Starting phenix.real_space_refine on Sat Mar 2 21:36:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ac7_11713/03_2024/7ac7_11713_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ac7_11713/03_2024/7ac7_11713.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ac7_11713/03_2024/7ac7_11713_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ac7_11713/03_2024/7ac7_11713_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ac7_11713/03_2024/7ac7_11713_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ac7_11713/03_2024/7ac7_11713.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ac7_11713/03_2024/7ac7_11713.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ac7_11713/03_2024/7ac7_11713_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ac7_11713/03_2024/7ac7_11713_updated.pdb" } resolution = 3.08 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 5015 5.49 5 Mg 441 5.21 5 S 156 5.16 5 C 77357 2.51 5 N 28740 2.21 5 O 43172 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "5 GLU 23": "OE1" <-> "OE2" Residue "5 ARG 45": "NH1" <-> "NH2" Residue "5 ARG 59": "NH1" <-> "NH2" Residue "5 ARG 88": "NH1" <-> "NH2" Residue "5 ARG 106": "NH1" <-> "NH2" Residue "5 ARG 153": "NH1" <-> "NH2" Residue "B ARG 52": "NH1" <-> "NH2" Residue "B ARG 63": "NH1" <-> "NH2" Residue "B ARG 80": "NH1" <-> "NH2" Residue "B ARG 156": "NH1" <-> "NH2" Residue "B ARG 167": "NH1" <-> "NH2" Residue "B ARG 177": "NH1" <-> "NH2" Residue "B ARG 182": "NH1" <-> "NH2" Residue "B ARG 189": "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 GLU 89": "OE1" <-> "OE2" Residue "C ARG 169": "NH1" <-> "NH2" Residue "C ARG 184": "NH1" <-> "NH2" Residue "D ARG 21": "NH1" <-> "NH2" Residue "D ARG 44": "NH1" <-> "NH2" Residue "D ARG 49": "NH1" <-> "NH2" Residue "D ARG 102": "NH1" <-> "NH2" Residue "D ARG 162": "NH1" <-> "NH2" Residue "D ARG 170": "NH1" <-> "NH2" Residue "E ARG 30": "NH1" <-> "NH2" Residue "E ARG 71": "NH1" <-> "NH2" Residue "E ARG 92": "NH1" <-> "NH2" Residue "E ARG 102": "NH1" <-> "NH2" Residue "E ARG 110": "NH1" <-> "NH2" Residue "E ARG 112": "NH1" <-> "NH2" Residue "E ARG 115": "NH1" <-> "NH2" Residue "E ARG 148": "NH1" <-> "NH2" Residue "F ARG 3": "NH1" <-> "NH2" Residue "F ARG 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 "G GLU 114": "OE1" <-> "OE2" Residue "G GLU 137": "OE1" <-> "OE2" Residue "H TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 124": "OD1" <-> "OD2" Residue "J ARG 13": "NH1" <-> "NH2" Residue "J ARG 34": "NH1" <-> "NH2" Residue "J ARG 37": "NH1" <-> "NH2" Residue "J ARG 95": "NH1" <-> "NH2" Residue "J ARG 96": "NH1" <-> "NH2" Residue "J ARG 120": "NH1" <-> "NH2" Residue "K ARG 17": "NH1" <-> "NH2" Residue "K ARG 18": "NH1" <-> "NH2" Residue "K GLU 92": "OE1" <-> "OE2" Residue "L ARG 21": "NH1" <-> "NH2" Residue "L ARG 33": "NH1" <-> "NH2" Residue "L ARG 41": "NH1" <-> "NH2" Residue "L ARG 47": "NH1" <-> "NH2" Residue "L ARG 60": "NH1" <-> "NH2" Residue "L ARG 78": "NH1" <-> "NH2" Residue "L ARG 123": "NH1" <-> "NH2" Residue "L ARG 126": "NH1" <-> "NH2" Residue "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 114": "NH1" <-> "NH2" Residue "N ARG 8": "NH1" <-> "NH2" Residue "N ARG 12": "NH1" <-> "NH2" Residue "N ARG 17": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "N 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 ARG 94": "NH1" <-> "NH2" Residue "O ARG 102": "NH1" <-> "NH2" Residue "O ARG 111": "NH1" <-> "NH2" Residue "P PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P GLU 68": "OE1" <-> "OE2" Residue "P ARG 89": "NH1" <-> "NH2" Residue "P ARG 101": "NH1" <-> "NH2" Residue "P ARG 109": "NH1" <-> "NH2" Residue "Q ARG 3": "NH1" <-> "NH2" Residue "Q ARG 6": "NH1" <-> "NH2" Residue "Q ARG 13": "NH1" <-> "NH2" Residue "Q ARG 33": "NH1" <-> "NH2" Residue "Q ARG 48": "NH1" <-> "NH2" Residue "Q ARG 70": "NH1" <-> "NH2" Residue "Q GLU 89": "OE1" <-> "OE2" Residue "Q GLU 111": "OE1" <-> "OE2" Residue "R ARG 21": "NH1" <-> "NH2" Residue "R GLU 46": "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 3": "NH1" <-> "NH2" Residue "T ARG 6": "NH1" <-> "NH2" Residue "U ARG 6": "NH1" <-> "NH2" Residue "U ARG 82": "NH1" <-> "NH2" Residue "U ARG 86": "NH1" <-> "NH2" Residue "U ARG 94": "NH1" <-> "NH2" Residue "V ARG 19": "NH1" <-> "NH2" Residue "W PHE 1": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 3": "NH1" <-> "NH2" Residue "X ARG 18": "NH1" <-> "NH2" Residue "X ARG 37": "NH1" <-> "NH2" Residue "X ARG 45": "NH1" <-> "NH2" Residue "X ARG 50": "NH1" <-> "NH2" Residue "X ARG 57": "NH1" <-> "NH2" Residue "X ARG 74": "NH1" <-> "NH2" Residue "Y GLU 17": "OE1" <-> "OE2" Residue "Y ARG 29": "NH1" <-> "NH2" Residue "Y ARG 47": "NH1" <-> "NH2" Residue "Y ARG 52": "NH1" <-> "NH2" Residue "Z ARG 11": "NH1" <-> "NH2" Residue "Z ARG 30": "NH1" <-> "NH2" Residue "Z ARG 45": "NH1" <-> "NH2" Residue "a ARG 49": "NH1" <-> "NH2" Residue "a ARG 56": "NH1" <-> "NH2" Residue "a ARG 63": "NH1" <-> "NH2" Residue "b ARG 10": "NH1" <-> "NH2" Residue "b ARG 16": "NH1" <-> "NH2" Residue "b ARG 52": "NH1" <-> "NH2" Residue "c ARG 28": "NH1" <-> "NH2" Residue "c ARG 44": "NH1" <-> "NH2" Residue "d ARG 3": "NH1" <-> "NH2" Residue "d ARG 14": "NH1" <-> "NH2" Residue "d ARG 19": "NH1" <-> "NH2" Residue "d ARG 21": "NH1" <-> "NH2" Residue "d ARG 33": "NH1" <-> "NH2" Residue "d ARG 41": "NH1" <-> "NH2" Residue "e ARG 13": "NH1" <-> "NH2" Residue "e ARG 30": "NH1" <-> "NH2" Residue "e ARG 40": "NH1" <-> "NH2" Residue "e ARG 42": "NH1" <-> "NH2" Residue "f ARG 24": "NH1" <-> "NH2" Residue "g ARG 63": "NH1" <-> "NH2" Residue "g ARG 74": "NH1" <-> "NH2" Residue "g GLU 78": "OE1" <-> "OE2" 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 "h ARG 164": "NH1" <-> "NH2" Residue "i ARG 73": "NH1" <-> "NH2" Residue "i ARG 81": "NH1" <-> "NH2" Residue "i PHE 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j ARG 68": "NH1" <-> "NH2" Residue "j ARG 69": "NH1" <-> "NH2" Residue "j ARG 93": "NH1" <-> "NH2" Residue "j ARG 157": "NH1" <-> "NH2" Residue "k ARG 45": "NH1" <-> "NH2" Residue "k ARG 79": "NH1" <-> "NH2" Residue "k ARG 91": "NH1" <-> "NH2" Residue "l ARG 4": "NH1" <-> "NH2" Residue "l ARG 53": "NH1" <-> "NH2" Residue "l GLU 58": "OE1" <-> "OE2" Residue "l ARG 78": "NH1" <-> "NH2" Residue "l ARG 79": "NH1" <-> "NH2" Residue "l ARG 92": "NH1" <-> "NH2" Residue "n ARG 11": "NH1" <-> "NH2" Residue "n ARG 41": "NH1" <-> "NH2" Residue "o ARG 5": "NH1" <-> "NH2" Residue "o ARG 45": "NH1" <-> "NH2" Residue "o ARG 89": "NH1" <-> "NH2" Residue "p ARG 37": "NH1" <-> "NH2" Residue "p ARG 69": "NH1" <-> "NH2" Residue "p ARG 93": "NH1" <-> "NH2" Residue "p ARG 106": "NH1" <-> "NH2" Residue "q ARG 9": "NH1" <-> "NH2" Residue "q ARG 14": "NH1" <-> "NH2" Residue "q ARG 50": "NH1" <-> "NH2" Residue "q ARG 83": "NH1" <-> "NH2" Residue "r ARG 29": "NH1" <-> "NH2" Residue "r ARG 70": "NH1" <-> "NH2" Residue "r ARG 87": "NH1" <-> "NH2" Residue "r ARG 109": "NH1" <-> "NH2" Residue "s ARG 59": "NH1" <-> "NH2" Residue "s ARG 63": "NH1" <-> "NH2" Residue "s ARG 65": "NH1" <-> "NH2" Residue "s ARG 69": "NH1" <-> "NH2" Residue "s ARG 85": "NH1" <-> "NH2" Residue "t ARG 72": "NH1" <-> "NH2" Residue "t ARG 89": "NH1" <-> "NH2" Residue "u ARG 28": "NH1" <-> "NH2" Residue "u 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 ARG 33": "NH1" <-> "NH2" Residue "z ARG 45": "NH1" <-> "NH2" Residue "z ARG 55": "NH1" <-> "NH2" Residue "z ARG 62": "NH1" <-> "NH2" Residue "z ARG 67": "NH1" <-> "NH2" Residue "z ARG 69": "NH1" <-> "NH2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 154883 Number of models: 1 Model: "" Number of chains: 71 Chain: "1" Number of atoms: 62336 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2903, 62336 Classifications: {'RNA': 2903} Modifications used: {'rna2p': 5, 'rna2p_pur': 284, 'rna2p_pyr': 165, 'rna3p': 17, 'rna3p_pur': 1383, 'rna3p_pyr': 1049} Link IDs: {'rna2p': 453, 'rna3p': 2449} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 9 Chain: "2" Number of atoms: 33049 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1540, 33049 Classifications: {'RNA': 1540} Modifications used: {'rna2p': 2, 'rna2p_pur': 118, 'rna2p_pyr': 92, 'rna3p': 9, 'rna3p_pur': 751, 'rna3p_pyr': 567} Link IDs: {'rna2p': 212, 'rna3p': 1327} Unresolved chain link dihedrals: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 37 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 2 Chain: "3" Number of atoms: 2569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2569 Classifications: {'RNA': 120} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 6, 'rna3p_pur': 56, 'rna3p_pyr': 50} Link IDs: {'rna2p': 13, 'rna3p': 106} Chain: "4" Number of atoms: 7759 Number of conformers: 1 Conformer: "" Number of residues, atoms: 363, 7759 Classifications: {'RNA': 363} Modifications used: {'rna2p_pur': 36, 'rna2p_pyr': 22, 'rna3p': 3, 'rna3p_pur': 162, 'rna3p_pyr': 140} Link IDs: {'rna2p': 58, 'rna3p': 304} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "5" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1191 Classifications: {'peptide': 147} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain: "7" Number of atoms: 1635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 1635 Classifications: {'RNA': 76} Modifications used: {'5*END': 1, 'rna2p': 1, 'rna2p_pur': 7, 'rna2p_pyr': 2, 'rna3p': 9, 'rna3p_pur': 30, 'rna3p_pyr': 27} Link IDs: {'rna2p': 9, 'rna3p': 66} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 3 Chain: "8" Number of atoms: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 324 Classifications: {'RNA': 15} Modifications used: {'5*END': 1, 'rna2p_pur': 2, 'rna3p_pur': 8, 'rna3p_pyr': 5} Link IDs: {'rna2p': 2, 'rna3p': 12} Chain: "A" Number of atoms: 634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 634 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "B" Number of atoms: 2083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2083 Classifications: {'peptide': 271} Modifications used: {'COO': 1} 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: 1411 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1411 Classifications: {'peptide': 177} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 170} Chain: "F" Number of atoms: 1313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1313 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain: "G" Number of atoms: 1111 Number of conformers: 1 Conformer: "" Number of residues, atoms: 149, 1111 Classifications: {'peptide': 149} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 145} Chain: "H" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 980 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 5, 'TRANS': 124} Chain: "J" Number of atoms: 1121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1121 Classifications: {'peptide': 141} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 134} 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: 884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 884 Classifications: {'peptide': 115} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 112} 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: 849 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 849 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 106} 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: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 477 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "Z" Number of atoms: 434 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 434 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "a" Number of atoms: 522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 522 Classifications: {'peptide': 66} Link IDs: {'PTRANS': 2, 'TRANS': 63} Chain: "b" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 54, 429 Classifications: {'peptide': 54} Link IDs: {'PTRANS': 1, 'TRANS': 52} 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: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 297 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "g" Number of atoms: 1760 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1760 Classifications: {'peptide': 225} Link IDs: {'PTRANS': 7, 'TRANS': 217} Chain: "h" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1636 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 7, 'TRANS': 200} Chain: "i" Number of atoms: 1643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1643 Classifications: {'peptide': 205} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain: "j" Number of atoms: 1152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1152 Classifications: {'peptide': 156} Link IDs: {'PTRANS': 5, 'TRANS': 150} Chain: "k" Number of atoms: 848 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 848 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "l" Number of atoms: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} Chain: "m" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 979 Classifications: {'peptide': 129} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 123} Chain: "n" Number of atoms: 1010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 1010 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} 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: 957 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 957 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 115} 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: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 891 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 4, 'TRANS': 110} 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: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 708 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'TRANS': 86} Chain: "u" Number of atoms: 643 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 643 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 2, 'TRANS': 78} Chain: "v" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 649 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 77} Chain: "w" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 535 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 2, 'TRANS': 62} Chain: "x" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "y" Number of atoms: 664 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 664 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} 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: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 303 Unusual residues: {' MG': 303} Classifications: {'undetermined': 303} Link IDs: {None: 302} Chain: "2" Number of atoms: 118 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 118 Unusual residues: {' MG': 118} Classifications: {'undetermined': 118} Link IDs: {None: 117} Chain: "3" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' MG': 9} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "7" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" 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: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 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} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0PHS SG CYS a 16 127.816 62.831 51.629 1.00118.01 S ATOM A0PI4 SG CYS a 18 126.172 63.218 48.263 1.00118.69 S ATOM A0PM2 SG CYS a 37 129.541 64.841 48.909 1.00115.85 S ATOM A0PMN SG CYS a 40 126.468 66.294 50.503 1.00116.70 S ATOM A0R79 SG CYS f 11 175.751 163.840 62.710 1.00 89.32 S ATOM A0RAT SG CYS f 27 176.766 165.974 63.682 1.00 88.06 S Time building chain proxies: 58.26, per 1000 atoms: 0.38 Number of scatterers: 154883 At special positions: 0 Unit cell: (315.12, 270.4, 231.92, 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 156 16.00 P 5015 15.00 Mg 441 11.99 O 43172 8.00 N 28740 7.00 C 77357 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 63.69 Conformation dependent library (CDL) restraints added in 7.6 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 18 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 16 " pdb="ZN ZN a 101 " - pdb=" SG CYS a 40 " pdb=" ZN f 101 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 27 " pdb="ZN ZN f 101 " - pdb=" SG CYS f 11 " pdb="ZN ZN f 101 " - pdb=" ND1 HIS f 33 " Number of angles added : 6 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10986 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: 180 helices and 72 sheets defined 38.7% alpha, 19.3% beta 1407 base pairs and 2186 stacking pairs defined. Time for finding SS restraints: 72.05 Creating SS restraints... Processing helix chain '5' and resid 18 through 24 Processing helix chain '5' and resid 38 through 45 removed outlier: 4.404A pdb=" N LYS 5 42 " --> pdb=" O GLY 5 38 " (cutoff:3.500A) Processing helix chain '5' and resid 93 through 107 removed outlier: 4.629A pdb=" N GLU 5 107 " --> pdb=" O ARG 5 103 " (cutoff:3.500A) Processing helix chain '5' and resid 138 through 157 removed outlier: 3.907A pdb=" N ARG 5 145 " --> pdb=" O ASP 5 141 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASN 5 157 " --> pdb=" O ARG 5 153 " (cutoff:3.500A) Processing helix chain 'B' and resid 12 through 17 removed outlier: 5.187A pdb=" N VAL B 16 " --> pdb=" O GLY B 12 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N VAL B 17 " --> pdb=" O ARG B 13 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 12 through 17' 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: 3.877A pdb=" N ALA B 211 " --> pdb=" O LYS B 207 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N ARG B 214 " --> pdb=" O ALA B 210 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLY B 215 " --> pdb=" O ALA B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 221 through 226 removed outlier: 3.726A pdb=" N MET B 225 " --> pdb=" O ARG B 221 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N ASN B 226 " --> pdb=" O GLY B 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 221 through 226' Processing helix chain 'B' and resid 260 through 268 removed outlier: 4.868A pdb=" N ASP B 264 " --> pdb=" O ASN B 260 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N LYS B 265 " --> pdb=" O LYS B 261 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N PHE B 266 " --> pdb=" O ARG B 262 " (cutoff:3.500A) removed outlier: 5.002A pdb=" N VAL B 268 " --> pdb=" O ASP B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 202 removed outlier: 4.401A pdb=" N MET B 201 " --> pdb=" O ALA B 198 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 5.952A pdb=" N THR C 61 " --> pdb=" O ALA C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 72 removed outlier: 3.756A pdb=" N ALA C 71 " --> pdb=" O HIS C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 98 through 103 removed outlier: 4.639A pdb=" N ALA C 102 " --> pdb=" O VAL C 98 " (cutoff:3.500A) removed outlier: 5.249A 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 24 through 41 removed outlier: 5.418A 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: 3.820A pdb=" N LEU D 134 " --> pdb=" O LYS D 130 " (cutoff:3.500A) Processing helix chain 'D' and resid 154 through 165 removed outlier: 4.299A pdb=" N ASN D 163 " --> pdb=" O LEU D 159 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N LEU D 164 " --> pdb=" O ALA D 160 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N HIS D 165 " --> pdb=" O ALA D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 176 through 183 Processing helix chain 'D' and resid 189 through 201 removed outlier: 3.879A pdb=" N GLN D 195 " --> pdb=" O ASP D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 21 Processing helix chain 'E' and resid 2 through 21 removed outlier: 5.320A pdb=" N VAL E 13 " --> pdb=" O LYS E 9 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N LYS E 14 " --> pdb=" O ASP E 10 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N LYS E 15 " --> pdb=" O GLU E 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 29 removed outlier: 3.960A pdb=" N VAL E 28 " --> pdb=" O SER E 24 " (cutoff:3.500A) Proline residue: E 29 - end of helix No H-bonds generated for 'chain 'E' and resid 24 through 29' Processing helix chain 'E' and resid 42 through 47 removed outlier: 4.105A pdb=" N ASP E 46 " --> pdb=" O GLU E 42 " (cutoff:3.500A) removed outlier: 3.936A 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 removed outlier: 3.640A pdb=" N ALA E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE E 60 " --> pdb=" O ASP E 56 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N GLY E 62 " --> pdb=" O ALA E 58 " (cutoff:3.500A) Processing helix chain 'E' and resid 93 through 111 removed outlier: 4.977A pdb=" N VAL E 108 " --> pdb=" O ILE E 104 " (cutoff:3.500A) Proline residue: E 109 - end of helix Processing helix chain 'E' and resid 162 through 174 Processing helix chain 'E' and resid 134 through 139 removed outlier: 4.593A pdb=" N ILE E 137 " --> pdb=" O GLU E 134 " (cutoff:3.500A) Proline residue: E 139 - end of helix Processing helix chain 'F' and resid 2 through 8 Proline residue: F 8 - end of helix Processing helix chain 'F' and resid 60 through 81 removed outlier: 4.112A pdb=" N GLN F 64 " --> pdb=" O ASP F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 153 removed outlier: 4.054A pdb=" N ILE F 141 " --> pdb=" O ASP F 137 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG F 152 " --> pdb=" O LEU F 148 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 28 Processing helix chain 'G' and resid 29 through 34 Processing helix chain 'G' and resid 40 through 48 removed outlier: 3.922A pdb=" N GLU G 45 " --> pdb=" O LYS G 41 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N PHE G 46 " --> pdb=" O LYS G 42 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE G 47 " --> pdb=" O ASN G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 51 through 76 removed outlier: 4.311A pdb=" N ALA G 64 " --> pdb=" O GLU G 60 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N ALA G 65 " --> pdb=" O VAL G 61 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N ASN G 66 " --> pdb=" O LEU G 62 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N ALA G 67 " --> pdb=" O ALA G 63 " (cutoff:3.500A) removed outlier: 5.393A pdb=" N ILE G 72 " --> pdb=" O ARG G 68 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 removed outlier: 4.194A pdb=" N ALA G 105 " --> pdb=" O ASP G 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 3 through 21 removed outlier: 3.720A pdb=" N LYS H 20 " --> pdb=" O SER H 16 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 48 removed outlier: 3.879A pdb=" N THR H 39 " --> pdb=" O VAL H 35 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N ARG H 42 " --> pdb=" O MET H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 71 removed outlier: 3.591A pdb=" N THR H 67 " --> pdb=" O ALA H 63 " (cutoff:3.500A) Proline residue: H 68 - end of helix removed outlier: 3.895A pdb=" N CYS H 71 " --> pdb=" O THR H 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 72 through 79 removed outlier: 4.924A pdb=" N PHE H 76 " --> pdb=" O LEU H 72 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N VAL H 77 " --> pdb=" O LYS H 73 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N GLY H 78 " --> pdb=" O ASP H 74 " (cutoff:3.500A) Proline residue: H 79 - end of helix No H-bonds generated for 'chain 'H' and resid 72 through 79' Processing helix chain 'H' and resid 94 through 106 removed outlier: 3.922A pdb=" N PHE H 99 " --> pdb=" O LEU H 95 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N ALA H 100 " --> pdb=" O PHE H 96 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N PHE H 106 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 109 through 114 removed outlier: 6.588A pdb=" N ALA H 112 " --> pdb=" O LYS H 109 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU H 114 " --> pdb=" O ALA H 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 38 removed outlier: 4.360A pdb=" N THR J 30 " --> pdb=" O GLY J 26 " (cutoff:3.500A) removed outlier: 4.442A pdb=" N GLU J 31 " --> pdb=" O ARG J 27 " (cutoff:3.500A) Processing helix chain 'J' and resid 67 through 72 Processing helix chain 'J' and resid 88 through 96 Processing helix chain 'J' and resid 97 through 110 removed outlier: 4.716A pdb=" N ILE J 101 " --> pdb=" O PRO J 97 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU J 102 " --> pdb=" O GLU J 98 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N ILE J 103 " --> pdb=" O ARG J 99 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA J 104 " --> pdb=" O VAL J 100 " (cutoff:3.500A) Proline residue: J 110 - end of helix Processing helix chain 'J' and resid 112 through 122 removed outlier: 3.951A pdb=" N LYS J 121 " --> pdb=" O ALA J 117 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LEU J 122 " --> pdb=" O MET J 118 " (cutoff:3.500A) Processing helix chain 'K' and resid 112 through 120 removed outlier: 3.776A pdb=" N ILE K 116 " --> pdb=" O PHE K 112 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N SER K 117 " --> pdb=" O MET K 113 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU K 118 " --> pdb=" O LYS K 114 " (cutoff:3.500A) Proline residue: K 120 - end of helix Processing helix chain 'L' and resid 56 through 61 Processing helix chain 'L' and resid 68 through 75 removed outlier: 4.141A pdb=" N ALA L 72 " --> pdb=" O SER L 68 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE L 73 " --> pdb=" O ARG L 69 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N ALA L 75 " --> pdb=" O ALA L 71 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 85 removed outlier: 4.469A pdb=" N LEU L 82 " --> pdb=" O ARG L 78 " (cutoff:3.500A) removed outlier: 5.104A pdb=" N ALA L 83 " --> pdb=" O LEU L 79 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N LYS L 84 " --> pdb=" O SER L 80 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N VAL L 85 " --> pdb=" O ASP L 81 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 78 through 85' Processing helix chain 'L' and resid 91 through 99 Processing helix chain 'L' and resid 128 through 139 removed outlier: 3.881A pdb=" N GLU L 136 " --> pdb=" O ARG L 132 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA L 137 " --> pdb=" O ALA L 133 " (cutoff:3.500A) Processing helix chain 'M' and resid 42 through 58 removed outlier: 3.803A pdb=" N ILE M 46 " --> pdb=" O THR M 42 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU M 47 " --> pdb=" O ALA M 43 " (cutoff:3.500A) Processing helix chain 'M' and resid 109 through 125 removed outlier: 4.114A pdb=" N GLU M 115 " --> pdb=" O GLU M 111 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA M 120 " --> pdb=" O ALA M 116 " (cutoff:3.500A) Proline residue: M 125 - end of helix Processing helix chain 'N' and resid 13 through 32 removed outlier: 3.864A pdb=" N ALA N 19 " --> pdb=" O SER N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 38 through 57 removed outlier: 3.940A pdb=" N ARG N 45 " --> pdb=" O ALA N 41 " (cutoff:3.500A) removed outlier: 4.362A pdb=" N ARG N 46 " --> pdb=" O LYS N 42 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL N 47 " --> pdb=" O GLU N 43 " (cutoff:3.500A) Proline residue: N 50 - end of helix removed outlier: 4.041A pdb=" N THR N 57 " --> pdb=" O THR N 53 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 71 removed outlier: 3.761A pdb=" N ARG N 63 " --> pdb=" O SER N 59 " (cutoff:3.500A) Processing helix chain 'N' and resid 72 through 88 removed outlier: 3.784A pdb=" N LYS N 78 " --> pdb=" O GLU N 74 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU N 83 " --> pdb=" O LEU N 79 " (cutoff:3.500A) removed outlier: 4.655A 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 3 through 20 removed outlier: 3.931A pdb=" N ARG O 7 " --> pdb=" O LYS O 3 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG O 13 " --> pdb=" O ARG O 9 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA O 14 " --> pdb=" O ARG O 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 55 through 63 removed outlier: 5.424A pdb=" N GLN O 61 " --> pdb=" O ALA O 57 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N LEU O 62 " --> pdb=" O ILE O 58 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N LYS O 63 " --> pdb=" O ALA O 59 " (cutoff:3.500A) Processing helix chain 'O' and resid 67 through 86 removed outlier: 4.002A pdb=" N LYS O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 114 Processing helix chain 'P' and resid 2 through 13 removed outlier: 4.186A pdb=" N GLN P 7 " --> pdb=" O ASN P 3 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N GLN P 10 " --> pdb=" O LYS P 6 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N GLU P 11 " --> pdb=" O GLN P 7 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N GLN P 12 " --> pdb=" O LEU P 8 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N MET P 13 " --> pdb=" O GLU P 9 " (cutoff:3.500A) Processing helix chain 'P' and resid 97 through 104 removed outlier: 5.081A pdb=" N ARG P 101 " --> pdb=" O LEU P 97 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N GLU P 102 " --> pdb=" O TYR P 98 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N ARG P 103 " --> pdb=" O TYR P 99 " (cutoff:3.500A) removed outlier: 5.438A pdb=" N THR P 104 " --> pdb=" O LEU P 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 97 through 104' Processing helix chain 'Q' and resid 6 through 22 removed outlier: 3.778A pdb=" N ALA Q 10 " --> pdb=" O ARG Q 6 " (cutoff:3.500A) Processing helix chain 'Q' and resid 26 through 31 removed outlier: 3.982A pdb=" N ARG Q 30 " --> pdb=" O GLY Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 39 through 73 removed outlier: 3.672A pdb=" N ARG Q 48 " --> pdb=" O GLN Q 44 " (cutoff:3.500A) removed outlier: 4.798A pdb=" N ARG Q 51 " --> pdb=" O TYR Q 47 " (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: 4.001A pdb=" N VAL S 17 " --> pdb=" O SER S 13 " (cutoff:3.500A) removed outlier: 4.736A pdb=" N ARG S 18 " --> pdb=" O ALA S 14 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N LEU S 19 " --> pdb=" O GLN S 15 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N VAL S 20 " --> pdb=" O LYS S 16 " (cutoff:3.500A) removed outlier: 4.514A pdb=" N LEU S 23 " --> pdb=" O LEU S 19 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N ILE S 24 " --> pdb=" O VAL S 20 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ARG S 25 " --> pdb=" O ALA S 21 " (cutoff:3.500A) Processing helix chain 'S' and resid 28 through 39 removed outlier: 3.554A pdb=" N ASP S 34 " --> pdb=" O SER S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 41 through 61 removed outlier: 4.269A pdb=" N VAL S 45 " --> pdb=" O LYS S 41 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LEU S 46 " --> pdb=" O LYS S 42 " (cutoff:3.500A) Processing helix chain 'T' and resid 3 through 11 removed outlier: 3.698A pdb=" N LEU T 7 " --> pdb=" O ARG T 3 " (cutoff:3.500A) removed outlier: 4.457A 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 50 Processing helix chain 'U' and resid 66 through 71 removed outlier: 3.839A pdb=" N VAL U 70 " --> pdb=" O GLN U 66 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ALA U 71 " --> pdb=" O VAL U 67 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 66 through 71' Processing helix chain 'V' and resid 13 through 24 removed outlier: 3.649A pdb=" N ASN V 24 " --> pdb=" O LEU V 20 " (cutoff:3.500A) Processing helix chain 'V' and resid 43 through 52 removed outlier: 3.697A pdb=" N VAL V 47 " --> pdb=" O ASP V 43 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N MET V 50 " --> pdb=" O LYS V 46 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N ALA V 52 " --> pdb=" O MET V 48 " (cutoff:3.500A) Processing helix chain 'V' and resid 53 through 59 removed outlier: 4.500A pdb=" N TYR V 57 " --> pdb=" O LYS V 53 " (cutoff:3.500A) removed outlier: 3.912A 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 5 through 10 removed outlier: 5.186A pdb=" N LYS Y 9 " --> pdb=" O GLU Y 5 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N SER Y 10 " --> pdb=" O LEU Y 6 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 5 through 10' Processing helix chain 'Y' and resid 11 through 35 removed outlier: 3.606A pdb=" N SER Y 34 " --> pdb=" O MET Y 30 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N GLY Y 35 " --> pdb=" O GLN Y 31 " (cutoff:3.500A) Processing helix chain 'Y' and resid 40 through 60 removed outlier: 4.128A pdb=" N LYS Y 44 " --> pdb=" O SER Y 40 " (cutoff:3.500A) Processing helix chain 'Z' and resid 17 through 28 removed outlier: 3.646A pdb=" N LEU Z 24 " --> pdb=" O HIS Z 20 " (cutoff:3.500A) Processing helix chain 'Z' and resid 41 through 52 Processing helix chain 'a' and resid 41 through 46 Processing helix chain 'a' and resid 55 through 64 removed outlier: 4.438A pdb=" N ARG a 59 " --> pdb=" O GLY a 55 " (cutoff:3.500A) Processing helix chain 'b' and resid 9 through 21 removed outlier: 4.489A pdb=" N HIS b 19 " --> pdb=" O MET b 15 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N ASP b 20 " --> pdb=" O ARG b 16 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N ALA b 21 " --> pdb=" O ARG b 17 " (cutoff:3.500A) Processing helix chain 'd' and resid 8 through 16 removed outlier: 3.535A pdb=" N SER d 15 " --> pdb=" O LYS d 11 " (cutoff:3.500A) Processing helix chain 'd' and resid 17 through 25 removed outlier: 3.788A pdb=" N ALA d 23 " --> pdb=" O ARG d 19 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N THR d 24 " --> pdb=" O ALA d 20 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N LYS d 25 " --> pdb=" O ARG d 21 " (cutoff:3.500A) Processing helix chain 'd' and resid 26 through 38 Processing helix chain 'e' and resid 7 through 14 Processing helix chain 'e' and resid 32 through 37 removed outlier: 4.651A pdb=" N LYS e 36 " --> pdb=" O ILE e 32 " (cutoff:3.500A) removed outlier: 4.938A pdb=" N ALA e 37 " --> pdb=" O LEU e 33 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 32 through 37' Processing helix chain 'e' and resid 38 through 46 Proline residue: e 46 - end of helix Processing helix chain 'e' and resid 51 through 63 removed outlier: 4.588A pdb=" N GLY e 56 " --> pdb=" O LYS e 52 " (cutoff:3.500A) removed outlier: 5.653A pdb=" N LEU e 57 " --> pdb=" O GLY e 53 " (cutoff:3.500A) removed outlier: 4.095A 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 24 through 29 removed outlier: 4.256A pdb=" N LYS g 28 " --> pdb=" O ASN g 24 " (cutoff:3.500A) Proline residue: g 29 - end of helix No H-bonds generated for 'chain 'g' and resid 24 through 29' Processing helix chain 'g' and resid 42 through 64 Proline residue: g 48 - end of helix removed outlier: 3.907A pdb=" N ARG g 63 " --> pdb=" O LYS g 59 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS g 64 " --> pdb=" O ILE g 60 " (cutoff:3.500A) Processing helix chain 'g' and resid 73 through 88 removed outlier: 6.271A pdb=" N SER g 77 " --> pdb=" O LYS g 73 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N GLU g 78 " --> pdb=" O ARG g 74 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N ALA g 79 " --> pdb=" O ALA g 75 " (cutoff:3.500A) Processing helix chain 'g' and resid 103 through 123 removed outlier: 4.620A pdb=" N GLN g 109 " --> pdb=" O LYS g 105 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N SER g 110 " --> pdb=" O THR g 106 " (cutoff:3.500A) Processing helix chain 'g' and resid 130 through 148 removed outlier: 3.771A pdb=" N SER g 147 " --> pdb=" O LYS g 143 " (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 Processing helix chain 'h' and resid 6 through 12 removed outlier: 3.501A pdb=" N LEU h 12 " --> pdb=" O ASN h 8 " (cutoff:3.500A) Processing helix chain 'h' and resid 28 through 48 removed outlier: 4.317A pdb=" N ALA h 48 " --> pdb=" O THR h 44 " (cutoff:3.500A) Processing helix chain 'h' and resid 72 through 78 Processing helix chain 'h' and resid 81 through 96 removed outlier: 3.533A pdb=" N GLU h 85 " --> pdb=" O GLY h 81 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N LYS h 86 " --> pdb=" O GLU h 82 " (cutoff:3.500A) Processing helix chain 'h' and resid 108 through 113 removed outlier: 4.224A pdb=" N ASP h 112 " --> pdb=" O LYS h 108 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N ALA h 113 " --> pdb=" O PRO h 109 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 108 through 113' Processing helix chain 'h' and resid 114 through 127 Processing helix chain 'h' and resid 129 through 145 removed outlier: 4.067A pdb=" N GLY h 145 " --> pdb=" O ALA h 141 " (cutoff:3.500A) Processing helix chain 'i' and resid 7 through 16 removed outlier: 4.205A pdb=" N LEU i 11 " --> pdb=" O PRO i 7 " (cutoff:3.500A) Processing helix chain 'i' and resid 27 through 32 removed outlier: 3.633A pdb=" N LYS i 31 " --> pdb=" O ALA i 27 " (cutoff:3.500A) Processing helix chain 'i' and resid 49 through 66 removed outlier: 3.507A pdb=" N VAL i 61 " --> pdb=" O GLU i 57 " (cutoff:3.500A) Processing helix chain 'i' and resid 68 through 83 removed outlier: 3.761A pdb=" N ASN i 74 " --> pdb=" O ARG i 70 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR i 75 " --> pdb=" O GLN i 71 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N LYS i 83 " --> pdb=" O ALA i 79 " (cutoff:3.500A) Processing helix chain 'i' and resid 85 through 97 removed outlier: 3.539A 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 Processing helix chain 'i' and resid 152 through 166 removed outlier: 3.846A pdb=" N LEU i 159 " --> pdb=" O VAL i 155 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN i 164 " --> pdb=" O GLU i 160 " (cutoff:3.500A) removed outlier: 4.474A pdb=" N GLU i 166 " --> pdb=" O ALA i 162 " (cutoff:3.500A) Processing helix chain 'i' and resid 187 through 192 removed outlier: 3.843A pdb=" N LEU i 191 " --> pdb=" O GLU i 187 " (cutoff:3.500A) removed outlier: 5.145A pdb=" N SER i 192 " --> pdb=" O ARG i 188 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 187 through 192' Processing helix chain 'i' and resid 196 through 206 removed outlier: 4.496A pdb=" N ILE i 200 " --> pdb=" O ASN i 196 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N VAL i 201 " --> pdb=" O GLU i 197 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU i 202 " --> pdb=" O HIS i 198 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N LEU i 203 " --> pdb=" O LEU i 199 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LYS i 206 " --> pdb=" O GLU i 202 " (cutoff:3.500A) Processing helix chain 'j' and resid 55 through 71 removed outlier: 3.714A pdb=" N ARG j 69 " --> pdb=" O GLU j 65 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N ASN j 70 " --> pdb=" O LYS j 66 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N MET j 71 " --> pdb=" O ALA j 67 " (cutoff:3.500A) Processing helix chain 'j' and resid 109 through 119 removed outlier: 3.741A pdb=" N ALA j 113 " --> pdb=" O GLY j 109 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU j 116 " --> pdb=" O ARG j 112 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N VAL j 117 " --> pdb=" O ALA j 113 " (cutoff:3.500A) Processing helix chain 'j' and resid 132 through 147 removed outlier: 3.601A pdb=" N ARG j 138 " --> pdb=" O ILE j 134 " (cutoff:3.500A) removed outlier: 3.696A 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 Processing helix chain 'k' and resid 17 through 33 Processing helix chain 'k' and resid 67 through 82 removed outlier: 3.656A pdb=" N ILE k 71 " --> pdb=" O PRO k 67 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N ASP k 82 " --> pdb=" O PHE k 78 " (cutoff:3.500A) Processing helix chain 'l' and resid 20 through 31 removed outlier: 4.463A pdb=" N ALA l 24 " --> pdb=" O SER l 20 " (cutoff:3.500A) Processing helix chain 'l' and resid 35 through 55 Processing helix chain 'l' and resid 57 through 70 Processing helix chain 'l' and resid 92 through 111 Processing helix chain 'l' and resid 115 through 130 Processing helix chain 'l' and resid 132 through 149 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 removed outlier: 3.818A pdb=" N GLN m 118 " --> pdb=" O ARG m 114 " (cutoff:3.500A) Processing helix chain 'n' and resid 34 through 39 Processing helix chain 'n' and resid 41 through 56 removed outlier: 3.739A pdb=" N ARG n 45 " --> pdb=" O ARG n 41 " (cutoff:3.500A) Proline residue: n 51 - end of helix removed outlier: 4.120A pdb=" N ASP n 56 " --> pdb=" O LEU n 52 " (cutoff:3.500A) Processing helix chain 'n' and resid 71 through 91 Processing helix chain 'n' and resid 94 through 102 removed outlier: 3.575A pdb=" N LYS n 100 " --> pdb=" O SER n 96 " (cutoff:3.500A) Processing helix chain 'o' and resid 14 through 33 Processing helix chain 'o' and resid 80 through 91 removed outlier: 5.659A pdb=" N ASP o 91 " --> pdb=" O LEU o 87 " (cutoff:3.500A) Processing helix chain 'p' and resid 46 through 51 removed outlier: 4.316A pdb=" N GLY p 51 " --> pdb=" O ALA p 47 " (cutoff:3.500A) Processing helix chain 'p' and resid 54 through 59 removed outlier: 4.712A pdb=" N SER p 58 " --> pdb=" O GLY p 54 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N THR p 59 " --> pdb=" O SER p 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 54 through 59' Processing helix chain 'p' and resid 60 through 75 Processing helix chain 'p' and resid 91 through 104 removed outlier: 4.307A pdb=" N SER p 95 " --> pdb=" O PRO p 91 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N ILE p 97 " --> pdb=" O ARG p 93 " (cutoff:3.500A) removed outlier: 3.960A 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: 3.945A pdb=" N TYR q 117 " --> pdb=" O ALA q 113 " (cutoff:3.500A) Processing helix chain 'r' and resid 14 through 22 removed outlier: 3.686A pdb=" N SER r 21 " --> pdb=" O ILE r 17 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ILE r 22 " --> pdb=" O ALA r 18 " (cutoff:3.500A) Processing helix chain 'r' and resid 26 through 38 removed outlier: 3.532A pdb=" N ILE r 33 " --> pdb=" O ARG r 29 " (cutoff:3.500A) Processing helix chain 'r' and resid 49 through 64 removed outlier: 4.073A pdb=" N ILE r 53 " --> pdb=" O SER r 49 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS r 62 " --> pdb=" O ASP r 58 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N PHE r 63 " --> pdb=" O GLU r 59 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N VAL r 64 " --> pdb=" O VAL r 60 " (cutoff:3.500A) Processing helix chain 'r' and resid 66 through 84 removed outlier: 3.616A pdb=" N ARG r 70 " --> pdb=" O GLU r 66 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N ARG r 71 " --> pdb=" O GLY r 67 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 94 Processing helix chain 'r' and resid 106 through 111 Processing helix chain 's' and resid 3 through 21 Processing helix chain 's' and resid 22 through 33 Processing helix chain 's' and resid 37 through 51 removed outlier: 3.663A pdb=" N TRP s 42 " --> pdb=" O ASP s 38 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N THR s 50 " --> pdb=" O LEU s 46 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU s 51 " --> pdb=" O LYS s 47 " (cutoff:3.500A) Processing helix chain 's' and resid 80 through 91 removed outlier: 3.553A pdb=" N ARG s 90 " --> pdb=" O GLU s 86 " (cutoff:3.500A) Processing helix chain 't' and resid 4 through 16 Processing helix chain 't' and resid 24 through 43 removed outlier: 4.290A pdb=" N GLY t 41 " --> pdb=" O ASN t 37 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N HIS t 42 " --> pdb=" O HIS t 38 " (cutoff:3.500A) Processing helix chain 't' and resid 49 through 74 removed outlier: 4.498A pdb=" N GLY t 55 " --> pdb=" O HIS t 51 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 86 Processing helix chain 'u' and resid 53 through 64 removed outlier: 3.806A pdb=" N GLN u 63 " --> pdb=" O HIS u 59 " (cutoff:3.500A) Processing helix chain 'u' and resid 68 through 81 removed outlier: 4.459A pdb=" N ALA u 81 " --> pdb=" O GLU u 77 " (cutoff:3.500A) Processing helix chain 'w' and resid 11 through 17 removed outlier: 4.821A pdb=" N ALA w 15 " --> pdb=" O CYS w 11 " (cutoff:3.500A) Processing helix chain 'w' and resid 25 through 34 removed outlier: 4.407A pdb=" N ASN w 31 " --> pdb=" O ALA w 27 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N THR w 34 " --> pdb=" O LYS w 30 " (cutoff:3.500A) Processing helix chain 'w' and resid 41 through 46 removed outlier: 3.887A pdb=" N THR w 45 " --> pdb=" O PRO w 41 " (cutoff:3.500A) Processing helix chain 'w' and resid 48 through 66 removed outlier: 3.749A pdb=" N GLN w 54 " --> pdb=" O LYS w 50 " (cutoff:3.500A) Processing helix chain 'x' and resid 12 through 26 removed outlier: 3.963A pdb=" N LYS x 18 " --> pdb=" O HIS x 14 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU x 24 " --> pdb=" O GLU x 20 " (cutoff:3.500A) Processing helix chain 'x' and resid 70 through 76 removed outlier: 4.598A pdb=" N PHE x 74 " --> pdb=" O LYS x 70 " (cutoff:3.500A) removed outlier: 4.612A 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: 3.807A pdb=" N ILE y 12 " --> pdb=" O LYS y 8 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLU y 15 " --> pdb=" O ALA y 11 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N PHE y 31 " --> pdb=" O MET y 27 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N GLU y 40 " --> pdb=" O TYR y 36 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA y 41 " --> pdb=" O ALA y 37 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY y 42 " --> pdb=" O ALA y 38 " (cutoff:3.500A) Processing helix chain 'y' and resid 44 through 65 removed outlier: 4.055A pdb=" N GLN y 48 " --> pdb=" O LYS y 44 " (cutoff:3.500A) Proline residue: y 56 - end of helix Processing helix chain 'y' and resid 68 through 86 removed outlier: 3.552A pdb=" N LYS y 85 " --> pdb=" O ALA y 81 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N LEU y 86 " --> pdb=" O GLN y 82 " (cutoff:3.500A) Processing helix chain 'z' and resid 11 through 27 removed outlier: 3.701A pdb=" N ALA z 15 " --> pdb=" O PRO z 11 " (cutoff:3.500A) Processing helix chain 'z' and resid 28 through 38 removed outlier: 4.198A pdb=" N PHE z 37 " --> pdb=" O ARG z 33 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N TYR z 38 " --> pdb=" O ARG z 34 " (cutoff:3.500A) Processing helix chain 'z' and resid 40 through 66 removed outlier: 4.066A pdb=" N ARG z 66 " --> pdb=" O ARG z 62 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain '5' and resid 49 through 52 No H-bonds generated for sheet with id= 1 Processing sheet with id= 2, first strand: chain '5' and resid 89 through 92 removed outlier: 4.899A pdb=" N LYS 5 89 " --> pdb=" O ALA 5 35 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLY 5 33 " --> pdb=" O LEU 5 91 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N GLU 5 28 " --> pdb=" O VAL 5 129 " (cutoff:3.500A) removed outlier: 4.746A pdb=" N LYS 5 126 " --> pdb=" O LEU 5 114 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 51 through 54 removed outlier: 3.564A pdb=" N GLY A 54 " --> pdb=" O THR A 58 " (cutoff:3.500A) removed outlier: 4.726A pdb=" N THR A 58 " --> pdb=" O GLY A 54 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 65 through 71 Processing sheet with id= 5, first strand: chain 'B' and resid 33 through 36 No H-bonds generated for sheet with id= 5 Processing sheet with id= 6, first strand: chain 'B' and resid 80 through 83 removed outlier: 3.927A pdb=" N ARG B 80 " --> pdb=" O LEU B 93 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU B 93 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N ILE B 74 " --> pdb=" O SER B 118 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N SER B 118 " --> pdb=" O ILE B 74 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ASP B 114 " --> pdb=" O VAL B 78 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 138 through 142 removed outlier: 4.180A pdb=" N SER B 139 " --> pdb=" O ILE B 164 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR B 173 " --> pdb=" O VAL B 165 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N GLU B 180 " --> pdb=" O LEU B 176 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 91 through 96 removed outlier: 4.416A pdb=" N GLU B 100 " --> pdb=" O TYR B 96 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'C' and resid 3 through 9 removed outlier: 4.176A pdb=" N SER C 199 " --> pdb=" O LYS C 8 " (cutoff:3.500A) removed outlier: 13.409A pdb=" N GLY C 198 " --> pdb=" O LYS C 114 " (cutoff:3.500A) removed outlier: 11.714A pdb=" N LYS C 114 " --> pdb=" O GLY C 198 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP C 200 " --> pdb=" O THR C 112 " (cutoff:3.500A) removed outlier: 4.710A pdb=" N THR C 112 " --> pdb=" O ASP C 200 " (cutoff:3.500A) removed outlier: 4.648A pdb=" N GLU C 168 " --> pdb=" O SER C 113 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'C' and resid 11 through 16 removed outlier: 3.761A pdb=" N VAL C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N VAL C 189 " --> pdb=" O THR C 25 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ARG C 179 " --> pdb=" O LEU C 188 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 36 through 40 removed outlier: 3.751A pdb=" N GLN C 36 " --> pdb=" O GLN C 49 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU C 40 " --> pdb=" O TYR C 45 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N TYR C 45 " --> pdb=" O LEU C 40 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N GLN C 49 " --> pdb=" O THR C 35 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N GLN C 94 " --> pdb=" O VAL C 34 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 46 through 51 removed outlier: 5.706A pdb=" N ARG C 46 " --> pdb=" O LEU C 84 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 105 through 108 removed outlier: 6.519A pdb=" N LYS C 105 " --> pdb=" O VAL C 177 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'D' and resid 1 through 6 removed outlier: 4.686A pdb=" N SER D 10 " --> pdb=" O LEU D 5 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'D' and resid 117 through 120 removed outlier: 5.698A pdb=" N ARG D 117 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASP D 168 " --> pdb=" O VAL D 146 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'E' and resid 65 through 69 removed outlier: 3.768A pdb=" N GLY E 86 " --> pdb=" O THR E 68 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N ILE E 85 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 5.726A pdb=" N GLY E 39 " --> pdb=" O GLY E 151 " (cutoff:3.500A) removed outlier: 8.091A pdb=" N GLY E 151 " --> pdb=" O GLY E 39 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU E 152 " --> pdb=" O VAL E 132 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'F' and resid 16 through 19 Processing sheet with id= 18, first strand: chain 'F' and resid 41 through 45 Processing sheet with id= 19, first strand: chain 'F' and resid 94 through 98 removed outlier: 4.184A pdb=" N ARG F 95 " --> pdb=" O SER F 106 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N SER F 106 " --> pdb=" O ARG F 95 " (cutoff:3.500A) Processing sheet with id= 20, first strand: chain 'F' and resid 121 through 125 removed outlier: 5.364A pdb=" N THR F 129 " --> pdb=" O LEU F 89 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ARG F 163 " --> pdb=" O GLN F 88 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'G' and resid 18 through 21 removed outlier: 4.441A pdb=" N MET G 1 " --> pdb=" O VAL G 21 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N GLN G 2 " --> pdb=" O ALA G 39 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LYS G 35 " --> pdb=" O LEU G 6 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'G' and resid 77 through 82 removed outlier: 6.448A pdb=" N VAL G 138 " --> pdb=" O VAL G 134 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLY G 126 " --> pdb=" O VAL G 146 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'H' and resid 24 through 28 removed outlier: 3.562A pdb=" N ALA H 25 " --> pdb=" O SER H 85 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N VAL H 27 " --> pdb=" O ALA H 83 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'J' and resid 52 through 57 removed outlier: 4.887A pdb=" N ASP J 19 " --> pdb=" O LEU J 140 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'K' and resid 56 through 60 removed outlier: 4.648A pdb=" N ASP K 56 " --> pdb=" O ILE K 43 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LYS K 40 " --> pdb=" O ILE K 22 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N THR K 6 " --> pdb=" O CYS K 21 " (cutoff:3.500A) removed outlier: 5.913A pdb=" N ASN K 82 " --> pdb=" O MET K 7 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'L' and resid 120 through 123 removed outlier: 4.195A pdb=" N LYS L 141 " --> pdb=" O VAL L 120 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'M' and resid 37 through 40 No H-bonds generated for sheet with id= 27 Processing sheet with id= 28, first strand: chain 'M' and resid 62 through 65 removed outlier: 3.703A pdb=" N TYR M 103 " --> pdb=" O LEU M 33 " (cutoff:3.500A) removed outlier: 7.853A pdb=" N SER M 30 " --> pdb=" O LYS M 133 " (cutoff:3.500A) removed outlier: 6.811A 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: 4.810A pdb=" N ARG N 103 " --> pdb=" O ASN N 107 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N GLY N 101 " --> pdb=" O PRO N 109 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N ALA N 111 " --> pdb=" O LYS N 99 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LYS N 99 " --> pdb=" O ALA N 111 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE N 113 " --> pdb=" O ILE N 97 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N ILE N 97 " --> pdb=" O ILE N 113 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N LEU N 115 " --> pdb=" O THR N 95 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR N 95 " --> pdb=" O LEU N 115 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'O' and resid 49 through 53 removed outlier: 4.136A pdb=" N VAL O 49 " --> pdb=" O VAL O 39 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ILE O 35 " --> pdb=" O THR O 53 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N HIS O 34 " --> pdb=" O THR O 31 " (cutoff:3.500A) removed outlier: 3.537A 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: 6.570A pdb=" N THR P 25 " --> pdb=" O LYS P 87 " (cutoff:3.500A) removed outlier: 3.869A 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 52 removed outlier: 4.343A pdb=" N ALA P 49 " --> pdb=" O THR P 60 " (cutoff:3.500A) removed outlier: 7.651A 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: 3.595A pdb=" N MET R 40 " --> pdb=" O VAL R 4 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LEU R 39 " --> pdb=" O GLY R 50 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASN R 43 " --> pdb=" O GLU R 46 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N GLU R 46 " --> pdb=" O ASN R 43 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'R' and resid 19 through 22 Processing sheet with id= 35, first strand: chain 'R' and resid 31 through 36 removed outlier: 4.405A pdb=" N GLU R 31 " --> pdb=" O VAL R 63 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'R' and resid 71 through 78 removed outlier: 4.415A pdb=" N TYR R 83 " --> pdb=" O ARG R 78 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'S' and resid 2 through 8 removed outlier: 4.806A pdb=" N THR S 3 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N VAL S 107 " --> pdb=" O THR S 3 " (cutoff:3.500A) removed outlier: 5.232A pdb=" N THR S 100 " --> pdb=" O GLY S 79 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLY S 79 " --> pdb=" O THR S 100 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'T' and resid 12 through 15 removed outlier: 5.343A pdb=" N VAL T 31 " --> pdb=" O HIS T 15 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N ASN T 28 " --> pdb=" O LEU T 87 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS T 81 " --> pdb=" O VAL T 34 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LYS T 66 " --> pdb=" O ARG T 77 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N ASP T 79 " --> pdb=" O LYS T 64 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N LYS T 64 " --> pdb=" O ASP T 79 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N LYS T 81 " --> pdb=" O VAL T 62 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N VAL T 62 " --> pdb=" O LYS T 81 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ALA T 83 " --> pdb=" O THR T 60 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N THR T 60 " --> pdb=" O ALA T 83 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL T 85 " --> pdb=" O VAL T 58 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N VAL T 58 " --> pdb=" O VAL T 85 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'U' and resid 40 through 46 removed outlier: 4.964A pdb=" N ASN U 40 " --> pdb=" O ALA U 63 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLN U 46 " --> pdb=" O GLY U 57 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'U' and resid 83 through 86 removed outlier: 3.701A pdb=" N PHE U 95 " --> pdb=" O GLY U 84 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'V' and resid 75 through 78 removed outlier: 3.758A pdb=" N HIS V 88 " --> pdb=" O GLN V 78 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N ILE V 89 " --> pdb=" O PRO V 27 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N ALA V 39 " --> pdb=" O ARG V 9 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N PHE V 2 " --> pdb=" O VAL V 60 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'V' and resid 71 through 74 removed outlier: 5.220A pdb=" N LYS V 71 " --> pdb=" O ALA V 94 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'X' and resid 12 through 19 removed outlier: 4.638A pdb=" N ASN X 23 " --> pdb=" O SER X 19 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'X' and resid 34 through 41 removed outlier: 3.599A pdb=" N VAL X 51 " --> pdb=" O HIS X 34 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG X 45 " --> pdb=" O VAL X 40 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'Z' and resid 33 through 39 removed outlier: 4.340A pdb=" N HIS Z 34 " --> pdb=" O GLN Z 9 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLN Z 9 " --> pdb=" O HIS Z 34 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N LYS Z 6 " --> pdb=" O GLU Z 58 " (cutoff:3.500A) removed outlier: 7.326A pdb=" N MET Z 54 " --> pdb=" O THR Z 10 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'a' and resid 20 through 25 removed outlier: 4.503A pdb=" N ASN a 20 " --> pdb=" O CYS a 16 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N CYS a 16 " --> pdb=" O ASN a 20 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'c' and resid 19 through 24 removed outlier: 5.926A pdb=" N HIS c 19 " --> pdb=" O SER c 13 " (cutoff:3.500A) removed outlier: 6.279A pdb=" N LEU c 34 " --> pdb=" O GLU c 51 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'e' and resid 22 through 25 No H-bonds generated for sheet with id= 48 Processing sheet with id= 49, first strand: chain 'f' and resid 1 through 4 removed outlier: 6.905A pdb=" N ILE f 23 " --> pdb=" O GLN f 37 " (cutoff:3.500A) removed outlier: 8.024A pdb=" N ASN f 13 " --> pdb=" O SER f 28 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'g' and resid 15 through 18 removed outlier: 5.717A pdb=" N HIS g 15 " --> pdb=" O ILE g 41 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N HIS g 39 " --> pdb=" O GLY g 17 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'g' and resid 89 through 93 removed outlier: 3.620A pdb=" N ILE g 186 " --> pdb=" O VAL g 163 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'h' and resid 54 through 59 Processing sheet with id= 53, first strand: chain 'h' and resid 164 through 169 removed outlier: 5.844A pdb=" N ARG h 164 " --> pdb=" O GLY h 155 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLY h 148 " --> pdb=" O PHE h 203 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N ASP h 181 " --> pdb=" O LYS h 204 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'i' and resid 141 through 145 removed outlier: 3.593A pdb=" N ASP i 141 " --> pdb=" O PHE i 182 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N MET i 178 " --> pdb=" O ILE i 145 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'j' and resid 11 through 16 removed outlier: 3.876A pdb=" N GLY j 40 " --> pdb=" O GLN j 12 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N LEU j 36 " --> pdb=" O ILE j 16 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'j' and resid 84 through 88 removed outlier: 3.636A pdb=" N ALA j 99 " --> pdb=" O ASN j 122 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASN j 122 " --> pdb=" O ALA j 99 " (cutoff:3.500A) Processing sheet with id= 57, first strand: chain 'j' and resid 33 through 40 Processing sheet with id= 58, first strand: chain 'k' and resid 38 through 42 removed outlier: 3.753A pdb=" N ARG k 38 " --> pdb=" O ASN k 63 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N TYR k 59 " --> pdb=" O TRP k 42 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N HIS k 3 " --> pdb=" O THR k 92 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N ARG k 86 " --> pdb=" O MET k 9 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'k' and resid 43 through 47 removed outlier: 3.972A pdb=" N GLY k 43 " --> pdb=" O TYR k 59 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR k 59 " --> pdb=" O GLY k 43 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N HIS k 55 " --> pdb=" O LEU k 47 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'l' and resid 73 through 79 No H-bonds generated for sheet with id= 60 Processing sheet with id= 61, first strand: chain 'm' and resid 23 through 29 removed outlier: 6.370A pdb=" N ALA m 23 " --> pdb=" O LEU m 63 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N ASP m 48 " --> pdb=" O THR m 62 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'm' and resid 74 through 77 removed outlier: 3.539A pdb=" N TYR m 128 " --> pdb=" O GLN m 76 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N CYS m 127 " --> pdb=" O VAL m 103 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL m 103 " --> pdb=" O ILE m 126 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'n' and resid 5 through 11 Processing sheet with id= 64, first strand: chain 'o' and resid 39 through 42 removed outlier: 4.557A pdb=" N LEU o 71 " --> pdb=" O LEU o 42 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'o' and resid 44 through 52 Processing sheet with id= 66, first strand: chain 'p' and resid 29 through 36 removed outlier: 4.077A pdb=" N ASN p 29 " --> pdb=" O SER p 26 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'q' and resid 29 through 32 removed outlier: 5.145A pdb=" N LEU q 81 " --> pdb=" O VAL q 98 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N HIS q 96 " --> pdb=" O ARG q 83 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 'q' and resid 36 through 41 removed outlier: 4.786A pdb=" N LYS q 51 " --> pdb=" O ILE q 67 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 'u' and resid 4 through 10 removed outlier: 4.140A pdb=" N GLY u 37 " --> pdb=" O VAL u 19 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 'v' and resid 7 through 11 removed outlier: 3.591A pdb=" N LEU v 8 " --> pdb=" O ILE v 61 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N SER v 72 " --> pdb=" O CYS v 64 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'v' and resid 19 through 31 No H-bonds generated for sheet with id= 71 Processing sheet with id= 72, first strand: chain 'x' and resid 30 through 34 1932 hydrogen bonds defined for protein. 5718 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3598 hydrogen bonds 5988 hydrogen bond angles 0 basepair planarities 1407 basepair parallelities 2186 stacking parallelities Total time for adding SS restraints: 230.87 Time building geometry restraints manager: 69.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 12376 1.29 - 1.42: 71640 1.42 - 1.55: 73637 1.55 - 1.68: 10057 1.68 - 1.82: 275 Bond restraints: 167985 Sorted by residual: bond pdb=" C5 5MU 4 341 " pdb=" C6 5MU 4 341 " ideal model delta sigma weight residual 1.155 1.441 -0.286 2.00e-02 2.50e+03 2.04e+02 bond pdb=" C5 5MU 11939 " pdb=" C6 5MU 11939 " ideal model delta sigma weight residual 1.155 1.440 -0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C5 5MU 1 747 " pdb=" C6 5MU 1 747 " ideal model delta sigma weight residual 1.155 1.440 -0.285 2.00e-02 2.50e+03 2.03e+02 bond pdb=" C5 5MU 7 54 " pdb=" C6 5MU 7 54 " ideal model delta sigma weight residual 1.155 1.438 -0.283 2.00e-02 2.50e+03 2.01e+02 bond pdb=" C13 MIA 7 37 " pdb=" C14 MIA 7 37 " ideal model delta sigma weight residual 1.317 1.529 -0.212 2.00e-02 2.50e+03 1.12e+02 ... (remaining 167980 not shown) Histogram of bond angle deviations from ideal: 98.64 - 109.18: 66321 109.18 - 119.72: 112032 119.72 - 130.25: 70841 130.25 - 140.79: 2452 140.79 - 151.33: 3 Bond angle restraints: 251649 Sorted by residual: angle pdb=" C1' OMG 12251 " pdb=" N9 OMG 12251 " pdb=" C8 OMG 12251 " ideal model delta sigma weight residual 142.82 102.27 40.55 3.00e+00 1.11e-01 1.83e+02 angle pdb=" C1' OMG 12251 " pdb=" N9 OMG 12251 " pdb=" C4 OMG 12251 " ideal model delta sigma weight residual 108.29 147.96 -39.67 3.00e+00 1.11e-01 1.75e+02 angle pdb=" N VAL 5 112 " pdb=" CA VAL 5 112 " pdb=" CB VAL 5 112 " ideal model delta sigma weight residual 110.53 98.71 11.82 1.09e+00 8.42e-01 1.18e+02 angle pdb=" C1' G7M 7 46 " pdb=" N9 G7M 7 46 " pdb=" C8 G7M 7 46 " ideal model delta sigma weight residual 94.96 126.23 -31.27 3.00e+00 1.11e-01 1.09e+02 angle pdb=" N VAL X 67 " pdb=" CA VAL X 67 " pdb=" C VAL X 67 " ideal model delta sigma weight residual 110.62 120.22 -9.60 1.02e+00 9.61e-01 8.86e+01 ... (remaining 251644 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.79: 94466 35.79 - 71.58: 11539 71.58 - 107.37: 1401 107.37 - 143.15: 36 143.15 - 178.94: 49 Dihedral angle restraints: 107491 sinusoidal: 90465 harmonic: 17026 Sorted by residual: dihedral pdb=" C5* PSU 2 516 " pdb=" C4* PSU 2 516 " pdb=" C3* PSU 2 516 " pdb=" O3* PSU 2 516 " ideal model delta sinusoidal sigma weight residual 147.00 76.76 70.24 1 8.00e+00 1.56e-02 9.93e+01 dihedral pdb=" C4' A 8 9 " pdb=" C3' A 8 9 " pdb=" C2' A 8 9 " pdb=" C1' A 8 9 " ideal model delta sinusoidal sigma weight residual -35.00 34.85 -69.85 1 8.00e+00 1.56e-02 9.83e+01 dihedral pdb=" C4' U 12506 " pdb=" C3' U 12506 " pdb=" C2' U 12506 " pdb=" C1' U 12506 " ideal model delta sinusoidal sigma weight residual -35.00 34.78 -69.78 1 8.00e+00 1.56e-02 9.82e+01 ... (remaining 107488 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.113: 31636 0.113 - 0.226: 415 0.226 - 0.339: 38 0.339 - 0.453: 7 0.453 - 0.566: 4 Chirality restraints: 32100 Sorted by residual: chirality pdb=" C3' C 4 78 " pdb=" C4' C 4 78 " pdb=" O3' C 4 78 " pdb=" C2' C 4 78 " both_signs ideal model delta sigma weight residual False -2.74 -2.18 -0.57 2.00e-01 2.50e+01 8.00e+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 1.97 0.55 2.00e-01 2.50e+01 7.65e+00 chirality pdb=" C3' C 4 314 " pdb=" C4' C 4 314 " pdb=" O3' C 4 314 " pdb=" C2' C 4 314 " both_signs ideal model delta sigma weight residual False -2.74 -2.20 -0.54 2.00e-01 2.50e+01 7.33e+00 ... (remaining 32097 not shown) Planarity restraints: 13244 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21516 " -0.053 2.00e-02 2.50e+03 6.00e-01 8.09e+03 pdb=" C4' 2MG 21516 " -0.444 2.00e-02 2.50e+03 pdb=" O4' 2MG 21516 " -0.669 2.00e-02 2.50e+03 pdb=" C3' 2MG 21516 " 0.594 2.00e-02 2.50e+03 pdb=" O3' 2MG 21516 " 0.622 2.00e-02 2.50e+03 pdb=" C2' 2MG 21516 " 0.191 2.00e-02 2.50e+03 pdb=" O2' 2MG 21516 " -0.953 2.00e-02 2.50e+03 pdb=" C1' 2MG 21516 " -0.215 2.00e-02 2.50e+03 pdb=" N9 2MG 21516 " 0.927 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 12445 " 0.008 2.00e-02 2.50e+03 5.92e-01 7.88e+03 pdb=" C4' 2MG 12445 " -0.472 2.00e-02 2.50e+03 pdb=" O4' 2MG 12445 " -0.879 2.00e-02 2.50e+03 pdb=" C3' 2MG 12445 " 0.570 2.00e-02 2.50e+03 pdb=" O3' 2MG 12445 " 0.487 2.00e-02 2.50e+03 pdb=" C2' 2MG 12445 " 0.298 2.00e-02 2.50e+03 pdb=" O2' 2MG 12445 " -0.771 2.00e-02 2.50e+03 pdb=" C1' 2MG 12445 " -0.178 2.00e-02 2.50e+03 pdb=" N9 2MG 12445 " 0.938 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 21207 " 0.035 2.00e-02 2.50e+03 5.88e-01 7.79e+03 pdb=" C4' 2MG 21207 " 0.444 2.00e-02 2.50e+03 pdb=" O4' 2MG 21207 " 0.687 2.00e-02 2.50e+03 pdb=" C3' 2MG 21207 " -0.590 2.00e-02 2.50e+03 pdb=" O3' 2MG 21207 " -0.584 2.00e-02 2.50e+03 pdb=" C2' 2MG 21207 " -0.213 2.00e-02 2.50e+03 pdb=" O2' 2MG 21207 " 0.916 2.00e-02 2.50e+03 pdb=" C1' 2MG 21207 " 0.214 2.00e-02 2.50e+03 pdb=" N9 2MG 21207 " -0.908 2.00e-02 2.50e+03 ... (remaining 13241 not shown) Histogram of nonbonded interaction distances: 1.18 - 1.93: 17 1.93 - 2.67: 8285 2.67 - 3.41: 197224 3.41 - 4.16: 493365 4.16 - 4.90: 690005 Nonbonded interactions: 1388896 Sorted by model distance: nonbonded pdb=" N6 A 11046 " pdb=" OD1 ASN H 4 " model vdw 1.183 2.520 nonbonded pdb=" O ASN G 66 " pdb=" OE1 GLU G 70 " model vdw 1.247 3.040 nonbonded pdb=" OP1 U 11083 " pdb=" CB LEU H 41 " model vdw 1.254 3.440 nonbonded pdb=" OE2 GLU n 42 " pdb=" NH1 ARG n 45 " model vdw 1.254 2.520 nonbonded pdb=" O3' A 4 363 " pdb=" C ALA W 2 " model vdw 1.285 3.270 ... (remaining 1388891 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: 4.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 25.170 Check model and map are aligned: 1.560 Set scattering table: 0.930 Process input model: 551.030 Find NCS groups from input model: 3.040 Set up NCS constraints: 0.360 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:2.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 588.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 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 0.286 167985 Z= 0.181 Angle : 0.561 40.554 251649 Z= 0.311 Chirality : 0.032 0.566 32100 Planarity : 0.019 0.600 13244 Dihedral : 23.019 178.942 96505 Min Nonbonded Distance : 1.183 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.20 % Allowed : 3.05 % Favored : 96.74 % Rotamer: Outliers : 0.66 % Allowed : 3.48 % Favored : 95.86 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.11), residues: 5865 helix: 1.34 (0.13), residues: 1928 sheet: -0.56 (0.15), residues: 1174 loop : -1.33 (0.11), residues: 2763 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP 5 147 HIS 0.006 0.001 HIS 5 136 PHE 0.011 0.001 PHE k 8 TYR 0.009 0.001 TYR 5 101 ARG 0.004 0.000 ARG K 30 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1887 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1855 time to evaluate : 6.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 5 24 TYR cc_start: 0.7331 (m-10) cc_final: 0.7125 (m-80) REVERT: 5 27 GLU cc_start: 0.7696 (mp0) cc_final: 0.7491 (mp0) REVERT: 5 65 LEU cc_start: 0.7214 (tp) cc_final: 0.6875 (tp) REVERT: 5 70 ILE cc_start: 0.7059 (pp) cc_final: 0.6632 (pp) REVERT: 5 93 ASN cc_start: 0.7315 (t0) cc_final: 0.7096 (t0) REVERT: 5 138 LYS cc_start: 0.9258 (OUTLIER) cc_final: 0.9045 (mttt) REVERT: 5 139 ARG cc_start: 0.8853 (OUTLIER) cc_final: 0.8397 (mtm180) REVERT: A 5 LYS cc_start: 0.7082 (OUTLIER) cc_final: 0.6576 (tmtt) REVERT: A 78 LYS cc_start: 0.8331 (mmmt) cc_final: 0.7997 (mttm) REVERT: D 163 ASN cc_start: 0.8971 (t0) cc_final: 0.8542 (t0) REVERT: D 194 LYS cc_start: 0.8395 (mmmt) cc_final: 0.7242 (mttm) REVERT: E 7 TYR cc_start: 0.8719 (t80) cc_final: 0.8260 (t80) REVERT: E 23 ASN cc_start: 0.8222 (t0) cc_final: 0.7929 (t0) REVERT: E 52 ASN cc_start: 0.8509 (m-40) cc_final: 0.8082 (m110) REVERT: F 42 GLU cc_start: 0.7308 (tt0) cc_final: 0.6657 (pt0) REVERT: F 75 MET cc_start: 0.8719 (mtp) cc_final: 0.8491 (mtp) REVERT: F 130 GLU cc_start: 0.7581 (tt0) cc_final: 0.7043 (tt0) REVERT: G 122 LEU cc_start: 0.4903 (mt) cc_final: 0.4492 (pt) REVERT: G 129 GLU cc_start: 0.7981 (mt-10) cc_final: 0.7418 (mm-30) REVERT: H 38 MET cc_start: -0.1119 (mtm) cc_final: -0.1445 (mmm) REVERT: H 86 MET cc_start: 0.2975 (mmm) cc_final: 0.2767 (mmm) REVERT: J 14 ASP cc_start: 0.8179 (m-30) cc_final: 0.7831 (m-30) REVERT: J 70 THR cc_start: 0.8872 (p) cc_final: 0.8610 (p) REVERT: J 106 LYS cc_start: 0.8552 (ttpt) cc_final: 0.8297 (ttmm) REVERT: J 125 TYR cc_start: 0.8341 (m-10) cc_final: 0.8104 (m-80) REVERT: K 114 LYS cc_start: 0.8856 (tptt) cc_final: 0.8611 (tppt) REVERT: M 7 THR cc_start: 0.8925 (m) cc_final: 0.8688 (p) REVERT: M 82 MET cc_start: 0.8900 (mmp) cc_final: 0.8598 (mmp) REVERT: M 88 ASN cc_start: 0.8768 (m110) cc_final: 0.8211 (m110) REVERT: N 57 THR cc_start: 0.9061 (m) cc_final: 0.8762 (p) REVERT: N 74 GLU cc_start: 0.7833 (pm20) cc_final: 0.6759 (pm20) REVERT: O 19 GLN cc_start: 0.8339 (tt0) cc_final: 0.8095 (tt0) REVERT: O 84 GLU cc_start: 0.8285 (pp20) cc_final: 0.7996 (pp20) REVERT: O 85 LYS cc_start: 0.8634 (mttm) cc_final: 0.8279 (mttt) REVERT: O 88 LYS cc_start: 0.8293 (mtmt) cc_final: 0.8002 (mtpt) REVERT: Q 11 ARG cc_start: 0.7272 (ttm170) cc_final: 0.6887 (tpp-160) REVERT: R 43 ASN cc_start: 0.7855 (p0) cc_final: 0.7582 (p0) REVERT: S 38 TYR cc_start: 0.7977 (m-10) cc_final: 0.7747 (m-10) REVERT: T 1 MET cc_start: 0.7227 (tpt) cc_final: 0.6736 (tpt) REVERT: T 37 ASP cc_start: 0.7738 (t0) cc_final: 0.7374 (t0) REVERT: U 81 ASP cc_start: 0.7479 (m-30) cc_final: 0.7186 (m-30) REVERT: V 7 GLU cc_start: 0.7393 (mp0) cc_final: 0.6764 (mp0) REVERT: V 41 GLU cc_start: 0.7871 (mt-10) cc_final: 0.7484 (mt-10) REVERT: V 62 THR cc_start: 0.8038 (p) cc_final: 0.7444 (p) REVERT: Y 10 SER cc_start: 0.7986 (m) cc_final: 0.7257 (p) REVERT: Y 45 GLN cc_start: 0.8379 (mt0) cc_final: 0.7936 (mt0) REVERT: Z 6 LYS cc_start: 0.8342 (mmmt) cc_final: 0.7510 (mmtp) REVERT: a 23 LYS cc_start: 0.8832 (mtpp) cc_final: 0.8240 (mtpp) REVERT: a 24 ILE cc_start: 0.8994 (tp) cc_final: 0.8577 (mm) REVERT: a 26 SER cc_start: 0.8535 (t) cc_final: 0.8012 (p) REVERT: b 17 ARG cc_start: 0.8298 (mtt180) cc_final: 0.8092 (mtt180) REVERT: c 22 THR cc_start: 0.9109 (p) cc_final: 0.8812 (p) REVERT: f 15 LYS cc_start: 0.8426 (mmtm) cc_final: 0.8196 (ttmt) REVERT: g 49 MET cc_start: 0.8193 (mtt) cc_final: 0.7532 (mtm) REVERT: g 136 MET cc_start: 0.8210 (ttp) cc_final: 0.7734 (ttp) REVERT: g 145 GLU cc_start: 0.8139 (mm-30) cc_final: 0.7911 (tp30) REVERT: g 182 PRO cc_start: 0.9167 (Cg_exo) cc_final: 0.8871 (Cg_endo) REVERT: h 42 TYR cc_start: 0.8064 (t80) cc_final: 0.7772 (t80) REVERT: h 85 GLU cc_start: 0.7482 (tp30) cc_final: 0.6718 (tp30) REVERT: h 183 ASP cc_start: 0.8089 (t70) cc_final: 0.7706 (t70) REVERT: h 186 THR cc_start: 0.8798 (p) cc_final: 0.8473 (m) REVERT: i 78 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7693 (mm-30) REVERT: i 85 ASN cc_start: 0.8637 (t0) cc_final: 0.7817 (t0) REVERT: i 141 ASP cc_start: 0.8640 (m-30) cc_final: 0.8256 (m-30) REVERT: j 64 MET cc_start: 0.8942 (mmt) cc_final: 0.8303 (mmt) REVERT: k 17 GLN cc_start: 0.8056 (mp10) cc_final: 0.7600 (mp10) REVERT: k 23 GLU cc_start: 0.8154 (tm-30) cc_final: 0.7942 (tp30) REVERT: k 65 GLU cc_start: 0.8100 (tp30) cc_final: 0.7728 (tp30) REVERT: k 90 MET cc_start: 0.7663 (mtm) cc_final: 0.7226 (mtm) REVERT: l 89 VAL cc_start: 0.8730 (p) cc_final: 0.8377 (m) REVERT: l 125 SER cc_start: 0.8911 (m) cc_final: 0.8541 (p) REVERT: l 135 VAL cc_start: 0.8307 (OUTLIER) cc_final: 0.8081 (m) REVERT: m 21 ASN cc_start: 0.8714 (m-40) cc_final: 0.8463 (m-40) REVERT: n 129 LYS cc_start: 0.5981 (pttp) cc_final: 0.5754 (pttp) REVERT: o 68 ARG cc_start: 0.7795 (mtt180) cc_final: 0.7471 (mtt90) REVERT: o 77 VAL cc_start: 0.7564 (t) cc_final: 0.7358 (p) REVERT: p 26 SER cc_start: 0.9043 (t) cc_final: 0.8747 (m) REVERT: p 64 GLN cc_start: 0.8618 (pt0) cc_final: 0.8414 (pt0) REVERT: p 77 TYR cc_start: 0.8857 (m-80) cc_final: 0.8571 (m-80) REVERT: p 98 ARG cc_start: 0.8399 (mmm-85) cc_final: 0.7707 (tpp-160) REVERT: q 18 LYS cc_start: 0.8244 (tptm) cc_final: 0.7990 (tttm) REVERT: q 41 THR cc_start: 0.9200 (m) cc_final: 0.8951 (p) REVERT: q 76 GLU cc_start: 0.7340 (tm-30) cc_final: 0.6673 (tm-30) REVERT: q 77 HIS cc_start: 0.7910 (m-70) cc_final: 0.7615 (m-70) REVERT: q 105 SER cc_start: 0.8708 (p) cc_final: 0.8394 (p) REVERT: q 108 LYS cc_start: 0.8894 (mptt) cc_final: 0.8650 (mtmm) REVERT: s 43 ASN cc_start: 0.8261 (m110) cc_final: 0.6747 (m-40) REVERT: t 20 ASN cc_start: 0.7978 (t0) cc_final: 0.7636 (t0) REVERT: t 37 ASN cc_start: 0.8972 (m-40) cc_final: 0.8721 (m-40) REVERT: u 23 ASP cc_start: 0.7488 (t0) cc_final: 0.7274 (t70) REVERT: v 11 ARG cc_start: 0.8286 (mmt180) cc_final: 0.8070 (ttm-80) REVERT: x 34 TRP cc_start: 0.8423 (m-90) cc_final: 0.7816 (m-90) REVERT: x 63 THR cc_start: 0.8865 (p) cc_final: 0.8380 (p) REVERT: x 73 GLU cc_start: 0.8583 (mt-10) cc_final: 0.8337 (mt-10) REVERT: y 21 ASN cc_start: 0.8696 (m110) cc_final: 0.8372 (m110) outliers start: 32 outliers final: 6 residues processed: 1874 average time/residue: 1.5630 time to fit residues: 4963.5151 Evaluate side-chains 1224 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1214 time to evaluate : 6.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 37 GLN Chi-restraints excluded: chain 5 residue 110 THR Chi-restraints excluded: chain 5 residue 138 LYS Chi-restraints excluded: chain 5 residue 139 ARG Chi-restraints excluded: chain A residue 3 HIS Chi-restraints excluded: chain A residue 5 LYS Chi-restraints excluded: chain H residue 122 GLN Chi-restraints excluded: chain W residue 1 PHE Chi-restraints excluded: chain c residue 43 VAL Chi-restraints excluded: chain l residue 135 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 906 optimal weight: 10.0000 chunk 813 optimal weight: 20.0000 chunk 451 optimal weight: 10.0000 chunk 277 optimal weight: 10.0000 chunk 548 optimal weight: 3.9990 chunk 434 optimal weight: 10.0000 chunk 841 optimal weight: 3.9990 chunk 325 optimal weight: 10.0000 chunk 511 optimal weight: 0.9990 chunk 625 optimal weight: 4.9990 chunk 974 optimal weight: 4.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 GLN ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 ASN C 130 GLN C 173 GLN E 127 ASN F 104 ASN H 122 GLN J 58 ASN L 38 GLN O 38 GLN Q 37 GLN X 34 HIS Y 20 ASN Y 31 GLN Z 20 HIS b 42 HIS c 19 HIS f 37 GLN g 39 HIS i 116 GLN i 131 ASN l 68 ASN ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 56 HIS q 46 ASN u 26 ASN x 14 HIS y 3 ASN y 61 GLN y 75 HIS y 82 GLN y 84 ASN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.2618 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 167985 Z= 0.303 Angle : 0.662 17.027 251649 Z= 0.352 Chirality : 0.035 0.411 32100 Planarity : 0.006 0.141 13244 Dihedral : 23.682 179.414 84783 Min Nonbonded Distance : 1.053 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.60 % Favored : 96.27 % Rotamer: Outliers : 3.87 % Allowed : 12.18 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.11), residues: 5865 helix: 1.07 (0.12), residues: 1974 sheet: -0.53 (0.15), residues: 1123 loop : -1.22 (0.11), residues: 2768 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP M 64 HIS 0.012 0.002 HIS x 14 PHE 0.021 0.002 PHE g 90 TYR 0.018 0.002 TYR 5 101 ARG 0.011 0.001 ARG 5 95 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1519 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 1330 time to evaluate : 6.341 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: 5 70 ILE cc_start: 0.6462 (pp) cc_final: 0.6060 (pp) REVERT: 5 118 TRP cc_start: 0.5197 (OUTLIER) cc_final: 0.3231 (m-90) REVERT: 5 139 ARG cc_start: 0.8755 (OUTLIER) cc_final: 0.8203 (mtm180) REVERT: 5 148 GLN cc_start: 0.8159 (mm-40) cc_final: 0.7923 (mm-40) REVERT: C 4 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8917 (mp) REVERT: D 115 GLN cc_start: 0.8635 (mt0) cc_final: 0.8300 (mt0) REVERT: D 163 ASN cc_start: 0.9141 (t0) cc_final: 0.8684 (t0) REVERT: D 194 LYS cc_start: 0.8553 (mmmt) cc_final: 0.7949 (mttp) REVERT: E 32 GLU cc_start: 0.7691 (mp0) cc_final: 0.7404 (mp0) REVERT: E 52 ASN cc_start: 0.8446 (m-40) cc_final: 0.8051 (m110) REVERT: E 128 TYR cc_start: 0.9036 (t80) cc_final: 0.8685 (t80) REVERT: E 133 ARG cc_start: 0.7831 (mpp80) cc_final: 0.7470 (mmt90) REVERT: E 170 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8535 (mm) REVERT: F 130 GLU cc_start: 0.8017 (tt0) cc_final: 0.7588 (tt0) REVERT: G 122 LEU cc_start: 0.4694 (mt) cc_final: 0.4453 (pt) REVERT: G 129 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7337 (mm-30) REVERT: H 38 MET cc_start: -0.0485 (mtm) cc_final: -0.0987 (mmm) REVERT: J 14 ASP cc_start: 0.8093 (m-30) cc_final: 0.7873 (m-30) REVERT: J 16 TYR cc_start: 0.8881 (m-80) cc_final: 0.8661 (m-80) REVERT: J 61 LYS cc_start: 0.9145 (mmtp) cc_final: 0.8867 (mmtm) REVERT: J 106 LYS cc_start: 0.9043 (ttpt) cc_final: 0.8707 (ttmm) REVERT: L 58 TYR cc_start: 0.8919 (p90) cc_final: 0.8535 (p90) REVERT: M 136 MET cc_start: 0.7633 (tmm) cc_final: 0.7225 (ppp) REVERT: N 72 ASP cc_start: 0.8329 (OUTLIER) cc_final: 0.7865 (t0) REVERT: N 74 GLU cc_start: 0.7789 (pm20) cc_final: 0.7290 (pm20) REVERT: O 56 LYS cc_start: 0.8655 (ptpp) cc_final: 0.8304 (ptpp) REVERT: O 83 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8736 (mm) REVERT: O 85 LYS cc_start: 0.8978 (mttm) cc_final: 0.8618 (mttp) REVERT: P 6 LYS cc_start: 0.8299 (mtmt) cc_final: 0.7917 (mtpp) REVERT: Q 11 ARG cc_start: 0.8038 (ttm170) cc_final: 0.7472 (tpp-160) REVERT: Q 49 ASP cc_start: 0.7760 (m-30) cc_final: 0.7474 (m-30) REVERT: S 96 ILE cc_start: 0.9289 (pt) cc_final: 0.9027 (mt) REVERT: T 3 ARG cc_start: 0.8261 (mtm180) cc_final: 0.7970 (mtp-110) REVERT: U 60 GLU cc_start: 0.7970 (OUTLIER) cc_final: 0.7498 (mp0) REVERT: V 7 GLU cc_start: 0.7355 (mp0) cc_final: 0.7155 (mp0) REVERT: Y 45 GLN cc_start: 0.8515 (mt0) cc_final: 0.8289 (mt0) REVERT: Z 6 LYS cc_start: 0.8651 (mmmt) cc_final: 0.8081 (mtmm) REVERT: a 23 LYS cc_start: 0.8974 (mtpp) cc_final: 0.8432 (mtpp) REVERT: a 26 SER cc_start: 0.8626 (t) cc_final: 0.8211 (p) REVERT: c 30 LYS cc_start: 0.8523 (mtmm) cc_final: 0.8311 (mtmt) REVERT: f 9 LYS cc_start: 0.8883 (mtpm) cc_final: 0.8577 (mtpm) REVERT: f 15 LYS cc_start: 0.8539 (mmtm) cc_final: 0.8214 (mttt) REVERT: g 136 MET cc_start: 0.7809 (ttp) cc_final: 0.7487 (mmp) REVERT: g 182 PRO cc_start: 0.9087 (Cg_exo) cc_final: 0.8771 (Cg_endo) REVERT: h 72 ARG cc_start: 0.7118 (mmm-85) cc_final: 0.6653 (mmm-85) REVERT: h 183 ASP cc_start: 0.8249 (t70) cc_final: 0.7778 (t70) REVERT: h 187 SER cc_start: 0.9165 (t) cc_final: 0.8818 (t) REVERT: h 188 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.7623 (mt-10) REVERT: i 51 TYR cc_start: 0.9071 (t80) cc_final: 0.8833 (t80) REVERT: i 78 GLU cc_start: 0.8104 (mm-30) cc_final: 0.7709 (mm-30) REVERT: i 85 ASN cc_start: 0.8453 (t0) cc_final: 0.8142 (t0) REVERT: i 141 ASP cc_start: 0.8585 (m-30) cc_final: 0.8155 (m-30) REVERT: j 101 GLU cc_start: 0.7899 (mm-30) cc_final: 0.7666 (mm-30) REVERT: k 9 MET cc_start: 0.8650 (mtp) cc_final: 0.8430 (mtp) REVERT: k 14 GLN cc_start: 0.8800 (mm-40) cc_final: 0.8494 (mm110) REVERT: k 23 GLU cc_start: 0.8334 (tm-30) cc_final: 0.8100 (tp30) REVERT: k 88 MET cc_start: 0.8444 (ttp) cc_final: 0.8175 (ttp) REVERT: l 89 VAL cc_start: 0.8845 (p) cc_final: 0.8633 (m) REVERT: l 149 LYS cc_start: 0.7728 (OUTLIER) cc_final: 0.7493 (ptmm) REVERT: m 21 ASN cc_start: 0.8796 (m-40) cc_final: 0.8539 (m-40) REVERT: n 22 LYS cc_start: 0.8601 (mtpp) cc_final: 0.8276 (mtmm) REVERT: n 36 GLU cc_start: 0.8523 (mm-30) cc_final: 0.8302 (mm-30) REVERT: n 129 LYS cc_start: 0.6652 (pttp) cc_final: 0.6417 (pttp) REVERT: o 14 ASP cc_start: 0.7818 (t0) cc_final: 0.7215 (t70) REVERT: p 15 GLN cc_start: 0.7439 (mm-40) cc_final: 0.7213 (tp-100) REVERT: p 81 ASN cc_start: 0.8962 (p0) cc_final: 0.8706 (p0) REVERT: q 18 LYS cc_start: 0.8458 (tptm) cc_final: 0.8175 (tttm) REVERT: q 29 GLN cc_start: 0.9122 (mp10) cc_final: 0.8813 (mp10) REVERT: q 41 THR cc_start: 0.9274 (m) cc_final: 0.9025 (p) REVERT: q 56 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7736 (ttm-80) REVERT: q 62 GLU cc_start: 0.8223 (mm-30) cc_final: 0.7991 (tp30) REVERT: q 77 HIS cc_start: 0.8130 (m-70) cc_final: 0.7789 (m-70) REVERT: r 65 VAL cc_start: 0.8511 (t) cc_final: 0.8011 (t) REVERT: s 43 ASN cc_start: 0.7890 (m110) cc_final: 0.7646 (m-40) REVERT: t 20 ASN cc_start: 0.8303 (t0) cc_final: 0.7946 (t0) REVERT: u 48 GLU cc_start: 0.8245 (tt0) cc_final: 0.7681 (tt0) REVERT: u 51 ARG cc_start: 0.7655 (ttm110) cc_final: 0.7007 (ttm-80) REVERT: v 18 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7183 (tm-30) REVERT: w 24 LYS cc_start: 0.8265 (mttt) cc_final: 0.8047 (mttt) REVERT: w 38 LYS cc_start: 0.8971 (mtmt) cc_final: 0.8753 (mttt) REVERT: w 66 SER cc_start: 0.9018 (t) cc_final: 0.8778 (p) REVERT: x 70 LYS cc_start: 0.7979 (mmtm) cc_final: 0.7011 (mmtm) REVERT: y 21 ASN cc_start: 0.8959 (m110) cc_final: 0.8301 (m-40) outliers start: 189 outliers final: 103 residues processed: 1427 average time/residue: 1.3552 time to fit residues: 3349.7977 Evaluate side-chains 1321 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 1209 time to evaluate : 6.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 75 VAL Chi-restraints excluded: chain 5 residue 118 TRP Chi-restraints excluded: chain 5 residue 139 ARG Chi-restraints excluded: chain A residue 3 HIS Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain K residue 42 THR Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain N residue 72 ASP Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 62 LEU Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 72 ILE Chi-restraints excluded: chain U residue 77 THR Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain a residue 27 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain f residue 8 LYS Chi-restraints excluded: chain g residue 52 GLU Chi-restraints excluded: chain g residue 205 ASP Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 26 THR Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 63 SER Chi-restraints excluded: chain h residue 188 GLU Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain j residue 73 ASN Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 61 LEU Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 33 ASP Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 144 MET Chi-restraints excluded: chain l residue 149 LYS Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 25 ILE Chi-restraints excluded: chain o residue 28 THR Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain p residue 76 GLU Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain s residue 35 ASN Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 38 SER Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain y residue 3 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 541 optimal weight: 3.9990 chunk 302 optimal weight: 10.0000 chunk 810 optimal weight: 2.9990 chunk 663 optimal weight: 6.9990 chunk 268 optimal weight: 7.9990 chunk 976 optimal weight: 1.9990 chunk 1054 optimal weight: 3.9990 chunk 869 optimal weight: 9.9990 chunk 968 optimal weight: 3.9990 chunk 332 optimal weight: 10.0000 chunk 783 optimal weight: 10.0000 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN H 88 HIS J 138 GLN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 12 GLN i 116 GLN ** i 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 68 GLN ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 5 GLN r 105 ASN t 38 HIS t 46 HIS t 80 GLN ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 13 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8485 moved from start: 0.3076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 167985 Z= 0.263 Angle : 0.603 14.408 251649 Z= 0.325 Chirality : 0.034 0.302 32100 Planarity : 0.006 0.135 13244 Dihedral : 23.618 179.036 84764 Min Nonbonded Distance : 1.039 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.48 % Favored : 96.42 % Rotamer: Outliers : 3.75 % Allowed : 15.52 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.11), residues: 5865 helix: 1.15 (0.12), residues: 1983 sheet: -0.40 (0.15), residues: 1113 loop : -1.11 (0.11), residues: 2769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP h 201 HIS 0.008 0.001 HIS x 14 PHE 0.013 0.001 PHE k 8 TYR 0.015 0.002 TYR w 51 ARG 0.011 0.001 ARG X 74 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1444 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 1261 time to evaluate : 6.344 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: 5 53 ASP cc_start: 0.6527 (OUTLIER) cc_final: 0.6159 (p0) REVERT: 5 139 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8338 (mtm180) REVERT: A 78 LYS cc_start: 0.8299 (mmmt) cc_final: 0.7935 (mttm) REVERT: C 4 LEU cc_start: 0.9126 (OUTLIER) cc_final: 0.8923 (mp) REVERT: C 126 ASN cc_start: 0.8510 (m110) cc_final: 0.8266 (m110) REVERT: D 115 GLN cc_start: 0.8647 (mt0) cc_final: 0.8446 (mt0) REVERT: D 163 ASN cc_start: 0.9051 (t0) cc_final: 0.8649 (t0) REVERT: D 194 LYS cc_start: 0.8542 (mmmt) cc_final: 0.7872 (mttp) REVERT: E 17 MET cc_start: 0.8285 (mmm) cc_final: 0.8019 (mmm) REVERT: E 52 ASN cc_start: 0.8553 (m-40) cc_final: 0.8152 (m110) REVERT: E 128 TYR cc_start: 0.9040 (t80) cc_final: 0.8701 (t80) REVERT: E 133 ARG cc_start: 0.7875 (mpp80) cc_final: 0.7558 (mmt90) REVERT: E 170 LEU cc_start: 0.8939 (OUTLIER) cc_final: 0.8569 (mm) REVERT: F 130 GLU cc_start: 0.8031 (tt0) cc_final: 0.7564 (tt0) REVERT: F 155 GLU cc_start: 0.8200 (pm20) cc_final: 0.7998 (pm20) REVERT: G 122 LEU cc_start: 0.4631 (mt) cc_final: 0.4404 (pt) REVERT: G 129 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7481 (pt0) REVERT: H 38 MET cc_start: -0.0385 (mtm) cc_final: -0.1347 (tpp) REVERT: H 86 MET cc_start: 0.3619 (mmm) cc_final: 0.3366 (mmm) REVERT: J 14 ASP cc_start: 0.8086 (m-30) cc_final: 0.7882 (m-30) REVERT: J 61 LYS cc_start: 0.9133 (mmtp) cc_final: 0.8791 (mmtm) REVERT: J 106 LYS cc_start: 0.8952 (ttpt) cc_final: 0.8621 (ttmm) REVERT: J 108 MET cc_start: 0.8545 (mtt) cc_final: 0.8164 (mtt) REVERT: J 125 TYR cc_start: 0.8226 (m-80) cc_final: 0.7712 (m-80) REVERT: L 58 TYR cc_start: 0.8949 (p90) cc_final: 0.8669 (p90) REVERT: L 123 ARG cc_start: 0.7708 (ttp-110) cc_final: 0.7415 (ptp-170) REVERT: M 136 MET cc_start: 0.7716 (tmm) cc_final: 0.7230 (tmm) REVERT: N 72 ASP cc_start: 0.8390 (t0) cc_final: 0.7660 (t0) REVERT: N 74 GLU cc_start: 0.7877 (pm20) cc_final: 0.7142 (pm20) REVERT: N 82 GLU cc_start: 0.8598 (mp0) cc_final: 0.8248 (mp0) REVERT: Q 11 ARG cc_start: 0.8046 (ttm170) cc_final: 0.7576 (tpp-160) REVERT: Q 49 ASP cc_start: 0.7986 (m-30) cc_final: 0.7713 (m-30) REVERT: Q 102 ASP cc_start: 0.8501 (t0) cc_final: 0.8185 (t0) REVERT: R 24 LYS cc_start: 0.8924 (ttpp) cc_final: 0.8588 (ttpt) REVERT: R 43 ASN cc_start: 0.7778 (p0) cc_final: 0.7286 (p0) REVERT: S 31 GLN cc_start: 0.8222 (mt0) cc_final: 0.8013 (mt0) REVERT: U 60 GLU cc_start: 0.7996 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: U 81 ASP cc_start: 0.7708 (m-30) cc_final: 0.7400 (m-30) REVERT: X 56 MET cc_start: 0.9004 (mtm) cc_final: 0.8593 (mtm) REVERT: X 60 ASP cc_start: 0.7374 (m-30) cc_final: 0.7076 (m-30) REVERT: a 26 SER cc_start: 0.8678 (t) cc_final: 0.8338 (p) REVERT: b 12 LYS cc_start: 0.8697 (ttmt) cc_final: 0.8419 (mtpp) REVERT: d 12 ARG cc_start: 0.8371 (ttm-80) cc_final: 0.8085 (ttm170) REVERT: f 9 LYS cc_start: 0.8919 (mtpm) cc_final: 0.8611 (mtpm) REVERT: f 15 LYS cc_start: 0.8583 (mmtm) cc_final: 0.8281 (mttt) REVERT: g 136 MET cc_start: 0.7806 (ttp) cc_final: 0.7510 (mmp) REVERT: g 182 PRO cc_start: 0.9131 (Cg_exo) cc_final: 0.8863 (Cg_endo) REVERT: h 183 ASP cc_start: 0.8253 (t70) cc_final: 0.7814 (t70) REVERT: h 188 GLU cc_start: 0.7797 (OUTLIER) cc_final: 0.7516 (mt-10) REVERT: i 73 ARG cc_start: 0.8305 (ttm-80) cc_final: 0.7714 (ttm-80) REVERT: i 85 ASN cc_start: 0.8472 (t0) cc_final: 0.8233 (t0) REVERT: i 141 ASP cc_start: 0.8548 (m-30) cc_final: 0.8053 (m-30) REVERT: j 101 GLU cc_start: 0.8068 (mm-30) cc_final: 0.7808 (mm-30) REVERT: k 14 GLN cc_start: 0.8809 (mm-40) cc_final: 0.8487 (mm110) REVERT: k 23 GLU cc_start: 0.8367 (tm-30) cc_final: 0.8148 (tp30) REVERT: k 65 GLU cc_start: 0.7936 (tp30) cc_final: 0.7527 (tp30) REVERT: l 57 SER cc_start: 0.7792 (p) cc_final: 0.5909 (t) REVERT: l 89 VAL cc_start: 0.8872 (p) cc_final: 0.8538 (m) REVERT: l 149 LYS cc_start: 0.7725 (OUTLIER) cc_final: 0.7475 (ptmm) REVERT: m 90 ASP cc_start: 0.8268 (p0) cc_final: 0.7948 (p0) REVERT: n 22 LYS cc_start: 0.8647 (mtpp) cc_final: 0.8370 (mtmm) REVERT: n 106 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.4825 (tpt90) REVERT: n 129 LYS cc_start: 0.6653 (pttp) cc_final: 0.6450 (pttp) REVERT: o 48 ARG cc_start: 0.8597 (mtt180) cc_final: 0.8062 (mtt-85) REVERT: o 68 ARG cc_start: 0.7772 (mtt180) cc_final: 0.7531 (mtt90) REVERT: o 72 ARG cc_start: 0.8665 (mmt-90) cc_final: 0.8176 (mmt180) REVERT: p 18 ASP cc_start: 0.7911 (OUTLIER) cc_final: 0.7221 (p0) REVERT: p 56 ARG cc_start: 0.7443 (mmm-85) cc_final: 0.7234 (mtp-110) REVERT: p 81 ASN cc_start: 0.8542 (OUTLIER) cc_final: 0.8273 (p0) REVERT: q 18 LYS cc_start: 0.8493 (tptm) cc_final: 0.8214 (tttm) REVERT: q 29 GLN cc_start: 0.9102 (mp10) cc_final: 0.8799 (mp10) REVERT: q 41 THR cc_start: 0.9299 (m) cc_final: 0.9038 (p) REVERT: q 56 ARG cc_start: 0.7910 (ttm-80) cc_final: 0.7530 (ttm-80) REVERT: q 76 GLU cc_start: 0.7699 (tm-30) cc_final: 0.7104 (tm-30) REVERT: q 77 HIS cc_start: 0.8246 (m-70) cc_final: 0.7968 (m-70) REVERT: s 43 ASN cc_start: 0.7922 (m110) cc_final: 0.7658 (m-40) REVERT: t 20 ASN cc_start: 0.8483 (t0) cc_final: 0.8156 (t0) REVERT: t 68 ASP cc_start: 0.8008 (m-30) cc_final: 0.7636 (m-30) REVERT: u 31 ARG cc_start: 0.8493 (ttt180) cc_final: 0.8278 (ttt-90) REVERT: u 48 GLU cc_start: 0.8097 (tt0) cc_final: 0.7504 (tt0) REVERT: u 51 ARG cc_start: 0.7571 (ttm110) cc_final: 0.7169 (ttm-80) REVERT: u 77 GLU cc_start: 0.8128 (mt-10) cc_final: 0.7877 (tt0) REVERT: v 17 MET cc_start: 0.8445 (mmm) cc_final: 0.8218 (mmm) REVERT: v 18 GLU cc_start: 0.7533 (tm-30) cc_final: 0.7218 (tm-30) REVERT: w 38 LYS cc_start: 0.8940 (mtmt) cc_final: 0.8716 (mtmt) REVERT: w 66 SER cc_start: 0.9026 (t) cc_final: 0.8799 (p) REVERT: x 70 LYS cc_start: 0.8314 (mmtm) cc_final: 0.7989 (mmtm) REVERT: y 4 ILE cc_start: 0.8519 (mm) cc_final: 0.8120 (mt) REVERT: y 21 ASN cc_start: 0.9028 (m110) cc_final: 0.8324 (m-40) outliers start: 183 outliers final: 126 residues processed: 1361 average time/residue: 1.3503 time to fit residues: 3173.8873 Evaluate side-chains 1337 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 136 poor density : 1201 time to evaluate : 6.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 53 ASP Chi-restraints excluded: chain 5 residue 139 ARG Chi-restraints excluded: chain 5 residue 141 ASP Chi-restraints excluded: chain A residue 3 HIS Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 53 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 60 GLU Chi-restraints excluded: chain K residue 14 SER Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 72 ILE Chi-restraints excluded: chain U residue 77 THR Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain Z residue 54 MET Chi-restraints excluded: chain a residue 27 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 120 GLN Chi-restraints excluded: chain g residue 159 ASP Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 205 ASP Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 26 THR Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 93 ASP Chi-restraints excluded: chain h residue 188 GLU Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain i residue 190 ASP Chi-restraints excluded: chain j residue 73 ASN Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 62 MET Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 33 ASP Chi-restraints excluded: chain l residue 45 SER Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 75 VAL Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain l residue 144 MET Chi-restraints excluded: chain l residue 149 LYS Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 43 THR Chi-restraints excluded: chain n residue 106 ARG Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 28 THR Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 78 GLU Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain p residue 81 ASN Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 65 SER Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain r residue 69 LEU Chi-restraints excluded: chain s residue 32 SER Chi-restraints excluded: chain s residue 35 ASN Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 47 LYS Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 72 SER Chi-restraints excluded: chain w residue 36 SER Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 38 SER Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain z residue 20 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 964 optimal weight: 8.9990 chunk 733 optimal weight: 9.9990 chunk 506 optimal weight: 20.0000 chunk 108 optimal weight: 40.0000 chunk 465 optimal weight: 50.0000 chunk 655 optimal weight: 2.9990 chunk 979 optimal weight: 2.9990 chunk 1037 optimal weight: 10.0000 chunk 511 optimal weight: 10.0000 chunk 928 optimal weight: 0.0170 chunk 279 optimal weight: 20.0000 overall best weight: 5.0026 ------------------------------------------------------------------------------- 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 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN J 128 ASN K 5 GLN N 11 ASN ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 48 GLN V 12 GLN Y 45 GLN c 45 GLN g 42 ASN i 131 ASN j 73 ASN ** j 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 68 GLN l 130 ASN ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 5 GLN n 81 HIS s 49 GLN v 9 GLN ** y 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 82 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.3781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.091 167985 Z= 0.378 Angle : 0.677 13.978 251649 Z= 0.362 Chirality : 0.038 0.342 32100 Planarity : 0.007 0.138 13244 Dihedral : 23.666 179.817 84764 Min Nonbonded Distance : 0.993 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.16 % Favored : 95.74 % Rotamer: Outliers : 4.52 % Allowed : 16.36 % Favored : 79.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.11), residues: 5865 helix: 1.00 (0.12), residues: 1988 sheet: -0.41 (0.16), residues: 1123 loop : -1.13 (0.11), residues: 2754 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP 5 147 HIS 0.008 0.001 HIS x 14 PHE 0.017 0.002 PHE W 1 TYR 0.018 0.002 TYR S 38 ARG 0.010 0.001 ARG F 153 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1498 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 221 poor density : 1277 time to evaluate : 6.315 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: 5 28 GLU cc_start: 0.8332 (mt-10) cc_final: 0.8112 (mt-10) REVERT: 5 40 GLU cc_start: 0.8834 (mm-30) cc_final: 0.8408 (mm-30) REVERT: 5 118 TRP cc_start: 0.5791 (OUTLIER) cc_final: 0.3947 (m-90) REVERT: 5 139 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8351 (mtm180) REVERT: A 5 LYS cc_start: 0.7279 (tmtt) cc_final: 0.6825 (tptp) REVERT: A 78 LYS cc_start: 0.8346 (mmmt) cc_final: 0.7940 (mttm) REVERT: C 4 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8728 (mp) REVERT: D 6 LYS cc_start: 0.8607 (tttm) cc_final: 0.8389 (tttt) REVERT: D 115 GLN cc_start: 0.8694 (mt0) cc_final: 0.8468 (mt0) REVERT: D 163 ASN cc_start: 0.9186 (t0) cc_final: 0.8752 (t0) REVERT: D 194 LYS cc_start: 0.8528 (mmmt) cc_final: 0.7978 (mttp) REVERT: E 52 ASN cc_start: 0.8631 (m-40) cc_final: 0.8203 (m110) REVERT: E 128 TYR cc_start: 0.8978 (t80) cc_final: 0.8613 (t80) REVERT: E 133 ARG cc_start: 0.7953 (mpp80) cc_final: 0.7689 (mmt90) REVERT: E 170 LEU cc_start: 0.8981 (OUTLIER) cc_final: 0.8659 (mm) REVERT: F 130 GLU cc_start: 0.8099 (tt0) cc_final: 0.7624 (tt0) REVERT: F 153 ARG cc_start: 0.8201 (ttm110) cc_final: 0.7831 (mtp-110) REVERT: F 155 GLU cc_start: 0.8088 (pm20) cc_final: 0.7848 (pm20) REVERT: G 129 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7630 (pt0) REVERT: H 38 MET cc_start: -0.0064 (mtm) cc_final: -0.1117 (tpp) REVERT: H 86 MET cc_start: 0.3757 (mmm) cc_final: 0.2798 (mmm) REVERT: J 106 LYS cc_start: 0.8989 (ttpt) cc_final: 0.8641 (ttmm) REVERT: K 17 ARG cc_start: 0.7658 (mtm180) cc_final: 0.7432 (mmm-85) REVERT: L 99 ASN cc_start: 0.8809 (p0) cc_final: 0.8357 (t0) REVERT: L 123 ARG cc_start: 0.7775 (ttp-110) cc_final: 0.7328 (ptp-170) REVERT: L 141 LYS cc_start: 0.7903 (ttpt) cc_final: 0.7649 (ttpp) REVERT: M 136 MET cc_start: 0.7725 (tmm) cc_final: 0.7148 (tmm) REVERT: N 13 ASN cc_start: 0.8588 (OUTLIER) cc_final: 0.8384 (p0) REVERT: N 14 SER cc_start: 0.9048 (m) cc_final: 0.8808 (t) REVERT: N 72 ASP cc_start: 0.8380 (t0) cc_final: 0.7411 (t0) REVERT: N 74 GLU cc_start: 0.8044 (pm20) cc_final: 0.7268 (pm20) REVERT: N 82 GLU cc_start: 0.8514 (mp0) cc_final: 0.7878 (mp0) REVERT: Q 11 ARG cc_start: 0.8162 (ttm170) cc_final: 0.7659 (tpp-160) REVERT: Q 49 ASP cc_start: 0.7918 (m-30) cc_final: 0.7557 (m-30) REVERT: R 24 LYS cc_start: 0.8845 (ttpp) cc_final: 0.8294 (ttpt) REVERT: S 38 TYR cc_start: 0.8935 (m-80) cc_final: 0.8688 (m-80) REVERT: T 42 GLU cc_start: 0.8143 (OUTLIER) cc_final: 0.7904 (mt-10) REVERT: U 60 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7550 (mp0) REVERT: U 81 ASP cc_start: 0.7786 (m-30) cc_final: 0.7527 (m-30) REVERT: X 56 MET cc_start: 0.9103 (mtm) cc_final: 0.8619 (mtm) REVERT: X 60 ASP cc_start: 0.7374 (m-30) cc_final: 0.7117 (m-30) REVERT: X 76 GLU cc_start: 0.7546 (mp0) cc_final: 0.7199 (mp0) REVERT: a 1 MET cc_start: 0.8238 (mtm) cc_final: 0.7951 (mmm) REVERT: a 59 ARG cc_start: 0.8546 (ptm-80) cc_final: 0.8097 (ptm-80) REVERT: b 12 LYS cc_start: 0.8688 (ttmt) cc_final: 0.8284 (mtpp) REVERT: d 12 ARG cc_start: 0.8494 (ttm-80) cc_final: 0.8089 (ttm170) REVERT: f 9 LYS cc_start: 0.8933 (mtpm) cc_final: 0.8652 (mtpm) REVERT: f 15 LYS cc_start: 0.8646 (mmtm) cc_final: 0.8325 (mttt) REVERT: g 136 MET cc_start: 0.7917 (ttp) cc_final: 0.7551 (mmp) REVERT: g 182 PRO cc_start: 0.9109 (Cg_exo) cc_final: 0.8840 (Cg_endo) REVERT: h 183 ASP cc_start: 0.8296 (t70) cc_final: 0.7890 (t70) REVERT: h 188 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7601 (mt-10) REVERT: i 44 ARG cc_start: 0.8466 (ptp90) cc_final: 0.8155 (ptp90) REVERT: i 85 ASN cc_start: 0.8655 (t0) cc_final: 0.8435 (t0) REVERT: i 141 ASP cc_start: 0.8579 (m-30) cc_final: 0.8099 (m-30) REVERT: i 177 LYS cc_start: 0.8298 (mtpp) cc_final: 0.8008 (mtpp) REVERT: k 9 MET cc_start: 0.8321 (mtp) cc_final: 0.8066 (mtp) REVERT: k 14 GLN cc_start: 0.8883 (mm-40) cc_final: 0.8394 (mm110) REVERT: k 24 ARG cc_start: 0.8923 (mtm-85) cc_final: 0.8653 (mtt90) REVERT: k 65 GLU cc_start: 0.7898 (tp30) cc_final: 0.7547 (tp30) REVERT: l 5 ARG cc_start: 0.7854 (tmm-80) cc_final: 0.7478 (ptt90) REVERT: l 89 VAL cc_start: 0.8836 (p) cc_final: 0.8474 (m) REVERT: l 149 LYS cc_start: 0.7748 (OUTLIER) cc_final: 0.7465 (ptmm) REVERT: m 90 ASP cc_start: 0.8463 (p0) cc_final: 0.8162 (p0) REVERT: n 22 LYS cc_start: 0.8566 (mtpp) cc_final: 0.8266 (mtmm) REVERT: n 38 TYR cc_start: 0.9203 (t80) cc_final: 0.8758 (t80) REVERT: n 129 LYS cc_start: 0.6821 (pttp) cc_final: 0.6573 (pttp) REVERT: o 14 ASP cc_start: 0.7927 (t0) cc_final: 0.7490 (t0) REVERT: o 16 ARG cc_start: 0.7776 (ptp-110) cc_final: 0.7568 (ptp-110) REVERT: o 31 ARG cc_start: 0.8066 (ttp80) cc_final: 0.7841 (ttp80) REVERT: o 48 ARG cc_start: 0.8643 (mtt180) cc_final: 0.8134 (mtt-85) REVERT: o 72 ARG cc_start: 0.8862 (mmt-90) cc_final: 0.8402 (mmt180) REVERT: p 18 ASP cc_start: 0.7962 (OUTLIER) cc_final: 0.7185 (p0) REVERT: p 94 GLU cc_start: 0.7749 (tm-30) cc_final: 0.7223 (tm-30) REVERT: p 98 ARG cc_start: 0.8569 (mmm-85) cc_final: 0.8247 (tpp80) REVERT: q 18 LYS cc_start: 0.8526 (tptm) cc_final: 0.8265 (tttm) REVERT: q 29 GLN cc_start: 0.9043 (mp10) cc_final: 0.8714 (mp10) REVERT: q 41 THR cc_start: 0.9332 (m) cc_final: 0.9106 (p) REVERT: q 56 ARG cc_start: 0.8053 (ttm-80) cc_final: 0.7496 (ttm-80) REVERT: q 59 ASN cc_start: 0.9029 (p0) cc_final: 0.8813 (p0) REVERT: q 62 GLU cc_start: 0.8189 (mm-30) cc_final: 0.7570 (mm-30) REVERT: q 103 ASP cc_start: 0.8415 (m-30) cc_final: 0.7984 (m-30) REVERT: r 74 SER cc_start: 0.8538 (m) cc_final: 0.8309 (p) REVERT: s 39 GLU cc_start: 0.8069 (tm-30) cc_final: 0.7809 (tm-30) REVERT: s 43 ASN cc_start: 0.8035 (m110) cc_final: 0.7667 (m-40) REVERT: t 68 ASP cc_start: 0.8100 (m-30) cc_final: 0.7742 (m-30) REVERT: u 48 GLU cc_start: 0.8136 (tt0) cc_final: 0.7754 (tt0) REVERT: v 18 GLU cc_start: 0.7704 (tm-30) cc_final: 0.7230 (tm-30) REVERT: w 38 LYS cc_start: 0.8973 (mtmt) cc_final: 0.8738 (mtmt) REVERT: x 65 GLU cc_start: 0.8511 (mm-30) cc_final: 0.8163 (mm-30) REVERT: x 70 LYS cc_start: 0.8496 (mmtm) cc_final: 0.7823 (mmtm) REVERT: y 21 ASN cc_start: 0.8997 (m110) cc_final: 0.8251 (m-40) outliers start: 221 outliers final: 161 residues processed: 1396 average time/residue: 1.3237 time to fit residues: 3208.0097 Evaluate side-chains 1385 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1214 time to evaluate : 6.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 64 PHE Chi-restraints excluded: chain 5 residue 75 VAL Chi-restraints excluded: chain 5 residue 118 TRP Chi-restraints excluded: chain 5 residue 139 ARG Chi-restraints excluded: chain 5 residue 141 ASP Chi-restraints excluded: chain A residue 3 HIS Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 38 VAL Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 38 ASN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 13 ASN Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 72 ILE Chi-restraints excluded: chain U residue 77 THR Chi-restraints excluded: chain V residue 5 ASN Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain Z residue 54 MET Chi-restraints excluded: chain a residue 27 THR Chi-restraints excluded: chain b residue 25 VAL Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain f residue 8 LYS Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 159 ASP Chi-restraints excluded: chain g residue 187 VAL Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 205 ASP Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 26 THR Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 63 SER Chi-restraints excluded: chain h residue 93 ASP Chi-restraints excluded: chain h residue 188 GLU Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 73 ASN Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain j residue 147 MET Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 62 MET Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 33 ASP Chi-restraints excluded: chain l residue 45 SER Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 75 VAL Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain l residue 149 LYS Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 43 THR Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 32 THR Chi-restraints excluded: chain o residue 78 GLU Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 58 THR Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain r residue 34 LEU Chi-restraints excluded: chain r residue 65 VAL Chi-restraints excluded: chain r residue 69 LEU Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain s residue 35 ASN Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain t residue 13 SER Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain u residue 55 ASP Chi-restraints excluded: chain v residue 9 GLN Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 28 PHE Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 59 VAL Chi-restraints excluded: chain v residue 61 ILE Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 72 SER Chi-restraints excluded: chain w residue 36 SER Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 38 SER Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 63 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 863 optimal weight: 1.9990 chunk 588 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 772 optimal weight: 5.9990 chunk 427 optimal weight: 10.0000 chunk 885 optimal weight: 6.9990 chunk 716 optimal weight: 5.9990 chunk 1 optimal weight: 8.9990 chunk 529 optimal weight: 3.9990 chunk 930 optimal weight: 1.9990 chunk 261 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN J 128 ASN ** S 9 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 12 GLN g 146 ASN i 131 ASN j 73 ASN k 68 GLN ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 5 GLN s 49 GLN ** t 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 3 ASN y 13 GLN y 82 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 167985 Z= 0.276 Angle : 0.615 14.185 251649 Z= 0.334 Chirality : 0.035 0.312 32100 Planarity : 0.006 0.132 13244 Dihedral : 23.631 179.686 84764 Min Nonbonded Distance : 1.011 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.72 % Favored : 96.18 % Rotamer: Outliers : 4.50 % Allowed : 17.65 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.11), residues: 5865 helix: 1.18 (0.12), residues: 1986 sheet: -0.38 (0.16), residues: 1129 loop : -1.06 (0.11), residues: 2750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP h 201 HIS 0.006 0.001 HIS x 14 PHE 0.015 0.001 PHE k 8 TYR 0.015 0.002 TYR S 38 ARG 0.012 0.001 ARG j 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1497 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 220 poor density : 1277 time to evaluate : 6.485 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: 5 23 GLU cc_start: 0.7220 (tm-30) cc_final: 0.7001 (tm-30) REVERT: 5 25 PHE cc_start: 0.6933 (t80) cc_final: 0.6309 (t80) REVERT: 5 28 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8092 (mt-10) REVERT: 5 40 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8597 (mm-30) REVERT: 5 53 ASP cc_start: 0.6462 (OUTLIER) cc_final: 0.6012 (p0) REVERT: 5 70 ILE cc_start: 0.6997 (pp) cc_final: 0.6704 (pp) REVERT: 5 101 TYR cc_start: 0.6973 (m-80) cc_final: 0.6307 (m-80) REVERT: 5 118 TRP cc_start: 0.5985 (OUTLIER) cc_final: 0.4282 (m-90) REVERT: 5 139 ARG cc_start: 0.8723 (OUTLIER) cc_final: 0.8492 (mtp180) REVERT: A 78 LYS cc_start: 0.8357 (mmmt) cc_final: 0.7930 (mttm) REVERT: C 4 LEU cc_start: 0.9088 (OUTLIER) cc_final: 0.8695 (mp) REVERT: D 6 LYS cc_start: 0.8531 (tttm) cc_final: 0.8306 (tttt) REVERT: D 163 ASN cc_start: 0.9085 (t0) cc_final: 0.8693 (t0) REVERT: D 194 LYS cc_start: 0.8514 (mmmt) cc_final: 0.7984 (mttp) REVERT: E 52 ASN cc_start: 0.8614 (m-40) cc_final: 0.8197 (m110) REVERT: E 133 ARG cc_start: 0.7954 (mpp80) cc_final: 0.7742 (mmt90) REVERT: E 170 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8674 (mm) REVERT: E 178 ARG cc_start: 0.7790 (mtt90) cc_final: 0.7572 (mtt90) REVERT: F 130 GLU cc_start: 0.8042 (tt0) cc_final: 0.7596 (tt0) REVERT: F 153 ARG cc_start: 0.8233 (ttm110) cc_final: 0.7933 (mtp-110) REVERT: F 155 GLU cc_start: 0.7980 (pm20) cc_final: 0.7732 (pm20) REVERT: G 129 GLU cc_start: 0.8199 (mt-10) cc_final: 0.7732 (pt0) REVERT: H 81 LEU cc_start: 0.2099 (OUTLIER) cc_final: 0.1616 (tt) REVERT: J 96 ARG cc_start: 0.7965 (mmm160) cc_final: 0.7481 (mtp85) REVERT: J 106 LYS cc_start: 0.8958 (ttpt) cc_final: 0.8598 (ttmm) REVERT: J 108 MET cc_start: 0.8588 (mtt) cc_final: 0.8193 (mtt) REVERT: J 125 TYR cc_start: 0.8156 (m-80) cc_final: 0.7809 (m-80) REVERT: K 17 ARG cc_start: 0.7641 (mtm180) cc_final: 0.7398 (mmt90) REVERT: K 89 ASN cc_start: 0.8799 (m-40) cc_final: 0.8589 (m-40) REVERT: L 99 ASN cc_start: 0.8784 (p0) cc_final: 0.8297 (t0) REVERT: L 123 ARG cc_start: 0.7766 (ttp-110) cc_final: 0.7400 (ptp-170) REVERT: L 141 LYS cc_start: 0.7908 (ttpt) cc_final: 0.7636 (ttpp) REVERT: M 104 GLU cc_start: 0.8417 (mt-10) cc_final: 0.8077 (mt-10) REVERT: M 136 MET cc_start: 0.7777 (tmm) cc_final: 0.7256 (tmm) REVERT: N 14 SER cc_start: 0.9027 (OUTLIER) cc_final: 0.8784 (t) REVERT: N 72 ASP cc_start: 0.8356 (t0) cc_final: 0.7600 (t0) REVERT: N 74 GLU cc_start: 0.7958 (pm20) cc_final: 0.7190 (pm20) REVERT: N 82 GLU cc_start: 0.8606 (mp0) cc_final: 0.7949 (mp0) REVERT: P 27 GLU cc_start: 0.8479 (OUTLIER) cc_final: 0.7714 (tt0) REVERT: P 44 GLU cc_start: 0.8095 (tp30) cc_final: 0.7724 (tp30) REVERT: Q 11 ARG cc_start: 0.8073 (ttm170) cc_final: 0.7621 (tpp-160) REVERT: Q 49 ASP cc_start: 0.7890 (m-30) cc_final: 0.7606 (m-30) REVERT: R 24 LYS cc_start: 0.8834 (ttpp) cc_final: 0.8210 (ttpt) REVERT: S 85 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8799 (mt) REVERT: U 60 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7553 (mp0) REVERT: U 81 ASP cc_start: 0.7748 (m-30) cc_final: 0.7516 (m-30) REVERT: X 56 MET cc_start: 0.9135 (mtm) cc_final: 0.8659 (mtm) REVERT: X 60 ASP cc_start: 0.7362 (m-30) cc_final: 0.7085 (m-30) REVERT: Y 44 LYS cc_start: 0.8694 (tttp) cc_final: 0.8141 (tttt) REVERT: a 1 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7923 (mmm) REVERT: a 56 ARG cc_start: 0.7428 (mmm160) cc_final: 0.7135 (mmm160) REVERT: a 59 ARG cc_start: 0.8513 (ptm-80) cc_final: 0.8203 (ptm-80) REVERT: b 12 LYS cc_start: 0.8658 (ttmt) cc_final: 0.8262 (mtpp) REVERT: d 12 ARG cc_start: 0.8480 (ttm-80) cc_final: 0.8267 (ttm170) REVERT: f 9 LYS cc_start: 0.8907 (OUTLIER) cc_final: 0.8642 (mtpm) REVERT: f 15 LYS cc_start: 0.8570 (mmtm) cc_final: 0.8289 (mttt) REVERT: g 136 MET cc_start: 0.7939 (ttp) cc_final: 0.7572 (mmp) REVERT: g 146 ASN cc_start: 0.8029 (t0) cc_final: 0.7770 (t0) REVERT: g 182 PRO cc_start: 0.9146 (Cg_exo) cc_final: 0.8897 (Cg_endo) REVERT: h 183 ASP cc_start: 0.8292 (t70) cc_final: 0.7909 (t70) REVERT: h 188 GLU cc_start: 0.7833 (OUTLIER) cc_final: 0.7575 (mt-10) REVERT: i 85 ASN cc_start: 0.8631 (t0) cc_final: 0.8405 (t0) REVERT: i 136 GLN cc_start: 0.9049 (mm-40) cc_final: 0.8792 (mm110) REVERT: i 141 ASP cc_start: 0.8571 (m-30) cc_final: 0.8111 (m-30) REVERT: k 14 GLN cc_start: 0.8855 (mm-40) cc_final: 0.8457 (mm-40) REVERT: k 65 GLU cc_start: 0.7804 (tp30) cc_final: 0.7490 (tp30) REVERT: l 5 ARG cc_start: 0.7887 (tmm-80) cc_final: 0.7502 (ptt90) REVERT: l 89 VAL cc_start: 0.8857 (p) cc_final: 0.8428 (m) REVERT: l 149 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7449 (ptmm) REVERT: m 90 ASP cc_start: 0.8496 (p0) cc_final: 0.8174 (p0) REVERT: n 22 LYS cc_start: 0.8557 (mtpp) cc_final: 0.8298 (mtmm) REVERT: n 106 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.5764 (ttt90) REVERT: n 129 LYS cc_start: 0.6655 (pttp) cc_final: 0.6425 (pttp) REVERT: o 14 ASP cc_start: 0.7891 (t0) cc_final: 0.7500 (t0) REVERT: p 94 GLU cc_start: 0.7719 (tm-30) cc_final: 0.7171 (tm-30) REVERT: p 98 ARG cc_start: 0.8549 (mmm-85) cc_final: 0.8261 (tpp80) REVERT: q 18 LYS cc_start: 0.8466 (tptm) cc_final: 0.8194 (tttm) REVERT: q 29 GLN cc_start: 0.9002 (mp10) cc_final: 0.8742 (mp10) REVERT: q 41 THR cc_start: 0.9359 (m) cc_final: 0.9124 (p) REVERT: q 56 ARG cc_start: 0.7993 (ttm-80) cc_final: 0.7416 (ttm-80) REVERT: q 62 GLU cc_start: 0.8198 (mm-30) cc_final: 0.7573 (mm-30) REVERT: q 77 HIS cc_start: 0.8294 (m-70) cc_final: 0.8070 (m-70) REVERT: q 103 ASP cc_start: 0.8423 (m-30) cc_final: 0.8101 (m-30) REVERT: r 74 SER cc_start: 0.8603 (m) cc_final: 0.8395 (p) REVERT: r 104 THR cc_start: 0.8517 (OUTLIER) cc_final: 0.8193 (p) REVERT: s 39 GLU cc_start: 0.8083 (tm-30) cc_final: 0.7730 (tm-30) REVERT: s 43 ASN cc_start: 0.8014 (m110) cc_final: 0.7558 (m-40) REVERT: t 68 ASP cc_start: 0.8089 (m-30) cc_final: 0.7728 (m-30) REVERT: u 48 GLU cc_start: 0.8054 (tt0) cc_final: 0.7837 (tt0) REVERT: v 17 MET cc_start: 0.8362 (mmm) cc_final: 0.8076 (mmm) REVERT: v 18 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7414 (tm-30) REVERT: v 80 GLU cc_start: 0.7999 (mp0) cc_final: 0.7640 (tm-30) REVERT: v 83 VAL cc_start: 0.7267 (m) cc_final: 0.6909 (t) REVERT: x 65 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8084 (mm-30) REVERT: x 70 LYS cc_start: 0.8372 (mmtm) cc_final: 0.7693 (mmtm) REVERT: y 21 ASN cc_start: 0.9032 (m110) cc_final: 0.8265 (m-40) outliers start: 220 outliers final: 164 residues processed: 1392 average time/residue: 1.3295 time to fit residues: 3217.0528 Evaluate side-chains 1416 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1236 time to evaluate : 6.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 53 ASP Chi-restraints excluded: chain 5 residue 56 VAL Chi-restraints excluded: chain 5 residue 64 PHE Chi-restraints excluded: chain 5 residue 112 VAL Chi-restraints excluded: chain 5 residue 118 TRP Chi-restraints excluded: chain 5 residue 139 ARG Chi-restraints excluded: chain 5 residue 141 ASP Chi-restraints excluded: chain A residue 3 HIS Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain J residue 100 VAL Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain N residue 14 SER Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 85 ILE Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 77 THR Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Y residue 58 ASN Chi-restraints excluded: chain Z residue 12 SER Chi-restraints excluded: chain Z residue 54 MET Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 27 THR Chi-restraints excluded: chain a residue 35 ASP Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain f residue 9 LYS Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 205 ASP Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 93 ASP Chi-restraints excluded: chain h residue 188 GLU Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain i residue 190 ASP Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain j residue 147 MET Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 62 MET Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 33 ASP Chi-restraints excluded: chain l residue 45 SER Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 75 VAL Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain l residue 149 LYS Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 43 THR Chi-restraints excluded: chain n residue 52 LEU Chi-restraints excluded: chain n residue 106 ARG Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 28 THR Chi-restraints excluded: chain o residue 77 VAL Chi-restraints excluded: chain o residue 78 GLU Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 92 LEU Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain r residue 30 SER Chi-restraints excluded: chain r residue 34 LEU Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 5 SER Chi-restraints excluded: chain s residue 35 ASN Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 47 LYS Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain u residue 55 ASP Chi-restraints excluded: chain v residue 28 PHE Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 61 ILE Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 72 SER Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 38 SER Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 3 ASN Chi-restraints excluded: chain y residue 39 ILE Chi-restraints excluded: chain z residue 20 LYS Chi-restraints excluded: chain z residue 22 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 348 optimal weight: 10.0000 chunk 934 optimal weight: 6.9990 chunk 205 optimal weight: 7.9990 chunk 608 optimal weight: 8.9990 chunk 256 optimal weight: 8.9990 chunk 1038 optimal weight: 5.9990 chunk 861 optimal weight: 5.9990 chunk 480 optimal weight: 50.0000 chunk 86 optimal weight: 8.9990 chunk 343 optimal weight: 10.0000 chunk 545 optimal weight: 2.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 200 HIS ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN G 20 ASN J 128 ASN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 9 HIS V 12 GLN Y 45 GLN a 20 ASN g 146 ASN i 131 ASN i 140 ASN k 63 ASN k 68 GLN ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 5 GLN n 75 GLN p 22 HIS ** t 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 9 GLN y 13 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.4161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.100 167985 Z= 0.445 Angle : 0.710 13.780 251649 Z= 0.377 Chirality : 0.040 0.347 32100 Planarity : 0.007 0.143 13244 Dihedral : 23.678 179.429 84764 Min Nonbonded Distance : 0.972 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.38 % Favored : 95.53 % Rotamer: Outliers : 5.45 % Allowed : 17.69 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.11), residues: 5865 helix: 0.95 (0.12), residues: 1998 sheet: -0.43 (0.16), residues: 1127 loop : -1.18 (0.11), residues: 2740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP 5 122 HIS 0.006 0.001 HIS x 83 PHE 0.017 0.002 PHE k 8 TYR 0.021 0.002 TYR S 38 ARG 0.011 0.001 ARG p 69 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1508 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1242 time to evaluate : 6.543 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: 5 23 GLU cc_start: 0.7415 (tm-30) cc_final: 0.7123 (tm-30) REVERT: 5 25 PHE cc_start: 0.7185 (t80) cc_final: 0.6742 (t80) REVERT: 5 53 ASP cc_start: 0.6435 (OUTLIER) cc_final: 0.5841 (p0) REVERT: 5 101 TYR cc_start: 0.6875 (m-80) cc_final: 0.6432 (m-80) REVERT: 5 139 ARG cc_start: 0.8653 (OUTLIER) cc_final: 0.8348 (mtp180) REVERT: A 56 ASP cc_start: 0.8018 (t0) cc_final: 0.7796 (t0) REVERT: A 78 LYS cc_start: 0.8367 (mmmt) cc_final: 0.7964 (mttm) REVERT: C 4 LEU cc_start: 0.9123 (OUTLIER) cc_final: 0.8693 (mp) REVERT: D 80 SER cc_start: 0.8908 (OUTLIER) cc_final: 0.8707 (t) REVERT: D 163 ASN cc_start: 0.9226 (t0) cc_final: 0.8780 (t0) REVERT: D 194 LYS cc_start: 0.8562 (mmmt) cc_final: 0.8029 (mttp) REVERT: E 32 GLU cc_start: 0.7448 (mp0) cc_final: 0.6685 (mp0) REVERT: E 133 ARG cc_start: 0.8092 (mpp80) cc_final: 0.7880 (mpt-90) REVERT: E 170 LEU cc_start: 0.9004 (OUTLIER) cc_final: 0.8680 (mm) REVERT: F 130 GLU cc_start: 0.8052 (tt0) cc_final: 0.7611 (tt0) REVERT: F 155 GLU cc_start: 0.7901 (pm20) cc_final: 0.7616 (pm20) REVERT: G 129 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7765 (pt0) REVERT: H 38 MET cc_start: -0.0329 (ptm) cc_final: -0.0747 (tpp) REVERT: H 81 LEU cc_start: 0.2362 (OUTLIER) cc_final: 0.1831 (tt) REVERT: J 96 ARG cc_start: 0.8054 (mmm160) cc_final: 0.7560 (mtp85) REVERT: J 106 LYS cc_start: 0.9060 (ttpt) cc_final: 0.8691 (ttmm) REVERT: J 125 TYR cc_start: 0.8238 (m-80) cc_final: 0.7932 (m-80) REVERT: K 17 ARG cc_start: 0.7643 (mtm180) cc_final: 0.7423 (mmt90) REVERT: L 99 ASN cc_start: 0.8744 (p0) cc_final: 0.8311 (t0) REVERT: L 123 ARG cc_start: 0.7813 (ttp-110) cc_final: 0.7382 (ptp-170) REVERT: M 104 GLU cc_start: 0.8430 (mt-10) cc_final: 0.8028 (mt-10) REVERT: M 136 MET cc_start: 0.7783 (tmm) cc_final: 0.7185 (tmm) REVERT: N 72 ASP cc_start: 0.8380 (t0) cc_final: 0.7663 (t0) REVERT: N 74 GLU cc_start: 0.7904 (pm20) cc_final: 0.7550 (pm20) REVERT: N 82 GLU cc_start: 0.8583 (mp0) cc_final: 0.7921 (mp0) REVERT: O 83 LEU cc_start: 0.9060 (OUTLIER) cc_final: 0.8735 (mm) REVERT: P 27 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: P 44 GLU cc_start: 0.8156 (tp30) cc_final: 0.7752 (tp30) REVERT: Q 11 ARG cc_start: 0.8168 (ttm170) cc_final: 0.7658 (tpp-160) REVERT: Q 49 ASP cc_start: 0.7995 (m-30) cc_final: 0.7646 (m-30) REVERT: R 24 LYS cc_start: 0.8857 (ttpp) cc_final: 0.8289 (ttpt) REVERT: R 26 ASP cc_start: 0.7960 (p0) cc_final: 0.7675 (p0) REVERT: S 38 TYR cc_start: 0.8962 (m-80) cc_final: 0.8675 (m-80) REVERT: T 42 GLU cc_start: 0.8085 (OUTLIER) cc_final: 0.7858 (mt-10) REVERT: U 60 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7635 (mp0) REVERT: X 56 MET cc_start: 0.9191 (mtm) cc_final: 0.8712 (mtm) REVERT: X 60 ASP cc_start: 0.7404 (m-30) cc_final: 0.7115 (m-30) REVERT: Y 44 LYS cc_start: 0.8769 (tttp) cc_final: 0.8274 (tttt) REVERT: a 1 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7943 (mmm) REVERT: a 56 ARG cc_start: 0.7491 (mmm160) cc_final: 0.7173 (mmm160) REVERT: a 59 ARG cc_start: 0.8549 (ptm-80) cc_final: 0.8256 (ptm-80) REVERT: b 12 LYS cc_start: 0.8685 (ttmt) cc_final: 0.8269 (mtpp) REVERT: f 9 LYS cc_start: 0.8910 (OUTLIER) cc_final: 0.8616 (mtpm) REVERT: f 15 LYS cc_start: 0.8582 (mmtm) cc_final: 0.8305 (mttt) REVERT: g 136 MET cc_start: 0.7974 (ttp) cc_final: 0.7639 (mmp) REVERT: g 182 PRO cc_start: 0.9130 (Cg_exo) cc_final: 0.8876 (Cg_endo) REVERT: h 183 ASP cc_start: 0.8371 (t70) cc_final: 0.7980 (t70) REVERT: i 136 GLN cc_start: 0.9047 (mm-40) cc_final: 0.8770 (mm110) REVERT: i 141 ASP cc_start: 0.8547 (m-30) cc_final: 0.8071 (m-30) REVERT: k 65 GLU cc_start: 0.7911 (tp30) cc_final: 0.7675 (tp30) REVERT: l 5 ARG cc_start: 0.7898 (tmm-80) cc_final: 0.7498 (ptt90) REVERT: l 15 ASP cc_start: 0.8566 (p0) cc_final: 0.8295 (p0) REVERT: l 149 LYS cc_start: 0.7742 (OUTLIER) cc_final: 0.7453 (ptmm) REVERT: m 72 VAL cc_start: 0.9487 (t) cc_final: 0.9250 (p) REVERT: m 90 ASP cc_start: 0.8578 (p0) cc_final: 0.8257 (p0) REVERT: n 18 ARG cc_start: 0.8354 (OUTLIER) cc_final: 0.8046 (mtm180) REVERT: n 22 LYS cc_start: 0.8603 (mtpp) cc_final: 0.8269 (mtmm) REVERT: n 106 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.6038 (ttt90) REVERT: o 14 ASP cc_start: 0.7996 (t0) cc_final: 0.7510 (t0) REVERT: p 18 ASP cc_start: 0.7972 (OUTLIER) cc_final: 0.7142 (p0) REVERT: q 18 LYS cc_start: 0.8555 (tptm) cc_final: 0.8279 (tttm) REVERT: q 56 ARG cc_start: 0.8030 (ttm-80) cc_final: 0.7438 (ttm-80) REVERT: q 103 ASP cc_start: 0.8500 (m-30) cc_final: 0.7914 (m-30) REVERT: s 39 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7767 (tm-30) REVERT: s 43 ASN cc_start: 0.8129 (m110) cc_final: 0.7596 (m-40) REVERT: t 24 SER cc_start: 0.8550 (m) cc_final: 0.8265 (t) REVERT: t 68 ASP cc_start: 0.8127 (m-30) cc_final: 0.7755 (m-30) REVERT: u 31 ARG cc_start: 0.8637 (ttt-90) cc_final: 0.8337 (ttt180) REVERT: u 48 GLU cc_start: 0.8113 (tt0) cc_final: 0.7845 (tt0) REVERT: v 17 MET cc_start: 0.8365 (mmm) cc_final: 0.8117 (mmm) REVERT: v 18 GLU cc_start: 0.7850 (tm-30) cc_final: 0.7359 (tm-30) REVERT: v 83 VAL cc_start: 0.7521 (m) cc_final: 0.7142 (t) REVERT: w 38 LYS cc_start: 0.9097 (mtmt) cc_final: 0.8880 (mttt) REVERT: x 65 GLU cc_start: 0.8564 (mm-30) cc_final: 0.8189 (mm-30) REVERT: x 70 LYS cc_start: 0.8417 (mmtm) cc_final: 0.7798 (mmtm) REVERT: y 21 ASN cc_start: 0.9016 (m110) cc_final: 0.8287 (m-40) outliers start: 266 outliers final: 206 residues processed: 1387 average time/residue: 1.3247 time to fit residues: 3195.0331 Evaluate side-chains 1436 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 222 poor density : 1214 time to evaluate : 6.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 53 ASP Chi-restraints excluded: chain 5 residue 56 VAL Chi-restraints excluded: chain 5 residue 64 PHE Chi-restraints excluded: chain 5 residue 75 VAL Chi-restraints excluded: chain 5 residue 112 VAL Chi-restraints excluded: chain 5 residue 118 TRP Chi-restraints excluded: chain 5 residue 139 ARG Chi-restraints excluded: chain 5 residue 141 ASP Chi-restraints excluded: chain A residue 3 HIS Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 139 SER Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 170 VAL Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 10 SER Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 80 SER Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 158 THR Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 38 ASN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 106 SER Chi-restraints excluded: chain F residue 107 LEU Chi-restraints excluded: chain F residue 131 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain G residue 144 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain J residue 141 ASP Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 39 LYS Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 46 VAL Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 31 VAL Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 104 VAL Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 68 ASP Chi-restraints excluded: chain S residue 101 SER Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 72 ILE Chi-restraints excluded: chain U residue 77 THR Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 54 MET Chi-restraints excluded: chain a residue 1 MET Chi-restraints excluded: chain a residue 24 ILE Chi-restraints excluded: chain a residue 26 SER Chi-restraints excluded: chain a residue 27 THR Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain f residue 8 LYS Chi-restraints excluded: chain f residue 9 LYS Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain g residue 68 LEU Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 159 ASP Chi-restraints excluded: chain g residue 187 VAL Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 205 ASP Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 63 SER Chi-restraints excluded: chain h residue 93 ASP Chi-restraints excluded: chain i residue 34 ILE Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain i residue 190 ASP Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain j residue 147 MET Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 33 ASP Chi-restraints excluded: chain l residue 45 SER Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 75 VAL Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain l residue 144 MET Chi-restraints excluded: chain l residue 149 LYS Chi-restraints excluded: chain m residue 83 LEU Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 18 ARG Chi-restraints excluded: chain n residue 43 THR Chi-restraints excluded: chain n residue 52 LEU Chi-restraints excluded: chain n residue 106 ARG Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 28 THR Chi-restraints excluded: chain o residue 77 VAL Chi-restraints excluded: chain o residue 78 GLU Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 92 LEU Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain p residue 87 LYS Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 65 SER Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain r residue 30 SER Chi-restraints excluded: chain r residue 34 LEU Chi-restraints excluded: chain r residue 69 LEU Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 5 SER Chi-restraints excluded: chain s residue 32 SER Chi-restraints excluded: chain s residue 35 ASN Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain t residue 75 VAL Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain u residue 55 ASP Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 28 PHE Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 44 LEU Chi-restraints excluded: chain v residue 59 VAL Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain v residue 72 SER Chi-restraints excluded: chain w residue 71 THR Chi-restraints excluded: chain x residue 38 SER Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 3 ASN Chi-restraints excluded: chain y residue 12 ILE Chi-restraints excluded: chain z residue 6 VAL Chi-restraints excluded: chain z residue 20 LYS Chi-restraints excluded: chain z residue 22 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 1000 optimal weight: 5.9990 chunk 117 optimal weight: 20.0000 chunk 591 optimal weight: 9.9990 chunk 758 optimal weight: 0.5980 chunk 587 optimal weight: 1.9990 chunk 873 optimal weight: 7.9990 chunk 579 optimal weight: 0.8980 chunk 1034 optimal weight: 5.9990 chunk 647 optimal weight: 0.9980 chunk 630 optimal weight: 20.0000 chunk 477 optimal weight: 50.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- 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** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN J 128 ASN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 38 GLN V 12 GLN Y 45 GLN i 131 ASN i 140 ASN k 68 GLN ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 5 GLN n 50 GLN t 80 GLN ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 13 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 167985 Z= 0.178 Angle : 0.583 14.259 251649 Z= 0.320 Chirality : 0.033 0.279 32100 Planarity : 0.006 0.125 13244 Dihedral : 23.620 179.160 84764 Min Nonbonded Distance : 1.051 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.31 % Favored : 96.59 % Rotamer: Outliers : 3.79 % Allowed : 19.94 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.12 (0.11), residues: 5865 helix: 1.27 (0.12), residues: 2007 sheet: -0.25 (0.16), residues: 1110 loop : -1.01 (0.11), residues: 2748 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP h 201 HIS 0.007 0.001 HIS q 77 PHE 0.016 0.001 PHE k 8 TYR 0.025 0.001 TYR G 25 ARG 0.013 0.000 ARG F 153 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1475 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 185 poor density : 1290 time to evaluate : 6.367 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: 5 23 GLU cc_start: 0.7477 (tm-30) cc_final: 0.7239 (tm-30) REVERT: 5 25 PHE cc_start: 0.7213 (t80) cc_final: 0.6860 (t80) REVERT: 5 53 ASP cc_start: 0.6258 (OUTLIER) cc_final: 0.5971 (p0) REVERT: 5 101 TYR cc_start: 0.6888 (m-80) cc_final: 0.6467 (m-80) REVERT: 5 139 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.8275 (mtm180) REVERT: A 78 LYS cc_start: 0.8340 (mmmt) cc_final: 0.7949 (mttm) REVERT: B 101 ARG cc_start: 0.8400 (mtt180) cc_final: 0.8155 (mtt-85) REVERT: B 269 ARG cc_start: 0.8367 (ttm-80) cc_final: 0.8150 (ttm-80) REVERT: C 4 LEU cc_start: 0.9023 (OUTLIER) cc_final: 0.8603 (mp) REVERT: D 163 ASN cc_start: 0.9046 (t0) cc_final: 0.8680 (t0) REVERT: D 194 LYS cc_start: 0.8491 (mmmt) cc_final: 0.7990 (mttp) REVERT: E 32 GLU cc_start: 0.7524 (OUTLIER) cc_final: 0.6837 (mp0) REVERT: E 52 ASN cc_start: 0.8573 (m-40) cc_final: 0.8065 (m110) REVERT: E 96 MET cc_start: 0.8522 (ttm) cc_final: 0.8266 (ttm) REVERT: E 133 ARG cc_start: 0.8011 (mpp80) cc_final: 0.7628 (mmt90) REVERT: E 170 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8568 (mm) REVERT: F 130 GLU cc_start: 0.7992 (tt0) cc_final: 0.7557 (tt0) REVERT: F 155 GLU cc_start: 0.7735 (pm20) cc_final: 0.7491 (pm20) REVERT: H 38 MET cc_start: -0.0223 (ptm) cc_final: -0.0868 (tpp) REVERT: H 52 MET cc_start: -0.1998 (tpp) cc_final: -0.3169 (ptm) REVERT: H 81 LEU cc_start: 0.2525 (OUTLIER) cc_final: 0.2041 (tt) REVERT: J 96 ARG cc_start: 0.7959 (mmm160) cc_final: 0.7492 (mtp85) REVERT: J 106 LYS cc_start: 0.8948 (ttpt) cc_final: 0.8576 (ttmm) REVERT: J 108 MET cc_start: 0.8424 (mtt) cc_final: 0.7939 (mtt) REVERT: J 125 TYR cc_start: 0.8149 (m-80) cc_final: 0.7831 (m-80) REVERT: K 17 ARG cc_start: 0.7596 (mtm180) cc_final: 0.7372 (mmt90) REVERT: L 99 ASN cc_start: 0.8662 (p0) cc_final: 0.8254 (t0) REVERT: L 123 ARG cc_start: 0.7738 (ttp-110) cc_final: 0.7436 (ptp-170) REVERT: M 104 GLU cc_start: 0.8412 (mt-10) cc_final: 0.8087 (mt-10) REVERT: N 24 MET cc_start: 0.8963 (ttm) cc_final: 0.8720 (ttp) REVERT: N 72 ASP cc_start: 0.8332 (t0) cc_final: 0.7538 (t0) REVERT: N 74 GLU cc_start: 0.7804 (pm20) cc_final: 0.7089 (pm20) REVERT: N 82 GLU cc_start: 0.8623 (mp0) cc_final: 0.8005 (mp0) REVERT: O 17 LYS cc_start: 0.9284 (tptt) cc_final: 0.9072 (tppt) REVERT: O 83 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8717 (mm) REVERT: P 27 GLU cc_start: 0.8488 (OUTLIER) cc_final: 0.7667 (tt0) REVERT: P 44 GLU cc_start: 0.8096 (tp30) cc_final: 0.7724 (tp30) REVERT: Q 11 ARG cc_start: 0.8041 (ttm170) cc_final: 0.7471 (tpp-160) REVERT: Q 49 ASP cc_start: 0.7989 (m-30) cc_final: 0.7699 (m-30) REVERT: R 24 LYS cc_start: 0.8814 (ttpp) cc_final: 0.8098 (ttpp) REVERT: R 26 ASP cc_start: 0.7940 (p0) cc_final: 0.7608 (p0) REVERT: S 85 ILE cc_start: 0.9142 (pt) cc_final: 0.8919 (mt) REVERT: T 1 MET cc_start: 0.7896 (tpt) cc_final: 0.7161 (tpt) REVERT: U 18 ASP cc_start: 0.8330 (p0) cc_final: 0.7883 (p0) REVERT: U 46 GLN cc_start: 0.8410 (tp-100) cc_final: 0.8177 (tp-100) REVERT: U 60 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: X 56 MET cc_start: 0.9105 (mtm) cc_final: 0.8613 (mtm) REVERT: X 60 ASP cc_start: 0.7306 (m-30) cc_final: 0.6996 (m-30) REVERT: X 76 GLU cc_start: 0.7566 (mp0) cc_final: 0.7306 (mp0) REVERT: Y 44 LYS cc_start: 0.8581 (tttp) cc_final: 0.8156 (tttt) REVERT: Z 37 GLU cc_start: 0.8310 (tp30) cc_final: 0.7877 (tp30) REVERT: a 1 MET cc_start: 0.8094 (mtm) cc_final: 0.7817 (mmm) REVERT: a 56 ARG cc_start: 0.7469 (mmm160) cc_final: 0.7257 (mmm160) REVERT: a 59 ARG cc_start: 0.8494 (ptm-80) cc_final: 0.8169 (ptm-80) REVERT: f 9 LYS cc_start: 0.8894 (OUTLIER) cc_final: 0.8645 (mtpm) REVERT: f 15 LYS cc_start: 0.8525 (mmtm) cc_final: 0.8274 (mttt) REVERT: g 27 MET cc_start: 0.8168 (mmm) cc_final: 0.7957 (mtp) REVERT: g 136 MET cc_start: 0.8002 (ttp) cc_final: 0.7768 (mmp) REVERT: g 182 PRO cc_start: 0.9147 (Cg_exo) cc_final: 0.8925 (Cg_endo) REVERT: h 183 ASP cc_start: 0.8284 (t70) cc_final: 0.7867 (t70) REVERT: i 85 ASN cc_start: 0.8664 (t0) cc_final: 0.8422 (t0) REVERT: i 136 GLN cc_start: 0.9041 (mm-40) cc_final: 0.8771 (mm110) REVERT: l 5 ARG cc_start: 0.7847 (tmm-80) cc_final: 0.7507 (ptt180) REVERT: l 89 VAL cc_start: 0.8878 (p) cc_final: 0.8452 (m) REVERT: l 144 MET cc_start: 0.8350 (OUTLIER) cc_final: 0.8025 (mmp) REVERT: l 149 LYS cc_start: 0.7613 (OUTLIER) cc_final: 0.7314 (ptmm) REVERT: m 36 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8815 (mt) REVERT: m 72 VAL cc_start: 0.9484 (t) cc_final: 0.9252 (p) REVERT: m 90 ASP cc_start: 0.8528 (p0) cc_final: 0.8218 (p0) REVERT: n 22 LYS cc_start: 0.8611 (mtpp) cc_final: 0.8365 (mtmm) REVERT: n 75 GLN cc_start: 0.8528 (mt0) cc_final: 0.8247 (mt0) REVERT: o 14 ASP cc_start: 0.7880 (t0) cc_final: 0.7503 (t0) REVERT: o 28 THR cc_start: 0.8384 (OUTLIER) cc_final: 0.8052 (m) REVERT: p 94 GLU cc_start: 0.7773 (tm-30) cc_final: 0.7100 (tm-30) REVERT: p 98 ARG cc_start: 0.8589 (mmm-85) cc_final: 0.8388 (tpp80) REVERT: q 18 LYS cc_start: 0.8385 (tptm) cc_final: 0.8118 (tttm) REVERT: q 56 ARG cc_start: 0.8107 (ttm-80) cc_final: 0.7655 (ttm-80) REVERT: q 62 GLU cc_start: 0.8271 (mm-30) cc_final: 0.7735 (tp30) REVERT: q 103 ASP cc_start: 0.8478 (m-30) cc_final: 0.8225 (m-30) REVERT: r 104 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8200 (p) REVERT: s 39 GLU cc_start: 0.8090 (tm-30) cc_final: 0.7707 (tm-30) REVERT: s 43 ASN cc_start: 0.8172 (m110) cc_final: 0.7655 (m-40) REVERT: t 20 ASN cc_start: 0.8565 (t0) cc_final: 0.8335 (t0) REVERT: t 68 ASP cc_start: 0.8066 (m-30) cc_final: 0.7711 (m-30) REVERT: u 48 GLU cc_start: 0.8074 (tt0) cc_final: 0.7672 (tt0) REVERT: v 18 GLU cc_start: 0.7901 (tm-30) cc_final: 0.7425 (tm-30) REVERT: v 57 ASP cc_start: 0.8272 (t0) cc_final: 0.8063 (m-30) REVERT: v 80 GLU cc_start: 0.8066 (mp0) cc_final: 0.7787 (tm-30) REVERT: v 83 VAL cc_start: 0.7566 (m) cc_final: 0.7186 (t) REVERT: x 65 GLU cc_start: 0.8555 (mm-30) cc_final: 0.8113 (mm-30) REVERT: x 70 LYS cc_start: 0.8364 (mmtm) cc_final: 0.7658 (mmtm) REVERT: y 21 ASN cc_start: 0.9050 (m110) cc_final: 0.8284 (m-40) outliers start: 185 outliers final: 130 residues processed: 1377 average time/residue: 1.3357 time to fit residues: 3197.7236 Evaluate side-chains 1388 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1243 time to evaluate : 6.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 53 ASP Chi-restraints excluded: chain 5 residue 56 VAL Chi-restraints excluded: chain 5 residue 64 PHE Chi-restraints excluded: chain 5 residue 112 VAL Chi-restraints excluded: chain 5 residue 139 ARG Chi-restraints excluded: chain 5 residue 141 ASP Chi-restraints excluded: chain A residue 3 HIS Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 15 GLN Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 51 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain Y residue 19 LEU Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 54 MET Chi-restraints excluded: chain a residue 27 THR Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain f residue 9 LYS Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 205 ASP Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 93 ASP Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain j residue 147 MET Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 33 ASP Chi-restraints excluded: chain l residue 45 SER Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 130 ASN Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain l residue 144 MET Chi-restraints excluded: chain l residue 149 LYS Chi-restraints excluded: chain m residue 36 ILE Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain m residue 118 GLN Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 43 THR Chi-restraints excluded: chain n residue 54 LEU Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 28 THR Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 92 LEU Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain r residue 30 SER Chi-restraints excluded: chain r residue 34 LEU Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 5 SER Chi-restraints excluded: chain s residue 35 ASN Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 55 ASP Chi-restraints excluded: chain u residue 75 ILE Chi-restraints excluded: chain v residue 28 PHE Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain x residue 32 ARG Chi-restraints excluded: chain x residue 38 SER Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain y residue 39 ILE Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain z residue 20 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 639 optimal weight: 30.0000 chunk 412 optimal weight: 10.0000 chunk 617 optimal weight: 8.9990 chunk 311 optimal weight: 20.0000 chunk 203 optimal weight: 8.9990 chunk 200 optimal weight: 7.9990 chunk 657 optimal weight: 6.9990 chunk 704 optimal weight: 1.9990 chunk 511 optimal weight: 9.9990 chunk 96 optimal weight: 7.9990 chunk 812 optimal weight: 0.5980 overall best weight: 5.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 5 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN F 104 ASN J 128 ASN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 54 GLN V 12 GLN Y 45 GLN c 45 GLN i 116 GLN i 131 ASN i 140 ASN k 68 GLN ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 5 GLN n 126 GLN q 77 HIS r 8 ASN ** t 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 9 GLN ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** x 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 13 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.079 167985 Z= 0.379 Angle : 0.667 13.751 251649 Z= 0.357 Chirality : 0.038 0.332 32100 Planarity : 0.006 0.139 13244 Dihedral : 23.622 179.133 84764 Min Nonbonded Distance : 0.989 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.13 % Favored : 95.77 % Rotamer: Outliers : 4.59 % Allowed : 19.33 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.25 (0.11), residues: 5865 helix: 1.13 (0.12), residues: 2005 sheet: -0.33 (0.16), residues: 1132 loop : -1.05 (0.11), residues: 2728 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP h 201 HIS 0.009 0.001 HIS t 46 PHE 0.024 0.002 PHE k 78 TYR 0.029 0.002 TYR k 59 ARG 0.011 0.001 ARG p 69 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1452 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 224 poor density : 1228 time to evaluate : 6.425 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: 5 23 GLU cc_start: 0.7517 (tm-30) cc_final: 0.7231 (tm-30) REVERT: 5 25 PHE cc_start: 0.7246 (t80) cc_final: 0.6803 (t80) REVERT: 5 53 ASP cc_start: 0.6350 (OUTLIER) cc_final: 0.5787 (p0) REVERT: 5 101 TYR cc_start: 0.6849 (m-80) cc_final: 0.6353 (m-80) REVERT: 5 118 TRP cc_start: 0.6191 (OUTLIER) cc_final: 0.5707 (t-100) REVERT: 5 139 ARG cc_start: 0.8732 (OUTLIER) cc_final: 0.8123 (mtm180) REVERT: A 78 LYS cc_start: 0.8390 (mmmt) cc_final: 0.7983 (mttm) REVERT: C 4 LEU cc_start: 0.9114 (OUTLIER) cc_final: 0.8649 (mp) REVERT: D 115 GLN cc_start: 0.8613 (mt0) cc_final: 0.8402 (mt0) REVERT: D 163 ASN cc_start: 0.9215 (t0) cc_final: 0.8799 (t0) REVERT: D 194 LYS cc_start: 0.8538 (mmmt) cc_final: 0.8042 (mttp) REVERT: E 32 GLU cc_start: 0.7469 (mp0) cc_final: 0.6844 (mp0) REVERT: E 133 ARG cc_start: 0.8063 (mpp80) cc_final: 0.7770 (mmt90) REVERT: E 170 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8666 (mm) REVERT: F 42 GLU cc_start: 0.7071 (pt0) cc_final: 0.6433 (pt0) REVERT: F 44 LYS cc_start: 0.7949 (mptt) cc_final: 0.7310 (mmtt) REVERT: F 130 GLU cc_start: 0.7999 (tt0) cc_final: 0.7602 (tt0) REVERT: F 155 GLU cc_start: 0.7682 (pm20) cc_final: 0.7387 (pm20) REVERT: H 38 MET cc_start: -0.0307 (ptm) cc_final: -0.1132 (tpp) REVERT: H 81 LEU cc_start: 0.2473 (OUTLIER) cc_final: 0.1990 (tt) REVERT: J 96 ARG cc_start: 0.8002 (mmm160) cc_final: 0.7525 (mtp85) REVERT: J 106 LYS cc_start: 0.9021 (ttpt) cc_final: 0.8636 (ttmm) REVERT: K 17 ARG cc_start: 0.7640 (mtm180) cc_final: 0.7408 (mmt90) REVERT: L 99 ASN cc_start: 0.8681 (p0) cc_final: 0.8302 (t0) REVERT: L 123 ARG cc_start: 0.7786 (ttp-110) cc_final: 0.7354 (ptp-170) REVERT: M 104 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8048 (mt-10) REVERT: M 136 MET cc_start: 0.7965 (tmm) cc_final: 0.7258 (ppp) REVERT: N 72 ASP cc_start: 0.8347 (t0) cc_final: 0.7629 (t0) REVERT: N 74 GLU cc_start: 0.7891 (pm20) cc_final: 0.7199 (pm20) REVERT: N 82 GLU cc_start: 0.8575 (mp0) cc_final: 0.7922 (mp0) REVERT: O 17 LYS cc_start: 0.9296 (tptt) cc_final: 0.9068 (tppt) REVERT: O 83 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8738 (mm) REVERT: P 27 GLU cc_start: 0.8494 (OUTLIER) cc_final: 0.7664 (tt0) REVERT: P 44 GLU cc_start: 0.8108 (tp30) cc_final: 0.7713 (tp30) REVERT: Q 11 ARG cc_start: 0.8144 (ttm170) cc_final: 0.7682 (tpp-160) REVERT: Q 49 ASP cc_start: 0.7999 (m-30) cc_final: 0.7700 (m-30) REVERT: R 26 ASP cc_start: 0.8011 (p0) cc_final: 0.7722 (p0) REVERT: T 42 GLU cc_start: 0.8084 (OUTLIER) cc_final: 0.7883 (mt-10) REVERT: U 60 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7645 (mp0) REVERT: X 56 MET cc_start: 0.9182 (mtm) cc_final: 0.8698 (mtm) REVERT: X 60 ASP cc_start: 0.7324 (m-30) cc_final: 0.7023 (m-30) REVERT: Y 44 LYS cc_start: 0.8715 (tttp) cc_final: 0.8337 (tttt) REVERT: Z 6 LYS cc_start: 0.8497 (mtmm) cc_final: 0.8289 (mtmm) REVERT: Z 37 GLU cc_start: 0.8259 (tp30) cc_final: 0.8041 (tp30) REVERT: a 1 MET cc_start: 0.8200 (mtm) cc_final: 0.7907 (mmm) REVERT: a 59 ARG cc_start: 0.8537 (ptm-80) cc_final: 0.8203 (ptm-80) REVERT: b 12 LYS cc_start: 0.8644 (ttmt) cc_final: 0.8248 (mtpp) REVERT: f 9 LYS cc_start: 0.8919 (OUTLIER) cc_final: 0.8655 (mtpm) REVERT: f 15 LYS cc_start: 0.8560 (mmtm) cc_final: 0.8293 (mttt) REVERT: g 136 MET cc_start: 0.7975 (ttp) cc_final: 0.7668 (mmp) REVERT: g 182 PRO cc_start: 0.9139 (Cg_exo) cc_final: 0.8896 (Cg_endo) REVERT: h 51 SER cc_start: 0.9023 (m) cc_final: 0.8486 (p) REVERT: h 183 ASP cc_start: 0.8389 (t70) cc_final: 0.7983 (t70) REVERT: i 136 GLN cc_start: 0.9032 (mm-40) cc_final: 0.8826 (mm-40) REVERT: k 1 MET cc_start: 0.7722 (tpp) cc_final: 0.7365 (tpp) REVERT: l 5 ARG cc_start: 0.7858 (tmm-80) cc_final: 0.7528 (ptt180) REVERT: l 144 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.8042 (mmp) REVERT: l 149 LYS cc_start: 0.7660 (OUTLIER) cc_final: 0.7408 (ptmm) REVERT: m 36 ILE cc_start: 0.9027 (OUTLIER) cc_final: 0.8777 (mt) REVERT: m 72 VAL cc_start: 0.9491 (t) cc_final: 0.9248 (p) REVERT: m 90 ASP cc_start: 0.8584 (p0) cc_final: 0.8253 (p0) REVERT: n 6 TYR cc_start: 0.8072 (m-80) cc_final: 0.7738 (m-80) REVERT: n 22 LYS cc_start: 0.8610 (mtpp) cc_final: 0.8377 (mtmm) REVERT: n 106 ARG cc_start: 0.8058 (OUTLIER) cc_final: 0.6197 (ttt90) REVERT: o 14 ASP cc_start: 0.7982 (t0) cc_final: 0.7573 (t0) REVERT: o 28 THR cc_start: 0.8367 (OUTLIER) cc_final: 0.8134 (m) REVERT: p 94 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7300 (tm-30) REVERT: p 98 ARG cc_start: 0.8599 (mmm-85) cc_final: 0.8374 (tpp80) REVERT: q 18 LYS cc_start: 0.8517 (tptm) cc_final: 0.8206 (tttm) REVERT: q 56 ARG cc_start: 0.8103 (ttm-80) cc_final: 0.7621 (ttm-80) REVERT: q 62 GLU cc_start: 0.8240 (mm-30) cc_final: 0.7717 (tp30) REVERT: q 103 ASP cc_start: 0.8525 (m-30) cc_final: 0.7955 (m-30) REVERT: r 104 THR cc_start: 0.8593 (OUTLIER) cc_final: 0.8272 (p) REVERT: s 39 GLU cc_start: 0.8168 (tm-30) cc_final: 0.7783 (tm-30) REVERT: s 43 ASN cc_start: 0.8059 (m110) cc_final: 0.7502 (m-40) REVERT: t 20 ASN cc_start: 0.8616 (t0) cc_final: 0.8360 (t0) REVERT: t 68 ASP cc_start: 0.8108 (m-30) cc_final: 0.7741 (m-30) REVERT: u 50 THR cc_start: 0.9174 (m) cc_final: 0.8821 (m) REVERT: v 18 GLU cc_start: 0.8070 (tm-30) cc_final: 0.7356 (tm-30) REVERT: v 80 GLU cc_start: 0.8096 (mp0) cc_final: 0.7548 (tm-30) REVERT: v 83 VAL cc_start: 0.7694 (m) cc_final: 0.7352 (t) REVERT: x 65 GLU cc_start: 0.8601 (mm-30) cc_final: 0.8167 (mm-30) REVERT: x 70 LYS cc_start: 0.8381 (mmtm) cc_final: 0.7748 (mmtm) REVERT: y 21 ASN cc_start: 0.9036 (m110) cc_final: 0.8248 (m-40) outliers start: 224 outliers final: 175 residues processed: 1351 average time/residue: 1.4316 time to fit residues: 3394.9979 Evaluate side-chains 1412 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1220 time to evaluate : 6.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 53 ASP Chi-restraints excluded: chain 5 residue 56 VAL Chi-restraints excluded: chain 5 residue 64 PHE Chi-restraints excluded: chain 5 residue 75 VAL Chi-restraints excluded: chain 5 residue 91 LEU Chi-restraints excluded: chain 5 residue 112 VAL Chi-restraints excluded: chain 5 residue 118 TRP Chi-restraints excluded: chain 5 residue 139 ARG Chi-restraints excluded: chain 5 residue 141 ASP Chi-restraints excluded: chain A residue 3 HIS Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 42 ASN Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain D residue 43 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 38 ASN Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 89 SER Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 28 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 77 THR Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 60 VAL Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 49 ASN Chi-restraints excluded: chain Z residue 54 MET Chi-restraints excluded: chain a residue 9 TYR Chi-restraints excluded: chain a residue 24 ILE Chi-restraints excluded: chain a residue 27 THR Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain f residue 9 LYS Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain g residue 68 LEU Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 205 ASP Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 63 SER Chi-restraints excluded: chain h residue 93 ASP Chi-restraints excluded: chain i residue 67 VAL Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain i residue 174 ASP Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain i residue 190 ASP Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain j residue 147 MET Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 39 LEU Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 33 ASP Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 45 SER Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 130 ASN Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain l residue 144 MET Chi-restraints excluded: chain l residue 149 LYS Chi-restraints excluded: chain m residue 36 ILE Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 43 THR Chi-restraints excluded: chain n residue 106 ARG Chi-restraints excluded: chain o residue 28 THR Chi-restraints excluded: chain o residue 77 VAL Chi-restraints excluded: chain o residue 78 GLU Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 92 LEU Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain r residue 30 SER Chi-restraints excluded: chain r residue 34 LEU Chi-restraints excluded: chain r residue 97 VAL Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 5 SER Chi-restraints excluded: chain s residue 30 ILE Chi-restraints excluded: chain s residue 32 SER Chi-restraints excluded: chain s residue 35 ASN Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain v residue 9 GLN Chi-restraints excluded: chain v residue 28 PHE Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 44 LEU Chi-restraints excluded: chain v residue 59 VAL Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain x residue 27 ASP Chi-restraints excluded: chain x residue 38 SER Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain y residue 39 ILE Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain z residue 20 LYS Chi-restraints excluded: chain z residue 22 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 940 optimal weight: 6.9990 chunk 990 optimal weight: 6.9990 chunk 903 optimal weight: 3.9990 chunk 963 optimal weight: 2.9990 chunk 580 optimal weight: 3.9990 chunk 419 optimal weight: 10.0000 chunk 756 optimal weight: 6.9990 chunk 295 optimal weight: 10.0000 chunk 870 optimal weight: 1.9990 chunk 911 optimal weight: 0.9980 chunk 960 optimal weight: 7.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 104 ASN G 20 ASN J 128 ASN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 54 GLN V 12 GLN Y 45 GLN c 45 GLN i 116 GLN i 131 ASN i 140 ASN k 52 ASN k 68 GLN ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 5 GLN n 50 GLN t 80 GLN u 26 ASN v 9 GLN ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 14 HIS ** y 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.4130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 167985 Z= 0.223 Angle : 0.600 14.555 251649 Z= 0.327 Chirality : 0.034 0.296 32100 Planarity : 0.006 0.128 13244 Dihedral : 23.611 179.391 84764 Min Nonbonded Distance : 1.032 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.55 % Favored : 96.35 % Rotamer: Outliers : 4.07 % Allowed : 20.33 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.11 (0.11), residues: 5865 helix: 1.25 (0.12), residues: 2005 sheet: -0.24 (0.16), residues: 1123 loop : -0.98 (0.11), residues: 2737 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP h 201 HIS 0.009 0.001 HIS q 77 PHE 0.027 0.001 PHE k 78 TYR 0.030 0.002 TYR k 59 ARG 0.010 0.000 ARG p 69 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1460 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 199 poor density : 1261 time to evaluate : 6.469 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: 5 23 GLU cc_start: 0.7473 (tm-30) cc_final: 0.7264 (tm-30) REVERT: 5 25 PHE cc_start: 0.7270 (t80) cc_final: 0.6923 (t80) REVERT: 5 53 ASP cc_start: 0.6221 (OUTLIER) cc_final: 0.5862 (p0) REVERT: 5 101 TYR cc_start: 0.6785 (m-80) cc_final: 0.6382 (m-80) REVERT: 5 118 TRP cc_start: 0.6291 (OUTLIER) cc_final: 0.5684 (t-100) REVERT: A 78 LYS cc_start: 0.8359 (mmmt) cc_final: 0.7956 (mttm) REVERT: B 101 ARG cc_start: 0.8424 (mtt180) cc_final: 0.8171 (mtt90) REVERT: C 4 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8631 (mp) REVERT: D 163 ASN cc_start: 0.9137 (t0) cc_final: 0.8757 (t0) REVERT: D 194 LYS cc_start: 0.8504 (mmmt) cc_final: 0.8007 (mttp) REVERT: E 32 GLU cc_start: 0.7434 (OUTLIER) cc_final: 0.6651 (mp0) REVERT: E 52 ASN cc_start: 0.8620 (m-40) cc_final: 0.8101 (m110) REVERT: E 98 GLU cc_start: 0.8253 (mt-10) cc_final: 0.8035 (mt-10) REVERT: E 133 ARG cc_start: 0.8059 (mpp80) cc_final: 0.7767 (mmt90) REVERT: E 170 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8612 (mm) REVERT: F 130 GLU cc_start: 0.8049 (tt0) cc_final: 0.7644 (tt0) REVERT: F 155 GLU cc_start: 0.7597 (pm20) cc_final: 0.7307 (pm20) REVERT: G 129 GLU cc_start: 0.8139 (mt-10) cc_final: 0.7713 (pt0) REVERT: H 38 MET cc_start: -0.0317 (ptm) cc_final: -0.1133 (tpp) REVERT: H 52 MET cc_start: -0.2140 (tpp) cc_final: -0.3241 (ptm) REVERT: H 81 LEU cc_start: 0.2442 (OUTLIER) cc_final: 0.1962 (tt) REVERT: J 96 ARG cc_start: 0.7989 (mmm160) cc_final: 0.7512 (mtp85) REVERT: J 106 LYS cc_start: 0.8971 (ttpt) cc_final: 0.8607 (ttmm) REVERT: J 125 TYR cc_start: 0.8300 (m-80) cc_final: 0.7800 (m-80) REVERT: K 17 ARG cc_start: 0.7606 (mtm180) cc_final: 0.7390 (mmt90) REVERT: L 99 ASN cc_start: 0.8689 (p0) cc_final: 0.8237 (t0) REVERT: L 123 ARG cc_start: 0.7742 (ttp-110) cc_final: 0.7374 (ptp-170) REVERT: M 104 GLU cc_start: 0.8390 (mt-10) cc_final: 0.8072 (mt-10) REVERT: N 72 ASP cc_start: 0.8308 (t0) cc_final: 0.7580 (t0) REVERT: N 74 GLU cc_start: 0.7800 (pm20) cc_final: 0.7105 (pm20) REVERT: N 82 GLU cc_start: 0.8614 (mp0) cc_final: 0.7955 (mp0) REVERT: O 17 LYS cc_start: 0.9306 (tptt) cc_final: 0.9078 (tppt) REVERT: O 83 LEU cc_start: 0.9071 (OUTLIER) cc_final: 0.8758 (mm) REVERT: P 27 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.7647 (tt0) REVERT: P 44 GLU cc_start: 0.8103 (tp30) cc_final: 0.7720 (tp30) REVERT: Q 11 ARG cc_start: 0.8075 (ttm170) cc_final: 0.7497 (tpp-160) REVERT: Q 49 ASP cc_start: 0.8013 (m-30) cc_final: 0.7709 (m-30) REVERT: R 26 ASP cc_start: 0.7992 (p0) cc_final: 0.7671 (p0) REVERT: T 1 MET cc_start: 0.7911 (tpt) cc_final: 0.7165 (tpt) REVERT: U 60 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7578 (mp0) REVERT: X 56 MET cc_start: 0.9130 (mtm) cc_final: 0.8643 (mtm) REVERT: X 60 ASP cc_start: 0.7281 (m-30) cc_final: 0.6965 (m-30) REVERT: Y 44 LYS cc_start: 0.8593 (tttp) cc_final: 0.8291 (tttt) REVERT: a 1 MET cc_start: 0.8063 (mtm) cc_final: 0.7781 (mmm) REVERT: a 25 ARG cc_start: 0.8311 (ttm-80) cc_final: 0.8094 (ttp80) REVERT: a 59 ARG cc_start: 0.8503 (ptm-80) cc_final: 0.8185 (ptm-80) REVERT: b 12 LYS cc_start: 0.8607 (ttmt) cc_final: 0.8205 (mtpp) REVERT: f 9 LYS cc_start: 0.8874 (OUTLIER) cc_final: 0.8615 (mtpm) REVERT: f 15 LYS cc_start: 0.8528 (mmtm) cc_final: 0.8286 (mttt) REVERT: g 136 MET cc_start: 0.7973 (ttp) cc_final: 0.7752 (mmp) REVERT: g 182 PRO cc_start: 0.9147 (Cg_exo) cc_final: 0.8924 (Cg_endo) REVERT: h 183 ASP cc_start: 0.8301 (t70) cc_final: 0.7889 (t70) REVERT: i 85 ASN cc_start: 0.8699 (t0) cc_final: 0.8441 (t0) REVERT: i 136 GLN cc_start: 0.9011 (mm-40) cc_final: 0.8810 (mm-40) REVERT: k 1 MET cc_start: 0.7765 (tpp) cc_final: 0.7411 (tpp) REVERT: k 65 GLU cc_start: 0.7841 (tp30) cc_final: 0.7340 (tp30) REVERT: l 5 ARG cc_start: 0.7806 (tmm-80) cc_final: 0.7475 (ptt180) REVERT: l 144 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8029 (mmp) REVERT: l 149 LYS cc_start: 0.7601 (OUTLIER) cc_final: 0.7384 (ptmm) REVERT: m 72 VAL cc_start: 0.9487 (t) cc_final: 0.9263 (p) REVERT: m 90 ASP cc_start: 0.8565 (p0) cc_final: 0.8239 (p0) REVERT: n 6 TYR cc_start: 0.8054 (m-80) cc_final: 0.7735 (m-80) REVERT: n 18 ARG cc_start: 0.8060 (OUTLIER) cc_final: 0.7589 (mtm180) REVERT: n 22 LYS cc_start: 0.8592 (mtpp) cc_final: 0.8341 (mtmm) REVERT: n 75 GLN cc_start: 0.8680 (mt0) cc_final: 0.8353 (mt0) REVERT: o 14 ASP cc_start: 0.7912 (t0) cc_final: 0.7526 (t0) REVERT: o 28 THR cc_start: 0.8337 (m) cc_final: 0.8083 (m) REVERT: p 87 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8268 (ttpt) REVERT: p 94 GLU cc_start: 0.7740 (tm-30) cc_final: 0.7322 (tm-30) REVERT: q 18 LYS cc_start: 0.8449 (tptm) cc_final: 0.8176 (tttm) REVERT: q 56 ARG cc_start: 0.8080 (ttm-80) cc_final: 0.7509 (ttm-80) REVERT: q 62 GLU cc_start: 0.8219 (mm-30) cc_final: 0.7590 (mm-30) REVERT: q 103 ASP cc_start: 0.8474 (m-30) cc_final: 0.8043 (m-30) REVERT: r 104 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8220 (p) REVERT: s 39 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7751 (tm-30) REVERT: s 43 ASN cc_start: 0.8066 (m110) cc_final: 0.7497 (m-40) REVERT: s 92 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7507 (mp0) REVERT: t 68 ASP cc_start: 0.8067 (m-30) cc_final: 0.7728 (m-30) REVERT: u 48 GLU cc_start: 0.8038 (tt0) cc_final: 0.7493 (tt0) REVERT: v 18 GLU cc_start: 0.8280 (tm-30) cc_final: 0.7396 (tm-30) REVERT: v 57 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.8053 (m-30) REVERT: v 77 ARG cc_start: 0.8484 (ttp80) cc_final: 0.8255 (ttp80) REVERT: v 80 GLU cc_start: 0.8100 (mp0) cc_final: 0.7671 (tm-30) REVERT: v 83 VAL cc_start: 0.7703 (m) cc_final: 0.7356 (t) REVERT: x 65 GLU cc_start: 0.8582 (mm-30) cc_final: 0.8238 (mm-30) REVERT: x 70 LYS cc_start: 0.8385 (mmtm) cc_final: 0.7729 (mmtm) REVERT: y 21 ASN cc_start: 0.9039 (m110) cc_final: 0.8259 (m-40) outliers start: 199 outliers final: 167 residues processed: 1359 average time/residue: 1.3301 time to fit residues: 3147.2227 Evaluate side-chains 1415 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 184 poor density : 1231 time to evaluate : 6.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 53 ASP Chi-restraints excluded: chain 5 residue 56 VAL Chi-restraints excluded: chain 5 residue 64 PHE Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 112 VAL Chi-restraints excluded: chain 5 residue 118 TRP Chi-restraints excluded: chain 5 residue 141 ASP Chi-restraints excluded: chain A residue 3 HIS Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 143 ASN Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 32 GLU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 20 ASN Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain J residue 81 ILE Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 77 THR Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 54 MET Chi-restraints excluded: chain a residue 27 THR Chi-restraints excluded: chain a residue 35 ASP Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain b residue 36 GLU Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain f residue 9 LYS Chi-restraints excluded: chain g residue 6 MET Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain g residue 68 LEU Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 205 ASP Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 93 ASP Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain j residue 147 MET Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 23 LEU Chi-restraints excluded: chain l residue 33 ASP Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 45 SER Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 75 VAL Chi-restraints excluded: chain l residue 130 ASN Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain l residue 144 MET Chi-restraints excluded: chain l residue 149 LYS Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain m residue 111 MET Chi-restraints excluded: chain m residue 118 GLN Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 18 ARG Chi-restraints excluded: chain n residue 43 THR Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain o residue 8 ILE Chi-restraints excluded: chain o residue 78 GLU Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 92 LEU Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain p residue 87 LYS Chi-restraints excluded: chain p residue 113 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain r residue 30 SER Chi-restraints excluded: chain r residue 34 LEU Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 5 SER Chi-restraints excluded: chain s residue 32 SER Chi-restraints excluded: chain s residue 35 ASN Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 92 GLU Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 28 PHE Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 44 LEU Chi-restraints excluded: chain v residue 57 ASP Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain x residue 38 SER Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain x residue 79 THR Chi-restraints excluded: chain y residue 39 ILE Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain z residue 20 LYS Chi-restraints excluded: chain z residue 22 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 632 optimal weight: 30.0000 chunk 1019 optimal weight: 5.9990 chunk 622 optimal weight: 0.0970 chunk 483 optimal weight: 50.0000 chunk 708 optimal weight: 0.8980 chunk 1068 optimal weight: 20.0000 chunk 983 optimal weight: 1.9990 chunk 851 optimal weight: 5.9990 chunk 88 optimal weight: 30.0000 chunk 657 optimal weight: 6.9990 chunk 521 optimal weight: 7.9990 overall best weight: 2.9984 ------------------------------------------------------------------------------- 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** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 127 ASN J 128 ASN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 54 GLN V 12 GLN c 45 GLN i 131 ASN ** j 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** k 68 GLN ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 50 GLN ** t 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 26 ASN ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.4163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 167985 Z= 0.240 Angle : 0.604 14.685 251649 Z= 0.329 Chirality : 0.034 0.295 32100 Planarity : 0.006 0.131 13244 Dihedral : 23.586 179.381 84760 Min Nonbonded Distance : 1.027 Molprobity Statistics. All-atom Clashscore : 8.38 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.82 % Favored : 96.08 % Rotamer: Outliers : 3.95 % Allowed : 20.52 % Favored : 75.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.07 (0.11), residues: 5865 helix: 1.28 (0.12), residues: 2000 sheet: -0.23 (0.16), residues: 1122 loop : -0.94 (0.11), residues: 2743 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP h 201 HIS 0.007 0.001 HIS q 77 PHE 0.025 0.001 PHE k 78 TYR 0.031 0.002 TYR k 59 ARG 0.013 0.000 ARG t 17 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11730 Ramachandran restraints generated. 5865 Oldfield, 0 Emsley, 5865 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1437 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1244 time to evaluate : 6.652 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: 5 23 GLU cc_start: 0.7501 (tm-30) cc_final: 0.7294 (tm-30) REVERT: 5 25 PHE cc_start: 0.7222 (t80) cc_final: 0.6802 (t80) REVERT: 5 53 ASP cc_start: 0.6271 (OUTLIER) cc_final: 0.5907 (p0) REVERT: 5 101 TYR cc_start: 0.6800 (m-80) cc_final: 0.6403 (m-80) REVERT: 5 118 TRP cc_start: 0.6261 (OUTLIER) cc_final: 0.5640 (t-100) REVERT: A 78 LYS cc_start: 0.8361 (mmmt) cc_final: 0.7960 (mttm) REVERT: B 101 ARG cc_start: 0.8436 (mtt180) cc_final: 0.8198 (mtt90) REVERT: C 4 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8643 (mp) REVERT: D 115 GLN cc_start: 0.8597 (mt0) cc_final: 0.8292 (mt0) REVERT: D 163 ASN cc_start: 0.9157 (t0) cc_final: 0.8752 (t0) REVERT: D 194 LYS cc_start: 0.8509 (mmmt) cc_final: 0.8006 (mttp) REVERT: E 52 ASN cc_start: 0.8652 (m-40) cc_final: 0.8123 (m110) REVERT: E 133 ARG cc_start: 0.8097 (mpp80) cc_final: 0.7839 (mmt90) REVERT: E 170 LEU cc_start: 0.8990 (OUTLIER) cc_final: 0.8610 (mm) REVERT: F 44 LYS cc_start: 0.7819 (mptt) cc_final: 0.7509 (mmtt) REVERT: F 130 GLU cc_start: 0.8055 (tt0) cc_final: 0.7672 (tt0) REVERT: F 155 GLU cc_start: 0.7556 (pm20) cc_final: 0.7273 (pm20) REVERT: G 129 GLU cc_start: 0.8143 (mt-10) cc_final: 0.7706 (pt0) REVERT: H 38 MET cc_start: -0.0296 (ptm) cc_final: -0.1120 (tpp) REVERT: H 52 MET cc_start: -0.1996 (tpp) cc_final: -0.3264 (ptm) REVERT: H 81 LEU cc_start: 0.2250 (OUTLIER) cc_final: 0.1766 (tt) REVERT: J 96 ARG cc_start: 0.7988 (mmm160) cc_final: 0.7515 (mtp85) REVERT: J 106 LYS cc_start: 0.8975 (ttpt) cc_final: 0.8604 (ttmm) REVERT: K 17 ARG cc_start: 0.7621 (mtm180) cc_final: 0.7401 (mmt90) REVERT: L 99 ASN cc_start: 0.8688 (p0) cc_final: 0.8238 (t0) REVERT: L 123 ARG cc_start: 0.7729 (ttp-110) cc_final: 0.7347 (ptp-170) REVERT: M 104 GLU cc_start: 0.8388 (mt-10) cc_final: 0.8071 (mt-10) REVERT: N 72 ASP cc_start: 0.8311 (t0) cc_final: 0.7643 (t0) REVERT: N 74 GLU cc_start: 0.7760 (pm20) cc_final: 0.7078 (pm20) REVERT: N 82 GLU cc_start: 0.8617 (mp0) cc_final: 0.7900 (mp0) REVERT: O 17 LYS cc_start: 0.9307 (tptt) cc_final: 0.9067 (tppt) REVERT: O 83 LEU cc_start: 0.9058 (OUTLIER) cc_final: 0.8739 (mm) REVERT: O 108 ASP cc_start: 0.8550 (m-30) cc_final: 0.8196 (m-30) REVERT: P 27 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.7633 (tt0) REVERT: P 44 GLU cc_start: 0.8092 (tp30) cc_final: 0.7714 (tp30) REVERT: Q 11 ARG cc_start: 0.8099 (ttm170) cc_final: 0.7628 (tpp-160) REVERT: Q 49 ASP cc_start: 0.7940 (m-30) cc_final: 0.7638 (m-30) REVERT: R 26 ASP cc_start: 0.7994 (p0) cc_final: 0.7665 (p0) REVERT: T 42 GLU cc_start: 0.8027 (OUTLIER) cc_final: 0.7742 (mt-10) REVERT: U 60 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7592 (mp0) REVERT: X 56 MET cc_start: 0.9141 (mtm) cc_final: 0.8661 (mtm) REVERT: X 60 ASP cc_start: 0.7301 (m-30) cc_final: 0.6991 (m-30) REVERT: Z 37 GLU cc_start: 0.8292 (tp30) cc_final: 0.7969 (tp30) REVERT: a 1 MET cc_start: 0.8046 (mtm) cc_final: 0.7774 (mmm) REVERT: a 59 ARG cc_start: 0.8503 (ptm-80) cc_final: 0.8189 (ptm-80) REVERT: b 12 LYS cc_start: 0.8616 (ttmt) cc_final: 0.8218 (mtpp) REVERT: c 30 LYS cc_start: 0.8616 (mttp) cc_final: 0.8362 (mtmt) REVERT: f 9 LYS cc_start: 0.8880 (OUTLIER) cc_final: 0.8618 (mtpm) REVERT: f 15 LYS cc_start: 0.8535 (mmtm) cc_final: 0.8288 (mttt) REVERT: g 136 MET cc_start: 0.7978 (ttp) cc_final: 0.7758 (mmp) REVERT: g 182 PRO cc_start: 0.9142 (Cg_exo) cc_final: 0.8916 (Cg_endo) REVERT: h 183 ASP cc_start: 0.8333 (t70) cc_final: 0.7918 (t70) REVERT: i 85 ASN cc_start: 0.8689 (t0) cc_final: 0.8435 (t0) REVERT: i 136 GLN cc_start: 0.9013 (mm-40) cc_final: 0.8810 (mm-40) REVERT: k 1 MET cc_start: 0.7779 (tpp) cc_final: 0.7405 (tpp) REVERT: k 65 GLU cc_start: 0.7790 (tp30) cc_final: 0.7303 (tp30) REVERT: l 5 ARG cc_start: 0.7811 (tmm-80) cc_final: 0.7493 (ptt180) REVERT: l 126 ASP cc_start: 0.8378 (m-30) cc_final: 0.8003 (t0) REVERT: l 144 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.8027 (mmp) REVERT: l 149 LYS cc_start: 0.7606 (OUTLIER) cc_final: 0.7390 (ptmm) REVERT: m 72 VAL cc_start: 0.9497 (t) cc_final: 0.9265 (p) REVERT: m 90 ASP cc_start: 0.8569 (p0) cc_final: 0.8240 (p0) REVERT: n 6 TYR cc_start: 0.8088 (m-80) cc_final: 0.7716 (m-80) REVERT: n 18 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7545 (mtm180) REVERT: n 75 GLN cc_start: 0.8669 (mt0) cc_final: 0.8351 (mt0) REVERT: o 14 ASP cc_start: 0.7919 (t0) cc_final: 0.7529 (t0) REVERT: o 28 THR cc_start: 0.8356 (m) cc_final: 0.8107 (m) REVERT: p 18 ASP cc_start: 0.7896 (OUTLIER) cc_final: 0.7050 (p0) REVERT: p 87 LYS cc_start: 0.8547 (OUTLIER) cc_final: 0.8245 (ttpt) REVERT: q 18 LYS cc_start: 0.8465 (tptm) cc_final: 0.8196 (tttm) REVERT: q 56 ARG cc_start: 0.8081 (ttm-80) cc_final: 0.7590 (ttm-80) REVERT: q 62 GLU cc_start: 0.8207 (mm-30) cc_final: 0.7699 (tp30) REVERT: q 103 ASP cc_start: 0.8458 (m-30) cc_final: 0.7929 (m-30) REVERT: r 104 THR cc_start: 0.8577 (OUTLIER) cc_final: 0.8246 (p) REVERT: s 39 GLU cc_start: 0.8146 (tm-30) cc_final: 0.7745 (tm-30) REVERT: s 43 ASN cc_start: 0.8104 (m110) cc_final: 0.7543 (m-40) REVERT: s 92 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7517 (mp0) REVERT: t 68 ASP cc_start: 0.8076 (m-30) cc_final: 0.7720 (m-30) REVERT: u 51 ARG cc_start: 0.7411 (ttm-80) cc_final: 0.7200 (ttm-80) REVERT: v 18 GLU cc_start: 0.8366 (tm-30) cc_final: 0.8110 (tm-30) REVERT: v 27 ARG cc_start: 0.8590 (ptt90) cc_final: 0.8327 (ptt-90) REVERT: v 57 ASP cc_start: 0.8254 (t0) cc_final: 0.8038 (m-30) REVERT: v 77 ARG cc_start: 0.8479 (ttp80) cc_final: 0.8231 (ttp80) REVERT: v 83 VAL cc_start: 0.7766 (m) cc_final: 0.7426 (t) REVERT: x 65 GLU cc_start: 0.8629 (mm-30) cc_final: 0.8349 (mm-30) REVERT: x 70 LYS cc_start: 0.8378 (mmtm) cc_final: 0.7739 (mmtm) REVERT: y 21 ASN cc_start: 0.9043 (m110) cc_final: 0.8269 (m-40) outliers start: 193 outliers final: 163 residues processed: 1346 average time/residue: 1.3280 time to fit residues: 3119.8013 Evaluate side-chains 1406 residues out of total 4884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 180 poor density : 1226 time to evaluate : 6.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 5 residue 53 ASP Chi-restraints excluded: chain 5 residue 56 VAL Chi-restraints excluded: chain 5 residue 97 LEU Chi-restraints excluded: chain 5 residue 112 VAL Chi-restraints excluded: chain 5 residue 118 TRP Chi-restraints excluded: chain 5 residue 141 ASP Chi-restraints excluded: chain A residue 3 HIS Chi-restraints excluded: chain A residue 17 GLU Chi-restraints excluded: chain A residue 29 GLU Chi-restraints excluded: chain A residue 30 SER Chi-restraints excluded: chain A residue 53 CYS Chi-restraints excluded: chain B residue 34 LEU Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 130 LEU Chi-restraints excluded: chain B residue 245 VAL Chi-restraints excluded: chain C residue 4 LEU Chi-restraints excluded: chain C residue 18 ASP Chi-restraints excluded: chain C residue 97 SER Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain C residue 161 MET Chi-restraints excluded: chain C residue 207 VAL Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 84 THR Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain E residue 13 VAL Chi-restraints excluded: chain E residue 19 GLU Chi-restraints excluded: chain E residue 68 THR Chi-restraints excluded: chain E residue 130 MET Chi-restraints excluded: chain E residue 132 VAL Chi-restraints excluded: chain E residue 144 ASP Chi-restraints excluded: chain E residue 152 LEU Chi-restraints excluded: chain E residue 170 LEU Chi-restraints excluded: chain F residue 72 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 103 ILE Chi-restraints excluded: chain F residue 133 LEU Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 108 VAL Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain J residue 86 GLN Chi-restraints excluded: chain K residue 80 ASP Chi-restraints excluded: chain K residue 86 LEU Chi-restraints excluded: chain K residue 90 ASN Chi-restraints excluded: chain K residue 97 THR Chi-restraints excluded: chain K residue 104 THR Chi-restraints excluded: chain K residue 109 SER Chi-restraints excluded: chain K residue 116 ILE Chi-restraints excluded: chain L residue 23 ILE Chi-restraints excluded: chain L residue 30 THR Chi-restraints excluded: chain L residue 40 SER Chi-restraints excluded: chain L residue 42 SER Chi-restraints excluded: chain L residue 77 ILE Chi-restraints excluded: chain L residue 85 VAL Chi-restraints excluded: chain L residue 111 ILE Chi-restraints excluded: chain M residue 7 THR Chi-restraints excluded: chain M residue 74 THR Chi-restraints excluded: chain M residue 89 VAL Chi-restraints excluded: chain M residue 93 VAL Chi-restraints excluded: chain M residue 105 MET Chi-restraints excluded: chain N residue 51 LEU Chi-restraints excluded: chain N residue 83 LEU Chi-restraints excluded: chain N residue 100 CYS Chi-restraints excluded: chain N residue 116 VAL Chi-restraints excluded: chain O residue 54 VAL Chi-restraints excluded: chain O residue 58 ILE Chi-restraints excluded: chain O residue 83 LEU Chi-restraints excluded: chain O residue 90 VAL Chi-restraints excluded: chain O residue 91 SER Chi-restraints excluded: chain O residue 95 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 27 GLU Chi-restraints excluded: chain P residue 52 ASN Chi-restraints excluded: chain P residue 60 THR Chi-restraints excluded: chain P residue 80 VAL Chi-restraints excluded: chain P residue 83 SER Chi-restraints excluded: chain P residue 102 GLU Chi-restraints excluded: chain P residue 114 LEU Chi-restraints excluded: chain Q residue 75 SER Chi-restraints excluded: chain Q residue 110 VAL Chi-restraints excluded: chain R residue 6 GLN Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 19 THR Chi-restraints excluded: chain R residue 54 VAL Chi-restraints excluded: chain R residue 99 THR Chi-restraints excluded: chain R residue 102 SER Chi-restraints excluded: chain S residue 4 ILE Chi-restraints excluded: chain S residue 62 ASP Chi-restraints excluded: chain S residue 108 SER Chi-restraints excluded: chain T residue 42 GLU Chi-restraints excluded: chain T residue 78 SER Chi-restraints excluded: chain U residue 15 THR Chi-restraints excluded: chain U residue 60 GLU Chi-restraints excluded: chain U residue 77 THR Chi-restraints excluded: chain V residue 8 VAL Chi-restraints excluded: chain V residue 10 LYS Chi-restraints excluded: chain V residue 20 LEU Chi-restraints excluded: chain V residue 61 LEU Chi-restraints excluded: chain V residue 90 ASP Chi-restraints excluded: chain X residue 30 LEU Chi-restraints excluded: chain Y residue 55 THR Chi-restraints excluded: chain Z residue 7 ILE Chi-restraints excluded: chain Z residue 54 MET Chi-restraints excluded: chain a residue 24 ILE Chi-restraints excluded: chain a residue 27 THR Chi-restraints excluded: chain b residue 29 SER Chi-restraints excluded: chain c residue 9 ILE Chi-restraints excluded: chain c residue 42 VAL Chi-restraints excluded: chain d residue 15 SER Chi-restraints excluded: chain d residue 42 LEU Chi-restraints excluded: chain f residue 9 LYS Chi-restraints excluded: chain g residue 6 MET Chi-restraints excluded: chain g residue 31 ILE Chi-restraints excluded: chain g residue 68 LEU Chi-restraints excluded: chain g residue 72 THR Chi-restraints excluded: chain g residue 199 VAL Chi-restraints excluded: chain g residue 205 ASP Chi-restraints excluded: chain h residue 21 THR Chi-restraints excluded: chain h residue 52 VAL Chi-restraints excluded: chain h residue 93 ASP Chi-restraints excluded: chain i residue 93 LEU Chi-restraints excluded: chain i residue 181 THR Chi-restraints excluded: chain j residue 38 VAL Chi-restraints excluded: chain j residue 120 VAL Chi-restraints excluded: chain j residue 131 THR Chi-restraints excluded: chain j residue 147 MET Chi-restraints excluded: chain k residue 18 VAL Chi-restraints excluded: chain k residue 97 THR Chi-restraints excluded: chain l residue 20 SER Chi-restraints excluded: chain l residue 33 ASP Chi-restraints excluded: chain l residue 38 THR Chi-restraints excluded: chain l residue 45 SER Chi-restraints excluded: chain l residue 47 LEU Chi-restraints excluded: chain l residue 59 LEU Chi-restraints excluded: chain l residue 73 VAL Chi-restraints excluded: chain l residue 75 VAL Chi-restraints excluded: chain l residue 130 ASN Chi-restraints excluded: chain l residue 135 VAL Chi-restraints excluded: chain l residue 144 MET Chi-restraints excluded: chain l residue 149 LYS Chi-restraints excluded: chain m residue 107 SER Chi-restraints excluded: chain m residue 111 MET Chi-restraints excluded: chain n residue 15 SER Chi-restraints excluded: chain n residue 18 ARG Chi-restraints excluded: chain n residue 43 THR Chi-restraints excluded: chain n residue 47 VAL Chi-restraints excluded: chain o residue 78 GLU Chi-restraints excluded: chain o residue 83 THR Chi-restraints excluded: chain o residue 92 LEU Chi-restraints excluded: chain o residue 98 VAL Chi-restraints excluded: chain p residue 18 ASP Chi-restraints excluded: chain p residue 87 LYS Chi-restraints excluded: chain p residue 113 VAL Chi-restraints excluded: chain q residue 35 THR Chi-restraints excluded: chain q residue 40 THR Chi-restraints excluded: chain q residue 74 LEU Chi-restraints excluded: chain r residue 30 SER Chi-restraints excluded: chain r residue 34 LEU Chi-restraints excluded: chain r residue 104 THR Chi-restraints excluded: chain s residue 5 SER Chi-restraints excluded: chain s residue 32 SER Chi-restraints excluded: chain s residue 35 ASN Chi-restraints excluded: chain s residue 37 SER Chi-restraints excluded: chain s residue 45 VAL Chi-restraints excluded: chain s residue 92 GLU Chi-restraints excluded: chain u residue 2 VAL Chi-restraints excluded: chain u residue 24 SER Chi-restraints excluded: chain v residue 14 SER Chi-restraints excluded: chain v residue 28 PHE Chi-restraints excluded: chain v residue 42 THR Chi-restraints excluded: chain v residue 44 LEU Chi-restraints excluded: chain v residue 67 LEU Chi-restraints excluded: chain x residue 38 SER Chi-restraints excluded: chain x residue 48 THR Chi-restraints excluded: chain x residue 49 ILE Chi-restraints excluded: chain x residue 63 THR Chi-restraints excluded: chain y residue 39 ILE Chi-restraints excluded: chain y residue 54 MET Chi-restraints excluded: chain z residue 20 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1073 random chunks: chunk 676 optimal weight: 0.9980 chunk 906 optimal weight: 5.9990 chunk 260 optimal weight: 8.9990 chunk 784 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 236 optimal weight: 8.9990 chunk 852 optimal weight: 9.9990 chunk 356 optimal weight: 10.0000 chunk 875 optimal weight: 3.9990 chunk 107 optimal weight: 50.0000 chunk 157 optimal weight: 10.0000 overall best weight: 4.5988 ------------------------------------------------------------------------------- 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** ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 128 ASN ** L 99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 54 GLN V 12 GLN c 45 GLN i 131 ASN k 52 ASN k 68 GLN ** m 18 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 5 GLN n 50 GLN ** t 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** y 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.101235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.065667 restraints weight = 303735.678| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 1.10 r_work: 0.2736 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2641 rms_B_bonded: 3.22 restraints_weight: 0.2500 r_work (final): 0.2641 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.4325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 167985 Z= 0.343 Angle : 0.655 14.754 251649 Z= 0.351 Chirality : 0.037 0.323 32100 Planarity : 0.006 0.137 13244 Dihedral : 23.604 179.527 84760 Min Nonbonded Distance : 0.997 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.10 % Allowed : 3.99 % Favored : 95.91 % Rotamer: Outliers : 4.05 % Allowed : 20.60 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.11), residues: 5865 helix: 1.16 (0.12), residues: 2000 sheet: -0.28 (0.16), residues: 1125 loop : -0.98 (0.11), residues: 2740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP k 42 HIS 0.007 0.001 HIS t 46 PHE 0.025 0.002 PHE k 78 TYR 0.024 0.002 TYR G 25 ARG 0.011 0.001 ARG t 17 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 49087.05 seconds wall clock time: 853 minutes 4.17 seconds (51184.17 seconds total)