (pt) cc_final: 0.6445 (pt) REVERT: v 43 LYS cc_start: 0.7586 (mtpp) cc_final: 0.7117 (mtpp) REVERT: v 80 GLU cc_start: 0.7641 (tm-30) cc_final: 0.7003 (tm-30) REVERT: w 50 LYS cc_start: 0.8569 (tttt) cc_final: 0.8234 (ttpt) REVERT: x 71 LEU cc_start: 0.6537 (mt) cc_final: 0.6150 (mt) REVERT: y 76 LYS cc_start: 0.7645 (mttt) cc_final: 0.7342 (mptt) REVERT: z 5 LYS cc_start: 0.7836 (pttm) cc_final: 0.6977 (pttp) REVERT: z 63 GLU cc_start: 0.6471 (pm20) cc_final: 0.6055 (tm-30) outliers start: 2 outliers final: 1 residues processed: 1423 average time/residue: 1.3572 time to fit residues: 3335.4584 Evaluate side-chains 1139 residues out of total 4987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1138 time to evaluate : 6.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 869 optimal weight: 20.0000 chunk 592 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 777 optimal weight: 6.9990 chunk 430 optimal weight: 9.9990 chunk 890 optimal weight: 10.0000 chunk 721 optimal weight: 1.9990 chunk 1 optimal weight: 10.0000 chunk 533 optimal weight: 20.0000 chunk 937 optimal weight: 20.0000 chunk 263 optimal weight: 10.0000 overall best weight: 7.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 79 HIS B 15 HIS B 58 HIS B 70 ASN ** C 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 GLN D 41 GLN D 97 ASN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 GLN G 2 GLN ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN N 81 ASN O 38 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 91 GLN ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN ** a 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 168 HIS h 69 HIS ** h 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 54 GLN ** i 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 121 HIS k 81 ASN m 16 ASN ** r 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.238 166754 Z= 0.421 Angle : 0.911 13.868 249500 Z= 0.462 Chirality : 0.045 0.545 31820 Planarity : 0.007 0.131 13336 Dihedral : 25.428 179.636 83395 Min Nonbonded Distance : 1.537 Molprobity Statistics. All-atom Clashscore : 28.71 Ramachandran Plot: Outliers : 0.03 % Allowed : 14.30 % Favored : 85.67 % Rotamer: Outliers : 0.02 % Allowed : 5.15 % Favored : 94.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.64 (0.10), residues: 6021 helix: -1.82 (0.11), residues: 1718 sheet: -2.35 (0.16), residues: 932 loop : -2.83 (0.10), residues: 3371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP M 64 HIS 0.012 0.002 HIS J 76 PHE 0.027 0.003 PHE d 18 TYR 0.041 0.003 TYR J 75 ARG 0.013 0.001 ARG t 63 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1349 residues out of total 4987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1348 time to evaluate : 6.959 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 142 ILE cc_start: 0.8680 (mt) cc_final: 0.7718 (mt) REVERT: B 60 GLN cc_start: 0.8493 (mt0) cc_final: 0.8166 (mt0) REVERT: B 67 PHE cc_start: 0.7777 (m-10) cc_final: 0.7388 (m-10) REVERT: B 145 GLU cc_start: 0.8364 (mt-10) cc_final: 0.7961 (mt-10) REVERT: B 153 GLN cc_start: 0.7135 (pm20) cc_final: 0.6858 (pm20) REVERT: B 156 ARG cc_start: 0.8439 (ttp-170) cc_final: 0.8136 (ttp-170) REVERT: B 180 GLU cc_start: 0.8597 (mp0) cc_final: 0.7882 (mp0) REVERT: B 201 MET cc_start: 0.9002 (ptt) cc_final: 0.7254 (tpp) REVERT: C 2 ILE cc_start: 0.9225 (pt) cc_final: 0.9010 (pt) REVERT: C 21 SER cc_start: 0.9288 (t) cc_final: 0.8928 (p) REVERT: C 77 ARG cc_start: 0.7991 (mtm-85) cc_final: 0.7430 (mmm160) REVERT: C 149 ASN cc_start: 0.8508 (t0) cc_final: 0.8190 (t0) REVERT: C 169 ARG cc_start: 0.8605 (mtp85) cc_final: 0.8160 (mtp85) REVERT: D 72 SER cc_start: 0.9316 (t) cc_final: 0.8778 (m) REVERT: D 97 ASN cc_start: 0.8142 (m110) cc_final: 0.7719 (m-40) REVERT: E 5 HIS cc_start: 0.8107 (t70) cc_final: 0.7441 (t70) REVERT: E 19 GLU cc_start: 0.9205 (tm-30) cc_final: 0.8808 (tm-30) REVERT: E 26 MET cc_start: 0.8637 (mtp) cc_final: 0.8244 (mtp) REVERT: E 33 LYS cc_start: 0.8325 (pttm) cc_final: 0.7898 (pttm) REVERT: E 96 MET cc_start: 0.8126 (ttp) cc_final: 0.7917 (tpp) REVERT: E 98 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7806 (tt0) REVERT: E 130 MET cc_start: 0.7553 (pmm) cc_final: 0.7223 (pmm) REVERT: H 38 MET cc_start: 0.0503 (mtt) cc_final: 0.0065 (tpp) REVERT: H 52 MET cc_start: 0.3666 (tmm) cc_final: 0.2608 (tmm) REVERT: H 65 GLU cc_start: 0.8333 (tm-30) cc_final: 0.8098 (tm-30) REVERT: I 116 MET cc_start: 0.4122 (mtp) cc_final: 0.3064 (mtp) REVERT: I 133 ARG cc_start: 0.7950 (ttm170) cc_final: 0.7685 (ttp-170) REVERT: K 39 ILE cc_start: 0.9080 (pt) cc_final: 0.8804 (pt) REVERT: K 67 LYS cc_start: 0.9027 (tptp) cc_final: 0.8569 (tptp) REVERT: K 82 ASN cc_start: 0.8608 (m-40) cc_final: 0.8405 (p0) REVERT: K 108 ARG cc_start: 0.7135 (ptm160) cc_final: 0.4844 (ppt170) REVERT: L 29 LYS cc_start: 0.8320 (pttt) cc_final: 0.8041 (pttt) REVERT: L 50 PHE cc_start: 0.8752 (t80) cc_final: 0.8309 (t80) REVERT: M 10 ARG cc_start: 0.7922 (ttm-80) cc_final: 0.7439 (mtm-85) REVERT: M 17 ASN cc_start: 0.9183 (t0) cc_final: 0.8894 (t0) REVERT: M 103 TYR cc_start: 0.7232 (m-80) cc_final: 0.6617 (m-80) REVERT: N 71 ARG cc_start: 0.8659 (mmm-85) cc_final: 0.8052 (tpp80) REVERT: O 9 ARG cc_start: 0.8232 (ttp80) cc_final: 0.7002 (ttp80) REVERT: O 17 LYS cc_start: 0.7942 (tptt) cc_final: 0.7585 (tttt) REVERT: P 34 GLU cc_start: 0.6259 (pt0) cc_final: 0.5483 (pt0) REVERT: P 56 HIS cc_start: 0.8101 (m-70) cc_final: 0.7795 (m170) REVERT: Q 37 GLN cc_start: 0.8592 (tt0) cc_final: 0.8038 (tt0) REVERT: Q 66 ASN cc_start: 0.8244 (t0) cc_final: 0.7757 (t0) REVERT: R 77 PHE cc_start: 0.8678 (t80) cc_final: 0.8438 (t80) REVERT: R 79 ARG cc_start: 0.7946 (mtm180) cc_final: 0.7610 (mtm180) REVERT: R 97 LYS cc_start: 0.6136 (tttt) cc_final: 0.5277 (mttm) REVERT: S 52 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7879 (mm-30) REVERT: S 110 ARG cc_start: 0.7556 (mpt90) cc_final: 0.6701 (ptm160) REVERT: T 40 LYS cc_start: 0.6933 (ptmt) cc_final: 0.6511 (ptpt) REVERT: T 70 HIS cc_start: 0.8477 (t70) cc_final: 0.8093 (t70) REVERT: U 6 ARG cc_start: 0.8790 (mmt180) cc_final: 0.8442 (tpp-160) REVERT: U 47 LYS cc_start: 0.8742 (mmtm) cc_final: 0.8471 (mmtt) REVERT: U 101 GLU cc_start: 0.7757 (tt0) cc_final: 0.7457 (mt-10) REVERT: V 45 ASP cc_start: 0.8771 (m-30) cc_final: 0.8442 (t0) REVERT: W 56 ASP cc_start: 0.8022 (p0) cc_final: 0.7570 (p0) REVERT: W 70 GLU cc_start: 0.8027 (pt0) cc_final: 0.7141 (pt0) REVERT: W 72 LYS cc_start: 0.8883 (mtpt) cc_final: 0.8554 (mtmt) REVERT: X 71 LEU cc_start: 0.9404 (mt) cc_final: 0.9178 (mt) REVERT: d 2 LYS cc_start: 0.8152 (ttmt) cc_final: 0.7801 (ttpt) REVERT: d 6 GLN cc_start: 0.8824 (mm-40) cc_final: 0.8584 (mm110) REVERT: f 1 MET cc_start: 0.9004 (tpp) cc_final: 0.8585 (tpp) REVERT: f 19 ARG cc_start: 0.8516 (mtt180) cc_final: 0.7348 (mtt180) REVERT: g 9 MET cc_start: 0.5282 (tpp) cc_final: 0.4413 (tpp) REVERT: g 49 MET cc_start: 0.7306 (mtp) cc_final: 0.7008 (mtt) REVERT: g 208 ARG cc_start: 0.7230 (mtm110) cc_final: 0.6864 (mtp-110) REVERT: i 71 GLN cc_start: 0.7893 (tt0) cc_final: 0.7632 (tm-30) REVERT: j 61 GLN cc_start: 0.8242 (tm-30) cc_final: 0.7941 (tm-30) REVERT: j 95 PHE cc_start: 0.8619 (t80) cc_final: 0.8064 (t80) REVERT: j 112 ARG cc_start: 0.8414 (ttm-80) cc_final: 0.8088 (mtp85) REVERT: j 147 MET cc_start: 0.7775 (ttt) cc_final: 0.7568 (ttt) REVERT: j 156 LYS cc_start: 0.9135 (tptt) cc_final: 0.8831 (mmmt) REVERT: k 11 HIS cc_start: 0.8070 (t70) cc_final: 0.7723 (t70) REVERT: k 13 ASP cc_start: 0.7900 (m-30) cc_final: 0.7274 (m-30) REVERT: l 102 ARG cc_start: 0.8206 (ttm110) cc_final: 0.7877 (mtp85) REVERT: m 27 MET cc_start: 0.8728 (ppp) cc_final: 0.8193 (ppp) REVERT: m 59 LEU cc_start: 0.8036 (tp) cc_final: 0.7617 (tt) REVERT: m 128 TYR cc_start: 0.7569 (m-10) cc_final: 0.7338 (m-10) REVERT: n 114 LYS cc_start: 0.5561 (tttm) cc_final: 0.5274 (tttt) REVERT: o 63 ASP cc_start: 0.6592 (p0) cc_final: 0.6316 (p0) REVERT: p 116 ILE cc_start: 0.9066 (mm) cc_final: 0.8767 (mm) REVERT: q 34 CYS cc_start: 0.7709 (m) cc_final: 0.7009 (m) REVERT: q 39 THR cc_start: 0.9035 (m) cc_final: 0.8631 (p) REVERT: q 49 LEU cc_start: 0.8526 (mp) cc_final: 0.8231 (mp) REVERT: q 81 LEU cc_start: 0.9208 (tp) cc_final: 0.8909 (tp) REVERT: r 79 ARG cc_start: 0.5193 (tmt170) cc_final: 0.3333 (mtt90) REVERT: r 81 MET cc_start: 0.8152 (mmm) cc_final: 0.7071 (mmm) REVERT: r 101 ARG cc_start: 0.6812 (mtp180) cc_final: 0.6567 (mpt180) REVERT: s 6 MET cc_start: 0.7898 (mmm) cc_final: 0.7539 (mmt) REVERT: s 76 LYS cc_start: 0.9056 (tttp) cc_final: 0.8389 (mptt) REVERT: s 77 PHE cc_start: 0.8439 (m-80) cc_final: 0.8175 (m-80) REVERT: s 83 LYS cc_start: 0.8000 (ptpp) cc_final: 0.6883 (ptpp) REVERT: t 65 LYS cc_start: 0.7906 (tppt) cc_final: 0.7439 (tppt) REVERT: u 16 PHE cc_start: 0.9179 (t80) cc_final: 0.8846 (t80) REVERT: v 27 ARG cc_start: 0.6562 (mmt180) cc_final: 0.6105 (mmt180) REVERT: v 43 LYS cc_start: 0.7567 (mtpp) cc_final: 0.7178 (mtpp) REVERT: v 80 GLU cc_start: 0.7665 (tm-30) cc_final: 0.6889 (tm-30) REVERT: w 50 LYS cc_start: 0.8553 (tttt) cc_final: 0.8207 (ttpt) REVERT: z 5 LYS cc_start: 0.7805 (pttm) cc_final: 0.6850 (pttp) REVERT: z 63 GLU cc_start: 0.6695 (pm20) cc_final: 0.6487 (tm-30) outliers start: 1 outliers final: 1 residues processed: 1349 average time/residue: 1.3579 time to fit residues: 3164.1069 Evaluate side-chains 1081 residues out of total 4987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1080 time to evaluate : 6.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 351 optimal weight: 10.0000 chunk 940 optimal weight: 8.9990 chunk 206 optimal weight: 7.9990 chunk 612 optimal weight: 6.9990 chunk 257 optimal weight: 6.9990 chunk 1044 optimal weight: 20.0000 chunk 867 optimal weight: 2.9990 chunk 483 optimal weight: 5.9990 chunk 86 optimal weight: 9.9990 chunk 345 optimal weight: 10.0000 chunk 548 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 HIS ** B 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 134 HIS ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 9 GLN D 41 GLN D 115 GLN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 GLN ** H 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN K 13 ASN L 54 GLN ** L 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 3 GLN N 81 ASN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN ** T 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 28 ASN ** T 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 46 HIS Y 58 ASN ** a 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 19 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 19 GLN g 39 HIS ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 69 HIS ** h 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 16 ASN ** s 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 20 HIS y 68 HIS Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.181 166754 Z= 0.342 Angle : 0.826 13.896 249500 Z= 0.425 Chirality : 0.042 0.515 31820 Planarity : 0.007 0.129 13336 Dihedral : 25.340 179.681 83395 Min Nonbonded Distance : 1.418 Molprobity Statistics. All-atom Clashscore : 25.32 Ramachandran Plot: Outliers : 0.02 % Allowed : 12.86 % Favored : 87.13 % Rotamer: Outliers : 0.04 % Allowed : 4.05 % Favored : 95.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.10), residues: 6021 helix: -1.72 (0.11), residues: 1734 sheet: -2.31 (0.16), residues: 921 loop : -2.79 (0.10), residues: 3366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP g 104 HIS 0.013 0.002 HIS W 46 PHE 0.039 0.002 PHE d 18 TYR 0.042 0.003 TYR r 23 ARG 0.011 0.001 ARG h 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1355 residues out of total 4987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1353 time to evaluate : 6.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 142 ILE cc_start: 0.8603 (mt) cc_final: 0.8254 (mm) REVERT: 5 151 LYS cc_start: 0.7548 (mmpt) cc_final: 0.7086 (tppt) REVERT: B 60 GLN cc_start: 0.8493 (mt0) cc_final: 0.8128 (mt0) REVERT: B 153 GLN cc_start: 0.7090 (pm20) cc_final: 0.6646 (pm20) REVERT: B 180 GLU cc_start: 0.8732 (mp0) cc_final: 0.8291 (mp0) REVERT: B 201 MET cc_start: 0.8937 (ptt) cc_final: 0.7345 (tpp) REVERT: C 49 GLN cc_start: 0.8462 (pt0) cc_final: 0.8080 (pt0) REVERT: C 77 ARG cc_start: 0.8003 (mtm-85) cc_final: 0.7441 (mmm160) REVERT: C 149 ASN cc_start: 0.8421 (t0) cc_final: 0.8091 (t0) REVERT: D 9 GLN cc_start: 0.8303 (mp-120) cc_final: 0.8086 (mp10) REVERT: D 72 SER cc_start: 0.9288 (t) cc_final: 0.8691 (m) REVERT: D 88 ARG cc_start: 0.7813 (mmp80) cc_final: 0.7491 (mmt180) REVERT: D 97 ASN cc_start: 0.8097 (m110) cc_final: 0.7641 (m-40) REVERT: E 5 HIS cc_start: 0.7995 (t70) cc_final: 0.7416 (t70) REVERT: E 26 MET cc_start: 0.8218 (mtp) cc_final: 0.7860 (mtp) REVERT: E 33 LYS cc_start: 0.8348 (pttm) cc_final: 0.7878 (pttm) REVERT: E 66 LEU cc_start: 0.8509 (tp) cc_final: 0.8209 (tt) REVERT: E 90 THR cc_start: 0.7986 (p) cc_final: 0.7771 (p) REVERT: E 164 GLU cc_start: 0.7281 (tm-30) cc_final: 0.7080 (tm-30) REVERT: F 107 LEU cc_start: 0.8828 (tp) cc_final: 0.8349 (mm) REVERT: F 124 GLU cc_start: 0.8282 (pp20) cc_final: 0.8043 (pp20) REVERT: H 52 MET cc_start: 0.3853 (tmm) cc_final: 0.2692 (tmm) REVERT: H 65 GLU cc_start: 0.8652 (tm-30) cc_final: 0.8401 (tm-30) REVERT: I 116 MET cc_start: 0.4146 (mtp) cc_final: 0.2982 (mtp) REVERT: I 133 ARG cc_start: 0.7880 (ttm170) cc_final: 0.7654 (ttp-170) REVERT: J 136 GLN cc_start: 0.8998 (mt0) cc_final: 0.8174 (pm20) REVERT: K 67 LYS cc_start: 0.8972 (tptp) cc_final: 0.8696 (tptp) REVERT: K 108 ARG cc_start: 0.7044 (ptm160) cc_final: 0.4726 (ppt170) REVERT: L 1 MET cc_start: 0.5892 (mmt) cc_final: 0.5226 (mmt) REVERT: L 29 LYS cc_start: 0.8379 (pttt) cc_final: 0.8032 (pttt) REVERT: L 50 PHE cc_start: 0.8707 (t80) cc_final: 0.8313 (t80) REVERT: M 10 ARG cc_start: 0.7873 (ttm-80) cc_final: 0.7385 (mtm-85) REVERT: M 17 ASN cc_start: 0.9147 (t0) cc_final: 0.8780 (t0) REVERT: M 103 TYR cc_start: 0.7184 (m-80) cc_final: 0.6590 (m-80) REVERT: O 9 ARG cc_start: 0.8339 (ttp80) cc_final: 0.7084 (ttp80) REVERT: O 17 LYS cc_start: 0.7830 (tptt) cc_final: 0.7541 (tttt) REVERT: O 67 ASN cc_start: 0.8162 (p0) cc_final: 0.7456 (p0) REVERT: O 69 ASP cc_start: 0.7509 (m-30) cc_final: 0.7266 (m-30) REVERT: P 34 GLU cc_start: 0.6141 (pt0) cc_final: 0.5292 (pt0) REVERT: P 56 HIS cc_start: 0.8300 (m-70) cc_final: 0.7983 (m170) REVERT: Q 37 GLN cc_start: 0.8474 (tt0) cc_final: 0.7930 (tt0) REVERT: Q 66 ASN cc_start: 0.8097 (t0) cc_final: 0.7659 (t0) REVERT: Q 83 LEU cc_start: 0.9033 (mm) cc_final: 0.8785 (mm) REVERT: R 16 GLU cc_start: 0.6717 (mp0) cc_final: 0.6438 (mp0) REVERT: R 79 ARG cc_start: 0.7895 (mtm180) cc_final: 0.7574 (mtm180) REVERT: R 82 HIS cc_start: 0.9398 (t70) cc_final: 0.9185 (t70) REVERT: R 97 LYS cc_start: 0.6041 (tttt) cc_final: 0.5181 (mttm) REVERT: R 98 ILE cc_start: 0.8373 (mm) cc_final: 0.8099 (mm) REVERT: S 52 GLU cc_start: 0.8054 (mm-30) cc_final: 0.7827 (mm-30) REVERT: S 110 ARG cc_start: 0.7544 (mpt90) cc_final: 0.6660 (ptm160) REVERT: T 40 LYS cc_start: 0.6898 (ptmt) cc_final: 0.6490 (ptpt) REVERT: T 70 HIS cc_start: 0.8390 (t70) cc_final: 0.8081 (t70) REVERT: U 6 ARG cc_start: 0.8791 (mmt180) cc_final: 0.8402 (tpp-160) REVERT: U 101 GLU cc_start: 0.7677 (tt0) cc_final: 0.7404 (mt-10) REVERT: V 45 ASP cc_start: 0.8768 (m-30) cc_final: 0.8409 (t0) REVERT: W 56 ASP cc_start: 0.7697 (p0) cc_final: 0.7435 (p0) REVERT: W 70 GLU cc_start: 0.8015 (pt0) cc_final: 0.7588 (pt0) REVERT: W 72 LYS cc_start: 0.8877 (mtpt) cc_final: 0.8654 (mtmt) REVERT: Z 12 SER cc_start: 0.8266 (t) cc_final: 0.8026 (p) REVERT: d 2 LYS cc_start: 0.8088 (ttmt) cc_final: 0.7771 (ttpt) REVERT: e 22 PHE cc_start: 0.8389 (m-80) cc_final: 0.8135 (m-80) REVERT: f 19 ARG cc_start: 0.8503 (mtt180) cc_final: 0.8070 (mtt180) REVERT: g 23 TRP cc_start: 0.9390 (p-90) cc_final: 0.9151 (p-90) REVERT: g 49 MET cc_start: 0.7250 (mtp) cc_final: 0.7015 (mtt) REVERT: g 208 ARG cc_start: 0.7363 (mtm110) cc_final: 0.7004 (mtp-110) REVERT: h 23 PHE cc_start: 0.6595 (t80) cc_final: 0.6330 (t80) REVERT: j 61 GLN cc_start: 0.8257 (tm-30) cc_final: 0.7956 (tm-30) REVERT: j 69 ARG cc_start: 0.7094 (mtm110) cc_final: 0.6411 (ttp-170) REVERT: j 95 PHE cc_start: 0.8477 (t80) cc_final: 0.7761 (t80) REVERT: j 112 ARG cc_start: 0.8337 (ttm-80) cc_final: 0.8027 (mtp-110) REVERT: j 147 MET cc_start: 0.8020 (ttt) cc_final: 0.7667 (ttt) REVERT: j 156 LYS cc_start: 0.9086 (tptt) cc_final: 0.8789 (mmmt) REVERT: k 11 HIS cc_start: 0.8119 (t70) cc_final: 0.7872 (t70) REVERT: k 13 ASP cc_start: 0.7931 (m-30) cc_final: 0.7384 (m-30) REVERT: l 102 ARG cc_start: 0.8266 (ttm110) cc_final: 0.7840 (mtt-85) REVERT: l 116 MET cc_start: 0.5452 (mpp) cc_final: 0.5039 (mpp) REVERT: n 83 ILE cc_start: 0.7095 (tp) cc_final: 0.6775 (pt) REVERT: n 114 LYS cc_start: 0.5746 (tttm) cc_final: 0.5481 (ttpt) REVERT: p 116 ILE cc_start: 0.9042 (mm) cc_final: 0.8733 (mm) REVERT: q 25 GLU cc_start: 0.7814 (mp0) cc_final: 0.7598 (mp0) REVERT: q 34 CYS cc_start: 0.7822 (m) cc_final: 0.7334 (m) REVERT: q 39 THR cc_start: 0.8910 (m) cc_final: 0.8466 (p) REVERT: q 49 LEU cc_start: 0.8562 (mp) cc_final: 0.8228 (mp) REVERT: r 44 LYS cc_start: 0.6458 (mtmt) cc_final: 0.6232 (mptt) REVERT: r 79 ARG cc_start: 0.5273 (tmt170) cc_final: 0.3469 (mtt90) REVERT: r 81 MET cc_start: 0.8128 (mmm) cc_final: 0.6982 (mmm) REVERT: r 101 ARG cc_start: 0.6784 (mtp180) cc_final: 0.6489 (mpt180) REVERT: r 109 ARG cc_start: 0.7633 (tpt170) cc_final: 0.5688 (ttt-90) REVERT: s 6 MET cc_start: 0.8135 (mmm) cc_final: 0.7806 (mmt) REVERT: s 48 LEU cc_start: 0.5390 (mt) cc_final: 0.5115 (mt) REVERT: s 76 LYS cc_start: 0.8763 (tttp) cc_final: 0.8330 (mptt) REVERT: s 83 LYS cc_start: 0.8353 (ptpp) cc_final: 0.7359 (ptpp) REVERT: s 90 ARG cc_start: 0.6780 (mtt-85) cc_final: 0.6562 (mtm-85) REVERT: u 16 PHE cc_start: 0.9123 (t80) cc_final: 0.8894 (t80) REVERT: v 43 LYS cc_start: 0.7482 (mtpp) cc_final: 0.7071 (mtpp) REVERT: v 80 GLU cc_start: 0.7722 (tm-30) cc_final: 0.7019 (tm-30) REVERT: w 50 LYS cc_start: 0.8548 (tttt) cc_final: 0.8223 (ttpt) REVERT: x 70 LYS cc_start: 0.5274 (mtpt) cc_final: 0.4951 (mtpp) REVERT: z 5 LYS cc_start: 0.7805 (pttm) cc_final: 0.6937 (pttp) REVERT: z 38 TYR cc_start: 0.8682 (t80) cc_final: 0.8245 (t80) outliers start: 2 outliers final: 1 residues processed: 1355 average time/residue: 1.3491 time to fit residues: 3160.8802 Evaluate side-chains 1112 residues out of total 4987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1111 time to evaluate : 6.893 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 1007 optimal weight: 7.9990 chunk 117 optimal weight: 20.0000 chunk 595 optimal weight: 6.9990 chunk 763 optimal weight: 9.9990 chunk 591 optimal weight: 5.9990 chunk 879 optimal weight: 9.9990 chunk 583 optimal weight: 6.9990 chunk 1040 optimal weight: 2.9990 chunk 651 optimal weight: 7.9990 chunk 634 optimal weight: 1.9990 chunk 480 optimal weight: 0.0000 overall best weight: 3.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 HIS ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 GLN K 13 ASN M 3 GLN ** M 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 62 ASN S 57 ASN ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 HIS Y 58 ASN ** a 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 19 HIS g 39 HIS ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 69 HIS ** h 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 54 GLN ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 81 ASN m 16 ASN ** r 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 166754 Z= 0.225 Angle : 0.715 13.879 249500 Z= 0.375 Chirality : 0.038 0.439 31820 Planarity : 0.006 0.126 13336 Dihedral : 25.149 179.604 83395 Min Nonbonded Distance : 1.462 Molprobity Statistics. All-atom Clashscore : 20.12 Ramachandran Plot: Outliers : 0.02 % Allowed : 10.60 % Favored : 89.39 % Rotamer: Outliers : 0.04 % Allowed : 2.35 % Favored : 97.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.27 (0.10), residues: 6021 helix: -1.42 (0.12), residues: 1738 sheet: -2.20 (0.16), residues: 932 loop : -2.65 (0.10), residues: 3351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 92 HIS 0.013 0.001 HIS X 20 PHE 0.025 0.002 PHE C 118 TYR 0.030 0.002 TYR q 38 ARG 0.010 0.001 ARG V 93 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1369 residues out of total 4987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1367 time to evaluate : 6.936 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 142 ILE cc_start: 0.8497 (mt) cc_final: 0.7697 (mt) REVERT: 5 151 LYS cc_start: 0.7374 (mmpt) cc_final: 0.6856 (tppt) REVERT: B 100 GLU cc_start: 0.7174 (tt0) cc_final: 0.6705 (tt0) REVERT: B 180 GLU cc_start: 0.8643 (mp0) cc_final: 0.8141 (mp0) REVERT: B 201 MET cc_start: 0.8920 (ptt) cc_final: 0.7460 (tpp) REVERT: C 49 GLN cc_start: 0.8385 (pt0) cc_final: 0.8116 (pt0) REVERT: C 149 ASN cc_start: 0.8280 (t0) cc_final: 0.7937 (t0) REVERT: D 1 MET cc_start: 0.4655 (tpt) cc_final: 0.3594 (ttm) REVERT: D 72 SER cc_start: 0.9268 (t) cc_final: 0.8629 (m) REVERT: D 97 ASN cc_start: 0.8037 (m110) cc_final: 0.7512 (m-40) REVERT: E 5 HIS cc_start: 0.7945 (t70) cc_final: 0.7360 (t70) REVERT: E 26 MET cc_start: 0.8047 (mtp) cc_final: 0.7737 (mtp) REVERT: E 33 LYS cc_start: 0.8195 (pttm) cc_final: 0.7580 (pttm) REVERT: E 66 LEU cc_start: 0.8472 (tp) cc_final: 0.8169 (tt) REVERT: E 90 THR cc_start: 0.7796 (p) cc_final: 0.7545 (p) REVERT: F 107 LEU cc_start: 0.8833 (tp) cc_final: 0.8363 (mm) REVERT: F 124 GLU cc_start: 0.8301 (pp20) cc_final: 0.7917 (pp20) REVERT: H 52 MET cc_start: 0.3724 (tmm) cc_final: 0.2593 (tmm) REVERT: I 116 MET cc_start: 0.3944 (mtp) cc_final: 0.2604 (mtp) REVERT: I 133 ARG cc_start: 0.7783 (ttm170) cc_final: 0.7522 (ttp-170) REVERT: J 102 GLU cc_start: 0.9053 (pm20) cc_final: 0.8669 (pm20) REVERT: J 136 GLN cc_start: 0.8978 (mt0) cc_final: 0.8199 (pm20) REVERT: K 70 ARG cc_start: 0.8308 (tpt-90) cc_final: 0.7983 (tpt-90) REVERT: K 108 ARG cc_start: 0.6971 (ptm160) cc_final: 0.4725 (ppt170) REVERT: L 1 MET cc_start: 0.5801 (mmt) cc_final: 0.5205 (mmt) REVERT: L 29 LYS cc_start: 0.8316 (pttt) cc_final: 0.7931 (pttt) REVERT: L 61 LEU cc_start: 0.9090 (mp) cc_final: 0.8797 (mp) REVERT: M 10 ARG cc_start: 0.7919 (ttm-80) cc_final: 0.7429 (mtm-85) REVERT: M 17 ASN cc_start: 0.9174 (t0) cc_final: 0.8752 (t0) REVERT: M 40 ARG cc_start: 0.9069 (ptp-110) cc_final: 0.8616 (mtm180) REVERT: M 103 TYR cc_start: 0.6899 (m-80) cc_final: 0.6568 (m-80) REVERT: O 9 ARG cc_start: 0.8341 (ttp80) cc_final: 0.7134 (ttp80) REVERT: O 17 LYS cc_start: 0.7759 (tptt) cc_final: 0.7514 (tttt) REVERT: O 67 ASN cc_start: 0.7985 (p0) cc_final: 0.7387 (p0) REVERT: O 69 ASP cc_start: 0.7678 (m-30) cc_final: 0.7447 (m-30) REVERT: O 99 TYR cc_start: 0.9050 (t80) cc_final: 0.8548 (t80) REVERT: P 34 GLU cc_start: 0.6087 (pt0) cc_final: 0.5197 (pt0) REVERT: Q 11 ARG cc_start: 0.7740 (tpp80) cc_final: 0.7437 (tpp80) REVERT: Q 37 GLN cc_start: 0.8285 (tt0) cc_final: 0.7717 (tt0) REVERT: Q 66 ASN cc_start: 0.8018 (t0) cc_final: 0.7552 (t0) REVERT: Q 83 LEU cc_start: 0.8918 (mm) cc_final: 0.8710 (mm) REVERT: R 79 ARG cc_start: 0.7946 (mtm180) cc_final: 0.7746 (mtm180) REVERT: R 97 LYS cc_start: 0.6033 (tttt) cc_final: 0.5135 (mttt) REVERT: R 98 ILE cc_start: 0.8427 (mm) cc_final: 0.8166 (mm) REVERT: S 13 SER cc_start: 0.8396 (p) cc_final: 0.7995 (m) REVERT: S 94 ASP cc_start: 0.7479 (t0) cc_final: 0.7259 (t0) REVERT: S 110 ARG cc_start: 0.7477 (mpt90) cc_final: 0.6456 (ptm160) REVERT: T 40 LYS cc_start: 0.6893 (ptmt) cc_final: 0.6533 (ptpt) REVERT: T 70 HIS cc_start: 0.8295 (t70) cc_final: 0.7995 (t70) REVERT: U 6 ARG cc_start: 0.8777 (mmt180) cc_final: 0.8366 (tpp-160) REVERT: U 37 GLU cc_start: 0.6452 (mt-10) cc_final: 0.6200 (mt-10) REVERT: U 101 GLU cc_start: 0.7664 (tt0) cc_final: 0.7338 (mt-10) REVERT: V 45 ASP cc_start: 0.8833 (m-30) cc_final: 0.8424 (t0) REVERT: W 56 ASP cc_start: 0.7879 (p0) cc_final: 0.7652 (p0) REVERT: W 70 GLU cc_start: 0.7952 (pt0) cc_final: 0.7559 (pt0) REVERT: Y 16 THR cc_start: 0.8918 (p) cc_final: 0.8538 (t) REVERT: Z 12 SER cc_start: 0.8351 (t) cc_final: 0.8002 (p) REVERT: Z 38 ARG cc_start: 0.8334 (mmp80) cc_final: 0.7855 (mmt-90) REVERT: d 31 LEU cc_start: 0.9162 (mm) cc_final: 0.8957 (mm) REVERT: d 35 ARG cc_start: 0.8287 (mmt-90) cc_final: 0.8082 (mmt90) REVERT: d 42 LEU cc_start: 0.8815 (tt) cc_final: 0.8610 (tt) REVERT: e 13 ARG cc_start: 0.8767 (mtt180) cc_final: 0.8017 (mtm-85) REVERT: e 22 PHE cc_start: 0.8494 (m-80) cc_final: 0.8284 (m-80) REVERT: f 1 MET cc_start: 0.9003 (tpp) cc_final: 0.8507 (tpp) REVERT: f 19 ARG cc_start: 0.8421 (mtt180) cc_final: 0.8029 (mtt180) REVERT: g 9 MET cc_start: 0.5372 (tpp) cc_final: 0.4756 (tpp) REVERT: g 49 MET cc_start: 0.7372 (mtp) cc_final: 0.7111 (mtt) REVERT: g 59 LYS cc_start: 0.6859 (tppp) cc_final: 0.5960 (mmtm) REVERT: g 208 ARG cc_start: 0.7303 (mtm110) cc_final: 0.6996 (mtp-110) REVERT: j 61 GLN cc_start: 0.8227 (tm-30) cc_final: 0.7899 (tm-30) REVERT: j 69 ARG cc_start: 0.7324 (mtm110) cc_final: 0.6803 (tmm160) REVERT: j 95 PHE cc_start: 0.8433 (t80) cc_final: 0.7907 (t80) REVERT: j 112 ARG cc_start: 0.8361 (ttm-80) cc_final: 0.8153 (mtp-110) REVERT: j 156 LYS cc_start: 0.9033 (tptt) cc_final: 0.8759 (mmmt) REVERT: k 13 ASP cc_start: 0.7858 (m-30) cc_final: 0.7459 (m-30) REVERT: l 11 LYS cc_start: 0.7106 (mmtt) cc_final: 0.6779 (mmmt) REVERT: l 102 ARG cc_start: 0.7925 (ttm110) cc_final: 0.7586 (mtp85) REVERT: l 116 MET cc_start: 0.5344 (mpp) cc_final: 0.5038 (mpp) REVERT: m 26 THR cc_start: 0.9153 (t) cc_final: 0.8845 (t) REVERT: m 27 MET cc_start: 0.8615 (ppp) cc_final: 0.8363 (ppp) REVERT: m 95 VAL cc_start: 0.9194 (t) cc_final: 0.8959 (t) REVERT: m 124 GLU cc_start: 0.6571 (mt-10) cc_final: 0.6305 (mt-10) REVERT: m 128 TYR cc_start: 0.7463 (m-10) cc_final: 0.7184 (m-10) REVERT: n 83 ILE cc_start: 0.7021 (tp) cc_final: 0.6722 (pt) REVERT: n 118 LEU cc_start: 0.7365 (pt) cc_final: 0.7064 (pt) REVERT: p 116 ILE cc_start: 0.8981 (mm) cc_final: 0.8690 (mm) REVERT: q 25 GLU cc_start: 0.7737 (mp0) cc_final: 0.7520 (mp0) REVERT: q 34 CYS cc_start: 0.7695 (m) cc_final: 0.7285 (m) REVERT: q 49 LEU cc_start: 0.8442 (mp) cc_final: 0.8218 (mp) REVERT: r 23 TYR cc_start: 0.4560 (t80) cc_final: 0.4192 (t80) REVERT: r 66 GLU cc_start: 0.7179 (tp30) cc_final: 0.6891 (tp30) REVERT: r 75 MET cc_start: 0.6598 (ptp) cc_final: 0.5632 (mmt) REVERT: r 79 ARG cc_start: 0.5093 (tmt170) cc_final: 0.3257 (mtt90) REVERT: r 81 MET cc_start: 0.8081 (mmm) cc_final: 0.6865 (mmm) REVERT: r 101 ARG cc_start: 0.6577 (mtp180) cc_final: 0.6313 (mpt180) REVERT: r 109 ARG cc_start: 0.7712 (tpt170) cc_final: 0.5730 (ttt-90) REVERT: s 6 MET cc_start: 0.8104 (mmm) cc_final: 0.7772 (mmt) REVERT: s 21 PHE cc_start: 0.6414 (p90) cc_final: 0.5792 (p90) REVERT: s 48 LEU cc_start: 0.5367 (mt) cc_final: 0.4988 (mt) REVERT: s 76 LYS cc_start: 0.8920 (tttp) cc_final: 0.8440 (mptt) REVERT: s 83 LYS cc_start: 0.8280 (ptpp) cc_final: 0.7144 (ptpp) REVERT: u 35 ARG cc_start: 0.8772 (ptp-110) cc_final: 0.8030 (ptp-110) REVERT: u 69 ASP cc_start: 0.8140 (m-30) cc_final: 0.7718 (t70) REVERT: v 38 ILE cc_start: 0.6736 (pt) cc_final: 0.6501 (pt) REVERT: v 43 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7588 (mtpt) REVERT: v 80 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7124 (tm-30) REVERT: w 50 LYS cc_start: 0.8512 (tttt) cc_final: 0.8144 (ttpt) REVERT: x 44 MET cc_start: 0.8804 (mmm) cc_final: 0.8501 (mmm) REVERT: y 76 LYS cc_start: 0.7563 (mttt) cc_final: 0.7149 (mptt) REVERT: z 5 LYS cc_start: 0.7802 (pttm) cc_final: 0.6929 (pttp) REVERT: z 38 TYR cc_start: 0.8678 (t80) cc_final: 0.8350 (t80) outliers start: 2 outliers final: 0 residues processed: 1369 average time/residue: 1.3517 time to fit residues: 3202.2845 Evaluate side-chains 1135 residues out of total 4987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1135 time to evaluate : 6.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 643 optimal weight: 0.6980 chunk 415 optimal weight: 20.0000 chunk 621 optimal weight: 8.9990 chunk 313 optimal weight: 9.9990 chunk 204 optimal weight: 10.0000 chunk 201 optimal weight: 9.9990 chunk 661 optimal weight: 0.6980 chunk 709 optimal weight: 5.9990 chunk 514 optimal weight: 2.9990 chunk 97 optimal weight: 10.0000 chunk 818 optimal weight: 0.9990 overall best weight: 2.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 135 GLN ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 116 GLN F 139 GLN I 30 GLN K 13 ASN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 57 ASN ** S 102 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN ** a 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 69 HIS h 100 GLN ** h 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 54 GLN ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 16 ASN ** r 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** r 91 HIS ** u 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 20 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.097 166754 Z= 0.173 Angle : 0.653 13.865 249500 Z= 0.345 Chirality : 0.035 0.370 31820 Planarity : 0.006 0.124 13336 Dihedral : 24.909 179.953 83395 Min Nonbonded Distance : 1.569 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 8.80 % Favored : 91.18 % Rotamer: Outliers : 0.04 % Allowed : 1.12 % Favored : 98.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.10), residues: 6021 helix: -1.04 (0.12), residues: 1705 sheet: -1.96 (0.16), residues: 935 loop : -2.45 (0.10), residues: 3381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP p 44 HIS 0.009 0.001 HIS P 56 PHE 0.030 0.002 PHE h 23 TYR 0.028 0.002 TYR k 59 ARG 0.026 0.001 ARG B 156 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1386 residues out of total 4987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1384 time to evaluate : 6.956 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 142 ILE cc_start: 0.8372 (mt) cc_final: 0.7730 (mt) REVERT: B 60 GLN cc_start: 0.8356 (mt0) cc_final: 0.8021 (mt0) REVERT: B 100 GLU cc_start: 0.7026 (tt0) cc_final: 0.6496 (tt0) REVERT: B 201 MET cc_start: 0.8926 (ptt) cc_final: 0.7556 (tpp) REVERT: C 80 TRP cc_start: 0.8446 (m-90) cc_final: 0.8092 (m-90) REVERT: C 149 ASN cc_start: 0.8162 (t0) cc_final: 0.7795 (t0) REVERT: C 169 ARG cc_start: 0.8584 (mtp85) cc_final: 0.8249 (mtp-110) REVERT: D 72 SER cc_start: 0.9207 (t) cc_final: 0.8432 (m) REVERT: D 97 ASN cc_start: 0.7995 (m110) cc_final: 0.7306 (m-40) REVERT: D 171 ASP cc_start: 0.8890 (t0) cc_final: 0.8481 (t70) REVERT: D 173 THR cc_start: 0.8845 (p) cc_final: 0.8599 (p) REVERT: D 195 GLN cc_start: 0.8855 (mp10) cc_final: 0.8510 (mp10) REVERT: E 5 HIS cc_start: 0.7796 (t70) cc_final: 0.7395 (t70) REVERT: E 26 MET cc_start: 0.7833 (mtp) cc_final: 0.7571 (mtp) REVERT: E 33 LYS cc_start: 0.8151 (pttm) cc_final: 0.7593 (pttm) REVERT: E 66 LEU cc_start: 0.8496 (tp) cc_final: 0.8221 (tt) REVERT: E 128 TYR cc_start: 0.8114 (t80) cc_final: 0.7790 (t80) REVERT: F 124 GLU cc_start: 0.8291 (pp20) cc_final: 0.8008 (pp20) REVERT: H 52 MET cc_start: 0.3791 (tmm) cc_final: 0.2622 (tmm) REVERT: I 116 MET cc_start: 0.4044 (mtp) cc_final: 0.2746 (mtp) REVERT: I 133 ARG cc_start: 0.7701 (ttm170) cc_final: 0.7382 (ttp-170) REVERT: J 102 GLU cc_start: 0.9064 (pm20) cc_final: 0.8602 (pm20) REVERT: J 136 GLN cc_start: 0.8915 (mt0) cc_final: 0.8201 (pm20) REVERT: K 70 ARG cc_start: 0.8415 (tpt-90) cc_final: 0.7886 (tpt-90) REVERT: K 105 ARG cc_start: 0.8232 (tpm170) cc_final: 0.5987 (tpm170) REVERT: K 108 ARG cc_start: 0.6674 (ptm160) cc_final: 0.4289 (ptm160) REVERT: L 1 MET cc_start: 0.5931 (mmt) cc_final: 0.5225 (mmt) REVERT: L 29 LYS cc_start: 0.8319 (pttt) cc_final: 0.7982 (pttt) REVERT: M 10 ARG cc_start: 0.7911 (ttm-80) cc_final: 0.7400 (mtm-85) REVERT: M 17 ASN cc_start: 0.9142 (t0) cc_final: 0.8793 (t0) REVERT: M 63 ILE cc_start: 0.8227 (mm) cc_final: 0.7999 (mm) REVERT: M 64 TRP cc_start: 0.7853 (m-90) cc_final: 0.7621 (m-10) REVERT: M 103 TYR cc_start: 0.6686 (m-80) cc_final: 0.6408 (m-80) REVERT: N 71 ARG cc_start: 0.8477 (mmm-85) cc_final: 0.7823 (tpp80) REVERT: O 9 ARG cc_start: 0.8395 (ttp80) cc_final: 0.7113 (ttp80) REVERT: O 17 LYS cc_start: 0.7658 (tptt) cc_final: 0.7330 (tttt) REVERT: O 67 ASN cc_start: 0.7949 (p0) cc_final: 0.7373 (p0) REVERT: O 69 ASP cc_start: 0.7488 (m-30) cc_final: 0.7251 (m-30) REVERT: O 99 TYR cc_start: 0.9033 (t80) cc_final: 0.8498 (t80) REVERT: Q 66 ASN cc_start: 0.7952 (t0) cc_final: 0.7478 (t0) REVERT: Q 81 ASN cc_start: 0.8475 (t0) cc_final: 0.8122 (t0) REVERT: R 27 ILE cc_start: 0.8877 (mt) cc_final: 0.8618 (mm) REVERT: R 39 LEU cc_start: 0.8243 (mp) cc_final: 0.7771 (mt) REVERT: R 97 LYS cc_start: 0.5992 (tttt) cc_final: 0.5176 (mttt) REVERT: R 98 ILE cc_start: 0.8392 (mm) cc_final: 0.8173 (mm) REVERT: S 13 SER cc_start: 0.8356 (p) cc_final: 0.7897 (m) REVERT: S 94 ASP cc_start: 0.7189 (t0) cc_final: 0.6788 (t0) REVERT: S 110 ARG cc_start: 0.7331 (mpt90) cc_final: 0.6329 (ptm160) REVERT: T 40 LYS cc_start: 0.6602 (ptmt) cc_final: 0.6253 (ptpt) REVERT: T 42 GLU cc_start: 0.8042 (pm20) cc_final: 0.7764 (pm20) REVERT: T 70 HIS cc_start: 0.8205 (t70) cc_final: 0.7913 (t70) REVERT: U 6 ARG cc_start: 0.8759 (mmt180) cc_final: 0.6686 (tpp-160) REVERT: U 22 ARG cc_start: 0.5670 (ptp-110) cc_final: 0.5247 (ppt170) REVERT: U 101 GLU cc_start: 0.7635 (tt0) cc_final: 0.7316 (mt-10) REVERT: V 45 ASP cc_start: 0.8861 (m-30) cc_final: 0.8444 (t0) REVERT: V 86 LEU cc_start: 0.9300 (mm) cc_final: 0.8981 (mm) REVERT: W 70 GLU cc_start: 0.7753 (pt0) cc_final: 0.6983 (pt0) REVERT: W 72 LYS cc_start: 0.8774 (mtpt) cc_final: 0.8517 (mtmt) REVERT: X 67 VAL cc_start: 0.9581 (t) cc_final: 0.9317 (p) REVERT: Y 16 THR cc_start: 0.8965 (p) cc_final: 0.8644 (t) REVERT: Z 12 SER cc_start: 0.8259 (t) cc_final: 0.7952 (p) REVERT: Z 38 ARG cc_start: 0.8366 (mmp80) cc_final: 0.7728 (mpp-170) REVERT: c 10 LYS cc_start: 0.5248 (ptmt) cc_final: 0.4654 (tttt) REVERT: d 31 LEU cc_start: 0.9167 (mm) cc_final: 0.8943 (mm) REVERT: d 35 ARG cc_start: 0.8201 (mmt-90) cc_final: 0.7958 (mmt90) REVERT: d 42 LEU cc_start: 0.8756 (tt) cc_final: 0.8452 (tt) REVERT: e 13 ARG cc_start: 0.8762 (mtt180) cc_final: 0.8387 (mtm180) REVERT: f 1 MET cc_start: 0.8969 (tpp) cc_final: 0.8493 (tpp) REVERT: f 19 ARG cc_start: 0.8332 (mtt180) cc_final: 0.7939 (mtt180) REVERT: g 9 MET cc_start: 0.5354 (tpp) cc_final: 0.4799 (mmm) REVERT: g 49 MET cc_start: 0.7334 (mtp) cc_final: 0.7050 (mtt) REVERT: g 59 LYS cc_start: 0.6762 (tppp) cc_final: 0.5752 (mmtm) REVERT: g 208 ARG cc_start: 0.7214 (mtm110) cc_final: 0.6945 (mtp-110) REVERT: j 52 LYS cc_start: 0.9038 (tmtt) cc_final: 0.8792 (tppt) REVERT: j 61 GLN cc_start: 0.8151 (tm-30) cc_final: 0.7828 (tm-30) REVERT: j 135 ASN cc_start: 0.8066 (t0) cc_final: 0.7750 (t0) REVERT: j 156 LYS cc_start: 0.8906 (tptt) cc_final: 0.8613 (mmmt) REVERT: k 13 ASP cc_start: 0.8084 (m-30) cc_final: 0.7708 (m-30) REVERT: l 11 LYS cc_start: 0.7138 (mmtt) cc_final: 0.6847 (mmmt) REVERT: l 102 ARG cc_start: 0.7955 (ttm110) cc_final: 0.7569 (mtt-85) REVERT: l 116 MET cc_start: 0.5601 (mpp) cc_final: 0.5275 (mpp) REVERT: m 26 THR cc_start: 0.9110 (t) cc_final: 0.8779 (t) REVERT: m 27 MET cc_start: 0.8658 (ppp) cc_final: 0.8445 (ppp) REVERT: m 59 LEU cc_start: 0.7823 (tt) cc_final: 0.7538 (tt) REVERT: m 95 VAL cc_start: 0.9228 (t) cc_final: 0.8830 (t) REVERT: m 128 TYR cc_start: 0.7407 (m-10) cc_final: 0.7153 (m-10) REVERT: n 57 MET cc_start: 0.4382 (mtp) cc_final: 0.3733 (ttm) REVERT: n 83 ILE cc_start: 0.7053 (tp) cc_final: 0.6792 (pt) REVERT: o 64 GLN cc_start: 0.7162 (tp40) cc_final: 0.6575 (mm-40) REVERT: p 116 ILE cc_start: 0.8924 (mm) cc_final: 0.8637 (mm) REVERT: q 25 GLU cc_start: 0.7649 (mp0) cc_final: 0.7356 (tm-30) REVERT: q 34 CYS cc_start: 0.7606 (m) cc_final: 0.7269 (m) REVERT: q 53 CYS cc_start: 0.7846 (t) cc_final: 0.6778 (t) REVERT: q 81 LEU cc_start: 0.8946 (tp) cc_final: 0.8071 (mp) REVERT: r 66 GLU cc_start: 0.6858 (tp30) cc_final: 0.6559 (tp30) REVERT: r 75 MET cc_start: 0.6386 (ptp) cc_final: 0.6032 (mmt) REVERT: r 81 MET cc_start: 0.8010 (mmm) cc_final: 0.6788 (mmm) REVERT: r 109 ARG cc_start: 0.7447 (tpt170) cc_final: 0.5993 (ttt-90) REVERT: s 6 MET cc_start: 0.7620 (mmm) cc_final: 0.7329 (mmt) REVERT: s 47 LYS cc_start: 0.4707 (tptt) cc_final: 0.3927 (mmmt) REVERT: s 76 LYS cc_start: 0.8989 (tttp) cc_final: 0.8456 (mptt) REVERT: s 83 LYS cc_start: 0.8111 (ptpp) cc_final: 0.7099 (ptpp) REVERT: u 53 ASP cc_start: 0.8808 (t70) cc_final: 0.8452 (t0) REVERT: u 69 ASP cc_start: 0.8036 (m-30) cc_final: 0.7814 (t70) REVERT: v 80 GLU cc_start: 0.7669 (tm-30) cc_final: 0.7145 (tm-30) REVERT: w 50 LYS cc_start: 0.8542 (tttt) cc_final: 0.8180 (ttpt) REVERT: y 15 GLU cc_start: 0.7873 (mt-10) cc_final: 0.7637 (mt-10) REVERT: y 76 LYS cc_start: 0.7533 (mttt) cc_final: 0.7191 (mptt) REVERT: z 5 LYS cc_start: 0.7935 (pttm) cc_final: 0.7113 (pttp) REVERT: z 13 ASP cc_start: 0.7398 (m-30) cc_final: 0.7091 (m-30) outliers start: 2 outliers final: 0 residues processed: 1386 average time/residue: 1.3920 time to fit residues: 3307.4006 Evaluate side-chains 1138 residues out of total 4987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1138 time to evaluate : 6.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 946 optimal weight: 0.3980 chunk 997 optimal weight: 10.0000 chunk 909 optimal weight: 10.0000 chunk 970 optimal weight: 30.0000 chunk 996 optimal weight: 1.9990 chunk 583 optimal weight: 10.0000 chunk 422 optimal weight: 20.0000 chunk 761 optimal weight: 10.0000 chunk 297 optimal weight: 20.0000 chunk 876 optimal weight: 8.9990 chunk 917 optimal weight: 0.8980 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 37 ASN B 58 HIS ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 GLN ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 138 GLN O 38 GLN O 100 HIS S 57 ASN ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 20 HIS Y 58 ASN ** a 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 6 GLN ** g 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 69 HIS ** h 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 54 GLN ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 16 ASN ** r 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 21 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7792 moved from start: 0.2922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.093 166754 Z= 0.260 Angle : 0.723 13.790 249500 Z= 0.376 Chirality : 0.037 0.451 31820 Planarity : 0.006 0.188 13336 Dihedral : 24.972 179.357 83395 Min Nonbonded Distance : 1.389 Molprobity Statistics. All-atom Clashscore : 21.54 Ramachandran Plot: Outliers : 0.02 % Allowed : 11.14 % Favored : 88.84 % Rotamer: Outliers : 0.04 % Allowed : 0.96 % Favored : 99.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.97 (0.10), residues: 6021 helix: -1.15 (0.12), residues: 1727 sheet: -1.96 (0.16), residues: 924 loop : -2.48 (0.10), residues: 3370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP x 34 HIS 0.010 0.001 HIS r 91 PHE 0.026 0.002 PHE G 46 TYR 0.028 0.002 TYR r 23 ARG 0.011 0.001 ARG U 6 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1332 residues out of total 4987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 1330 time to evaluate : 6.782 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 GLN cc_start: 0.8432 (mt0) cc_final: 0.8090 (mt0) REVERT: B 132 MET cc_start: 0.8440 (mtt) cc_final: 0.8212 (mtp) REVERT: B 201 MET cc_start: 0.8944 (ptt) cc_final: 0.7585 (tpp) REVERT: C 149 ASN cc_start: 0.8359 (t0) cc_final: 0.7980 (t0) REVERT: C 164 GLN cc_start: 0.8482 (mm-40) cc_final: 0.6696 (tt0) REVERT: D 72 SER cc_start: 0.9215 (t) cc_final: 0.8497 (m) REVERT: D 97 ASN cc_start: 0.8062 (m110) cc_final: 0.7470 (m-40) REVERT: D 147 LEU cc_start: 0.8594 (tp) cc_final: 0.8380 (tp) REVERT: D 195 GLN cc_start: 0.8922 (mp10) cc_final: 0.8620 (mp10) REVERT: E 5 HIS cc_start: 0.7876 (t70) cc_final: 0.7496 (t70) REVERT: E 26 MET cc_start: 0.7975 (mtp) cc_final: 0.7648 (mtp) REVERT: E 33 LYS cc_start: 0.8128 (pttm) cc_final: 0.7553 (pttm) REVERT: E 38 MET cc_start: 0.7427 (tpt) cc_final: 0.7003 (tpt) REVERT: F 124 GLU cc_start: 0.8228 (pp20) cc_final: 0.7870 (pp20) REVERT: H 52 MET cc_start: 0.3832 (tmm) cc_final: 0.2688 (tmm) REVERT: H 86 MET cc_start: 0.7188 (tpt) cc_final: 0.6852 (tpp) REVERT: I 52 LEU cc_start: 0.6355 (tp) cc_final: 0.6097 (tp) REVERT: I 116 MET cc_start: 0.4119 (mtp) cc_final: 0.2882 (mtp) REVERT: I 133 ARG cc_start: 0.7695 (ttm170) cc_final: 0.7372 (ttp-170) REVERT: J 80 HIS cc_start: 0.8756 (m90) cc_final: 0.8456 (m-70) REVERT: J 136 GLN cc_start: 0.8968 (mt0) cc_final: 0.8209 (pm20) REVERT: K 82 ASN cc_start: 0.8388 (p0) cc_final: 0.8109 (p0) REVERT: K 108 ARG cc_start: 0.6699 (ptm160) cc_final: 0.4438 (ppt170) REVERT: L 1 MET cc_start: 0.5716 (mmt) cc_final: 0.5123 (mmt) REVERT: L 29 LYS cc_start: 0.8322 (pttt) cc_final: 0.7924 (pttt) REVERT: M 10 ARG cc_start: 0.7898 (ttm-80) cc_final: 0.7472 (mtm-85) REVERT: M 17 ASN cc_start: 0.9136 (t0) cc_final: 0.8726 (t0) REVERT: M 103 TYR cc_start: 0.6910 (m-80) cc_final: 0.6457 (m-80) REVERT: N 71 ARG cc_start: 0.8559 (mmm-85) cc_final: 0.7988 (tpp80) REVERT: O 9 ARG cc_start: 0.8335 (ttp80) cc_final: 0.7098 (ttp80) REVERT: O 17 LYS cc_start: 0.7710 (tptt) cc_final: 0.7278 (tttm) REVERT: O 67 ASN cc_start: 0.8085 (p0) cc_final: 0.7477 (p0) REVERT: O 69 ASP cc_start: 0.7612 (m-30) cc_final: 0.7347 (m-30) REVERT: O 99 TYR cc_start: 0.8972 (t80) cc_final: 0.8575 (t80) REVERT: P 34 GLU cc_start: 0.6199 (pt0) cc_final: 0.5738 (pt0) REVERT: Q 48 ARG cc_start: 0.8381 (ttp80) cc_final: 0.7939 (ttp80) REVERT: Q 66 ASN cc_start: 0.8057 (t0) cc_final: 0.7604 (t0) REVERT: Q 83 LEU cc_start: 0.8970 (mm) cc_final: 0.8666 (mm) REVERT: R 79 ARG cc_start: 0.8010 (mtm180) cc_final: 0.7755 (mtm180) REVERT: R 95 ASP cc_start: 0.8325 (t0) cc_final: 0.6930 (p0) REVERT: R 97 LYS cc_start: 0.6070 (tttt) cc_final: 0.5304 (mttm) REVERT: R 98 ILE cc_start: 0.8377 (mm) cc_final: 0.8174 (mm) REVERT: S 13 SER cc_start: 0.8350 (p) cc_final: 0.8009 (m) REVERT: S 94 ASP cc_start: 0.7499 (t0) cc_final: 0.7297 (t0) REVERT: S 110 ARG cc_start: 0.7400 (mpt90) cc_final: 0.6381 (ptm160) REVERT: T 15 HIS cc_start: 0.8116 (t70) cc_final: 0.7632 (t70) REVERT: T 33 LYS cc_start: 0.8212 (mttt) cc_final: 0.7688 (mttp) REVERT: T 40 LYS cc_start: 0.6668 (ptmt) cc_final: 0.6240 (ptpt) REVERT: T 70 HIS cc_start: 0.8232 (t70) cc_final: 0.7896 (t70) REVERT: U 6 ARG cc_start: 0.8308 (mmt180) cc_final: 0.7991 (tpt170) REVERT: U 22 ARG cc_start: 0.5725 (ptp-110) cc_final: 0.5438 (ppt170) REVERT: U 101 GLU cc_start: 0.7602 (tt0) cc_final: 0.7307 (mt-10) REVERT: V 2 PHE cc_start: 0.6959 (m-10) cc_final: 0.5725 (m-10) REVERT: V 45 ASP cc_start: 0.8803 (m-30) cc_final: 0.8433 (t0) REVERT: V 86 LEU cc_start: 0.9205 (mm) cc_final: 0.8854 (mm) REVERT: W 70 GLU cc_start: 0.7842 (pt0) cc_final: 0.7154 (pt0) REVERT: W 72 LYS cc_start: 0.8892 (mtpt) cc_final: 0.8641 (mtmt) REVERT: X 44 LYS cc_start: 0.7450 (tmmt) cc_final: 0.7177 (tmmt) REVERT: X 67 VAL cc_start: 0.9613 (t) cc_final: 0.9339 (p) REVERT: Y 16 THR cc_start: 0.8979 (p) cc_final: 0.8666 (t) REVERT: Z 12 SER cc_start: 0.8311 (t) cc_final: 0.8010 (p) REVERT: Z 38 ARG cc_start: 0.8437 (mmp80) cc_final: 0.7797 (mpp-170) REVERT: d 31 LEU cc_start: 0.9218 (mm) cc_final: 0.8984 (mm) REVERT: d 35 ARG cc_start: 0.8340 (mmt-90) cc_final: 0.8138 (mmt90) REVERT: d 42 LEU cc_start: 0.8775 (tt) cc_final: 0.8314 (tt) REVERT: e 22 PHE cc_start: 0.8301 (m-80) cc_final: 0.8049 (m-80) REVERT: e 23 LYS cc_start: 0.8568 (pttt) cc_final: 0.8360 (pttt) REVERT: f 1 MET cc_start: 0.8985 (tpp) cc_final: 0.8475 (tpp) REVERT: f 19 ARG cc_start: 0.8381 (mtt180) cc_final: 0.7993 (mtt180) REVERT: g 9 MET cc_start: 0.5090 (tpp) cc_final: 0.4650 (mmm) REVERT: g 27 MET cc_start: 0.7269 (ttp) cc_final: 0.6976 (ttp) REVERT: g 49 MET cc_start: 0.7369 (mtp) cc_final: 0.7059 (mtt) REVERT: g 208 ARG cc_start: 0.7248 (mtm110) cc_final: 0.6992 (mtp-110) REVERT: h 23 PHE cc_start: 0.6399 (t80) cc_final: 0.6158 (t80) REVERT: i 55 LEU cc_start: 0.7970 (tt) cc_final: 0.7100 (tp) REVERT: j 29 ARG cc_start: 0.8312 (mtm-85) cc_final: 0.7927 (mtm-85) REVERT: j 52 LYS cc_start: 0.9133 (tmtt) cc_final: 0.8848 (tppt) REVERT: j 61 GLN cc_start: 0.8220 (tm-30) cc_final: 0.7893 (tm-30) REVERT: j 64 MET cc_start: 0.7771 (mmm) cc_final: 0.7536 (mmm) REVERT: j 135 ASN cc_start: 0.8085 (t0) cc_final: 0.7831 (t0) REVERT: j 156 LYS cc_start: 0.8949 (tptt) cc_final: 0.8648 (mmmt) REVERT: k 7 VAL cc_start: 0.7820 (t) cc_final: 0.7550 (t) REVERT: k 13 ASP cc_start: 0.7874 (m-30) cc_final: 0.7406 (m-30) REVERT: l 11 LYS cc_start: 0.7164 (mmtt) cc_final: 0.6920 (mmmt) REVERT: l 102 ARG cc_start: 0.8143 (ttm110) cc_final: 0.7738 (mtt-85) REVERT: l 116 MET cc_start: 0.5384 (mpp) cc_final: 0.5170 (mpp) REVERT: m 10 MET cc_start: 0.8000 (ttp) cc_final: 0.7748 (ttp) REVERT: m 26 THR cc_start: 0.9206 (t) cc_final: 0.8750 (t) REVERT: m 59 LEU cc_start: 0.7804 (tt) cc_final: 0.7600 (tt) REVERT: m 95 VAL cc_start: 0.9187 (t) cc_final: 0.8964 (t) REVERT: m 128 TYR cc_start: 0.7431 (m-10) cc_final: 0.7216 (m-10) REVERT: n 57 MET cc_start: 0.4380 (mtp) cc_final: 0.3702 (ttm) REVERT: n 83 ILE cc_start: 0.6995 (tp) cc_final: 0.6764 (pt) REVERT: n 115 LYS cc_start: 0.7711 (mmtp) cc_final: 0.7198 (mmtm) REVERT: p 29 ASN cc_start: 0.8152 (t0) cc_final: 0.7904 (t0) REVERT: p 116 ILE cc_start: 0.8987 (mm) cc_final: 0.8680 (mm) REVERT: q 34 CYS cc_start: 0.7731 (m) cc_final: 0.7259 (m) REVERT: q 49 LEU cc_start: 0.8764 (mp) cc_final: 0.8518 (mp) REVERT: q 53 CYS cc_start: 0.7973 (t) cc_final: 0.7176 (t) REVERT: q 81 LEU cc_start: 0.9047 (tp) cc_final: 0.8148 (mp) REVERT: r 66 GLU cc_start: 0.7160 (tp30) cc_final: 0.6927 (tp30) REVERT: r 75 MET cc_start: 0.6656 (ptp) cc_final: 0.6265 (mmt) REVERT: r 81 MET cc_start: 0.8048 (mmm) cc_final: 0.6802 (mmm) REVERT: r 101 ARG cc_start: 0.6833 (mpt180) cc_final: 0.6435 (mmp80) REVERT: r 109 ARG cc_start: 0.7538 (tpt170) cc_final: 0.6135 (ttt-90) REVERT: s 6 MET cc_start: 0.7896 (mmm) cc_final: 0.7615 (mmt) REVERT: s 47 LYS cc_start: 0.4841 (tptt) cc_final: 0.4202 (mmmt) REVERT: s 76 LYS cc_start: 0.9076 (tttp) cc_final: 0.8457 (mptt) REVERT: s 83 LYS cc_start: 0.8052 (ptpp) cc_final: 0.7278 (ptpp) REVERT: v 43 LYS cc_start: 0.8005 (mtpp) cc_final: 0.7644 (mppt) REVERT: v 80 GLU cc_start: 0.7725 (tm-30) cc_final: 0.7072 (tm-30) REVERT: w 50 LYS cc_start: 0.8553 (tttt) cc_final: 0.8181 (ttpt) REVERT: y 15 GLU cc_start: 0.7893 (mt-10) cc_final: 0.7639 (mt-10) REVERT: y 76 LYS cc_start: 0.7475 (mttt) cc_final: 0.7022 (mptt) REVERT: z 5 LYS cc_start: 0.7826 (pttm) cc_final: 0.7054 (pttp) REVERT: z 38 TYR cc_start: 0.8693 (t80) cc_final: 0.8342 (t80) outliers start: 2 outliers final: 0 residues processed: 1332 average time/residue: 1.3389 time to fit residues: 3102.9193 Evaluate side-chains 1103 residues out of total 4987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1103 time to evaluate : 6.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 966 optimal weight: 0.5980 chunk 636 optimal weight: 8.9990 chunk 1025 optimal weight: 0.8980 chunk 626 optimal weight: 10.0000 chunk 486 optimal weight: 0.3980 chunk 713 optimal weight: 3.9990 chunk 1075 optimal weight: 20.0000 chunk 990 optimal weight: 7.9990 chunk 856 optimal weight: 6.9990 chunk 88 optimal weight: 30.0000 chunk 661 optimal weight: 3.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 GLN ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 104 GLN O 100 HIS S 57 ASN ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN ** a 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 6 GLN ** g 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 39 HIS h 69 HIS ** h 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 54 GLN ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 16 ASN ** p 22 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 35 GLN ** t 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 20 HIS y 55 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7709 moved from start: 0.3134 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 166754 Z= 0.159 Angle : 0.638 13.890 249500 Z= 0.338 Chirality : 0.034 0.362 31820 Planarity : 0.006 0.124 13336 Dihedral : 24.810 179.692 83395 Min Nonbonded Distance : 1.592 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.62 % Favored : 92.38 % Rotamer: Outliers : 0.08 % Allowed : 0.40 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.72 (0.10), residues: 6021 helix: -0.91 (0.12), residues: 1726 sheet: -1.85 (0.16), residues: 930 loop : -2.34 (0.10), residues: 3365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP x 34 HIS 0.009 0.001 HIS r 91 PHE 0.035 0.002 PHE B 30 TYR 0.028 0.002 TYR F 164 ARG 0.010 0.001 ARG n 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 12042 Ramachandran restraints generated. 6021 Oldfield, 0 Emsley, 6021 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1377 residues out of total 4987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 1373 time to evaluate : 6.970 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 60 GLN cc_start: 0.8350 (mt0) cc_final: 0.7967 (mt0) REVERT: B 147 LYS cc_start: 0.8138 (mmtt) cc_final: 0.7728 (mmtt) REVERT: B 201 MET cc_start: 0.8966 (ptt) cc_final: 0.7654 (tpp) REVERT: C 149 ASN cc_start: 0.8128 (t0) cc_final: 0.7837 (t0) REVERT: C 151 THR cc_start: 0.8590 (m) cc_final: 0.8258 (p) REVERT: C 164 GLN cc_start: 0.8185 (mm-40) cc_final: 0.6492 (tt0) REVERT: D 72 SER cc_start: 0.9187 (t) cc_final: 0.8441 (m) REVERT: D 97 ASN cc_start: 0.7916 (m110) cc_final: 0.7282 (m-40) REVERT: D 171 ASP cc_start: 0.8890 (t0) cc_final: 0.8412 (t70) REVERT: D 173 THR cc_start: 0.8865 (p) cc_final: 0.8611 (p) REVERT: E 5 HIS cc_start: 0.7773 (t70) cc_final: 0.7423 (t70) REVERT: E 19 GLU cc_start: 0.9161 (tm-30) cc_final: 0.8355 (tm-30) REVERT: E 33 LYS cc_start: 0.8033 (pttm) cc_final: 0.7334 (pttm) REVERT: E 38 MET cc_start: 0.7409 (tpt) cc_final: 0.6997 (tpt) REVERT: E 66 LEU cc_start: 0.8397 (tp) cc_final: 0.8161 (tt) REVERT: E 98 GLU cc_start: 0.7918 (mt-10) cc_final: 0.7611 (tt0) REVERT: F 107 LEU cc_start: 0.8688 (tp) cc_final: 0.8070 (mt) REVERT: F 124 GLU cc_start: 0.8284 (pp20) cc_final: 0.7992 (pp20) REVERT: G 68 ARG cc_start: 0.6434 (ptt90) cc_final: 0.6002 (ptt-90) REVERT: H 52 MET cc_start: 0.3707 (tmm) cc_final: 0.2623 (tmm) REVERT: H 97 LYS cc_start: 0.5959 (mttt) cc_final: 0.4735 (mmmt) REVERT: I 116 MET cc_start: 0.4170 (mtp) cc_final: 0.2911 (mtp) REVERT: I 133 ARG cc_start: 0.7630 (ttm170) cc_final: 0.7322 (ttp-170) REVERT: J 61 LYS cc_start: 0.8066 (mtpt) cc_final: 0.7807 (mtpt) REVERT: J 98 GLU cc_start: 0.8255 (pp20) cc_final: 0.8041 (pp20) REVERT: J 102 GLU cc_start: 0.9043 (pm20) cc_final: 0.8599 (pm20) REVERT: J 136 GLN cc_start: 0.8912 (mt0) cc_final: 0.8102 (pm20) REVERT: K 70 ARG cc_start: 0.8415 (tpt-90) cc_final: 0.7933 (tpt-90) REVERT: K 105 ARG cc_start: 0.8223 (tpm170) cc_final: 0.6233 (tpm170) REVERT: K 108 ARG cc_start: 0.6646 (ptm160) cc_final: 0.4369 (ptm160) REVERT: L 1 MET cc_start: 0.5757 (mmt) cc_final: 0.5151 (mmt) REVERT: L 7 SER cc_start: 0.8860 (p) cc_final: 0.8365 (m) REVERT: M 10 ARG cc_start: 0.7906 (ttm-80) cc_final: 0.7431 (mtm-85) REVERT: M 17 ASN cc_start: 0.9121 (t0) cc_final: 0.8741 (t0) REVERT: M 103 TYR cc_start: 0.6587 (m-80) cc_final: 0.6346 (m-80) REVERT: M 131 VAL cc_start: 0.8906 (m) cc_final: 0.8603 (t) REVERT: N 57 THR cc_start: 0.7879 (p) cc_final: 0.7650 (p) REVERT: N 114 GLU cc_start: 0.7067 (tt0) cc_final: 0.6669 (tt0) REVERT: O 9 ARG cc_start: 0.8330 (ttp80) cc_final: 0.7166 (ttp80) REVERT: O 17 LYS cc_start: 0.7695 (tptt) cc_final: 0.7334 (tptt) REVERT: O 26 LEU cc_start: 0.8774 (tp) cc_final: 0.8557 (tp) REVERT: O 67 ASN cc_start: 0.7986 (p0) cc_final: 0.7549 (p0) REVERT: O 99 TYR cc_start: 0.8956 (t80) cc_final: 0.8728 (t80) REVERT: Q 48 ARG cc_start: 0.8351 (ttp80) cc_final: 0.7656 (ttp80) REVERT: Q 66 ASN cc_start: 0.7936 (t0) cc_final: 0.7426 (t0) REVERT: Q 81 ASN cc_start: 0.8474 (t0) cc_final: 0.8126 (t0) REVERT: Q 83 LEU cc_start: 0.8852 (mm) cc_final: 0.8591 (mm) REVERT: R 97 LYS cc_start: 0.5981 (tttt) cc_final: 0.5164 (mttt) REVERT: S 13 SER cc_start: 0.8201 (p) cc_final: 0.7828 (m) REVERT: S 110 ARG cc_start: 0.7294 (mpt90) cc_final: 0.6272 (ptm160) REVERT: T 6 ARG cc_start: 0.8117 (tpp80) cc_final: 0.7876 (ttm110) REVERT: T 15 HIS cc_start: 0.8048 (t70) cc_final: 0.7659 (t70) REVERT: T 33 LYS cc_start: 0.8188 (mttt) cc_final: 0.7661 (mttp) REVERT: T 40 LYS cc_start: 0.6455 (ptmt) cc_final: 0.6032 (ptpt) REVERT: T 70 HIS cc_start: 0.8162 (t70) cc_final: 0.7833 (t70) REVERT: T 93 LEU cc_start: 0.7699 (tp) cc_final: 0.7265 (tp) REVERT: U 6 ARG cc_start: 0.8407 (mmt180) cc_final: 0.8112 (mtt-85) REVERT: U 10 GLU cc_start: 0.8340 (tt0) cc_final: 0.8138 (tt0) REVERT: U 22 ARG cc_start: 0.5577 (ptp-110) cc_final: 0.5250 (ppt170) REVERT: U 94 ARG cc_start: 0.8160 (mpp-170) cc_final: 0.7415 (ptt-90) REVERT: U 101 GLU cc_start: 0.7584 (tt0) cc_final: 0.7272 (mt-10) REVERT: V 86 LEU cc_start: 0.9233 (mm) cc_final: 0.8825 (mm) REVERT: W 70 GLU cc_start: 0.7674 (pt0) cc_final: 0.7058 (pt0) REVERT: W 72 LYS cc_start: 0.8916 (mtpt) cc_final: 0.8692 (mtmt) REVERT: X 67 VAL cc_start: 0.9569 (t) cc_final: 0.9281 (p) REVERT: X 71 LEU cc_start: 0.9226 (tp) cc_final: 0.8983 (tp) REVERT: Y 16 THR cc_start: 0.8963 (p) cc_final: 0.8629 (t) REVERT: Z 12 SER cc_start: 0.8240 (t) cc_final: 0.7924 (p) REVERT: Z 38 ARG cc_start: 0.8352 (mmp80) cc_final: 0.7687 (mpp-170) REVERT: c 10 LYS cc_start: 0.4944 (ptmt) cc_final: 0.3889 (ttpt) REVERT: d 31 LEU cc_start: 0.9177 (mm) cc_final: 0.8961 (mm) REVERT: d 35 ARG cc_start: 0.8186 (mmt-90) cc_final: 0.7950 (mmt90) REVERT: d 42 LEU cc_start: 0.8718 (tt) cc_final: 0.8315 (tt) REVERT: e 22 PHE cc_start: 0.8317 (m-80) cc_final: 0.8081 (m-80) REVERT: f 1 MET cc_start: 0.8926 (tpp) cc_final: 0.8459 (tpp) REVERT: f 19 ARG cc_start: 0.8298 (mtt180) cc_final: 0.7927 (mtt180) REVERT: g 9 MET cc_start: 0.5078 (tpp) cc_final: 0.4702 (mmm) REVERT: g 23 TRP cc_start: 0.9337 (p-90) cc_final: 0.9102 (p-90) REVERT: g 27 MET cc_start: 0.6937 (ttp) cc_final: 0.6585 (ttp) REVERT: g 49 MET cc_start: 0.7387 (mtp) cc_final: 0.7092 (mtt) REVERT: g 208 ARG cc_start: 0.7202 (mtm110) cc_final: 0.6915 (mtp-110) REVERT: i 58 LYS cc_start: 0.8256 (tttt) cc_final: 0.7998 (tptt) REVERT: i 189 SER cc_start: 0.8746 (p) cc_final: 0.8124 (m) REVERT: j 11 LEU cc_start: 0.7164 (pt) cc_final: 0.6799 (pt) REVERT: j 52 LYS cc_start: 0.9042 (tmtt) cc_final: 0.8816 (tppt) REVERT: j 61 GLN cc_start: 0.8171 (tm-30) cc_final: 0.7854 (tm-30) REVERT: j 95 PHE cc_start: 0.8077 (t80) cc_final: 0.7683 (t80) REVERT: j 156 LYS cc_start: 0.8805 (tptt) cc_final: 0.8506 (mmmt) REVERT: k 13 ASP cc_start: 0.7897 (m-30) cc_final: 0.7587 (m-30) REVERT: k 38 ARG cc_start: 0.6409 (ptt180) cc_final: 0.6176 (ptt180) REVERT: l 11 LYS cc_start: 0.7049 (mmtt) cc_final: 0.6813 (mmmt) REVERT: l 102 ARG cc_start: 0.8111 (ttm110) cc_final: 0.7687 (mtt-85) REVERT: m 26 THR cc_start: 0.9114 (t) cc_final: 0.8659 (t) REVERT: m 27 MET cc_start: 0.8610 (ppp) cc_final: 0.8065 (ppp) REVERT: m 59 LEU cc_start: 0.7924 (tt) cc_final: 0.7619 (tt) REVERT: m 95 VAL cc_start: 0.9167 (t) cc_final: 0.8668 (t) REVERT: m 128 TYR cc_start: 0.7418 (m-10) cc_final: 0.7181 (m-10) REVERT: n 57 MET cc_start: 0.4334 (mtp) cc_final: 0.3815 (ttm) REVERT: n 83 ILE cc_start: 0.6958 (tp) cc_final: 0.6733 (pt) REVERT: n 115 LYS cc_start: 0.7559 (mmtp) cc_final: 0.7113 (mmtm) REVERT: o 64 GLN cc_start: 0.6953 (tp40) cc_final: 0.6470 (mm-40) REVERT: o 71 LEU cc_start: 0.8293 (mm) cc_final: 0.7932 (mm) REVERT: p 116 ILE cc_start: 0.8902 (mm) cc_final: 0.8613 (mm) REVERT: q 34 CYS cc_start: 0.7613 (m) cc_final: 0.7290 (m) REVERT: q 53 CYS cc_start: 0.7881 (t) cc_final: 0.6907 (t) REVERT: q 54 ARG cc_start: 0.7645 (tpp80) cc_final: 0.7315 (ttp-110) REVERT: q 81 LEU cc_start: 0.9001 (tp) cc_final: 0.8104 (mp) REVERT: r 66 GLU cc_start: 0.6933 (tp30) cc_final: 0.6727 (tp30) REVERT: r 75 MET cc_start: 0.6381 (ptp) cc_final: 0.6085 (mmt) REVERT: r 81 MET cc_start: 0.8028 (mmm) cc_final: 0.6719 (mmm) REVERT: r 109 ARG cc_start: 0.7431 (tpt170) cc_final: 0.6039 (ttt-90) REVERT: s 6 MET cc_start: 0.7541 (mmm) cc_final: 0.7166 (mmt) REVERT: s 42 TRP cc_start: 0.6720 (m100) cc_final: 0.6216 (m100) REVERT: s 47 LYS cc_start: 0.4834 (tptt) cc_final: 0.4402 (mmmt) REVERT: s 76 LYS cc_start: 0.9016 (tttp) cc_final: 0.8455 (mptt) REVERT: s 83 LYS cc_start: 0.8003 (ptpp) cc_final: 0.7041 (ptpp) REVERT: u 16 PHE cc_start: 0.8292 (t80) cc_final: 0.7789 (t80) REVERT: v 38 ILE cc_start: 0.6812 (pt) cc_final: 0.6590 (pt) REVERT: v 80 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7213 (tm-30) REVERT: w 50 LYS cc_start: 0.8522 (tttt) cc_final: 0.8182 (ttpt) REVERT: x 44 MET cc_start: 0.8674 (mmm) cc_final: 0.8471 (mmm) REVERT: y 15 GLU cc_start: 0.7892 (mt-10) cc_final: 0.7658 (mt-10) REVERT: y 76 LYS cc_start: 0.7384 (mttt) cc_final: 0.6994 (mptt) REVERT: z 5 LYS cc_start: 0.7916 (pttm) cc_final: 0.7273 (pttp) outliers start: 4 outliers final: 1 residues processed: 1375 average time/residue: 1.3044 time to fit residues: 3131.0122 Evaluate side-chains 1138 residues out of total 4987 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 1137 time to evaluate : 6.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1080 random chunks: chunk 525 optimal weight: 0.0970 chunk 680 optimal weight: 8.9990 chunk 912 optimal weight: 6.9990 chunk 262 optimal weight: 10.0000 chunk 790 optimal weight: 10.0000 chunk 126 optimal weight: 10.0000 chunk 238 optimal weight: 10.0000 chunk 858 optimal weight: 0.6980 chunk 359 optimal weight: 10.0000 chunk 881 optimal weight: 20.0000 chunk 108 optimal weight: 30.0000 overall best weight: 5.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 58 HIS ** B 128 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 41 GLN ** D 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 139 GLN ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 80 HIS K 82 ASN ** L 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 15 GLN ** Q 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN S 57 ASN ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 49 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 87 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 58 ASN a 30 HIS ** a 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 61 ASN a 65 ASN ** g 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** h 69 HIS ** h 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 51 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** x 69 HIS y 20 HIS y 21 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.117380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.100766 restraints weight = 433799.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.102855 restraints weight = 222098.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.103336 restraints weight = 118923.936| |-----------------------------------------------------------------------------| r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.3100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 166754 Z= 0.304 Angle : 0.765 13.781 249500 Z= 0.394 Chirality : 0.039 0.495 31820 Planarity : 0.006 0.128 13336 Dihedral : 24.969 179.146 83395 Min Nonbonded Distance : 1.271 Molprobity Statistics. All-atom Clashscore : 23.40 Ramachandran Plot: Outliers : 0.03 % Allowed : 12.31 % Favored : 87.66 % Rotamer: Outliers : 0.04 % Allowed : 0.70 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.91 (0.10), residues: 6021 helix: -1.12 (0.12), residues: 1740 sheet: -1.90 (0.16), residues: 931 loop : -2.44 (0.10), residues: 3350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP x 34 HIS 0.009 0.002 HIS J 80 PHE 0.025 0.002 PHE H 69 TYR 0.028 0.002 TYR F 164 ARG 0.010 0.001 ARG h 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 42617.08 seconds wall clock time: 745 minutes 29.12 seconds (44729.12 seconds total)