Starting phenix.real_space_refine on Wed Mar 27 19:37:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acj_11717/03_2024/7acj_11717_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acj_11717/03_2024/7acj_11717.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acj_11717/03_2024/7acj_11717_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acj_11717/03_2024/7acj_11717_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acj_11717/03_2024/7acj_11717_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acj_11717/03_2024/7acj_11717.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acj_11717/03_2024/7acj_11717.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acj_11717/03_2024/7acj_11717_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acj_11717/03_2024/7acj_11717_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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 4919 5.49 5 Mg 308 5.21 5 S 153 5.16 5 C 75866 2.51 5 N 28222 2.21 5 O 42333 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 ARG 106": "NH1" <-> "NH2" Residue "5 ARG 139": "NH1" <-> "NH2" Residue "A ARG 11": "NH1" <-> "NH2" Residue "A ARG 20": "NH1" <-> "NH2" Residue "A ARG 25": "NH1" <-> "NH2" Residue "A GLU 29": "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 ARG 182": "NH1" <-> "NH2" Residue "B ARG 212": "NH1" <-> "NH2" Residue "B ARG 269": "NH1" <-> "NH2" Residue "C PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 33": "NH1" <-> "NH2" Residue "C ARG 59": "NH1" <-> "NH2" 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 170": "NH1" <-> "NH2" Residue "D GLU 198": "OE1" <-> "OE2" 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 115": "NH1" <-> "NH2" Residue "E ARG 125": "NH1" <-> "NH2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F ARG 55": "NH1" <-> "NH2" Residue "F ARG 95": "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 27": "NH1" <-> "NH2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 34": "NH1" <-> "NH2" Residue "J ARG 35": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K ARG 17": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K ARG 49": "NH1" <-> "NH2" Residue "K ARG 105": "NH1" <-> "NH2" 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 "M ARG 6": "NH1" <-> "NH2" 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 59": "NH1" <-> "NH2" Residue "M ARG 114": "NH1" <-> "NH2" Residue "N ARG 2": "NH1" <-> "NH2" Residue "N ARG 4": "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 ARG 63": "NH1" <-> "NH2" Residue "N ARG 64": "NH1" <-> "NH2" Residue "N ARG 69": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N ARG 103": "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 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 "P ARG 21": "NH1" <-> "NH2" Residue "P ARG 62": "NH1" <-> "NH2" 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 "Q ARG 92": "NH1" <-> "NH2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R GLU 62": "OE1" <-> "OE2" 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 "U ARG 82": "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 50": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 48": "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 "Z GLU 58": "OE1" <-> "OE2" Residue "a ARG 49": "NH1" <-> "NH2" Residue "a ARG 56": "NH1" <-> "NH2" Residue "a ARG 59": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "c ARG 6": "NH1" <-> "NH2" Residue "c ARG 28": "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 42": "NH1" <-> "NH2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "g ARG 139": "NH1" <-> "NH2" Residue "g ARG 208": "NH1" <-> "NH2" Residue "g ARG 225": "NH1" <-> "NH2" Residue "h ARG 54": "NH1" <-> "NH2" Residue "h ARG 72": "NH1" <-> "NH2" Residue "h ARG 127": "NH1" <-> "NH2" Residue "h ARG 131": "NH1" <-> "NH2" Residue "h ARG 132": "NH1" <-> "NH2" Residue "i ARG 14": "NH1" <-> "NH2" Residue "i GLU 15": "OE1" <-> "OE2" Residue "i ARG 73": "NH1" <-> "NH2" Residue "i ARG 81": "NH1" <-> "NH2" Residue "i ARG 146": "NH1" <-> "NH2" Residue "i GLU 202": "OE1" <-> "OE2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j ARG 54": "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 ARG 2": "NH1" <-> "NH2" Residue "k ARG 45": "NH1" <-> "NH2" Residue "k ARG 79": "NH1" <-> "NH2" Residue "l ARG 4": "NH1" <-> "NH2" Residue "l GLU 48": "OE1" <-> "OE2" 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 ARG 80": "NH1" <-> "NH2" Residue "n ARG 11": "NH1" <-> "NH2" Residue "n ARG 41": "NH1" <-> "NH2" Residue "n ARG 45": "NH1" <-> "NH2" Residue "n ARG 130": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o GLU 27": "OE1" <-> "OE2" Residue "o ARG 45": "NH1" <-> "NH2" Residue "o GLU 47": "OE1" <-> "OE2" 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 GLU 59": "OE1" <-> "OE2" Residue "r ARG 70": "NH1" <-> "NH2" Residue "r ARG 87": "NH1" <-> "NH2" Residue "r ARG 92": "NH1" <-> "NH2" Residue "r ARG 113": "NH1" <-> "NH2" Residue "s ARG 9": "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 "t ARG 72": "NH1" <-> "NH2" Residue "t ARG 89": "NH1" <-> "NH2" Residue "u ARG 28": "NH1" <-> "NH2" 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 ARG 12": "NH1" <-> "NH2" Residue "w ARG 48": "NH1" <-> "NH2" Residue "w ARG 61": "NH1" <-> "NH2" Residue "w TYR 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w ARG 73": "NH1" <-> "NH2" Residue "x ARG 32": "NH1" <-> "NH2" Residue "y ARG 24": "NH1" <-> "NH2" Residue "y ARG 60": "NH1" <-> "NH2" Residue "y ARG 74": "NH1" <-> "NH2" Residue "z ARG 45": "NH1" <-> "NH2" Residue "z ARG 55": "NH1" <-> "NH2" Residue "z ARG 66": "NH1" <-> "NH2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 151803 Number of models: 1 Model: "" Number of chains: 64 Chain: "1" Number of atoms: 62336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62336 Classifications: {'RNA': 2903} Modifications used: {'rna2p': 6, 'rna2p_pur': 299, 'rna2p_pyr': 165, 'rna3p': 16, 'rna3p_pur': 1368, 'rna3p_pyr': 1049} Link IDs: {'rna2p': 469, 'rna3p': 2433} 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': 2, 'rna2p_pur': 122, 'rna2p_pyr': 98, 'rna3p': 9, 'rna3p_pur': 747, 'rna3p_pyr': 555} Link IDs: {'rna2p': 222, 'rna3p': 1311} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 14 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': 9, 'rna2p_pyr': 8, 'rna3p_pur': 55, 'rna3p_pyr': 48} Link IDs: {'rna2p': 16, 'rna3p': 103} Chain: "4" Number of atoms: 7756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 7756 Classifications: {'RNA': 363} Modifications used: {'5*END': 1, 'rna2p_pur': 38, 'rna2p_pyr': 25, 'rna3p': 3, 'rna3p_pur': 160, 'rna3p_pyr': 137} Link IDs: {'rna2p': 62, 'rna3p': 300} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 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: "A" Number of atoms: 595 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 595 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} 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: {'PTRANS': 6, '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: 1110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1110 Classifications: {'peptide': 149} Link IDs: {'PTRANS': 3, 'TRANS': 145} 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: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1075 Classifications: {'peptide': 136} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 128} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'4D4:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "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: 16 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 16 Classifications: {'peptide': 2} Link IDs: {'TRANS': 1} 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: 514 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 514 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} 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: 1658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1658 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 7, 'TRANS': 204} 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: {'PTRANS': 7, '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: 553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 67, 553 Classifications: {'peptide': 67} Link IDs: {'PTRANS': 2, 'TRANS': 64} Chain: "x" Number of atoms: 685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 685 Classifications: {'peptide': 86} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 79} 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: "1" Number of atoms: 237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 237, 237 Unusual residues: {' MG': 237} Classifications: {'undetermined': 237} Link IDs: {None: 236} Chain: "2" Number of atoms: 57 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 57 Unusual residues: {' MG': 57} Classifications: {'undetermined': 57} Link IDs: {None: 56} Chain: "3" Number of atoms: 7 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 7 Unusual residues: {' MG': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Chain: "5" 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: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Unusual residues: {' MG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "f" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0N5S SG CYS a 16 123.685 93.179 40.799 1.00164.55 S ATOM A0N64 SG CYS a 18 123.633 94.526 37.217 1.00162.74 S ATOM A0NA2 SG CYS a 37 126.566 95.275 39.671 1.00159.12 S ATOM A0NAN SG CYS a 40 123.126 96.907 39.973 1.00163.35 S ATOM A0OVG SG CYS f 11 174.080 182.789 87.007 1.00106.21 S ATOM A0OW5 SG CYS f 14 177.535 181.833 88.319 1.00106.86 S ATOM A0OZ0 SG CYS f 27 175.607 184.744 89.904 1.00106.81 S Time building chain proxies: 58.43, per 1000 atoms: 0.38 Number of scatterers: 151803 At special positions: 0 Unit cell: (298.48, 264.16, 246.48, 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 153 16.00 P 4919 15.00 Mg 308 11.99 O 42333 8.00 N 28222 7.00 C 75866 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 67.53 Conformation dependent library (CDL) restraints added in 8.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 101 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 40 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 16 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 18 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 37 " pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 33 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 14 " Number of angles added : 9 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10774 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: 171 helices and 69 sheets defined 37.7% alpha, 18.2% beta 1421 base pairs and 2345 stacking pairs defined. Time for finding SS restraints: 78.77 Creating SS restraints... Processing helix chain '5' and resid 17 through 24 removed outlier: 3.727A pdb=" N ARG 5 21 " --> pdb=" O ASN 5 17 " (cutoff:3.500A) Processing helix chain '5' and resid 37 through 46 Processing helix chain '5' and resid 93 through 103 removed outlier: 3.898A pdb=" N ASP 5 98 " --> pdb=" O GLN 5 94 " (cutoff:3.500A) removed outlier: 5.283A pdb=" N SER 5 99 " --> pdb=" O ARG 5 95 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N LEU 5 100 " --> pdb=" O GLU 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 134 through 160 removed outlier: 3.513A pdb=" N LYS 5 138 " --> pdb=" O LYS 5 134 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER 5 140 " --> pdb=" O HIS 5 136 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N VAL 5 149 " --> pdb=" O ARG 5 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 16 removed outlier: 7.311A pdb=" N HIS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N VAL B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 11 through 16' Processing helix chain 'B' and resid 30 through 35 removed outlier: 3.618A pdb=" N LEU B 34 " --> pdb=" O PHE B 30 " (cutoff:3.500A) removed outlier: 5.563A pdb=" N GLU B 35 " --> pdb=" O ALA B 31 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 30 through 35' Processing helix chain 'B' and resid 131 through 136 removed outlier: 3.521A 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 207 through 215 removed outlier: 3.959A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 3.942A pdb=" N MET B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 5.238A pdb=" N ASN B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 226' Processing helix chain 'B' and resid 260 through 268 removed outlier: 4.706A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 4.944A pdb=" N ILE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.823A pdb=" N VAL B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 260 through 268' Processing helix chain 'B' and resid 197 through 202 removed outlier: 4.419A pdb=" N HIS B 200 " --> pdb=" O ASN B 197 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N MET B 201 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.655A pdb=" N VAL C 60 " --> pdb=" O LYS C 56 " (cutoff:3.500A) removed outlier: 6.156A pdb=" N THR C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 61' Processing helix chain 'C' and resid 62 through 72 Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'C' and resid 98 through 103 removed outlier: 5.969A pdb=" N PHE C 101 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ALA C 102 " --> pdb=" O GLU C 99 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N ASP C 103 " --> pdb=" O LEU C 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 103' Processing helix chain 'D' and resid 24 through 40 Processing helix chain 'D' and resid 97 through 116 Processing helix chain 'D' and resid 130 through 142 removed outlier: 3.594A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 163 removed outlier: 4.063A pdb=" N ARG D 162 " --> pdb=" O PHE D 158 " (cutoff:3.500A) removed outlier: 4.968A pdb=" N ASN D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 183 Processing helix chain 'D' and resid 189 through 201 Processing helix chain 'D' and resid 16 through 21 Processing helix chain 'E' and resid 2 through 21 removed outlier: 5.110A pdb=" N ASP E 10 " --> pdb=" O ASP E 6 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLU E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N THR E 18 " --> pdb=" O LYS E 14 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 62 removed outlier: 4.795A pdb=" N LEU E 50 " --> pdb=" O ASP E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 106 removed outlier: 3.630A pdb=" N ARG E 102 " --> pdb=" O GLU E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 142 through 147 removed outlier: 4.365A pdb=" N VAL E 146 " --> pdb=" O ASP E 142 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ASP E 147 " --> pdb=" O TYR E 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 142 through 147' Processing helix chain 'E' and resid 162 through 174 Processing helix chain 'E' and resid 134 through 139 removed outlier: 4.446A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Proline residue: E 139 - end of helix Processing helix chain 'F' and resid 60 through 81 removed outlier: 4.541A pdb=" N GLN F 64 " --> pdb=" O ASP F 60 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR F 67 " --> pdb=" O ALA F 63 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLY F 78 " --> pdb=" O SER F 74 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLU F 81 " --> pdb=" O ILE F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 4.106A pdb=" N ILE F 141 " --> pdb=" O ASP F 137 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N ARG F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 28 Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 40 through 51 removed outlier: 3.988A pdb=" N ARG G 51 " --> pdb=" O PHE G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 63 removed outlier: 5.481A pdb=" N ALA G 56 " --> pdb=" O ALA G 52 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS G 57 " --> pdb=" O GLU G 53 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA G 59 " --> pdb=" O GLU G 55 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N GLU G 60 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N VAL G 61 " --> pdb=" O LYS G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 74 removed outlier: 5.066A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N ALA G 74 " --> pdb=" O GLU G 70 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 69 through 74' Processing helix chain 'G' and resid 84 through 91 Processing helix chain 'G' and resid 98 through 107 removed outlier: 4.070A pdb=" N ALA G 102 " --> pdb=" O ASP G 98 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ALA G 105 " --> pdb=" O ASP G 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.314A pdb=" N ARG J 34 " --> pdb=" O THR J 30 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ARG J 35 " --> pdb=" O GLU J 31 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.533A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 3.616A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.690A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 119 Processing helix chain 'L' and resid 37 through 42 removed outlier: 3.554A pdb=" N ARG L 41 " --> pdb=" O GLY L 37 " (cutoff:3.500A) removed outlier: 5.797A pdb=" N SER L 42 " --> pdb=" O GLN L 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 37 through 42' Processing helix chain 'L' and resid 56 through 62 removed outlier: 3.508A pdb=" N LEU L 61 " --> pdb=" O LEU L 57 " (cutoff:3.500A) Proline residue: L 62 - end of helix Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.183A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 5.592A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 68 through 75' Processing helix chain 'L' and resid 78 through 85 removed outlier: 3.859A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.637A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 4.336A 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 Processing helix chain 'L' and resid 128 through 139 Processing helix chain 'M' and resid 42 through 58 Processing helix chain 'M' and resid 109 through 125 removed outlier: 3.826A pdb=" N LEU M 119 " --> pdb=" O GLU M 115 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ALA M 122 " --> pdb=" O LYS M 118 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 4.576A 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: 3.896A pdb=" N ASN N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 57 removed outlier: 4.375A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 3.777A pdb=" N LYS N 56 " --> pdb=" O ILE N 52 " (cutoff:3.500A) removed outlier: 5.364A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 Processing helix chain 'N' and resid 72 through 88 removed outlier: 3.955A pdb=" N PHE N 80 " --> pdb=" O VAL N 76 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N ASN N 81 " --> pdb=" O ALA N 77 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N GLY N 84 " --> pdb=" O PHE N 80 " (cutoff:3.500A) Proline residue: N 85 - end of helix Processing helix chain 'O' and resid 2 through 20 removed outlier: 4.537A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 5.665A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.751A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 removed outlier: 3.839A pdb=" N GLY O 114 " --> pdb=" O ALA O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 13 removed outlier: 3.637A pdb=" N GLU P 11 " --> pdb=" O GLN P 7 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 104 removed outlier: 4.632A pdb=" N ARG P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 99 through 104' Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.621A pdb=" N GLN Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ALA Q 21 " --> pdb=" O ILE Q 17 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 4.425A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 73 removed outlier: 3.766A pdb=" N ARG Q 48 " --> pdb=" O GLN Q 44 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 75 through 87 Processing helix chain 'Q' and resid 91 through 102 Processing helix chain 'Q' and resid 103 through 118 Processing helix chain 'S' and resid 13 through 25 removed outlier: 3.534A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.874A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ILE S 35 " --> pdb=" O GLN S 31 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 4.109A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N VAL S 50 " --> pdb=" O LEU S 46 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 11 removed outlier: 4.460A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 removed outlier: 4.043A pdb=" N GLU T 25 " --> pdb=" O SER T 21 " (cutoff:3.500A) Processing helix chain 'T' and resid 39 through 51 Processing helix chain 'U' and resid 66 through 71 removed outlier: 4.659A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 5.181A 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 removed outlier: 3.738A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 54 removed outlier: 3.733A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N ALA V 54 " --> pdb=" O MET V 50 " (cutoff:3.500A) Processing helix chain 'X' and resid 52 through 63 Processing helix chain 'X' and resid 64 through 75 Processing helix chain 'Y' and resid 2 through 10 removed outlier: 4.579A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) removed outlier: 5.388A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N SER Y 10 " --> pdb=" O LEU Y 6 " (cutoff:3.500A) Processing helix chain 'Y' and resid 11 through 35 Processing helix chain 'Y' and resid 40 through 61 removed outlier: 4.527A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 Processing helix chain 'Z' and resid 41 through 52 removed outlier: 3.628A pdb=" N VAL Z 51 " --> pdb=" O MET Z 47 " (cutoff:3.500A) Processing helix chain 'a' and resid 58 through 63 removed outlier: 4.978A pdb=" N ASN a 61 " --> pdb=" O ASP a 58 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS a 62 " --> pdb=" O ARG a 59 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N ARG a 63 " --> pdb=" O PHE a 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 58 through 63' Processing helix chain 'b' and resid 9 through 19 removed outlier: 5.009A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 Processing helix chain 'd' and resid 17 through 25 removed outlier: 4.046A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) removed outlier: 4.903A pdb=" N LYS d 25 " --> pdb=" O ARG d 21 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 38 Processing helix chain 'e' and resid 7 through 14 removed outlier: 3.748A pdb=" N LYS e 12 " --> pdb=" O ARG e 8 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ARG e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 46 removed outlier: 3.723A pdb=" N LEU e 44 " --> pdb=" O ARG e 40 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N ARG e 45 " --> pdb=" O LYS e 41 " (cutoff:3.500A) Proline residue: e 46 - end of helix Processing helix chain 'e' and resid 51 through 63 removed outlier: 4.564A pdb=" N GLY e 56 " --> pdb=" O LYS e 52 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N LEU e 57 " --> pdb=" O GLY e 53 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N VAL e 58 " --> pdb=" O ASP e 54 " (cutoff:3.500A) removed outlier: 3.570A 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: 4.048A pdb=" N MET g 9 " --> pdb=" O SER g 5 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU g 10 " --> pdb=" O MET g 6 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS g 11 " --> pdb=" O ARG g 7 " (cutoff:3.500A) Processing helix chain 'g' and resid 27 through 32 removed outlier: 5.135A pdb=" N PHE g 32 " --> pdb=" O LYS g 28 " (cutoff:3.500A) Processing helix chain 'g' and resid 42 through 64 Proline residue: g 48 - end of helix removed outlier: 4.137A pdb=" N ARG g 63 " --> pdb=" O LYS g 59 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LYS g 64 " --> pdb=" O ILE g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 76 through 88 Processing helix chain 'g' and resid 103 through 121 removed outlier: 4.749A pdb=" N GLN g 109 " --> pdb=" O LYS g 105 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N SER g 110 " --> pdb=" O THR g 106 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N LEU g 114 " --> pdb=" O SER g 110 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N LYS g 115 " --> pdb=" O ILE g 111 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N ASP g 116 " --> pdb=" O LYS g 112 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N LEU g 117 " --> pdb=" O ARG g 113 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLU g 118 " --> pdb=" O LEU g 114 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N GLN g 120 " --> pdb=" O ASP g 116 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N SER g 121 " --> pdb=" O LEU g 117 " (cutoff:3.500A) Processing helix chain 'g' and resid 131 through 149 removed outlier: 4.408A pdb=" N MET g 136 " --> pdb=" O LYS g 132 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER g 147 " --> pdb=" O LYS g 143 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU g 148 " --> pdb=" O LEU g 144 " (cutoff:3.500A) Processing helix chain 'g' and resid 165 through 170 removed outlier: 4.380A pdb=" N HIS g 170 " --> pdb=" O ALA g 166 " (cutoff:3.500A) Processing helix chain 'g' and resid 171 through 180 removed outlier: 3.582A pdb=" N ASN g 178 " --> pdb=" O LYS g 174 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU g 179 " --> pdb=" O GLU g 175 " (cutoff:3.500A) Processing helix chain 'g' and resid 206 through 226 removed outlier: 3.618A pdb=" N THR g 211 " --> pdb=" O ILE g 207 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N SER g 226 " --> pdb=" O ARG g 222 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 12 removed outlier: 3.881A pdb=" N ILE h 10 " --> pdb=" O HIS h 6 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ARG h 11 " --> pdb=" O PRO h 7 " (cutoff:3.500A) Processing helix chain 'h' and resid 25 through 48 removed outlier: 6.089A pdb=" N PHE h 29 " --> pdb=" O ASN h 25 " (cutoff:3.500A) removed outlier: 5.437A pdb=" N ALA h 30 " --> pdb=" O THR h 26 " (cutoff:3.500A) removed outlier: 6.135A pdb=" N ASP h 31 " --> pdb=" O LYS h 27 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA h 48 " --> pdb=" O THR h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 78 removed outlier: 4.592A pdb=" N VAL h 76 " --> pdb=" O ARG h 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 81 through 96 removed outlier: 4.099A pdb=" N GLU h 85 " --> pdb=" O GLY h 81 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS h 89 " --> pdb=" O GLU h 85 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N VAL h 90 " --> pdb=" O LYS h 86 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL h 91 " --> pdb=" O LEU h 87 " (cutoff:3.500A) Processing helix chain 'h' and resid 112 through 127 removed outlier: 4.715A pdb=" N SER h 119 " --> pdb=" O LEU h 115 " (cutoff:3.500A) removed outlier: 4.836A pdb=" N ILE h 120 " --> pdb=" O VAL h 116 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N THR h 121 " --> pdb=" O ALA h 117 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N SER h 122 " --> pdb=" O ASP h 118 " (cutoff:3.500A) Processing helix chain 'h' and resid 129 through 145 Processing helix chain 'i' and resid 7 through 16 removed outlier: 4.775A pdb=" N LEU i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N SER i 12 " --> pdb=" O LYS i 8 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 32 Processing helix chain 'i' and resid 49 through 66 removed outlier: 3.546A pdb=" N GLN i 54 " --> pdb=" O ASP i 50 " (cutoff:3.500A) Processing helix chain 'i' and resid 68 through 83 removed outlier: 5.004A pdb=" N LYS i 83 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 removed outlier: 4.087A 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: 3.754A pdb=" N LYS i 121 " --> pdb=" O LEU i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 146 through 151 removed outlier: 4.734A pdb=" N LYS i 151 " --> pdb=" O GLU i 147 " (cutoff:3.500A) Processing helix chain 'i' and resid 152 through 166 removed outlier: 4.346A pdb=" N GLU i 163 " --> pdb=" O LEU i 159 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N GLN i 164 " --> pdb=" O GLU i 160 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ARG i 165 " --> pdb=" O LEU i 161 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 4.614A pdb=" N SER i 192 " --> pdb=" O ARG i 188 " (cutoff:3.500A) Processing helix chain 'i' and resid 196 through 206 removed outlier: 4.142A pdb=" N ILE i 200 " --> pdb=" O ASN i 196 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL i 201 " --> pdb=" O GLU i 197 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LYS i 206 " --> pdb=" O GLU i 202 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 71 removed outlier: 3.720A pdb=" N GLN j 61 " --> pdb=" O PRO j 57 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N MET j 71 " --> pdb=" O ALA j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 110 through 119 removed outlier: 4.356A pdb=" N VAL j 114 " --> pdb=" O ALA j 110 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 148 removed outlier: 3.885A pdb=" N ARG j 138 " --> pdb=" O ILE j 134 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU j 144 " --> pdb=" O THR j 140 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N MET j 147 " --> pdb=" O GLY j 143 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N ASN j 148 " --> pdb=" O LEU j 144 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 158 Processing helix chain 'j' and resid 160 through 165 Processing helix chain 'k' and resid 14 through 33 removed outlier: 3.901A pdb=" N VAL k 18 " --> pdb=" O GLN k 14 " (cutoff:3.500A) Proline residue: k 19 - end of helix Processing helix chain 'k' and resid 67 through 82 removed outlier: 5.244A pdb=" N ASP k 82 " --> pdb=" O PHE k 78 " (cutoff:3.500A) Processing helix chain 'l' and resid 20 through 32 removed outlier: 5.638A pdb=" N VAL l 32 " --> pdb=" O ASN l 28 " (cutoff:3.500A) Processing helix chain 'l' and resid 35 through 55 removed outlier: 3.539A pdb=" N ALA l 39 " --> pdb=" O LYS l 35 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 70 removed outlier: 3.711A pdb=" N VAL l 64 " --> pdb=" O GLU l 60 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN l 68 " --> pdb=" O VAL l 64 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL l 69 " --> pdb=" O ALA l 65 " (cutoff:3.500A) Processing helix chain 'l' and resid 92 through 111 removed outlier: 3.674A pdb=" N ASN l 97 " --> pdb=" O PRO l 93 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA l 98 " --> pdb=" O VAL l 94 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG l 109 " --> pdb=" O VAL l 105 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N LYS l 110 " --> pdb=" O GLU l 106 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N ARG l 111 " --> pdb=" O ALA l 107 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 130 removed outlier: 3.540A pdb=" N ASN l 122 " --> pdb=" O LEU l 118 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU l 123 " --> pdb=" O ARG l 119 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA l 127 " --> pdb=" O GLU l 123 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N ALA l 128 " --> pdb=" O LEU l 124 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N GLU l 129 " --> pdb=" O SER l 125 " (cutoff:3.500A) Processing helix chain 'l' and resid 132 through 149 removed outlier: 3.954A pdb=" N LYS l 136 " --> pdb=" O GLY l 132 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ASP l 140 " --> pdb=" O LYS l 136 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ARG l 143 " --> pdb=" O GLU l 139 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA l 145 " --> pdb=" O VAL l 141 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLU l 146 " --> pdb=" O HIS l 142 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN l 148 " --> pdb=" O MET l 144 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N LYS l 149 " --> pdb=" O ALA l 145 " (cutoff:3.500A) Processing helix chain 'm' and resid 5 through 21 Processing helix chain 'm' and resid 30 through 44 removed outlier: 3.587A pdb=" N GLY m 44 " --> pdb=" O LEU m 40 " (cutoff:3.500A) Processing helix chain 'm' and resid 112 through 120 Processing helix chain 'n' and resid 34 through 39 removed outlier: 3.675A pdb=" N PHE n 39 " --> pdb=" O LEU n 35 " (cutoff:3.500A) Processing helix chain 'n' and resid 41 through 50 removed outlier: 3.920A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N ARG n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Processing helix chain 'n' and resid 51 through 56 removed outlier: 4.767A pdb=" N VAL n 55 " --> pdb=" O PRO n 51 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N ASP n 56 " --> pdb=" O LEU n 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'n' and resid 51 through 56' Processing helix chain 'n' and resid 71 through 92 Processing helix chain 'n' and resid 93 through 102 removed outlier: 4.787A pdb=" N GLU n 97 " --> pdb=" O SER n 93 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 33 removed outlier: 3.705A pdb=" N ILE o 18 " --> pdb=" O ASP o 14 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLN o 20 " --> pdb=" O ARG o 16 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA o 21 " --> pdb=" O LEU o 17 " (cutoff:3.500A) Processing helix chain 'o' and resid 80 through 89 removed outlier: 4.230A pdb=" N VAL o 84 " --> pdb=" O THR o 80 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASP o 85 " --> pdb=" O GLU o 81 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA o 86 " --> pdb=" O LYS o 82 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU o 87 " --> pdb=" O THR o 83 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ARG o 89 " --> pdb=" O ASP o 85 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 3.806A pdb=" N SER p 50 " --> pdb=" O THR p 46 " (cutoff:3.500A) removed outlier: 4.584A 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 54 through 59 removed outlier: 4.025A pdb=" N SER p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N THR p 59 " --> pdb=" O SER p 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 54 through 59' Processing helix chain 'p' and resid 60 through 75 removed outlier: 3.756A pdb=" N VAL p 74 " --> pdb=" O CYS p 70 " (cutoff:3.500A) removed outlier: 4.302A pdb=" N LYS p 75 " --> pdb=" O ALA p 71 " (cutoff:3.500A) Processing helix chain 'p' and resid 91 through 104 removed outlier: 4.128A pdb=" N SER p 95 " --> pdb=" O PRO p 91 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR p 96 " --> pdb=" O GLY p 92 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N ILE p 97 " --> pdb=" O ARG p 93 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLY p 104 " --> pdb=" O LEU p 100 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 11 removed outlier: 3.778A pdb=" N ARG q 9 " --> pdb=" O ASN q 5 " (cutoff:3.500A) Proline residue: q 11 - end of helix Processing helix chain 'q' and resid 113 through 118 removed outlier: 3.811A pdb=" N TYR q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 23 removed outlier: 3.886A pdb=" N ILE r 22 " --> pdb=" O ALA r 18 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N TYR r 23 " --> pdb=" O LEU r 19 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 38 removed outlier: 4.310A pdb=" N SER r 30 " --> pdb=" O GLY r 26 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU r 34 " --> pdb=" O SER r 30 " (cutoff:3.500A) Processing helix chain 'r' and resid 49 through 64 removed outlier: 3.820A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N VAL r 64 " --> pdb=" O VAL r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 84 removed outlier: 3.793A pdb=" N LEU r 80 " --> pdb=" O SER r 76 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N MET r 81 " --> pdb=" O ILE r 77 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 94 Processing helix chain 's' and resid 3 through 21 removed outlier: 3.532A pdb=" N VAL s 11 " --> pdb=" O LYS s 7 " (cutoff:3.500A) Processing helix chain 's' and resid 22 through 33 removed outlier: 3.552A pdb=" N GLU s 26 " --> pdb=" O ALA s 22 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N ILE s 30 " --> pdb=" O GLU s 26 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE s 31 " --> pdb=" O LEU s 27 " (cutoff:3.500A) Processing helix chain 's' and resid 37 through 51 removed outlier: 3.898A pdb=" N GLN s 49 " --> pdb=" O VAL s 45 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU s 51 " --> pdb=" O LYS s 47 " (cutoff:3.500A) Processing helix chain 's' and resid 80 through 91 Processing helix chain 't' and resid 4 through 16 Processing helix chain 't' and resid 24 through 44 removed outlier: 3.981A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA t 44 " --> pdb=" O GLN t 40 " (cutoff:3.500A) Processing helix chain 't' and resid 49 through 74 removed outlier: 4.441A pdb=" N GLY t 55 " --> pdb=" O HIS t 51 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 86 removed outlier: 6.056A pdb=" N THR t 79 " --> pdb=" O VAL t 75 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLN t 80 " --> pdb=" O ALA t 76 " (cutoff:3.500A) Processing helix chain 'u' and resid 53 through 64 Processing helix chain 'u' and resid 68 through 82 removed outlier: 3.728A pdb=" N LYS u 76 " --> pdb=" O ALA u 72 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU u 77 " --> pdb=" O ALA u 73 " (cutoff:3.500A) Processing helix chain 'w' and resid 26 through 34 removed outlier: 4.896A pdb=" N ASN w 31 " --> pdb=" O ALA w 27 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N TYR w 32 " --> pdb=" O THR w 28 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N ILE w 33 " --> pdb=" O LEU w 29 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N THR w 34 " --> pdb=" O LYS w 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 41 through 46 Processing helix chain 'w' and resid 48 through 66 removed outlier: 3.505A pdb=" N ARG w 57 " --> pdb=" O ARG w 53 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 25 removed outlier: 3.633A pdb=" N LEU x 16 " --> pdb=" O ASP x 12 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N LYS x 17 " --> pdb=" O LEU x 13 " (cutoff:3.500A) Processing helix chain 'x' and resid 70 through 76 removed outlier: 4.525A pdb=" N PHE x 74 " --> pdb=" O LYS x 70 " (cutoff:3.500A) removed outlier: 4.718A 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 70 through 76' Processing helix chain 'y' and resid 4 through 41 removed outlier: 3.604A pdb=" N ILE y 12 " --> pdb=" O LYS y 8 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N SER y 23 " --> pdb=" O LYS y 19 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ARG y 24 " --> pdb=" O HIS y 20 " (cutoff:3.500A) Processing helix chain 'y' and resid 44 through 65 removed outlier: 4.245A pdb=" N GLU y 53 " --> pdb=" O LYS y 49 " (cutoff:3.500A) Proline residue: y 56 - end of helix removed outlier: 4.203A pdb=" N GLN y 61 " --> pdb=" O ILE y 57 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N ALA y 62 " --> pdb=" O VAL y 58 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N ALA y 63 " --> pdb=" O ASP y 59 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS y 64 " --> pdb=" O ARG y 60 " (cutoff:3.500A) Processing helix chain 'y' and resid 68 through 86 Processing helix chain 'z' and resid 11 through 27 Processing helix chain 'z' and resid 28 through 38 removed outlier: 3.591A pdb=" N VAL z 32 " --> pdb=" O VAL z 28 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ARG z 33 " --> pdb=" O LEU z 29 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ARG z 34 " --> pdb=" O ALA z 30 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N PHE z 37 " --> pdb=" O ARG z 33 " (cutoff:3.500A) removed outlier: 5.608A pdb=" N TYR z 38 " --> pdb=" O ARG z 34 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 69 removed outlier: 3.724A pdb=" N ARG z 66 " --> pdb=" O ARG z 62 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N ARG z 67 " --> pdb=" O GLU z 63 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N THR z 68 " --> pdb=" O ASN z 64 " (cutoff:3.500A) removed outlier: 5.345A pdb=" N ARG z 69 " --> pdb=" O ALA z 65 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '5' and resid 48 through 51 removed outlier: 5.043A pdb=" N LYS 5 48 " --> pdb=" O THR 5 71 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain '5' and resid 56 through 59 removed outlier: 4.194A pdb=" N PHE 5 64 " --> pdb=" O LEU 5 57 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ARG 5 59 " --> pdb=" O GLU 5 62 " (cutoff:3.500A) removed outlier: 5.951A pdb=" N GLU 5 62 " --> pdb=" O ARG 5 59 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '5' and resid 89 through 92 removed outlier: 3.968A pdb=" N LYS 5 89 " --> pdb=" O ALA 5 35 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA 5 35 " --> pdb=" O LYS 5 89 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N GLU 5 28 " --> pdb=" O VAL 5 129 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N VAL 5 129 " --> pdb=" O GLU 5 28 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ALA 5 32 " --> pdb=" O VAL 5 125 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N LYS 5 126 " --> pdb=" O LEU 5 114 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain '5' and resid 115 through 119 removed outlier: 4.001A pdb=" N SER 5 115 " --> pdb=" O LYS 5 126 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'A' and resid 51 through 54 removed outlier: 4.317A pdb=" N THR A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'A' and resid 65 through 71 Processing sheet with id= 7, first strand: chain 'B' and resid 2 through 5 Processing sheet with id= 8, first strand: chain 'B' and resid 80 through 83 removed outlier: 3.896A pdb=" N ARG B 80 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N LEU B 93 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N ILE B 74 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N SER B 118 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP B 114 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 138 through 142 removed outlier: 4.381A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR B 173 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 91 through 96 removed outlier: 4.686A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 11 through 16 removed outlier: 4.253A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N VAL C 26 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 201 " --> pdb=" O GLY C 6 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N SER C 199 " --> pdb=" O LYS C 8 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ASP C 200 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N THR C 112 " --> pdb=" O ASP C 200 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 79 through 84 removed outlier: 5.620A pdb=" N ARG C 46 " --> pdb=" O LEU C 84 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N GLN C 49 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N ASN C 32 " --> pdb=" O ILE C 96 " (cutoff:3.500A) removed outlier: 4.937A pdb=" N GLN C 94 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 179 through 182 Processing sheet with id= 14, first strand: chain 'C' and resid 105 through 108 removed outlier: 7.288A pdb=" N LYS C 105 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'D' and resid 1 through 6 removed outlier: 4.624A pdb=" N SER D 10 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'D' and resid 117 through 120 removed outlier: 5.884A pdb=" N ARG D 117 " --> pdb=" O ASP D 184 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'E' and resid 33 through 40 removed outlier: 3.669A pdb=" N CYS E 87 " --> pdb=" O MET E 38 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N VAL E 40 " --> pdb=" O ILE E 85 " (cutoff:3.500A) removed outlier: 5.307A pdb=" N ILE E 85 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 4.740A pdb=" N GLY E 86 " --> pdb=" O THR E 68 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'E' and resid 127 through 133 removed outlier: 4.444A pdb=" N TYR E 128 " --> pdb=" O ILE E 156 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'F' and resid 16 through 19 removed outlier: 4.744A pdb=" N ASP F 16 " --> pdb=" O LYS F 27 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LYS F 27 " --> pdb=" O ASP F 16 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LYS F 18 " --> pdb=" O THR F 25 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'F' and resid 41 through 45 removed outlier: 3.896A pdb=" N GLY F 53 " --> pdb=" O GLU F 42 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LYS F 44 " --> pdb=" O THR F 51 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'F' and resid 82 through 89 removed outlier: 5.925A pdb=" N THR F 129 " --> pdb=" O LEU F 89 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'F' and resid 94 through 98 Processing sheet with id= 23, first strand: chain 'G' and resid 17 through 20 removed outlier: 5.873A pdb=" N GLN G 2 " --> pdb=" O ALA G 39 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'G' and resid 128 through 134 removed outlier: 4.659A pdb=" N HIS G 128 " --> pdb=" O VAL G 144 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N PHE G 132 " --> pdb=" O ALA G 140 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL G 138 " --> pdb=" O VAL G 134 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'K' and resid 18 through 21 removed outlier: 3.703A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'M' and resid 63 through 66 removed outlier: 7.270A pdb=" N LEU M 102 " --> pdb=" O ARG M 66 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'M' and resid 71 through 74 Processing sheet with id= 28, first strand: chain 'N' and resid 33 through 37 removed outlier: 5.504A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) removed outlier: 9.035A pdb=" N TYR N 94 " --> pdb=" O VAL N 116 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'O' and resid 49 through 52 removed outlier: 4.164A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N HIS O 29 " --> pdb=" O TYR O 36 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG O 25 " --> pdb=" O ILE O 40 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'P' and resid 38 through 45 removed outlier: 5.168A pdb=" N ARG P 39 " --> pdb=" O VAL P 32 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'P' and resid 49 through 52 removed outlier: 3.867A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'R' and resid 11 through 15 Processing sheet with id= 33, first strand: chain 'R' and resid 18 through 22 removed outlier: 3.864A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'R' and resid 65 through 68 removed outlier: 3.636A pdb=" N GLY R 67 " --> pdb=" O PHE R 93 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'R' and resid 69 through 78 removed outlier: 5.320A pdb=" N GLU R 70 " --> pdb=" O GLN R 91 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLN R 91 " --> pdb=" O GLU R 70 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'S' and resid 2 through 8 removed outlier: 5.807A pdb=" N HIS S 102 " --> pdb=" O ASP S 77 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'S' and resid 79 through 88 No H-bonds generated for sheet with id= 37 Processing sheet with id= 38, first strand: chain 'T' and resid 28 through 33 removed outlier: 5.894A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N HIS T 70 " --> pdb=" O ARG T 73 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.549A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'U' and resid 40 through 45 No H-bonds generated for sheet with id= 39 Processing sheet with id= 40, first strand: chain 'U' and resid 83 through 87 Processing sheet with id= 41, first strand: chain 'V' and resid 69 through 72 removed outlier: 3.813A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'X' and resid 12 through 19 removed outlier: 3.669A pdb=" N ARG X 27 " --> pdb=" O GLY X 15 " (cutoff:3.500A) removed outlier: 4.506A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'Z' and resid 33 through 39 removed outlier: 4.156A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LYS Z 6 " --> pdb=" O GLU Z 58 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'c' and resid 8 through 13 removed outlier: 5.920A pdb=" N HIS c 19 " --> pdb=" O SER c 13 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'c' and resid 34 through 39 removed outlier: 5.949A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'e' and resid 22 through 25 removed outlier: 5.766A pdb=" N PHE e 22 " --> pdb=" O VAL e 50 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'f' and resid 13 through 19 removed outlier: 8.497A pdb=" N ASN f 13 " --> pdb=" O SER f 28 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'g' and resid 67 through 71 removed outlier: 4.111A pdb=" N VAL g 163 " --> pdb=" O PHE g 184 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'h' and resid 54 through 59 removed outlier: 3.903A pdb=" N VAL h 66 " --> pdb=" O GLN h 100 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'h' and resid 164 through 169 removed outlier: 6.009A pdb=" N ARG h 164 " --> pdb=" O GLY h 155 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY h 194 " --> pdb=" O THR h 191 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N VAL h 200 " --> pdb=" O ASN h 185 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASN h 185 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP h 183 " --> pdb=" O ILE h 202 " (cutoff:3.500A) removed outlier: 6.970A pdb=" N ASP h 181 " --> pdb=" O LYS h 204 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'i' and resid 140 through 145 removed outlier: 3.986A pdb=" N ASP i 141 " --> pdb=" O PHE i 182 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N PHE i 182 " --> pdb=" O ASP i 141 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N MET i 178 " --> pdb=" O ILE i 145 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N TRP i 170 " --> pdb=" O LYS i 183 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'j' and resid 12 through 16 removed outlier: 4.852A pdb=" N GLY j 40 " --> pdb=" O GLN j 12 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'j' and resid 84 through 88 removed outlier: 3.778A pdb=" N ALA j 99 " --> pdb=" O ASN j 122 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'j' and resid 33 through 40 Processing sheet with id= 55, first strand: chain 'k' and resid 38 through 42 removed outlier: 5.718A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'k' and resid 43 through 47 removed outlier: 3.748A pdb=" N GLY k 43 " --> pdb=" O TYR k 59 " (cutoff:3.500A) removed outlier: 7.104A pdb=" N HIS k 55 " --> pdb=" O LEU k 47 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'l' and resid 73 through 77 Processing sheet with id= 58, first strand: chain 'm' and resid 23 through 29 removed outlier: 6.521A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU m 60 " --> pdb=" O LYS m 50 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N LYS m 50 " --> pdb=" O GLU m 60 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'm' and resid 74 through 77 removed outlier: 3.866A pdb=" N CYS m 127 " --> pdb=" O VAL m 103 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'n' and resid 7 through 11 removed outlier: 3.510A pdb=" N ARG n 18 " --> pdb=" O THR n 66 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N PHE n 20 " --> pdb=" O TYR n 64 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N TYR n 64 " --> pdb=" O PHE n 20 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU n 61 " --> pdb=" O ASN n 25 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LYS n 27 " --> pdb=" O LEU n 61 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE n 65 " --> pdb=" O VAL n 29 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'o' and resid 39 through 42 removed outlier: 4.376A pdb=" N LEU o 71 " --> pdb=" O LEU o 42 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N ILE o 6 " --> pdb=" O ILE o 76 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ARG o 5 " --> pdb=" O GLY o 103 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'o' and resid 44 through 53 removed outlier: 7.837A pdb=" N ALA o 61 " --> pdb=" O ILE o 53 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'p' and resid 29 through 36 removed outlier: 4.319A pdb=" N ASN p 29 " --> pdb=" O SER p 26 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N ILE p 31 " --> pdb=" O HIS p 24 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N ASN p 109 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N GLY p 88 " --> pdb=" O VAL p 113 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'q' and resid 29 through 32 removed outlier: 4.834A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'q' and resid 36 through 41 removed outlier: 5.096A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'u' and resid 4 through 9 removed outlier: 5.981A pdb=" N PHE u 16 " --> pdb=" O HIS u 9 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL u 19 " --> pdb=" O GLY u 37 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY u 37 " --> pdb=" O VAL u 19 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'v' and resid 7 through 11 removed outlier: 7.127A pdb=" N GLU v 60 " --> pdb=" O VAL v 76 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'v' and resid 20 through 30 No H-bonds generated for sheet with id= 68 Processing sheet with id= 69, first strand: chain 'x' and resid 30 through 34 removed outlier: 3.681A pdb=" N THR x 33 " --> pdb=" O ALA x 50 " (cutoff:3.500A) 1753 hydrogen bonds defined for protein. 5190 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3582 hydrogen bonds 5624 hydrogen bond angles 0 basepair planarities 1421 basepair parallelities 2345 stacking parallelities Total time for adding SS restraints: 260.28 Time building geometry restraints manager: 72.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.08 - 1.22: 1000 1.22 - 1.37: 39898 1.37 - 1.52: 81336 1.52 - 1.66: 42275 1.66 - 1.81: 273 Bond restraints: 164782 Sorted by residual: bond pdb=" C5 5MU 1 747 " pdb=" C6 5MU 1 747 " ideal model delta sigma weight residual 1.155 1.436 -0.281 2.00e-02 2.50e+03 1.97e+02 bond pdb=" C5 5MU 4 341 " pdb=" C6 5MU 4 341 " ideal model delta sigma weight residual 1.155 1.435 -0.280 2.00e-02 2.50e+03 1.96e+02 bond pdb=" C5 5MU 11939 " pdb=" C6 5MU 11939 " ideal model delta sigma weight residual 1.155 1.434 -0.279 2.00e-02 2.50e+03 1.95e+02 bond pdb=" N PRO r 96 " pdb=" CD PRO r 96 " ideal model delta sigma weight residual 1.473 1.279 0.194 1.40e-02 5.10e+03 1.92e+02 bond pdb=" C ARG C 33 " pdb=" O ARG C 33 " ideal model delta sigma weight residual 1.236 1.076 0.160 1.20e-02 6.94e+03 1.77e+02 ... (remaining 164777 not shown) Histogram of bond angle deviations from ideal: 93.26 - 106.45: 29935 106.45 - 119.63: 141893 119.63 - 132.82: 74945 132.82 - 146.01: 67 146.01 - 159.19: 2 Bond angle restraints: 246842 Sorted by residual: angle pdb=" C1' OMG 12251 " pdb=" N9 OMG 12251 " pdb=" C4 OMG 12251 " ideal model delta sigma weight residual 108.29 159.19 -50.90 3.00e+00 1.11e-01 2.88e+02 angle pdb=" C1' OMG 12251 " pdb=" N9 OMG 12251 " pdb=" C8 OMG 12251 " ideal model delta sigma weight residual 142.82 93.26 49.56 3.00e+00 1.11e-01 2.73e+02 angle pdb=" N ILE r 73 " pdb=" CA ILE r 73 " pdb=" C ILE r 73 " ideal model delta sigma weight residual 110.62 123.14 -12.52 1.02e+00 9.61e-01 1.51e+02 angle pdb=" N LYS r 103 " pdb=" CA LYS r 103 " pdb=" C LYS r 103 " ideal model delta sigma weight residual 111.71 125.15 -13.44 1.15e+00 7.56e-01 1.37e+02 angle pdb=" N LEU C 100 " pdb=" CA LEU C 100 " pdb=" C LEU C 100 " ideal model delta sigma weight residual 112.54 126.19 -13.65 1.22e+00 6.72e-01 1.25e+02 ... (remaining 246837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.83: 92169 35.83 - 71.65: 11708 71.65 - 107.48: 1449 107.48 - 143.30: 50 143.30 - 179.13: 60 Dihedral angle restraints: 105436 sinusoidal: 88734 harmonic: 16702 Sorted by residual: dihedral pdb=" C4' G 12677 " pdb=" C3' G 12677 " pdb=" C2' G 12677 " pdb=" C1' G 12677 " ideal model delta sinusoidal sigma weight residual -35.00 34.12 -69.12 1 8.00e+00 1.56e-02 9.65e+01 dihedral pdb=" C4' G 3 51 " pdb=" C3' G 3 51 " pdb=" C2' G 3 51 " pdb=" C1' G 3 51 " ideal model delta sinusoidal sigma weight residual -35.00 34.04 -69.04 1 8.00e+00 1.56e-02 9.63e+01 dihedral pdb=" C5' G 12677 " pdb=" C4' G 12677 " pdb=" C3' G 12677 " pdb=" O3' G 12677 " ideal model delta sinusoidal sigma weight residual 147.00 78.58 68.42 1 8.00e+00 1.56e-02 9.48e+01 ... (remaining 105433 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.103: 30976 0.103 - 0.206: 413 0.206 - 0.309: 74 0.309 - 0.412: 25 0.412 - 0.515: 6 Chirality restraints: 31494 Sorted by residual: chirality pdb=" CA THR r 102 " pdb=" N THR r 102 " pdb=" C THR r 102 " pdb=" CB THR r 102 " both_signs ideal model delta sigma weight residual False 2.53 2.01 0.52 2.00e-01 2.50e+01 6.64e+00 chirality pdb=" CA LEU C 100 " pdb=" N LEU C 100 " pdb=" C LEU C 100 " pdb=" CB LEU C 100 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.59e+00 chirality pdb=" CA LYS C 154 " pdb=" N LYS C 154 " pdb=" C LYS C 154 " pdb=" CB LYS C 154 " both_signs ideal model delta sigma weight residual False 2.51 2.99 -0.48 2.00e-01 2.50e+01 5.67e+00 ... (remaining 31491 not shown) Planarity restraints: 12988 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MU 11939 " 0.932 2.00e-02 2.50e+03 6.09e-01 8.36e+03 pdb=" C4' 5MU 11939 " -0.192 2.00e-02 2.50e+03 pdb=" O4' 5MU 11939 " -0.808 2.00e-02 2.50e+03 pdb=" C3' 5MU 11939 " 0.236 2.00e-02 2.50e+03 pdb=" O3' 5MU 11939 " -0.885 2.00e-02 2.50e+03 pdb=" C2' 5MU 11939 " 0.608 2.00e-02 2.50e+03 pdb=" O2' 5MU 11939 " 0.599 2.00e-02 2.50e+03 pdb=" C1' 5MU 11939 " -0.466 2.00e-02 2.50e+03 pdb=" N1 5MU 11939 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21207 " 0.051 2.00e-02 2.50e+03 5.71e-01 7.34e+03 pdb=" C4' 2MG 21207 " 0.429 2.00e-02 2.50e+03 pdb=" O4' 2MG 21207 " 0.575 2.00e-02 2.50e+03 pdb=" C3' 2MG 21207 " -0.589 2.00e-02 2.50e+03 pdb=" O3' 2MG 21207 " -0.596 2.00e-02 2.50e+03 pdb=" C2' 2MG 21207 " -0.188 2.00e-02 2.50e+03 pdb=" O2' 2MG 21207 " 0.942 2.00e-02 2.50e+03 pdb=" C1' 2MG 21207 " 0.236 2.00e-02 2.50e+03 pdb=" N9 2MG 21207 " -0.860 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21516 " -0.046 2.00e-02 2.50e+03 5.58e-01 7.01e+03 pdb=" C4' 2MG 21516 " -0.423 2.00e-02 2.50e+03 pdb=" O4' 2MG 21516 " -0.550 2.00e-02 2.50e+03 pdb=" C3' 2MG 21516 " 0.588 2.00e-02 2.50e+03 pdb=" O3' 2MG 21516 " 0.575 2.00e-02 2.50e+03 pdb=" C2' 2MG 21516 " 0.196 2.00e-02 2.50e+03 pdb=" O2' 2MG 21516 " -0.930 2.00e-02 2.50e+03 pdb=" C1' 2MG 21516 " -0.237 2.00e-02 2.50e+03 pdb=" N9 2MG 21516 " 0.827 2.00e-02 2.50e+03 ... (remaining 12985 not shown) Histogram of nonbonded interaction distances: 0.85 - 1.66: 30 1.66 - 2.47: 1246 2.47 - 3.28: 157553 3.28 - 4.09: 481345 4.09 - 4.90: 722270 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1362444 Sorted by model distance: nonbonded pdb=" O3' A 11367 " pdb=" NZ LYS d 25 " model vdw 0.852 2.520 nonbonded pdb=" O3' U 12746 " pdb=" NZ LYS F 138 " model vdw 0.949 2.520 nonbonded pdb=" C3' U 12746 " pdb=" NZ LYS F 138 " model vdw 0.955 3.550 nonbonded pdb=" O3' U 12746 " pdb=" CE LYS F 138 " model vdw 1.146 3.440 nonbonded pdb=" OE1 GLU 5 28 " pdb=" CG2 VAL 5 129 " model vdw 1.191 3.460 ... (remaining 1362439 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 9.980 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: 0.140 Extract box with map and model: 29.550 Check model and map are aligned: 1.660 Set scattering table: 1.050 Process input model: 598.490 Find NCS groups from input model: 3.070 Set up NCS constraints: 0.400 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: 0.030 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 646.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7949 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 : 0.003 0.281 164782 Z= 0.181 Angle : 0.607 50.902 246842 Z= 0.346 Chirality : 0.033 0.515 31494 Planarity : 0.017 0.609 12988 Dihedral : 23.549 179.128 94662 Min Nonbonded Distance : 0.852 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.17 % Allowed : 5.09 % Favored : 94.74 % Rotamer: Outliers : 0.61 % Allowed : 5.61 % Favored : 93.78 % Cbeta Deviations : 0.35 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.11), residues: 5756 helix: 1.11 (0.13), residues: 1837 sheet: -1.04 (0.16), residues: 1058 loop : -1.72 (0.11), residues: 2861 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 78 HIS 0.003 0.000 HIS N 3 PHE 0.013 0.001 PHE N 80 TYR 0.009 0.001 TYR J 16 ARG 0.008 0.000 ARG C 33 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1983 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 1954 time to evaluate : 6.620 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: 5 31 GLU cc_start: 0.8147 (mp0) cc_final: 0.7847 (pp20) REVERT: 5 146 GLU cc_start: 0.7783 (tp30) cc_final: 0.7050 (tp30) REVERT: 5 151 LYS cc_start: 0.8928 (ttpp) cc_final: 0.8285 (ptmt) REVERT: A 44 LYS cc_start: 0.9264 (mtpp) cc_final: 0.8797 (mttm) REVERT: A 68 LYS cc_start: 0.8034 (tptt) cc_final: 0.7754 (tptt) REVERT: B 96 TYR cc_start: 0.7863 (m-80) cc_final: 0.7603 (m-80) REVERT: D 136 GLN cc_start: 0.8613 (tp40) cc_final: 0.8412 (tp40) REVERT: E 21 ASN cc_start: 0.8484 (t0) cc_final: 0.8211 (t0) REVERT: E 23 ASN cc_start: 0.8180 (p0) cc_final: 0.7802 (m110) REVERT: E 108 VAL cc_start: 0.4848 (OUTLIER) cc_final: 0.4619 (m) REVERT: F 75 MET cc_start: 0.8524 (ttp) cc_final: 0.8059 (ptm) REVERT: F 143 GLN cc_start: 0.8502 (tp40) cc_final: 0.8075 (tp40) REVERT: G 44 ILE cc_start: 0.8114 (tt) cc_final: 0.7717 (pt) REVERT: J 98 GLU cc_start: 0.8300 (pm20) cc_final: 0.8033 (pm20) REVERT: J 128 ASN cc_start: 0.8179 (p0) cc_final: 0.7601 (p0) REVERT: L 93 ASN cc_start: 0.9071 (m-40) cc_final: 0.8768 (m-40) REVERT: M 84 LYS cc_start: 0.8683 (mppt) cc_final: 0.8429 (mmtt) REVERT: N 43 GLU cc_start: 0.7364 (tp30) cc_final: 0.7153 (tp30) REVERT: O 17 LYS cc_start: 0.8841 (tptt) cc_final: 0.8310 (tptp) REVERT: O 47 VAL cc_start: 0.9202 (t) cc_final: 0.8368 (p) REVERT: O 48 LEU cc_start: 0.9113 (mt) cc_final: 0.8772 (mt) REVERT: O 69 ASP cc_start: 0.8727 (m-30) cc_final: 0.8460 (m-30) REVERT: O 76 LYS cc_start: 0.9048 (mmtt) cc_final: 0.8341 (mmtt) REVERT: P 83 SER cc_start: 0.8467 (m) cc_final: 0.8159 (t) REVERT: P 85 SER cc_start: 0.8420 (m) cc_final: 0.8168 (m) REVERT: Q 45 TYR cc_start: 0.8060 (m-10) cc_final: 0.7391 (m-10) REVERT: Q 85 LYS cc_start: 0.8155 (ttmm) cc_final: 0.7819 (mtpt) REVERT: R 15 SER cc_start: 0.8830 (t) cc_final: 0.8617 (p) REVERT: R 18 GLN cc_start: 0.8367 (pt0) cc_final: 0.8049 (pt0) REVERT: R 60 LYS cc_start: 0.7644 (mtmt) cc_final: 0.7418 (mttp) REVERT: S 15 GLN cc_start: 0.8201 (tt0) cc_final: 0.7959 (tt0) REVERT: S 94 ASP cc_start: 0.7027 (m-30) cc_final: 0.6749 (m-30) REVERT: T 11 LEU cc_start: 0.9031 (pt) cc_final: 0.8826 (pt) REVERT: T 43 ILE cc_start: 0.8467 (OUTLIER) cc_final: 0.8054 (mt) REVERT: U 37 GLU cc_start: 0.8866 (mp0) cc_final: 0.8385 (mp0) REVERT: V 51 GLN cc_start: 0.8559 (tm-30) cc_final: 0.8181 (tm-30) REVERT: X 20 HIS cc_start: 0.7701 (t-90) cc_final: 0.7468 (t-90) REVERT: X 66 THR cc_start: 0.9257 (p) cc_final: 0.8914 (p) REVERT: Y 10 SER cc_start: 0.8022 (t) cc_final: 0.7584 (t) REVERT: a 10 GLU cc_start: 0.7909 (pm20) cc_final: 0.7383 (pm20) REVERT: a 13 THR cc_start: 0.7630 (p) cc_final: 0.7295 (p) REVERT: b 17 ARG cc_start: 0.8176 (mtt180) cc_final: 0.7935 (mtt180) REVERT: c 45 GLN cc_start: 0.8354 (mm-40) cc_final: 0.8037 (mm-40) REVERT: f 31 PRO cc_start: 0.8917 (Cg_exo) cc_final: 0.8696 (Cg_endo) REVERT: g 18 HIS cc_start: 0.7584 (m90) cc_final: 0.7360 (m90) REVERT: g 32 PHE cc_start: 0.8215 (t80) cc_final: 0.7812 (t80) REVERT: g 44 GLU cc_start: 0.8588 (mt-10) cc_final: 0.8378 (pm20) REVERT: g 49 MET cc_start: 0.8550 (mtm) cc_final: 0.8074 (ptm) REVERT: g 105 LYS cc_start: 0.8880 (mttp) cc_final: 0.8270 (ttmt) REVERT: g 109 GLN cc_start: 0.9015 (mm-40) cc_final: 0.8428 (mp10) REVERT: g 175 GLU cc_start: 0.7872 (mt-10) cc_final: 0.7377 (mt-10) REVERT: h 42 TYR cc_start: 0.8598 (t80) cc_final: 0.8059 (t80) REVERT: h 44 THR cc_start: 0.9371 (m) cc_final: 0.9141 (p) REVERT: h 211 MET cc_start: 0.7337 (tpt) cc_final: 0.6967 (tpp) REVERT: i 70 ARG cc_start: 0.8252 (tpp80) cc_final: 0.7660 (tpp80) REVERT: i 73 ARG cc_start: 0.8635 (ttp80) cc_final: 0.8206 (ttp-110) REVERT: i 77 LYS cc_start: 0.9278 (mttm) cc_final: 0.8982 (mtmt) REVERT: j 20 ARG cc_start: 0.7920 (ttt-90) cc_final: 0.7702 (ttt-90) REVERT: j 50 TYR cc_start: 0.8404 (t80) cc_final: 0.8102 (t80) REVERT: j 134 ILE cc_start: 0.9207 (mp) cc_final: 0.8948 (mp) REVERT: j 142 ASP cc_start: 0.8424 (m-30) cc_final: 0.8173 (m-30) REVERT: k 25 TYR cc_start: 0.8491 (m-10) cc_final: 0.8218 (m-80) REVERT: k 44 ARG cc_start: 0.8224 (mtm110) cc_final: 0.7544 (mtm110) REVERT: k 56 LYS cc_start: 0.7689 (tttt) cc_final: 0.7218 (tttm) REVERT: k 97 THR cc_start: 0.9109 (p) cc_final: 0.8904 (p) REVERT: k 98 GLU cc_start: 0.8139 (mp0) cc_final: 0.7898 (mp0) REVERT: m 9 ASP cc_start: 0.8486 (t70) cc_final: 0.8271 (t0) REVERT: m 38 ASN cc_start: 0.8254 (m-40) cc_final: 0.7992 (m-40) REVERT: m 60 GLU cc_start: 0.8308 (tt0) cc_final: 0.8031 (tt0) REVERT: n 88 MET cc_start: 0.8569 (ttt) cc_final: 0.8367 (ptm) REVERT: n 128 SER cc_start: 0.7312 (p) cc_final: 0.6859 (t) REVERT: o 18 ILE cc_start: 0.7969 (tt) cc_final: 0.7748 (tp) REVERT: o 47 GLU cc_start: 0.7957 (tt0) cc_final: 0.7635 (tt0) REVERT: o 51 VAL cc_start: 0.9091 (t) cc_final: 0.8883 (p) REVERT: p 31 ILE cc_start: 0.9102 (mt) cc_final: 0.8857 (mm) REVERT: p 40 ASN cc_start: 0.8855 (m110) cc_final: 0.8556 (m-40) REVERT: p 77 TYR cc_start: 0.8879 (m-80) cc_final: 0.8636 (m-80) REVERT: p 108 THR cc_start: 0.8633 (p) cc_final: 0.8318 (p) REVERT: q 61 PHE cc_start: 0.8565 (m-80) cc_final: 0.8205 (m-80) REVERT: r 28 THR cc_start: 0.7925 (m) cc_final: 0.7684 (m) REVERT: r 90 ARG cc_start: 0.8200 (mmm160) cc_final: 0.7632 (mtm180) REVERT: r 100 GLN cc_start: 0.6504 (mp10) cc_final: 0.5300 (tm-30) REVERT: r 102 THR cc_start: 0.7677 (t) cc_final: 0.7345 (t) REVERT: s 20 TYR cc_start: 0.8793 (m-10) cc_final: 0.8424 (m-80) REVERT: s 61 ARG cc_start: 0.6439 (mmm-85) cc_final: 0.5707 (mmm160) REVERT: s 89 MET cc_start: 0.7591 (mmm) cc_final: 0.7274 (mmm) REVERT: s 98 LYS cc_start: 0.7975 (mmmm) cc_final: 0.7342 (mmmt) REVERT: t 80 GLN cc_start: 0.8576 (tm-30) cc_final: 0.8338 (tm-30) REVERT: u 12 LYS cc_start: 0.8447 (ttpt) cc_final: 0.8224 (tttt) REVERT: x 17 LYS cc_start: 0.8188 (mmtp) cc_final: 0.7965 (ptmt) REVERT: x 32 ARG cc_start: 0.6903 (ttm170) cc_final: 0.6143 (ttm-80) REVERT: x 34 TRP cc_start: 0.7810 (m-90) cc_final: 0.7333 (m-90) REVERT: y 28 MET cc_start: 0.8523 (ptm) cc_final: 0.8264 (ptm) REVERT: y 29 ARG cc_start: 0.8414 (mmt180) cc_final: 0.8162 (mmt90) REVERT: y 78 ASN cc_start: 0.9071 (m-40) cc_final: 0.8832 (m-40) REVERT: z 10 GLU cc_start: 0.7216 (mt-10) cc_final: 0.6986 (mm-30) REVERT: z 37 PHE cc_start: 0.8346 (m-10) cc_final: 0.7882 (m-10) REVERT: z 39 GLU cc_start: 0.7588 (pt0) cc_final: 0.7294 (pt0) REVERT: z 44 GLU cc_start: 0.8309 (tp30) cc_final: 0.8055 (tp30) outliers start: 29 outliers final: 9 residues processed: 1972 average time/residue: 1.5165 time to fit residues: 5144.4221 Evaluate side-chains 1301 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 1290 time to evaluate : 6.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain m residue 72 VAL Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain p residue 32 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 890 optimal weight: 7.9990 chunk 798 optimal weight: 10.0000 chunk 443 optimal weight: 20.0000 chunk 272 optimal weight: 10.0000 chunk 538 optimal weight: 0.5980 chunk 426 optimal weight: 20.0000 chunk 826 optimal weight: 10.0000 chunk 319 optimal weight: 10.0000 chunk 502 optimal weight: 5.9990 chunk 614 optimal weight: 1.9990 chunk 957 optimal weight: 8.9990 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 22 HIS C 32 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN C 148 GLN C 150 GLN C 173 GLN D 30 GLN E 52 ASN F 115 HIS G 33 GLN K 3 GLN K 93 GLN L 54 GLN ** N 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 34 HIS ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** S 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 75 GLN X 23 ASN Y 39 GLN b 6 ASN e 31 HIS f 35 GLN ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 146 ASN g 168 HIS h 19 ASN h 69 HIS h 123 GLN h 176 HIS ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 63 ASN ** l 86 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 67 GLN n 110 GLN o 58 ASN ** q 5 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 66 GLN ** v 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 61 GLN z 56 HIS Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.136 164782 Z= 0.319 Angle : 0.725 16.944 246842 Z= 0.376 Chirality : 0.038 0.365 31494 Planarity : 0.007 0.140 12988 Dihedral : 24.442 179.944 83136 Min Nonbonded Distance : 0.970 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.62 % Favored : 93.31 % Rotamer: Outliers : 4.15 % Allowed : 15.88 % Favored : 79.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.11), residues: 5756 helix: 0.65 (0.12), residues: 1865 sheet: -0.97 (0.16), residues: 1064 loop : -1.79 (0.11), residues: 2827 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP 5 39 HIS 0.012 0.002 HIS N 3 PHE 0.030 0.002 PHE E 138 TYR 0.023 0.002 TYR h 42 ARG 0.013 0.001 ARG y 10 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1532 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1333 time to evaluate : 6.498 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 31 GLU cc_start: 0.8360 (mp0) cc_final: 0.8090 (mp0) REVERT: 5 37 GLN cc_start: 0.7376 (mp10) cc_final: 0.6855 (mp10) REVERT: 5 69 ASN cc_start: 0.8840 (t0) cc_final: 0.8335 (t0) REVERT: 5 90 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8487 (mm) REVERT: 5 146 GLU cc_start: 0.7902 (tp30) cc_final: 0.7096 (tp30) REVERT: A 43 THR cc_start: 0.9329 (m) cc_final: 0.8908 (p) REVERT: A 44 LYS cc_start: 0.9394 (mtpp) cc_final: 0.8835 (mttm) REVERT: B 52 ARG cc_start: 0.7586 (ptt90) cc_final: 0.7311 (ptt90) REVERT: B 96 TYR cc_start: 0.8263 (m-80) cc_final: 0.7853 (m-80) REVERT: B 133 ARG cc_start: 0.7955 (mtp85) cc_final: 0.7528 (mtt90) REVERT: B 201 MET cc_start: 0.8703 (ptm) cc_final: 0.8500 (ptp) REVERT: D 1 MET cc_start: 0.7364 (ttm) cc_final: 0.7004 (ttm) REVERT: E 21 ASN cc_start: 0.8509 (t0) cc_final: 0.8214 (t0) REVERT: E 23 ASN cc_start: 0.8536 (p0) cc_final: 0.8035 (m110) REVERT: E 99 PHE cc_start: 0.8759 (t80) cc_final: 0.8067 (t80) REVERT: F 143 GLN cc_start: 0.8480 (tp40) cc_final: 0.8020 (tp40) REVERT: J 92 MET cc_start: 0.7535 (tpt) cc_final: 0.7302 (mmt) REVERT: J 98 GLU cc_start: 0.8523 (pm20) cc_final: 0.8175 (pm20) REVERT: J 106 LYS cc_start: 0.8927 (tmtt) cc_final: 0.8699 (tttm) REVERT: J 130 HIS cc_start: 0.6907 (t-90) cc_final: 0.6618 (t-170) REVERT: K 82 ASN cc_start: 0.7756 (OUTLIER) cc_final: 0.7312 (m-40) REVERT: N 43 GLU cc_start: 0.7524 (tp30) cc_final: 0.7307 (tp30) REVERT: O 76 LYS cc_start: 0.9060 (mmtt) cc_final: 0.8616 (mmtt) REVERT: O 98 GLN cc_start: 0.8695 (tm-30) cc_final: 0.8342 (tm-30) REVERT: R 60 LYS cc_start: 0.8341 (mtmt) cc_final: 0.8102 (mttp) REVERT: S 109 ASP cc_start: 0.8075 (t0) cc_final: 0.7835 (t0) REVERT: U 18 ASP cc_start: 0.7771 (p0) cc_final: 0.7306 (p0) REVERT: X 68 LEU cc_start: 0.9166 (mt) cc_final: 0.8916 (mt) REVERT: Z 40 ASP cc_start: 0.8161 (t0) cc_final: 0.7898 (t0) REVERT: a 31 ASP cc_start: 0.7923 (m-30) cc_final: 0.7528 (t0) REVERT: c 50 LYS cc_start: 0.8971 (mtpt) cc_final: 0.8724 (mmtp) REVERT: g 15 HIS cc_start: 0.8298 (m90) cc_final: 0.8082 (m90) REVERT: g 18 HIS cc_start: 0.7598 (m90) cc_final: 0.7353 (m90) REVERT: g 32 PHE cc_start: 0.8259 (t80) cc_final: 0.7896 (t80) REVERT: g 44 GLU cc_start: 0.8737 (mt-10) cc_final: 0.8516 (pm20) REVERT: g 49 MET cc_start: 0.8648 (mtm) cc_final: 0.8138 (mpp) REVERT: g 88 ASP cc_start: 0.8776 (t70) cc_final: 0.8543 (t0) REVERT: g 100 MET cc_start: 0.8934 (mmm) cc_final: 0.8709 (mmm) REVERT: g 105 LYS cc_start: 0.9039 (mttp) cc_final: 0.8288 (mmtt) REVERT: g 109 GLN cc_start: 0.8986 (mm-40) cc_final: 0.8418 (mp10) REVERT: h 168 TYR cc_start: 0.8016 (m-80) cc_final: 0.7795 (m-80) REVERT: h 182 ILE cc_start: 0.9018 (mm) cc_final: 0.8818 (mm) REVERT: h 211 MET cc_start: 0.7159 (tpt) cc_final: 0.6894 (tpp) REVERT: i 73 ARG cc_start: 0.8708 (ttp80) cc_final: 0.8428 (ttp-170) REVERT: i 77 LYS cc_start: 0.9334 (mttm) cc_final: 0.9043 (mtmt) REVERT: i 81 ARG cc_start: 0.8891 (ttp80) cc_final: 0.8511 (ptm-80) REVERT: j 50 TYR cc_start: 0.8400 (t80) cc_final: 0.8164 (t80) REVERT: j 66 LYS cc_start: 0.9249 (mttp) cc_final: 0.8993 (mmtt) REVERT: j 142 ASP cc_start: 0.8456 (m-30) cc_final: 0.8227 (m-30) REVERT: k 24 ARG cc_start: 0.8925 (ttm110) cc_final: 0.8692 (ptp-110) REVERT: k 25 TYR cc_start: 0.8609 (m-10) cc_final: 0.8206 (m-80) REVERT: k 97 THR cc_start: 0.9199 (p) cc_final: 0.8985 (p) REVERT: l 59 LEU cc_start: 0.6664 (OUTLIER) cc_final: 0.6197 (tp) REVERT: m 52 GLU cc_start: 0.6209 (pm20) cc_final: 0.5689 (pm20) REVERT: n 21 ILE cc_start: 0.6665 (OUTLIER) cc_final: 0.6342 (pt) REVERT: n 52 LEU cc_start: 0.9450 (mt) cc_final: 0.9139 (pp) REVERT: n 128 SER cc_start: 0.8006 (p) cc_final: 0.7314 (t) REVERT: o 57 VAL cc_start: 0.8571 (m) cc_final: 0.8352 (m) REVERT: o 99 GLN cc_start: 0.8222 (pt0) cc_final: 0.7999 (pm20) REVERT: p 31 ILE cc_start: 0.9167 (mt) cc_final: 0.8873 (mm) REVERT: p 83 GLU cc_start: 0.7960 (mp0) cc_final: 0.7462 (mp0) REVERT: p 101 ASN cc_start: 0.8301 (t0) cc_final: 0.7995 (t0) REVERT: r 72 GLU cc_start: 0.9131 (tm-30) cc_final: 0.8924 (pt0) REVERT: r 90 ARG cc_start: 0.8369 (mmm160) cc_final: 0.7679 (mtm180) REVERT: r 100 GLN cc_start: 0.6340 (mp10) cc_final: 0.5113 (tm-30) REVERT: s 61 ARG cc_start: 0.7218 (mmm-85) cc_final: 0.6335 (mmm160) REVERT: s 82 ILE cc_start: 0.6891 (OUTLIER) cc_final: 0.6581 (mt) REVERT: t 80 GLN cc_start: 0.8677 (tm-30) cc_final: 0.8311 (tm-30) REVERT: u 12 LYS cc_start: 0.8752 (ttpt) cc_final: 0.8518 (ttmm) REVERT: u 51 ARG cc_start: 0.7140 (ttp-170) cc_final: 0.6781 (ttm170) REVERT: x 32 ARG cc_start: 0.7500 (ttm170) cc_final: 0.6896 (ttm-80) REVERT: y 13 GLN cc_start: 0.8377 (mm110) cc_final: 0.8086 (mt0) REVERT: y 27 MET cc_start: 0.8273 (mtp) cc_final: 0.7946 (mtt) REVERT: y 78 ASN cc_start: 0.9083 (m-40) cc_final: 0.8745 (m110) REVERT: z 37 PHE cc_start: 0.8343 (m-10) cc_final: 0.7844 (m-10) REVERT: z 39 GLU cc_start: 0.7788 (pt0) cc_final: 0.7397 (pt0) REVERT: z 44 GLU cc_start: 0.8594 (tp30) cc_final: 0.8161 (tp30) REVERT: z 59 LYS cc_start: 0.8328 (mmtp) cc_final: 0.7941 (mmtp) outliers start: 199 outliers final: 141 residues processed: 1438 average time/residue: 1.3286 time to fit residues: 3333.5808 Evaluate side-chains 1340 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 1194 time to evaluate : 6.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 60 ASP Chi-restraints excluded: chain 5 residue 85 THR Chi-restraints excluded: chain 5 residue 90 LEU Chi-restraints excluded: chain 5 residue 92 LEU Chi-restraints excluded: chain 5 residue 120 ASN Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 84 LEU Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 108 VAL Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 9 VAL Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain O residue 116 GLN Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 74 ILE Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 87 GLN Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 40 ILE Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 70 ILE Chi-restraints excluded: chain V residue 79 ARG Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 27 THR Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 61 CYS Chi-restraints excluded: chain f residue 35 GLN Chi-restraints excluded: chain g residue 136 MET Chi-restraints excluded: chain h residue 25 ASN Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain i residue 30 THR Chi-restraints excluded: chain i residue 100 ASN Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain j residue 73 ASN Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain l residue 42 ILE Chi-restraints excluded: chain l residue 43 VAL Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 122 ASN Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain m residue 2 SER Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 55 THR Chi-restraints excluded: chain m residue 72 VAL Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 91 ASP Chi-restraints excluded: chain n residue 110 GLN Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 81 ASN Chi-restraints excluded: chain q residue 4 VAL Chi-restraints excluded: chain q residue 49 LEU Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain r residue 95 LEU Chi-restraints excluded: chain s residue 30 ILE Chi-restraints excluded: chain s residue 76 LYS Chi-restraints excluded: chain s residue 82 ILE Chi-restraints excluded: chain t residue 25 THR Chi-restraints excluded: chain u residue 23 ASP Chi-restraints excluded: chain v residue 6 ARG Chi-restraints excluded: chain v residue 8 LEU Chi-restraints excluded: chain v residue 41 THR Chi-restraints excluded: chain v residue 50 ASN Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain w residue 25 ASP Chi-restraints excluded: chain w residue 40 VAL Chi-restraints excluded: chain x residue 4 SER Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain y residue 58 VAL Chi-restraints excluded: chain y residue 80 THR Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 28 VAL Chi-restraints excluded: chain z residue 43 THR Chi-restraints excluded: chain z residue 56 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 531 optimal weight: 10.0000 chunk 297 optimal weight: 20.0000 chunk 796 optimal weight: 8.9990 chunk 651 optimal weight: 5.9990 chunk 264 optimal weight: 10.0000 chunk 958 optimal weight: 9.9990 chunk 1035 optimal weight: 20.0000 chunk 853 optimal weight: 1.9990 chunk 950 optimal weight: 5.9990 chunk 326 optimal weight: 10.0000 chunk 769 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 22 HIS B 46 ASN B 134 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN C 130 GLN ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 94 GLN E 81 GLN F 116 GLN G 28 ASN ** G 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 82 HIS R 86 GLN S 40 ASN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 78 GLN ** X 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN f 35 GLN ** g 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 131 ASN ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 86 GLN l 148 ASN n 50 GLN v 51 ASN ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 3 ASN y 61 GLN ** z 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.104 164782 Z= 0.347 Angle : 0.711 15.128 246842 Z= 0.372 Chirality : 0.039 0.402 31494 Planarity : 0.007 0.138 12988 Dihedral : 24.500 179.605 83133 Min Nonbonded Distance : 0.952 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.37 % Favored : 92.58 % Rotamer: Outliers : 5.67 % Allowed : 17.84 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.11), residues: 5756 helix: 0.38 (0.12), residues: 1875 sheet: -1.07 (0.16), residues: 1076 loop : -1.84 (0.11), residues: 2805 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 78 HIS 0.049 0.002 HIS e 31 PHE 0.028 0.002 PHE A 26 TYR 0.021 0.002 TYR z 71 ARG 0.016 0.001 ARG r 70 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1524 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1252 time to evaluate : 6.458 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: 5 31 GLU cc_start: 0.8388 (mp0) cc_final: 0.8126 (mp0) REVERT: 5 69 ASN cc_start: 0.8763 (t0) cc_final: 0.8185 (t0) REVERT: 5 146 GLU cc_start: 0.7833 (tp30) cc_final: 0.7273 (tp30) REVERT: 5 157 ASN cc_start: 0.8698 (m110) cc_final: 0.8447 (m110) REVERT: A 43 THR cc_start: 0.9345 (m) cc_final: 0.8907 (p) REVERT: A 44 LYS cc_start: 0.9364 (mtpp) cc_final: 0.8883 (mttm) REVERT: B 133 ARG cc_start: 0.8065 (mtp85) cc_final: 0.7605 (mmt90) REVERT: D 1 MET cc_start: 0.7403 (ttm) cc_final: 0.7083 (ttm) REVERT: D 145 ASP cc_start: 0.8044 (OUTLIER) cc_final: 0.7658 (p0) REVERT: D 149 ILE cc_start: 0.9439 (OUTLIER) cc_final: 0.9224 (mm) REVERT: E 21 ASN cc_start: 0.8684 (t0) cc_final: 0.8110 (t0) REVERT: E 23 ASN cc_start: 0.8511 (p0) cc_final: 0.8133 (m110) REVERT: E 99 PHE cc_start: 0.8734 (t80) cc_final: 0.8093 (t80) REVERT: J 37 ARG cc_start: 0.8773 (OUTLIER) cc_final: 0.7390 (ttm170) REVERT: J 106 LYS cc_start: 0.8970 (tmtt) cc_final: 0.8754 (tttm) REVERT: K 69 VAL cc_start: 0.9045 (OUTLIER) cc_final: 0.8799 (m) REVERT: O 17 LYS cc_start: 0.8927 (tptt) cc_final: 0.8597 (tptp) REVERT: O 56 LYS cc_start: 0.8391 (mmtm) cc_final: 0.7742 (mmtm) REVERT: O 76 LYS cc_start: 0.9208 (mmtt) cc_final: 0.8735 (mmtt) REVERT: O 98 GLN cc_start: 0.8706 (tm-30) cc_final: 0.8153 (tm-30) REVERT: S 77 ASP cc_start: 0.8198 (m-30) cc_final: 0.7308 (t0) REVERT: S 109 ASP cc_start: 0.8157 (t0) cc_final: 0.7932 (t0) REVERT: U 61 LYS cc_start: 0.9266 (OUTLIER) cc_final: 0.8979 (mtmt) REVERT: U 62 GLU cc_start: 0.7899 (pm20) cc_final: 0.7693 (pm20) REVERT: a 31 ASP cc_start: 0.7902 (m-30) cc_final: 0.7660 (t0) REVERT: c 50 LYS cc_start: 0.8811 (mtpt) cc_final: 0.8409 (mmtm) REVERT: g 7 ARG cc_start: 0.8855 (tpp-160) cc_final: 0.8651 (tpp-160) REVERT: g 18 HIS cc_start: 0.7550 (m90) cc_final: 0.7250 (m90) REVERT: g 32 PHE cc_start: 0.8273 (t80) cc_final: 0.7977 (t80) REVERT: g 44 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8346 (mp0) REVERT: g 49 MET cc_start: 0.8571 (mtm) cc_final: 0.8291 (ptp) REVERT: g 100 MET cc_start: 0.9041 (mmm) cc_final: 0.8807 (mmm) REVERT: g 105 LYS cc_start: 0.9105 (mttp) cc_final: 0.8671 (mmtt) REVERT: g 154 MET cc_start: 0.7617 (mpp) cc_final: 0.7330 (mpp) REVERT: h 58 GLU cc_start: 0.7550 (mp0) cc_final: 0.7247 (mp0) REVERT: h 168 TYR cc_start: 0.8032 (m-80) cc_final: 0.7759 (m-80) REVERT: h 193 TYR cc_start: 0.8279 (m-80) cc_final: 0.7986 (m-80) REVERT: h 211 MET cc_start: 0.7087 (tpt) cc_final: 0.6844 (tpp) REVERT: i 73 ARG cc_start: 0.8661 (ttp80) cc_final: 0.8313 (ttp-170) REVERT: i 77 LYS cc_start: 0.9339 (mttm) cc_final: 0.9041 (mtmt) REVERT: j 66 LYS cc_start: 0.9303 (mttp) cc_final: 0.8972 (mmtt) REVERT: k 5 GLU cc_start: 0.7532 (tp30) cc_final: 0.7226 (tp30) REVERT: k 25 TYR cc_start: 0.8546 (m-10) cc_final: 0.8248 (m-80) REVERT: l 31 MET cc_start: 0.8283 (tmm) cc_final: 0.8017 (tmm) REVERT: l 59 LEU cc_start: 0.6572 (OUTLIER) cc_final: 0.6058 (tp) REVERT: m 43 GLU cc_start: 0.8618 (mm-30) cc_final: 0.8294 (mm-30) REVERT: n 38 TYR cc_start: 0.6919 (OUTLIER) cc_final: 0.6521 (m-80) REVERT: n 89 GLU cc_start: 0.8588 (pp20) cc_final: 0.8099 (pp20) REVERT: n 110 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.7980 (pm20) REVERT: n 120 LYS cc_start: 0.8217 (mtmm) cc_final: 0.7884 (mtmm) REVERT: n 128 SER cc_start: 0.8134 (p) cc_final: 0.7448 (t) REVERT: o 82 LYS cc_start: 0.8039 (ttpp) cc_final: 0.7750 (ttpp) REVERT: o 99 GLN cc_start: 0.8432 (pt0) cc_final: 0.8065 (pm20) REVERT: p 18 ASP cc_start: 0.8260 (p0) cc_final: 0.7784 (p0) REVERT: p 31 ILE cc_start: 0.9241 (mt) cc_final: 0.8921 (mm) REVERT: p 83 GLU cc_start: 0.8025 (mp0) cc_final: 0.7615 (mp0) REVERT: p 101 ASN cc_start: 0.8471 (t0) cc_final: 0.8217 (t0) REVERT: r 90 ARG cc_start: 0.8303 (mmm160) cc_final: 0.7661 (mtm180) REVERT: s 61 ARG cc_start: 0.7113 (mmm-85) cc_final: 0.6886 (mmm160) REVERT: t 80 GLN cc_start: 0.8757 (tm-30) cc_final: 0.8328 (tm-30) REVERT: x 17 LYS cc_start: 0.8045 (mttm) cc_final: 0.7598 (ptmt) REVERT: x 32 ARG cc_start: 0.7488 (ttm170) cc_final: 0.6957 (ttm-80) REVERT: x 37 ARG cc_start: 0.8020 (ptt180) cc_final: 0.7773 (ptt180) REVERT: y 13 GLN cc_start: 0.8356 (mm110) cc_final: 0.8081 (mp10) REVERT: y 78 ASN cc_start: 0.9076 (m-40) cc_final: 0.8736 (m110) REVERT: z 4 ILE cc_start: 0.8107 (mp) cc_final: 0.7859 (mp) REVERT: z 39 GLU cc_start: 0.7863 (pt0) cc_final: 0.7487 (pt0) REVERT: z 44 GLU cc_start: 0.8601 (tp30) cc_final: 0.8094 (tp30) outliers start: 272 outliers final: 193 residues processed: 1409 average time/residue: 1.3349 time to fit residues: 3300.3703 Evaluate side-chains 1351 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1150 time to evaluate : 5.752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 14 ILE Chi-restraints excluded: chain 5 residue 60 ASP Chi-restraints excluded: chain 5 residue 85 THR Chi-restraints excluded: chain 5 residue 87 THR Chi-restraints excluded: chain 5 residue 92 LEU Chi-restraints excluded: chain 5 residue 120 ASN Chi-restraints excluded: chain 5 residue 127 ILE Chi-restraints excluded: chain 5 residue 141 ASP Chi-restraints excluded: chain A residue 23 VAL Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 25 THR Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 37 ARG Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 76 VAL Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain O residue 116 GLN Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 74 ILE Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 86 GLN Chi-restraints excluded: chain R residue 87 GLN Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 61 LYS Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 79 ARG Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain Y residue 50 VAL Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 27 THR Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain g residue 114 LEU Chi-restraints excluded: chain h residue 31 ASP Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain i residue 30 THR Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 174 ASP Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain i residue 203 LEU Chi-restraints excluded: chain j residue 43 ASN Chi-restraints excluded: chain j residue 56 VAL Chi-restraints excluded: chain j residue 73 ASN Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 42 ILE Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 84 THR Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 122 ASN Chi-restraints excluded: chain m residue 2 SER Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 55 THR Chi-restraints excluded: chain m residue 72 VAL Chi-restraints excluded: chain m residue 76 GLN Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain n residue 7 TYR Chi-restraints excluded: chain n residue 38 TYR Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 66 THR Chi-restraints excluded: chain n residue 91 ASP Chi-restraints excluded: chain n residue 110 GLN Chi-restraints excluded: chain o residue 24 GLU Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 50 THR Chi-restraints excluded: chain o residue 69 THR Chi-restraints excluded: chain o residue 73 LEU Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 75 LYS Chi-restraints excluded: chain p residue 80 LYS Chi-restraints excluded: chain p residue 81 ASN Chi-restraints excluded: chain p residue 108 THR Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 102 LEU Chi-restraints excluded: chain r residue 31 LYS Chi-restraints excluded: chain r residue 105 ASN Chi-restraints excluded: chain s residue 30 ILE Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain s residue 76 LYS Chi-restraints excluded: chain t residue 13 SER Chi-restraints excluded: chain u residue 23 ASP Chi-restraints excluded: chain v residue 6 ARG Chi-restraints excluded: chain v residue 50 ASN Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain w residue 25 ASP Chi-restraints excluded: chain w residue 34 THR Chi-restraints excluded: chain w residue 55 LEU Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain w residue 74 HIS Chi-restraints excluded: chain x residue 4 SER Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 15 LEU Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 67 VAL Chi-restraints excluded: chain y residue 58 VAL Chi-restraints excluded: chain y residue 67 ILE Chi-restraints excluded: chain y residue 80 THR Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 28 VAL Chi-restraints excluded: chain z residue 43 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 947 optimal weight: 4.9990 chunk 720 optimal weight: 7.9990 chunk 497 optimal weight: 4.9990 chunk 106 optimal weight: 50.0000 chunk 457 optimal weight: 20.0000 chunk 643 optimal weight: 5.9990 chunk 962 optimal weight: 5.9990 chunk 1018 optimal weight: 0.2980 chunk 502 optimal weight: 5.9990 chunk 912 optimal weight: 20.0000 chunk 274 optimal weight: 10.0000 overall best weight: 4.4588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 157 ASN B 134 ASN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN C 130 GLN ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 133 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS K 93 GLN ** M 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN Q 56 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 86 GLN S 7 HIS ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN a 33 ASN ** g 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 3 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** n 110 GLN ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 40 ASN ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 51 ASN ** x 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 61 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.3868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 164782 Z= 0.268 Angle : 0.663 15.281 246842 Z= 0.350 Chirality : 0.036 0.380 31494 Planarity : 0.006 0.130 12988 Dihedral : 24.484 179.533 83132 Min Nonbonded Distance : 0.968 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.38 % Favored : 92.56 % Rotamer: Outliers : 5.36 % Allowed : 19.49 % Favored : 75.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.11), residues: 5756 helix: 0.48 (0.12), residues: 1871 sheet: -1.00 (0.16), residues: 1070 loop : -1.79 (0.11), residues: 2815 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP k 42 HIS 0.015 0.001 HIS e 31 PHE 0.027 0.002 PHE m 66 TYR 0.025 0.002 TYR c 49 ARG 0.010 0.001 ARG a 25 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1495 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 257 poor density : 1238 time to evaluate : 6.580 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: 5 40 GLU cc_start: 0.8281 (mt-10) cc_final: 0.7658 (mp0) REVERT: 5 69 ASN cc_start: 0.8763 (t0) cc_final: 0.8187 (t0) REVERT: 5 134 LYS cc_start: 0.8479 (OUTLIER) cc_final: 0.8154 (mtmt) REVERT: A 43 THR cc_start: 0.9336 (m) cc_final: 0.8875 (p) REVERT: A 44 LYS cc_start: 0.9336 (mtpp) cc_final: 0.8747 (mttm) REVERT: B 96 TYR cc_start: 0.8828 (m-80) cc_final: 0.8508 (m-80) REVERT: B 133 ARG cc_start: 0.8069 (mtp85) cc_final: 0.7613 (mmt90) REVERT: B 163 GLN cc_start: 0.8183 (tp-100) cc_final: 0.7945 (tp-100) REVERT: D 1 MET cc_start: 0.7397 (ttm) cc_final: 0.7174 (ttm) REVERT: E 8 TYR cc_start: 0.8049 (m-80) cc_final: 0.6920 (m-80) REVERT: E 17 MET cc_start: 0.8492 (mtp) cc_final: 0.8279 (mtp) REVERT: E 21 ASN cc_start: 0.8703 (t0) cc_final: 0.8080 (t0) REVERT: E 23 ASN cc_start: 0.8451 (p0) cc_final: 0.8149 (m110) REVERT: E 99 PHE cc_start: 0.8778 (t80) cc_final: 0.8163 (t80) REVERT: F 143 GLN cc_start: 0.8966 (tp-100) cc_final: 0.8517 (tp40) REVERT: J 106 LYS cc_start: 0.8918 (tmtt) cc_final: 0.8703 (tttm) REVERT: K 69 VAL cc_start: 0.9038 (OUTLIER) cc_final: 0.8794 (m) REVERT: K 82 ASN cc_start: 0.7617 (OUTLIER) cc_final: 0.7285 (m-40) REVERT: L 12 SER cc_start: 0.8846 (t) cc_final: 0.8377 (p) REVERT: O 17 LYS cc_start: 0.8954 (tptt) cc_final: 0.8639 (tptp) REVERT: O 76 LYS cc_start: 0.8958 (mmtt) cc_final: 0.8723 (mmtt) REVERT: O 98 GLN cc_start: 0.8760 (tm-30) cc_final: 0.8185 (tm-30) REVERT: P 31 TRP cc_start: 0.8307 (m100) cc_final: 0.7869 (m100) REVERT: S 77 ASP cc_start: 0.8198 (OUTLIER) cc_final: 0.7272 (t0) REVERT: S 109 ASP cc_start: 0.8070 (t0) cc_final: 0.7798 (t0) REVERT: T 42 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7989 (mt-10) REVERT: U 61 LYS cc_start: 0.9288 (OUTLIER) cc_final: 0.8966 (mtmt) REVERT: V 48 MET cc_start: 0.8645 (tpp) cc_final: 0.8061 (tpp) REVERT: a 11 GLU cc_start: 0.8279 (tp30) cc_final: 0.8029 (tp30) REVERT: a 25 ARG cc_start: 0.7952 (mmm-85) cc_final: 0.7411 (mmm-85) REVERT: g 7 ARG cc_start: 0.8838 (tpp-160) cc_final: 0.8608 (tpp-160) REVERT: g 18 HIS cc_start: 0.7680 (m90) cc_final: 0.7360 (m90) REVERT: g 24 ASN cc_start: 0.9301 (t0) cc_final: 0.8997 (t0) REVERT: g 32 PHE cc_start: 0.8241 (t80) cc_final: 0.8037 (t80) REVERT: g 44 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8367 (mp0) REVERT: g 49 MET cc_start: 0.8625 (mtm) cc_final: 0.8219 (mpp) REVERT: g 100 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8841 (mmm) REVERT: h 58 GLU cc_start: 0.7498 (mp0) cc_final: 0.7179 (mp0) REVERT: h 168 TYR cc_start: 0.8143 (m-80) cc_final: 0.7690 (m-80) REVERT: h 193 TYR cc_start: 0.8357 (m-80) cc_final: 0.8134 (m-80) REVERT: h 211 MET cc_start: 0.7008 (tpt) cc_final: 0.6742 (tpp) REVERT: i 73 ARG cc_start: 0.8687 (ttp80) cc_final: 0.8331 (ttp-110) REVERT: i 77 LYS cc_start: 0.9325 (mttm) cc_final: 0.9023 (mtmt) REVERT: j 23 LYS cc_start: 0.8642 (tttt) cc_final: 0.8409 (tttt) REVERT: j 66 LYS cc_start: 0.9287 (mttp) cc_final: 0.8992 (mmtt) REVERT: j 146 ASN cc_start: 0.8305 (p0) cc_final: 0.8057 (p0) REVERT: k 5 GLU cc_start: 0.7696 (tp30) cc_final: 0.7315 (tp30) REVERT: k 24 ARG cc_start: 0.8915 (ttm110) cc_final: 0.8673 (ptp-110) REVERT: k 25 TYR cc_start: 0.8483 (m-10) cc_final: 0.8167 (m-80) REVERT: k 61 LEU cc_start: 0.8965 (tt) cc_final: 0.8758 (tp) REVERT: k 90 MET cc_start: 0.7763 (mmm) cc_final: 0.7450 (mmm) REVERT: l 31 MET cc_start: 0.8241 (tmm) cc_final: 0.7950 (tmm) REVERT: l 59 LEU cc_start: 0.6624 (OUTLIER) cc_final: 0.6076 (tp) REVERT: l 101 MET cc_start: 0.8957 (mmm) cc_final: 0.8505 (mpp) REVERT: l 144 MET cc_start: 0.6877 (mtt) cc_final: 0.6199 (mmp) REVERT: m 43 GLU cc_start: 0.8529 (mm-30) cc_final: 0.8100 (mm-30) REVERT: n 128 SER cc_start: 0.8096 (p) cc_final: 0.7258 (t) REVERT: o 82 LYS cc_start: 0.8033 (ttpp) cc_final: 0.7753 (ttpp) REVERT: o 99 GLN cc_start: 0.8414 (pt0) cc_final: 0.8043 (pm20) REVERT: p 31 ILE cc_start: 0.9251 (mt) cc_final: 0.8936 (mm) REVERT: p 83 GLU cc_start: 0.8019 (mp0) cc_final: 0.7520 (mp0) REVERT: p 107 ILE cc_start: 0.7991 (mp) cc_final: 0.7304 (mp) REVERT: p 109 ASN cc_start: 0.8228 (t0) cc_final: 0.7893 (t0) REVERT: r 13 LYS cc_start: 0.7720 (OUTLIER) cc_final: 0.7390 (ttpp) REVERT: r 90 ARG cc_start: 0.8258 (mmm160) cc_final: 0.7589 (mtm180) REVERT: s 6 MET cc_start: 0.8444 (mtp) cc_final: 0.8185 (mtp) REVERT: s 61 ARG cc_start: 0.7097 (mmm-85) cc_final: 0.6858 (mmm160) REVERT: s 89 MET cc_start: 0.7767 (mmm) cc_final: 0.7392 (mmm) REVERT: t 80 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8160 (tm-30) REVERT: u 75 ILE cc_start: 0.8938 (tp) cc_final: 0.8433 (tp) REVERT: u 79 ASN cc_start: 0.8594 (m-40) cc_final: 0.8225 (m-40) REVERT: x 17 LYS cc_start: 0.8036 (mttm) cc_final: 0.7623 (ptmt) REVERT: x 25 SER cc_start: 0.8433 (OUTLIER) cc_final: 0.7662 (p) REVERT: x 32 ARG cc_start: 0.7456 (ttm170) cc_final: 0.7052 (ttm-80) REVERT: y 13 GLN cc_start: 0.8356 (mm110) cc_final: 0.8070 (mp10) REVERT: y 78 ASN cc_start: 0.9064 (m-40) cc_final: 0.8715 (m110) REVERT: z 4 ILE cc_start: 0.8130 (mp) cc_final: 0.7888 (mp) REVERT: z 44 GLU cc_start: 0.8544 (tp30) cc_final: 0.8076 (tp30) outliers start: 257 outliers final: 184 residues processed: 1378 average time/residue: 1.2836 time to fit residues: 3114.0836 Evaluate side-chains 1356 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1163 time to evaluate : 6.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 14 ILE Chi-restraints excluded: chain 5 residue 23 GLU Chi-restraints excluded: chain 5 residue 60 ASP Chi-restraints excluded: chain 5 residue 78 THR Chi-restraints excluded: chain 5 residue 85 THR Chi-restraints excluded: chain 5 residue 92 LEU Chi-restraints excluded: chain 5 residue 120 ASN Chi-restraints excluded: chain 5 residue 127 ILE Chi-restraints excluded: chain 5 residue 134 LYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 43 ASP Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 18 THR Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 74 ILE Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 87 GLN Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 61 LYS Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 63 ILE Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 79 ARG Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 27 THR Chi-restraints excluded: chain a residue 33 ASN Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain e residue 51 SER Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain g residue 68 LEU Chi-restraints excluded: chain g residue 100 MET Chi-restraints excluded: chain g residue 165 ASP Chi-restraints excluded: chain g residue 187 VAL Chi-restraints excluded: chain h residue 25 ASN Chi-restraints excluded: chain h residue 31 ASP Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 174 ASP Chi-restraints excluded: chain j residue 43 ASN Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 42 ILE Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 122 ASN Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 72 VAL Chi-restraints excluded: chain m residue 76 GLN Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 113 ASP Chi-restraints excluded: chain n residue 6 TYR Chi-restraints excluded: chain n residue 7 TYR Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 66 THR Chi-restraints excluded: chain n residue 91 ASP Chi-restraints excluded: chain o residue 40 ILE Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 75 LYS Chi-restraints excluded: chain p residue 81 ASN Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 102 LEU Chi-restraints excluded: chain r residue 13 LYS Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 95 LEU Chi-restraints excluded: chain r residue 105 ASN Chi-restraints excluded: chain r residue 110 LYS Chi-restraints excluded: chain s residue 30 ILE Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain s residue 76 LYS Chi-restraints excluded: chain t residue 13 SER Chi-restraints excluded: chain u residue 23 ASP Chi-restraints excluded: chain u residue 29 ASN Chi-restraints excluded: chain u residue 67 ILE Chi-restraints excluded: chain v residue 50 ASN Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain w residue 25 ASP Chi-restraints excluded: chain w residue 55 LEU Chi-restraints excluded: chain x residue 4 SER Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 7 LYS Chi-restraints excluded: chain x residue 15 LEU Chi-restraints excluded: chain x residue 25 SER Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain x residue 67 VAL Chi-restraints excluded: chain y residue 58 VAL Chi-restraints excluded: chain y residue 80 THR Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 24 GLU Chi-restraints excluded: chain z residue 43 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 848 optimal weight: 5.9990 chunk 578 optimal weight: 4.9990 chunk 14 optimal weight: 10.0000 chunk 758 optimal weight: 0.9990 chunk 420 optimal weight: 20.0000 chunk 869 optimal weight: 6.9990 chunk 704 optimal weight: 3.9990 chunk 1 optimal weight: 10.0000 chunk 520 optimal weight: 0.9990 chunk 914 optimal weight: 7.9990 chunk 257 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN Q 56 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN e 31 HIS g 146 ASN g 168 HIS ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 123 GLN ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 75 GLN ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** p 15 GLN p 40 ASN ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 51 ASN ** x 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 61 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 164782 Z= 0.217 Angle : 0.636 14.796 246842 Z= 0.337 Chirality : 0.034 0.391 31494 Planarity : 0.006 0.129 12988 Dihedral : 24.457 179.925 83130 Min Nonbonded Distance : 1.005 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.11 % Favored : 92.84 % Rotamer: Outliers : 5.45 % Allowed : 20.57 % Favored : 73.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.11), residues: 5756 helix: 0.57 (0.12), residues: 1876 sheet: -0.95 (0.16), residues: 1073 loop : -1.73 (0.11), residues: 2807 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.002 TRP k 42 HIS 0.008 0.001 HIS b 38 PHE 0.028 0.002 PHE A 26 TYR 0.018 0.002 TYR c 49 ARG 0.011 0.000 ARG d 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1507 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1246 time to evaluate : 6.535 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: 5 37 GLN cc_start: 0.7240 (mt0) cc_final: 0.6586 (mt0) REVERT: 5 40 GLU cc_start: 0.8358 (mt-10) cc_final: 0.8076 (mp0) REVERT: 5 69 ASN cc_start: 0.8580 (t0) cc_final: 0.8026 (t0) REVERT: 5 134 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.8062 (mtmt) REVERT: 5 157 ASN cc_start: 0.8660 (m-40) cc_final: 0.8332 (m110) REVERT: A 43 THR cc_start: 0.9332 (m) cc_final: 0.8863 (p) REVERT: A 44 LYS cc_start: 0.9341 (mtpp) cc_final: 0.8759 (mttm) REVERT: B 133 ARG cc_start: 0.8106 (mtp85) cc_final: 0.7580 (mmt90) REVERT: E 7 TYR cc_start: 0.7420 (t80) cc_final: 0.7132 (t80) REVERT: E 8 TYR cc_start: 0.7562 (m-80) cc_final: 0.6919 (m-10) REVERT: E 21 ASN cc_start: 0.8707 (t0) cc_final: 0.8095 (t0) REVERT: E 23 ASN cc_start: 0.8437 (p0) cc_final: 0.8172 (m110) REVERT: E 99 PHE cc_start: 0.8813 (t80) cc_final: 0.8218 (t80) REVERT: F 128 GLN cc_start: 0.8482 (mm-40) cc_final: 0.8054 (mm-40) REVERT: J 37 ARG cc_start: 0.8705 (OUTLIER) cc_final: 0.7400 (ttm170) REVERT: J 106 LYS cc_start: 0.8913 (tmtt) cc_final: 0.8703 (tttm) REVERT: J 128 ASN cc_start: 0.8228 (p0) cc_final: 0.7894 (p0) REVERT: K 71 ARG cc_start: 0.8533 (OUTLIER) cc_final: 0.8250 (mtt-85) REVERT: K 82 ASN cc_start: 0.7748 (OUTLIER) cc_final: 0.7278 (m-40) REVERT: L 12 SER cc_start: 0.8876 (t) cc_final: 0.8340 (p) REVERT: O 17 LYS cc_start: 0.8963 (tptt) cc_final: 0.8656 (tptp) REVERT: O 76 LYS cc_start: 0.8950 (mmtt) cc_final: 0.8642 (mmtt) REVERT: O 98 GLN cc_start: 0.8746 (tm-30) cc_final: 0.8181 (tm-30) REVERT: P 31 TRP cc_start: 0.8256 (m100) cc_final: 0.7817 (m100) REVERT: S 77 ASP cc_start: 0.8208 (m-30) cc_final: 0.7313 (t0) REVERT: S 109 ASP cc_start: 0.7967 (t0) cc_final: 0.7612 (t0) REVERT: X 54 LYS cc_start: 0.8735 (ttpp) cc_final: 0.8440 (tttt) REVERT: Y 39 GLN cc_start: 0.8754 (mt0) cc_final: 0.8390 (mt0) REVERT: a 25 ARG cc_start: 0.7814 (mmm-85) cc_final: 0.7608 (mmm-85) REVERT: a 33 ASN cc_start: 0.8695 (t0) cc_final: 0.8414 (p0) REVERT: g 7 ARG cc_start: 0.8845 (tpp-160) cc_final: 0.8615 (tpp-160) REVERT: g 18 HIS cc_start: 0.7665 (m90) cc_final: 0.7317 (m90) REVERT: g 24 ASN cc_start: 0.9274 (t0) cc_final: 0.9026 (t0) REVERT: g 32 PHE cc_start: 0.8268 (t80) cc_final: 0.8022 (t80) REVERT: g 44 GLU cc_start: 0.8580 (mt-10) cc_final: 0.8060 (mp0) REVERT: g 49 MET cc_start: 0.8600 (mtm) cc_final: 0.8237 (mpp) REVERT: g 58 ASN cc_start: 0.7662 (t0) cc_final: 0.7308 (t0) REVERT: g 109 GLN cc_start: 0.8878 (mm-40) cc_final: 0.8245 (mp10) REVERT: h 58 GLU cc_start: 0.7469 (mp0) cc_final: 0.7173 (mp0) REVERT: h 168 TYR cc_start: 0.8198 (m-80) cc_final: 0.7639 (m-80) REVERT: h 193 TYR cc_start: 0.8355 (m-80) cc_final: 0.8115 (m-80) REVERT: h 211 MET cc_start: 0.6879 (tpt) cc_final: 0.6598 (tpp) REVERT: i 73 ARG cc_start: 0.8678 (ttp80) cc_final: 0.8317 (ttp-110) REVERT: i 77 LYS cc_start: 0.9306 (mttm) cc_final: 0.8993 (mtmt) REVERT: j 23 LYS cc_start: 0.8638 (tttt) cc_final: 0.8410 (tttt) REVERT: j 66 LYS cc_start: 0.9275 (mttp) cc_final: 0.8965 (mmtt) REVERT: k 5 GLU cc_start: 0.7679 (tp30) cc_final: 0.7333 (tp30) REVERT: k 25 TYR cc_start: 0.8461 (m-10) cc_final: 0.8183 (m-80) REVERT: k 61 LEU cc_start: 0.8977 (tt) cc_final: 0.8712 (tp) REVERT: k 90 MET cc_start: 0.7020 (mmm) cc_final: 0.6746 (mmm) REVERT: l 31 MET cc_start: 0.8269 (tmm) cc_final: 0.7971 (tmm) REVERT: l 59 LEU cc_start: 0.6656 (OUTLIER) cc_final: 0.6156 (tp) REVERT: m 43 GLU cc_start: 0.8565 (mm-30) cc_final: 0.8129 (mm-30) REVERT: m 126 ILE cc_start: 0.9258 (mt) cc_final: 0.9054 (mm) REVERT: n 38 TYR cc_start: 0.6879 (OUTLIER) cc_final: 0.6542 (m-80) REVERT: n 120 LYS cc_start: 0.8413 (mtmm) cc_final: 0.8167 (mtmm) REVERT: n 128 SER cc_start: 0.7904 (p) cc_final: 0.7109 (t) REVERT: o 82 LYS cc_start: 0.8024 (ttpp) cc_final: 0.7734 (ttpp) REVERT: o 99 GLN cc_start: 0.8381 (pt0) cc_final: 0.7963 (pm20) REVERT: p 31 ILE cc_start: 0.9257 (mt) cc_final: 0.8946 (mm) REVERT: p 83 GLU cc_start: 0.7972 (mp0) cc_final: 0.7527 (mp0) REVERT: p 106 ARG cc_start: 0.8139 (ttp80) cc_final: 0.7126 (tpt90) REVERT: p 107 ILE cc_start: 0.7682 (mp) cc_final: 0.7332 (mt) REVERT: r 90 ARG cc_start: 0.8250 (mmm160) cc_final: 0.7570 (mtm180) REVERT: s 6 MET cc_start: 0.8549 (mtp) cc_final: 0.8208 (mtp) REVERT: s 61 ARG cc_start: 0.7105 (mmm-85) cc_final: 0.6827 (mmm160) REVERT: s 89 MET cc_start: 0.7673 (mmm) cc_final: 0.7392 (mmm) REVERT: t 80 GLN cc_start: 0.8714 (tm-30) cc_final: 0.8124 (tm-30) REVERT: v 77 ARG cc_start: 0.8079 (ttp80) cc_final: 0.7833 (ttp80) REVERT: x 17 LYS cc_start: 0.8024 (mttm) cc_final: 0.7654 (ptmt) REVERT: x 32 ARG cc_start: 0.7417 (ttm170) cc_final: 0.7040 (ttm-80) REVERT: y 13 GLN cc_start: 0.8363 (mm110) cc_final: 0.8066 (mp10) REVERT: y 78 ASN cc_start: 0.9068 (m-40) cc_final: 0.8720 (m110) REVERT: z 12 PHE cc_start: 0.7796 (t80) cc_final: 0.7543 (t80) REVERT: z 44 GLU cc_start: 0.8514 (tp30) cc_final: 0.8066 (tp30) outliers start: 261 outliers final: 190 residues processed: 1390 average time/residue: 1.2999 time to fit residues: 3185.1110 Evaluate side-chains 1366 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1170 time to evaluate : 6.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 14 ILE Chi-restraints excluded: chain 5 residue 60 ASP Chi-restraints excluded: chain 5 residue 85 THR Chi-restraints excluded: chain 5 residue 87 THR Chi-restraints excluded: chain 5 residue 92 LEU Chi-restraints excluded: chain 5 residue 120 ASN Chi-restraints excluded: chain 5 residue 125 VAL Chi-restraints excluded: chain 5 residue 127 ILE Chi-restraints excluded: chain 5 residue 134 LYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 136 ILE Chi-restraints excluded: chain E residue 143 TYR Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 37 ARG Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 71 ARG Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain O residue 35 ILE Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 74 ILE Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 43 ASN Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 27 THR Chi-restraints excluded: chain a residue 44 PHE Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain g residue 19 GLN Chi-restraints excluded: chain g residue 68 LEU Chi-restraints excluded: chain g residue 187 VAL Chi-restraints excluded: chain h residue 31 ASP Chi-restraints excluded: chain h residue 33 LEU Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 174 ASP Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain j residue 43 ASN Chi-restraints excluded: chain j residue 73 ASN Chi-restraints excluded: chain j residue 80 THR Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 84 THR Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain m residue 2 SER Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 32 LEU Chi-restraints excluded: chain m residue 55 THR Chi-restraints excluded: chain m residue 72 VAL Chi-restraints excluded: chain m residue 76 GLN Chi-restraints excluded: chain m residue 85 ILE Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 113 ASP Chi-restraints excluded: chain n residue 6 TYR Chi-restraints excluded: chain n residue 7 TYR Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 38 TYR Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 66 THR Chi-restraints excluded: chain n residue 91 ASP Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 75 LYS Chi-restraints excluded: chain p residue 81 ASN Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain p residue 108 THR Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 102 LEU Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 95 LEU Chi-restraints excluded: chain r residue 105 ASN Chi-restraints excluded: chain s residue 30 ILE Chi-restraints excluded: chain s residue 35 ASN Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain s residue 76 LYS Chi-restraints excluded: chain u residue 23 ASP Chi-restraints excluded: chain u residue 29 ASN Chi-restraints excluded: chain u residue 67 ILE Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain w residue 25 ASP Chi-restraints excluded: chain w residue 55 LEU Chi-restraints excluded: chain x residue 4 SER Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 7 LYS Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain x residue 67 VAL Chi-restraints excluded: chain y residue 67 ILE Chi-restraints excluded: chain y residue 80 THR Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 43 THR Chi-restraints excluded: chain z residue 68 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 342 optimal weight: 10.0000 chunk 917 optimal weight: 30.0000 chunk 201 optimal weight: 10.0000 chunk 598 optimal weight: 9.9990 chunk 251 optimal weight: 10.0000 chunk 1019 optimal weight: 7.9990 chunk 846 optimal weight: 2.9990 chunk 472 optimal weight: 30.0000 chunk 84 optimal weight: 10.0000 chunk 337 optimal weight: 20.0000 chunk 535 optimal weight: 4.9990 overall best weight: 7.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 134 ASN B 239 ASN ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN C 130 GLN ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 56 GLN ** R 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 23 ASN Y 25 GLN ** a 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 42 HIS ** g 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 168 HIS ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 89 ASN ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 4 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 50 ASN v 51 ASN ** x 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 61 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.4512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.120 164782 Z= 0.409 Angle : 0.760 14.549 246842 Z= 0.395 Chirality : 0.041 0.428 31494 Planarity : 0.007 0.137 12988 Dihedral : 24.569 178.840 83130 Min Nonbonded Distance : 0.940 Molprobity Statistics. All-atom Clashscore : 17.79 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.69 % Favored : 91.26 % Rotamer: Outliers : 6.22 % Allowed : 20.57 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.11), residues: 5756 helix: 0.25 (0.12), residues: 1877 sheet: -1.07 (0.16), residues: 1060 loop : -1.83 (0.11), residues: 2819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP k 42 HIS 0.038 0.002 HIS e 31 PHE 0.039 0.002 PHE E 77 TYR 0.024 0.002 TYR E 8 ARG 0.012 0.001 ARG d 12 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1477 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 1179 time to evaluate : 6.509 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: 5 40 GLU cc_start: 0.8263 (mt-10) cc_final: 0.7935 (mp0) REVERT: 5 66 PHE cc_start: 0.8371 (t80) cc_final: 0.8098 (t80) REVERT: 5 69 ASN cc_start: 0.8623 (t0) cc_final: 0.7977 (t0) REVERT: 5 134 LYS cc_start: 0.8393 (OUTLIER) cc_final: 0.8094 (mtmt) REVERT: A 43 THR cc_start: 0.9314 (m) cc_final: 0.8853 (p) REVERT: A 44 LYS cc_start: 0.9345 (mtpp) cc_final: 0.8763 (mttm) REVERT: B 133 ARG cc_start: 0.8077 (mtp85) cc_final: 0.7771 (ttm110) REVERT: B 163 GLN cc_start: 0.8118 (tp-100) cc_final: 0.7866 (tp-100) REVERT: C 148 GLN cc_start: 0.8344 (OUTLIER) cc_final: 0.8098 (mp10) REVERT: E 7 TYR cc_start: 0.7544 (t80) cc_final: 0.7276 (t80) REVERT: E 8 TYR cc_start: 0.7998 (m-80) cc_final: 0.7143 (m-80) REVERT: E 21 ASN cc_start: 0.8766 (t0) cc_final: 0.8104 (t0) REVERT: E 23 ASN cc_start: 0.8575 (p0) cc_final: 0.8234 (m-40) REVERT: E 94 GLU cc_start: 0.8648 (pp20) cc_final: 0.7736 (pp20) REVERT: E 99 PHE cc_start: 0.8730 (t80) cc_final: 0.8268 (t80) REVERT: E 164 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.7913 (pm20) REVERT: F 143 GLN cc_start: 0.8859 (tp-100) cc_final: 0.8398 (tp40) REVERT: J 37 ARG cc_start: 0.8796 (OUTLIER) cc_final: 0.7408 (ttm170) REVERT: J 106 LYS cc_start: 0.9001 (tmtt) cc_final: 0.8790 (tttm) REVERT: K 82 ASN cc_start: 0.7709 (OUTLIER) cc_final: 0.7236 (m-40) REVERT: O 17 LYS cc_start: 0.8964 (tptt) cc_final: 0.8718 (tptp) REVERT: O 98 GLN cc_start: 0.8747 (tm-30) cc_final: 0.8250 (tm-30) REVERT: O 116 GLN cc_start: 0.6518 (OUTLIER) cc_final: 0.5359 (pm20) REVERT: S 77 ASP cc_start: 0.8264 (m-30) cc_final: 0.7366 (t0) REVERT: S 109 ASP cc_start: 0.8002 (t0) cc_final: 0.7714 (t0) REVERT: T 42 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8035 (mt-10) REVERT: V 48 MET cc_start: 0.8914 (tpp) cc_final: 0.8701 (mpp) REVERT: X 54 LYS cc_start: 0.8952 (ttpp) cc_final: 0.8718 (tttp) REVERT: c 50 LYS cc_start: 0.8672 (mtpt) cc_final: 0.8376 (mttp) REVERT: g 7 ARG cc_start: 0.8840 (tpp-160) cc_final: 0.8608 (tpp-160) REVERT: g 18 HIS cc_start: 0.7629 (m90) cc_final: 0.7296 (m90) REVERT: g 24 ASN cc_start: 0.9236 (t0) cc_final: 0.8989 (t0) REVERT: g 28 LYS cc_start: 0.8368 (tttt) cc_final: 0.8107 (mttt) REVERT: g 44 GLU cc_start: 0.8510 (mt-10) cc_final: 0.8140 (mp0) REVERT: g 49 MET cc_start: 0.8605 (mtm) cc_final: 0.8124 (mpp) REVERT: g 58 ASN cc_start: 0.7734 (t0) cc_final: 0.7496 (t0) REVERT: g 100 MET cc_start: 0.9033 (mmm) cc_final: 0.8573 (tpp) REVERT: g 109 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8251 (mp10) REVERT: h 58 GLU cc_start: 0.7576 (mp0) cc_final: 0.7249 (mp0) REVERT: h 168 TYR cc_start: 0.8211 (m-80) cc_final: 0.7701 (m-80) REVERT: h 211 MET cc_start: 0.6849 (tpt) cc_final: 0.6634 (tpp) REVERT: i 73 ARG cc_start: 0.8706 (ttp80) cc_final: 0.8350 (ttp-170) REVERT: i 77 LYS cc_start: 0.9342 (mttm) cc_final: 0.9030 (mtmt) REVERT: j 66 LYS cc_start: 0.9268 (mttp) cc_final: 0.8954 (mmtt) REVERT: k 5 GLU cc_start: 0.7751 (tp30) cc_final: 0.7372 (tp30) REVERT: k 24 ARG cc_start: 0.8966 (ttm110) cc_final: 0.8549 (ptp-110) REVERT: k 25 TYR cc_start: 0.8577 (m-10) cc_final: 0.8267 (m-80) REVERT: k 90 MET cc_start: 0.7101 (mmm) cc_final: 0.6428 (mmm) REVERT: l 59 LEU cc_start: 0.6642 (OUTLIER) cc_final: 0.6186 (tp) REVERT: l 144 MET cc_start: 0.7382 (ptp) cc_final: 0.6654 (mmp) REVERT: m 43 GLU cc_start: 0.8579 (mm-30) cc_final: 0.8170 (mm-30) REVERT: m 111 MET cc_start: 0.7192 (ptt) cc_final: 0.6855 (ptt) REVERT: m 124 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7432 (tm-30) REVERT: n 38 TYR cc_start: 0.6878 (OUTLIER) cc_final: 0.6669 (m-80) REVERT: n 59 GLU cc_start: 0.7940 (tp30) cc_final: 0.7689 (tp30) REVERT: n 128 SER cc_start: 0.8111 (p) cc_final: 0.7434 (t) REVERT: o 82 LYS cc_start: 0.8060 (ttpp) cc_final: 0.7737 (ttpp) REVERT: o 99 GLN cc_start: 0.8458 (pt0) cc_final: 0.7986 (pm20) REVERT: p 18 ASP cc_start: 0.8215 (p0) cc_final: 0.7966 (p0) REVERT: p 31 ILE cc_start: 0.9280 (mt) cc_final: 0.8943 (mm) REVERT: p 83 GLU cc_start: 0.7932 (mp0) cc_final: 0.7526 (mp0) REVERT: p 107 ILE cc_start: 0.7767 (mp) cc_final: 0.7466 (mp) REVERT: r 27 LYS cc_start: 0.8402 (tppp) cc_final: 0.8189 (tptm) REVERT: r 90 ARG cc_start: 0.8447 (mmm160) cc_final: 0.8050 (ttm170) REVERT: r 110 LYS cc_start: 0.6086 (OUTLIER) cc_final: 0.5753 (mmtm) REVERT: s 6 MET cc_start: 0.8405 (mtp) cc_final: 0.8081 (mtp) REVERT: s 89 MET cc_start: 0.7822 (mmm) cc_final: 0.7594 (mmm) REVERT: t 59 MET cc_start: 0.8218 (mtm) cc_final: 0.7737 (mtm) REVERT: t 80 GLN cc_start: 0.8715 (tm-30) cc_final: 0.8203 (tm-30) REVERT: u 8 ARG cc_start: 0.8454 (OUTLIER) cc_final: 0.8252 (mtp180) REVERT: u 77 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.7734 (tm-30) REVERT: w 32 TYR cc_start: 0.8188 (m-80) cc_final: 0.7920 (m-80) REVERT: x 17 LYS cc_start: 0.8100 (mttm) cc_final: 0.7722 (ptmt) REVERT: x 24 GLU cc_start: 0.8862 (mp0) cc_final: 0.8610 (mp0) REVERT: x 32 ARG cc_start: 0.7390 (ttm170) cc_final: 0.6970 (ttm-80) REVERT: y 13 GLN cc_start: 0.8392 (mm110) cc_final: 0.8108 (mp10) REVERT: y 78 ASN cc_start: 0.9075 (m-40) cc_final: 0.8748 (m110) REVERT: z 44 GLU cc_start: 0.8593 (tp30) cc_final: 0.8131 (tp30) outliers start: 298 outliers final: 229 residues processed: 1355 average time/residue: 1.3714 time to fit residues: 3300.8011 Evaluate side-chains 1377 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 240 poor density : 1137 time to evaluate : 6.480 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 60 ASP Chi-restraints excluded: chain 5 residue 78 THR Chi-restraints excluded: chain 5 residue 85 THR Chi-restraints excluded: chain 5 residue 87 THR Chi-restraints excluded: chain 5 residue 92 LEU Chi-restraints excluded: chain 5 residue 120 ASN Chi-restraints excluded: chain 5 residue 125 VAL Chi-restraints excluded: chain 5 residue 134 LYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 148 GLN Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 37 ARG Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 121 GLU Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain L residue 127 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain O residue 116 GLN Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 9 GLU Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 74 ILE Chi-restraints excluded: chain Q residue 87 SER Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 87 GLN Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 59 GLU Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 58 VAL Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 27 THR Chi-restraints excluded: chain a residue 31 ASP Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain b residue 15 MET Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain g residue 19 GLN Chi-restraints excluded: chain g residue 68 LEU Chi-restraints excluded: chain g residue 187 VAL Chi-restraints excluded: chain h residue 25 ASN Chi-restraints excluded: chain h residue 31 ASP Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain h residue 111 LEU Chi-restraints excluded: chain h residue 176 HIS Chi-restraints excluded: chain i residue 100 ASN Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 174 ASP Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain i residue 203 LEU Chi-restraints excluded: chain j residue 73 ASN Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain k residue 51 ILE Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 75 VAL Chi-restraints excluded: chain l residue 84 THR Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 116 MET Chi-restraints excluded: chain l residue 122 ASN Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain m residue 14 ILE Chi-restraints excluded: chain m residue 32 LEU Chi-restraints excluded: chain m residue 55 THR Chi-restraints excluded: chain m residue 72 VAL Chi-restraints excluded: chain m residue 76 GLN Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 113 ASP Chi-restraints excluded: chain n residue 6 TYR Chi-restraints excluded: chain n residue 7 TYR Chi-restraints excluded: chain n residue 38 TYR Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 66 THR Chi-restraints excluded: chain n residue 91 ASP Chi-restraints excluded: chain o residue 24 GLU Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain o residue 69 THR Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 75 LYS Chi-restraints excluded: chain p residue 81 ASN Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain p residue 108 THR Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 63 VAL Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 102 LEU Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 95 LEU Chi-restraints excluded: chain r residue 105 ASN Chi-restraints excluded: chain r residue 110 LYS Chi-restraints excluded: chain s residue 30 ILE Chi-restraints excluded: chain s residue 35 ASN Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain s residue 76 LYS Chi-restraints excluded: chain u residue 8 ARG Chi-restraints excluded: chain u residue 23 ASP Chi-restraints excluded: chain u residue 29 ASN Chi-restraints excluded: chain u residue 77 GLU Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain w residue 25 ASP Chi-restraints excluded: chain w residue 34 THR Chi-restraints excluded: chain w residue 55 LEU Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 4 SER Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 7 LYS Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain x residue 67 VAL Chi-restraints excluded: chain y residue 58 VAL Chi-restraints excluded: chain y residue 67 ILE Chi-restraints excluded: chain y residue 80 THR Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 24 GLU Chi-restraints excluded: chain z residue 36 GLU Chi-restraints excluded: chain z residue 43 THR Chi-restraints excluded: chain z residue 56 HIS Chi-restraints excluded: chain z residue 68 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 983 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 581 optimal weight: 8.9990 chunk 744 optimal weight: 4.9990 chunk 577 optimal weight: 5.9990 chunk 858 optimal weight: 5.9990 chunk 569 optimal weight: 4.9990 chunk 1015 optimal weight: 9.9990 chunk 635 optimal weight: 7.9990 chunk 619 optimal weight: 20.0000 chunk 469 optimal weight: 40.0000 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN Q 56 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 23 ASN Y 25 GLN ** a 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 51 ASN ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 50 ASN v 51 ASN ** x 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 61 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.4500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 164782 Z= 0.283 Angle : 0.684 14.593 246842 Z= 0.361 Chirality : 0.037 0.409 31494 Planarity : 0.006 0.131 12988 Dihedral : 24.555 179.162 83130 Min Nonbonded Distance : 0.983 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.56 % Favored : 92.39 % Rotamer: Outliers : 5.86 % Allowed : 21.51 % Favored : 72.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.11), residues: 5756 helix: 0.33 (0.12), residues: 1891 sheet: -1.07 (0.16), residues: 1081 loop : -1.78 (0.11), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP k 42 HIS 0.012 0.001 HIS N 3 PHE 0.028 0.002 PHE a 64 TYR 0.020 0.002 TYR k 59 ARG 0.010 0.001 ARG d 12 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1472 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 281 poor density : 1191 time to evaluate : 6.734 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: 5 23 GLU cc_start: 0.8141 (pm20) cc_final: 0.7579 (pm20) REVERT: 5 37 GLN cc_start: 0.7282 (mt0) cc_final: 0.6503 (mt0) REVERT: 5 40 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7936 (mp0) REVERT: 5 48 LYS cc_start: 0.6466 (OUTLIER) cc_final: 0.5815 (mmtm) REVERT: 5 66 PHE cc_start: 0.8342 (t80) cc_final: 0.8083 (t80) REVERT: 5 69 ASN cc_start: 0.8497 (t0) cc_final: 0.7874 (t0) REVERT: 5 134 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.8019 (mtmt) REVERT: A 43 THR cc_start: 0.9315 (m) cc_final: 0.8843 (p) REVERT: A 44 LYS cc_start: 0.9328 (mtpp) cc_final: 0.8726 (mttm) REVERT: B 163 GLN cc_start: 0.8129 (tp-100) cc_final: 0.7871 (tp-100) REVERT: E 8 TYR cc_start: 0.8021 (m-80) cc_final: 0.7636 (m-80) REVERT: E 21 ASN cc_start: 0.8727 (t0) cc_final: 0.8078 (t0) REVERT: E 23 ASN cc_start: 0.8586 (p0) cc_final: 0.8247 (m110) REVERT: E 164 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.7949 (pm20) REVERT: F 35 ARG cc_start: 0.7987 (tpp80) cc_final: 0.7457 (tpp80) REVERT: F 143 GLN cc_start: 0.8830 (tp-100) cc_final: 0.8406 (tp40) REVERT: J 37 ARG cc_start: 0.8731 (OUTLIER) cc_final: 0.7419 (ttm170) REVERT: J 128 ASN cc_start: 0.8256 (p0) cc_final: 0.7974 (p0) REVERT: K 82 ASN cc_start: 0.7897 (OUTLIER) cc_final: 0.7271 (m-40) REVERT: K 107 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8588 (pt) REVERT: L 12 SER cc_start: 0.8701 (t) cc_final: 0.8327 (p) REVERT: L 23 ILE cc_start: 0.8628 (OUTLIER) cc_final: 0.8425 (pt) REVERT: O 17 LYS cc_start: 0.8973 (tptt) cc_final: 0.8699 (tptp) REVERT: O 98 GLN cc_start: 0.8750 (tm-30) cc_final: 0.8244 (tm-30) REVERT: P 31 TRP cc_start: 0.8291 (m100) cc_final: 0.7867 (m100) REVERT: R 18 GLN cc_start: 0.8305 (pt0) cc_final: 0.7947 (pt0) REVERT: S 2 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8215 (mm-30) REVERT: S 77 ASP cc_start: 0.8224 (m-30) cc_final: 0.7333 (t0) REVERT: S 109 ASP cc_start: 0.7851 (t0) cc_final: 0.7508 (t0) REVERT: T 42 GLU cc_start: 0.8277 (mt-10) cc_final: 0.8005 (mt-10) REVERT: X 54 LYS cc_start: 0.8862 (ttpp) cc_final: 0.8605 (tttp) REVERT: a 1 MET cc_start: 0.8490 (tpp) cc_final: 0.8167 (mmp) REVERT: g 7 ARG cc_start: 0.8837 (tpp-160) cc_final: 0.8593 (tpp-160) REVERT: g 18 HIS cc_start: 0.7691 (m90) cc_final: 0.7317 (m90) REVERT: g 28 LYS cc_start: 0.8307 (tttt) cc_final: 0.8005 (mttm) REVERT: g 44 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8127 (mp0) REVERT: g 49 MET cc_start: 0.8604 (mtm) cc_final: 0.8100 (mpp) REVERT: g 109 GLN cc_start: 0.8871 (mm-40) cc_final: 0.8264 (mp10) REVERT: h 42 TYR cc_start: 0.8340 (t80) cc_final: 0.8125 (t80) REVERT: h 46 GLU cc_start: 0.7850 (mt-10) cc_final: 0.7641 (mt-10) REVERT: h 58 GLU cc_start: 0.7529 (mp0) cc_final: 0.7210 (mp0) REVERT: h 168 TYR cc_start: 0.8250 (m-80) cc_final: 0.7763 (m-80) REVERT: h 211 MET cc_start: 0.7087 (tpt) cc_final: 0.6792 (tpp) REVERT: i 73 ARG cc_start: 0.8678 (ttp80) cc_final: 0.8313 (ttp-110) REVERT: i 77 LYS cc_start: 0.9327 (mttm) cc_final: 0.9014 (mtmt) REVERT: j 55 GLU cc_start: 0.8466 (mp0) cc_final: 0.8245 (mp0) REVERT: j 66 LYS cc_start: 0.9279 (mttp) cc_final: 0.8918 (mmtt) REVERT: k 25 TYR cc_start: 0.8570 (m-10) cc_final: 0.8234 (m-80) REVERT: k 98 GLU cc_start: 0.8297 (mp0) cc_final: 0.8060 (mp0) REVERT: l 59 LEU cc_start: 0.6705 (OUTLIER) cc_final: 0.6209 (tp) REVERT: l 144 MET cc_start: 0.7410 (ptp) cc_final: 0.6682 (mmp) REVERT: m 42 GLU cc_start: 0.8781 (pt0) cc_final: 0.8554 (pt0) REVERT: m 111 MET cc_start: 0.7295 (ptt) cc_final: 0.7041 (ptt) REVERT: n 59 GLU cc_start: 0.7990 (tp30) cc_final: 0.7705 (tp30) REVERT: n 128 SER cc_start: 0.7964 (p) cc_final: 0.7294 (t) REVERT: o 82 LYS cc_start: 0.7994 (ttpp) cc_final: 0.7662 (ttpp) REVERT: o 99 GLN cc_start: 0.8398 (pt0) cc_final: 0.8036 (pm20) REVERT: p 31 ILE cc_start: 0.9270 (mt) cc_final: 0.8940 (mm) REVERT: p 40 ASN cc_start: 0.8998 (m-40) cc_final: 0.8281 (t0) REVERT: p 83 GLU cc_start: 0.7927 (mp0) cc_final: 0.7458 (mp0) REVERT: p 106 ARG cc_start: 0.8156 (ttp80) cc_final: 0.7127 (tpt90) REVERT: p 107 ILE cc_start: 0.7804 (mp) cc_final: 0.7351 (mp) REVERT: r 90 ARG cc_start: 0.8398 (mmm160) cc_final: 0.7974 (ttm170) REVERT: r 110 LYS cc_start: 0.5868 (OUTLIER) cc_final: 0.5604 (mmtm) REVERT: s 6 MET cc_start: 0.8422 (mtp) cc_final: 0.8048 (mtp) REVERT: t 80 GLN cc_start: 0.8684 (tm-30) cc_final: 0.8183 (tm-30) REVERT: v 39 LYS cc_start: 0.8765 (ptpt) cc_final: 0.8492 (mtmt) REVERT: w 32 TYR cc_start: 0.8215 (m-80) cc_final: 0.7947 (m-80) REVERT: x 17 LYS cc_start: 0.8047 (mttm) cc_final: 0.7694 (ptmt) REVERT: x 32 ARG cc_start: 0.7437 (ttm170) cc_final: 0.7023 (ttm-80) REVERT: y 13 GLN cc_start: 0.8375 (mm110) cc_final: 0.8081 (mp10) REVERT: y 78 ASN cc_start: 0.9078 (m-40) cc_final: 0.8741 (m110) REVERT: z 44 GLU cc_start: 0.8552 (tp30) cc_final: 0.8092 (tp30) outliers start: 281 outliers final: 234 residues processed: 1361 average time/residue: 1.2682 time to fit residues: 3042.0233 Evaluate side-chains 1387 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 1144 time to evaluate : 6.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 14 ILE Chi-restraints excluded: chain 5 residue 48 LYS Chi-restraints excluded: chain 5 residue 60 ASP Chi-restraints excluded: chain 5 residue 78 THR Chi-restraints excluded: chain 5 residue 85 THR Chi-restraints excluded: chain 5 residue 87 THR Chi-restraints excluded: chain 5 residue 92 LEU Chi-restraints excluded: chain 5 residue 120 ASN Chi-restraints excluded: chain 5 residue 125 VAL Chi-restraints excluded: chain 5 residue 127 ILE Chi-restraints excluded: chain 5 residue 134 LYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 70 ASN Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 172 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 176 ASP Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 199 MET Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 105 LEU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 61 VAL Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 37 ARG Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 5 ILE Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 74 ILE Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 87 GLN Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 96 ILE Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 24 ILE Chi-restraints excluded: chain a residue 31 ASP Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain b residue 15 MET Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain c residue 17 THR Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 59 ILE Chi-restraints excluded: chain g residue 19 GLN Chi-restraints excluded: chain g residue 68 LEU Chi-restraints excluded: chain g residue 187 VAL Chi-restraints excluded: chain h residue 31 ASP Chi-restraints excluded: chain h residue 33 LEU Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain h residue 111 LEU Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain h residue 176 HIS Chi-restraints excluded: chain i residue 100 ASN Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 174 ASP Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain j residue 73 ASN Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 75 VAL Chi-restraints excluded: chain l residue 84 THR Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 122 ASN Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 32 LEU Chi-restraints excluded: chain m residue 72 VAL Chi-restraints excluded: chain m residue 76 GLN Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 113 ASP Chi-restraints excluded: chain n residue 6 TYR Chi-restraints excluded: chain n residue 7 TYR Chi-restraints excluded: chain n residue 46 MET Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 66 THR Chi-restraints excluded: chain n residue 91 ASP Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 50 THR Chi-restraints excluded: chain o residue 54 SER Chi-restraints excluded: chain o residue 69 THR Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 81 ASN Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain p residue 108 THR Chi-restraints excluded: chain p residue 116 ILE Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 63 VAL Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 102 LEU Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 95 LEU Chi-restraints excluded: chain r residue 105 ASN Chi-restraints excluded: chain r residue 110 LYS Chi-restraints excluded: chain s residue 30 ILE Chi-restraints excluded: chain s residue 35 ASN Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain s residue 76 LYS Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain u residue 23 ASP Chi-restraints excluded: chain u residue 29 ASN Chi-restraints excluded: chain u residue 67 ILE Chi-restraints excluded: chain v residue 50 ASN Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain w residue 25 ASP Chi-restraints excluded: chain w residue 34 THR Chi-restraints excluded: chain w residue 55 LEU Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 4 SER Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 7 LYS Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain x residue 67 VAL Chi-restraints excluded: chain y residue 58 VAL Chi-restraints excluded: chain y residue 67 ILE Chi-restraints excluded: chain y residue 80 THR Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 24 GLU Chi-restraints excluded: chain z residue 43 THR Chi-restraints excluded: chain z residue 56 HIS Chi-restraints excluded: chain z residue 68 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 628 optimal weight: 0.2980 chunk 405 optimal weight: 20.0000 chunk 606 optimal weight: 7.9990 chunk 306 optimal weight: 10.0000 chunk 199 optimal weight: 10.0000 chunk 196 optimal weight: 9.9990 chunk 645 optimal weight: 0.8980 chunk 692 optimal weight: 0.9990 chunk 502 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 798 optimal weight: 6.9990 overall best weight: 3.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN C 130 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN a 33 ASN ** a 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 31 HIS ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 168 HIS ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 51 ASN ** x 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 61 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 164782 Z= 0.206 Angle : 0.643 14.598 246842 Z= 0.341 Chirality : 0.035 0.411 31494 Planarity : 0.006 0.127 12988 Dihedral : 24.495 179.485 83130 Min Nonbonded Distance : 1.027 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.70 % Favored : 92.25 % Rotamer: Outliers : 5.22 % Allowed : 22.72 % Favored : 72.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.11), residues: 5756 helix: 0.46 (0.12), residues: 1893 sheet: -0.99 (0.16), residues: 1067 loop : -1.65 (0.11), residues: 2796 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP 5 147 HIS 0.010 0.001 HIS v 47 PHE 0.048 0.002 PHE k 8 TYR 0.021 0.001 TYR p 77 ARG 0.009 0.000 ARG k 79 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1478 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1228 time to evaluate : 5.872 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: 5 37 GLN cc_start: 0.7200 (mt0) cc_final: 0.6469 (mt0) REVERT: 5 40 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7984 (mp0) REVERT: 5 48 LYS cc_start: 0.6311 (OUTLIER) cc_final: 0.5697 (mmtm) REVERT: 5 66 PHE cc_start: 0.8387 (t80) cc_final: 0.8131 (t80) REVERT: 5 69 ASN cc_start: 0.8522 (t0) cc_final: 0.7751 (t0) REVERT: 5 134 LYS cc_start: 0.8304 (OUTLIER) cc_final: 0.7771 (mtmm) REVERT: A 43 THR cc_start: 0.9339 (m) cc_final: 0.8853 (p) REVERT: A 44 LYS cc_start: 0.9324 (mtpp) cc_final: 0.8716 (mttm) REVERT: A 78 LYS cc_start: 0.8140 (mttp) cc_final: 0.7916 (mtpp) REVERT: B 96 TYR cc_start: 0.8882 (m-80) cc_final: 0.8573 (m-80) REVERT: B 163 GLN cc_start: 0.8116 (tp-100) cc_final: 0.7849 (tp-100) REVERT: C 108 ASP cc_start: 0.6881 (m-30) cc_final: 0.6455 (m-30) REVERT: E 8 TYR cc_start: 0.7796 (m-80) cc_final: 0.7497 (m-10) REVERT: E 21 ASN cc_start: 0.8736 (t0) cc_final: 0.8114 (t0) REVERT: E 23 ASN cc_start: 0.8529 (p0) cc_final: 0.8223 (m110) REVERT: F 143 GLN cc_start: 0.8722 (tp-100) cc_final: 0.8346 (tp-100) REVERT: J 96 ARG cc_start: 0.7521 (mtt90) cc_final: 0.7168 (mtt90) REVERT: J 108 MET cc_start: 0.7767 (OUTLIER) cc_final: 0.7357 (mtt) REVERT: J 128 ASN cc_start: 0.8148 (p0) cc_final: 0.7814 (p0) REVERT: K 82 ASN cc_start: 0.7893 (OUTLIER) cc_final: 0.7333 (m-40) REVERT: K 107 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8493 (pt) REVERT: L 12 SER cc_start: 0.8733 (t) cc_final: 0.8384 (p) REVERT: O 17 LYS cc_start: 0.8965 (tptt) cc_final: 0.8648 (tptp) REVERT: O 98 GLN cc_start: 0.8726 (tm-30) cc_final: 0.8215 (tm-30) REVERT: P 31 TRP cc_start: 0.8235 (m100) cc_final: 0.7817 (m100) REVERT: R 18 GLN cc_start: 0.8260 (pt0) cc_final: 0.7901 (pt0) REVERT: S 2 GLU cc_start: 0.8387 (mm-30) cc_final: 0.8128 (mm-30) REVERT: S 77 ASP cc_start: 0.8225 (m-30) cc_final: 0.7324 (t0) REVERT: S 109 ASP cc_start: 0.7704 (t0) cc_final: 0.7365 (t0) REVERT: T 42 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8035 (mt-10) REVERT: T 43 ILE cc_start: 0.8677 (OUTLIER) cc_final: 0.8278 (mt) REVERT: V 48 MET cc_start: 0.8808 (tpp) cc_final: 0.8512 (mpp) REVERT: X 54 LYS cc_start: 0.8759 (ttpp) cc_final: 0.8481 (tttp) REVERT: g 18 HIS cc_start: 0.7586 (m90) cc_final: 0.7258 (m90) REVERT: g 28 LYS cc_start: 0.8346 (tttt) cc_final: 0.8028 (mttm) REVERT: g 44 GLU cc_start: 0.8502 (mt-10) cc_final: 0.8194 (mp0) REVERT: g 49 MET cc_start: 0.8617 (mtm) cc_final: 0.8138 (mpp) REVERT: g 100 MET cc_start: 0.9034 (mmm) cc_final: 0.8567 (tpp) REVERT: g 109 GLN cc_start: 0.8861 (mm-40) cc_final: 0.8251 (mp10) REVERT: h 58 GLU cc_start: 0.7461 (mp0) cc_final: 0.7150 (mp0) REVERT: h 211 MET cc_start: 0.7165 (tpt) cc_final: 0.6791 (tpp) REVERT: i 73 ARG cc_start: 0.8664 (ttp80) cc_final: 0.8304 (ttp-110) REVERT: i 77 LYS cc_start: 0.9307 (mttm) cc_final: 0.8993 (mtmt) REVERT: j 55 GLU cc_start: 0.8423 (mp0) cc_final: 0.8175 (mp0) REVERT: j 66 LYS cc_start: 0.9281 (mttp) cc_final: 0.8960 (mmtt) REVERT: k 7 VAL cc_start: 0.9173 (t) cc_final: 0.8966 (p) REVERT: k 24 ARG cc_start: 0.8915 (ttm110) cc_final: 0.8542 (ptp-110) REVERT: k 25 TYR cc_start: 0.8492 (m-10) cc_final: 0.8263 (m-80) REVERT: k 98 GLU cc_start: 0.8261 (mp0) cc_final: 0.8008 (mp0) REVERT: l 59 LEU cc_start: 0.6843 (OUTLIER) cc_final: 0.6386 (tp) REVERT: l 144 MET cc_start: 0.7500 (ptp) cc_final: 0.6799 (mmp) REVERT: m 27 MET cc_start: 0.8172 (ptm) cc_final: 0.7514 (ppp) REVERT: m 42 GLU cc_start: 0.8774 (pt0) cc_final: 0.8433 (pt0) REVERT: n 115 LYS cc_start: 0.8180 (mmtm) cc_final: 0.7715 (mmtt) REVERT: n 128 SER cc_start: 0.7823 (p) cc_final: 0.7106 (t) REVERT: o 82 LYS cc_start: 0.8020 (ttpp) cc_final: 0.7648 (ttpp) REVERT: p 15 GLN cc_start: 0.7068 (tp-100) cc_final: 0.6833 (tp40) REVERT: p 31 ILE cc_start: 0.9276 (mt) cc_final: 0.8946 (mm) REVERT: p 38 GLN cc_start: 0.8245 (mp10) cc_final: 0.7900 (pm20) REVERT: p 40 ASN cc_start: 0.8950 (m-40) cc_final: 0.8393 (t0) REVERT: p 83 GLU cc_start: 0.7896 (mp0) cc_final: 0.7427 (mp0) REVERT: p 106 ARG cc_start: 0.8214 (ttp80) cc_final: 0.7184 (tpt90) REVERT: p 107 ILE cc_start: 0.7754 (mp) cc_final: 0.7294 (mp) REVERT: r 50 GLU cc_start: 0.8712 (mp0) cc_final: 0.8387 (tp30) REVERT: r 90 ARG cc_start: 0.8360 (mmm160) cc_final: 0.7582 (mtm180) REVERT: r 110 LYS cc_start: 0.5840 (OUTLIER) cc_final: 0.5613 (mmtm) REVERT: s 83 LYS cc_start: 0.8604 (OUTLIER) cc_final: 0.8198 (mmtp) REVERT: t 80 GLN cc_start: 0.8658 (tm-30) cc_final: 0.8179 (tm-30) REVERT: v 39 LYS cc_start: 0.8779 (ptpt) cc_final: 0.8531 (mtmt) REVERT: w 32 TYR cc_start: 0.8123 (m-80) cc_final: 0.7850 (m-80) REVERT: x 11 ILE cc_start: 0.8629 (pt) cc_final: 0.8381 (mp) REVERT: x 32 ARG cc_start: 0.7377 (ttm170) cc_final: 0.7004 (ttm-80) REVERT: y 13 GLN cc_start: 0.8388 (mm110) cc_final: 0.8097 (mp10) REVERT: y 78 ASN cc_start: 0.9069 (m-40) cc_final: 0.8801 (m-40) REVERT: z 44 GLU cc_start: 0.8503 (tp30) cc_final: 0.8063 (tp30) outliers start: 250 outliers final: 205 residues processed: 1368 average time/residue: 1.2994 time to fit residues: 3152.2410 Evaluate side-chains 1396 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 1182 time to evaluate : 6.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 14 ILE Chi-restraints excluded: chain 5 residue 48 LYS Chi-restraints excluded: chain 5 residue 60 ASP Chi-restraints excluded: chain 5 residue 78 THR Chi-restraints excluded: chain 5 residue 85 THR Chi-restraints excluded: chain 5 residue 87 THR Chi-restraints excluded: chain 5 residue 92 LEU Chi-restraints excluded: chain 5 residue 120 ASN Chi-restraints excluded: chain 5 residue 125 VAL Chi-restraints excluded: chain 5 residue 127 ILE Chi-restraints excluded: chain 5 residue 134 LYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 162 VAL Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain G residue 143 ILE Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 65 ILE Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 74 ILE Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 41 ILE Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 87 GLN Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 79 ARG Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 24 ILE Chi-restraints excluded: chain a residue 31 ASP Chi-restraints excluded: chain a residue 33 ASN Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain g residue 19 GLN Chi-restraints excluded: chain g residue 68 LEU Chi-restraints excluded: chain g residue 187 VAL Chi-restraints excluded: chain h residue 31 ASP Chi-restraints excluded: chain h residue 33 LEU Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain i residue 100 ASN Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 174 ASP Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain j residue 43 ASN Chi-restraints excluded: chain j residue 56 VAL Chi-restraints excluded: chain j residue 73 ASN Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 75 VAL Chi-restraints excluded: chain l residue 84 THR Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 122 ASN Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain m residue 12 THR Chi-restraints excluded: chain m residue 72 VAL Chi-restraints excluded: chain m residue 76 GLN Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 113 ASP Chi-restraints excluded: chain n residue 6 TYR Chi-restraints excluded: chain n residue 7 TYR Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 46 MET Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 66 THR Chi-restraints excluded: chain n residue 91 ASP Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain o residue 53 ILE Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 81 ASN Chi-restraints excluded: chain p residue 108 THR Chi-restraints excluded: chain p residue 116 ILE Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 63 VAL Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 102 LEU Chi-restraints excluded: chain r residue 8 ASN Chi-restraints excluded: chain r residue 13 LYS Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 95 LEU Chi-restraints excluded: chain r residue 105 ASN Chi-restraints excluded: chain r residue 110 LYS Chi-restraints excluded: chain s residue 30 ILE Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain s residue 76 LYS Chi-restraints excluded: chain s residue 83 LYS Chi-restraints excluded: chain u residue 29 ASN Chi-restraints excluded: chain u residue 67 ILE Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain w residue 25 ASP Chi-restraints excluded: chain w residue 55 LEU Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 4 SER Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 7 LYS Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain x residue 67 VAL Chi-restraints excluded: chain y residue 58 VAL Chi-restraints excluded: chain y residue 67 ILE Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 24 GLU Chi-restraints excluded: chain z residue 43 THR Chi-restraints excluded: chain z residue 68 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 924 optimal weight: 8.9990 chunk 973 optimal weight: 7.9990 chunk 887 optimal weight: 8.9990 chunk 946 optimal weight: 5.9990 chunk 972 optimal weight: 20.0000 chunk 569 optimal weight: 1.9990 chunk 412 optimal weight: 20.0000 chunk 743 optimal weight: 0.9980 chunk 290 optimal weight: 10.0000 chunk 855 optimal weight: 10.0000 chunk 895 optimal weight: 5.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN C 130 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 12 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN ** a 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 31 HIS g 15 HIS ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** l 52 GLN o 99 GLN ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 61 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8404 moved from start: 0.4567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 164782 Z= 0.279 Angle : 0.682 14.324 246842 Z= 0.360 Chirality : 0.037 0.418 31494 Planarity : 0.006 0.131 12988 Dihedral : 24.489 179.954 83130 Min Nonbonded Distance : 0.986 Molprobity Statistics. All-atom Clashscore : 16.17 Ramachandran Plot: Outliers : 0.05 % Allowed : 8.04 % Favored : 91.90 % Rotamer: Outliers : 5.07 % Allowed : 23.16 % Favored : 71.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.11), residues: 5756 helix: 0.41 (0.12), residues: 1894 sheet: -1.00 (0.16), residues: 1074 loop : -1.70 (0.11), residues: 2788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.074 0.002 TRP k 42 HIS 0.022 0.001 HIS e 31 PHE 0.033 0.002 PHE A 26 TYR 0.041 0.002 TYR l 44 ARG 0.010 0.001 ARG k 79 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1431 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 243 poor density : 1188 time to evaluate : 6.233 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: 5 37 GLN cc_start: 0.7256 (mt0) cc_final: 0.6494 (mt0) REVERT: 5 40 GLU cc_start: 0.8337 (mt-10) cc_final: 0.7995 (mp0) REVERT: 5 48 LYS cc_start: 0.6370 (OUTLIER) cc_final: 0.5744 (mmtm) REVERT: 5 66 PHE cc_start: 0.8423 (t80) cc_final: 0.8138 (t80) REVERT: 5 134 LYS cc_start: 0.8298 (OUTLIER) cc_final: 0.7807 (mtmm) REVERT: A 43 THR cc_start: 0.9311 (m) cc_final: 0.8841 (p) REVERT: A 44 LYS cc_start: 0.9308 (mtpp) cc_final: 0.8716 (mttm) REVERT: B 35 GLU cc_start: 0.7223 (tt0) cc_final: 0.6903 (tt0) REVERT: B 163 GLN cc_start: 0.8146 (tp-100) cc_final: 0.7871 (tp-100) REVERT: C 1 MET cc_start: 0.7609 (tpt) cc_final: 0.6769 (tpt) REVERT: C 108 ASP cc_start: 0.7217 (m-30) cc_final: 0.6588 (m-30) REVERT: E 21 ASN cc_start: 0.8727 (t0) cc_final: 0.8074 (t0) REVERT: E 23 ASN cc_start: 0.8592 (p0) cc_final: 0.8212 (m-40) REVERT: E 156 ILE cc_start: 0.9194 (tp) cc_final: 0.8952 (tp) REVERT: E 164 GLU cc_start: 0.8795 (OUTLIER) cc_final: 0.7908 (pm20) REVERT: F 35 ARG cc_start: 0.7902 (tpp80) cc_final: 0.7497 (ttt180) REVERT: F 143 GLN cc_start: 0.8761 (tp-100) cc_final: 0.8326 (tp-100) REVERT: J 108 MET cc_start: 0.7758 (OUTLIER) cc_final: 0.7374 (mtt) REVERT: J 128 ASN cc_start: 0.8193 (p0) cc_final: 0.7941 (p0) REVERT: K 82 ASN cc_start: 0.7887 (OUTLIER) cc_final: 0.7303 (m-40) REVERT: K 107 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8455 (pt) REVERT: L 12 SER cc_start: 0.8744 (t) cc_final: 0.8394 (p) REVERT: O 17 LYS cc_start: 0.8971 (tptt) cc_final: 0.8671 (tptp) REVERT: O 98 GLN cc_start: 0.8737 (tm-30) cc_final: 0.8231 (tm-30) REVERT: P 31 TRP cc_start: 0.8267 (m100) cc_final: 0.7814 (m100) REVERT: R 18 GLN cc_start: 0.8264 (pt0) cc_final: 0.7904 (pt0) REVERT: S 77 ASP cc_start: 0.8225 (m-30) cc_final: 0.7342 (t0) REVERT: S 109 ASP cc_start: 0.7806 (t0) cc_final: 0.7463 (t0) REVERT: T 42 GLU cc_start: 0.8384 (mt-10) cc_final: 0.8117 (mt-10) REVERT: X 54 LYS cc_start: 0.8857 (ttpp) cc_final: 0.8622 (tttp) REVERT: a 11 GLU cc_start: 0.8379 (tp30) cc_final: 0.8013 (tp30) REVERT: g 18 HIS cc_start: 0.7603 (m90) cc_final: 0.7281 (m90) REVERT: g 28 LYS cc_start: 0.8261 (tttt) cc_final: 0.7956 (mptt) REVERT: g 44 GLU cc_start: 0.8468 (mt-10) cc_final: 0.8167 (mp0) REVERT: g 49 MET cc_start: 0.8625 (mtm) cc_final: 0.8141 (mpp) REVERT: g 109 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8156 (mp10) REVERT: h 42 TYR cc_start: 0.8297 (t80) cc_final: 0.7844 (t80) REVERT: h 58 GLU cc_start: 0.7579 (mp0) cc_final: 0.7249 (mp0) REVERT: h 168 TYR cc_start: 0.7900 (m-80) cc_final: 0.7646 (m-80) REVERT: h 211 MET cc_start: 0.7150 (tpt) cc_final: 0.6801 (tpp) REVERT: i 73 ARG cc_start: 0.8670 (ttp80) cc_final: 0.8312 (ttp-110) REVERT: i 77 LYS cc_start: 0.9329 (mttm) cc_final: 0.9019 (mtmt) REVERT: j 66 LYS cc_start: 0.9261 (mttp) cc_final: 0.8918 (mmtt) REVERT: k 7 VAL cc_start: 0.9260 (t) cc_final: 0.9047 (p) REVERT: k 24 ARG cc_start: 0.8966 (ttm110) cc_final: 0.8511 (ptp-110) REVERT: k 25 TYR cc_start: 0.8562 (m-10) cc_final: 0.8269 (m-80) REVERT: l 59 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6289 (tp) REVERT: l 144 MET cc_start: 0.7503 (ptp) cc_final: 0.6772 (mmp) REVERT: m 42 GLU cc_start: 0.8774 (pt0) cc_final: 0.8443 (pt0) REVERT: n 120 LYS cc_start: 0.8648 (mtmm) cc_final: 0.8215 (ptpp) REVERT: n 128 SER cc_start: 0.7902 (p) cc_final: 0.7284 (t) REVERT: o 82 LYS cc_start: 0.7985 (ttpp) cc_final: 0.7614 (ttpp) REVERT: p 15 GLN cc_start: 0.7114 (tp-100) cc_final: 0.6850 (tp40) REVERT: p 31 ILE cc_start: 0.9276 (mt) cc_final: 0.8943 (mm) REVERT: p 40 ASN cc_start: 0.8988 (m-40) cc_final: 0.8336 (t0) REVERT: p 83 GLU cc_start: 0.7865 (mp0) cc_final: 0.7462 (mp0) REVERT: p 106 ARG cc_start: 0.8236 (ttp80) cc_final: 0.7243 (tpt90) REVERT: p 107 ILE cc_start: 0.7831 (mp) cc_final: 0.7358 (mp) REVERT: r 50 GLU cc_start: 0.8796 (mp0) cc_final: 0.8456 (tp30) REVERT: r 68 ASP cc_start: 0.8680 (p0) cc_final: 0.8407 (p0) REVERT: r 90 ARG cc_start: 0.8415 (mmm160) cc_final: 0.7974 (ttm170) REVERT: r 110 LYS cc_start: 0.5954 (OUTLIER) cc_final: 0.5574 (mmtm) REVERT: s 18 ASP cc_start: 0.8435 (t0) cc_final: 0.8021 (p0) REVERT: t 80 GLN cc_start: 0.8692 (tm-30) cc_final: 0.8174 (tm-30) REVERT: u 79 ASN cc_start: 0.8540 (m-40) cc_final: 0.8204 (m110) REVERT: v 39 LYS cc_start: 0.8783 (ptpt) cc_final: 0.8537 (mtmt) REVERT: w 32 TYR cc_start: 0.8171 (m-80) cc_final: 0.7892 (m-80) REVERT: y 13 GLN cc_start: 0.8400 (mm110) cc_final: 0.8088 (mp10) REVERT: y 78 ASN cc_start: 0.9092 (m-40) cc_final: 0.8823 (m-40) REVERT: z 44 GLU cc_start: 0.8515 (tp30) cc_final: 0.8090 (tp30) outliers start: 243 outliers final: 213 residues processed: 1336 average time/residue: 1.1698 time to fit residues: 2752.6760 Evaluate side-chains 1380 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1159 time to evaluate : 5.988 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 14 ILE Chi-restraints excluded: chain 5 residue 48 LYS Chi-restraints excluded: chain 5 residue 60 ASP Chi-restraints excluded: chain 5 residue 78 THR Chi-restraints excluded: chain 5 residue 85 THR Chi-restraints excluded: chain 5 residue 87 THR Chi-restraints excluded: chain 5 residue 92 LEU Chi-restraints excluded: chain 5 residue 120 ASN Chi-restraints excluded: chain 5 residue 125 VAL Chi-restraints excluded: chain 5 residue 127 ILE Chi-restraints excluded: chain 5 residue 134 LYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 110 LEU Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 149 ILE Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 90 THR Chi-restraints excluded: chain E residue 111 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 164 GLU Chi-restraints excluded: chain F residue 36 THR Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 103 VAL Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 95 LEU Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 47 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 118 ARG Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 74 ILE Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 87 GLN Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain T residue 22 THR Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 24 ASN Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 79 ARG Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 24 ILE Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain b residue 15 MET Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain c residue 12 VAL Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain h residue 31 ASP Chi-restraints excluded: chain h residue 33 LEU Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain h residue 165 THR Chi-restraints excluded: chain i residue 100 ASN Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 174 ASP Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain j residue 21 VAL Chi-restraints excluded: chain j residue 43 ASN Chi-restraints excluded: chain j residue 56 VAL Chi-restraints excluded: chain j residue 73 ASN Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 75 VAL Chi-restraints excluded: chain l residue 84 THR Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 106 GLU Chi-restraints excluded: chain l residue 122 ASN Chi-restraints excluded: chain l residue 125 SER Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 72 VAL Chi-restraints excluded: chain m residue 76 GLN Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 113 ASP Chi-restraints excluded: chain n residue 6 TYR Chi-restraints excluded: chain n residue 7 TYR Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 66 THR Chi-restraints excluded: chain n residue 91 ASP Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 81 ASN Chi-restraints excluded: chain p residue 108 THR Chi-restraints excluded: chain p residue 116 ILE Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 41 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 63 VAL Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 102 LEU Chi-restraints excluded: chain r residue 13 LYS Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 95 LEU Chi-restraints excluded: chain r residue 105 ASN Chi-restraints excluded: chain r residue 110 LYS Chi-restraints excluded: chain s residue 30 ILE Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain s residue 76 LYS Chi-restraints excluded: chain u residue 23 ASP Chi-restraints excluded: chain u residue 29 ASN Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain w residue 25 ASP Chi-restraints excluded: chain w residue 55 LEU Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 4 SER Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 7 LYS Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain x residue 67 VAL Chi-restraints excluded: chain y residue 58 VAL Chi-restraints excluded: chain y residue 67 ILE Chi-restraints excluded: chain y residue 80 THR Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 24 GLU Chi-restraints excluded: chain z residue 43 THR Chi-restraints excluded: chain z residue 56 HIS Chi-restraints excluded: chain z residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 943 optimal weight: 30.0000 chunk 621 optimal weight: 30.0000 chunk 1001 optimal weight: 6.9990 chunk 610 optimal weight: 9.9990 chunk 474 optimal weight: 50.0000 chunk 695 optimal weight: 0.9990 chunk 1050 optimal weight: 8.9990 chunk 966 optimal weight: 0.6980 chunk 836 optimal weight: 0.4980 chunk 86 optimal weight: 10.0000 chunk 645 optimal weight: 1.9990 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 58 ASN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 61 ASN ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN a 33 ASN e 31 HIS ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 168 HIS ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 50 ASN v 51 ASN y 61 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 164782 Z= 0.172 Angle : 0.637 15.554 246842 Z= 0.338 Chirality : 0.034 0.396 31494 Planarity : 0.006 0.125 12988 Dihedral : 24.455 179.033 83130 Min Nonbonded Distance : 1.048 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.23 % Favored : 92.72 % Rotamer: Outliers : 4.32 % Allowed : 24.14 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.11), residues: 5756 helix: 0.48 (0.12), residues: 1907 sheet: -0.95 (0.16), residues: 1064 loop : -1.64 (0.11), residues: 2785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.083 0.002 TRP k 42 HIS 0.013 0.001 HIS e 31 PHE 0.042 0.002 PHE F 52 TYR 0.029 0.001 TYR a 9 ARG 0.023 0.000 ARG C 59 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11512 Ramachandran restraints generated. 5756 Oldfield, 0 Emsley, 5756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1406 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1199 time to evaluate : 5.986 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: 5 37 GLN cc_start: 0.7266 (mt0) cc_final: 0.6518 (mt0) REVERT: 5 40 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8062 (mp0) REVERT: 5 48 LYS cc_start: 0.6217 (OUTLIER) cc_final: 0.5869 (mmtm) REVERT: 5 66 PHE cc_start: 0.8377 (t80) cc_final: 0.8113 (t80) REVERT: 5 134 LYS cc_start: 0.8253 (OUTLIER) cc_final: 0.7740 (mtmm) REVERT: A 43 THR cc_start: 0.9327 (m) cc_final: 0.8823 (p) REVERT: A 44 LYS cc_start: 0.9305 (mtpp) cc_final: 0.8735 (mttm) REVERT: A 78 LYS cc_start: 0.8123 (mttp) cc_final: 0.7904 (mtpp) REVERT: B 35 GLU cc_start: 0.7262 (tt0) cc_final: 0.6943 (tt0) REVERT: B 96 TYR cc_start: 0.8858 (m-80) cc_final: 0.8503 (m-80) REVERT: B 163 GLN cc_start: 0.8119 (tp-100) cc_final: 0.7858 (tp-100) REVERT: C 1 MET cc_start: 0.7534 (tpt) cc_final: 0.6694 (tpt) REVERT: C 108 ASP cc_start: 0.7032 (m-30) cc_final: 0.6494 (m-30) REVERT: E 21 ASN cc_start: 0.8710 (t0) cc_final: 0.8016 (t0) REVERT: E 23 ASN cc_start: 0.8562 (p0) cc_final: 0.8210 (m110) REVERT: E 156 ILE cc_start: 0.9190 (tp) cc_final: 0.8964 (tp) REVERT: F 35 ARG cc_start: 0.7948 (tpp80) cc_final: 0.7672 (ttt180) REVERT: F 143 GLN cc_start: 0.8678 (tp-100) cc_final: 0.8275 (tp-100) REVERT: J 108 MET cc_start: 0.7721 (OUTLIER) cc_final: 0.7357 (mtt) REVERT: J 128 ASN cc_start: 0.8071 (p0) cc_final: 0.7774 (p0) REVERT: K 82 ASN cc_start: 0.7836 (OUTLIER) cc_final: 0.7344 (m-40) REVERT: K 107 LEU cc_start: 0.8757 (OUTLIER) cc_final: 0.8448 (pt) REVERT: L 12 SER cc_start: 0.8762 (t) cc_final: 0.8429 (p) REVERT: L 106 GLU cc_start: 0.7487 (tm-30) cc_final: 0.7287 (tm-30) REVERT: O 17 LYS cc_start: 0.8989 (tptt) cc_final: 0.8667 (tptp) REVERT: O 98 GLN cc_start: 0.8718 (tm-30) cc_final: 0.8213 (tm-30) REVERT: P 31 TRP cc_start: 0.8165 (m100) cc_final: 0.7744 (m100) REVERT: R 18 GLN cc_start: 0.8245 (pt0) cc_final: 0.7877 (pt0) REVERT: S 77 ASP cc_start: 0.8204 (m-30) cc_final: 0.7339 (t0) REVERT: S 109 ASP cc_start: 0.7676 (t0) cc_final: 0.7333 (t0) REVERT: T 42 GLU cc_start: 0.8368 (mt-10) cc_final: 0.8086 (mt-10) REVERT: T 43 ILE cc_start: 0.8717 (OUTLIER) cc_final: 0.8373 (mt) REVERT: X 54 LYS cc_start: 0.8726 (ttpp) cc_final: 0.8383 (tttp) REVERT: g 18 HIS cc_start: 0.7575 (m90) cc_final: 0.7231 (m90) REVERT: g 28 LYS cc_start: 0.8261 (tttt) cc_final: 0.7874 (mptt) REVERT: g 44 GLU cc_start: 0.8456 (mt-10) cc_final: 0.8177 (mp0) REVERT: g 49 MET cc_start: 0.8595 (mtm) cc_final: 0.8126 (mpp) REVERT: g 100 MET cc_start: 0.8915 (mmm) cc_final: 0.8484 (tpp) REVERT: g 109 GLN cc_start: 0.8856 (mm-40) cc_final: 0.8152 (mp10) REVERT: h 42 TYR cc_start: 0.8238 (t80) cc_final: 0.7933 (t80) REVERT: h 58 GLU cc_start: 0.7594 (mp0) cc_final: 0.7268 (mp0) REVERT: h 134 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8904 (ptt) REVERT: h 211 MET cc_start: 0.7200 (tpt) cc_final: 0.6823 (tpp) REVERT: i 73 ARG cc_start: 0.8668 (ttp80) cc_final: 0.8351 (ttp-110) REVERT: i 77 LYS cc_start: 0.9298 (mttm) cc_final: 0.8987 (mtmt) REVERT: j 55 GLU cc_start: 0.8340 (mp0) cc_final: 0.8073 (mp0) REVERT: j 66 LYS cc_start: 0.9262 (mttp) cc_final: 0.8914 (mptt) REVERT: k 24 ARG cc_start: 0.8936 (ttm110) cc_final: 0.8492 (ptp-110) REVERT: k 25 TYR cc_start: 0.8522 (m-10) cc_final: 0.8280 (m-80) REVERT: l 59 LEU cc_start: 0.6823 (OUTLIER) cc_final: 0.6376 (tp) REVERT: m 27 MET cc_start: 0.8087 (ptm) cc_final: 0.7518 (ppp) REVERT: m 42 GLU cc_start: 0.8755 (pt0) cc_final: 0.8417 (pt0) REVERT: m 91 GLU cc_start: 0.7933 (mt-10) cc_final: 0.7471 (mp0) REVERT: n 128 SER cc_start: 0.7771 (p) cc_final: 0.6931 (t) REVERT: n 130 ARG cc_start: 0.7469 (mmp80) cc_final: 0.6926 (mmp-170) REVERT: o 82 LYS cc_start: 0.8054 (ttpp) cc_final: 0.7677 (ttpp) REVERT: o 88 MET cc_start: 0.7766 (ptt) cc_final: 0.7461 (ptt) REVERT: p 31 ILE cc_start: 0.9270 (mt) cc_final: 0.8941 (mm) REVERT: p 38 GLN cc_start: 0.8331 (mp10) cc_final: 0.8023 (pm20) REVERT: p 40 ASN cc_start: 0.8958 (m-40) cc_final: 0.8391 (t0) REVERT: p 83 GLU cc_start: 0.7830 (mp0) cc_final: 0.7412 (mp0) REVERT: p 106 ARG cc_start: 0.8217 (ttp80) cc_final: 0.7211 (tpt90) REVERT: p 107 ILE cc_start: 0.7749 (mp) cc_final: 0.7277 (mp) REVERT: p 126 LYS cc_start: 0.7774 (ttmm) cc_final: 0.7379 (mmtt) REVERT: r 50 GLU cc_start: 0.8846 (mp0) cc_final: 0.8470 (tp30) REVERT: r 68 ASP cc_start: 0.8627 (p0) cc_final: 0.8381 (p0) REVERT: r 78 LYS cc_start: 0.9266 (ptmm) cc_final: 0.8787 (tttp) REVERT: r 90 ARG cc_start: 0.8351 (mmm160) cc_final: 0.7571 (mtm180) REVERT: s 18 ASP cc_start: 0.8422 (t0) cc_final: 0.8071 (p0) REVERT: s 83 LYS cc_start: 0.8597 (OUTLIER) cc_final: 0.8137 (mmtp) REVERT: s 92 GLU cc_start: 0.8902 (mp0) cc_final: 0.8597 (mp0) REVERT: t 80 GLN cc_start: 0.8666 (tm-30) cc_final: 0.8126 (tm-30) REVERT: w 73 ARG cc_start: 0.7670 (ptt90) cc_final: 0.7462 (ptt90) REVERT: x 11 ILE cc_start: 0.8619 (pt) cc_final: 0.8146 (mp) REVERT: x 17 LYS cc_start: 0.7960 (mttt) cc_final: 0.7613 (ptmt) REVERT: x 66 MET cc_start: 0.6877 (ptp) cc_final: 0.6578 (ptp) REVERT: y 13 GLN cc_start: 0.8386 (mm110) cc_final: 0.8086 (mp10) REVERT: y 78 ASN cc_start: 0.9070 (m-40) cc_final: 0.8806 (m-40) REVERT: z 44 GLU cc_start: 0.8453 (tp30) cc_final: 0.8054 (tp30) outliers start: 207 outliers final: 178 residues processed: 1325 average time/residue: 1.1466 time to fit residues: 2672.4995 Evaluate side-chains 1347 residues out of total 4793 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 187 poor density : 1160 time to evaluate : 5.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 14 ILE Chi-restraints excluded: chain 5 residue 48 LYS Chi-restraints excluded: chain 5 residue 60 ASP Chi-restraints excluded: chain 5 residue 78 THR Chi-restraints excluded: chain 5 residue 87 THR Chi-restraints excluded: chain 5 residue 120 ASN Chi-restraints excluded: chain 5 residue 125 VAL Chi-restraints excluded: chain 5 residue 127 ILE Chi-restraints excluded: chain 5 residue 134 LYS Chi-restraints excluded: chain A residue 35 SER Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 72 ASP Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 58 ASN Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 180 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 199 SER Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 93 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain E residue 60 ILE Chi-restraints excluded: chain E residue 117 LEU Chi-restraints excluded: chain G residue 12 LEU Chi-restraints excluded: chain G residue 45 GLU Chi-restraints excluded: chain G residue 109 GLU Chi-restraints excluded: chain G residue 115 VAL Chi-restraints excluded: chain J residue 14 ASP Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 108 MET Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 82 ASN Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 68 SER Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 93 ASN Chi-restraints excluded: chain L residue 121 THR Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 12 MET Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 73 ILE Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 102 LEU Chi-restraints excluded: chain M residue 108 VAL Chi-restraints excluded: chain M residue 129 THR Chi-restraints excluded: chain M residue 132 THR Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 29 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain O residue 39 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain O residue 103 VAL Chi-restraints excluded: chain P residue 28 VAL Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 70 VAL Chi-restraints excluded: chain P residue 76 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 84 ILE Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain P residue 92 VAL Chi-restraints excluded: chain Q residue 8 VAL Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 22 LEU Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 87 GLN Chi-restraints excluded: chain R residue 96 VAL Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain T residue 24 MET Chi-restraints excluded: chain T residue 43 ILE Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain V residue 4 ILE Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 22 LEU Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain Z residue 19 LYS Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 36 VAL Chi-restraints excluded: chain Z residue 41 THR Chi-restraints excluded: chain a residue 13 THR Chi-restraints excluded: chain a residue 21 VAL Chi-restraints excluded: chain a residue 24 ILE Chi-restraints excluded: chain a residue 33 ASN Chi-restraints excluded: chain a residue 56 ARG Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 43 ILE Chi-restraints excluded: chain c residue 48 ILE Chi-restraints excluded: chain e residue 31 HIS Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain g residue 70 VAL Chi-restraints excluded: chain h residue 31 ASP Chi-restraints excluded: chain h residue 33 LEU Chi-restraints excluded: chain h residue 35 SER Chi-restraints excluded: chain h residue 66 VAL Chi-restraints excluded: chain h residue 67 THR Chi-restraints excluded: chain h residue 134 MET Chi-restraints excluded: chain h residue 176 HIS Chi-restraints excluded: chain i residue 100 ASN Chi-restraints excluded: chain i residue 101 VAL Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 174 ASP Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain j residue 43 ASN Chi-restraints excluded: chain j residue 56 VAL Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 30 THR Chi-restraints excluded: chain l residue 7 ILE Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 75 VAL Chi-restraints excluded: chain l residue 84 THR Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain l residue 89 VAL Chi-restraints excluded: chain l residue 122 ASN Chi-restraints excluded: chain m residue 72 VAL Chi-restraints excluded: chain m residue 76 GLN Chi-restraints excluded: chain m residue 104 VAL Chi-restraints excluded: chain m residue 113 ASP Chi-restraints excluded: chain n residue 6 TYR Chi-restraints excluded: chain n residue 7 TYR Chi-restraints excluded: chain n residue 21 ILE Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 58 VAL Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 66 THR Chi-restraints excluded: chain n residue 91 ASP Chi-restraints excluded: chain n residue 111 VAL Chi-restraints excluded: chain o residue 80 THR Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain p residue 32 VAL Chi-restraints excluded: chain p residue 81 ASN Chi-restraints excluded: chain p residue 108 THR Chi-restraints excluded: chain p residue 116 ILE Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 63 VAL Chi-restraints excluded: chain q residue 64 THR Chi-restraints excluded: chain q residue 102 LEU Chi-restraints excluded: chain r residue 13 LYS Chi-restraints excluded: chain r residue 64 VAL Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 95 LEU Chi-restraints excluded: chain r residue 105 ASN Chi-restraints excluded: chain s residue 30 ILE Chi-restraints excluded: chain s residue 48 LEU Chi-restraints excluded: chain s residue 51 LEU Chi-restraints excluded: chain s residue 54 ASP Chi-restraints excluded: chain s residue 76 LYS Chi-restraints excluded: chain s residue 83 LYS Chi-restraints excluded: chain u residue 29 ASN Chi-restraints excluded: chain v residue 50 ASN Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain w residue 34 THR Chi-restraints excluded: chain w residue 55 LEU Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 4 SER Chi-restraints excluded: chain x residue 5 LEU Chi-restraints excluded: chain x residue 7 LYS Chi-restraints excluded: chain x residue 51 VAL Chi-restraints excluded: chain x residue 62 VAL Chi-restraints excluded: chain x residue 67 VAL Chi-restraints excluded: chain y residue 58 VAL Chi-restraints excluded: chain y residue 67 ILE Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 43 THR Chi-restraints excluded: chain z residue 68 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 512 optimal weight: 3.9990 chunk 664 optimal weight: 7.9990 chunk 890 optimal weight: 0.4980 chunk 256 optimal weight: 10.0000 chunk 770 optimal weight: 6.9990 chunk 123 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 837 optimal weight: 8.9990 chunk 350 optimal weight: 10.0000 chunk 859 optimal weight: 8.9990 chunk 106 optimal weight: 50.0000 overall best weight: 5.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 130 GLN ** C 164 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 130 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 29 HIS ** O 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN ** R 11 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 GLN a 33 ASN g 15 HIS ** g 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 37 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 61 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.074976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 95)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.054172 restraints weight = 550535.576| |-----------------------------------------------------------------------------| r_work (start): 0.3176 rms_B_bonded: 1.52 r_work: 0.3068 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.4463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.389 164782 Z= 0.269 Angle : 0.686 59.170 246842 Z= 0.374 Chirality : 0.036 1.124 31494 Planarity : 0.006 0.175 12988 Dihedral : 24.452 179.058 83130 Min Nonbonded Distance : 1.044 Molprobity Statistics. All-atom Clashscore : 15.30 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.30 % Favored : 92.63 % Rotamer: Outliers : 4.17 % Allowed : 24.26 % Favored : 71.56 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 0.54 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.11), residues: 5756 helix: 0.48 (0.12), residues: 1908 sheet: -0.94 (0.16), residues: 1069 loop : -1.64 (0.11), residues: 2779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.091 0.003 TRP k 42 HIS 0.076 0.001 HIS e 31 PHE 0.035 0.002 PHE E 77 TYR 0.041 0.002 TYR l 44 ARG 0.019 0.000 ARG J 96 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 48559.41 seconds wall clock time: 844 minutes 27.76 seconds (50667.76 seconds total)