Starting phenix.real_space_refine on Wed Mar 27 17:58:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acr_11718/03_2024/7acr_11718_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acr_11718/03_2024/7acr_11718.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acr_11718/03_2024/7acr_11718_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.44 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acr_11718/03_2024/7acr_11718_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acr_11718/03_2024/7acr_11718_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acr_11718/03_2024/7acr_11718.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acr_11718/03_2024/7acr_11718.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acr_11718/03_2024/7acr_11718_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7acr_11718/03_2024/7acr_11718_updated.pdb" } resolution = 3.44 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 4916 5.49 5 Mg 212 5.21 5 S 153 5.16 5 C 75846 2.51 5 N 28215 2.21 5 O 42324 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 45": "NH1" <-> "NH2" Residue "5 ARG 106": "NH1" <-> "NH2" Residue "5 ARG 139": "NH1" <-> "NH2" Residue "A ARG 11": "NH1" <-> "NH2" 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 ARG 13": "NH1" <-> "NH2" 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 "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 152": "NH1" <-> "NH2" Residue "F ARG 153": "NH1" <-> "NH2" Residue "F ARG 163": "NH1" <-> "NH2" Residue "F ARG 170": "NH1" <-> "NH2" Residue "G ARG 50": "NH1" <-> "NH2" Residue "G ARG 51": "NH1" <-> "NH2" Residue "G ARG 68": "NH1" <-> "NH2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J GLU 31": "OE1" <-> "OE2" Residue "J ARG 34": "NH1" <-> "NH2" Residue "J ARG 35": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J TYR 74": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 "L ARG 126": "NH1" <-> "NH2" Residue "L GLU 136": "OE1" <-> "OE2" 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 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" 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 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 GLU 84": "OE1" <-> "OE2" Residue "O PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "P GLU 11": "OE1" <-> "OE2" 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 GLU 16": "OE1" <-> "OE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R GLU 23": "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 "S ARG 110": "NH1" <-> "NH2" Residue "T ARG 6": "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 "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 "b ARG 52": "NH1" <-> "NH2" Residue "c ARG 28": "NH1" <-> "NH2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 41": "NH1" <-> "NH2" Residue "e ARG 13": "NH1" <-> "NH2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 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 88": "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 ARG 73": "NH1" <-> "NH2" Residue "i ARG 81": "NH1" <-> "NH2" Residue "i ARG 146": "NH1" <-> "NH2" 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 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 GLU 59": "OE1" <-> "OE2" Residue "n GLU 89": "OE1" <-> "OE2" Residue "n GLU 97": "OE1" <-> "OE2" Residue "n ASP 107": "OD1" <-> "OD2" Residue "n GLU 112": "OE1" <-> "OE2" Residue "n ARG 113": "NH1" <-> "NH2" Residue "n ARG 119": "NH1" <-> "NH2" Residue "n ARG 124": "NH1" <-> "NH2" Residue "n ARG 130": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o ARG 45": "NH1" <-> "NH2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "p ARG 37": "NH1" <-> "NH2" Residue "p ARG 69": "NH1" <-> "NH2" Residue "p ARG 93": "NH1" <-> "NH2" Residue "p ARG 106": "NH1" <-> "NH2" Residue "q ARG 9": "NH1" <-> "NH2" Residue "q ARG 14": "NH1" <-> "NH2" Residue "q ARG 50": "NH1" <-> "NH2" Residue "q ARG 83": "NH1" <-> "NH2" Residue "r ARG 29": "NH1" <-> "NH2" Residue "r ARG 70": "NH1" <-> "NH2" Residue "r ARG 87": "NH1" <-> "NH2" Residue "r ARG 109": "NH1" <-> "NH2" Residue "s ARG 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 "s ARG 85": "NH1" <-> "NH2" Residue "t ARG 72": "NH1" <-> "NH2" Residue "t ARG 89": "NH1" <-> "NH2" Residue "u ARG 28": "NH1" <-> "NH2" Residue "u 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 61": "NH1" <-> "NH2" Residue "x ARG 32": "NH1" <-> "NH2" Residue "y ARG 60": "NH1" <-> "NH2" Residue "y ARG 74": "NH1" <-> "NH2" Residue "z GLU 39": "OE1" <-> "OE2" Residue "z ARG 45": "NH1" <-> "NH2" Residue "z ARG 55": "NH1" <-> "NH2" Residue "z ARG 66": "NH1" <-> "NH2" Residue "z ARG 67": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 151668 Number of models: 1 Model: "" Number of chains: 66 Chain: "1" Number of atoms: 62335 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62335 Classifications: {'RNA': 2903} Modifications used: {'rna2p': 6, 'rna2p_pur': 301, 'rna2p_pyr': 164, 'rna3p': 16, 'rna3p_pur': 1366, 'rna3p_pyr': 1050} Link IDs: {'rna2p': 470, 'rna3p': 2432} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 46 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 1 Chain: "2" Number of atoms: 32927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1534, 32927 Classifications: {'RNA': 1534} Modifications used: {'rna2p': 1, 'rna2p_pur': 121, 'rna2p_pyr': 98, 'rna3p': 10, 'rna3p_pur': 748, 'rna3p_pyr': 555} Link IDs: {'rna2p': 220, 'rna3p': 1313} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 4 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 41 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Chain: "3" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 7, 'rna3p_pur': 56, 'rna3p_pyr': 49} Link IDs: {'rna2p': 14, 'rna3p': 105} Chain: "4" Number of atoms: 7755 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 7755 Classifications: {'RNA': 363} Modifications used: {'5*END': 1, 'rna2p_pur': 38, 'rna2p_pyr': 30, 'rna3p': 3, 'rna3p_pur': 160, 'rna3p_pyr': 132} Link IDs: {'rna2p': 67, 'rna3p': 295} Unresolved chain links: 1 Unresolved chain link angles: 4 Unresolved chain link dihedrals: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 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: 582 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 582 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 74} Chain: "B" Number of atoms: 2082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2082 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 17, 'TRANS': 253} Chain: "C" Number of atoms: 1565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1565 Classifications: {'peptide': 209} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 202} Chain: "D" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1552 Classifications: {'peptide': 201} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 195} Chain: "E" Number of atoms: 1410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1410 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "F" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1313 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "G" Number of atoms: 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: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 114} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'0TD:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "r" Number of atoms: 867 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 867 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "s" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "t" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 714 Classifications: {'peptide': 88} Modifications used: {'COO': 1} Link IDs: {'TRANS': 87} Chain: "u" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 649 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 79} Chain: "v" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 648 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "w" Number of atoms: 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: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "y" Number of atoms: 669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 669 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "z" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 589 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 2, 'TRANS': 67} Chain: "1" Number of atoms: 172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 172 Unusual residues: {' MG': 172} Classifications: {'undetermined': 172} Link IDs: {None: 171} Chain: "2" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 31 Unusual residues: {' MG': 31} Classifications: {'undetermined': 31} Link IDs: {None: 30} Chain: "3" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' MG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "a" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "d" 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: "h" 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 A0N5B SG CYS a 16 126.811 95.456 37.757 1.00237.03 S ATOM A0N9L SG CYS a 37 129.296 97.891 38.776 1.00222.56 S ATOM A0NA6 SG CYS a 40 125.960 99.295 38.959 1.00226.25 S ATOM A0OUZ SG CYS f 11 179.228 183.683 89.100 1.00 99.87 S ATOM A0OVO SG CYS f 14 182.411 182.310 90.622 1.00103.32 S ATOM A0OYJ SG CYS f 27 180.788 185.488 92.084 1.00105.74 S Time building chain proxies: 59.30, per 1000 atoms: 0.39 Number of scatterers: 151668 At special positions: 0 Unit cell: (298.48, 266.24, 245.44, 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 4916 15.00 Mg 212 11.99 O 42324 8.00 N 28215 7.00 C 75846 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 Atom "ATOM 91769 O5' U 21372 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 67.97 Conformation dependent library (CDL) restraints added in 7.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN a 101 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 37 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 40 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 16 " 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 14 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " Number of angles added : 3 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10766 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: 170 helices and 73 sheets defined 37.7% alpha, 19.2% beta 1449 base pairs and 2379 stacking pairs defined. Time for finding SS restraints: 74.88 Creating SS restraints... Processing helix chain '5' and resid 17 through 24 removed outlier: 4.264A pdb=" N ARG 5 21 " --> pdb=" O ASN 5 17 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS 5 22 " --> pdb=" O LYS 5 18 " (cutoff:3.500A) Processing helix chain '5' and resid 37 through 47 removed outlier: 4.016A pdb=" N VAL 5 41 " --> pdb=" O GLN 5 37 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N LYS 5 42 " --> pdb=" O GLY 5 38 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N SER 5 43 " --> pdb=" O TRP 5 39 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG 5 45 " --> pdb=" O VAL 5 41 " (cutoff:3.500A) Processing helix chain '5' and resid 93 through 103 removed outlier: 3.896A pdb=" N ASP 5 98 " --> pdb=" O GLN 5 94 " (cutoff:3.500A) removed outlier: 5.456A pdb=" N SER 5 99 " --> pdb=" O ARG 5 95 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N LEU 5 100 " --> pdb=" O GLU 5 96 " (cutoff:3.500A) Processing helix chain '5' and resid 134 through 160 removed outlier: 6.507A pdb=" N LYS 5 138 " --> pdb=" O LYS 5 134 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG 5 139 " --> pdb=" O GLN 5 135 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N VAL 5 149 " --> pdb=" O ARG 5 145 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 16 removed outlier: 7.265A pdb=" N HIS B 15 " --> pdb=" O PRO B 11 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N VAL B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 136 Proline residue: B 136 - end of helix Processing helix chain 'B' and resid 207 through 215 removed outlier: 3.715A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ARG B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 4.816A pdb=" N ASN B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 268 removed outlier: 4.870A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 5.562A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ILE B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) removed outlier: 5.924A 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 'C' and resid 61 through 72 Processing helix chain 'C' and resid 98 through 103 removed outlier: 4.316A pdb=" N ALA C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ASP C 103 " --> pdb=" O GLU C 99 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 98 through 103' Processing helix chain 'C' and resid 120 through 125 Processing helix chain 'D' and resid 15 through 20 removed outlier: 3.739A pdb=" N PHE D 19 " --> pdb=" O SER D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 41 removed outlier: 3.612A pdb=" N ARG D 40 " --> pdb=" O ALA D 36 " (cutoff:3.500A) removed outlier: 5.746A pdb=" N GLN D 41 " --> pdb=" O ALA D 37 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 116 Processing helix chain 'D' and resid 130 through 142 removed outlier: 3.543A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 163 removed outlier: 3.712A pdb=" N ARG D 162 " --> pdb=" O PHE D 158 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N ASN D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 183 removed outlier: 3.891A pdb=" N LEU D 180 " --> pdb=" O ASP D 176 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE D 181 " --> pdb=" O PRO D 177 " (cutoff:3.500A) Processing helix chain 'D' and resid 189 through 201 Processing helix chain 'E' and resid 2 through 20 removed outlier: 4.090A pdb=" N GLU E 11 " --> pdb=" O TYR E 7 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LYS E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 42 through 47 removed outlier: 4.006A pdb=" N ASP E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS E 47 " --> pdb=" O ALA E 43 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 42 through 47' Processing helix chain 'E' and resid 48 through 62 Processing helix chain 'E' and resid 93 through 108 Processing helix chain 'E' and resid 162 through 174 removed outlier: 3.849A pdb=" N GLY E 166 " --> pdb=" O SER E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 removed outlier: 4.268A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N PHE E 138 " --> pdb=" O GLN E 135 " (cutoff:3.500A) Proline residue: E 139 - end of helix No H-bonds generated for 'chain 'E' and resid 134 through 139' Processing helix chain 'F' and resid 2 through 8 removed outlier: 3.990A pdb=" N ALA F 7 " --> pdb=" O ARG F 3 " (cutoff:3.500A) Proline residue: F 8 - end of helix Processing helix chain 'F' and resid 60 through 81 Processing helix chain 'F' and resid 137 through 153 removed outlier: 3.849A pdb=" N ARG F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 28 removed outlier: 3.840A pdb=" N ALA G 26 " --> pdb=" O LYS G 22 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG G 27 " --> pdb=" O ALA G 23 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASN G 28 " --> pdb=" O GLY G 24 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 22 through 28' Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 43 through 51 removed outlier: 3.512A pdb=" N PHE G 47 " --> pdb=" O ASN G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 63 removed outlier: 3.730A pdb=" N VAL G 61 " --> pdb=" O LYS G 57 " (cutoff:3.500A) Processing helix chain 'G' and resid 69 through 74 removed outlier: 5.283A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) removed outlier: 5.301A 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: 3.904A pdb=" N ALA G 102 " --> pdb=" O ASP G 98 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N ALA G 105 " --> pdb=" O ASP G 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.409A pdb=" N THR J 30 " --> pdb=" O GLY J 26 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 98 through 110 removed outlier: 4.961A pdb=" N GLU J 102 " --> pdb=" O GLU J 98 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N MET J 108 " --> pdb=" O ALA J 104 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU J 109 " --> pdb=" O VAL J 105 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 4.276A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.442A 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 56 through 62 removed outlier: 3.781A 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: 4.325A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N THR L 74 " --> pdb=" O LYS L 70 " (cutoff:3.500A) removed outlier: 6.242A 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 83 removed outlier: 3.939A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 83' 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: 4.171A pdb=" N LYS M 123 " --> pdb=" O LEU M 119 " (cutoff:3.500A) removed outlier: 4.331A 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: 3.515A pdb=" N ASN N 23 " --> pdb=" O ALA N 19 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG N 30 " --> pdb=" O GLY N 26 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 56 removed outlier: 3.888A pdb=" N GLU N 43 " --> pdb=" O PRO N 39 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU N 44 " --> pdb=" O LYS N 40 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N GLU N 49 " --> pdb=" O ARG N 45 " (cutoff:3.500A) Proline residue: N 50 - end of helix Processing helix chain 'N' and resid 59 through 71 Processing helix chain 'N' and resid 72 through 88 removed outlier: 4.218A 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 22 removed outlier: 4.418A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 62 removed outlier: 5.169A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 2 through 13 removed outlier: 4.052A pdb=" N GLN P 7 " --> pdb=" O ASN P 3 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N GLN P 10 " --> pdb=" O LYS P 6 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLU P 11 " --> pdb=" O GLN P 7 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N MET P 13 " --> pdb=" O GLU P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 98 through 104 removed outlier: 4.727A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ARG P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 98 through 104' Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.687A pdb=" N GLN Q 20 " --> pdb=" O LYS Q 16 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA Q 21 " --> pdb=" O ILE Q 17 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N LYS Q 22 " --> pdb=" O LEU Q 18 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 4.262A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 72 removed outlier: 3.680A pdb=" N ARG Q 48 " --> pdb=" O GLN Q 44 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LYS Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLN Q 59 " --> pdb=" O ARG Q 55 " (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: 3.890A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.704A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 62 removed outlier: 3.953A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER S 53 " --> pdb=" O LYS S 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 11 removed outlier: 3.822A pdb=" N VAL T 10 " --> pdb=" O ARG T 6 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU T 11 " --> pdb=" O LEU T 7 " (cutoff:3.500A) Processing helix chain 'T' and resid 17 through 27 Processing helix chain 'T' and resid 39 through 51 removed outlier: 4.130A pdb=" N ALA T 45 " --> pdb=" O ALA T 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.868A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ALA U 71 " --> pdb=" O VAL U 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 66 through 71' Processing helix chain 'V' and resid 13 through 24 Processing helix chain 'V' and resid 43 through 53 removed outlier: 4.236A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N LYS V 53 " --> pdb=" O ASN V 49 " (cutoff:3.500A) Processing helix chain 'V' and resid 54 through 59 removed outlier: 4.262A pdb=" N SER V 58 " --> pdb=" O ALA V 54 " (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 8 removed outlier: 4.107A pdb=" N ARG Y 7 " --> pdb=" O ALA Y 3 " (cutoff:3.500A) removed outlier: 5.331A pdb=" N GLU Y 8 " --> pdb=" O LYS Y 4 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 35 removed outlier: 4.804A pdb=" N LEU Y 14 " --> pdb=" O SER Y 10 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 39 through 62 removed outlier: 4.830A pdb=" N LEU Y 43 " --> pdb=" O GLN Y 39 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N GLY Y 62 " --> pdb=" O ASN Y 58 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 Processing helix chain 'Z' and resid 41 through 52 Processing helix chain 'b' and resid 9 through 19 removed outlier: 4.867A 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: 4.045A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) removed outlier: 4.946A 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 15 removed outlier: 3.885A pdb=" N LYS e 12 " --> pdb=" O ARG e 8 " (cutoff:3.500A) removed outlier: 4.859A pdb=" N ARG e 13 " --> pdb=" O GLY e 9 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N PHE e 14 " --> pdb=" O ALA e 10 " (cutoff:3.500A) removed outlier: 6.007A pdb=" N LYS e 15 " --> pdb=" O ALA e 11 " (cutoff:3.500A) Processing helix chain 'e' and resid 37 through 46 removed outlier: 3.536A 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: 4.030A pdb=" N LEU e 55 " --> pdb=" O SER e 51 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N GLY e 56 " --> pdb=" O LYS e 52 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LEU e 57 " --> pdb=" O GLY e 53 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N VAL e 58 " --> pdb=" O ASP e 54 " (cutoff:3.500A) Proline residue: e 63 - end of helix Processing helix chain 'g' and resid 5 through 13 Processing helix chain 'g' and resid 27 through 32 removed outlier: 4.467A pdb=" N ILE g 31 " --> pdb=" O MET g 27 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N PHE g 32 " --> pdb=" O LYS g 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 27 through 32' Processing helix chain 'g' and resid 42 through 64 Proline residue: g 48 - end of helix removed outlier: 3.512A pdb=" N LYS g 64 " --> pdb=" O ILE g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 76 through 88 removed outlier: 3.740A pdb=" N VAL g 80 " --> pdb=" O ALA g 76 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS g 81 " --> pdb=" O SER g 77 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER g 86 " --> pdb=" O ASP g 82 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 124 removed outlier: 4.644A pdb=" N GLU g 118 " --> pdb=" O LEU g 114 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N SER g 121 " --> pdb=" O LEU g 117 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N GLN g 122 " --> pdb=" O GLU g 118 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLY g 124 " --> pdb=" O GLN g 120 " (cutoff:3.500A) Processing helix chain 'g' and resid 125 through 130 removed outlier: 4.717A pdb=" N LEU g 129 " --> pdb=" O THR g 125 " (cutoff:3.500A) removed outlier: 6.215A pdb=" N THR g 130 " --> pdb=" O PHE g 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 125 through 130' Processing helix chain 'g' and resid 131 through 149 removed outlier: 3.509A pdb=" N LEU g 144 " --> pdb=" O GLU g 140 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N SER g 147 " --> pdb=" O LYS g 143 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU g 148 " --> pdb=" O LEU g 144 " (cutoff:3.500A) Processing helix chain 'g' and resid 165 through 170 Processing helix chain 'g' and resid 171 through 180 Processing helix chain 'g' and resid 206 through 227 removed outlier: 4.993A pdb=" N GLN g 227 " --> pdb=" O GLU g 223 " (cutoff:3.500A) Processing helix chain 'h' and resid 6 through 12 removed outlier: 3.802A pdb=" N ILE h 10 " --> pdb=" O HIS h 6 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 48 Processing helix chain 'h' and resid 72 through 78 removed outlier: 4.299A pdb=" N VAL h 76 " --> pdb=" O ARG h 72 " (cutoff:3.500A) Processing helix chain 'h' and resid 81 through 96 removed outlier: 5.295A pdb=" N GLU h 85 " --> pdb=" O GLY h 81 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL h 90 " --> pdb=" O LYS h 86 " (cutoff:3.500A) Processing helix chain 'h' and resid 112 through 127 removed outlier: 5.342A pdb=" N SER h 119 " --> pdb=" O LEU h 115 " (cutoff:3.500A) removed outlier: 5.508A pdb=" N ILE h 120 " --> pdb=" O VAL h 116 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N THR h 121 " --> pdb=" O ALA h 117 " (cutoff:3.500A) removed outlier: 6.103A pdb=" N SER h 122 " --> pdb=" O ASP h 118 " (cutoff:3.500A) Processing helix chain 'h' and resid 129 through 145 removed outlier: 3.966A pdb=" N LEU h 144 " --> pdb=" O ASN h 140 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N GLY h 145 " --> pdb=" O ALA h 141 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 16 removed outlier: 4.764A pdb=" N LEU i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) removed outlier: 4.387A 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 Processing helix chain 'i' and resid 68 through 83 removed outlier: 5.001A pdb=" N LYS i 83 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 removed outlier: 3.888A 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: 3.502A pdb=" N GLN i 116 " --> pdb=" O ALA i 112 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N LYS i 121 " --> pdb=" O LEU i 117 " (cutoff:3.500A) Processing helix chain 'i' and resid 146 through 152 removed outlier: 4.157A pdb=" N LYS i 151 " --> pdb=" O GLU i 147 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N GLN i 152 " --> pdb=" O LYS i 148 " (cutoff:3.500A) Processing helix chain 'i' and resid 153 through 166 removed outlier: 3.829A pdb=" N GLU i 163 " --> pdb=" O LEU i 159 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N GLN i 164 " --> pdb=" O GLU i 160 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ARG i 165 " --> pdb=" O LEU i 161 " (cutoff:3.500A) removed outlier: 5.287A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 4.581A pdb=" N SER i 192 " --> pdb=" O ARG i 188 " (cutoff:3.500A) Processing helix chain 'i' and resid 196 through 206 removed outlier: 3.770A pdb=" N ILE i 200 " --> pdb=" O ASN i 196 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N TYR i 204 " --> pdb=" O ILE i 200 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 71 removed outlier: 3.578A pdb=" N GLU j 65 " --> pdb=" O GLN j 61 " (cutoff:3.500A) Processing helix chain 'j' and resid 110 through 119 removed outlier: 3.639A pdb=" N VAL j 114 " --> pdb=" O ALA j 110 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 147 removed outlier: 3.861A pdb=" N ARG j 138 " --> pdb=" O ILE j 134 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N MET j 147 " --> pdb=" O GLY j 143 " (cutoff:3.500A) Processing helix chain 'j' and resid 149 through 158 Processing helix chain 'j' and resid 160 through 165 removed outlier: 3.717A pdb=" N LEU j 165 " --> pdb=" O VAL j 161 " (cutoff:3.500A) Processing helix chain 'k' and resid 14 through 33 removed outlier: 4.988A 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 81 Processing helix chain 'l' and resid 20 through 32 removed outlier: 6.116A pdb=" N VAL l 32 " --> pdb=" O ASN l 28 " (cutoff:3.500A) Processing helix chain 'l' and resid 35 through 55 removed outlier: 3.569A pdb=" N GLN l 52 " --> pdb=" O GLU l 48 " (cutoff:3.500A) Processing helix chain 'l' and resid 57 through 70 Processing helix chain 'l' and resid 92 through 112 removed outlier: 5.071A pdb=" N GLY l 112 " --> pdb=" O ALA l 108 " (cutoff:3.500A) Processing helix chain 'l' and resid 115 through 130 removed outlier: 4.429A pdb=" N GLU l 129 " --> pdb=" O SER l 125 " (cutoff:3.500A) Processing helix chain 'l' and resid 132 through 149 removed outlier: 5.080A pdb=" N LYS l 136 " --> pdb=" O GLY l 132 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N MET l 144 " --> pdb=" O ASP l 140 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ASN l 148 " --> pdb=" O MET l 144 " (cutoff:3.500A) removed outlier: 5.387A 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 Processing helix chain 'm' and resid 112 through 120 Processing helix chain 'n' and resid 34 through 39 Processing helix chain 'n' and resid 41 through 56 removed outlier: 3.542A pdb=" N MET n 46 " --> pdb=" O GLU n 42 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ARG n 49 " --> pdb=" O ARG n 45 " (cutoff:3.500A) Proline residue: n 51 - end of helix removed outlier: 3.677A pdb=" N ASP n 56 " --> pdb=" O LEU n 52 " (cutoff:3.500A) Processing helix chain 'n' and resid 73 through 92 removed outlier: 4.811A pdb=" N GLY n 77 " --> pdb=" O SER n 73 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE n 79 " --> pdb=" O GLN n 75 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N ARG n 80 " --> pdb=" O ALA n 76 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ASP n 91 " --> pdb=" O LEU n 87 " (cutoff:3.500A) Processing helix chain 'n' and resid 94 through 102 removed outlier: 3.515A pdb=" N GLY n 102 " --> pdb=" O LEU n 98 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 33 removed outlier: 3.604A pdb=" N ASP o 19 " --> pdb=" O HIS o 15 " (cutoff:3.500A) removed outlier: 4.581A pdb=" N GLN o 20 " --> pdb=" O ARG o 16 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N THR o 28 " --> pdb=" O GLU o 24 " (cutoff:3.500A) Processing helix chain 'o' and resid 82 through 90 removed outlier: 3.891A pdb=" N LEU o 90 " --> pdb=" O ALA o 86 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 4.139A pdb=" N GLY p 51 " --> pdb=" O ALA p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 54 through 59 removed outlier: 4.598A pdb=" N SER p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.294A 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 76 removed outlier: 3.603A pdb=" N LYS p 75 " --> pdb=" O ALA p 71 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N GLU p 76 " --> pdb=" O ASP p 72 " (cutoff:3.500A) Processing helix chain 'p' and resid 92 through 104 removed outlier: 4.559A pdb=" N ILE p 97 " --> pdb=" O ARG p 93 " (cutoff:3.500A) removed outlier: 4.140A pdb=" N GLY p 104 " --> pdb=" O LEU p 100 " (cutoff:3.500A) Processing helix chain 'q' and resid 3 through 11 Proline residue: q 11 - end of helix Processing helix chain 'q' and resid 113 through 118 removed outlier: 3.876A pdb=" N TYR q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 22 removed outlier: 3.539A pdb=" N SER r 21 " --> pdb=" O ILE r 17 " (cutoff:3.500A) removed outlier: 4.697A pdb=" N ILE r 22 " --> pdb=" O ALA r 18 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 38 removed outlier: 3.707A pdb=" N SER r 30 " --> pdb=" O GLY r 26 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N LYS r 31 " --> pdb=" O LYS r 27 " (cutoff:3.500A) Processing helix chain 'r' and resid 49 through 64 removed outlier: 3.667A pdb=" N ILE r 53 " --> pdb=" O SER r 49 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ASP r 54 " --> pdb=" O GLU r 50 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ALA r 61 " --> pdb=" O ARG r 57 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS r 62 " --> pdb=" O ASP r 58 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N VAL r 64 " --> pdb=" O VAL r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 65 through 84 Processing helix chain 'r' and resid 85 through 94 removed outlier: 3.922A pdb=" N ARG r 93 " --> pdb=" O LEU r 89 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY r 94 " --> pdb=" O ARG r 90 " (cutoff:3.500A) Processing helix chain 'r' and resid 106 through 111 removed outlier: 4.102A pdb=" N GLY r 111 " --> pdb=" O ARG r 107 " (cutoff:3.500A) Processing helix chain 's' and resid 3 through 21 removed outlier: 3.629A pdb=" N ALA s 8 " --> pdb=" O GLN s 4 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ARG s 9 " --> pdb=" O SER s 5 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU s 10 " --> pdb=" O MET s 6 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N VAL s 11 " --> pdb=" O LYS s 7 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA s 17 " --> pdb=" O ARG s 13 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N LYS s 19 " --> pdb=" O ALA s 15 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N TYR s 20 " --> pdb=" O LEU s 16 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE s 21 " --> pdb=" O ALA s 17 " (cutoff:3.500A) Processing helix chain 's' and resid 22 through 34 removed outlier: 5.190A pdb=" N VAL s 34 " --> pdb=" O ILE s 30 " (cutoff:3.500A) Processing helix chain 's' and resid 37 through 52 removed outlier: 3.716A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU s 51 " --> pdb=" O LYS s 47 " (cutoff:3.500A) Proline residue: s 52 - end of helix Processing helix chain 's' and resid 80 through 91 removed outlier: 3.601A pdb=" N GLU s 86 " --> pdb=" O ILE s 82 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 16 Processing helix chain 't' and resid 24 through 47 removed outlier: 4.437A pdb=" N VAL t 29 " --> pdb=" O THR t 25 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 50 through 74 removed outlier: 4.508A pdb=" N GLY t 55 " --> pdb=" O HIS t 51 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LEU t 56 " --> pdb=" O SER t 52 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 86 removed outlier: 5.441A pdb=" N THR t 79 " --> pdb=" O VAL t 75 " (cutoff:3.500A) Processing helix chain 'u' and resid 53 through 64 removed outlier: 3.816A pdb=" N GLN u 63 " --> pdb=" O HIS u 59 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N GLY u 64 " --> pdb=" O TRP u 60 " (cutoff:3.500A) Processing helix chain 'u' and resid 68 through 82 Processing helix chain 'w' and resid 11 through 17 Processing helix chain 'w' and resid 25 through 34 removed outlier: 4.482A pdb=" N LEU w 29 " --> pdb=" O ASP w 25 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N ASN w 31 " --> pdb=" O ALA w 27 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N TYR w 32 " --> pdb=" O THR w 28 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N ILE w 33 " --> pdb=" O LEU w 29 " (cutoff:3.500A) removed outlier: 5.454A 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: 3.708A pdb=" N ARG w 53 " --> pdb=" O ALA w 49 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLN w 54 " --> pdb=" O LYS w 50 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ARG w 57 " --> pdb=" O ARG w 53 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 26 Processing helix chain 'x' and resid 70 through 76 removed outlier: 4.963A pdb=" N PHE x 74 " --> pdb=" O LYS x 70 " (cutoff:3.500A) removed outlier: 4.695A 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 42 removed outlier: 3.761A pdb=" N HIS y 20 " --> pdb=" O LYS y 16 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N VAL y 35 " --> pdb=" O PHE y 31 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY y 42 " --> pdb=" O ALA y 38 " (cutoff:3.500A) Processing helix chain 'y' and resid 43 through 65 removed outlier: 3.762A pdb=" N ALA y 47 " --> pdb=" O ASP y 43 " (cutoff:3.500A) Proline residue: y 56 - end of helix removed outlier: 3.710A pdb=" N ARG y 60 " --> pdb=" O PRO y 56 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N GLY y 65 " --> pdb=" O GLN y 61 " (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 36 removed outlier: 3.787A pdb=" N VAL z 32 " --> pdb=" O VAL z 28 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N ARG z 33 " --> pdb=" O LEU z 29 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ARG z 34 " --> pdb=" O ALA z 30 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 65 removed outlier: 4.093A pdb=" N LYS z 59 " --> pdb=" O ARG z 55 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '5' and resid 48 through 51 removed outlier: 5.224A 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: 4.226A pdb=" N PHE 5 64 " --> pdb=" O LEU 5 57 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N ARG 5 59 " --> pdb=" O GLU 5 62 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N GLU 5 62 " --> pdb=" O ARG 5 59 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain '5' and resid 88 through 92 removed outlier: 3.821A pdb=" N GLU 5 28 " --> pdb=" O VAL 5 129 " (cutoff:3.500A) removed outlier: 6.822A 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: 3.774A 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: 3.927A pdb=" N PHE A 60 " --> pdb=" O GLY A 52 " (cutoff:3.500A) removed outlier: 4.481A 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 72 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 33 through 36 No H-bonds generated for sheet with id= 8 Processing sheet with id= 9, first strand: chain 'B' and resid 80 through 83 removed outlier: 3.973A pdb=" N ARG B 80 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N LEU B 93 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 4.727A pdb=" N ILE B 74 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 4.600A pdb=" N SER B 118 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N ASP B 114 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'B' and resid 138 through 142 removed outlier: 4.078A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N THR B 173 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'B' and resid 91 through 96 removed outlier: 4.461A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 3 through 6 removed outlier: 4.386A pdb=" N GLU C 168 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 10 through 16 removed outlier: 4.043A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N VAL C 189 " --> pdb=" O THR C 25 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU C 187 " --> pdb=" O ILE C 27 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ARG C 179 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'C' and resid 32 through 35 removed outlier: 5.602A pdb=" N THR C 51 " --> pdb=" O ARG C 33 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N GLN C 49 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLN C 36 " --> pdb=" O GLN C 49 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'C' and resid 46 through 51 removed outlier: 5.752A pdb=" N ARG C 46 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'C' and resid 105 through 108 removed outlier: 6.244A pdb=" N LYS C 105 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'D' and resid 1 through 6 removed outlier: 4.533A pdb=" N SER D 10 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'D' and resid 117 through 120 removed outlier: 5.493A pdb=" N ARG D 117 " --> pdb=" O ASP D 184 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'E' and resid 86 through 92 removed outlier: 3.924A pdb=" N ASN E 37 " --> pdb=" O ASP E 153 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N GLY E 39 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N GLY E 151 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR E 128 " --> pdb=" O ILE E 156 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'F' and resid 15 through 20 removed outlier: 4.157A pdb=" N VAL F 23 " --> pdb=" O ASN F 20 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLN F 22 " --> pdb=" O LEU F 37 " (cutoff:3.500A) removed outlier: 4.628A pdb=" N GLY F 31 " --> pdb=" O GLY F 28 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'F' and resid 40 through 43 removed outlier: 6.427A pdb=" N ALA F 40 " --> pdb=" O ARG F 55 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'F' and resid 82 through 89 removed outlier: 5.845A pdb=" N THR F 129 " --> pdb=" O LEU F 89 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'F' and resid 94 through 99 Processing sheet with id= 24, first strand: chain 'G' and resid 17 through 20 removed outlier: 4.222A pdb=" N ASP G 17 " --> pdb=" O LEU G 5 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N LYS G 35 " --> pdb=" O LEU G 6 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'G' and resid 127 through 133 removed outlier: 4.026A pdb=" N PHE G 132 " --> pdb=" O ALA G 140 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'J' and resid 14 through 19 Processing sheet with id= 27, first strand: chain 'K' and resid 18 through 21 removed outlier: 3.707A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'M' and resid 62 through 66 removed outlier: 7.185A pdb=" N LEU M 102 " --> pdb=" O ARG M 66 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LYS M 127 " --> pdb=" O VAL M 36 " (cutoff:3.500A) Processing sheet with id= 29, first strand: chain 'N' and resid 33 through 37 removed outlier: 4.993A pdb=" N MET N 110 " --> pdb=" O CYS N 100 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'O' and resid 49 through 52 removed outlier: 3.970A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N VAL O 28 " --> pdb=" O ASP O 93 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'P' and resid 38 through 45 removed outlier: 6.353A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N SER P 83 " --> pdb=" O LYS P 29 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'P' and resid 49 through 53 removed outlier: 3.737A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ARG P 53 " --> pdb=" O HIS P 56 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N HIS P 56 " --> pdb=" O ARG P 53 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N SER P 57 " --> pdb=" O THR P 76 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'R' and resid 11 through 15 removed outlier: 6.996A pdb=" N LEU R 39 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ASN R 43 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N GLU R 46 " --> pdb=" O ASN R 43 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'R' and resid 18 through 23 removed outlier: 4.338A pdb=" N GLN R 18 " --> pdb=" O ILE R 98 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N ASP R 95 " --> pdb=" O VAL R 64 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LYS R 60 " --> pdb=" O THR R 99 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'R' and resid 57 through 60 removed outlier: 5.482A pdb=" N LYS R 60 " --> pdb=" O GLY R 100 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'R' and resid 65 through 68 removed outlier: 3.914A pdb=" N ALA R 65 " --> pdb=" O ASP R 95 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N GLY R 67 " --> pdb=" O PHE R 93 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.653A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.378A pdb=" N VAL S 105 " --> pdb=" O ALA S 5 " (cutoff:3.500A) removed outlier: 5.743A pdb=" N HIS S 102 " --> pdb=" O ASP S 77 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'S' and resid 79 through 88 No H-bonds generated for sheet with id= 39 Processing sheet with id= 40, first strand: chain 'T' and resid 12 through 15 removed outlier: 3.586A pdb=" N ALA T 13 " --> pdb=" O LYS T 33 " (cutoff:3.500A) removed outlier: 5.429A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 4.612A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'U' and resid 11 through 14 removed outlier: 3.998A pdb=" N LYS U 21 " --> pdb=" O VAL U 13 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'U' and resid 40 through 46 removed outlier: 4.872A pdb=" N ASN U 40 " --> pdb=" O ALA U 63 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'U' and resid 83 through 87 Processing sheet with id= 44, first strand: chain 'V' and resid 1 through 6 removed outlier: 4.019A pdb=" N PHE V 2 " --> pdb=" O VAL V 60 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'V' and resid 37 through 42 removed outlier: 3.927A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ASP V 76 " --> pdb=" O ASP V 90 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'X' and resid 12 through 18 removed outlier: 4.238A pdb=" N THR X 25 " --> pdb=" O ASN X 17 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'Z' and resid 33 through 39 removed outlier: 4.314A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 7.024A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'a' and resid 11 through 16 removed outlier: 3.982A pdb=" N MET a 22 " --> pdb=" O ALA a 14 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N CYS a 16 " --> pdb=" O ASN a 20 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ASN a 20 " --> pdb=" O CYS a 16 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'c' and resid 8 through 13 removed outlier: 6.050A pdb=" N HIS c 19 " --> pdb=" O SER c 13 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'c' and resid 34 through 39 removed outlier: 6.045A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'e' and resid 22 through 25 removed outlier: 6.159A pdb=" N PHE e 22 " --> pdb=" O VAL e 50 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'f' and resid 1 through 5 removed outlier: 7.352A pdb=" N HIS f 33 " --> pdb=" O CYS f 27 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N CYS f 27 " --> pdb=" O HIS f 33 " (cutoff:3.500A) removed outlier: 5.052A pdb=" N ILE f 23 " --> pdb=" O GLN f 37 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N SER f 28 " --> pdb=" O ASN f 13 " (cutoff:3.500A) removed outlier: 8.520A pdb=" N ASN f 13 " --> pdb=" O SER f 28 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'g' and resid 15 through 18 removed outlier: 5.996A pdb=" N HIS g 15 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N HIS g 39 " --> pdb=" O GLY g 17 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'g' and resid 90 through 93 Processing sheet with id= 55, first strand: chain 'h' and resid 54 through 59 removed outlier: 3.556A pdb=" N ARG h 54 " --> pdb=" O HIS h 69 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N THR h 70 " --> pdb=" O ALA h 104 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'h' and resid 148 through 155 removed outlier: 4.012A pdb=" N GLY h 148 " --> pdb=" O PHE h 203 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N ASP h 181 " --> pdb=" O LYS h 204 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'i' and resid 141 through 144 removed outlier: 3.932A pdb=" N ASP i 141 " --> pdb=" O PHE i 182 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N THR i 181 " --> pdb=" O GLU i 172 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'j' and resid 11 through 16 removed outlier: 7.106A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'j' and resid 84 through 88 removed outlier: 3.654A pdb=" N ALA j 99 " --> pdb=" O ASN j 122 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'j' and resid 32 through 40 Processing sheet with id= 61, first strand: chain 'k' and resid 38 through 43 removed outlier: 4.138A pdb=" N ARG k 38 " --> pdb=" O ASN k 63 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) removed outlier: 4.675A pdb=" N MET k 90 " --> pdb=" O GLU k 5 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'l' and resid 73 through 77 Processing sheet with id= 63, first strand: chain 'm' and resid 23 through 29 removed outlier: 6.489A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LYS m 50 " --> pdb=" O GLU m 60 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'm' and resid 74 through 77 removed outlier: 3.895A pdb=" N CYS m 127 " --> pdb=" O VAL m 103 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'n' and resid 5 through 11 removed outlier: 3.567A pdb=" N VAL n 19 " --> pdb=" O GLY n 8 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N GLY n 10 " --> pdb=" O ALA n 17 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N ALA n 16 " --> pdb=" O LYS n 68 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N ARG n 18 " --> pdb=" O THR n 66 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N THR n 66 " --> pdb=" O ARG n 18 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR n 64 " --> pdb=" O PHE n 20 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LYS n 22 " --> pdb=" O ASP n 62 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'o' and resid 39 through 42 removed outlier: 4.689A pdb=" N LEU o 71 " --> pdb=" O LEU o 42 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ILE o 6 " --> pdb=" O ILE o 76 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N ARG o 5 " --> pdb=" O GLY o 103 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'o' and resid 44 through 53 removed outlier: 6.886A pdb=" N ALA o 61 " --> pdb=" O ILE o 53 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'p' and resid 30 through 35 removed outlier: 3.701A pdb=" N ASN p 109 " --> pdb=" O LEU p 82 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLY p 88 " --> pdb=" O VAL p 113 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'q' and resid 29 through 33 removed outlier: 4.955A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'q' and resid 35 through 41 removed outlier: 4.906A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'u' and resid 4 through 9 removed outlier: 5.665A pdb=" N PHE u 16 " --> pdb=" O HIS u 9 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY u 37 " --> pdb=" O VAL u 19 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'v' and resid 39 through 48 removed outlier: 4.561A pdb=" N LYS v 19 " --> pdb=" O ASP v 48 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL v 22 " --> pdb=" O VAL v 13 " (cutoff:3.500A) removed outlier: 5.068A pdb=" N GLU v 26 " --> pdb=" O GLN v 9 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N GLN v 9 " --> pdb=" O GLU v 26 " (cutoff:3.500A) removed outlier: 12.854A pdb=" N PHE v 28 " --> pdb=" O THR v 7 " (cutoff:3.500A) removed outlier: 15.849A pdb=" N THR v 7 " --> pdb=" O PHE v 28 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N GLU v 60 " --> pdb=" O VAL v 76 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N SER v 72 " --> pdb=" O CYS v 64 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'x' and resid 30 through 34 1851 hydrogen bonds defined for protein. 5496 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3658 hydrogen bonds 5782 hydrogen bond angles 0 basepair planarities 1449 basepair parallelities 2379 stacking parallelities Total time for adding SS restraints: 274.83 Time building geometry restraints manager: 73.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.28: 12120 1.28 - 1.41: 53770 1.41 - 1.55: 88587 1.55 - 1.68: 9984 1.68 - 1.81: 273 Bond restraints: 164734 Sorted by residual: bond pdb=" N PRO g 29 " pdb=" CD PRO g 29 " ideal model delta sigma weight residual 1.473 1.702 -0.229 1.40e-02 5.10e+03 2.67e+02 bond pdb=" C5 5MU 11939 " pdb=" C6 5MU 11939 " 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 1 747 " pdb=" C6 5MU 1 747 " ideal model delta sigma weight residual 1.155 1.435 -0.280 2.00e-02 2.50e+03 1.95e+02 bond pdb=" C5 5MU 4 341 " pdb=" C6 5MU 4 341 " ideal model delta sigma weight residual 1.155 1.434 -0.279 2.00e-02 2.50e+03 1.94e+02 bond pdb=" N PRO w 41 " pdb=" CD PRO w 41 " ideal model delta sigma weight residual 1.473 1.639 -0.166 1.40e-02 5.10e+03 1.40e+02 ... (remaining 164729 not shown) Histogram of bond angle deviations from ideal: 93.00 - 106.29: 28961 106.29 - 119.58: 141234 119.58 - 132.87: 76503 132.87 - 146.16: 71 146.16 - 159.45: 2 Bond angle restraints: 246771 Sorted by residual: angle pdb=" C1' OMG 12251 " pdb=" N9 OMG 12251 " pdb=" C4 OMG 12251 " ideal model delta sigma weight residual 108.29 159.45 -51.16 3.00e+00 1.11e-01 2.91e+02 angle pdb=" C1' OMG 12251 " pdb=" N9 OMG 12251 " pdb=" C8 OMG 12251 " ideal model delta sigma weight residual 142.82 93.00 49.82 3.00e+00 1.11e-01 2.76e+02 angle pdb=" N HIS x 14 " pdb=" CA HIS x 14 " pdb=" C HIS x 14 " ideal model delta sigma weight residual 111.28 123.79 -12.51 1.09e+00 8.42e-01 1.32e+02 angle pdb=" N VAL S 47 " pdb=" CA VAL S 47 " pdb=" C VAL S 47 " ideal model delta sigma weight residual 110.62 122.21 -11.59 1.02e+00 9.61e-01 1.29e+02 angle pdb=" C1' G7M 2 527 " pdb=" N9 G7M 2 527 " pdb=" C8 G7M 2 527 " ideal model delta sigma weight residual 112.61 144.56 -31.95 3.00e+00 1.11e-01 1.13e+02 ... (remaining 246766 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.89: 91928 35.89 - 71.77: 11970 71.77 - 107.66: 1407 107.66 - 143.55: 40 143.55 - 179.43: 47 Dihedral angle restraints: 105392 sinusoidal: 88704 harmonic: 16688 Sorted by residual: dihedral pdb=" C4' G 12308 " pdb=" C3' G 12308 " pdb=" C2' G 12308 " pdb=" C1' G 12308 " ideal model delta sinusoidal sigma weight residual -35.00 34.19 -69.19 1 8.00e+00 1.56e-02 9.67e+01 dihedral pdb=" C4' U 4 221 " pdb=" C3' U 4 221 " pdb=" C2' U 4 221 " pdb=" C1' U 4 221 " ideal model delta sinusoidal sigma weight residual -35.00 32.53 -67.53 1 8.00e+00 1.56e-02 9.27e+01 dihedral pdb=" C4' A 1 428 " pdb=" C3' A 1 428 " pdb=" C2' A 1 428 " pdb=" C1' A 1 428 " ideal model delta sinusoidal sigma weight residual -35.00 30.33 -65.33 1 8.00e+00 1.56e-02 8.74e+01 ... (remaining 105389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.099: 30622 0.099 - 0.199: 696 0.199 - 0.298: 126 0.298 - 0.397: 32 0.397 - 0.497: 11 Chirality restraints: 31487 Sorted by residual: chirality pdb=" CA LEU G 12 " pdb=" N LEU G 12 " pdb=" C LEU G 12 " pdb=" CB LEU G 12 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.17e+00 chirality pdb=" CA THR e 34 " pdb=" N THR e 34 " pdb=" C THR e 34 " pdb=" CB THR e 34 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.48 2.00e-01 2.50e+01 5.70e+00 chirality pdb=" CA GLU 5 107 " pdb=" N GLU 5 107 " pdb=" C GLU 5 107 " pdb=" CB GLU 5 107 " both_signs ideal model delta sigma weight residual False 2.51 2.04 0.47 2.00e-01 2.50e+01 5.61e+00 ... (remaining 31484 not shown) Planarity restraints: 12982 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21207 " 0.075 2.00e-02 2.50e+03 6.41e-01 9.25e+03 pdb=" C4' 2MG 21207 " 0.480 2.00e-02 2.50e+03 pdb=" O4' 2MG 21207 " 0.830 2.00e-02 2.50e+03 pdb=" C3' 2MG 21207 " -0.585 2.00e-02 2.50e+03 pdb=" O3' 2MG 21207 " -0.630 2.00e-02 2.50e+03 pdb=" C2' 2MG 21207 " -0.221 2.00e-02 2.50e+03 pdb=" O2' 2MG 21207 " 0.937 2.00e-02 2.50e+03 pdb=" C1' 2MG 21207 " 0.156 2.00e-02 2.50e+03 pdb=" N9 2MG 21207 " -1.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' OMG 12251 " 0.047 2.00e-02 2.50e+03 5.79e-01 7.54e+03 pdb=" C4' OMG 12251 " 0.428 2.00e-02 2.50e+03 pdb=" O4' OMG 12251 " 0.591 2.00e-02 2.50e+03 pdb=" C3' OMG 12251 " -0.593 2.00e-02 2.50e+03 pdb=" O3' OMG 12251 " -0.608 2.00e-02 2.50e+03 pdb=" C2' OMG 12251 " -0.183 2.00e-02 2.50e+03 pdb=" O2' OMG 12251 " 0.957 2.00e-02 2.50e+03 pdb=" C1' OMG 12251 " 0.232 2.00e-02 2.50e+03 pdb=" N9 OMG 12251 " -0.871 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 12445 " -0.038 2.00e-02 2.50e+03 5.74e-01 7.43e+03 pdb=" C4' 2MG 12445 " -0.433 2.00e-02 2.50e+03 pdb=" O4' 2MG 12445 " -0.624 2.00e-02 2.50e+03 pdb=" C3' 2MG 12445 " 0.590 2.00e-02 2.50e+03 pdb=" O3' 2MG 12445 " 0.580 2.00e-02 2.50e+03 pdb=" C2' 2MG 12445 " 0.203 2.00e-02 2.50e+03 pdb=" O2' 2MG 12445 " -0.924 2.00e-02 2.50e+03 pdb=" C1' 2MG 12445 " -0.227 2.00e-02 2.50e+03 pdb=" N9 2MG 12445 " 0.872 2.00e-02 2.50e+03 ... (remaining 12979 not shown) Histogram of nonbonded interaction distances: 0.44 - 1.34: 12 1.34 - 2.23: 234 2.23 - 3.12: 107232 3.12 - 4.01: 477649 4.01 - 4.90: 780217 Warning: very small nonbonded interaction distances. Nonbonded interactions: 1365344 Sorted by model distance: nonbonded pdb=" P U 21372 " pdb=" CB SER n 73 " model vdw 0.444 3.800 nonbonded pdb=" O LYS G 42 " pdb=" CE2 PHE G 46 " model vdw 0.891 3.340 nonbonded pdb=" OP1 U 21372 " pdb=" CA SER n 73 " model vdw 0.980 3.470 nonbonded pdb=" P U 21372 " pdb=" OG SER n 73 " model vdw 1.006 3.400 nonbonded pdb=" O5' U 21372 " pdb=" OG SER n 73 " model vdw 1.094 2.440 ... (remaining 1365339 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: 0.000 Normalize map: mean=0, sd=1: 8.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.190 Extract box with map and model: 27.710 Check model and map are aligned: 1.640 Set scattering table: 1.050 Process input model: 609.900 Find NCS groups from input model: 3.080 Set up NCS constraints: 0.420 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 655.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7705 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 0.280 164734 Z= 0.196 Angle : 0.653 51.156 246771 Z= 0.383 Chirality : 0.037 0.497 31487 Planarity : 0.017 0.641 12982 Dihedral : 23.548 179.432 94626 Min Nonbonded Distance : 0.444 Molprobity Statistics. All-atom Clashscore : 14.05 Ramachandran Plot: Outliers : 0.40 % Allowed : 5.34 % Favored : 94.26 % Rotamer: Outliers : 1.77 % Allowed : 5.47 % Favored : 92.76 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.11), residues: 5750 helix: 0.98 (0.13), residues: 1826 sheet: -1.17 (0.15), residues: 1091 loop : -1.59 (0.11), residues: 2833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP s 101 HIS 0.003 0.000 HIS t 50 PHE 0.018 0.001 PHE k 8 TYR 0.032 0.001 TYR n 7 ARG 0.009 0.000 ARG A 14 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1765 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 1680 time to evaluate : 6.632 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7392 (tm-30) cc_final: 0.7104 (tm-30) REVERT: 5 82 CYS cc_start: 0.8115 (m) cc_final: 0.7704 (t) REVERT: 5 83 ASP cc_start: 0.8577 (t70) cc_final: 0.8377 (t0) REVERT: 5 148 GLN cc_start: 0.8294 (mm-40) cc_final: 0.7211 (mm110) REVERT: A 56 ASP cc_start: 0.8202 (p0) cc_final: 0.7894 (p0) REVERT: B 96 TYR cc_start: 0.8116 (m-80) cc_final: 0.7415 (m-80) REVERT: B 115 GLN cc_start: 0.7763 (tt0) cc_final: 0.7415 (tm-30) REVERT: C 2 ILE cc_start: 0.8199 (pt) cc_final: 0.7997 (pt) REVERT: E 83 TYR cc_start: 0.7248 (t80) cc_final: 0.6933 (t80) REVERT: E 118 SER cc_start: 0.8758 (m) cc_final: 0.8313 (p) REVERT: E 127 ASN cc_start: 0.6980 (m-40) cc_final: 0.6563 (t0) REVERT: F 19 ILE cc_start: 0.7803 (mp) cc_final: 0.7602 (mm) REVERT: F 20 ASN cc_start: 0.8348 (m-40) cc_final: 0.7775 (p0) REVERT: G 8 LYS cc_start: 0.8426 (tptt) cc_final: 0.8124 (mmtt) REVERT: G 54 LEU cc_start: 0.7385 (mp) cc_final: 0.6923 (pt) REVERT: J 19 ASP cc_start: 0.6908 (t0) cc_final: 0.6573 (t0) REVERT: J 84 ILE cc_start: 0.7313 (tp) cc_final: 0.7104 (tp) REVERT: N 75 ILE cc_start: 0.9241 (mm) cc_final: 0.8955 (mm) REVERT: N 97 ILE cc_start: 0.7771 (mt) cc_final: 0.7392 (mt) REVERT: O 21 LEU cc_start: 0.8712 (mt) cc_final: 0.8114 (tt) REVERT: P 9 GLU cc_start: 0.7812 (pp20) cc_final: 0.7357 (pp20) REVERT: P 76 THR cc_start: 0.8787 (m) cc_final: 0.8249 (p) REVERT: S 78 GLU cc_start: 0.7770 (tt0) cc_final: 0.7414 (tt0) REVERT: T 43 ILE cc_start: 0.7876 (pt) cc_final: 0.7529 (mt) REVERT: V 69 GLU cc_start: 0.8571 (mp0) cc_final: 0.8098 (tm-30) REVERT: Z 4 THR cc_start: 0.8607 (m) cc_final: 0.8239 (m) REVERT: Z 11 ARG cc_start: 0.8699 (ttm170) cc_final: 0.8416 (mtt-85) REVERT: b 7 LYS cc_start: 0.8292 (tttt) cc_final: 0.8079 (tttp) REVERT: f 16 ILE cc_start: 0.7291 (mm) cc_final: 0.7058 (mm) REVERT: h 22 TRP cc_start: 0.4705 (p90) cc_final: 0.3906 (p90) REVERT: h 34 ASP cc_start: 0.8733 (m-30) cc_final: 0.8522 (m-30) REVERT: h 118 ASP cc_start: 0.8225 (m-30) cc_final: 0.7873 (m-30) REVERT: h 142 MET cc_start: 0.9391 (mmm) cc_final: 0.9114 (mmp) REVERT: h 178 LEU cc_start: 0.8961 (mt) cc_final: 0.8754 (mt) REVERT: h 181 ASP cc_start: 0.8726 (t70) cc_final: 0.8458 (t0) REVERT: h 184 TYR cc_start: 0.6530 (t80) cc_final: 0.5380 (t80) REVERT: h 201 TRP cc_start: 0.7340 (m-90) cc_final: 0.6812 (m-90) REVERT: j 50 TYR cc_start: 0.8129 (t80) cc_final: 0.7908 (t80) REVERT: k 6 ILE cc_start: 0.9092 (mp) cc_final: 0.8579 (mp) REVERT: k 65 GLU cc_start: 0.7396 (tt0) cc_final: 0.6905 (tt0) REVERT: k 88 MET cc_start: 0.6372 (tpp) cc_final: 0.5869 (tpt) REVERT: l 23 LEU cc_start: 0.8814 (mt) cc_final: 0.8242 (mp) REVERT: l 96 ARG cc_start: 0.8942 (ttp-170) cc_final: 0.8680 (ttp-110) REVERT: m 92 LEU cc_start: 0.8471 (mt) cc_final: 0.8136 (tp) REVERT: n 42 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.8345 (tp30) REVERT: n 46 MET cc_start: 0.8847 (OUTLIER) cc_final: 0.8111 (mtm) REVERT: n 54 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8013 (mt) REVERT: n 99 ARG cc_start: 0.7755 (OUTLIER) cc_final: 0.7512 (ttm170) REVERT: n 110 GLN cc_start: 0.9080 (OUTLIER) cc_final: 0.8802 (tm-30) REVERT: n 124 ARG cc_start: 0.9219 (OUTLIER) cc_final: 0.8987 (ttp80) REVERT: n 125 PRO cc_start: 0.6817 (OUTLIER) cc_final: 0.6304 (Cg_exo) REVERT: n 129 LYS cc_start: 0.4055 (OUTLIER) cc_final: 0.2826 (ptmt) REVERT: n 130 ARG cc_start: 0.7282 (OUTLIER) cc_final: 0.7037 (ptt-90) REVERT: o 15 HIS cc_start: 0.7576 (p90) cc_final: 0.7147 (p-80) REVERT: o 19 ASP cc_start: 0.7841 (p0) cc_final: 0.7518 (p0) REVERT: o 57 VAL cc_start: 0.5621 (OUTLIER) cc_final: 0.5357 (p) REVERT: p 38 GLN cc_start: 0.8522 (mp10) cc_final: 0.8206 (mp-120) REVERT: p 82 LEU cc_start: 0.8170 (mp) cc_final: 0.7854 (mp) REVERT: q 24 LEU cc_start: 0.8375 (mt) cc_final: 0.7317 (mt) REVERT: q 55 VAL cc_start: 0.8568 (OUTLIER) cc_final: 0.8248 (p) REVERT: q 103 ASP cc_start: 0.7534 (m-30) cc_final: 0.7164 (m-30) REVERT: s 28 LYS cc_start: 0.8165 (mptt) cc_final: 0.7816 (mmtm) REVERT: s 42 TRP cc_start: 0.7198 (t-100) cc_final: 0.6988 (t-100) REVERT: s 74 LEU cc_start: 0.7685 (tp) cc_final: 0.7316 (tp) REVERT: t 59 MET cc_start: 0.7985 (mtt) cc_final: 0.7689 (mtt) REVERT: u 9 HIS cc_start: 0.7583 (m90) cc_final: 0.7363 (m170) REVERT: u 17 TYR cc_start: 0.7651 (m-80) cc_final: 0.6862 (m-80) REVERT: u 53 ASP cc_start: 0.8598 (t70) cc_final: 0.8293 (t0) REVERT: u 75 ILE cc_start: 0.8106 (mt) cc_final: 0.7720 (tt) REVERT: v 40 ARG cc_start: 0.8161 (mmm160) cc_final: 0.7890 (mmt90) REVERT: w 32 TYR cc_start: 0.8486 (m-80) cc_final: 0.8136 (m-80) REVERT: y 57 ILE cc_start: 0.9207 (mm) cc_final: 0.8747 (mm) REVERT: z 20 LYS cc_start: 0.9185 (ttmt) cc_final: 0.8862 (tmtt) REVERT: z 40 LYS cc_start: 0.7643 (mttt) cc_final: 0.7353 (ttpp) REVERT: z 63 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7177 (mm-30) outliers start: 85 outliers final: 19 residues processed: 1737 average time/residue: 1.4996 time to fit residues: 4431.9524 Evaluate side-chains 1034 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1004 time to evaluate : 6.209 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 57 VAL Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain n residue 13 LYS Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 22 LYS Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 41 ARG Chi-restraints excluded: chain n residue 42 GLU Chi-restraints excluded: chain n residue 43 THR Chi-restraints excluded: chain n residue 46 MET Chi-restraints excluded: chain n residue 49 ARG Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 99 ARG Chi-restraints excluded: chain n residue 105 THR Chi-restraints excluded: chain n residue 106 ARG Chi-restraints excluded: chain n residue 110 GLN Chi-restraints excluded: chain n residue 113 ARG Chi-restraints excluded: chain n residue 114 LYS Chi-restraints excluded: chain n residue 120 LYS Chi-restraints excluded: chain n residue 123 ARG Chi-restraints excluded: chain n residue 124 ARG Chi-restraints excluded: chain n residue 125 PRO Chi-restraints excluded: chain n residue 129 LYS Chi-restraints excluded: chain n residue 130 ARG Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain q residue 55 VAL Chi-restraints excluded: chain s residue 96 LEU Chi-restraints excluded: chain s residue 101 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 890 optimal weight: 20.0000 chunk 798 optimal weight: 0.9980 chunk 443 optimal weight: 20.0000 chunk 272 optimal weight: 10.0000 chunk 538 optimal weight: 0.9990 chunk 426 optimal weight: 50.0000 chunk 826 optimal weight: 9.9990 chunk 319 optimal weight: 10.0000 chunk 502 optimal weight: 9.9990 chunk 614 optimal weight: 5.9990 chunk 957 optimal weight: 30.0000 overall best weight: 5.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 128 GLN ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 ASN ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 58 ASN K 9 ASN K 29 HIS K 93 GLN M 22 GLN N 107 ASN ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 12 GLN Q 52 GLN Q 56 GLN Q 59 GLN S 15 GLN T 48 GLN ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 ASN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 5 GLN b 6 ASN c 19 HIS e 28 ASN e 43 HIS ** f 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 42 ASN ** h 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 54 GLN j 73 ASN j 97 GLN k 58 HIS ** l 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 4 ASN n 50 GLN ** o 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 101 ASN p 119 ASN q 112 GLN ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 79 ASN v 50 ASN ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 9 ASN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.113 164734 Z= 0.292 Angle : 0.721 15.353 246771 Z= 0.375 Chirality : 0.036 0.495 31487 Planarity : 0.006 0.134 12982 Dihedral : 24.433 178.706 83176 Min Nonbonded Distance : 1.073 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.78 % Favored : 93.13 % Rotamer: Outliers : 4.34 % Allowed : 14.74 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.11), residues: 5750 helix: 0.37 (0.12), residues: 1896 sheet: -1.09 (0.16), residues: 1090 loop : -1.56 (0.11), residues: 2764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP J 15 HIS 0.016 0.002 HIS N 16 PHE 0.027 0.002 PHE k 8 TYR 0.024 0.002 TYR O 99 ARG 0.009 0.001 ARG t 58 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1060 time to evaluate : 5.846 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 31 GLU cc_start: 0.7703 (tm-30) cc_final: 0.7316 (tm-30) REVERT: 5 73 MET cc_start: 0.8055 (OUTLIER) cc_final: 0.7765 (mtm) REVERT: 5 82 CYS cc_start: 0.7896 (m) cc_final: 0.7627 (t) REVERT: 5 83 ASP cc_start: 0.8577 (t70) cc_final: 0.8349 (t0) REVERT: 5 143 LYS cc_start: 0.9154 (tttt) cc_final: 0.8745 (tptp) REVERT: 5 144 GLU cc_start: 0.8751 (tp30) cc_final: 0.7773 (tp30) REVERT: 5 148 GLN cc_start: 0.8350 (mm-40) cc_final: 0.7899 (mm110) REVERT: A 70 GLU cc_start: 0.7015 (mp0) cc_final: 0.6608 (mp0) REVERT: B 23 GLU cc_start: 0.6909 (tt0) cc_final: 0.6240 (tt0) REVERT: C 2 ILE cc_start: 0.8471 (pt) cc_final: 0.8216 (pt) REVERT: D 181 ILE cc_start: 0.8795 (OUTLIER) cc_final: 0.8557 (mt) REVERT: E 26 MET cc_start: 0.7435 (mtp) cc_final: 0.7195 (mtp) REVERT: E 83 TYR cc_start: 0.7321 (t80) cc_final: 0.6643 (t80) REVERT: E 96 MET cc_start: 0.7964 (tmm) cc_final: 0.7668 (tmm) REVERT: E 118 SER cc_start: 0.8770 (m) cc_final: 0.8292 (p) REVERT: E 127 ASN cc_start: 0.8217 (m-40) cc_final: 0.7376 (t0) REVERT: E 138 PHE cc_start: 0.8631 (m-80) cc_final: 0.8068 (m-80) REVERT: E 148 ARG cc_start: 0.6114 (OUTLIER) cc_final: 0.5857 (tmt170) REVERT: E 175 PHE cc_start: 0.8037 (t80) cc_final: 0.7716 (t80) REVERT: G 2 GLN cc_start: 0.8218 (tp40) cc_final: 0.7982 (tp40) REVERT: G 8 LYS cc_start: 0.8170 (tptt) cc_final: 0.7897 (mmtt) REVERT: G 15 LEU cc_start: 0.6291 (tt) cc_final: 0.5882 (tp) REVERT: G 42 LYS cc_start: 0.8069 (tptm) cc_final: 0.7644 (tmmt) REVERT: L 143 GLU cc_start: 0.7628 (tp30) cc_final: 0.7181 (mp0) REVERT: M 75 GLU cc_start: 0.7374 (mp0) cc_final: 0.7112 (mp0) REVERT: N 24 MET cc_start: 0.8470 (tpp) cc_final: 0.7902 (mpp) REVERT: O 21 LEU cc_start: 0.8844 (mt) cc_final: 0.8436 (tt) REVERT: P 6 LYS cc_start: 0.8435 (tttt) cc_final: 0.8210 (tppt) REVERT: P 9 GLU cc_start: 0.7936 (pp20) cc_final: 0.7229 (pp20) REVERT: P 71 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7618 (mp0) REVERT: P 102 GLU cc_start: 0.8171 (mp0) cc_final: 0.7953 (tm-30) REVERT: S 77 ASP cc_start: 0.7832 (m-30) cc_final: 0.7053 (t70) REVERT: S 78 GLU cc_start: 0.8212 (tt0) cc_final: 0.7719 (tt0) REVERT: T 70 HIS cc_start: 0.6941 (t-90) cc_final: 0.6577 (p-80) REVERT: Y 44 LYS cc_start: 0.8509 (ttmm) cc_final: 0.7880 (tttp) REVERT: Z 19 LYS cc_start: 0.8595 (mmmt) cc_final: 0.8102 (ttpp) REVERT: a 43 PHE cc_start: 0.6975 (t80) cc_final: 0.6475 (t80) REVERT: a 53 THR cc_start: 0.0200 (OUTLIER) cc_final: -0.0446 (t) REVERT: b 22 LEU cc_start: 0.8651 (OUTLIER) cc_final: 0.8405 (mp) REVERT: g 154 MET cc_start: 0.7684 (ttp) cc_final: 0.7071 (mtm) REVERT: g 213 TYR cc_start: 0.8234 (m-80) cc_final: 0.7734 (m-80) REVERT: h 29 PHE cc_start: 0.7994 (m-80) cc_final: 0.7678 (m-80) REVERT: h 34 ASP cc_start: 0.9095 (m-30) cc_final: 0.8702 (m-30) REVERT: h 142 MET cc_start: 0.9402 (mmm) cc_final: 0.9104 (mmt) REVERT: h 178 LEU cc_start: 0.9080 (mt) cc_final: 0.8853 (mt) REVERT: h 181 ASP cc_start: 0.8788 (t70) cc_final: 0.8542 (t0) REVERT: h 184 TYR cc_start: 0.7069 (t80) cc_final: 0.6866 (t80) REVERT: i 135 TYR cc_start: 0.7508 (t80) cc_final: 0.7300 (t80) REVERT: j 73 ASN cc_start: 0.8349 (OUTLIER) cc_final: 0.8147 (m-40) REVERT: k 35 LYS cc_start: 0.8767 (mppt) cc_final: 0.8266 (mppt) REVERT: k 36 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.9089 (mp) REVERT: k 68 GLN cc_start: 0.8862 (pm20) cc_final: 0.8447 (pp30) REVERT: k 88 MET cc_start: 0.6145 (tpp) cc_final: 0.5598 (tpp) REVERT: l 15 ASP cc_start: 0.5568 (t0) cc_final: 0.5216 (t0) REVERT: l 87 VAL cc_start: 0.4717 (OUTLIER) cc_final: 0.4515 (m) REVERT: l 96 ARG cc_start: 0.8904 (ttp-170) cc_final: 0.8693 (ttp80) REVERT: m 3 MET cc_start: 0.7913 (mmm) cc_final: 0.7612 (tpt) REVERT: n 4 ASN cc_start: 0.5957 (OUTLIER) cc_final: 0.5750 (p0) REVERT: n 42 GLU cc_start: 0.8852 (OUTLIER) cc_final: 0.8615 (tp30) REVERT: n 43 THR cc_start: 0.8464 (OUTLIER) cc_final: 0.7750 (p) REVERT: n 46 MET cc_start: 0.8817 (mmm) cc_final: 0.8452 (ptp) REVERT: n 52 LEU cc_start: 0.8780 (mt) cc_final: 0.8369 (tp) REVERT: n 110 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8687 (tm-30) REVERT: n 129 LYS cc_start: 0.4088 (OUTLIER) cc_final: 0.2923 (pttm) REVERT: n 130 ARG cc_start: 0.7183 (OUTLIER) cc_final: 0.6413 (ptt-90) REVERT: o 15 HIS cc_start: 0.7631 (p90) cc_final: 0.7390 (p-80) REVERT: o 66 GLU cc_start: 0.5562 (mt-10) cc_final: 0.5000 (mm-30) REVERT: p 53 ARG cc_start: 0.7268 (OUTLIER) cc_final: 0.6854 (tpm170) REVERT: p 82 LEU cc_start: 0.8404 (mp) cc_final: 0.7942 (mp) REVERT: q 103 ASP cc_start: 0.7459 (m-30) cc_final: 0.7099 (m-30) REVERT: r 75 MET cc_start: 0.8616 (ppp) cc_final: 0.8326 (ppp) REVERT: s 43 ASN cc_start: 0.8376 (t0) cc_final: 0.8106 (m-40) REVERT: t 18 ASP cc_start: 0.8393 (p0) cc_final: 0.8181 (p0) REVERT: t 47 LYS cc_start: 0.8285 (OUTLIER) cc_final: 0.7930 (pttt) REVERT: u 53 ASP cc_start: 0.8611 (t70) cc_final: 0.8321 (t0) REVERT: v 17 MET cc_start: 0.7724 (mtm) cc_final: 0.7489 (mtm) REVERT: v 40 ARG cc_start: 0.8441 (mmm160) cc_final: 0.8241 (mmt90) REVERT: w 32 TYR cc_start: 0.8331 (m-80) cc_final: 0.8123 (m-80) REVERT: w 38 LYS cc_start: 0.8890 (mtpt) cc_final: 0.8627 (mtpp) REVERT: z 49 LYS cc_start: 0.9083 (ttpp) cc_final: 0.8845 (ttpp) REVERT: z 54 LYS cc_start: 0.8313 (mtmt) cc_final: 0.8060 (mttt) outliers start: 208 outliers final: 129 residues processed: 1192 average time/residue: 1.3183 time to fit residues: 2726.7078 Evaluate side-chains 1054 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 146 poor density : 908 time to evaluate : 6.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 14 ILE Chi-restraints excluded: chain 5 residue 25 PHE Chi-restraints excluded: chain 5 residue 73 MET Chi-restraints excluded: chain 5 residue 80 VAL Chi-restraints excluded: chain 5 residue 115 SER Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 160 THR Chi-restraints excluded: chain B residue 162 VAL Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 111 GLU Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain E residue 148 ARG Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain F residue 10 VAL Chi-restraints excluded: chain F residue 16 ASP Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 24 THR 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 29 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 52 ILE Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain S residue 107 VAL Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 92 ASN Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 35 ILE Chi-restraints excluded: chain U residue 41 LEU Chi-restraints excluded: chain U residue 68 SER Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 55 GLU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain X residue 60 ASP Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Z residue 5 ILE Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 48 ILE Chi-restraints excluded: chain Z residue 49 ASN Chi-restraints excluded: chain a residue 24 ILE Chi-restraints excluded: chain a residue 53 THR Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain e residue 28 ASN Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 77 LYS Chi-restraints excluded: chain i residue 129 VAL Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain i residue 203 LEU Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 73 ASN Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 141 ILE Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 36 ILE Chi-restraints excluded: chain n residue 4 ASN Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 41 ARG Chi-restraints excluded: chain n residue 42 GLU Chi-restraints excluded: chain n residue 43 THR Chi-restraints excluded: chain n residue 49 ARG Chi-restraints excluded: chain n residue 53 GLU Chi-restraints excluded: chain n residue 63 LEU Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 105 THR Chi-restraints excluded: chain n residue 110 GLN Chi-restraints excluded: chain n residue 113 ARG Chi-restraints excluded: chain n residue 123 ARG Chi-restraints excluded: chain n residue 129 LYS Chi-restraints excluded: chain n residue 130 ARG Chi-restraints excluded: chain p residue 17 SER Chi-restraints excluded: chain p residue 53 ARG Chi-restraints excluded: chain p residue 72 ASP Chi-restraints excluded: chain p residue 108 THR Chi-restraints excluded: chain p residue 113 VAL Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 49 LEU Chi-restraints excluded: chain q residue 73 ASN Chi-restraints excluded: chain s residue 101 TRP Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 27 VAL Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain u residue 78 VAL Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 70 THR Chi-restraints excluded: chain w residue 59 ILE Chi-restraints excluded: chain y residue 67 ILE Chi-restraints excluded: chain z residue 13 ASP Chi-restraints excluded: chain z residue 53 VAL 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: 9.9990 chunk 297 optimal weight: 20.0000 chunk 796 optimal weight: 30.0000 chunk 651 optimal weight: 10.0000 chunk 264 optimal weight: 10.0000 chunk 958 optimal weight: 8.9990 chunk 1035 optimal weight: 10.0000 chunk 853 optimal weight: 8.9990 chunk 950 optimal weight: 6.9990 chunk 326 optimal weight: 10.0000 chunk 769 optimal weight: 8.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 90 GLN E 21 ASN ** F 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 135 GLN K 5 GLN O 38 GLN ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 56 GLN Q 59 GLN S 7 HIS T 59 ASN ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 24 ASN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 6 GLN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 61 ASN b 38 HIS b 42 HIS d 16 HIS ** f 13 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 37 GLN ** l 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 4 GLN ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 112 GLN ** r 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 9 HIS u 79 ASN v 50 ASN w 54 GLN z 9 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 164734 Z= 0.413 Angle : 0.829 13.832 246771 Z= 0.428 Chirality : 0.043 0.390 31487 Planarity : 0.007 0.143 12982 Dihedral : 24.753 179.710 83132 Min Nonbonded Distance : 1.140 Molprobity Statistics. All-atom Clashscore : 23.40 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.70 % Favored : 92.19 % Rotamer: Outliers : 5.80 % Allowed : 17.24 % Favored : 76.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -1.87 (0.10), residues: 5750 helix: -0.22 (0.11), residues: 1901 sheet: -1.32 (0.16), residues: 1057 loop : -1.92 (0.11), residues: 2792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.004 TRP l 103 HIS 0.021 0.002 HIS v 47 PHE 0.025 0.003 PHE J 119 TYR 0.028 0.003 TYR E 22 ARG 0.018 0.001 ARG y 25 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1260 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 278 poor density : 982 time to evaluate : 6.400 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: 5 27 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7503 (mt-10) REVERT: 5 31 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7377 (tm-30) REVERT: 5 62 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7890 (mp0) REVERT: 5 73 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7424 (mtm) REVERT: 5 96 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8719 (mp0) REVERT: 5 115 SER cc_start: 0.4899 (OUTLIER) cc_final: 0.4577 (m) REVERT: E 26 MET cc_start: 0.7426 (mtp) cc_final: 0.7177 (mtp) REVERT: E 83 TYR cc_start: 0.7538 (t80) cc_final: 0.6916 (t80) REVERT: E 118 SER cc_start: 0.8497 (m) cc_final: 0.7953 (p) REVERT: E 138 PHE cc_start: 0.8992 (m-80) cc_final: 0.8479 (m-80) REVERT: E 175 PHE cc_start: 0.8098 (t80) cc_final: 0.7608 (t80) REVERT: G 2 GLN cc_start: 0.8370 (tp40) cc_final: 0.8057 (tp40) REVERT: G 8 LYS cc_start: 0.8025 (tptt) cc_final: 0.7678 (mmtt) REVERT: G 27 ARG cc_start: 0.8839 (ptt-90) cc_final: 0.8513 (ptt90) REVERT: G 42 LYS cc_start: 0.7828 (tptm) cc_final: 0.7401 (tmmt) REVERT: J 19 ASP cc_start: 0.7199 (t0) cc_final: 0.6534 (t0) REVERT: K 45 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.7195 (tt0) REVERT: K 87 LEU cc_start: 0.8086 (mt) cc_final: 0.7741 (mt) REVERT: K 107 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.8121 (pp) REVERT: L 143 GLU cc_start: 0.7817 (tp30) cc_final: 0.7296 (mp0) REVERT: N 24 MET cc_start: 0.8466 (tpp) cc_final: 0.8001 (mpp) REVERT: N 74 GLU cc_start: 0.8437 (mp0) cc_final: 0.7937 (mp0) REVERT: N 89 SER cc_start: 0.8290 (OUTLIER) cc_final: 0.8064 (t) REVERT: O 48 LEU cc_start: 0.8903 (mt) cc_final: 0.8649 (mm) REVERT: P 3 ASN cc_start: 0.8547 (m110) cc_final: 0.8014 (t0) REVERT: P 6 LYS cc_start: 0.8407 (tttt) cc_final: 0.8104 (tppt) REVERT: P 9 GLU cc_start: 0.7950 (pp20) cc_final: 0.7371 (pp20) REVERT: P 13 MET cc_start: 0.7865 (mtm) cc_final: 0.7537 (mtm) REVERT: P 71 GLU cc_start: 0.7995 (OUTLIER) cc_final: 0.6177 (mp0) REVERT: S 66 ILE cc_start: 0.8956 (pt) cc_final: 0.8543 (mt) REVERT: Z 19 LYS cc_start: 0.8794 (mmmt) cc_final: 0.8202 (ttpp) REVERT: a 1 MET cc_start: 0.8924 (mmm) cc_final: 0.8708 (mmm) REVERT: a 43 PHE cc_start: 0.6719 (t80) cc_final: 0.6049 (t80) REVERT: a 53 THR cc_start: 0.0272 (OUTLIER) cc_final: -0.0301 (t) REVERT: b 22 LEU cc_start: 0.8765 (OUTLIER) cc_final: 0.8545 (mp) REVERT: b 52 ARG cc_start: 0.8318 (ptm-80) cc_final: 0.8087 (ptm-80) REVERT: g 213 TYR cc_start: 0.8522 (m-80) cc_final: 0.8142 (m-80) REVERT: h 29 PHE cc_start: 0.8668 (m-80) cc_final: 0.8070 (m-80) REVERT: h 34 ASP cc_start: 0.9139 (m-30) cc_final: 0.8676 (m-30) REVERT: h 42 TYR cc_start: 0.8933 (t80) cc_final: 0.8614 (t80) REVERT: h 84 VAL cc_start: 0.6441 (OUTLIER) cc_final: 0.6233 (t) REVERT: h 142 MET cc_start: 0.9357 (mmm) cc_final: 0.9069 (mmt) REVERT: h 181 ASP cc_start: 0.8853 (t70) cc_final: 0.8572 (t0) REVERT: i 124 MET cc_start: 0.6572 (mmt) cc_final: 0.6017 (mmt) REVERT: i 185 LYS cc_start: 0.8654 (tptt) cc_final: 0.8329 (tptt) REVERT: k 35 LYS cc_start: 0.9095 (mppt) cc_final: 0.8739 (mppt) REVERT: k 75 GLU cc_start: 0.8850 (tt0) cc_final: 0.8369 (tp30) REVERT: l 15 ASP cc_start: 0.6391 (t0) cc_final: 0.6067 (t0) REVERT: l 87 VAL cc_start: 0.4928 (OUTLIER) cc_final: 0.4728 (m) REVERT: l 116 MET cc_start: 0.8569 (mmm) cc_final: 0.8086 (mtt) REVERT: n 4 ASN cc_start: 0.7746 (OUTLIER) cc_final: 0.7523 (p0) REVERT: n 42 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8616 (tp30) REVERT: o 57 VAL cc_start: 0.6072 (OUTLIER) cc_final: 0.5355 (p) REVERT: q 103 ASP cc_start: 0.7247 (m-30) cc_final: 0.6822 (m-30) REVERT: r 86 TYR cc_start: 0.6321 (t80) cc_final: 0.6063 (t80) REVERT: s 66 GLN cc_start: 0.8333 (tt0) cc_final: 0.8021 (mt0) REVERT: s 89 MET cc_start: 0.8149 (tpp) cc_final: 0.7711 (tpp) REVERT: u 53 ASP cc_start: 0.8553 (t70) cc_final: 0.8323 (t0) REVERT: v 11 ARG cc_start: 0.7861 (mpt180) cc_final: 0.7619 (mpt180) REVERT: v 34 TYR cc_start: 0.8739 (m-80) cc_final: 0.8519 (m-80) REVERT: v 80 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7741 (tm-30) REVERT: w 38 LYS cc_start: 0.8924 (mtpt) cc_final: 0.8650 (mtpp) REVERT: y 57 ILE cc_start: 0.9187 (mp) cc_final: 0.8781 (tp) REVERT: y 61 GLN cc_start: 0.9142 (mm-40) cc_final: 0.8858 (mm-40) REVERT: z 36 GLU cc_start: 0.7810 (pm20) cc_final: 0.7563 (pm20) REVERT: z 54 LYS cc_start: 0.8311 (mtmt) cc_final: 0.8096 (mtmt) outliers start: 278 outliers final: 173 residues processed: 1156 average time/residue: 1.3292 time to fit residues: 2704.5053 Evaluate side-chains 1056 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 186 poor density : 870 time to evaluate : 6.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 22 HIS Chi-restraints excluded: chain 5 residue 25 PHE Chi-restraints excluded: chain 5 residue 73 MET Chi-restraints excluded: chain 5 residue 80 VAL Chi-restraints excluded: chain 5 residue 81 VAL Chi-restraints excluded: chain 5 residue 85 THR Chi-restraints excluded: chain 5 residue 115 SER Chi-restraints excluded: chain 5 residue 125 VAL Chi-restraints excluded: chain 5 residue 140 SER Chi-restraints excluded: chain 5 residue 149 VAL Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 105 LEU 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 B residue 272 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 73 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 100 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain E residue 154 ILE Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain J residue 49 ASP Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 45 GLU Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR 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 29 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 25 THR Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain Q residue 74 ILE Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 41 LEU Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 89 ASP Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 55 GLU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 59 ILE Chi-restraints excluded: chain X residue 60 ASP Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 23 THR Chi-restraints excluded: chain Z residue 24 LEU Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 48 ILE Chi-restraints excluded: chain a residue 51 VAL Chi-restraints excluded: chain a residue 53 THR Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 15 MET Chi-restraints excluded: chain b residue 22 LEU Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 46 ASP Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain g residue 6 MET Chi-restraints excluded: chain g residue 57 LEU Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain h residue 84 VAL Chi-restraints excluded: chain h residue 116 VAL Chi-restraints excluded: chain h residue 121 THR Chi-restraints excluded: chain h residue 153 VAL Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain i residue 203 LEU Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 90 MET Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 30 LEU Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain m residue 26 THR Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 36 ILE Chi-restraints excluded: chain m residue 63 LEU Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 4 ASN Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 42 GLU Chi-restraints excluded: chain n residue 60 LYS Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 72 ILE Chi-restraints excluded: chain n residue 83 ILE Chi-restraints excluded: chain n residue 105 THR Chi-restraints excluded: chain n residue 123 ARG Chi-restraints excluded: chain n residue 129 LYS Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 63 ASP Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain p residue 17 SER Chi-restraints excluded: chain p residue 72 ASP Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 49 LEU Chi-restraints excluded: chain q residue 73 ASN Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 78 SER Chi-restraints excluded: chain s residue 101 TRP Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 27 VAL Chi-restraints excluded: chain u residue 21 VAL Chi-restraints excluded: chain u residue 78 VAL Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain w residue 59 ILE Chi-restraints excluded: chain y residue 67 ILE Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 14 VAL Chi-restraints excluded: chain z residue 28 VAL Chi-restraints excluded: chain z residue 53 VAL Chi-restraints excluded: chain z residue 56 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 947 optimal weight: 20.0000 chunk 720 optimal weight: 0.9990 chunk 497 optimal weight: 30.0000 chunk 106 optimal weight: 50.0000 chunk 457 optimal weight: 30.0000 chunk 643 optimal weight: 7.9990 chunk 962 optimal weight: 5.9990 chunk 1018 optimal weight: 8.9990 chunk 502 optimal weight: 10.0000 chunk 912 optimal weight: 7.9990 chunk 274 optimal weight: 10.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 159 HIS B 143 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 97 ASN ** F 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 64 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 73 ASN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 13 ASN ** l 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 4 GLN ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 GLN n 75 GLN ** o 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 112 GLN r 52 GLN ** r 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 80 GLN ** v 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 9 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.4435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.121 164734 Z= 0.307 Angle : 0.715 14.041 246771 Z= 0.376 Chirality : 0.038 0.403 31487 Planarity : 0.006 0.131 12982 Dihedral : 24.630 179.960 83110 Min Nonbonded Distance : 1.152 Molprobity Statistics. All-atom Clashscore : 19.55 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.39 % Favored : 92.52 % Rotamer: Outliers : 4.82 % Allowed : 20.13 % Favored : 75.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.74 (0.11), residues: 5750 helix: -0.04 (0.12), residues: 1902 sheet: -1.37 (0.15), residues: 1064 loop : -1.84 (0.11), residues: 2784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.003 TRP l 103 HIS 0.013 0.002 HIS t 46 PHE 0.021 0.002 PHE m 66 TYR 0.041 0.002 TYR l 44 ARG 0.008 0.001 ARG E 148 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1171 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 940 time to evaluate : 6.441 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.7548 (tm-30) cc_final: 0.7295 (tm-30) REVERT: 5 146 GLU cc_start: 0.8325 (tt0) cc_final: 0.7762 (tp30) REVERT: 5 150 ASP cc_start: 0.8676 (p0) cc_final: 0.7407 (p0) REVERT: A 56 ASP cc_start: 0.8271 (p0) cc_final: 0.8050 (p0) REVERT: B 236 GLU cc_start: 0.7481 (tp30) cc_final: 0.7271 (tp30) REVERT: D 141 MET cc_start: 0.8195 (mpp) cc_final: 0.7987 (mtm) REVERT: E 26 MET cc_start: 0.7229 (mtp) cc_final: 0.6909 (mtp) REVERT: E 31 VAL cc_start: 0.8224 (OUTLIER) cc_final: 0.7905 (p) REVERT: E 83 TYR cc_start: 0.7475 (t80) cc_final: 0.6858 (t80) REVERT: E 96 MET cc_start: 0.7925 (tmm) cc_final: 0.7575 (tmm) REVERT: E 118 SER cc_start: 0.8690 (m) cc_final: 0.8151 (p) REVERT: E 127 ASN cc_start: 0.8553 (m-40) cc_final: 0.7691 (m-40) REVERT: E 138 PHE cc_start: 0.8889 (m-80) cc_final: 0.8329 (m-80) REVERT: E 175 PHE cc_start: 0.8107 (t80) cc_final: 0.7790 (t80) REVERT: G 2 GLN cc_start: 0.8425 (tp40) cc_final: 0.8087 (tp40) REVERT: J 19 ASP cc_start: 0.7042 (t0) cc_final: 0.6463 (t0) REVERT: K 87 LEU cc_start: 0.8065 (mt) cc_final: 0.7664 (mt) REVERT: K 107 LEU cc_start: 0.8361 (OUTLIER) cc_final: 0.8150 (pp) REVERT: L 143 GLU cc_start: 0.7654 (tp30) cc_final: 0.7242 (mp0) REVERT: N 24 MET cc_start: 0.8349 (tpp) cc_final: 0.8066 (mpp) REVERT: N 89 SER cc_start: 0.8258 (OUTLIER) cc_final: 0.8017 (t) REVERT: O 48 LEU cc_start: 0.8890 (mt) cc_final: 0.8666 (mm) REVERT: P 3 ASN cc_start: 0.8545 (m110) cc_final: 0.8144 (t0) REVERT: P 6 LYS cc_start: 0.8429 (tttt) cc_final: 0.8073 (tppt) REVERT: P 9 GLU cc_start: 0.7942 (pp20) cc_final: 0.7395 (pp20) REVERT: P 71 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.6913 (mp0) REVERT: Q 57 PHE cc_start: 0.8844 (m-80) cc_final: 0.8640 (m-80) REVERT: S 66 ILE cc_start: 0.8917 (pt) cc_final: 0.8512 (mt) REVERT: U 66 GLN cc_start: 0.8585 (mt0) cc_final: 0.8344 (mt0) REVERT: Z 19 LYS cc_start: 0.8716 (mmmt) cc_final: 0.8130 (ttpp) REVERT: Z 47 MET cc_start: 0.7430 (mmt) cc_final: 0.7191 (mmt) REVERT: a 1 MET cc_start: 0.8885 (mmm) cc_final: 0.8665 (mmm) REVERT: b 52 ARG cc_start: 0.8325 (ptm-80) cc_final: 0.7801 (ptm-80) REVERT: d 42 LEU cc_start: 0.8760 (tp) cc_final: 0.8513 (tp) REVERT: f 13 ASN cc_start: 0.8261 (OUTLIER) cc_final: 0.7950 (t0) REVERT: g 213 TYR cc_start: 0.8582 (m-80) cc_final: 0.8308 (m-80) REVERT: h 29 PHE cc_start: 0.8655 (m-80) cc_final: 0.8365 (m-80) REVERT: h 142 MET cc_start: 0.9345 (mmm) cc_final: 0.9108 (mmt) REVERT: h 181 ASP cc_start: 0.8885 (t70) cc_final: 0.8641 (t0) REVERT: h 183 ASP cc_start: 0.7013 (t0) cc_final: 0.6687 (t0) REVERT: i 124 MET cc_start: 0.6847 (mmp) cc_final: 0.6226 (mmt) REVERT: i 185 LYS cc_start: 0.8672 (tptt) cc_final: 0.8269 (tptt) REVERT: k 35 LYS cc_start: 0.9036 (mppt) cc_final: 0.8634 (mppt) REVERT: k 75 GLU cc_start: 0.8833 (tt0) cc_final: 0.8306 (tp30) REVERT: l 15 ASP cc_start: 0.6716 (t0) cc_final: 0.6323 (t0) REVERT: l 87 VAL cc_start: 0.4895 (OUTLIER) cc_final: 0.4692 (m) REVERT: l 116 MET cc_start: 0.8769 (mmm) cc_final: 0.8370 (mtm) REVERT: n 110 GLN cc_start: 0.8779 (tt0) cc_final: 0.8495 (mm-40) REVERT: o 57 VAL cc_start: 0.5802 (OUTLIER) cc_final: 0.5501 (p) REVERT: o 58 ASN cc_start: 0.7122 (m110) cc_final: 0.6790 (m-40) REVERT: q 103 ASP cc_start: 0.7146 (m-30) cc_final: 0.6749 (m-30) REVERT: r 86 TYR cc_start: 0.6407 (t80) cc_final: 0.6198 (t80) REVERT: s 43 ASN cc_start: 0.8419 (t0) cc_final: 0.8103 (m-40) REVERT: s 89 MET cc_start: 0.8265 (tpp) cc_final: 0.7935 (tpp) REVERT: u 53 ASP cc_start: 0.8514 (t70) cc_final: 0.8314 (t0) REVERT: v 11 ARG cc_start: 0.7808 (mpt180) cc_final: 0.7580 (mpt180) REVERT: v 80 GLU cc_start: 0.8052 (tm-30) cc_final: 0.7753 (tm-30) REVERT: w 38 LYS cc_start: 0.8855 (mtpt) cc_final: 0.8528 (mtpt) REVERT: y 57 ILE cc_start: 0.9180 (mp) cc_final: 0.8916 (tp) REVERT: z 36 GLU cc_start: 0.7941 (pm20) cc_final: 0.7668 (pm20) REVERT: z 63 GLU cc_start: 0.8501 (mm-30) cc_final: 0.8292 (mm-30) outliers start: 231 outliers final: 170 residues processed: 1082 average time/residue: 1.2635 time to fit residues: 2408.9532 Evaluate side-chains 1047 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 177 poor density : 870 time to evaluate : 5.676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 22 HIS Chi-restraints excluded: chain 5 residue 25 PHE Chi-restraints excluded: chain 5 residue 52 SER Chi-restraints excluded: chain 5 residue 85 THR Chi-restraints excluded: chain 5 residue 115 SER Chi-restraints excluded: chain 5 residue 149 VAL Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain G residue 139 PHE Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 49 ASP Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain K residue 107 LEU Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 75 GLU Chi-restraints excluded: chain M residue 115 GLU 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 37 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 63 VAL Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 41 LEU Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 42 LEU Chi-restraints excluded: chain V residue 55 GLU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 60 ASP Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 48 ILE Chi-restraints excluded: chain a residue 53 THR Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 46 ASP Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 32 ILE Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain f residue 12 ARG Chi-restraints excluded: chain f residue 13 ASN Chi-restraints excluded: chain g residue 6 MET Chi-restraints excluded: chain g residue 36 ASN Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain g residue 157 LEU Chi-restraints excluded: chain h residue 153 VAL Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 20 PHE Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain i residue 203 LEU Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 76 LEU Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 87 VAL Chi-restraints excluded: chain m residue 9 ASP Chi-restraints excluded: chain m residue 26 THR Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 36 ILE Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 114 LYS Chi-restraints excluded: chain n residue 129 LYS Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 36 VAL Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 63 ASP Chi-restraints excluded: chain o residue 78 GLU Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain p residue 17 SER Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 49 LEU Chi-restraints excluded: chain q residue 73 ASN Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 78 SER Chi-restraints excluded: chain s residue 101 TRP Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 27 VAL Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain u residue 21 VAL Chi-restraints excluded: chain u residue 47 GLU Chi-restraints excluded: chain u residue 78 VAL Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 47 HIS Chi-restraints excluded: chain w residue 59 ILE Chi-restraints excluded: chain y residue 67 ILE Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 13 ASP Chi-restraints excluded: chain z residue 28 VAL Chi-restraints excluded: chain z residue 53 VAL Chi-restraints excluded: chain z residue 56 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 848 optimal weight: 0.9990 chunk 578 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 758 optimal weight: 9.9990 chunk 420 optimal weight: 40.0000 chunk 869 optimal weight: 1.9990 chunk 704 optimal weight: 8.9990 chunk 1 optimal weight: 10.0000 chunk 520 optimal weight: 8.9990 chunk 914 optimal weight: 30.0000 chunk 257 optimal weight: 10.0000 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 159 HIS ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 22 GLN ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 145 ASN ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** T 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 87 GLN ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 13 ASN j 97 GLN ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 4 ASN ** n 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 79 ASN ** v 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 9 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.4575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 164734 Z= 0.269 Angle : 0.690 14.028 246771 Z= 0.364 Chirality : 0.037 0.392 31487 Planarity : 0.006 0.131 12982 Dihedral : 24.598 179.782 83102 Min Nonbonded Distance : 1.172 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.53 % Favored : 92.38 % Rotamer: Outliers : 5.30 % Allowed : 20.98 % Favored : 73.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.11), residues: 5750 helix: 0.11 (0.12), residues: 1895 sheet: -1.40 (0.16), residues: 1063 loop : -1.82 (0.11), residues: 2792 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.067 0.002 TRP l 103 HIS 0.010 0.001 HIS t 46 PHE 0.020 0.002 PHE G 47 TYR 0.053 0.002 TYR l 44 ARG 0.009 0.001 ARG c 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 254 poor density : 906 time to evaluate : 6.401 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: 5 31 GLU cc_start: 0.7493 (tm-30) cc_final: 0.7253 (tm-30) REVERT: 5 73 MET cc_start: 0.7695 (mtm) cc_final: 0.7446 (mtm) REVERT: 5 146 GLU cc_start: 0.8284 (tt0) cc_final: 0.7700 (tp30) REVERT: 5 150 ASP cc_start: 0.8671 (p0) cc_final: 0.7242 (p0) REVERT: B 39 LYS cc_start: 0.7520 (OUTLIER) cc_final: 0.6941 (ptpp) REVERT: E 26 MET cc_start: 0.7360 (mtp) cc_final: 0.7112 (mtm) REVERT: E 31 VAL cc_start: 0.8134 (OUTLIER) cc_final: 0.7781 (p) REVERT: E 83 TYR cc_start: 0.7519 (t80) cc_final: 0.6919 (t80) REVERT: E 89 VAL cc_start: 0.6975 (OUTLIER) cc_final: 0.6692 (p) REVERT: E 96 MET cc_start: 0.7986 (tmm) cc_final: 0.7597 (tmm) REVERT: E 118 SER cc_start: 0.8604 (m) cc_final: 0.8062 (p) REVERT: E 127 ASN cc_start: 0.8575 (m-40) cc_final: 0.7710 (m-40) REVERT: E 138 PHE cc_start: 0.8919 (m-80) cc_final: 0.8382 (m-80) REVERT: E 175 PHE cc_start: 0.8021 (t80) cc_final: 0.7662 (t80) REVERT: G 2 GLN cc_start: 0.8520 (tp40) cc_final: 0.8299 (mm110) REVERT: J 19 ASP cc_start: 0.7039 (t0) cc_final: 0.6490 (t0) REVERT: J 102 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8035 (mt-10) REVERT: K 87 LEU cc_start: 0.8185 (mt) cc_final: 0.7840 (mt) REVERT: L 143 GLU cc_start: 0.7611 (tp30) cc_final: 0.7225 (mp0) REVERT: N 24 MET cc_start: 0.8311 (tpp) cc_final: 0.7935 (mpp) REVERT: N 89 SER cc_start: 0.8298 (OUTLIER) cc_final: 0.8043 (t) REVERT: N 114 GLU cc_start: 0.8170 (OUTLIER) cc_final: 0.7628 (pm20) REVERT: O 48 LEU cc_start: 0.8887 (mt) cc_final: 0.8677 (mm) REVERT: P 3 ASN cc_start: 0.8575 (m110) cc_final: 0.8139 (t0) REVERT: P 6 LYS cc_start: 0.8429 (tttt) cc_final: 0.8073 (tppt) REVERT: P 9 GLU cc_start: 0.7954 (pp20) cc_final: 0.7441 (pp20) REVERT: P 13 MET cc_start: 0.7535 (mtm) cc_final: 0.7268 (mtm) REVERT: P 71 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.6943 (mp0) REVERT: S 66 ILE cc_start: 0.8818 (pt) cc_final: 0.8423 (mt) REVERT: U 66 GLN cc_start: 0.8521 (mt0) cc_final: 0.8241 (mt0) REVERT: Z 19 LYS cc_start: 0.8653 (mmmt) cc_final: 0.8125 (ttpp) REVERT: Z 47 MET cc_start: 0.7464 (mmt) cc_final: 0.7141 (mmt) REVERT: b 52 ARG cc_start: 0.8335 (ptm-80) cc_final: 0.7798 (ptm-80) REVERT: d 42 LEU cc_start: 0.8762 (tp) cc_final: 0.8495 (tp) REVERT: g 145 GLU cc_start: 0.8919 (tm-30) cc_final: 0.8685 (pp20) REVERT: g 213 TYR cc_start: 0.8596 (m-80) cc_final: 0.8328 (m-80) REVERT: h 25 ASN cc_start: 0.8131 (t0) cc_final: 0.7928 (p0) REVERT: h 29 PHE cc_start: 0.8611 (m-80) cc_final: 0.8339 (m-80) REVERT: h 142 MET cc_start: 0.9309 (mmm) cc_final: 0.9101 (mmt) REVERT: h 181 ASP cc_start: 0.8878 (t70) cc_final: 0.8626 (t0) REVERT: h 183 ASP cc_start: 0.6987 (t0) cc_final: 0.6654 (t0) REVERT: h 184 TYR cc_start: 0.7346 (t80) cc_final: 0.6976 (t80) REVERT: i 105 MET cc_start: 0.7936 (ttm) cc_final: 0.7722 (ttm) REVERT: i 124 MET cc_start: 0.6971 (mmp) cc_final: 0.5881 (mmt) REVERT: i 135 TYR cc_start: 0.8150 (t80) cc_final: 0.7804 (t80) REVERT: i 185 LYS cc_start: 0.8693 (tptt) cc_final: 0.8297 (tptt) REVERT: k 35 LYS cc_start: 0.9029 (mppt) cc_final: 0.8691 (mppt) REVERT: k 75 GLU cc_start: 0.8871 (tt0) cc_final: 0.8329 (tp30) REVERT: l 15 ASP cc_start: 0.6611 (t0) cc_final: 0.6320 (t0) REVERT: n 4 ASN cc_start: 0.7912 (OUTLIER) cc_final: 0.7636 (p0) REVERT: n 42 GLU cc_start: 0.8322 (tp30) cc_final: 0.8054 (tp30) REVERT: n 46 MET cc_start: 0.8017 (ptt) cc_final: 0.7711 (ptp) REVERT: n 110 GLN cc_start: 0.8807 (tt0) cc_final: 0.8476 (mm110) REVERT: o 57 VAL cc_start: 0.5811 (OUTLIER) cc_final: 0.5414 (p) REVERT: o 58 ASN cc_start: 0.7295 (m110) cc_final: 0.6997 (m-40) REVERT: q 103 ASP cc_start: 0.7243 (m-30) cc_final: 0.6853 (m-30) REVERT: s 21 PHE cc_start: 0.8124 (m-10) cc_final: 0.7878 (m-80) REVERT: s 89 MET cc_start: 0.8218 (tpp) cc_final: 0.7921 (tpp) REVERT: v 9 GLN cc_start: 0.7778 (mp10) cc_final: 0.7090 (tm-30) REVERT: v 11 ARG cc_start: 0.7746 (mpt180) cc_final: 0.7494 (mpt180) REVERT: v 34 TYR cc_start: 0.8649 (m-80) cc_final: 0.8422 (m-80) REVERT: v 57 ASP cc_start: 0.6504 (t0) cc_final: 0.6283 (t0) REVERT: w 38 LYS cc_start: 0.8874 (mtpt) cc_final: 0.8639 (mtpp) REVERT: x 55 ARG cc_start: 0.6338 (OUTLIER) cc_final: 0.5666 (mmp80) REVERT: z 36 GLU cc_start: 0.7915 (pm20) cc_final: 0.7697 (pm20) REVERT: z 54 LYS cc_start: 0.8455 (mtmt) cc_final: 0.8088 (ttmt) outliers start: 254 outliers final: 192 residues processed: 1070 average time/residue: 1.2765 time to fit residues: 2412.1567 Evaluate side-chains 1063 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 862 time to evaluate : 6.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 22 HIS Chi-restraints excluded: chain 5 residue 25 PHE Chi-restraints excluded: chain 5 residue 52 SER Chi-restraints excluded: chain 5 residue 80 VAL Chi-restraints excluded: chain 5 residue 85 THR Chi-restraints excluded: chain 5 residue 115 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 32 ASN Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 197 THR Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 49 ASP Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 3 GLN Chi-restraints excluded: chain M residue 24 THR Chi-restraints excluded: chain M residue 115 GLU 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 37 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain R residue 49 ILE Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 41 LEU Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 87 PHE Chi-restraints excluded: chain V residue 3 THR Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 55 GLU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 60 ASP Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 48 ILE Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 15 MET Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 46 ASP Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain f residue 12 ARG Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 147 SER Chi-restraints excluded: chain g residue 157 LEU Chi-restraints excluded: chain h residue 122 SER Chi-restraints excluded: chain h residue 151 VAL Chi-restraints excluded: chain h residue 153 VAL Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 102 VAL Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 21 VAL Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 76 LEU Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain k residue 13 ASP Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 63 GLU Chi-restraints excluded: chain m residue 9 ASP Chi-restraints excluded: chain m residue 26 THR Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 63 LEU Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 4 ASN Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 60 LYS Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 72 ILE Chi-restraints excluded: chain n residue 129 LYS Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 36 VAL Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 63 ASP Chi-restraints excluded: chain o residue 78 GLU Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain p residue 17 SER Chi-restraints excluded: chain p residue 97 ILE Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 49 LEU Chi-restraints excluded: chain q residue 73 ASN Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 78 SER Chi-restraints excluded: chain s residue 96 LEU Chi-restraints excluded: chain s residue 101 TRP Chi-restraints excluded: chain t residue 22 THR Chi-restraints excluded: chain t residue 27 VAL Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain u residue 47 GLU Chi-restraints excluded: chain u residue 78 VAL Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 47 HIS Chi-restraints excluded: chain w residue 59 ILE Chi-restraints excluded: chain x residue 55 ARG Chi-restraints excluded: chain y residue 67 ILE Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 13 ASP Chi-restraints excluded: chain z residue 28 VAL Chi-restraints excluded: chain z residue 53 VAL Chi-restraints excluded: chain z residue 56 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 342 optimal weight: 20.0000 chunk 917 optimal weight: 0.8980 chunk 201 optimal weight: 10.0000 chunk 598 optimal weight: 3.9990 chunk 251 optimal weight: 10.0000 chunk 1019 optimal weight: 10.0000 chunk 846 optimal weight: 6.9990 chunk 472 optimal weight: 40.0000 chunk 84 optimal weight: 10.0000 chunk 337 optimal weight: 20.0000 chunk 535 optimal weight: 4.9990 overall best weight: 5.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 159 HIS ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 134 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 75 GLN ** R 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** T 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 49 ASN ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 9 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8180 moved from start: 0.4715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 164734 Z= 0.267 Angle : 0.689 15.619 246771 Z= 0.363 Chirality : 0.037 0.391 31487 Planarity : 0.006 0.130 12982 Dihedral : 24.591 179.695 83102 Min Nonbonded Distance : 1.176 Molprobity Statistics. All-atom Clashscore : 19.30 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.74 % Favored : 92.17 % Rotamer: Outliers : 5.49 % Allowed : 21.67 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.64 (0.11), residues: 5750 helix: 0.12 (0.12), residues: 1900 sheet: -1.42 (0.16), residues: 1061 loop : -1.79 (0.11), residues: 2789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.076 0.002 TRP l 103 HIS 0.009 0.001 HIS V 80 PHE 0.023 0.002 PHE z 12 TYR 0.052 0.002 TYR i 76 ARG 0.012 0.001 ARG c 28 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1160 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 263 poor density : 897 time to evaluate : 6.407 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: 5 31 GLU cc_start: 0.7394 (tm-30) cc_final: 0.7169 (tm-30) REVERT: 5 73 MET cc_start: 0.7268 (mtm) cc_final: 0.7041 (mtm) REVERT: 5 146 GLU cc_start: 0.8297 (tt0) cc_final: 0.7683 (tp30) REVERT: 5 150 ASP cc_start: 0.8640 (p0) cc_final: 0.7154 (p0) REVERT: A 56 ASP cc_start: 0.8306 (p0) cc_final: 0.8058 (p0) REVERT: B 39 LYS cc_start: 0.7504 (OUTLIER) cc_final: 0.6926 (ptpp) REVERT: C 116 LYS cc_start: 0.8227 (mmtm) cc_final: 0.7882 (mmtm) REVERT: D 145 ASP cc_start: 0.7945 (OUTLIER) cc_final: 0.7546 (p0) REVERT: E 26 MET cc_start: 0.7089 (mtp) cc_final: 0.6743 (mtp) REVERT: E 31 VAL cc_start: 0.8094 (OUTLIER) cc_final: 0.7716 (p) REVERT: E 83 TYR cc_start: 0.7554 (t80) cc_final: 0.6930 (t80) REVERT: E 89 VAL cc_start: 0.7037 (OUTLIER) cc_final: 0.6785 (p) REVERT: E 96 MET cc_start: 0.8038 (tmm) cc_final: 0.7624 (tmm) REVERT: E 118 SER cc_start: 0.8595 (m) cc_final: 0.8011 (p) REVERT: E 127 ASN cc_start: 0.8584 (m-40) cc_final: 0.7701 (m-40) REVERT: E 138 PHE cc_start: 0.8936 (m-80) cc_final: 0.8408 (m-80) REVERT: G 2 GLN cc_start: 0.8583 (tp40) cc_final: 0.8375 (mm110) REVERT: J 19 ASP cc_start: 0.7035 (t0) cc_final: 0.6501 (t0) REVERT: J 102 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8096 (mt-10) REVERT: K 87 LEU cc_start: 0.8234 (mt) cc_final: 0.7856 (mt) REVERT: L 143 GLU cc_start: 0.7545 (tp30) cc_final: 0.7217 (mp0) REVERT: M 1 MET cc_start: 0.7727 (tpp) cc_final: 0.7442 (tpt) REVERT: N 89 SER cc_start: 0.8300 (OUTLIER) cc_final: 0.8062 (t) REVERT: N 114 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7636 (pm20) REVERT: O 48 LEU cc_start: 0.8905 (mt) cc_final: 0.8695 (mm) REVERT: P 3 ASN cc_start: 0.8588 (m110) cc_final: 0.8137 (t0) REVERT: P 6 LYS cc_start: 0.8444 (tttt) cc_final: 0.8078 (tppt) REVERT: P 9 GLU cc_start: 0.7991 (pp20) cc_final: 0.7499 (pp20) REVERT: P 13 MET cc_start: 0.7487 (mtm) cc_final: 0.7209 (mtm) REVERT: P 71 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.6910 (mp0) REVERT: P 76 THR cc_start: 0.9207 (m) cc_final: 0.8933 (p) REVERT: Q 57 PHE cc_start: 0.8782 (m-80) cc_final: 0.8421 (m-80) REVERT: Q 95 LEU cc_start: 0.8771 (mt) cc_final: 0.8547 (mm) REVERT: S 66 ILE cc_start: 0.8785 (pt) cc_final: 0.8426 (mt) REVERT: T 37 ASP cc_start: 0.8088 (OUTLIER) cc_final: 0.7668 (p0) REVERT: U 66 GLN cc_start: 0.8552 (mt0) cc_final: 0.8184 (mt0) REVERT: Z 19 LYS cc_start: 0.8614 (mmmt) cc_final: 0.8115 (ttpp) REVERT: Z 47 MET cc_start: 0.7491 (mmt) cc_final: 0.7187 (mmt) REVERT: b 52 ARG cc_start: 0.8341 (ptm-80) cc_final: 0.7794 (ptm-80) REVERT: d 42 LEU cc_start: 0.8753 (tp) cc_final: 0.8482 (tp) REVERT: f 1 MET cc_start: 0.8035 (mmp) cc_final: 0.7674 (mmp) REVERT: g 145 GLU cc_start: 0.8944 (tm-30) cc_final: 0.8736 (pp20) REVERT: g 213 TYR cc_start: 0.8585 (m-80) cc_final: 0.8132 (m-80) REVERT: h 29 PHE cc_start: 0.8625 (m-80) cc_final: 0.8409 (m-80) REVERT: h 57 ILE cc_start: 0.7364 (OUTLIER) cc_final: 0.7054 (tp) REVERT: h 181 ASP cc_start: 0.8889 (t70) cc_final: 0.8652 (t0) REVERT: h 183 ASP cc_start: 0.7012 (t0) cc_final: 0.6672 (t0) REVERT: h 184 TYR cc_start: 0.7277 (t80) cc_final: 0.6937 (t80) REVERT: i 76 TYR cc_start: 0.8493 (t80) cc_final: 0.7866 (t80) REVERT: i 124 MET cc_start: 0.7788 (mmp) cc_final: 0.7095 (mmt) REVERT: i 135 TYR cc_start: 0.8078 (t80) cc_final: 0.7780 (t80) REVERT: i 185 LYS cc_start: 0.8700 (tptt) cc_final: 0.8307 (tptt) REVERT: k 35 LYS cc_start: 0.9085 (mppt) cc_final: 0.8707 (mppt) REVERT: k 42 TRP cc_start: 0.7596 (m-10) cc_final: 0.7378 (m-10) REVERT: k 75 GLU cc_start: 0.8875 (tt0) cc_final: 0.8333 (tp30) REVERT: k 90 MET cc_start: 0.8002 (pmm) cc_final: 0.7786 (pmm) REVERT: l 15 ASP cc_start: 0.6609 (t0) cc_final: 0.6388 (t0) REVERT: n 4 ASN cc_start: 0.8215 (OUTLIER) cc_final: 0.8009 (p0) REVERT: n 42 GLU cc_start: 0.8189 (tp30) cc_final: 0.7950 (tp30) REVERT: n 46 MET cc_start: 0.7900 (ptt) cc_final: 0.7590 (ptp) REVERT: n 110 GLN cc_start: 0.8816 (tt0) cc_final: 0.8484 (mm110) REVERT: o 57 VAL cc_start: 0.5948 (OUTLIER) cc_final: 0.5533 (p) REVERT: o 58 ASN cc_start: 0.7378 (m110) cc_final: 0.7062 (m-40) REVERT: s 21 PHE cc_start: 0.8246 (m-80) cc_final: 0.7990 (m-80) REVERT: s 89 MET cc_start: 0.8202 (tpp) cc_final: 0.7905 (tpp) REVERT: v 9 GLN cc_start: 0.7838 (mp10) cc_final: 0.7259 (tm-30) REVERT: v 11 ARG cc_start: 0.7774 (mpt180) cc_final: 0.7555 (mpt180) REVERT: v 77 ARG cc_start: 0.7787 (tmm-80) cc_final: 0.7296 (tmm-80) REVERT: w 38 LYS cc_start: 0.8831 (mtpt) cc_final: 0.8536 (mtpp) REVERT: w 51 TYR cc_start: 0.7779 (m-80) cc_final: 0.7572 (m-80) REVERT: x 55 ARG cc_start: 0.6399 (OUTLIER) cc_final: 0.5736 (mmp80) REVERT: y 61 GLN cc_start: 0.9141 (mm-40) cc_final: 0.8830 (mm-40) REVERT: z 31 GLU cc_start: 0.7865 (tp30) cc_final: 0.7329 (tm-30) REVERT: z 36 GLU cc_start: 0.7903 (pm20) cc_final: 0.7676 (pm20) REVERT: z 49 LYS cc_start: 0.9113 (ttpp) cc_final: 0.8872 (ttpp) outliers start: 263 outliers final: 206 residues processed: 1069 average time/residue: 1.2683 time to fit residues: 2382.9876 Evaluate side-chains 1076 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 858 time to evaluate : 6.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 25 PHE Chi-restraints excluded: chain 5 residue 52 SER Chi-restraints excluded: chain 5 residue 80 VAL Chi-restraints excluded: chain 5 residue 85 THR Chi-restraints excluded: chain 5 residue 115 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain D residue 181 ILE Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 139 PHE Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 49 ASP Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 2 LEU 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 29 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 7 HIS Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 41 LEU Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 87 PHE Chi-restraints excluded: chain U residue 103 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 55 GLU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 60 ASP Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 48 ILE Chi-restraints excluded: chain a residue 24 ILE Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 15 MET Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 46 ASP Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain f residue 12 ARG Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain g residue 36 ASN Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 157 LEU Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain h residue 122 SER Chi-restraints excluded: chain h residue 124 LEU Chi-restraints excluded: chain h residue 151 VAL Chi-restraints excluded: chain h residue 153 VAL Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 20 PHE Chi-restraints excluded: chain i residue 102 VAL Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain i residue 203 LEU Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 21 VAL Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 76 LEU Chi-restraints excluded: chain j residue 117 VAL Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 137 VAL Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain l residue 30 LEU Chi-restraints excluded: chain l residue 63 GLU Chi-restraints excluded: chain m residue 9 ASP Chi-restraints excluded: chain m residue 26 THR Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 63 LEU Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 4 ASN Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 60 LYS Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 72 ILE Chi-restraints excluded: chain n residue 114 LYS Chi-restraints excluded: chain n residue 129 LYS Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 36 VAL Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 63 ASP Chi-restraints excluded: chain o residue 76 ILE Chi-restraints excluded: chain o residue 78 GLU Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain p residue 17 SER Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 49 LEU Chi-restraints excluded: chain q residue 73 ASN Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 78 SER Chi-restraints excluded: chain q residue 98 VAL Chi-restraints excluded: chain s residue 96 LEU Chi-restraints excluded: chain t residue 27 VAL Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 47 GLU Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 78 VAL Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 47 HIS Chi-restraints excluded: chain w residue 59 ILE Chi-restraints excluded: chain x residue 55 ARG Chi-restraints excluded: chain y residue 67 ILE Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 13 ASP Chi-restraints excluded: chain z residue 28 VAL Chi-restraints excluded: chain z residue 53 VAL Chi-restraints excluded: chain z residue 56 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 983 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 581 optimal weight: 9.9990 chunk 744 optimal weight: 10.0000 chunk 577 optimal weight: 3.9990 chunk 858 optimal weight: 50.0000 chunk 569 optimal weight: 5.9990 chunk 1015 optimal weight: 8.9990 chunk 635 optimal weight: 2.9990 chunk 619 optimal weight: 2.9990 chunk 469 optimal weight: 50.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 159 HIS ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN B 134 ASN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** i 54 GLN ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 4 ASN n 50 GLN ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 28 GLN ** v 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 9 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.103 164734 Z= 0.253 Angle : 0.679 14.010 246771 Z= 0.359 Chirality : 0.036 0.384 31487 Planarity : 0.006 0.129 12982 Dihedral : 24.579 179.527 83100 Min Nonbonded Distance : 1.185 Molprobity Statistics. All-atom Clashscore : 19.21 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.90 % Favored : 92.02 % Rotamer: Outliers : 5.57 % Allowed : 22.48 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.57 (0.11), residues: 5750 helix: 0.21 (0.12), residues: 1894 sheet: -1.42 (0.16), residues: 1065 loop : -1.76 (0.11), residues: 2791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.095 0.002 TRP l 103 HIS 0.024 0.001 HIS S 7 PHE 0.023 0.002 PHE o 13 TYR 0.038 0.002 TYR l 44 ARG 0.012 0.001 ARG c 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1159 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 267 poor density : 892 time to evaluate : 6.340 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: 5 146 GLU cc_start: 0.8269 (tt0) cc_final: 0.7650 (tp30) REVERT: 5 150 ASP cc_start: 0.8631 (p0) cc_final: 0.7175 (p0) REVERT: A 56 ASP cc_start: 0.8296 (p0) cc_final: 0.8078 (p0) REVERT: B 39 LYS cc_start: 0.7483 (OUTLIER) cc_final: 0.6914 (ptpp) REVERT: D 141 MET cc_start: 0.8154 (mpp) cc_final: 0.7798 (mtm) REVERT: D 145 ASP cc_start: 0.7944 (OUTLIER) cc_final: 0.7542 (p0) REVERT: E 26 MET cc_start: 0.7105 (mtp) cc_final: 0.6724 (mtp) REVERT: E 31 VAL cc_start: 0.8051 (OUTLIER) cc_final: 0.7658 (p) REVERT: E 83 TYR cc_start: 0.7550 (t80) cc_final: 0.6977 (t80) REVERT: E 96 MET cc_start: 0.8071 (tmm) cc_final: 0.7654 (tmm) REVERT: E 118 SER cc_start: 0.8458 (m) cc_final: 0.7900 (p) REVERT: E 127 ASN cc_start: 0.8610 (m-40) cc_final: 0.7732 (m-40) REVERT: E 138 PHE cc_start: 0.8931 (m-80) cc_final: 0.8411 (m-80) REVERT: F 32 GLU cc_start: 0.8036 (tp30) cc_final: 0.7271 (tp30) REVERT: G 2 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.8375 (mm110) REVERT: J 19 ASP cc_start: 0.7029 (t0) cc_final: 0.6500 (t0) REVERT: J 44 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.8537 (t80) REVERT: J 102 GLU cc_start: 0.8354 (mt-10) cc_final: 0.8141 (mt-10) REVERT: K 87 LEU cc_start: 0.8261 (mt) cc_final: 0.7815 (mt) REVERT: L 143 GLU cc_start: 0.7489 (tp30) cc_final: 0.7141 (mp0) REVERT: M 53 MET cc_start: 0.8020 (mtm) cc_final: 0.7815 (mtm) REVERT: N 24 MET cc_start: 0.8246 (tpp) cc_final: 0.7567 (mpp) REVERT: N 89 SER cc_start: 0.8277 (OUTLIER) cc_final: 0.8069 (t) REVERT: N 114 GLU cc_start: 0.8057 (OUTLIER) cc_final: 0.7648 (pm20) REVERT: O 48 LEU cc_start: 0.8901 (mt) cc_final: 0.8695 (mm) REVERT: P 3 ASN cc_start: 0.8586 (m110) cc_final: 0.8137 (t0) REVERT: P 6 LYS cc_start: 0.8429 (tttt) cc_final: 0.8072 (tppt) REVERT: P 9 GLU cc_start: 0.7972 (pp20) cc_final: 0.7503 (pp20) REVERT: P 13 MET cc_start: 0.7480 (mtm) cc_final: 0.7197 (mtm) REVERT: P 71 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7068 (mp0) REVERT: P 76 THR cc_start: 0.9198 (m) cc_final: 0.8937 (p) REVERT: Q 57 PHE cc_start: 0.8798 (m-80) cc_final: 0.8396 (m-80) REVERT: Q 95 LEU cc_start: 0.8773 (mt) cc_final: 0.8547 (mm) REVERT: S 66 ILE cc_start: 0.8769 (pt) cc_final: 0.8375 (mt) REVERT: T 37 ASP cc_start: 0.8081 (OUTLIER) cc_final: 0.7676 (p0) REVERT: V 8 VAL cc_start: 0.8091 (OUTLIER) cc_final: 0.7834 (p) REVERT: V 87 GLN cc_start: 0.7976 (mt0) cc_final: 0.7552 (mt0) REVERT: Z 19 LYS cc_start: 0.8598 (mmmt) cc_final: 0.8131 (ttpp) REVERT: Z 47 MET cc_start: 0.7505 (mmt) cc_final: 0.7169 (mmt) REVERT: b 52 ARG cc_start: 0.8362 (ptm-80) cc_final: 0.7821 (ptm-80) REVERT: d 42 LEU cc_start: 0.8741 (tp) cc_final: 0.8471 (tp) REVERT: f 1 MET cc_start: 0.8064 (mmp) cc_final: 0.7734 (mmp) REVERT: g 213 TYR cc_start: 0.8576 (m-80) cc_final: 0.8359 (m-80) REVERT: h 57 ILE cc_start: 0.7408 (OUTLIER) cc_final: 0.7186 (tp) REVERT: h 181 ASP cc_start: 0.8884 (t70) cc_final: 0.8682 (t0) REVERT: h 183 ASP cc_start: 0.6964 (t0) cc_final: 0.6716 (t0) REVERT: h 184 TYR cc_start: 0.7155 (t80) cc_final: 0.6847 (t80) REVERT: i 124 MET cc_start: 0.7668 (mmp) cc_final: 0.6882 (mmt) REVERT: i 185 LYS cc_start: 0.8695 (tptt) cc_final: 0.8292 (tptt) REVERT: k 35 LYS cc_start: 0.9091 (mppt) cc_final: 0.8698 (mppt) REVERT: k 75 GLU cc_start: 0.8877 (tt0) cc_final: 0.8323 (tp30) REVERT: l 15 ASP cc_start: 0.6756 (t0) cc_final: 0.6498 (t0) REVERT: n 4 ASN cc_start: 0.7989 (OUTLIER) cc_final: 0.7753 (p0) REVERT: n 19 VAL cc_start: 0.5334 (OUTLIER) cc_final: 0.4977 (p) REVERT: n 52 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8302 (tp) REVERT: o 57 VAL cc_start: 0.5974 (OUTLIER) cc_final: 0.5525 (p) REVERT: o 58 ASN cc_start: 0.7366 (m110) cc_final: 0.7036 (m-40) REVERT: s 21 PHE cc_start: 0.8292 (m-10) cc_final: 0.8035 (m-80) REVERT: s 89 MET cc_start: 0.8246 (tpp) cc_final: 0.7947 (tpp) REVERT: t 10 LYS cc_start: 0.8936 (mtmm) cc_final: 0.8730 (mtmm) REVERT: u 76 LYS cc_start: 0.8944 (tttm) cc_final: 0.8614 (tttm) REVERT: v 9 GLN cc_start: 0.7935 (mp10) cc_final: 0.7258 (tm-30) REVERT: v 11 ARG cc_start: 0.7744 (mpt180) cc_final: 0.7541 (mpt180) REVERT: v 47 HIS cc_start: 0.7798 (OUTLIER) cc_final: 0.7596 (p90) REVERT: w 38 LYS cc_start: 0.8831 (mtpt) cc_final: 0.8559 (mtpp) REVERT: x 44 MET cc_start: 0.3977 (tpp) cc_final: 0.1998 (mmt) REVERT: x 55 ARG cc_start: 0.6494 (OUTLIER) cc_final: 0.5782 (mmp80) REVERT: y 61 GLN cc_start: 0.9164 (mm-40) cc_final: 0.8954 (mm-40) REVERT: z 24 GLU cc_start: 0.8185 (pt0) cc_final: 0.7846 (pt0) REVERT: z 36 GLU cc_start: 0.7856 (pm20) cc_final: 0.7643 (pm20) REVERT: z 49 LYS cc_start: 0.9111 (ttpp) cc_final: 0.8874 (ttpp) outliers start: 267 outliers final: 209 residues processed: 1071 average time/residue: 1.3614 time to fit residues: 2592.6648 Evaluate side-chains 1080 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 854 time to evaluate : 5.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 22 HIS Chi-restraints excluded: chain 5 residue 25 PHE Chi-restraints excluded: chain 5 residue 80 VAL Chi-restraints excluded: chain 5 residue 85 THR Chi-restraints excluded: chain 5 residue 115 SER Chi-restraints excluded: chain 5 residue 140 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 120 VAL Chi-restraints excluded: chain B residue 134 ASN Chi-restraints excluded: chain B residue 137 VAL Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 32 ASN Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain G residue 2 GLN Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 139 PHE Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain J residue 49 ASP Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 2 LEU Chi-restraints excluded: chain M residue 3 GLN 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 29 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 41 LEU Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 87 PHE Chi-restraints excluded: chain U residue 103 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 55 GLU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 60 ASP Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 48 ILE Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 15 MET Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 46 ASP Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 7 GLU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain f residue 12 ARG Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain g residue 36 ASN Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 157 LEU Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain h residue 122 SER Chi-restraints excluded: chain h residue 124 LEU Chi-restraints excluded: chain h residue 151 VAL Chi-restraints excluded: chain h residue 153 VAL Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 20 PHE Chi-restraints excluded: chain i residue 102 VAL Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain i residue 203 LEU Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 21 VAL Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 76 LEU Chi-restraints excluded: chain j residue 117 VAL Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 137 VAL Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 68 GLN Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain l residue 63 GLU Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain m residue 9 ASP Chi-restraints excluded: chain m residue 26 THR Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 63 LEU Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 4 ASN Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 52 LEU Chi-restraints excluded: chain n residue 60 LYS Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 72 ILE Chi-restraints excluded: chain n residue 105 THR Chi-restraints excluded: chain n residue 114 LYS Chi-restraints excluded: chain n residue 129 LYS Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 63 ASP Chi-restraints excluded: chain o residue 69 THR Chi-restraints excluded: chain o residue 76 ILE Chi-restraints excluded: chain o residue 78 GLU Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain p residue 17 SER Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 49 LEU Chi-restraints excluded: chain q residue 73 ASN Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 78 SER Chi-restraints excluded: chain q residue 98 VAL Chi-restraints excluded: chain s residue 96 LEU Chi-restraints excluded: chain t residue 27 VAL Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain t residue 83 GLU Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 78 VAL Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain v residue 47 HIS Chi-restraints excluded: chain w residue 33 ILE Chi-restraints excluded: chain w residue 59 ILE Chi-restraints excluded: chain x residue 55 ARG Chi-restraints excluded: chain y residue 67 ILE Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 13 ASP Chi-restraints excluded: chain z residue 28 VAL Chi-restraints excluded: chain z residue 53 VAL Chi-restraints excluded: chain z residue 56 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 628 optimal weight: 20.0000 chunk 405 optimal weight: 30.0000 chunk 606 optimal weight: 10.0000 chunk 306 optimal weight: 20.0000 chunk 199 optimal weight: 10.0000 chunk 196 optimal weight: 10.0000 chunk 645 optimal weight: 0.7980 chunk 692 optimal weight: 8.9990 chunk 502 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 798 optimal weight: 7.9990 overall best weight: 6.7590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 159 HIS ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN ** C 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 11 ASN ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 7 HIS ** T 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 80 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 4 ASN ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 79 ASN ** v 47 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 9 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.5019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.093 164734 Z= 0.321 Angle : 0.733 14.044 246771 Z= 0.383 Chirality : 0.039 0.397 31487 Planarity : 0.006 0.131 12982 Dihedral : 24.635 179.689 83100 Min Nonbonded Distance : 1.182 Molprobity Statistics. All-atom Clashscore : 21.29 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.49 % Favored : 91.43 % Rotamer: Outliers : 5.66 % Allowed : 22.59 % Favored : 71.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.11), residues: 5750 helix: 0.04 (0.12), residues: 1896 sheet: -1.48 (0.15), residues: 1080 loop : -1.86 (0.11), residues: 2774 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.101 0.003 TRP l 103 HIS 0.011 0.002 HIS V 80 PHE 0.028 0.002 PHE G 46 TYR 0.036 0.002 TYR l 44 ARG 0.013 0.001 ARG c 28 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1145 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 874 time to evaluate : 6.258 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: 5 31 GLU cc_start: 0.7108 (tm-30) cc_final: 0.6847 (tm-30) REVERT: 5 146 GLU cc_start: 0.8316 (tt0) cc_final: 0.7679 (tp30) REVERT: 5 150 ASP cc_start: 0.8662 (p0) cc_final: 0.7180 (p0) REVERT: B 39 LYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7007 (ptpp) REVERT: D 141 MET cc_start: 0.8188 (mpp) cc_final: 0.7965 (mtm) REVERT: D 145 ASP cc_start: 0.7976 (OUTLIER) cc_final: 0.7556 (p0) REVERT: E 26 MET cc_start: 0.7142 (mtp) cc_final: 0.6891 (mtp) REVERT: E 31 VAL cc_start: 0.8061 (OUTLIER) cc_final: 0.7660 (p) REVERT: E 83 TYR cc_start: 0.7543 (t80) cc_final: 0.6954 (t80) REVERT: E 96 MET cc_start: 0.8030 (tmm) cc_final: 0.7590 (tmm) REVERT: E 127 ASN cc_start: 0.8579 (m-40) cc_final: 0.7686 (m-40) REVERT: E 138 PHE cc_start: 0.8972 (m-80) cc_final: 0.8398 (m-80) REVERT: F 69 ARG cc_start: 0.8859 (ttt180) cc_final: 0.7703 (ttp80) REVERT: G 2 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.8369 (mm110) REVERT: J 19 ASP cc_start: 0.7029 (t0) cc_final: 0.6507 (t0) REVERT: J 44 TYR cc_start: 0.8869 (OUTLIER) cc_final: 0.8588 (t80) REVERT: J 102 GLU cc_start: 0.8391 (mt-10) cc_final: 0.8183 (mt-10) REVERT: K 87 LEU cc_start: 0.8345 (mt) cc_final: 0.7891 (mt) REVERT: L 143 GLU cc_start: 0.7463 (tp30) cc_final: 0.7070 (mp0) REVERT: M 1 MET cc_start: 0.7929 (tpp) cc_final: 0.7550 (tpt) REVERT: N 114 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7863 (pm20) REVERT: P 3 ASN cc_start: 0.8596 (m110) cc_final: 0.8161 (t0) REVERT: P 6 LYS cc_start: 0.8432 (tttt) cc_final: 0.8082 (tppt) REVERT: P 9 GLU cc_start: 0.8021 (pp20) cc_final: 0.7551 (pp20) REVERT: P 13 MET cc_start: 0.7515 (mtm) cc_final: 0.7268 (mtm) REVERT: P 71 GLU cc_start: 0.8114 (OUTLIER) cc_final: 0.6902 (mp0) REVERT: Q 57 PHE cc_start: 0.8849 (m-80) cc_final: 0.8492 (m-80) REVERT: S 66 ILE cc_start: 0.8801 (pt) cc_final: 0.8468 (mt) REVERT: T 37 ASP cc_start: 0.8112 (OUTLIER) cc_final: 0.7679 (p0) REVERT: Z 19 LYS cc_start: 0.8645 (mmmt) cc_final: 0.8136 (ttpp) REVERT: Z 47 MET cc_start: 0.7564 (mmt) cc_final: 0.7198 (mmt) REVERT: d 42 LEU cc_start: 0.8768 (tp) cc_final: 0.8498 (tp) REVERT: f 1 MET cc_start: 0.8098 (mmp) cc_final: 0.7754 (mmp) REVERT: g 145 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8711 (pp20) REVERT: g 213 TYR cc_start: 0.8607 (m-80) cc_final: 0.8353 (m-80) REVERT: h 25 ASN cc_start: 0.8636 (t0) cc_final: 0.8266 (p0) REVERT: h 57 ILE cc_start: 0.7480 (OUTLIER) cc_final: 0.7216 (tp) REVERT: h 183 ASP cc_start: 0.6967 (t0) cc_final: 0.6702 (t0) REVERT: i 124 MET cc_start: 0.7767 (mmp) cc_final: 0.6984 (mmt) REVERT: k 35 LYS cc_start: 0.9143 (mppt) cc_final: 0.8719 (mppt) REVERT: k 75 GLU cc_start: 0.8883 (tt0) cc_final: 0.8341 (tp30) REVERT: k 90 MET cc_start: 0.8227 (pmm) cc_final: 0.7811 (pmm) REVERT: l 15 ASP cc_start: 0.6679 (t0) cc_final: 0.6412 (t0) REVERT: n 19 VAL cc_start: 0.5492 (OUTLIER) cc_final: 0.5151 (p) REVERT: n 52 LEU cc_start: 0.9184 (tp) cc_final: 0.8748 (tp) REVERT: n 57 MET cc_start: 0.7256 (pmm) cc_final: 0.6596 (pmm) REVERT: o 57 VAL cc_start: 0.6064 (OUTLIER) cc_final: 0.5607 (p) REVERT: o 58 ASN cc_start: 0.7462 (m110) cc_final: 0.7156 (m-40) REVERT: s 21 PHE cc_start: 0.8247 (m-10) cc_final: 0.8012 (m-80) REVERT: s 89 MET cc_start: 0.8300 (tpp) cc_final: 0.7998 (tpp) REVERT: t 10 LYS cc_start: 0.8941 (mtmm) cc_final: 0.8730 (mtmm) REVERT: u 76 LYS cc_start: 0.8857 (tttm) cc_final: 0.8474 (tttm) REVERT: v 11 ARG cc_start: 0.7717 (mpt180) cc_final: 0.7492 (mpt180) REVERT: v 77 ARG cc_start: 0.7983 (tmm-80) cc_final: 0.7558 (tmm-80) REVERT: w 38 LYS cc_start: 0.8838 (mtpt) cc_final: 0.8492 (mtpt) REVERT: w 51 TYR cc_start: 0.7599 (m-80) cc_final: 0.7328 (m-80) REVERT: x 44 MET cc_start: 0.4505 (tpp) cc_final: 0.2474 (mmt) REVERT: x 55 ARG cc_start: 0.6441 (OUTLIER) cc_final: 0.5687 (mmp80) REVERT: y 10 ARG cc_start: 0.8423 (ttt90) cc_final: 0.7821 (ttt90) REVERT: y 61 GLN cc_start: 0.9197 (mm-40) cc_final: 0.8965 (mm-40) REVERT: z 36 GLU cc_start: 0.7831 (pm20) cc_final: 0.7630 (pm20) outliers start: 271 outliers final: 223 residues processed: 1048 average time/residue: 1.3561 time to fit residues: 2521.4992 Evaluate side-chains 1085 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 235 poor density : 850 time to evaluate : 6.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 22 HIS Chi-restraints excluded: chain 5 residue 25 PHE Chi-restraints excluded: chain 5 residue 52 SER Chi-restraints excluded: chain 5 residue 80 VAL Chi-restraints excluded: chain 5 residue 85 THR Chi-restraints excluded: chain 5 residue 115 SER Chi-restraints excluded: chain 5 residue 140 SER Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 17 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 39 LYS Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 90 ASN Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 228 VAL Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 32 ASN Chi-restraints excluded: chain C residue 34 VAL Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain D residue 164 LEU Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 128 TYR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain G residue 2 GLN Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 139 PHE Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain J residue 49 ASP Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain J residue 142 ILE Chi-restraints excluded: chain K residue 4 GLU Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 3 GLN 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 29 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 115 LEU Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 9 ILE Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain Q residue 39 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 13 SER Chi-restraints excluded: chain S residue 24 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 7 LEU Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 17 SER Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 37 ASP Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 41 LEU Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 87 PHE 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 55 GLU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 65 VAL Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 60 ASP Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 8 THR Chi-restraints excluded: chain Z residue 25 LEU Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 48 ILE Chi-restraints excluded: chain a residue 16 CYS Chi-restraints excluded: chain a residue 24 ILE Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 15 MET Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 46 ASP Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 7 GLU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 24 THR Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain c residue 53 LYS Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain f residue 12 ARG Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain g residue 36 ASN Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 157 LEU Chi-restraints excluded: chain g residue 196 VAL Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain h residue 122 SER Chi-restraints excluded: chain h residue 124 LEU Chi-restraints excluded: chain h residue 151 VAL Chi-restraints excluded: chain h residue 153 VAL Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain i residue 17 THR Chi-restraints excluded: chain i residue 20 PHE Chi-restraints excluded: chain i residue 102 VAL Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain i residue 203 LEU Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 21 VAL Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 76 LEU Chi-restraints excluded: chain j residue 117 VAL Chi-restraints excluded: chain j residue 134 ILE Chi-restraints excluded: chain j residue 137 VAL Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 68 GLN Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain l residue 63 GLU Chi-restraints excluded: chain l residue 80 VAL Chi-restraints excluded: chain m residue 9 ASP Chi-restraints excluded: chain m residue 26 THR Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 63 LEU Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 30 ILE Chi-restraints excluded: chain n residue 60 LYS Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 72 ILE Chi-restraints excluded: chain n residue 105 THR Chi-restraints excluded: chain n residue 114 LYS Chi-restraints excluded: chain n residue 129 LYS Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 36 VAL Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 63 ASP Chi-restraints excluded: chain o residue 69 THR Chi-restraints excluded: chain o residue 76 ILE Chi-restraints excluded: chain o residue 78 GLU Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain p residue 17 SER Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 49 LEU Chi-restraints excluded: chain q residue 73 ASN Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 78 SER Chi-restraints excluded: chain q residue 98 VAL Chi-restraints excluded: chain s residue 96 LEU Chi-restraints excluded: chain t residue 27 VAL Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain t residue 83 GLU Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 78 VAL Chi-restraints excluded: chain v residue 13 VAL Chi-restraints excluded: chain w residue 33 ILE Chi-restraints excluded: chain w residue 59 ILE Chi-restraints excluded: chain x residue 55 ARG Chi-restraints excluded: chain y residue 67 ILE Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 13 ASP Chi-restraints excluded: chain z residue 28 VAL Chi-restraints excluded: chain z residue 53 VAL Chi-restraints excluded: chain z residue 56 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 924 optimal weight: 2.9990 chunk 973 optimal weight: 10.0000 chunk 887 optimal weight: 20.0000 chunk 946 optimal weight: 0.0770 chunk 972 optimal weight: 5.9990 chunk 569 optimal weight: 3.9990 chunk 412 optimal weight: 50.0000 chunk 743 optimal weight: 9.9990 chunk 290 optimal weight: 20.0000 chunk 855 optimal weight: 5.9990 chunk 895 optimal weight: 5.9990 overall best weight: 3.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 159 HIS ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 90 ASN C 36 GLN ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN U 54 GLN ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 79 ASN z 9 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.4911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 164734 Z= 0.209 Angle : 0.662 14.010 246771 Z= 0.351 Chirality : 0.035 0.379 31487 Planarity : 0.006 0.126 12982 Dihedral : 24.562 179.818 83100 Min Nonbonded Distance : 1.201 Molprobity Statistics. All-atom Clashscore : 18.33 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.30 % Favored : 92.61 % Rotamer: Outliers : 4.63 % Allowed : 23.99 % Favored : 71.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.11), residues: 5750 helix: 0.24 (0.12), residues: 1893 sheet: -1.29 (0.16), residues: 1077 loop : -1.75 (0.11), residues: 2780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.104 0.002 TRP l 103 HIS 0.008 0.001 HIS V 80 PHE 0.025 0.002 PHE z 19 TYR 0.040 0.002 TYR G 25 ARG 0.015 0.000 ARG c 28 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1119 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 897 time to evaluate : 6.360 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 31 GLU cc_start: 0.7237 (tm-30) cc_final: 0.6923 (tm-30) REVERT: 5 146 GLU cc_start: 0.8275 (tt0) cc_final: 0.7631 (tp30) REVERT: 5 150 ASP cc_start: 0.8603 (p0) cc_final: 0.7145 (p0) REVERT: B 248 TRP cc_start: 0.7983 (m-10) cc_final: 0.7683 (m-10) REVERT: D 145 ASP cc_start: 0.7927 (OUTLIER) cc_final: 0.7527 (p0) REVERT: E 26 MET cc_start: 0.7224 (mtp) cc_final: 0.6959 (mtp) REVERT: E 31 VAL cc_start: 0.7931 (OUTLIER) cc_final: 0.7538 (p) REVERT: E 83 TYR cc_start: 0.7515 (t80) cc_final: 0.6969 (t80) REVERT: E 96 MET cc_start: 0.8069 (tmm) cc_final: 0.7658 (tmm) REVERT: E 118 SER cc_start: 0.8540 (m) cc_final: 0.7974 (p) REVERT: E 127 ASN cc_start: 0.8551 (m-40) cc_final: 0.7679 (m-40) REVERT: E 138 PHE cc_start: 0.8889 (m-80) cc_final: 0.8383 (m-80) REVERT: F 20 ASN cc_start: 0.8458 (m-40) cc_final: 0.7939 (p0) REVERT: F 32 GLU cc_start: 0.8133 (tp30) cc_final: 0.7280 (tp30) REVERT: F 72 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8524 (mm) REVERT: G 27 ARG cc_start: 0.8682 (ptt-90) cc_final: 0.8063 (ptt90) REVERT: J 19 ASP cc_start: 0.7001 (t0) cc_final: 0.6479 (t0) REVERT: J 25 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7898 (tp) REVERT: J 44 TYR cc_start: 0.8805 (OUTLIER) cc_final: 0.8500 (t80) REVERT: J 102 GLU cc_start: 0.8334 (mt-10) cc_final: 0.8110 (mt-10) REVERT: K 87 LEU cc_start: 0.8260 (mt) cc_final: 0.7825 (mt) REVERT: L 1 MET cc_start: 0.6759 (ttt) cc_final: 0.6476 (ttt) REVERT: L 143 GLU cc_start: 0.7412 (tp30) cc_final: 0.6986 (mp0) REVERT: N 24 MET cc_start: 0.8310 (tpp) cc_final: 0.7619 (mpp) REVERT: N 114 GLU cc_start: 0.8049 (OUTLIER) cc_final: 0.7821 (pm20) REVERT: P 3 ASN cc_start: 0.8553 (m110) cc_final: 0.8115 (t0) REVERT: P 6 LYS cc_start: 0.8416 (tttt) cc_final: 0.8062 (tppt) REVERT: P 9 GLU cc_start: 0.7968 (pp20) cc_final: 0.7533 (pp20) REVERT: P 13 MET cc_start: 0.7482 (mtm) cc_final: 0.7180 (mtm) REVERT: P 71 GLU cc_start: 0.7942 (OUTLIER) cc_final: 0.6962 (mp0) REVERT: P 76 THR cc_start: 0.9174 (m) cc_final: 0.8933 (p) REVERT: Q 57 PHE cc_start: 0.8793 (m-80) cc_final: 0.8392 (m-80) REVERT: Q 95 LEU cc_start: 0.8743 (mt) cc_final: 0.8514 (mm) REVERT: S 66 ILE cc_start: 0.8707 (pt) cc_final: 0.8342 (mt) REVERT: V 8 VAL cc_start: 0.7942 (OUTLIER) cc_final: 0.7711 (p) REVERT: Z 19 LYS cc_start: 0.8588 (mmmt) cc_final: 0.8137 (ttpp) REVERT: Z 47 MET cc_start: 0.7540 (mmt) cc_final: 0.7238 (mmt) REVERT: a 43 PHE cc_start: 0.6585 (t80) cc_final: 0.5607 (t80) REVERT: d 42 LEU cc_start: 0.8805 (tp) cc_final: 0.8506 (tp) REVERT: g 145 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8712 (pp20) REVERT: g 213 TYR cc_start: 0.8607 (m-80) cc_final: 0.8359 (m-80) REVERT: h 25 ASN cc_start: 0.8681 (t0) cc_final: 0.8276 (p0) REVERT: h 57 ILE cc_start: 0.7451 (OUTLIER) cc_final: 0.7212 (tp) REVERT: h 124 LEU cc_start: 0.7936 (OUTLIER) cc_final: 0.7665 (mm) REVERT: h 183 ASP cc_start: 0.6940 (t0) cc_final: 0.6688 (t0) REVERT: i 124 MET cc_start: 0.7866 (mmp) cc_final: 0.7091 (mmt) REVERT: j 29 ARG cc_start: 0.7833 (ptp90) cc_final: 0.7585 (ptp90) REVERT: j 54 ARG cc_start: 0.7231 (mpt180) cc_final: 0.6840 (mpt180) REVERT: j 147 MET cc_start: 0.7811 (ttp) cc_final: 0.7471 (ttp) REVERT: k 35 LYS cc_start: 0.9049 (mppt) cc_final: 0.8611 (mppt) REVERT: k 75 GLU cc_start: 0.8859 (tt0) cc_final: 0.8341 (tp30) REVERT: k 90 MET cc_start: 0.8127 (pmm) cc_final: 0.7675 (pmm) REVERT: l 15 ASP cc_start: 0.6878 (t0) cc_final: 0.6619 (t0) REVERT: l 63 GLU cc_start: 0.8703 (OUTLIER) cc_final: 0.8035 (pp20) REVERT: n 19 VAL cc_start: 0.5163 (OUTLIER) cc_final: 0.4815 (p) REVERT: n 52 LEU cc_start: 0.8952 (tp) cc_final: 0.8658 (tp) REVERT: n 57 MET cc_start: 0.7654 (pmm) cc_final: 0.7224 (pmm) REVERT: n 110 GLN cc_start: 0.8810 (tt0) cc_final: 0.8487 (mm110) REVERT: o 57 VAL cc_start: 0.6075 (OUTLIER) cc_final: 0.5608 (p) REVERT: o 58 ASN cc_start: 0.7374 (m110) cc_final: 0.7072 (m-40) REVERT: s 21 PHE cc_start: 0.8283 (m-10) cc_final: 0.8010 (m-80) REVERT: s 89 MET cc_start: 0.8278 (tpp) cc_final: 0.7961 (tpp) REVERT: u 76 LYS cc_start: 0.8857 (tttm) cc_final: 0.8453 (tttm) REVERT: v 9 GLN cc_start: 0.7922 (mp10) cc_final: 0.7503 (tm-30) REVERT: v 47 HIS cc_start: 0.7582 (OUTLIER) cc_final: 0.7218 (p90) REVERT: x 44 MET cc_start: 0.4680 (tpp) cc_final: 0.2885 (mmt) REVERT: x 55 ARG cc_start: 0.6557 (OUTLIER) cc_final: 0.5772 (mmp80) REVERT: y 10 ARG cc_start: 0.8435 (ttt90) cc_final: 0.7841 (ttt90) REVERT: y 61 GLN cc_start: 0.9186 (mm-40) cc_final: 0.8936 (mm-40) REVERT: z 31 GLU cc_start: 0.7768 (tp30) cc_final: 0.7513 (tm-30) REVERT: z 54 LYS cc_start: 0.8437 (mtmt) cc_final: 0.8051 (ttmt) outliers start: 222 outliers final: 179 residues processed: 1043 average time/residue: 1.2627 time to fit residues: 2332.6230 Evaluate side-chains 1055 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 194 poor density : 861 time to evaluate : 6.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 22 HIS Chi-restraints excluded: chain 5 residue 25 PHE Chi-restraints excluded: chain 5 residue 52 SER Chi-restraints excluded: chain 5 residue 85 THR Chi-restraints excluded: chain 5 residue 115 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 32 ASN Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 108 ILE Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 128 TYR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 139 PHE Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain J residue 49 ASP Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 3 GLN 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 29 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain R residue 74 ILE Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 41 LEU Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 87 PHE 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 55 GLU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 48 ILE Chi-restraints excluded: chain a residue 16 CYS Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 46 ASP Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 7 GLU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain f residue 12 ARG Chi-restraints excluded: chain g residue 36 ASN Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 157 LEU Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain h residue 122 SER Chi-restraints excluded: chain h residue 124 LEU Chi-restraints excluded: chain h residue 151 VAL Chi-restraints excluded: chain h residue 153 VAL Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain i residue 20 PHE Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain i residue 203 LEU Chi-restraints excluded: chain j residue 13 GLU Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 21 VAL Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 76 LEU Chi-restraints excluded: chain j residue 137 VAL Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 68 GLN Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain l residue 63 GLU Chi-restraints excluded: chain m residue 9 ASP Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 63 LEU Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 60 LYS Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 105 THR Chi-restraints excluded: chain n residue 114 LYS Chi-restraints excluded: chain n residue 129 LYS Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 63 ASP Chi-restraints excluded: chain o residue 69 THR Chi-restraints excluded: chain o residue 76 ILE Chi-restraints excluded: chain o residue 78 GLU Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain p residue 17 SER Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 49 LEU Chi-restraints excluded: chain q residue 73 ASN Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 78 SER Chi-restraints excluded: chain q residue 98 VAL Chi-restraints excluded: chain s residue 96 LEU Chi-restraints excluded: chain t residue 27 VAL Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain t residue 83 GLU Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 78 VAL Chi-restraints excluded: chain v residue 47 HIS Chi-restraints excluded: chain w residue 33 ILE Chi-restraints excluded: chain w residue 59 ILE Chi-restraints excluded: chain x residue 55 ARG Chi-restraints excluded: chain y residue 67 ILE Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 13 ASP Chi-restraints excluded: chain z residue 53 VAL Chi-restraints excluded: chain z residue 56 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 943 optimal weight: 10.0000 chunk 621 optimal weight: 9.9990 chunk 1001 optimal weight: 0.8980 chunk 610 optimal weight: 9.9990 chunk 474 optimal weight: 50.0000 chunk 695 optimal weight: 9.9990 chunk 1050 optimal weight: 2.9990 chunk 966 optimal weight: 20.0000 chunk 836 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 645 optimal weight: 5.9990 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 5 159 HIS ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN ** T 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 80 HIS ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 9 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.5097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 164734 Z= 0.292 Angle : 0.714 14.040 246771 Z= 0.374 Chirality : 0.037 0.388 31487 Planarity : 0.006 0.130 12982 Dihedral : 24.592 179.718 83100 Min Nonbonded Distance : 1.193 Molprobity Statistics. All-atom Clashscore : 20.67 Ramachandran Plot: Outliers : 0.09 % Allowed : 8.43 % Favored : 91.48 % Rotamer: Outliers : 4.38 % Allowed : 24.61 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.67 (0.11), residues: 5750 helix: 0.05 (0.12), residues: 1890 sheet: -1.31 (0.16), residues: 1078 loop : -1.83 (0.11), residues: 2782 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.098 0.003 TRP l 103 HIS 0.010 0.001 HIS g 94 PHE 0.021 0.002 PHE G 46 TYR 0.038 0.002 TYR G 25 ARG 0.015 0.001 ARG c 28 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11500 Ramachandran restraints generated. 5750 Oldfield, 0 Emsley, 5750 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1067 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 857 time to evaluate : 6.339 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: 5 31 GLU cc_start: 0.7113 (tm-30) cc_final: 0.6797 (tm-30) REVERT: 5 146 GLU cc_start: 0.8297 (tt0) cc_final: 0.7667 (tp30) REVERT: 5 150 ASP cc_start: 0.8645 (p0) cc_final: 0.7132 (p0) REVERT: B 248 TRP cc_start: 0.8138 (m-10) cc_final: 0.7890 (m-10) REVERT: D 145 ASP cc_start: 0.7966 (OUTLIER) cc_final: 0.7548 (p0) REVERT: E 31 VAL cc_start: 0.7988 (OUTLIER) cc_final: 0.7585 (p) REVERT: E 83 TYR cc_start: 0.7563 (t80) cc_final: 0.7020 (t80) REVERT: E 96 MET cc_start: 0.8030 (tmm) cc_final: 0.7579 (tmm) REVERT: E 118 SER cc_start: 0.8651 (m) cc_final: 0.8169 (p) REVERT: E 127 ASN cc_start: 0.8577 (m-40) cc_final: 0.7673 (m-40) REVERT: E 130 MET cc_start: 0.8203 (mmm) cc_final: 0.7892 (mpp) REVERT: E 138 PHE cc_start: 0.8953 (m-80) cc_final: 0.8381 (m-80) REVERT: F 69 ARG cc_start: 0.8845 (ttt180) cc_final: 0.7720 (ttp80) REVERT: J 19 ASP cc_start: 0.7038 (t0) cc_final: 0.6520 (t0) REVERT: J 44 TYR cc_start: 0.8853 (OUTLIER) cc_final: 0.8541 (t80) REVERT: L 143 GLU cc_start: 0.7424 (tp30) cc_final: 0.7026 (mp0) REVERT: N 114 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7835 (pm20) REVERT: P 3 ASN cc_start: 0.8565 (m110) cc_final: 0.8142 (t0) REVERT: P 6 LYS cc_start: 0.8414 (tttt) cc_final: 0.8078 (tppt) REVERT: P 9 GLU cc_start: 0.8000 (pp20) cc_final: 0.7577 (pp20) REVERT: P 71 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7049 (mp0) REVERT: P 76 THR cc_start: 0.9215 (m) cc_final: 0.8940 (p) REVERT: S 66 ILE cc_start: 0.8741 (pt) cc_final: 0.8400 (mt) REVERT: U 101 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7645 (tm-30) REVERT: V 1 MET cc_start: 0.5337 (tpp) cc_final: 0.4873 (tpp) REVERT: Z 19 LYS cc_start: 0.8587 (mmmt) cc_final: 0.8120 (ttpp) REVERT: Z 47 MET cc_start: 0.7572 (mmt) cc_final: 0.7235 (mmt) REVERT: d 42 LEU cc_start: 0.8757 (tp) cc_final: 0.8462 (tp) REVERT: g 145 GLU cc_start: 0.8969 (tm-30) cc_final: 0.8747 (pp20) REVERT: g 213 TYR cc_start: 0.8604 (m-80) cc_final: 0.8347 (m-80) REVERT: h 25 ASN cc_start: 0.8724 (t0) cc_final: 0.8305 (p0) REVERT: h 34 ASP cc_start: 0.8867 (m-30) cc_final: 0.8175 (m-30) REVERT: h 57 ILE cc_start: 0.7562 (OUTLIER) cc_final: 0.7287 (tp) REVERT: h 183 ASP cc_start: 0.6859 (t0) cc_final: 0.6571 (t0) REVERT: i 124 MET cc_start: 0.7881 (mmp) cc_final: 0.7038 (mmt) REVERT: i 178 MET cc_start: 0.5279 (ptt) cc_final: 0.5004 (ptt) REVERT: j 29 ARG cc_start: 0.7854 (ptp90) cc_final: 0.7552 (ptp90) REVERT: j 54 ARG cc_start: 0.7152 (mpt180) cc_final: 0.6793 (mpt180) REVERT: k 35 LYS cc_start: 0.9046 (mppt) cc_final: 0.8775 (mppt) REVERT: k 75 GLU cc_start: 0.8884 (tt0) cc_final: 0.8370 (tp30) REVERT: k 90 MET cc_start: 0.8001 (pmm) cc_final: 0.7606 (pmm) REVERT: l 15 ASP cc_start: 0.6757 (t0) cc_final: 0.6509 (t0) REVERT: l 62 PHE cc_start: 0.7619 (t80) cc_final: 0.7407 (t80) REVERT: l 63 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.7954 (pp20) REVERT: n 19 VAL cc_start: 0.5365 (OUTLIER) cc_final: 0.5013 (p) REVERT: n 52 LEU cc_start: 0.8979 (tp) cc_final: 0.8763 (tp) REVERT: o 57 VAL cc_start: 0.6130 (OUTLIER) cc_final: 0.5665 (p) REVERT: o 58 ASN cc_start: 0.7383 (m110) cc_final: 0.7095 (m-40) REVERT: r 103 LYS cc_start: 0.7579 (mttt) cc_final: 0.7330 (mttt) REVERT: s 21 PHE cc_start: 0.8276 (m-10) cc_final: 0.8043 (m-80) REVERT: s 89 MET cc_start: 0.8284 (tpp) cc_final: 0.7985 (tpp) REVERT: u 76 LYS cc_start: 0.8942 (tttm) cc_final: 0.8602 (tttm) REVERT: v 9 GLN cc_start: 0.7898 (mp10) cc_final: 0.7557 (tm-30) REVERT: v 47 HIS cc_start: 0.7528 (OUTLIER) cc_final: 0.7252 (p90) REVERT: x 44 MET cc_start: 0.5217 (tpp) cc_final: 0.3443 (mmt) REVERT: x 55 ARG cc_start: 0.6526 (OUTLIER) cc_final: 0.5718 (mmp80) REVERT: y 10 ARG cc_start: 0.8417 (ttt90) cc_final: 0.7824 (ttt90) REVERT: y 61 GLN cc_start: 0.9198 (mm-40) cc_final: 0.8941 (mm-40) REVERT: z 31 GLU cc_start: 0.7911 (tp30) cc_final: 0.7652 (tm-30) REVERT: z 49 LYS cc_start: 0.9126 (ttpp) cc_final: 0.8891 (ttpp) REVERT: z 54 LYS cc_start: 0.8482 (mtmt) cc_final: 0.8095 (ttmt) outliers start: 210 outliers final: 188 residues processed: 997 average time/residue: 1.2578 time to fit residues: 2217.8545 Evaluate side-chains 1043 residues out of total 4790 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 844 time to evaluate : 6.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 22 HIS Chi-restraints excluded: chain 5 residue 25 PHE Chi-restraints excluded: chain 5 residue 85 THR Chi-restraints excluded: chain 5 residue 115 SER Chi-restraints excluded: chain B residue 16 VAL Chi-restraints excluded: chain B residue 19 VAL Chi-restraints excluded: chain B residue 64 ILE Chi-restraints excluded: chain B residue 74 ILE Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 117 GLN Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 272 SER Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 9 VAL Chi-restraints excluded: chain C residue 32 ASN Chi-restraints excluded: chain C residue 60 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 92 VAL Chi-restraints excluded: chain C residue 99 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 178 VAL Chi-restraints excluded: chain C residue 187 LEU Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 48 THR Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 75 SER Chi-restraints excluded: chain D residue 145 ASP Chi-restraints excluded: chain E residue 31 VAL Chi-restraints excluded: chain E residue 128 TYR Chi-restraints excluded: chain E residue 155 THR Chi-restraints excluded: chain E residue 157 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 127 THR Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 139 PHE Chi-restraints excluded: chain J residue 10 THR Chi-restraints excluded: chain J residue 25 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 44 TYR Chi-restraints excluded: chain J residue 49 ASP Chi-restraints excluded: chain J residue 55 ILE Chi-restraints excluded: chain J residue 73 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 124 VAL Chi-restraints excluded: chain J residue 130 HIS Chi-restraints excluded: chain J residue 131 ASN Chi-restraints excluded: chain J residue 136 GLN Chi-restraints excluded: chain K residue 10 VAL Chi-restraints excluded: chain K residue 69 VAL Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 61 LEU Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 118 THR Chi-restraints excluded: chain M residue 3 GLN 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 29 VAL Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 48 VAL Chi-restraints excluded: chain N residue 54 LEU Chi-restraints excluded: chain N residue 79 LEU Chi-restraints excluded: chain N residue 95 THR Chi-restraints excluded: chain N residue 114 GLU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 47 VAL Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 30 VAL Chi-restraints excluded: chain P residue 33 VAL Chi-restraints excluded: chain P residue 50 ILE Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 71 GLU Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 34 VAL Chi-restraints excluded: chain R residue 45 GLU Chi-restraints excluded: chain S residue 3 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 39 THR Chi-restraints excluded: chain S residue 45 VAL Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 74 ILE Chi-restraints excluded: chain S residue 76 VAL Chi-restraints excluded: chain S residue 77 ASP Chi-restraints excluded: chain S residue 97 LEU Chi-restraints excluded: chain S residue 109 ASP Chi-restraints excluded: chain T residue 11 LEU Chi-restraints excluded: chain T residue 32 LEU Chi-restraints excluded: chain T residue 39 THR Chi-restraints excluded: chain T residue 60 THR Chi-restraints excluded: chain T residue 93 LEU Chi-restraints excluded: chain U residue 14 LEU Chi-restraints excluded: chain U residue 41 LEU Chi-restraints excluded: chain U residue 59 VAL Chi-restraints excluded: chain U residue 83 VAL Chi-restraints excluded: chain U residue 93 VAL 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 55 GLU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain X residue 13 VAL Chi-restraints excluded: chain X residue 40 VAL Chi-restraints excluded: chain X residue 60 ASP Chi-restraints excluded: chain X residue 65 ASP Chi-restraints excluded: chain Z residue 4 THR Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 32 ILE Chi-restraints excluded: chain Z residue 48 ILE Chi-restraints excluded: chain a residue 16 CYS Chi-restraints excluded: chain b residue 3 VAL Chi-restraints excluded: chain b residue 9 THR Chi-restraints excluded: chain b residue 15 MET Chi-restraints excluded: chain b residue 26 THR Chi-restraints excluded: chain b residue 46 ASP Chi-restraints excluded: chain b residue 55 ILE Chi-restraints excluded: chain c residue 7 GLU Chi-restraints excluded: chain c residue 11 LEU Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain d residue 4 THR Chi-restraints excluded: chain d residue 24 THR Chi-restraints excluded: chain e residue 29 LEU Chi-restraints excluded: chain e residue 58 VAL Chi-restraints excluded: chain f residue 12 ARG Chi-restraints excluded: chain f residue 17 VAL Chi-restraints excluded: chain g residue 36 ASN Chi-restraints excluded: chain g residue 125 THR Chi-restraints excluded: chain g residue 129 LEU Chi-restraints excluded: chain g residue 157 LEU Chi-restraints excluded: chain h residue 57 ILE Chi-restraints excluded: chain h residue 122 SER Chi-restraints excluded: chain h residue 124 LEU Chi-restraints excluded: chain h residue 153 VAL Chi-restraints excluded: chain h residue 186 THR Chi-restraints excluded: chain i residue 20 PHE Chi-restraints excluded: chain i residue 169 THR Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain i residue 203 LEU Chi-restraints excluded: chain j residue 18 VAL Chi-restraints excluded: chain j residue 21 VAL Chi-restraints excluded: chain j residue 30 ILE Chi-restraints excluded: chain j residue 74 VAL Chi-restraints excluded: chain j residue 76 LEU Chi-restraints excluded: chain j residue 137 VAL Chi-restraints excluded: chain k residue 5 GLU Chi-restraints excluded: chain k residue 21 MET Chi-restraints excluded: chain k residue 36 ILE Chi-restraints excluded: chain k residue 68 GLN Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 22 LEU Chi-restraints excluded: chain l residue 63 GLU Chi-restraints excluded: chain m residue 30 SER Chi-restraints excluded: chain m residue 36 ILE Chi-restraints excluded: chain m residue 63 LEU Chi-restraints excluded: chain m residue 75 ILE Chi-restraints excluded: chain m residue 90 ASP Chi-restraints excluded: chain n residue 19 VAL Chi-restraints excluded: chain n residue 29 VAL Chi-restraints excluded: chain n residue 60 LYS Chi-restraints excluded: chain n residue 65 ILE Chi-restraints excluded: chain n residue 72 ILE Chi-restraints excluded: chain n residue 105 THR Chi-restraints excluded: chain n residue 114 LYS Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 47 GLU Chi-restraints excluded: chain o residue 57 VAL Chi-restraints excluded: chain o residue 63 ASP Chi-restraints excluded: chain o residue 69 THR Chi-restraints excluded: chain o residue 76 ILE Chi-restraints excluded: chain o residue 78 GLU Chi-restraints excluded: chain o residue 84 VAL Chi-restraints excluded: chain p residue 17 SER Chi-restraints excluded: chain p residue 129 VAL Chi-restraints excluded: chain q residue 3 THR Chi-restraints excluded: chain q residue 19 SER Chi-restraints excluded: chain q residue 49 LEU Chi-restraints excluded: chain q residue 73 ASN Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain q residue 78 SER Chi-restraints excluded: chain q residue 98 VAL Chi-restraints excluded: chain s residue 96 LEU Chi-restraints excluded: chain t residue 27 VAL Chi-restraints excluded: chain t residue 47 LYS Chi-restraints excluded: chain t residue 83 GLU Chi-restraints excluded: chain t residue 85 LEU Chi-restraints excluded: chain u residue 57 ILE Chi-restraints excluded: chain u residue 78 VAL Chi-restraints excluded: chain v residue 47 HIS Chi-restraints excluded: chain w residue 33 ILE Chi-restraints excluded: chain w residue 59 ILE Chi-restraints excluded: chain x residue 55 ARG Chi-restraints excluded: chain y residue 67 ILE Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 13 ASP Chi-restraints excluded: chain z residue 28 VAL Chi-restraints excluded: chain z residue 53 VAL Chi-restraints excluded: chain z residue 56 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1054 random chunks: chunk 512 optimal weight: 6.9990 chunk 664 optimal weight: 5.9990 chunk 890 optimal weight: 8.9990 chunk 256 optimal weight: 10.0000 chunk 770 optimal weight: 0.5980 chunk 123 optimal weight: 10.0000 chunk 232 optimal weight: 10.0000 chunk 837 optimal weight: 0.9990 chunk 350 optimal weight: 10.0000 chunk 859 optimal weight: 8.9990 chunk 106 optimal weight: 50.0000 overall best weight: 4.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 167 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 87 GLN ** T 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 36 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** k 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** l 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** n 4 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 9 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.064115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.046144 restraints weight = 831133.565| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 2.32 r_work: 0.3203 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.3203 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.5099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 164734 Z= 0.241 Angle : 0.682 14.020 246771 Z= 0.360 Chirality : 0.036 0.384 31487 Planarity : 0.006 0.128 12982 Dihedral : 24.564 179.907 83096 Min Nonbonded Distance : 1.051 Molprobity Statistics. All-atom Clashscore : 19.39 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.77 % Favored : 92.14 % Rotamer: Outliers : 4.49 % Allowed : 24.45 % Favored : 71.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.60 (0.11), residues: 5750 helix: 0.10 (0.12), residues: 1889 sheet: -1.24 (0.16), residues: 1064 loop : -1.81 (0.11), residues: 2797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.087 0.002 TRP B 248 HIS 0.018 0.001 HIS g 94 PHE 0.021 0.002 PHE t 43 TYR 0.035 0.002 TYR G 25 ARG 0.015 0.001 ARG c 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 40265.92 seconds wall clock time: 705 minutes 43.22 seconds (42343.22 seconds total)