Starting phenix.real_space_refine on Sun Mar 24 15:06:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfx_12303/03_2024/7nfx_12303_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfx_12303/03_2024/7nfx_12303.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfx_12303/03_2024/7nfx_12303.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfx_12303/03_2024/7nfx_12303.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfx_12303/03_2024/7nfx_12303_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7nfx_12303/03_2024/7nfx_12303_neut_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 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 5 6.06 5 P 4021 5.49 5 Mg 2 5.21 5 S 290 5.16 5 C 77612 2.51 5 N 27743 2.21 5 O 38559 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "B ARG 10": "NH1" <-> "NH2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C GLU 146": "OE1" <-> "OE2" Residue "C GLU 149": "OE1" <-> "OE2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C ARG 306": "NH1" <-> "NH2" Residue "C ARG 323": "NH1" <-> "NH2" Residue "C ARG 337": "NH1" <-> "NH2" Residue "D ARG 15": "NH1" <-> "NH2" Residue "D ARG 23": "NH1" <-> "NH2" Residue "D ARG 24": "NH1" <-> "NH2" Residue "D ARG 33": "NH1" <-> "NH2" Residue "D ARG 50": "NH1" <-> "NH2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D ARG 108": "NH1" <-> "NH2" Residue "D GLU 124": "OE1" <-> "OE2" Residue "D ARG 179": "NH1" <-> "NH2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "E GLU 225": "OE1" <-> "OE2" Residue "F ARG 48": "NH1" <-> "NH2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "F ARG 159": "NH1" <-> "NH2" Residue "F GLU 231": "OE1" <-> "OE2" Residue "F ARG 238": "NH1" <-> "NH2" Residue "F ARG 247": "NH1" <-> "NH2" Residue "G ARG 89": "NH1" <-> "NH2" Residue "G ARG 113": "NH1" <-> "NH2" Residue "G GLU 148": "OE1" <-> "OE2" Residue "G ARG 189": "NH1" <-> "NH2" Residue "G GLU 220": "OE1" <-> "OE2" Residue "G ARG 234": "NH1" <-> "NH2" Residue "H ARG 23": "NH1" <-> "NH2" Residue "H ARG 89": "NH1" <-> "NH2" Residue "I ARG 4": "NH1" <-> "NH2" Residue "I ARG 69": "NH1" <-> "NH2" Residue "I ARG 98": "NH1" <-> "NH2" Residue "I ARG 116": "NH1" <-> "NH2" Residue "I ARG 153": "NH1" <-> "NH2" Residue "I ARG 162": "NH1" <-> "NH2" Residue "I ARG 203": "NH1" <-> "NH2" Residue "I ARG 210": "NH1" <-> "NH2" Residue "J GLU 41": "OE1" <-> "OE2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J GLU 80": "OE1" <-> "OE2" Residue "J GLU 111": "OE1" <-> "OE2" Residue "J ARG 146": "NH1" <-> "NH2" Residue "J ARG 164": "NH1" <-> "NH2" Residue "L ARG 31": "NH1" <-> "NH2" Residue "L GLU 80": "OE1" <-> "OE2" Residue "L ARG 102": "NH1" <-> "NH2" Residue "L ARG 116": "NH1" <-> "NH2" Residue "L ARG 158": "NH1" <-> "NH2" Residue "L GLU 164": "OE1" <-> "OE2" Residue "L GLU 171": "OE1" <-> "OE2" Residue "M ARG 11": "NH1" <-> "NH2" Residue "M ARG 98": "NH1" <-> "NH2" Residue "M ARG 109": "NH1" <-> "NH2" Residue "M ARG 119": "NH1" <-> "NH2" Residue "M ARG 121": "NH1" <-> "NH2" Residue "N ARG 24": "NH1" <-> "NH2" Residue "N ARG 50": "NH1" <-> "NH2" Residue "N ARG 65": "NH1" <-> "NH2" Residue "N ARG 96": "NH1" <-> "NH2" Residue "N GLU 131": "OE1" <-> "OE2" Residue "N ARG 169": "NH1" <-> "NH2" Residue "N ARG 189": "NH1" <-> "NH2" Residue "N ARG 194": "NH1" <-> "NH2" Residue "O ARG 78": "NH1" <-> "NH2" Residue "O ARG 128": "NH1" <-> "NH2" Residue "O ARG 140": "NH1" <-> "NH2" Residue "O GLU 144": "OE1" <-> "OE2" Residue "P GLU 31": "OE1" <-> "OE2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "Q ARG 37": "NH1" <-> "NH2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q ARG 91": "NH1" <-> "NH2" Residue "Q GLU 175": "OE1" <-> "OE2" Residue "Q ARG 180": "NH1" <-> "NH2" Residue "Q ARG 181": "NH1" <-> "NH2" Residue "R ARG 38": "NH1" <-> "NH2" Residue "R ARG 42": "NH1" <-> "NH2" Residue "R ARG 74": "NH1" <-> "NH2" Residue "R ARG 117": "NH1" <-> "NH2" Residue "R ARG 173": "NH1" <-> "NH2" Residue "R ARG 176": "NH1" <-> "NH2" Residue "S GLU 9": "OE1" <-> "OE2" Residue "S ARG 31": "NH1" <-> "NH2" Residue "S ARG 43": "NH1" <-> "NH2" Residue "S ARG 83": "NH1" <-> "NH2" Residue "S ARG 111": "NH1" <-> "NH2" Residue "S ARG 118": "NH1" <-> "NH2" Residue "S GLU 131": "OE1" <-> "OE2" Residue "S ARG 139": "NH1" <-> "NH2" Residue "T ARG 130": "NH1" <-> "NH2" Residue "T ARG 136": "NH1" <-> "NH2" Residue "V ARG 48": "NH1" <-> "NH2" Residue "V ARG 51": "NH1" <-> "NH2" Residue "V ARG 89": "NH1" <-> "NH2" Residue "V ARG 131": "NH1" <-> "NH2" Residue "W GLU 4": "OE1" <-> "OE2" Residue "W ARG 19": "NH1" <-> "NH2" Residue "X ARG 53": "NH1" <-> "NH2" Residue "X ARG 129": "NH1" <-> "NH2" Residue "X ARG 139": "NH1" <-> "NH2" Residue "Y ARG 27": "NH1" <-> "NH2" Residue "Y GLU 54": "OE1" <-> "OE2" Residue "Y ARG 87": "NH1" <-> "NH2" Residue "Z ARG 65": "NH1" <-> "NH2" Residue "a ARG 9": "NH1" <-> "NH2" Residue "a ARG 21": "NH1" <-> "NH2" Residue "a ARG 65": "NH1" <-> "NH2" Residue "a ARG 105": "NH1" <-> "NH2" Residue "b ARG 14": "NH1" <-> "NH2" Residue "b ARG 18": "NH1" <-> "NH2" Residue "b ARG 28": "NH1" <-> "NH2" Residue "c ARG 39": "NH1" <-> "NH2" Residue "c TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 90": "NH1" <-> "NH2" Residue "e ARG 36": "NH1" <-> "NH2" Residue "e ARG 39": "NH1" <-> "NH2" Residue "e ARG 128": "NH1" <-> "NH2" Residue "f ARG 89": "NH1" <-> "NH2" Residue "g ARG 29": "NH1" <-> "NH2" Residue "g ARG 60": "NH1" <-> "NH2" Residue "h ARG 7": "NH1" <-> "NH2" Residue "h ARG 94": "NH1" <-> "NH2" Residue "i ARG 45": "NH1" <-> "NH2" Residue "i ARG 68": "NH1" <-> "NH2" Residue "i ARG 76": "NH1" <-> "NH2" Residue "j ARG 20": "NH1" <-> "NH2" Residue "j ARG 45": "NH1" <-> "NH2" Residue "j ARG 55": "NH1" <-> "NH2" Residue "j ARG 56": "NH1" <-> "NH2" Residue "j ARG 72": "NH1" <-> "NH2" Residue "j ARG 79": "NH1" <-> "NH2" Residue "k ARG 3": "NH1" <-> "NH2" Residue "k GLU 7": "OE1" <-> "OE2" Residue "k GLU 54": "OE1" <-> "OE2" Residue "l ARG 28": "NH1" <-> "NH2" Residue "m ARG 97": "NH1" <-> "NH2" Residue "m ARG 111": "NH1" <-> "NH2" Residue "n ARG 2": "NH1" <-> "NH2" Residue "n ARG 23": "NH1" <-> "NH2" Residue "o ARG 40": "NH1" <-> "NH2" Residue "o ARG 43": "NH1" <-> "NH2" Residue "o ARG 78": "NH1" <-> "NH2" Residue "p ARG 17": "NH1" <-> "NH2" Residue "p ARG 49": "NH1" <-> "NH2" Residue "p ARG 84": "NH1" <-> "NH2" Residue "q GLU 71": "OE1" <-> "OE2" Residue "r GLU 28": "OE1" <-> "OE2" Residue "r ARG 35": "NH1" <-> "NH2" Residue "r ARG 112": "NH1" <-> "NH2" Residue "r ARG 113": "NH1" <-> "NH2" Residue "u ARG 76": "NH1" <-> "NH2" Residue "u ARG 93": "NH1" <-> "NH2" Residue "u ARG 105": "NH1" <-> "NH2" Residue "u GLU 144": "OE1" <-> "OE2" Residue "u ARG 171": "NH1" <-> "NH2" Residue "u GLU 228": "OE1" <-> "OE2" Residue "v GLU 130": "OE1" <-> "OE2" Residue "v GLU 198": "OE1" <-> "OE2" Residue "v GLU 200": "OE1" <-> "OE2" Residue "x GLU 34": "OE1" <-> "OE2" Residue "x PHE 106": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x PHE 159": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x GLU 165": "OE1" <-> "OE2" Residue "x GLU 182": "OE1" <-> "OE2" Residue "x ASP 222": "OD1" <-> "OD2" Residue "x PHE 236": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "x ASP 241": "OD1" <-> "OD2" Residue "x ASP 280": "OD1" <-> "OD2" Residue "x ARG 371": "NH1" <-> "NH2" Residue "y ARG 34": "NH1" <-> "NH2" Residue "y ARG 41": "NH1" <-> "NH2" Time to flip residues: 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 148232 Number of models: 1 Model: "" Number of chains: 62 Chain: "1" Number of atoms: 5341 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 5341 Classifications: {'RNA': 249} Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 12, 'rna3p_pur': 124, 'rna3p_pyr': 101} Link IDs: {'rna2p': 24, 'rna3p': 224} Chain breaks: 3 Chain: "5" Number of atoms: 74854 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3493, 74854 Classifications: {'RNA': 3493} Modifications used: {'5*END': 1, 'rna2p_pur': 325, 'rna2p_pyr': 214, 'rna3p_pur': 1579, 'rna3p_pyr': 1374} Link IDs: {'rna2p': 539, 'rna3p': 2953} Chain breaks: 15 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {' U:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "7" Number of atoms: 2558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 2558 Classifications: {'RNA': 120} Modifications used: {'5*END': 1, 'rna2p_pur': 6, 'rna2p_pyr': 6, 'rna3p_pur': 55, 'rna3p_pyr': 53} Link IDs: {'rna2p': 12, 'rna3p': 107} Chain: "8" Number of atoms: 3314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 3314 Classifications: {'RNA': 156} Modifications used: {'5*END': 1, 'rna2p_pur': 14, 'rna2p_pyr': 13, 'rna3p_pur': 62, 'rna3p_pyr': 67} Link IDs: {'rna2p': 26, 'rna3p': 129} Chain: "A" Number of atoms: 1868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 1868 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 14, 'TRANS': 229} Chain: "B" Number of atoms: 3148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3148 Classifications: {'peptide': 394} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 15, 'TRANS': 378} Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "C" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 362, 2883 Classifications: {'peptide': 362} Link IDs: {'PTRANS': 18, 'TRANS': 343} Chain: "D" Number of atoms: 2386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2386 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain: "E" Number of atoms: 1898 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1898 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 15, 'TRANS': 220} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "F" Number of atoms: 1870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1870 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 7, 'TRANS': 217} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "G" Number of atoms: 1934 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1934 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1} Link IDs: {'PTRANS': 14, 'TRANS': 226} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 1516 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1516 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "I" Number of atoms: 1655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1655 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 192} Chain breaks: 1 Chain: "J" Number of atoms: 1353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 169, 1353 Classifications: {'peptide': 169} Link IDs: {'PTRANS': 5, 'TRANS': 163} Chain: "L" Number of atoms: 1703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1703 Classifications: {'peptide': 210} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 14, 'TRANS': 195} Chain: "M" Number of atoms: 1137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1137 Classifications: {'peptide': 138} Link IDs: {'PTRANS': 4, 'TRANS': 133} Chain: "N" Number of atoms: 1701 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1701 Classifications: {'peptide': 203} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain: "O" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1638 Classifications: {'peptide': 199} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 189} Chain: "P" Number of atoms: 1242 Number of conformers: 1 Conformer: "" Number of residues, atoms: 153, 1242 Classifications: {'peptide': 153} Link IDs: {'PTRANS': 7, 'TRANS': 145} Chain: "Q" Number of atoms: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1506 Classifications: {'peptide': 187} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 10, 'TRANS': 176} Chain: "R" Number of atoms: 1508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1508 Classifications: {'peptide': 180} Link IDs: {'PTRANS': 3, 'TRANS': 176} Chain: "S" Number of atoms: 1454 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1454 Classifications: {'peptide': 175} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 163} Chain: "T" Number of atoms: 1298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1298 Classifications: {'peptide': 159} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 149} Chain: "U" Number of atoms: 808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 808 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 2, 'TRANS': 96} Chain: "V" Number of atoms: 979 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 979 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 124} Chain: "W" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 528 Classifications: {'peptide': 63} Link IDs: {'PTRANS': 2, 'TRANS': 60} Chain: "X" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 976 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 110} Chain: "Y" Number of atoms: 1115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1115 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "Z" Number of atoms: 1107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 135, 1107 Classifications: {'peptide': 135} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 128} Chain: "a" Number of atoms: 1162 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1162 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "b" Number of atoms: 609 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 609 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Chain: "c" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 732 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "d" Number of atoms: 888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 888 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "e" Number of atoms: 1053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1053 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 6, 'TRANS': 121} Chain: "f" Number of atoms: 876 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 876 Classifications: {'peptide': 109} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain: "g" Number of atoms: 906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 906 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "h" Number of atoms: 1013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1013 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "i" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 830 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "j" Number of atoms: 705 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 705 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "k" Number of atoms: 569 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 569 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 66} Chain: "l" Number of atoms: 444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 444 Classifications: {'peptide': 50} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 47} Chain: "m" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 429 Classifications: {'peptide': 52} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 48} Chain: "n" Number of atoms: 222 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 222 Classifications: {'peptide': 23} Link IDs: {'TRANS': 22} Chain: "o" Number of atoms: 851 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 851 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 4, 'TRANS': 99} Chain: "p" Number of atoms: 708 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 708 Classifications: {'peptide': 91} Modifications used: {'COO': 1} Link IDs: {'TRANS': 90} Chain: "q" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 842 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "r" Number of atoms: 1001 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1001 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 5, 'TRANS': 119} Chain: "s" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 105 Classifications: {'peptide': 21} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'TRANS': 20} Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'UNK:plan-1': 21} Unresolved non-hydrogen planarities: 21 Chain: "t" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 693 Classifications: {'peptide': 88} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 85} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 9 Chain: "u" Number of atoms: 1637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1637 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 2, 'TRANS': 193} Chain: "v" Number of atoms: 1455 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1455 Classifications: {'peptide': 186} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 182} Chain breaks: 1 Chain: "w" Number of atoms: 623 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 75, 617 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} Conformer: "B" Number of residues, atoms: 75, 617 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 1, 'TRANS': 73} bond proxies already assigned to first conformer: 621 Chain: "x" Number of atoms: 3236 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3236 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 10, 'TRANS': 406} Chain breaks: 1 Chain: "y" Number of atoms: 1133 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1133 Classifications: {'peptide': 147} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 2, 'TRANS': 144} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 57 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 3, 'ARG:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "z" Number of atoms: 161 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 161 Classifications: {'peptide': 19} Link IDs: {'PTRANS': 5, 'TRANS': 13} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "j" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "m" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "o" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "p" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "v" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GTP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "x" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 33 Unusual residues: {' MG': 1, 'GNP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM A0NW4 SG CYS g 46 59.310 120.371 111.920 1.00 26.61 S ATOM A0NWL SG CYS g 49 58.613 118.736 115.335 1.00 28.99 S ATOM A0O3W SG CYS g 83 58.475 116.594 112.270 1.00 25.18 S ATOM A0O4G SG CYS g 86 55.862 119.270 112.685 1.00 26.45 S ATOM A0PU7 SG CYS j 19 107.649 141.850 86.862 1.00 16.45 S ATOM A0PUZ SG CYS j 22 111.021 143.664 86.815 1.00 12.78 S ATOM A0PXI SG CYS j 34 108.198 144.958 88.968 1.00 15.07 S ATOM A0PY1 SG CYS j 37 108.029 145.263 85.173 1.00 16.57 S ATOM A0R6J SG CYS m 96 154.212 197.458 177.169 1.00 24.69 S ATOM A0R79 SG CYS m 99 155.028 193.799 176.575 1.00 23.47 S ATOM A0R9R SG CYS m 110 157.793 196.064 177.663 1.00 25.02 S ATOM A0RAZ SG CYS m 115 156.352 196.402 174.168 1.00 23.66 S ATOM A0RMN SG CYS o 12 98.752 236.607 88.385 1.00 29.84 S ATOM A0RNB SG CYS o 15 97.474 239.431 86.234 1.00 29.12 S ATOM A0S0C SG CYS o 72 95.245 237.989 89.049 1.00 27.99 S ATOM A0S1D SG CYS o 77 96.027 236.034 85.814 1.00 29.97 S ATOM A0SG3 SG CYS p 39 54.129 129.736 125.390 1.00 15.59 S ATOM A0SGQ SG CYS p 42 53.880 126.304 127.094 1.00 17.02 S ATOM A0SK4 SG CYS p 57 57.009 127.377 125.102 1.00 15.86 S ATOM A0SKK SG CYS p 60 53.610 126.353 123.526 1.00 17.83 S Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ACYS w 39 " occ=0.50 ... (10 atoms not shown) pdb=" SG BCYS w 39 " occ=0.50 Time building chain proxies: 58.19, per 1000 atoms: 0.39 Number of scatterers: 148232 At special positions: 0 Unit cell: (255.942, 309.042, 270.81, 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 5 29.99 S 290 16.00 P 4021 15.00 Mg 2 11.99 O 38559 8.00 N 27743 7.00 C 77612 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: 64.77 Conformation dependent library (CDL) restraints added in 8.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN g 201 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 86 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 83 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 49 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 46 " pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " pdb=" ZN m 201 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 99 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 110 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 115 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 96 " pdb=" ZN o 201 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 15 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 77 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 12 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 72 " pdb=" ZN p 100 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 42 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 60 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 57 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 39 " Number of angles added : 30 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14376 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: 270 helices and 67 sheets defined 44.7% alpha, 13.2% beta 1237 base pairs and 1953 stacking pairs defined. Time for finding SS restraints: 80.81 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.815A pdb=" N ARG A 9 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N LYS A 10 " --> pdb=" O ARG A 6 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N GLY A 11 " --> pdb=" O GLY A 7 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ALA A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLY A 13 " --> pdb=" O ARG A 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 5 through 13' Processing helix chain 'A' and resid 33 through 39 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.727A pdb=" N MET A 107 " --> pdb=" O PRO A 103 " (cutoff:3.500A) Proline residue: A 108 - end of helix No H-bonds generated for 'chain 'A' and resid 103 through 108' Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.830A pdb=" N ALA A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ALA A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N LYS A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 4.971A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 120 removed outlier: 4.010A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N PHE B 118 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N TYR B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N LYS B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 139 removed outlier: 3.876A pdb=" N CYS B 134 " --> pdb=" O PHE B 130 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N LYS B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N LYS B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TRP B 137 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLN B 138 " --> pdb=" O CYS B 134 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 156 Processing helix chain 'B' and resid 167 through 172 removed outlier: 4.480A pdb=" N LEU B 171 " --> pdb=" O GLN B 167 " (cutoff:3.500A) Proline residue: B 172 - end of helix No H-bonds generated for 'chain 'B' and resid 167 through 172' Processing helix chain 'B' and resid 189 through 201 Processing helix chain 'B' and resid 206 through 211 removed outlier: 3.947A pdb=" N VAL B 210 " --> pdb=" O PRO B 206 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 235 Processing helix chain 'B' and resid 299 through 304 removed outlier: 4.481A pdb=" N ALA B 303 " --> pdb=" O ILE B 299 " (cutoff:3.500A) Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.742A pdb=" N GLU B 361 " --> pdb=" O ARG B 357 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 390 Processing helix chain 'C' and resid 25 through 30 removed outlier: 4.013A pdb=" N LYS C 29 " --> pdb=" O PRO C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 33 through 49 removed outlier: 4.046A pdb=" N LYS C 46 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASN C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N ASN C 48 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ARG C 49 " --> pdb=" O ARG C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 133 removed outlier: 4.039A pdb=" N ALA C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N LEU C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Processing helix chain 'C' and resid 134 through 141 removed outlier: 3.587A pdb=" N GLY C 141 " --> pdb=" O VAL C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 162 removed outlier: 4.281A pdb=" N GLY C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LYS C 162 " --> pdb=" O VAL C 158 " (cutoff:3.500A) Processing helix chain 'C' and resid 163 through 175 Processing helix chain 'C' and resid 176 through 187 removed outlier: 4.008A pdb=" N ILE C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 Processing helix chain 'C' and resid 216 through 223 removed outlier: 4.887A pdb=" N ASN C 223 " --> pdb=" O LYS C 219 " (cutoff:3.500A) Processing helix chain 'C' and resid 236 through 242 Proline residue: C 242 - end of helix Processing helix chain 'C' and resid 253 through 264 removed outlier: 4.303A pdb=" N ASP C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N ASP C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 removed outlier: 3.511A pdb=" N ILE C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LYS C 294 " --> pdb=" O SER C 290 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 303 removed outlier: 4.049A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N LEU C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N ARG C 303 " --> pdb=" O GLN C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 322 removed outlier: 4.533A pdb=" N LEU C 322 " --> pdb=" O PRO C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 323 through 329 Processing helix chain 'C' and resid 330 through 363 removed outlier: 4.177A pdb=" N THR C 334 " --> pdb=" O PRO C 330 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N THR C 339 " --> pdb=" O MET C 335 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N ILE C 340 " --> pdb=" O ARG C 336 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N LEU C 341 " --> pdb=" O ARG C 337 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N ARG C 342 " --> pdb=" O ASN C 338 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N GLN C 343 " --> pdb=" O THR C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 58 through 63 removed outlier: 5.298A pdb=" N GLN C 61 " --> pdb=" O ALA C 58 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N THR C 62 " --> pdb=" O GLY C 59 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N SER C 63 " --> pdb=" O HIS C 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 58 through 63' Processing helix chain 'D' and resid 9 through 16 Processing helix chain 'D' and resid 20 through 26 Processing helix chain 'D' and resid 29 through 37 removed outlier: 4.082A pdb=" N ARG D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 removed outlier: 4.493A pdb=" N LEU D 83 " --> pdb=" O TYR D 79 " (cutoff:3.500A) Proline residue: D 84 - end of helix Processing helix chain 'D' and resid 94 through 114 Processing helix chain 'D' and resid 115 through 120 removed outlier: 4.805A pdb=" N TYR D 119 " --> pdb=" O MET D 115 " (cutoff:3.500A) removed outlier: 5.054A pdb=" N GLU D 120 " --> pdb=" O ASP D 116 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 115 through 120' Processing helix chain 'D' and resid 157 through 170 Processing helix chain 'D' and resid 191 through 201 removed outlier: 6.573A pdb=" N HIS D 195 " --> pdb=" O ASN D 191 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ARG D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 215 Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 225 through 230 removed outlier: 4.577A pdb=" N ASN D 229 " --> pdb=" O GLN D 225 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N ASN D 230 " --> pdb=" O TYR D 226 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 225 through 230' Processing helix chain 'D' and resid 232 through 250 removed outlier: 3.518A pdb=" N MET D 236 " --> pdb=" O THR D 232 " (cutoff:3.500A) removed outlier: 4.795A pdb=" N GLU D 237 " --> pdb=" O PRO D 233 " (cutoff:3.500A) removed outlier: 4.834A pdb=" N GLU D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 294 removed outlier: 4.435A pdb=" N ARG D 293 " --> pdb=" O ARG D 289 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ALA D 294 " --> pdb=" O ALA D 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 63 removed outlier: 3.566A pdb=" N MET E 58 " --> pdb=" O SER E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 186 through 191 removed outlier: 5.332A pdb=" N ILE E 191 " --> pdb=" O GLN E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 214 removed outlier: 4.170A pdb=" N LYS E 214 " --> pdb=" O ASP E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 258 removed outlier: 3.716A pdb=" N LYS E 243 " --> pdb=" O THR E 239 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N GLN E 252 " --> pdb=" O ALA E 248 " (cutoff:3.500A) Proline residue: E 255 - end of helix Processing helix chain 'E' and resid 262 through 270 removed outlier: 4.976A pdb=" N VAL E 270 " --> pdb=" O TYR E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 283 removed outlier: 5.154A pdb=" N VAL E 283 " --> pdb=" O PRO E 279 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 179 Processing helix chain 'F' and resid 26 through 81 removed outlier: 3.520A pdb=" N ILE F 71 " --> pdb=" O TYR F 67 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA F 80 " --> pdb=" O MET F 76 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N GLY F 81 " --> pdb=" O ALA F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 115 Processing helix chain 'F' and resid 128 through 139 Processing helix chain 'F' and resid 148 through 158 Processing helix chain 'F' and resid 173 through 181 removed outlier: 4.272A pdb=" N ILE F 177 " --> pdb=" O ASP F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 199 removed outlier: 4.079A pdb=" N VAL F 199 " --> pdb=" O GLU F 195 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 211 removed outlier: 5.002A pdb=" N TRP F 211 " --> pdb=" O ASN F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 239 through 250 removed outlier: 4.891A pdb=" N ASN F 243 " --> pdb=" O GLU F 239 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ARG F 244 " --> pdb=" O ASP F 240 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 74 removed outlier: 3.645A pdb=" N ALA G 68 " --> pdb=" O GLN G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 removed outlier: 5.211A pdb=" N PHE G 83 " --> pdb=" O ALA G 79 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N THR G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N GLN G 85 " --> pdb=" O ASN G 81 " (cutoff:3.500A) removed outlier: 5.377A pdb=" N VAL G 86 " --> pdb=" O GLN G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 103 removed outlier: 4.042A pdb=" N LYS G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N TYR G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 123 removed outlier: 3.750A pdb=" N LYS G 110 " --> pdb=" O THR G 106 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N LYS G 111 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N GLN G 112 " --> pdb=" O GLN G 108 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N ALA G 122 " --> pdb=" O ALA G 118 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA G 123 " --> pdb=" O GLU G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 150 Processing helix chain 'G' and resid 167 through 178 Proline residue: G 171 - end of helix Processing helix chain 'G' and resid 186 through 195 removed outlier: 3.720A pdb=" N LEU G 193 " --> pdb=" O ARG G 189 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N VAL G 194 " --> pdb=" O LEU G 190 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N HIS G 195 " --> pdb=" O CYS G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 226 removed outlier: 4.658A pdb=" N GLY G 213 " --> pdb=" O SER G 209 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ALA G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 236 Processing helix chain 'G' and resid 243 through 262 removed outlier: 3.917A pdb=" N LEU G 261 " --> pdb=" O LYS G 257 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 86 removed outlier: 3.996A pdb=" N THR H 69 " --> pdb=" O LYS H 65 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N VAL H 70 " --> pdb=" O GLU H 66 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N ARG H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N THR H 72 " --> pdb=" O ALA H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 166 removed outlier: 4.141A pdb=" N THR H 165 " --> pdb=" O ILE H 161 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N THR H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 176 removed outlier: 4.073A pdb=" N LEU H 176 " --> pdb=" O ILE H 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 10 removed outlier: 4.128A pdb=" N TYR I 9 " --> pdb=" O PRO I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 47 removed outlier: 4.067A pdb=" N PHE I 46 " --> pdb=" O LYS I 42 " (cutoff:3.500A) Proline residue: I 47 - end of helix No H-bonds generated for 'chain 'I' and resid 42 through 47' Processing helix chain 'I' and resid 61 through 80 Processing helix chain 'I' and resid 144 through 160 removed outlier: 3.911A pdb=" N PHE I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) removed outlier: 4.332A pdb=" N LYS I 158 " --> pdb=" O ARG I 154 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N PHE I 159 " --> pdb=" O ALA I 155 " (cutoff:3.500A) Proline residue: I 160 - end of helix Processing helix chain 'I' and resid 177 through 188 removed outlier: 4.315A pdb=" N GLU I 182 " --> pdb=" O ALA I 178 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N ASP I 183 " --> pdb=" O ASP I 179 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 214 removed outlier: 4.149A pdb=" N HIS I 213 " --> pdb=" O TRP I 209 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N SER I 214 " --> pdb=" O ARG I 210 " (cutoff:3.500A) Processing helix chain 'J' and resid 30 through 45 Processing helix chain 'J' and resid 76 through 91 Processing helix chain 'J' and resid 111 through 116 removed outlier: 4.525A pdb=" N LEU J 115 " --> pdb=" O GLU J 111 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N GLY J 116 " --> pdb=" O HIS J 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 111 through 116' Processing helix chain 'J' and resid 139 through 144 removed outlier: 4.703A pdb=" N ASP J 143 " --> pdb=" O PHE J 139 " (cutoff:3.500A) Processing helix chain 'J' and resid 158 through 170 Processing helix chain 'L' and resid 17 through 22 removed outlier: 3.786A pdb=" N ARG L 21 " --> pdb=" O ASP L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 27 through 47 removed outlier: 3.863A pdb=" N ALA L 47 " --> pdb=" O ALA L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 77 through 85 Processing helix chain 'L' and resid 87 through 95 removed outlier: 3.592A pdb=" N ARG L 92 " --> pdb=" O LYS L 88 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 124 removed outlier: 3.908A pdb=" N LEU L 110 " --> pdb=" O SER L 106 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 147 removed outlier: 3.963A pdb=" N GLU L 143 " --> pdb=" O SER L 139 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N LEU L 144 " --> pdb=" O SER L 140 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LYS L 145 " --> pdb=" O ALA L 141 " (cutoff:3.500A) removed outlier: 5.577A pdb=" N LEU L 146 " --> pdb=" O GLU L 142 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA L 147 " --> pdb=" O GLU L 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 139 through 147' Processing helix chain 'L' and resid 170 through 176 Processing helix chain 'L' and resid 177 through 192 Processing helix chain 'L' and resid 193 through 211 removed outlier: 3.586A pdb=" N LYS L 210 " --> pdb=" O ASP L 206 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS L 211 " --> pdb=" O VAL L 207 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 56 removed outlier: 4.013A pdb=" N MET M 55 " --> pdb=" O PRO M 51 " (cutoff:3.500A) removed outlier: 5.046A pdb=" N GLN M 56 " --> pdb=" O PHE M 52 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 51 through 56' Processing helix chain 'M' and resid 69 through 81 removed outlier: 6.464A pdb=" N VAL M 73 " --> pdb=" O ARG M 69 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG M 74 " --> pdb=" O GLN M 70 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 90 removed outlier: 5.392A pdb=" N ARG M 90 " --> pdb=" O TRP M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 104 Processing helix chain 'M' and resid 106 through 139 Processing helix chain 'N' and resid 2 through 14 removed outlier: 3.929A pdb=" N TYR N 6 " --> pdb=" O GLY N 2 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N LYS N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 34 removed outlier: 4.713A pdb=" N SER N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 Processing helix chain 'N' and resid 83 through 88 removed outlier: 3.969A pdb=" N HIS N 87 " --> pdb=" O LYS N 83 " (cutoff:3.500A) removed outlier: 4.943A pdb=" N GLY N 88 " --> pdb=" O PRO N 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 83 through 88' Processing helix chain 'N' and resid 97 through 111 removed outlier: 3.710A pdb=" N GLY N 111 " --> pdb=" O GLY N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 139 through 146 removed outlier: 4.110A pdb=" N ASN N 145 " --> pdb=" O ALA N 141 " (cutoff:3.500A) Proline residue: N 146 - end of helix Processing helix chain 'N' and resid 158 through 163 Processing helix chain 'N' and resid 165 through 173 removed outlier: 3.615A pdb=" N LYS N 170 " --> pdb=" O SER N 166 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N SER N 171 " --> pdb=" O ALA N 167 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG N 172 " --> pdb=" O GLY N 168 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLY N 173 " --> pdb=" O ARG N 169 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 197 Processing helix chain 'N' and resid 147 through 152 removed outlier: 4.547A pdb=" N TRP N 150 " --> pdb=" O ASP N 147 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ILE N 151 " --> pdb=" O THR N 148 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 30 removed outlier: 3.717A pdb=" N ILE O 22 " --> pdb=" O ARG O 18 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N LEU O 29 " --> pdb=" O LYS O 25 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLY O 30 " --> pdb=" O GLN O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 46 through 61 removed outlier: 5.322A pdb=" N ARG O 61 " --> pdb=" O PHE O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 70 removed outlier: 3.709A pdb=" N GLY O 69 " --> pdb=" O ASN O 65 " (cutoff:3.500A) Proline residue: O 70 - end of helix No H-bonds generated for 'chain 'O' and resid 65 through 70' Processing helix chain 'O' and resid 75 through 89 removed outlier: 3.540A pdb=" N MET O 87 " --> pdb=" O THR O 83 " (cutoff:3.500A) Proline residue: O 89 - end of helix Processing helix chain 'O' and resid 92 through 103 removed outlier: 5.095A pdb=" N LYS O 103 " --> pdb=" O LEU O 99 " (cutoff:3.500A) Processing helix chain 'O' and resid 124 through 129 Processing helix chain 'O' and resid 137 through 146 Processing helix chain 'O' and resid 150 through 190 removed outlier: 5.492A pdb=" N LYS O 187 " --> pdb=" O LYS O 183 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N LYS O 188 " --> pdb=" O ASN O 184 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ILE O 189 " --> pdb=" O VAL O 185 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 200 removed outlier: 3.775A pdb=" N VAL O 195 " --> pdb=" O ARG O 191 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS O 199 " --> pdb=" O VAL O 195 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLY O 200 " --> pdb=" O LEU O 196 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 37 Processing helix chain 'P' and resid 40 through 54 Processing helix chain 'P' and resid 70 through 77 removed outlier: 4.455A pdb=" N LYS P 74 " --> pdb=" O CYS P 70 " (cutoff:3.500A) removed outlier: 4.630A pdb=" N GLN P 75 " --> pdb=" O ALA P 71 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N TRP P 76 " --> pdb=" O GLN P 72 " (cutoff:3.500A) Processing helix chain 'P' and resid 84 through 106 Processing helix chain 'Q' and resid 22 through 39 removed outlier: 3.571A pdb=" N ARG Q 26 " --> pdb=" O ASP Q 22 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 54 removed outlier: 4.225A pdb=" N GLN Q 45 " --> pdb=" O SER Q 41 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N SER Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 72 removed outlier: 3.858A pdb=" N LEU Q 72 " --> pdb=" O ARG Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 117 Processing helix chain 'Q' and resid 122 through 130 Processing helix chain 'Q' and resid 146 through 153 removed outlier: 4.276A pdb=" N ARG Q 150 " --> pdb=" O ARG Q 146 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N HIS Q 151 " --> pdb=" O GLU Q 147 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N PHE Q 152 " --> pdb=" O VAL Q 148 " (cutoff:3.500A) removed outlier: 5.395A pdb=" N GLY Q 153 " --> pdb=" O TYR Q 149 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 146 through 153' Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 18 through 23 removed outlier: 6.509A pdb=" N VAL R 22 " --> pdb=" O GLY R 18 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N TRP R 23 " --> pdb=" O LYS R 19 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 18 through 23' Processing helix chain 'R' and resid 28 through 36 removed outlier: 3.758A pdb=" N ILE R 32 " --> pdb=" O GLU R 28 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ALA R 35 " --> pdb=" O GLU R 31 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N ASN R 36 " --> pdb=" O ILE R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 48 removed outlier: 3.830A pdb=" N ILE R 41 " --> pdb=" O SER R 37 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ARG R 42 " --> pdb=" O ARG R 38 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS R 43 " --> pdb=" O GLN R 39 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 73 Processing helix chain 'R' and resid 84 through 113 Proline residue: R 90 - end of helix removed outlier: 6.600A pdb=" N VAL R 93 " --> pdb=" O MET R 89 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 130 Processing helix chain 'R' and resid 134 through 181 removed outlier: 3.502A pdb=" N LEU R 138 " --> pdb=" O ASN R 134 " (cutoff:3.500A) Processing helix chain 'S' and resid 36 through 52 Processing helix chain 'S' and resid 101 through 117 Processing helix chain 'S' and resid 120 through 125 removed outlier: 5.096A pdb=" N GLN S 125 " --> pdb=" O ALA S 121 " (cutoff:3.500A) Processing helix chain 'S' and resid 139 through 147 removed outlier: 4.622A pdb=" N PHE S 145 " --> pdb=" O ALA S 141 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N HIS S 146 " --> pdb=" O VAL S 142 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N ASP S 147 " --> pdb=" O LYS S 143 " (cutoff:3.500A) Processing helix chain 'S' and resid 161 through 166 Proline residue: S 165 - end of helix No H-bonds generated for 'chain 'S' and resid 161 through 166' Processing helix chain 'T' and resid 11 through 16 removed outlier: 3.529A pdb=" N PHE T 15 " --> pdb=" O THR T 11 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N SER T 16 " --> pdb=" O ARG T 12 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 11 through 16' Processing helix chain 'T' and resid 26 through 32 removed outlier: 4.388A pdb=" N TYR T 30 " --> pdb=" O PRO T 26 " (cutoff:3.500A) Processing helix chain 'T' and resid 54 through 59 removed outlier: 3.652A pdb=" N HIS T 58 " --> pdb=" O HIS T 54 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N GLY T 59 " --> pdb=" O LYS T 55 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 54 through 59' Processing helix chain 'T' and resid 92 through 97 removed outlier: 4.078A pdb=" N ILE T 96 " --> pdb=" O ARG T 92 " (cutoff:3.500A) removed outlier: 5.316A pdb=" N LYS T 97 " --> pdb=" O ILE T 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 92 through 97' Processing helix chain 'T' and resid 99 through 121 removed outlier: 4.259A pdb=" N ASP T 103 " --> pdb=" O SER T 99 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N ALA T 119 " --> pdb=" O LYS T 115 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N LYS T 120 " --> pdb=" O LYS T 116 " (cutoff:3.500A) removed outlier: 5.019A pdb=" N GLU T 121 " --> pdb=" O LYS T 117 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 32 removed outlier: 4.882A pdb=" N VAL U 29 " --> pdb=" O CYS U 25 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N GLU U 30 " --> pdb=" O THR U 26 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N ASP U 31 " --> pdb=" O HIS U 27 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY U 32 " --> pdb=" O PRO U 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 25 through 32' Processing helix chain 'U' and resid 35 through 47 Processing helix chain 'U' and resid 55 through 60 removed outlier: 5.142A pdb=" N GLY U 59 " --> pdb=" O ASN U 55 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL U 60 " --> pdb=" O LEU U 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 55 through 60' Processing helix chain 'U' and resid 79 through 95 removed outlier: 4.182A pdb=" N LEU U 83 " --> pdb=" O SER U 79 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LYS U 84 " --> pdb=" O LYS U 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 69 through 74 removed outlier: 5.395A pdb=" N LYS V 74 " --> pdb=" O PRO V 70 " (cutoff:3.500A) Processing helix chain 'V' and resid 122 through 130 Proline residue: V 130 - end of helix Processing helix chain 'V' and resid 131 through 136 Processing helix chain 'W' and resid 33 through 43 removed outlier: 3.694A pdb=" N LYS W 43 " --> pdb=" O ALA W 39 " (cutoff:3.500A) Processing helix chain 'W' and resid 45 through 50 removed outlier: 4.053A pdb=" N ILE W 49 " --> pdb=" O ASN W 45 " (cutoff:3.500A) removed outlier: 5.601A pdb=" N ASN W 50 " --> pdb=" O PRO W 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'W' and resid 45 through 50' Processing helix chain 'W' and resid 52 through 60 Processing helix chain 'X' and resid 72 through 78 removed outlier: 3.910A pdb=" N ILE X 77 " --> pdb=" O HIS X 73 " (cutoff:3.500A) removed outlier: 5.029A pdb=" N LYS X 78 " --> pdb=" O TYR X 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 83 through 93 Processing helix chain 'X' and resid 105 through 117 Processing helix chain 'X' and resid 145 through 154 Processing helix chain 'Y' and resid 10 through 21 Processing helix chain 'Y' and resid 22 through 31 removed outlier: 4.321A pdb=" N SER Y 31 " --> pdb=" O ARG Y 27 " (cutoff:3.500A) Processing helix chain 'Y' and resid 35 through 43 Processing helix chain 'Y' and resid 100 through 105 removed outlier: 4.026A pdb=" N VAL Y 104 " --> pdb=" O HIS Y 100 " (cutoff:3.500A) removed outlier: 5.156A pdb=" N VAL Y 105 " --> pdb=" O PRO Y 101 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 100 through 105' Processing helix chain 'Y' and resid 112 through 134 Processing helix chain 'Z' and resid 58 through 67 removed outlier: 4.498A pdb=" N ILE Z 62 " --> pdb=" O GLY Z 58 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N LYS Z 67 " --> pdb=" O ALA Z 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 81 removed outlier: 3.655A pdb=" N LEU Z 80 " --> pdb=" O ASN Z 76 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N MET Z 81 " --> pdb=" O TYR Z 77 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 76 through 81' Processing helix chain 'Z' and resid 92 through 97 removed outlier: 3.560A pdb=" N VAL Z 96 " --> pdb=" O ASP Z 92 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ASN Z 97 " --> pdb=" O LYS Z 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 92 through 97' Processing helix chain 'Z' and resid 98 through 104 removed outlier: 4.930A pdb=" N ARG Z 102 " --> pdb=" O LYS Z 98 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N ASP Z 103 " --> pdb=" O ASP Z 99 " (cutoff:3.500A) Proline residue: Z 104 - end of helix No H-bonds generated for 'chain 'Z' and resid 98 through 104' Processing helix chain 'Z' and resid 105 through 124 removed outlier: 3.802A pdb=" N LYS Z 123 " --> pdb=" O GLU Z 119 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N THR Z 124 " --> pdb=" O GLU Z 120 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 133 removed outlier: 3.743A pdb=" N PHE Z 131 " --> pdb=" O ASN Z 127 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N GLN Z 132 " --> pdb=" O LYS Z 128 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LYS Z 133 " --> pdb=" O TRP Z 129 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 127 through 133' Processing helix chain 'a' and resid 2 through 7 removed outlier: 5.363A pdb=" N LYS a 7 " --> pdb=" O SER a 3 " (cutoff:3.500A) Processing helix chain 'a' and resid 41 through 48 Processing helix chain 'a' and resid 64 through 69 removed outlier: 3.936A pdb=" N SER a 68 " --> pdb=" O LYS a 64 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 83 removed outlier: 3.792A pdb=" N LEU a 78 " --> pdb=" O ASN a 74 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N TRP a 79 " --> pdb=" O LEU a 75 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N THR a 80 " --> pdb=" O ASP a 76 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LEU a 81 " --> pdb=" O LYS a 77 " (cutoff:3.500A) removed outlier: 4.437A pdb=" N VAL a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N SER a 83 " --> pdb=" O TRP a 79 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 74 through 83' Processing helix chain 'a' and resid 84 through 91 removed outlier: 3.890A pdb=" N ALA a 90 " --> pdb=" O THR a 86 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N ALA a 91 " --> pdb=" O ARG a 87 " (cutoff:3.500A) Processing helix chain 'a' and resid 102 through 107 Processing helix chain 'a' and resid 130 through 141 Processing helix chain 'b' and resid 11 through 20 removed outlier: 4.224A pdb=" N ASN b 19 " --> pdb=" O LYS b 15 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY b 20 " --> pdb=" O TRP b 16 " (cutoff:3.500A) Processing helix chain 'b' and resid 36 through 51 removed outlier: 4.629A pdb=" N LYS b 51 " --> pdb=" O LYS b 47 " (cutoff:3.500A) Processing helix chain 'b' and resid 53 through 76 Processing helix chain 'c' and resid 13 through 24 removed outlier: 3.885A pdb=" N ARG c 17 " --> pdb=" O SER c 13 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 41 removed outlier: 4.014A pdb=" N THR c 34 " --> pdb=" O GLY c 30 " (cutoff:3.500A) Processing helix chain 'c' and resid 53 through 68 Processing helix chain 'c' and resid 77 through 86 Processing helix chain 'd' and resid 28 through 34 removed outlier: 3.857A pdb=" N ARG d 32 " --> pdb=" O ASN d 28 " (cutoff:3.500A) Processing helix chain 'd' and resid 37 through 57 removed outlier: 3.663A pdb=" N ARG d 41 " --> pdb=" O GLY d 37 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ALA d 42 " --> pdb=" O PHE d 38 " (cutoff:3.500A) Proline residue: d 43 - end of helix Processing helix chain 'd' and resid 65 through 74 Processing helix chain 'e' and resid 24 through 29 removed outlier: 3.631A pdb=" N TYR e 28 " --> pdb=" O GLN e 24 " (cutoff:3.500A) removed outlier: 5.128A pdb=" N VAL e 29 " --> pdb=" O SER e 25 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 24 through 29' Processing helix chain 'e' and resid 43 through 48 Processing helix chain 'e' and resid 81 through 90 removed outlier: 4.344A pdb=" N VAL e 87 " --> pdb=" O LYS e 83 " (cutoff:3.500A) removed outlier: 4.653A pdb=" N LEU e 88 " --> pdb=" O GLU e 84 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LEU e 89 " --> pdb=" O LEU e 85 " (cutoff:3.500A) removed outlier: 5.281A pdb=" N MET e 90 " --> pdb=" O GLU e 86 " (cutoff:3.500A) Processing helix chain 'e' and resid 104 through 119 removed outlier: 3.579A pdb=" N ALA e 110 " --> pdb=" O LYS e 106 " (cutoff:3.500A) Processing helix chain 'f' and resid 35 through 40 removed outlier: 4.046A pdb=" N THR f 39 " --> pdb=" O ALA f 35 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU f 40 " --> pdb=" O ARG f 36 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 35 through 40' Processing helix chain 'g' and resid 60 through 68 removed outlier: 3.610A pdb=" N MET g 65 " --> pdb=" O PRO g 61 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ARG g 66 " --> pdb=" O LYS g 62 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N SER g 68 " --> pdb=" O LEU g 64 " (cutoff:3.500A) Processing helix chain 'g' and resid 83 through 115 Processing helix chain 'h' and resid 5 through 13 removed outlier: 4.296A pdb=" N GLY h 11 " --> pdb=" O ARG h 7 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LYS h 12 " --> pdb=" O ASP h 8 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N LYS h 13 " --> pdb=" O LEU h 9 " (cutoff:3.500A) Processing helix chain 'h' and resid 14 through 38 Processing helix chain 'h' and resid 40 through 74 removed outlier: 3.554A pdb=" N LYS h 46 " --> pdb=" O SER h 42 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N ILE h 47 " --> pdb=" O LYS h 43 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N ARG h 48 " --> pdb=" O LEU h 44 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N VAL h 49 " --> pdb=" O SER h 45 " (cutoff:3.500A) Processing helix chain 'h' and resid 80 through 85 Proline residue: h 85 - end of helix Processing helix chain 'h' and resid 88 through 94 removed outlier: 3.883A pdb=" N ARG h 93 " --> pdb=" O ARG h 89 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG h 94 " --> pdb=" O ALA h 90 " (cutoff:3.500A) Processing helix chain 'h' and resid 96 through 103 removed outlier: 6.377A pdb=" N GLU h 100 " --> pdb=" O ASN h 96 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N SER h 101 " --> pdb=" O LYS h 97 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N LYS h 103 " --> pdb=" O GLU h 99 " (cutoff:3.500A) Processing helix chain 'h' and resid 104 through 115 Proline residue: h 115 - end of helix Processing helix chain 'i' and resid 25 through 30 removed outlier: 4.278A pdb=" N ARG i 29 " --> pdb=" O ARG i 25 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N ARG i 30 " --> pdb=" O HIS i 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 25 through 30' Processing helix chain 'i' and resid 34 through 49 removed outlier: 3.652A pdb=" N VAL i 47 " --> pdb=" O MET i 43 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 64 removed outlier: 3.519A pdb=" N VAL i 63 " --> pdb=" O GLU i 59 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N SER i 64 " --> pdb=" O LEU i 60 " (cutoff:3.500A) Processing helix chain 'i' and resid 65 through 77 Processing helix chain 'i' and resid 79 through 103 removed outlier: 4.301A pdb=" N LYS i 103 " --> pdb=" O LYS i 99 " (cutoff:3.500A) Processing helix chain 'j' and resid 4 through 11 removed outlier: 3.592A pdb=" N GLY j 9 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N LYS j 10 " --> pdb=" O SER j 6 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N ARG j 11 " --> pdb=" O SER j 7 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 removed outlier: 3.823A pdb=" N ASN j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N THR j 58 " --> pdb=" O LYS j 54 " (cutoff:3.500A) Processing helix chain 'j' and resid 64 through 77 removed outlier: 4.327A pdb=" N ILE j 69 " --> pdb=" O ARG j 65 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 17 removed outlier: 3.782A pdb=" N ARG k 17 " --> pdb=" O LEU k 13 " (cutoff:3.500A) Processing helix chain 'k' and resid 49 through 60 removed outlier: 3.620A pdb=" N ALA k 53 " --> pdb=" O ASP k 49 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN k 58 " --> pdb=" O GLU k 54 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N SER k 59 " --> pdb=" O LYS k 55 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LEU k 60 " --> pdb=" O LEU k 56 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 21 removed outlier: 3.598A pdb=" N ASN l 20 " --> pdb=" O LYS l 16 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ARG l 21 " --> pdb=" O GLN l 17 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 30 removed outlier: 4.416A pdb=" N ARG l 28 " --> pdb=" O PRO l 24 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N MET l 29 " --> pdb=" O GLN l 25 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N LYS l 30 " --> pdb=" O TRP l 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'l' and resid 24 through 30' Processing helix chain 'm' and resid 79 through 91 removed outlier: 3.629A pdb=" N TYR m 89 " --> pdb=" O LEU m 85 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 24 removed outlier: 3.811A pdb=" N ARG n 23 " --> pdb=" O LYS n 19 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N SER n 24 " --> pdb=" O MET n 20 " (cutoff:3.500A) Processing helix chain 'o' and resid 35 through 46 Processing helix chain 'p' and resid 19 through 35 removed outlier: 4.116A pdb=" N LYS p 28 " --> pdb=" O LYS p 24 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ILE p 29 " --> pdb=" O MET p 25 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 92 Processing helix chain 'q' and resid 19 through 24 removed outlier: 4.232A pdb=" N LEU q 23 " --> pdb=" O TYR q 19 " (cutoff:3.500A) Processing helix chain 'q' and resid 45 through 57 removed outlier: 3.566A pdb=" N ASP q 51 " --> pdb=" O THR q 47 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL q 52 " --> pdb=" O GLU q 48 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ALA q 55 " --> pdb=" O ASP q 51 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N VAL q 56 " --> pdb=" O VAL q 52 " (cutoff:3.500A) Processing helix chain 'q' and resid 75 through 80 removed outlier: 5.423A pdb=" N GLY q 80 " --> pdb=" O VAL q 76 " (cutoff:3.500A) Processing helix chain 'q' and resid 100 through 117 removed outlier: 3.975A pdb=" N VAL q 104 " --> pdb=" O SER q 100 " (cutoff:3.500A) Proline residue: q 113 - end of helix removed outlier: 3.646A pdb=" N LYS q 116 " --> pdb=" O ILE q 112 " (cutoff:3.500A) Processing helix chain 'r' and resid 2 through 13 removed outlier: 4.130A pdb=" N GLN r 6 " --> pdb=" O SER r 2 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ASN r 12 " --> pdb=" O MET r 8 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N CYS r 13 " --> pdb=" O VAL r 9 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 98 removed outlier: 6.060A pdb=" N THR r 89 " --> pdb=" O ASN r 85 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N LEU r 90 " --> pdb=" O ALA r 86 " (cutoff:3.500A) Processing helix chain 'r' and resid 103 through 122 removed outlier: 4.010A pdb=" N ARG r 107 " --> pdb=" O HIS r 103 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N MET r 108 " --> pdb=" O PRO r 104 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N ALA r 109 " --> pdb=" O ASP r 105 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N LYS r 122 " --> pdb=" O LEU r 118 " (cutoff:3.500A) Processing helix chain 't' and resid 5 through 22 removed outlier: 3.537A pdb=" N THR t 11 " --> pdb=" O GLU t 7 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ARG t 21 " --> pdb=" O PHE t 17 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N THR t 22 " --> pdb=" O GLN t 18 " (cutoff:3.500A) Processing helix chain 't' and resid 75 through 91 removed outlier: 4.218A pdb=" N MET t 81 " --> pdb=" O ASN t 77 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA t 82 " --> pdb=" O LYS t 78 " (cutoff:3.500A) Processing helix chain 'u' and resid 61 through 74 removed outlier: 3.525A pdb=" N GLN u 72 " --> pdb=" O GLU u 68 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N GLY u 74 " --> pdb=" O GLN u 70 " (cutoff:3.500A) Processing helix chain 'u' and resid 79 through 99 removed outlier: 3.636A pdb=" N TYR u 83 " --> pdb=" O ASP u 79 " (cutoff:3.500A) Processing helix chain 'u' and resid 114 through 119 removed outlier: 3.968A pdb=" N LEU u 118 " --> pdb=" O THR u 114 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N THR u 119 " --> pdb=" O GLU u 115 " (cutoff:3.500A) No H-bonds generated for 'chain 'u' and resid 114 through 119' Processing helix chain 'u' and resid 122 through 149 removed outlier: 3.768A pdb=" N LEU u 126 " --> pdb=" O ARG u 122 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL u 127 " --> pdb=" O TYR u 123 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N ASN u 146 " --> pdb=" O LYS u 142 " (cutoff:3.500A) removed outlier: 5.424A pdb=" N THR u 147 " --> pdb=" O GLN u 143 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N GLU u 148 " --> pdb=" O GLU u 144 " (cutoff:3.500A) Proline residue: u 149 - end of helix Processing helix chain 'u' and resid 150 through 175 removed outlier: 4.137A pdb=" N HIS u 154 " --> pdb=" O ARG u 150 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL u 163 " --> pdb=" O LEU u 159 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N LYS u 164 " --> pdb=" O ARG u 160 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N GLU u 174 " --> pdb=" O GLU u 170 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N SER u 175 " --> pdb=" O ARG u 171 " (cutoff:3.500A) Processing helix chain 'u' and resid 179 through 202 removed outlier: 4.247A pdb=" N LYS u 183 " --> pdb=" O ASP u 179 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N LEU u 184 " --> pdb=" O ALA u 180 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU u 185 " --> pdb=" O LYS u 181 " (cutoff:3.500A) Processing helix chain 'u' and resid 204 through 226 removed outlier: 3.651A pdb=" N GLU u 209 " --> pdb=" O LYS u 205 " (cutoff:3.500A) removed outlier: 4.723A pdb=" N THR u 226 " --> pdb=" O ALA u 222 " (cutoff:3.500A) Processing helix chain 'u' and resid 227 through 252 removed outlier: 3.509A pdb=" N VAL u 231 " --> pdb=" O GLU u 227 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N LEU u 232 " --> pdb=" O GLU u 228 " (cutoff:3.500A) removed outlier: 4.724A pdb=" N TYR u 233 " --> pdb=" O GLN u 229 " (cutoff:3.500A) Proline residue: u 242 - end of helix removed outlier: 4.320A pdb=" N ILE u 251 " --> pdb=" O CYS u 247 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N GLY u 252 " --> pdb=" O ALA u 248 " (cutoff:3.500A) Processing helix chain 'v' and resid 76 through 86 removed outlier: 3.565A pdb=" N LEU v 84 " --> pdb=" O LEU v 80 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU v 85 " --> pdb=" O PHE v 81 " (cutoff:3.500A) Processing helix chain 'v' and resid 124 through 133 removed outlier: 3.502A pdb=" N PHE v 128 " --> pdb=" O LEU v 124 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ARG v 131 " --> pdb=" O GLN v 127 " (cutoff:3.500A) Processing helix chain 'v' and resid 147 through 152 removed outlier: 3.659A pdb=" N GLU v 151 " --> pdb=" O ALA v 147 " (cutoff:3.500A) Processing helix chain 'v' and resid 153 through 169 removed outlier: 3.984A pdb=" N LEU v 169 " --> pdb=" O ASP v 165 " (cutoff:3.500A) Processing helix chain 'v' and resid 189 through 207 removed outlier: 3.547A pdb=" N THR v 203 " --> pdb=" O LYS v 199 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N VAL v 206 " --> pdb=" O ASN v 202 " (cutoff:3.500A) Processing helix chain 'v' and resid 233 through 238 Proline residue: v 238 - end of helix Processing helix chain 'v' and resid 260 through 271 removed outlier: 5.468A pdb=" N GLU v 264 " --> pdb=" O ILE v 260 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS v 265 " --> pdb=" O GLN v 261 " (cutoff:3.500A) Processing helix chain 'v' and resid 251 through 256 removed outlier: 4.196A pdb=" N ASP v 254 " --> pdb=" O GLY v 251 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N VAL v 255 " --> pdb=" O ARG v 252 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N GLY v 256 " --> pdb=" O GLY v 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'v' and resid 251 through 256' Processing helix chain 'w' and resid 6 through 22 removed outlier: 3.555A pdb=" N ASP w 21 " --> pdb=" O LEU w 17 " (cutoff:3.500A) Proline residue: w 22 - end of helix Processing helix chain 'w' and resid 55 through 76 removed outlier: 4.579A pdb=" N VAL w 59 " --> pdb=" O GLN w 55 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N LYS w 60 " --> pdb=" O ALA w 56 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N LYS w 61 " --> pdb=" O GLN w 57 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N LYS w 76 " --> pdb=" O LEU w 72 " (cutoff:3.500A) Processing helix chain 'x' and resid 3 through 20 removed outlier: 6.612A pdb=" N GLY x 7 " --> pdb=" O LEU x 3 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG x 8 " --> pdb=" O ALA x 4 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ALA x 13 " --> pdb=" O LYS x 9 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N ASN x 19 " --> pdb=" O ARG x 15 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA x 20 " --> pdb=" O SER x 16 " (cutoff:3.500A) Processing helix chain 'x' and resid 24 through 43 Processing helix chain 'x' and resid 45 through 61 removed outlier: 4.338A pdb=" N ASP x 61 " --> pdb=" O LYS x 57 " (cutoff:3.500A) Processing helix chain 'x' and resid 70 through 88 Processing helix chain 'x' and resid 113 through 129 Processing helix chain 'x' and resid 143 through 156 Processing helix chain 'x' and resid 167 through 183 Processing helix chain 'x' and resid 198 through 213 Processing helix chain 'x' and resid 227 through 240 removed outlier: 4.762A pdb=" N ALA x 231 " --> pdb=" O GLN x 227 " (cutoff:3.500A) Processing helix chain 'x' and resid 257 through 267 removed outlier: 4.056A pdb=" N SER x 261 " --> pdb=" O GLY x 257 " (cutoff:3.500A) Processing helix chain 'x' and resid 287 through 296 removed outlier: 4.874A pdb=" N ILE x 291 " --> pdb=" O THR x 287 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N GLY x 296 " --> pdb=" O SER x 292 " (cutoff:3.500A) Processing helix chain 'x' and resid 299 through 311 removed outlier: 4.268A pdb=" N LEU x 303 " --> pdb=" O ASP x 299 " (cutoff:3.500A) Processing helix chain 'x' and resid 314 through 325 removed outlier: 5.463A pdb=" N LEU x 318 " --> pdb=" O ASP x 314 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N ILE x 319 " --> pdb=" O ASN x 315 " (cutoff:3.500A) Processing helix chain 'x' and resid 328 through 343 removed outlier: 4.137A pdb=" N GLY x 343 " --> pdb=" O ILE x 339 " (cutoff:3.500A) Processing helix chain 'x' and resid 363 through 382 removed outlier: 5.316A pdb=" N GLU x 367 " --> pdb=" O GLY x 363 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER x 381 " --> pdb=" O THR x 377 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N MET x 382 " --> pdb=" O ILE x 378 " (cutoff:3.500A) Processing helix chain 'x' and resid 383 through 389 Processing helix chain 'x' and resid 391 through 400 removed outlier: 3.678A pdb=" N LYS x 398 " --> pdb=" O LYS x 394 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N GLN x 399 " --> pdb=" O VAL x 395 " (cutoff:3.500A) Proline residue: x 400 - end of helix Processing helix chain 'x' and resid 401 through 410 removed outlier: 3.637A pdb=" N GLY x 409 " --> pdb=" O ARG x 405 " (cutoff:3.500A) Processing helix chain 'x' and resid 413 through 437 removed outlier: 3.539A pdb=" N VAL x 417 " --> pdb=" O SER x 413 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N GLN x 418 " --> pdb=" O THR x 414 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE x 437 " --> pdb=" O LYS x 433 " (cutoff:3.500A) Processing helix chain 'y' and resid 27 through 38 removed outlier: 4.005A pdb=" N ALA y 31 " --> pdb=" O GLY y 27 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N LEU y 32 " --> pdb=" O PRO y 28 " (cutoff:3.500A) Processing helix chain 'y' and resid 77 through 94 removed outlier: 4.091A pdb=" N LYS y 81 " --> pdb=" O THR y 77 " (cutoff:3.500A) Processing helix chain 'y' and resid 95 through 101 removed outlier: 3.847A pdb=" N GLN y 100 " --> pdb=" O THR y 96 " (cutoff:3.500A) removed outlier: 5.505A pdb=" N GLN y 101 " --> pdb=" O GLU y 97 " (cutoff:3.500A) Processing helix chain 'y' and resid 102 through 110 removed outlier: 4.283A pdb=" N LEU y 106 " --> pdb=" O SER y 102 " (cutoff:3.500A) removed outlier: 5.398A pdb=" N THR y 110 " --> pdb=" O LEU y 106 " (cutoff:3.500A) Processing helix chain 'y' and resid 113 through 129 Processing helix chain 'z' and resid 562 through 569 Proline residue: z 568 - end of helix Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.545A pdb=" N ASP A 47 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.932A pdb=" N LYS A 60 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N GLN A 86 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 110 through 114 removed outlier: 3.859A pdb=" N THR A 111 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N ARG A 147 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N SER A 138 " --> pdb=" O ARG A 147 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 58 through 64 Processing sheet with id= 4, first strand: chain 'A' and resid 145 through 150 removed outlier: 4.125A pdb=" N SER A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 40 through 43 removed outlier: 4.709A pdb=" N HIS B 179 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU B 163 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLN B 203 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 53 through 59 removed outlier: 6.760A pdb=" N ILE B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ARG B 343 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 7.446A pdb=" N VAL B 344 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N VAL B 222 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 98 through 102 removed outlier: 6.683A pdb=" N GLY B 91 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N LYS B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 286 through 290 removed outlier: 3.579A pdb=" N LYS B 286 " --> pdb=" O MET B 332 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY B 290 " --> pdb=" O ASN B 328 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N ASN B 328 " --> pdb=" O GLY B 290 " (cutoff:3.500A) Processing sheet with id= 9, first strand: chain 'B' and resid 76 through 80 No H-bonds generated for sheet with id= 9 Processing sheet with id= 10, first strand: chain 'B' and resid 88 through 93 No H-bonds generated for sheet with id= 10 Processing sheet with id= 11, first strand: chain 'B' and resid 215 through 218 removed outlier: 4.059A pdb=" N GLU B 215 " --> pdb=" O ILE B 284 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 6 through 10 removed outlier: 5.165A pdb=" N LYS C 20 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'C' and resid 226 through 232 removed outlier: 3.904A pdb=" N THR C 228 " --> pdb=" O PRO C 207 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N PHE C 249 " --> pdb=" O GLY C 206 " (cutoff:3.500A) Processing sheet with id= 14, first strand: chain 'D' and resid 60 through 66 Processing sheet with id= 15, first strand: chain 'E' and resid 143 through 149 removed outlier: 4.005A pdb=" N THR E 144 " --> pdb=" O PHE E 160 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS E 156 " --> pdb=" O ILE E 148 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 142 through 146 removed outlier: 5.445A pdb=" N PHE F 120 " --> pdb=" O LEU F 215 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 180 through 185 removed outlier: 3.913A pdb=" N LEU G 154 " --> pdb=" O PHE G 204 " (cutoff:3.500A) Processing sheet with id= 18, first strand: chain 'H' and resid 5 through 12 removed outlier: 5.837A pdb=" N LYS H 53 " --> pdb=" O ILE H 12 " (cutoff:3.500A) Processing sheet with id= 19, first strand: chain 'H' and resid 17 through 20 Processing sheet with id= 20, first strand: chain 'H' and resid 102 through 106 removed outlier: 6.672A pdb=" N LEU H 111 " --> pdb=" O GLN H 106 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N SER H 110 " --> pdb=" O MET H 128 " (cutoff:3.500A) Processing sheet with id= 21, first strand: chain 'H' and resid 132 through 136 removed outlier: 6.039A pdb=" N ASP H 142 " --> pdb=" O SER H 94 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'I' and resid 34 through 37 removed outlier: 6.261A pdb=" N PHE I 34 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ILE I 135 " --> pdb=" O ARG I 90 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N MET I 136 " --> pdb=" O MET I 52 " (cutoff:3.500A) removed outlier: 6.287A pdb=" N THR I 140 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 5.716A pdb=" N CYS I 49 " --> pdb=" O SER I 168 " (cutoff:3.500A) Processing sheet with id= 23, first strand: chain 'I' and resid 95 through 98 removed outlier: 3.628A pdb=" N GLY I 124 " --> pdb=" O ILE I 97 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'I' and resid 189 through 192 removed outlier: 5.501A pdb=" N ARG I 189 " --> pdb=" O ILE I 200 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'J' and resid 48 through 52 removed outlier: 3.677A pdb=" N VAL J 49 " --> pdb=" O HIS J 71 " (cutoff:3.500A) removed outlier: 5.434A pdb=" N CYS J 25 " --> pdb=" O GLY J 127 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N GLY J 127 " --> pdb=" O CYS J 25 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'M' and resid 10 through 16 removed outlier: 4.116A pdb=" N ARG M 11 " --> pdb=" O ILE M 27 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N LYS M 23 " --> pdb=" O VAL M 15 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N LEU M 37 " --> pdb=" O VAL M 28 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N GLY M 40 " --> pdb=" O ARG M 46 " (cutoff:3.500A) removed outlier: 5.227A pdb=" N ARG M 46 " --> pdb=" O GLY M 40 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'N' and resid 113 through 116 removed outlier: 6.855A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N PHE N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASN N 117 " --> pdb=" O ILE N 133 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'O' and resid 6 through 10 Processing sheet with id= 29, first strand: chain 'P' and resid 14 through 20 removed outlier: 6.592A pdb=" N ILE P 149 " --> pdb=" O GLU P 115 " (cutoff:3.500A) Processing sheet with id= 30, first strand: chain 'P' and resid 57 through 60 removed outlier: 3.609A pdb=" N PHE P 60 " --> pdb=" O GLN P 80 " (cutoff:3.500A) removed outlier: 4.960A pdb=" N GLN P 80 " --> pdb=" O PHE P 60 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'P' and resid 116 through 122 Processing sheet with id= 32, first strand: chain 'P' and resid 124 through 130 removed outlier: 4.117A pdb=" N MET P 125 " --> pdb=" O SER P 141 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'Q' and resid 78 through 82 Processing sheet with id= 34, first strand: chain 'S' and resid 27 through 33 removed outlier: 6.806A pdb=" N VAL S 13 " --> pdb=" O VAL S 62 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'S' and resid 92 through 99 removed outlier: 4.055A pdb=" N ASN S 77 " --> pdb=" O ILE S 132 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N LYS S 128 " --> pdb=" O TRP S 81 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'S' and resid 9 through 13 removed outlier: 4.596A pdb=" N GLU S 9 " --> pdb=" O VAL S 67 " (cutoff:3.500A) Processing sheet with id= 37, first strand: chain 'T' and resid 39 through 42 removed outlier: 4.088A pdb=" N LYS T 60 " --> pdb=" O ILE T 42 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'T' and resid 73 through 80 removed outlier: 3.897A pdb=" N LYS T 83 " --> pdb=" O VAL T 80 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'U' and resid 61 through 65 removed outlier: 4.171A pdb=" N ILE U 70 " --> pdb=" O LEU U 23 " (cutoff:3.500A) removed outlier: 5.514A pdb=" N GLU U 108 " --> pdb=" O LYS U 20 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LEU U 112 " --> pdb=" O ASP U 24 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE U 115 " --> pdb=" O TRP U 99 " (cutoff:3.500A) removed outlier: 8.037A pdb=" N TRP U 99 " --> pdb=" O PHE U 115 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'V' and resid 24 through 27 removed outlier: 4.364A pdb=" N ALA V 24 " --> pdb=" O ILE V 39 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'V' and resid 59 through 64 removed outlier: 4.277A pdb=" N ASP V 59 " --> pdb=" O VAL V 81 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N ASP V 100 " --> pdb=" O ARG V 85 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ARG V 85 " --> pdb=" O ASP V 100 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'V' and resid 87 through 90 removed outlier: 4.473A pdb=" N VAL V 94 " --> pdb=" O ARG V 90 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'W' and resid 3 through 6 removed outlier: 6.559A pdb=" N GLU W 4 " --> pdb=" O LYS W 12 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS W 12 " --> pdb=" O GLU W 4 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N CYS W 6 " --> pdb=" O GLY W 10 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'W' and resid 18 through 22 Processing sheet with id= 45, first strand: chain 'X' and resid 95 through 100 Processing sheet with id= 46, first strand: chain 'Y' and resid 53 through 56 removed outlier: 4.711A pdb=" N ASP Y 53 " --> pdb=" O VAL Y 70 " (cutoff:3.500A) Processing sheet with id= 47, first strand: chain 'Y' and resid 71 through 75 Processing sheet with id= 48, first strand: chain 'Y' and resid 85 through 89 removed outlier: 6.009A pdb=" N VAL Y 85 " --> pdb=" O VAL Y 97 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N THR Y 93 " --> pdb=" O LYS Y 89 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'Z' and resid 9 through 14 removed outlier: 4.817A pdb=" N LYS Z 9 " --> pdb=" O ILE Z 25 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N ARG Z 21 " --> pdb=" O VAL Z 13 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N LEU Z 42 " --> pdb=" O VAL Z 26 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N HIS Z 40 " --> pdb=" O ILE Z 29 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'Z' and resid 42 through 45 Processing sheet with id= 51, first strand: chain 'c' and resid 26 through 29 removed outlier: 6.627A pdb=" N LYS c 26 " --> pdb=" O ILE c 97 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N GLY c 70 " --> pdb=" O LYS c 44 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'd' and resid 20 through 27 removed outlier: 4.269A pdb=" N VAL d 21 " --> pdb=" O ARG d 90 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N ARG d 85 " --> pdb=" O VAL d 109 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N TYR d 103 " --> pdb=" O LYS d 91 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'e' and resid 74 through 80 Processing sheet with id= 54, first strand: chain 'f' and resid 9 through 12 removed outlier: 6.657A pdb=" N LEU f 27 " --> pdb=" O ALA f 12 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N ARG f 85 " --> pdb=" O THR f 75 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS f 45 " --> pdb=" O VAL f 74 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ARG f 46 " --> pdb=" O MET f 104 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'f' and resid 6 through 12 removed outlier: 4.222A pdb=" N HIS f 99 " --> pdb=" O PHE f 11 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'g' and resid 20 through 24 Processing sheet with id= 57, first strand: chain 'k' and resid 2 through 5 removed outlier: 3.540A pdb=" N ARG k 3 " --> pdb=" O LEU k 42 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL k 46 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL k 32 " --> pdb=" O ILE k 47 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LYS k 67 " --> pdb=" O VAL k 23 " (cutoff:3.500A) removed outlier: 4.240A pdb=" N ILE k 25 " --> pdb=" O LYS k 67 " (cutoff:3.500A) removed outlier: 5.107A pdb=" N LYS k 27 " --> pdb=" O LEU k 69 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'm' and resid 100 through 104 removed outlier: 4.432A pdb=" N ALA m 101 " --> pdb=" O CYS m 96 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N LYS m 93 " --> pdb=" O LYS m 124 " (cutoff:3.500A) removed outlier: 8.436A pdb=" N ASN m 120 " --> pdb=" O ARG m 97 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'o' and resid 7 through 10 removed outlier: 5.362A pdb=" N VAL o 67 " --> pdb=" O TYR o 26 " (cutoff:3.500A) Processing sheet with id= 60, first strand: chain 'p' and resid 46 through 50 removed outlier: 8.260A pdb=" N LYS p 46 " --> pdb=" O GLY p 58 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ILE p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N GLY p 53 " --> pdb=" O GLY p 66 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N LYS p 62 " --> pdb=" O CYS p 57 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'q' and resid 15 through 18 removed outlier: 3.699A pdb=" N GLN q 85 " --> pdb=" O ASN q 59 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N ASN q 59 " --> pdb=" O GLN q 85 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'r' and resid 48 through 53 removed outlier: 4.786A pdb=" N THR r 48 " --> pdb=" O LYS r 65 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N SER r 76 " --> pdb=" O ARG r 66 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 't' and resid 27 through 32 Processing sheet with id= 64, first strand: chain 'v' and resid 97 through 105 removed outlier: 7.364A pdb=" N THR v 97 " --> pdb=" O PRO v 119 " (cutoff:3.500A) removed outlier: 4.889A pdb=" N ASN v 111 " --> pdb=" O VAL v 105 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ARG v 65 " --> pdb=" O SER v 112 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU v 118 " --> pdb=" O LEU v 69 " (cutoff:3.500A) removed outlier: 6.069A pdb=" N GLY v 71 " --> pdb=" O LEU v 118 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'w' and resid 26 through 32 Processing sheet with id= 66, first strand: chain 'x' and resid 158 through 161 removed outlier: 4.709A pdb=" N PHE x 106 " --> pdb=" O VAL x 189 " (cutoff:3.500A) removed outlier: 4.349A pdb=" N THR x 191 " --> pdb=" O PHE x 106 " (cutoff:3.500A) removed outlier: 7.290A pdb=" N GLY x 108 " --> pdb=" O THR x 191 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ASN x 216 " --> pdb=" O VAL x 103 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 'y' and resid 3 through 7 2502 hydrogen bonds defined for protein. 7417 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3239 hydrogen bonds 5552 hydrogen bond angles 0 basepair planarities 1237 basepair parallelities 1953 stacking parallelities Total time for adding SS restraints: 341.24 Time building geometry restraints manager: 69.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 19751 1.33 - 1.45: 63387 1.45 - 1.57: 67900 1.57 - 1.69: 8020 1.69 - 1.81: 463 Bond restraints: 159521 Sorted by residual: bond pdb=" N GLU x 226 " pdb=" CA GLU x 226 " ideal model delta sigma weight residual 1.457 1.488 -0.031 6.40e-03 2.44e+04 2.41e+01 bond pdb=" N3B GNP x 601 " pdb=" PG GNP x 601 " ideal model delta sigma weight residual 1.801 1.710 0.091 2.00e-02 2.50e+03 2.09e+01 bond pdb=" O5' GNP x 601 " pdb=" PA GNP x 601 " ideal model delta sigma weight residual 1.660 1.573 0.087 2.00e-02 2.50e+03 1.91e+01 bond pdb=" N ILE x 157 " pdb=" CA ILE x 157 " ideal model delta sigma weight residual 1.456 1.494 -0.038 8.70e-03 1.32e+04 1.89e+01 bond pdb=" N LYS x 286 " pdb=" CA LYS x 286 " ideal model delta sigma weight residual 1.457 1.501 -0.044 1.29e-02 6.01e+03 1.16e+01 ... (remaining 159516 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.72: 24994 106.72 - 113.60: 94015 113.60 - 120.47: 61565 120.47 - 127.35: 45767 127.35 - 134.22: 8443 Bond angle restraints: 234784 Sorted by residual: angle pdb=" N PRO y 245 " pdb=" CA PRO y 245 " pdb=" CB PRO y 245 " ideal model delta sigma weight residual 103.25 110.84 -7.59 1.05e+00 9.07e-01 5.23e+01 angle pdb=" CA PHE x 285 " pdb=" C PHE x 285 " pdb=" O PHE x 285 " ideal model delta sigma weight residual 120.51 113.11 7.40 1.43e+00 4.89e-01 2.68e+01 angle pdb=" C3' A 55061 " pdb=" O3' A 55061 " pdb=" P G 55062 " ideal model delta sigma weight residual 120.20 127.81 -7.61 1.50e+00 4.44e-01 2.58e+01 angle pdb=" CA ILE x 187 " pdb=" C ILE x 187 " pdb=" O ILE x 187 " ideal model delta sigma weight residual 122.63 118.39 4.24 8.70e-01 1.32e+00 2.37e+01 angle pdb=" N ASP x 5 " pdb=" CA ASP x 5 " pdb=" C ASP x 5 " ideal model delta sigma weight residual 113.12 107.37 5.75 1.25e+00 6.40e-01 2.11e+01 ... (remaining 234779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 91328 35.97 - 71.94: 10271 71.94 - 107.91: 1414 107.91 - 143.87: 46 143.87 - 179.84: 99 Dihedral angle restraints: 103158 sinusoidal: 80881 harmonic: 22277 Sorted by residual: dihedral pdb=" CA GLY x 298 " pdb=" C GLY x 298 " pdb=" N ASP x 299 " pdb=" CA ASP x 299 " ideal model delta harmonic sigma weight residual 180.00 122.89 57.11 0 5.00e+00 4.00e-02 1.30e+02 dihedral pdb=" C4' U 55022 " pdb=" C3' U 55022 " pdb=" C2' U 55022 " pdb=" C1' U 55022 " ideal model delta sinusoidal sigma weight residual -35.00 33.61 -68.61 1 8.00e+00 1.56e-02 9.53e+01 dihedral pdb=" C5' U 55022 " pdb=" C4' U 55022 " pdb=" C3' U 55022 " pdb=" O3' U 55022 " ideal model delta sinusoidal sigma weight residual 147.00 79.03 67.97 1 8.00e+00 1.56e-02 9.37e+01 ... (remaining 103155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.075: 27862 0.075 - 0.150: 1227 0.150 - 0.225: 120 0.225 - 0.300: 6 0.300 - 0.375: 1 Chirality restraints: 29216 Sorted by residual: chirality pdb=" C3' U 55022 " pdb=" C4' U 55022 " pdb=" O3' U 55022 " pdb=" C2' U 55022 " both_signs ideal model delta sigma weight residual False -2.74 -2.37 -0.38 2.00e-01 2.50e+01 3.52e+00 chirality pdb=" CA ILE x 135 " pdb=" N ILE x 135 " pdb=" C ILE x 135 " pdb=" CB ILE x 135 " both_signs ideal model delta sigma weight residual False 2.43 2.71 -0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB VAL x 240 " pdb=" CA VAL x 240 " pdb=" CG1 VAL x 240 " pdb=" CG2 VAL x 240 " both_signs ideal model delta sigma weight residual False -2.63 -2.37 -0.26 2.00e-01 2.50e+01 1.65e+00 ... (remaining 29213 not shown) Planarity restraints: 14749 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER i 92 " -0.022 2.00e-02 2.50e+03 4.39e-02 1.92e+01 pdb=" C SER i 92 " 0.076 2.00e-02 2.50e+03 pdb=" O SER i 92 " -0.028 2.00e-02 2.50e+03 pdb=" N VAL i 93 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER i 91 " -0.018 2.00e-02 2.50e+03 3.65e-02 1.33e+01 pdb=" C SER i 91 " 0.063 2.00e-02 2.50e+03 pdb=" O SER i 91 " -0.024 2.00e-02 2.50e+03 pdb=" N SER i 92 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR f 106 " -0.055 5.00e-02 4.00e+02 8.42e-02 1.14e+01 pdb=" N PRO f 107 " 0.146 5.00e-02 4.00e+02 pdb=" CA PRO f 107 " -0.045 5.00e-02 4.00e+02 pdb=" CD PRO f 107 " -0.045 5.00e-02 4.00e+02 ... (remaining 14746 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 5162 2.66 - 3.22: 127052 3.22 - 3.78: 285209 3.78 - 4.34: 374629 4.34 - 4.90: 527811 Nonbonded interactions: 1319863 Sorted by model distance: nonbonded pdb=" O6 G 52624 " pdb=" O2 U 52632 " model vdw 2.097 2.432 nonbonded pdb=" OG SER v 95 " pdb="MG MG v 300 " model vdw 2.106 2.170 nonbonded pdb=" O1B GNP x 601 " pdb="MG MG x 602 " model vdw 2.108 2.170 nonbonded pdb=" O2' U 55022 " pdb=" O5' C 55023 " model vdw 2.111 2.440 nonbonded pdb=" OP2 A 51326 " pdb=" O2' U 54445 " model vdw 2.116 2.440 ... (remaining 1319858 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 8.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.160 Extract box with map and model: 24.380 Check model and map are aligned: 1.720 Set scattering table: 1.060 Process input model: 679.320 Find NCS groups from input model: 3.650 Set up NCS constraints: 0.480 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: 0.040 Load rotamer database and sin/cos tables:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 721.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 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 : 0.002 0.091 159521 Z= 0.149 Angle : 0.526 10.910 234784 Z= 0.304 Chirality : 0.032 0.375 29216 Planarity : 0.003 0.084 14749 Dihedral : 23.446 179.842 88782 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.15 % Allowed : 4.89 % Favored : 94.96 % Rotamer: Outliers : 3.98 % Allowed : 7.58 % Favored : 88.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.01 % 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: 0.36 (0.10), residues: 7563 helix: 1.93 (0.10), residues: 2783 sheet: -0.16 (0.16), residues: 1049 loop : -0.98 (0.10), residues: 3731 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP z 577 HIS 0.004 0.001 HIS x 195 PHE 0.015 0.001 PHE J 130 TYR 0.014 0.001 TYR D 44 ARG 0.004 0.000 ARG T 9 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2075 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 262 poor density : 1813 time to evaluate : 7.914 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: B 328 ASN cc_start: 0.8332 (m-40) cc_final: 0.8089 (m110) REVERT: C 281 MET cc_start: 0.8018 (mmt) cc_final: 0.7402 (mmm) REVERT: D 221 LYS cc_start: 0.8163 (tmmm) cc_final: 0.7653 (mtmm) REVERT: D 277 LYS cc_start: 0.7637 (tptt) cc_final: 0.7371 (mtmm) REVERT: E 203 LYS cc_start: 0.7983 (tmmt) cc_final: 0.7372 (ptpt) REVERT: E 246 GLN cc_start: 0.7894 (tp40) cc_final: 0.7673 (tp40) REVERT: H 169 ASN cc_start: 0.7944 (m110) cc_final: 0.7738 (m-40) REVERT: I 36 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8096 (mp) REVERT: I 119 PHE cc_start: 0.8234 (t80) cc_final: 0.8026 (t80) REVERT: I 163 GLN cc_start: 0.7525 (OUTLIER) cc_final: 0.6714 (pm20) REVERT: L 69 LYS cc_start: 0.7964 (mmtp) cc_final: 0.7722 (mmtt) REVERT: L 103 ARG cc_start: 0.7792 (ptp-110) cc_final: 0.7435 (mtm110) REVERT: M 70 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.6572 (tm-30) REVERT: N 32 GLN cc_start: 0.7821 (OUTLIER) cc_final: 0.7034 (mp10) REVERT: N 174 LEU cc_start: 0.8422 (OUTLIER) cc_final: 0.8140 (pp) REVERT: O 16 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8537 (tp) REVERT: O 42 ASN cc_start: 0.8162 (OUTLIER) cc_final: 0.7863 (p0) REVERT: O 186 GLU cc_start: 0.6166 (OUTLIER) cc_final: 0.5645 (pt0) REVERT: R 74 ARG cc_start: 0.7068 (OUTLIER) cc_final: 0.4439 (mtm180) REVERT: R 99 MET cc_start: 0.7608 (mmp) cc_final: 0.7256 (mmt) REVERT: R 119 MET cc_start: 0.7169 (ttp) cc_final: 0.6965 (ttm) REVERT: R 162 ARG cc_start: 0.6575 (mtt90) cc_final: 0.5586 (tmt170) REVERT: T 83 LYS cc_start: 0.5698 (pttp) cc_final: 0.5293 (mttt) REVERT: T 90 ASN cc_start: 0.8432 (m-40) cc_final: 0.8196 (m-40) REVERT: T 125 TRP cc_start: 0.5957 (t60) cc_final: 0.5599 (t-100) REVERT: V 16 ILE cc_start: 0.7870 (OUTLIER) cc_final: 0.7602 (pt) REVERT: V 18 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8419 (pp) REVERT: W 1 MET cc_start: 0.5491 (pmm) cc_final: 0.5151 (mpp) REVERT: X 43 SER cc_start: 0.8452 (t) cc_final: 0.8173 (p) REVERT: X 71 LEU cc_start: 0.8512 (OUTLIER) cc_final: 0.8301 (tt) REVERT: Z 81 MET cc_start: 0.8730 (tpt) cc_final: 0.8401 (tpt) REVERT: d 18 ASN cc_start: 0.4765 (m-40) cc_final: 0.4550 (m-40) REVERT: e 22 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.7941 (ttp80) REVERT: f 5 LEU cc_start: 0.8977 (mm) cc_final: 0.8658 (mt) REVERT: g 34 TYR cc_start: 0.8838 (m-80) cc_final: 0.8553 (m-80) REVERT: h 23 ASP cc_start: 0.7317 (m-30) cc_final: 0.7076 (m-30) REVERT: h 96 ASN cc_start: 0.7562 (t0) cc_final: 0.7105 (t0) REVERT: i 63 VAL cc_start: 0.7911 (OUTLIER) cc_final: 0.7665 (t) REVERT: k 43 TYR cc_start: 0.8636 (m-80) cc_final: 0.8356 (m-80) REVERT: n 11 ARG cc_start: 0.6634 (mtm180) cc_final: 0.6028 (tpt-90) REVERT: n 14 LYS cc_start: 0.8360 (mtpt) cc_final: 0.7176 (mmtt) REVERT: n 19 LYS cc_start: 0.7879 (ttpp) cc_final: 0.7641 (mmmt) REVERT: n 21 ARG cc_start: 0.7913 (ttt180) cc_final: 0.6494 (mmt180) REVERT: o 34 TYR cc_start: 0.7713 (m-80) cc_final: 0.7064 (m-80) REVERT: p 8 VAL cc_start: 0.7805 (OUTLIER) cc_final: 0.7581 (m) REVERT: p 50 ARG cc_start: 0.8197 (ttm170) cc_final: 0.7956 (ttp-170) REVERT: r 103 HIS cc_start: 0.7466 (OUTLIER) cc_final: 0.6668 (m-70) REVERT: t 10 LEU cc_start: 0.6870 (mt) cc_final: 0.6482 (pp) REVERT: u 228 GLU cc_start: -0.0054 (OUTLIER) cc_final: -0.0265 (mt-10) REVERT: x 104 ILE cc_start: 0.1297 (mp) cc_final: 0.1076 (mt) REVERT: x 120 LYS cc_start: 0.4307 (OUTLIER) cc_final: 0.3561 (mmtt) REVERT: x 131 LYS cc_start: 0.2312 (OUTLIER) cc_final: 0.2028 (mttt) REVERT: x 149 LYS cc_start: 0.3812 (OUTLIER) cc_final: 0.3193 (ptpp) REVERT: x 207 GLN cc_start: 0.2091 (OUTLIER) cc_final: 0.1393 (pp30) REVERT: x 208 VAL cc_start: 0.2058 (t) cc_final: 0.1638 (p) REVERT: x 342 MET cc_start: 0.4180 (mtp) cc_final: 0.3804 (tmm) REVERT: x 369 MET cc_start: 0.2470 (mtm) cc_final: 0.2266 (ptt) REVERT: y 55 LYS cc_start: 0.2669 (OUTLIER) cc_final: 0.2463 (ptpt) REVERT: z 580 MET cc_start: 0.1246 (ppp) cc_final: 0.0975 (mmt) outliers start: 262 outliers final: 71 residues processed: 1977 average time/residue: 1.6502 time to fit residues: 5410.2723 Evaluate side-chains 1218 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 1125 time to evaluate : 7.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 126 ARG Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain M residue 56 GLN Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 70 GLN Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain N residue 32 GLN Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 174 LEU Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 42 ASN Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain P residue 69 ARG Chi-restraints excluded: chain Q residue 10 ASP Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain R residue 74 ARG Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain U residue 99 TRP Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 79 VAL Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 57 MET Chi-restraints excluded: chain b residue 60 ASN Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 102 LEU Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 13 VAL Chi-restraints excluded: chain e residue 22 ARG Chi-restraints excluded: chain g residue 32 TYR Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain h residue 88 THR Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain i residue 63 VAL Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain p residue 8 VAL Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain r residue 67 ARG Chi-restraints excluded: chain r residue 78 VAL Chi-restraints excluded: chain r residue 103 HIS Chi-restraints excluded: chain t residue 76 VAL Chi-restraints excluded: chain u residue 228 GLU Chi-restraints excluded: chain x residue 18 SER Chi-restraints excluded: chain x residue 33 LYS Chi-restraints excluded: chain x residue 71 LYS Chi-restraints excluded: chain x residue 82 GLU Chi-restraints excluded: chain x residue 97 THR Chi-restraints excluded: chain x residue 120 LYS Chi-restraints excluded: chain x residue 127 ARG Chi-restraints excluded: chain x residue 131 LYS Chi-restraints excluded: chain x residue 149 LYS Chi-restraints excluded: chain x residue 169 VAL Chi-restraints excluded: chain x residue 185 GLU Chi-restraints excluded: chain x residue 198 GLU Chi-restraints excluded: chain x residue 202 PHE Chi-restraints excluded: chain x residue 207 GLN Chi-restraints excluded: chain x residue 240 VAL Chi-restraints excluded: chain x residue 245 VAL Chi-restraints excluded: chain x residue 260 LEU Chi-restraints excluded: chain x residue 279 ILE Chi-restraints excluded: chain x residue 300 ILE Chi-restraints excluded: chain y residue 55 LYS Chi-restraints excluded: chain y residue 68 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 966 optimal weight: 8.9990 chunk 867 optimal weight: 9.9990 chunk 481 optimal weight: 10.0000 chunk 296 optimal weight: 10.0000 chunk 585 optimal weight: 3.9990 chunk 463 optimal weight: 10.0000 chunk 897 optimal weight: 5.9990 chunk 347 optimal weight: 10.0000 chunk 545 optimal weight: 0.0980 chunk 667 optimal weight: 6.9990 chunk 1039 optimal weight: 10.0000 overall best weight: 5.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS A 95 GLN A 162 ASN A 194 ASN B 3 HIS B 175 GLN B 184 GLN ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 213 GLN B 376 HIS ** C 21 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN C 215 ASN C 299 GLN D 9 ASN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 ASN ** E 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN F 241 GLN G 112 GLN G 149 ASN H 39 ASN H 78 GLN J 65 ASN J 98 ASN ** M 56 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 196 ASN O 72 HIS O 180 GLN ** P 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN Q 125 GLN R 130 ASN S 66 GLN T 3 ASN T 66 ASN U 38 ASN W 45 ASN X 105 ASN Y 56 GLN Y 86 GLN Z 78 ASN ** a 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 57 ASN f 80 ASN h 30 GLN h 62 ASN j 76 HIS ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 ASN r 21 ASN ** r 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** r 100 ASN ** w 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** x 19 ASN x 76 GLN x 338 ASN y 44 ASN y 45 ASN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.2261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 159521 Z= 0.318 Angle : 0.689 16.105 234784 Z= 0.348 Chirality : 0.040 0.319 29216 Planarity : 0.006 0.095 14749 Dihedral : 24.614 179.900 72684 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.61 % Favored : 94.31 % Rotamer: Outliers : 4.53 % Allowed : 13.08 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.01 % 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: -0.04 (0.10), residues: 7563 helix: 1.48 (0.10), residues: 2788 sheet: -0.25 (0.16), residues: 1033 loop : -1.14 (0.10), residues: 3742 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP N 120 HIS 0.009 0.002 HIS a 40 PHE 0.025 0.002 PHE U 42 TYR 0.028 0.002 TYR D 44 ARG 0.011 0.001 ARG L 167 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1467 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 298 poor density : 1169 time to evaluate : 7.979 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: B 314 ILE cc_start: 0.8354 (OUTLIER) cc_final: 0.8063 (pp) REVERT: D 64 ILE cc_start: 0.8562 (mt) cc_final: 0.8309 (mt) REVERT: D 221 LYS cc_start: 0.8257 (tmmm) cc_final: 0.7779 (mtmm) REVERT: D 277 LYS cc_start: 0.7642 (tptt) cc_final: 0.7334 (mtmm) REVERT: E 203 LYS cc_start: 0.8260 (tmmt) cc_final: 0.7560 (ptpt) REVERT: F 76 MET cc_start: 0.8170 (ttm) cc_final: 0.7923 (ttm) REVERT: F 139 GLU cc_start: 0.7923 (tt0) cc_final: 0.7508 (tt0) REVERT: H 48 LEU cc_start: 0.7641 (OUTLIER) cc_final: 0.7381 (mp) REVERT: I 102 MET cc_start: 0.8337 (mmp) cc_final: 0.7880 (mmt) REVERT: I 163 GLN cc_start: 0.7635 (OUTLIER) cc_final: 0.6952 (pm20) REVERT: L 9 ILE cc_start: 0.7978 (OUTLIER) cc_final: 0.7631 (tp) REVERT: L 69 LYS cc_start: 0.8234 (mmtp) cc_final: 0.7952 (mmtt) REVERT: M 81 ASP cc_start: 0.7980 (t0) cc_final: 0.7372 (m-30) REVERT: N 32 GLN cc_start: 0.8141 (OUTLIER) cc_final: 0.7217 (mp10) REVERT: N 174 LEU cc_start: 0.8744 (OUTLIER) cc_final: 0.8316 (pp) REVERT: N 188 ARG cc_start: 0.7877 (mtm-85) cc_final: 0.7617 (mtt90) REVERT: O 27 VAL cc_start: 0.9011 (OUTLIER) cc_final: 0.8502 (m) REVERT: O 42 ASN cc_start: 0.8766 (OUTLIER) cc_final: 0.8072 (p0) REVERT: O 186 GLU cc_start: 0.6448 (OUTLIER) cc_final: 0.5840 (pt0) REVERT: R 74 ARG cc_start: 0.8113 (OUTLIER) cc_final: 0.5516 (mtm180) REVERT: R 116 ASP cc_start: 0.8022 (p0) cc_final: 0.7789 (p0) REVERT: R 148 ASP cc_start: 0.7642 (m-30) cc_final: 0.7412 (m-30) REVERT: T 34 TYR cc_start: 0.8793 (m-80) cc_final: 0.8570 (m-80) REVERT: T 125 TRP cc_start: 0.6188 (t60) cc_final: 0.5938 (t-100) REVERT: V 16 ILE cc_start: 0.8182 (OUTLIER) cc_final: 0.7836 (pt) REVERT: V 18 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8596 (pp) REVERT: W 1 MET cc_start: 0.5927 (OUTLIER) cc_final: 0.5073 (pmm) REVERT: Z 73 LYS cc_start: 0.8368 (tptp) cc_final: 0.8167 (mtpp) REVERT: Z 81 MET cc_start: 0.8818 (tpt) cc_final: 0.8587 (tpt) REVERT: a 4 ARG cc_start: 0.8523 (OUTLIER) cc_final: 0.8239 (ttp80) REVERT: b 52 LYS cc_start: 0.7779 (ttmt) cc_final: 0.7493 (mtpp) REVERT: c 22 MET cc_start: 0.9272 (mmt) cc_final: 0.8792 (mmt) REVERT: e 22 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8210 (ttt180) REVERT: e 86 GLU cc_start: 0.7673 (mt-10) cc_final: 0.7343 (mt-10) REVERT: f 5 LEU cc_start: 0.9013 (mm) cc_final: 0.8719 (mt) REVERT: h 23 ASP cc_start: 0.7630 (OUTLIER) cc_final: 0.7398 (m-30) REVERT: h 63 GLN cc_start: 0.8233 (mt0) cc_final: 0.7973 (mt0) REVERT: h 96 ASN cc_start: 0.7826 (t0) cc_final: 0.7227 (t0) REVERT: h 114 TYR cc_start: 0.7915 (m-80) cc_final: 0.7681 (m-80) REVERT: k 43 TYR cc_start: 0.8631 (m-80) cc_final: 0.8413 (m-80) REVERT: m 120 ASN cc_start: 0.8294 (OUTLIER) cc_final: 0.8007 (m-40) REVERT: n 11 ARG cc_start: 0.6858 (mtm180) cc_final: 0.5901 (tpt170) REVERT: n 14 LYS cc_start: 0.8696 (mtpt) cc_final: 0.7499 (mmtt) REVERT: n 19 LYS cc_start: 0.7783 (ttpp) cc_final: 0.7548 (mmmt) REVERT: r 103 HIS cc_start: 0.7619 (OUTLIER) cc_final: 0.6865 (m-70) REVERT: t 10 LEU cc_start: 0.6926 (mt) cc_final: 0.6484 (pp) REVERT: x 43 ASP cc_start: 0.3190 (OUTLIER) cc_final: 0.2867 (m-30) REVERT: x 74 MET cc_start: 0.6787 (mtt) cc_final: 0.6515 (mtt) REVERT: x 82 GLU cc_start: 0.5382 (OUTLIER) cc_final: 0.4987 (mm-30) REVERT: x 154 LYS cc_start: 0.3682 (OUTLIER) cc_final: 0.2707 (mmtt) REVERT: x 185 GLU cc_start: 0.0819 (OUTLIER) cc_final: 0.0585 (pt0) REVERT: x 329 LEU cc_start: 0.3623 (mt) cc_final: 0.3246 (mp) REVERT: x 369 MET cc_start: 0.2260 (mtm) cc_final: 0.1233 (ptt) REVERT: x 430 MET cc_start: 0.1752 (ptm) cc_final: 0.0893 (ttm) outliers start: 298 outliers final: 170 residues processed: 1363 average time/residue: 1.3327 time to fit residues: 3112.8388 Evaluate side-chains 1237 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 192 poor density : 1045 time to evaluate : 7.684 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 139 ASP Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 233 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain D residue 9 ASN Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain F residue 42 LYS Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 186 THR Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain I residue 202 ASN Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 50 MET Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 32 GLN Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 174 LEU Chi-restraints excluded: chain N residue 196 ASN Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 42 ASN Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 166 ILE Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 186 GLU Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 25 HIS Chi-restraints excluded: chain P residue 69 ARG Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 125 MET Chi-restraints excluded: chain Q residue 75 ARG Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain Q residue 111 SER Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 74 ARG Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 130 ASN Chi-restraints excluded: chain R residue 139 MET Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 49 ILE Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 52 ASP Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 79 VAL Chi-restraints excluded: chain Y residue 102 SER Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 57 MET Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain a residue 4 ARG Chi-restraints excluded: chain a residue 8 THR Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain b residue 60 ASN Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain d residue 21 VAL Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 86 VAL Chi-restraints excluded: chain d residue 106 VAL Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain d residue 112 THR Chi-restraints excluded: chain d residue 113 THR Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 13 VAL Chi-restraints excluded: chain e residue 22 ARG Chi-restraints excluded: chain e residue 123 THR Chi-restraints excluded: chain f residue 31 GLU Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain g residue 32 TYR Chi-restraints excluded: chain g residue 35 THR Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 67 GLU Chi-restraints excluded: chain h residue 82 ASP Chi-restraints excluded: chain h residue 88 THR Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain i residue 13 LYS Chi-restraints excluded: chain k residue 30 ASP Chi-restraints excluded: chain k residue 70 LYS Chi-restraints excluded: chain l residue 11 ARG Chi-restraints excluded: chain m residue 120 ASN Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 18 HIS Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain r residue 58 LYS Chi-restraints excluded: chain r residue 60 VAL Chi-restraints excluded: chain r residue 78 VAL Chi-restraints excluded: chain r residue 80 THR Chi-restraints excluded: chain r residue 103 HIS Chi-restraints excluded: chain r residue 105 ASP Chi-restraints excluded: chain u residue 169 LEU Chi-restraints excluded: chain v residue 114 THR Chi-restraints excluded: chain w residue 27 VAL Chi-restraints excluded: chain x residue 12 SER Chi-restraints excluded: chain x residue 43 ASP Chi-restraints excluded: chain x residue 62 LEU Chi-restraints excluded: chain x residue 69 LEU Chi-restraints excluded: chain x residue 82 GLU Chi-restraints excluded: chain x residue 146 ASP Chi-restraints excluded: chain x residue 154 LYS Chi-restraints excluded: chain x residue 166 MET Chi-restraints excluded: chain x residue 169 VAL Chi-restraints excluded: chain x residue 185 GLU Chi-restraints excluded: chain x residue 198 GLU Chi-restraints excluded: chain x residue 220 VAL Chi-restraints excluded: chain x residue 222 ASP Chi-restraints excluded: chain x residue 240 VAL Chi-restraints excluded: chain x residue 245 VAL Chi-restraints excluded: chain x residue 279 ILE Chi-restraints excluded: chain x residue 292 SER Chi-restraints excluded: chain x residue 300 ILE Chi-restraints excluded: chain x residue 307 VAL Chi-restraints excluded: chain x residue 328 THR Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain y residue 55 LYS Chi-restraints excluded: chain y residue 68 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 577 optimal weight: 9.9990 chunk 322 optimal weight: 10.0000 chunk 865 optimal weight: 7.9990 chunk 708 optimal weight: 2.9990 chunk 286 optimal weight: 20.0000 chunk 1041 optimal weight: 9.9990 chunk 1125 optimal weight: 9.9990 chunk 927 optimal weight: 10.0000 chunk 1032 optimal weight: 10.0000 chunk 355 optimal weight: 20.0000 chunk 835 optimal weight: 6.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 HIS C 94 ASN D 195 HIS ** D 225 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 39 HIS E 124 HIS ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN E 275 ASN ** E 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN G 236 HIS J 65 ASN J 104 ASN L 115 GLN M 33 GLN N 37 HIS O 46 ASN P 34 GLN Q 57 ASN Q 125 GLN R 39 GLN ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 37 HIS S 92 ASN S 125 GLN T 69 GLN T 98 HIS T 144 ASN U 50 ASN X 73 HIS X 94 ASN X 105 ASN ** a 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 93 ASN b 60 ASN ** c 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 57 ASN e 102 ASN g 28 ASN g 100 GLN h 30 GLN l 19 GLN ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 51 GLN ** r 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.3171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.089 159521 Z= 0.417 Angle : 0.757 16.082 234784 Z= 0.381 Chirality : 0.044 0.357 29216 Planarity : 0.006 0.107 14749 Dihedral : 24.711 179.807 72612 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.02 % Favored : 93.92 % Rotamer: Outliers : 5.85 % Allowed : 15.06 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.08 % 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 (0.09), residues: 7563 helix: 1.02 (0.10), residues: 2798 sheet: -0.36 (0.16), residues: 1021 loop : -1.35 (0.10), residues: 3744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP R 95 HIS 0.009 0.002 HIS I 51 PHE 0.032 0.002 PHE R 132 TYR 0.036 0.003 TYR x 125 ARG 0.014 0.001 ARG u 152 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1445 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 385 poor density : 1060 time to evaluate : 7.953 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: B 204 GLN cc_start: 0.8423 (OUTLIER) cc_final: 0.7752 (mt0) REVERT: B 314 ILE cc_start: 0.8328 (OUTLIER) cc_final: 0.8104 (pp) REVERT: C 281 MET cc_start: 0.8055 (mmt) cc_final: 0.7818 (mmt) REVERT: D 64 ILE cc_start: 0.8557 (mt) cc_final: 0.8294 (mt) REVERT: D 122 GLN cc_start: 0.7275 (OUTLIER) cc_final: 0.7045 (tt0) REVERT: D 277 LYS cc_start: 0.7787 (tptt) cc_final: 0.7526 (mtmm) REVERT: E 119 ARG cc_start: 0.7081 (OUTLIER) cc_final: 0.6844 (ptm160) REVERT: E 203 LYS cc_start: 0.8365 (tmmt) cc_final: 0.7530 (ptpt) REVERT: E 241 GLN cc_start: 0.8219 (tp40) cc_final: 0.7928 (tp-100) REVERT: E 282 LEU cc_start: 0.8764 (OUTLIER) cc_final: 0.8455 (pt) REVERT: F 38 LYS cc_start: 0.8200 (mmtm) cc_final: 0.7821 (ttpt) REVERT: F 139 GLU cc_start: 0.8106 (tt0) cc_final: 0.7734 (tt0) REVERT: H 118 LEU cc_start: 0.8746 (mt) cc_final: 0.8518 (mt) REVERT: I 210 ARG cc_start: 0.7171 (OUTLIER) cc_final: 0.6587 (mtt90) REVERT: I 214 SER cc_start: 0.7817 (p) cc_final: 0.7141 (t) REVERT: L 9 ILE cc_start: 0.7989 (OUTLIER) cc_final: 0.7627 (tp) REVERT: L 69 LYS cc_start: 0.8311 (mmtp) cc_final: 0.8035 (mmtt) REVERT: L 103 ARG cc_start: 0.8032 (OUTLIER) cc_final: 0.7574 (ptp-110) REVERT: M 81 ASP cc_start: 0.8046 (OUTLIER) cc_final: 0.7496 (m-30) REVERT: N 32 GLN cc_start: 0.8334 (OUTLIER) cc_final: 0.7417 (mp10) REVERT: N 174 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8455 (pp) REVERT: O 42 ASN cc_start: 0.8753 (OUTLIER) cc_final: 0.8467 (m-40) REVERT: O 87 MET cc_start: 0.9033 (mtt) cc_final: 0.8749 (mtt) REVERT: Q 121 LEU cc_start: 0.8751 (OUTLIER) cc_final: 0.8535 (mt) REVERT: R 3 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7368 (tmm) REVERT: R 148 ASP cc_start: 0.7793 (m-30) cc_final: 0.7268 (m-30) REVERT: S 108 GLN cc_start: 0.8965 (tt0) cc_final: 0.8736 (mt0) REVERT: U 99 TRP cc_start: 0.6893 (OUTLIER) cc_final: 0.4845 (m-90) REVERT: V 16 ILE cc_start: 0.8229 (OUTLIER) cc_final: 0.7914 (pt) REVERT: V 18 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8614 (pp) REVERT: W 1 MET cc_start: 0.6567 (OUTLIER) cc_final: 0.5680 (pmm) REVERT: W 15 PRO cc_start: 0.7818 (Cg_endo) cc_final: 0.7592 (Cg_exo) REVERT: Z 73 LYS cc_start: 0.8351 (tptp) cc_final: 0.8068 (mtpp) REVERT: Z 81 MET cc_start: 0.8766 (tpt) cc_final: 0.8494 (tpt) REVERT: a 12 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.8253 (mmp-170) REVERT: b 52 LYS cc_start: 0.7666 (ttmt) cc_final: 0.7349 (mtpp) REVERT: c 37 MET cc_start: 0.7729 (tpp) cc_final: 0.7177 (mmt) REVERT: e 22 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8136 (ttt180) REVERT: e 86 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7469 (mt-10) REVERT: f 5 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8742 (mt) REVERT: f 14 TYR cc_start: 0.8449 (m-80) cc_final: 0.8180 (m-80) REVERT: f 100 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8500 (tpp80) REVERT: g 5 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8722 (pp) REVERT: h 23 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7454 (m-30) REVERT: h 77 LYS cc_start: 0.8884 (OUTLIER) cc_final: 0.8328 (tttp) REVERT: h 96 ASN cc_start: 0.7626 (t0) cc_final: 0.7016 (t0) REVERT: n 10 MET cc_start: 0.5035 (ttt) cc_final: 0.4591 (ttt) REVERT: n 11 ARG cc_start: 0.6954 (mtm180) cc_final: 0.5992 (tpt170) REVERT: n 14 LYS cc_start: 0.8750 (mtpt) cc_final: 0.7617 (mmtt) REVERT: o 51 GLN cc_start: 0.8534 (OUTLIER) cc_final: 0.6835 (tp-100) REVERT: r 103 HIS cc_start: 0.7642 (OUTLIER) cc_final: 0.6914 (m-70) REVERT: t 10 LEU cc_start: 0.6931 (mt) cc_final: 0.6531 (pp) REVERT: u 148 GLU cc_start: 0.3211 (mm-30) cc_final: 0.2445 (tm-30) REVERT: x 82 GLU cc_start: 0.5363 (OUTLIER) cc_final: 0.4671 (mm-30) REVERT: x 86 LEU cc_start: 0.4463 (OUTLIER) cc_final: 0.4094 (mp) REVERT: x 150 GLN cc_start: 0.5152 (pm20) cc_final: 0.4922 (pm20) REVERT: x 185 GLU cc_start: 0.1338 (OUTLIER) cc_final: 0.0402 (pt0) REVERT: x 342 MET cc_start: 0.4581 (mtp) cc_final: 0.4045 (tmm) REVERT: x 369 MET cc_start: 0.2528 (mtm) cc_final: 0.2149 (tpt) outliers start: 385 outliers final: 236 residues processed: 1329 average time/residue: 1.3473 time to fit residues: 3097.2628 Evaluate side-chains 1246 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 980 time to evaluate : 7.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 155 THR Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 119 ARG Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 42 LYS Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 18 ILE Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 186 THR Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain I residue 202 ASN Chi-restraints excluded: chain I residue 210 ARG Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 103 ARG Chi-restraints excluded: chain L residue 130 LYS Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 63 LYS Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 32 GLN Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 174 LEU Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 42 ASN Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 108 ILE Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 25 HIS Chi-restraints excluded: chain P residue 69 ARG Chi-restraints excluded: chain P residue 91 LEU Chi-restraints excluded: chain P residue 125 MET Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain Q residue 75 ARG Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 95 VAL Chi-restraints excluded: chain Q residue 111 SER Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain R residue 3 MET Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 39 GLN Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 74 ARG Chi-restraints excluded: chain R residue 78 ILE Chi-restraints excluded: chain R residue 130 ASN Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 49 SER Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 92 ASN Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 169 THR Chi-restraints excluded: chain T residue 32 ARG Chi-restraints excluded: chain T residue 33 ILE Chi-restraints excluded: chain T residue 40 VAL Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain U residue 20 LYS Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 76 VAL Chi-restraints excluded: chain U residue 79 SER Chi-restraints excluded: chain U residue 99 TRP Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 49 ILE Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 52 ASP Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 79 VAL Chi-restraints excluded: chain Y residue 102 SER Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Z residue 35 ASP Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 57 MET Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain a residue 12 ARG Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain c residue 15 ASN Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain d residue 21 VAL Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 102 LEU Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain d residue 112 THR Chi-restraints excluded: chain d residue 113 THR Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 13 VAL Chi-restraints excluded: chain e residue 22 ARG Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 123 THR Chi-restraints excluded: chain f residue 5 LEU Chi-restraints excluded: chain f residue 31 GLU Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain f residue 47 CYS Chi-restraints excluded: chain f residue 100 ARG Chi-restraints excluded: chain f residue 108 SER Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 32 TYR Chi-restraints excluded: chain g residue 35 THR Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain g residue 100 GLN Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 67 GLU Chi-restraints excluded: chain h residue 77 LYS Chi-restraints excluded: chain h residue 82 ASP Chi-restraints excluded: chain h residue 88 THR Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain i residue 3 LEU Chi-restraints excluded: chain i residue 81 ILE Chi-restraints excluded: chain j residue 61 THR Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain k residue 30 ASP Chi-restraints excluded: chain k residue 70 LYS Chi-restraints excluded: chain l residue 11 ARG Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 18 HIS Chi-restraints excluded: chain o residue 51 GLN Chi-restraints excluded: chain o residue 66 ILE Chi-restraints excluded: chain o residue 77 CYS Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain r residue 58 LYS Chi-restraints excluded: chain r residue 60 VAL Chi-restraints excluded: chain r residue 71 ARG Chi-restraints excluded: chain r residue 78 VAL Chi-restraints excluded: chain r residue 80 THR Chi-restraints excluded: chain r residue 103 HIS Chi-restraints excluded: chain r residue 105 ASP Chi-restraints excluded: chain u residue 94 LEU Chi-restraints excluded: chain u residue 141 LEU Chi-restraints excluded: chain u residue 169 LEU Chi-restraints excluded: chain u residue 184 LEU Chi-restraints excluded: chain v residue 88 LEU Chi-restraints excluded: chain v residue 114 THR Chi-restraints excluded: chain v residue 162 VAL Chi-restraints excluded: chain x residue 12 SER Chi-restraints excluded: chain x residue 36 CYS Chi-restraints excluded: chain x residue 43 ASP Chi-restraints excluded: chain x residue 82 GLU Chi-restraints excluded: chain x residue 84 VAL Chi-restraints excluded: chain x residue 86 LEU Chi-restraints excluded: chain x residue 97 THR Chi-restraints excluded: chain x residue 146 ASP Chi-restraints excluded: chain x residue 169 VAL Chi-restraints excluded: chain x residue 185 GLU Chi-restraints excluded: chain x residue 220 VAL Chi-restraints excluded: chain x residue 240 VAL Chi-restraints excluded: chain x residue 245 VAL Chi-restraints excluded: chain x residue 260 LEU Chi-restraints excluded: chain x residue 279 ILE Chi-restraints excluded: chain x residue 300 ILE Chi-restraints excluded: chain x residue 307 VAL Chi-restraints excluded: chain x residue 412 VAL Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain y residue 55 LYS Chi-restraints excluded: chain y residue 68 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 1029 optimal weight: 6.9990 chunk 783 optimal weight: 6.9990 chunk 540 optimal weight: 6.9990 chunk 115 optimal weight: 10.0000 chunk 497 optimal weight: 9.9990 chunk 699 optimal weight: 0.7980 chunk 1045 optimal weight: 20.0000 chunk 1106 optimal weight: 30.0000 chunk 546 optimal weight: 0.1980 chunk 990 optimal weight: 2.9990 chunk 298 optimal weight: 10.0000 overall best weight: 3.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN C 21 ASN ** E 178 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN E 275 ASN ** E 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 GLN J 65 ASN J 104 ASN M 33 GLN N 37 HIS N 196 ASN Q 125 GLN S 92 ASN T 114 GLN X 73 HIS X 105 ASN X 111 GLN ** a 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 33 GLN e 57 ASN g 28 ASN h 30 GLN ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 ASN ** m 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 51 GLN ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 159521 Z= 0.218 Angle : 0.610 14.264 234784 Z= 0.312 Chirality : 0.037 0.305 29216 Planarity : 0.005 0.092 14749 Dihedral : 24.624 179.955 72604 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.56 % Favored : 94.39 % Rotamer: Outliers : 4.68 % Allowed : 17.46 % Favored : 77.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.16 (0.10), residues: 7563 helix: 1.38 (0.10), residues: 2796 sheet: -0.26 (0.16), residues: 1023 loop : -1.24 (0.10), residues: 3744 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 120 HIS 0.007 0.001 HIS E 124 PHE 0.024 0.001 PHE S 176 TYR 0.024 0.002 TYR E 212 ARG 0.007 0.000 ARG L 167 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1354 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 308 poor density : 1046 time to evaluate : 7.881 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: B 314 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.8057 (pp) REVERT: C 352 GLU cc_start: 0.7525 (mm-30) cc_final: 0.7227 (mm-30) REVERT: D 64 ILE cc_start: 0.8548 (mt) cc_final: 0.8311 (mt) REVERT: E 203 LYS cc_start: 0.8368 (tmmt) cc_final: 0.7466 (ptpt) REVERT: E 241 GLN cc_start: 0.8141 (tp40) cc_final: 0.7831 (tp-100) REVERT: E 282 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8300 (pt) REVERT: F 32 ILE cc_start: 0.7935 (OUTLIER) cc_final: 0.7561 (mp) REVERT: F 38 LYS cc_start: 0.8137 (mmtm) cc_final: 0.7727 (mtpt) REVERT: F 139 GLU cc_start: 0.8060 (tt0) cc_final: 0.7717 (tt0) REVERT: J 18 ARG cc_start: 0.8360 (OUTLIER) cc_final: 0.7641 (mtp85) REVERT: L 103 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7388 (ptp-110) REVERT: L 155 MET cc_start: 0.8792 (OUTLIER) cc_final: 0.8320 (mtm) REVERT: M 8 GLU cc_start: 0.7092 (OUTLIER) cc_final: 0.6195 (tm-30) REVERT: M 81 ASP cc_start: 0.8052 (OUTLIER) cc_final: 0.7544 (m-30) REVERT: N 32 GLN cc_start: 0.8157 (OUTLIER) cc_final: 0.7272 (mp10) REVERT: N 174 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8466 (pp) REVERT: O 87 MET cc_start: 0.8987 (mtt) cc_final: 0.8729 (mtt) REVERT: Q 121 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8432 (mt) REVERT: R 6 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7774 (tp) REVERT: R 148 ASP cc_start: 0.7769 (m-30) cc_final: 0.7392 (m-30) REVERT: S 108 GLN cc_start: 0.8863 (tt0) cc_final: 0.8469 (mt0) REVERT: T 32 ARG cc_start: 0.7831 (OUTLIER) cc_final: 0.7435 (ptm160) REVERT: U 20 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7483 (ttpt) REVERT: U 50 ASN cc_start: 0.8169 (m110) cc_final: 0.7717 (m-40) REVERT: U 96 LEU cc_start: 0.8183 (mm) cc_final: 0.7916 (mt) REVERT: V 16 ILE cc_start: 0.8176 (OUTLIER) cc_final: 0.7874 (pt) REVERT: V 18 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8575 (pp) REVERT: V 90 ARG cc_start: 0.7849 (mtt180) cc_final: 0.7620 (mtm180) REVERT: V 124 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.6629 (mm-30) REVERT: W 1 MET cc_start: 0.6561 (OUTLIER) cc_final: 0.5776 (pmm) REVERT: Y 75 ARG cc_start: 0.8979 (OUTLIER) cc_final: 0.8499 (mtm180) REVERT: Z 73 LYS cc_start: 0.8346 (tptp) cc_final: 0.8140 (mtpp) REVERT: Z 81 MET cc_start: 0.8835 (tpt) cc_final: 0.8582 (tpt) REVERT: a 12 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.7513 (mmp-170) REVERT: a 32 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.8365 (mtt-85) REVERT: c 37 MET cc_start: 0.7737 (tpp) cc_final: 0.7187 (mmt) REVERT: e 22 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8190 (ttt180) REVERT: e 86 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7411 (mt-10) REVERT: f 5 LEU cc_start: 0.9017 (OUTLIER) cc_final: 0.8711 (mt) REVERT: f 100 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.8202 (tpp80) REVERT: g 5 LEU cc_start: 0.8979 (OUTLIER) cc_final: 0.8724 (pp) REVERT: h 23 ASP cc_start: 0.7621 (OUTLIER) cc_final: 0.7360 (m-30) REVERT: h 96 ASN cc_start: 0.7539 (OUTLIER) cc_final: 0.6904 (t0) REVERT: i 4 ARG cc_start: 0.6910 (OUTLIER) cc_final: 0.6064 (tpt-90) REVERT: n 11 ARG cc_start: 0.6870 (mtm180) cc_final: 0.5842 (tpt-90) REVERT: n 14 LYS cc_start: 0.8643 (mtpt) cc_final: 0.7463 (mmtt) REVERT: p 29 ILE cc_start: 0.9199 (mm) cc_final: 0.8871 (mt) REVERT: r 28 GLU cc_start: 0.8307 (pm20) cc_final: 0.7984 (pm20) REVERT: r 103 HIS cc_start: 0.7518 (OUTLIER) cc_final: 0.6818 (m-70) REVERT: t 10 LEU cc_start: 0.7005 (mt) cc_final: 0.6633 (pp) REVERT: u 154 HIS cc_start: 0.2666 (OUTLIER) cc_final: 0.1986 (m-70) REVERT: x 65 MET cc_start: 0.5524 (tpp) cc_final: 0.5266 (tpp) REVERT: x 82 GLU cc_start: 0.5346 (OUTLIER) cc_final: 0.4733 (mm-30) REVERT: x 86 LEU cc_start: 0.4435 (OUTLIER) cc_final: 0.4052 (mp) REVERT: x 150 GLN cc_start: 0.4504 (OUTLIER) cc_final: 0.4228 (pm20) REVERT: x 185 GLU cc_start: 0.2011 (OUTLIER) cc_final: 0.1038 (pt0) REVERT: x 342 MET cc_start: 0.4514 (mtp) cc_final: 0.3969 (tmm) REVERT: x 369 MET cc_start: 0.2604 (mtm) cc_final: 0.2125 (tpt) REVERT: x 430 MET cc_start: 0.2148 (ptm) cc_final: 0.1314 (ttm) outliers start: 308 outliers final: 202 residues processed: 1254 average time/residue: 1.3406 time to fit residues: 2901.3214 Evaluate side-chains 1229 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 236 poor density : 993 time to evaluate : 7.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 120 LYS Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 18 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 202 ASN Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 103 ARG Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 155 MET Chi-restraints excluded: chain M residue 8 GLU Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 32 GLN Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 174 LEU Chi-restraints excluded: chain N residue 196 ASN Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain P residue 14 SER Chi-restraints excluded: chain P residue 25 HIS Chi-restraints excluded: chain P residue 69 ARG Chi-restraints excluded: chain P residue 104 LEU Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain Q residue 111 SER Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 74 ARG Chi-restraints excluded: chain R residue 149 LYS Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 49 SER Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 92 ASN Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain S residue 169 THR Chi-restraints excluded: chain S residue 174 THR Chi-restraints excluded: chain T residue 32 ARG Chi-restraints excluded: chain T residue 33 ILE Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain U residue 20 LYS Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 79 SER Chi-restraints excluded: chain U residue 111 GLU Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 124 GLU Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 52 ASP Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 75 ARG Chi-restraints excluded: chain Y residue 79 VAL Chi-restraints excluded: chain Y residue 102 SER Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 57 MET Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 115 LYS Chi-restraints excluded: chain a residue 12 ARG Chi-restraints excluded: chain a residue 32 ARG Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 135 GLU Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 92 CYS Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain d residue 21 VAL Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 97 ASP Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain d residue 112 THR Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 13 VAL Chi-restraints excluded: chain e residue 22 ARG Chi-restraints excluded: chain e residue 41 ILE Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 123 THR Chi-restraints excluded: chain f residue 5 LEU Chi-restraints excluded: chain f residue 31 GLU Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain f residue 47 CYS Chi-restraints excluded: chain f residue 100 ARG Chi-restraints excluded: chain f residue 108 SER Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 32 TYR Chi-restraints excluded: chain g residue 35 THR Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 67 GLU Chi-restraints excluded: chain h residue 82 ASP Chi-restraints excluded: chain h residue 88 THR Chi-restraints excluded: chain h residue 96 ASN Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain i residue 4 ARG Chi-restraints excluded: chain j residue 13 ASN Chi-restraints excluded: chain k residue 30 ASP Chi-restraints excluded: chain l residue 11 ARG Chi-restraints excluded: chain l residue 49 LEU Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 66 ILE Chi-restraints excluded: chain o residue 77 CYS Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain q residue 52 VAL Chi-restraints excluded: chain r residue 58 LYS Chi-restraints excluded: chain r residue 60 VAL Chi-restraints excluded: chain r residue 78 VAL Chi-restraints excluded: chain r residue 80 THR Chi-restraints excluded: chain r residue 89 THR Chi-restraints excluded: chain r residue 103 HIS Chi-restraints excluded: chain r residue 105 ASP Chi-restraints excluded: chain u residue 94 LEU Chi-restraints excluded: chain u residue 127 VAL Chi-restraints excluded: chain u residue 141 LEU Chi-restraints excluded: chain u residue 154 HIS Chi-restraints excluded: chain u residue 169 LEU Chi-restraints excluded: chain u residue 184 LEU Chi-restraints excluded: chain v residue 68 LEU Chi-restraints excluded: chain v residue 88 LEU Chi-restraints excluded: chain v residue 114 THR Chi-restraints excluded: chain v residue 183 ASP Chi-restraints excluded: chain w residue 53 THR Chi-restraints excluded: chain x residue 12 SER Chi-restraints excluded: chain x residue 82 GLU Chi-restraints excluded: chain x residue 86 LEU Chi-restraints excluded: chain x residue 97 THR Chi-restraints excluded: chain x residue 150 GLN Chi-restraints excluded: chain x residue 169 VAL Chi-restraints excluded: chain x residue 185 GLU Chi-restraints excluded: chain x residue 220 VAL Chi-restraints excluded: chain x residue 222 ASP Chi-restraints excluded: chain x residue 240 VAL Chi-restraints excluded: chain x residue 245 VAL Chi-restraints excluded: chain x residue 260 LEU Chi-restraints excluded: chain x residue 279 ILE Chi-restraints excluded: chain x residue 307 VAL Chi-restraints excluded: chain x residue 328 THR Chi-restraints excluded: chain x residue 384 ASP Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain y residue 55 LYS Chi-restraints excluded: chain y residue 68 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 921 optimal weight: 2.9990 chunk 628 optimal weight: 9.9990 chunk 16 optimal weight: 50.0000 chunk 824 optimal weight: 6.9990 chunk 456 optimal weight: 10.0000 chunk 944 optimal weight: 6.9990 chunk 765 optimal weight: 0.9990 chunk 1 optimal weight: 40.0000 chunk 565 optimal weight: 7.9990 chunk 993 optimal weight: 1.9990 chunk 279 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 178 ASN E 246 GLN ** E 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN J 104 ASN M 125 ASN N 37 HIS N 196 ASN Q 125 GLN R 130 ASN S 92 ASN T 114 GLN X 105 ASN X 111 GLN ** a 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 57 ASN g 28 ASN ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 ASN ** m 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** o 51 GLN q 50 GLN ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 44 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 159521 Z= 0.243 Angle : 0.613 14.389 234784 Z= 0.313 Chirality : 0.037 0.307 29216 Planarity : 0.005 0.089 14749 Dihedral : 24.575 179.995 72599 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.03 % Favored : 93.93 % Rotamer: Outliers : 5.24 % Allowed : 17.83 % Favored : 76.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.10), residues: 7563 helix: 1.46 (0.10), residues: 2782 sheet: -0.27 (0.16), residues: 1023 loop : -1.21 (0.10), residues: 3758 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 120 HIS 0.009 0.001 HIS S 91 PHE 0.026 0.001 PHE S 176 TYR 0.024 0.002 TYR E 212 ARG 0.008 0.000 ARG L 167 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1365 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 345 poor density : 1020 time to evaluate : 7.981 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: B 204 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7739 (mt0) REVERT: B 314 ILE cc_start: 0.8272 (OUTLIER) cc_final: 0.8030 (pp) REVERT: C 352 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7210 (mm-30) REVERT: D 64 ILE cc_start: 0.8565 (mt) cc_final: 0.8343 (mt) REVERT: D 271 MET cc_start: 0.8354 (ttm) cc_final: 0.8030 (mtp) REVERT: E 203 LYS cc_start: 0.8393 (tmmt) cc_final: 0.7502 (ptpt) REVERT: E 282 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8225 (pt) REVERT: F 32 ILE cc_start: 0.7947 (OUTLIER) cc_final: 0.7544 (mp) REVERT: F 38 LYS cc_start: 0.8142 (mmtm) cc_final: 0.7801 (ttpt) REVERT: F 139 GLU cc_start: 0.8037 (tt0) cc_final: 0.7679 (tt0) REVERT: I 210 ARG cc_start: 0.7116 (OUTLIER) cc_final: 0.6466 (mtt90) REVERT: L 9 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7430 (tp) REVERT: L 103 ARG cc_start: 0.7906 (OUTLIER) cc_final: 0.7415 (ptp-110) REVERT: L 155 MET cc_start: 0.8775 (OUTLIER) cc_final: 0.8271 (mtm) REVERT: L 198 ARG cc_start: 0.7743 (OUTLIER) cc_final: 0.6133 (mpt-90) REVERT: M 8 GLU cc_start: 0.7112 (OUTLIER) cc_final: 0.6263 (tm-30) REVERT: M 81 ASP cc_start: 0.8015 (OUTLIER) cc_final: 0.7512 (m-30) REVERT: N 32 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7314 (mp10) REVERT: N 174 LEU cc_start: 0.8760 (OUTLIER) cc_final: 0.8420 (pp) REVERT: O 87 MET cc_start: 0.9108 (mtt) cc_final: 0.8888 (mtt) REVERT: O 196 LEU cc_start: 0.8797 (OUTLIER) cc_final: 0.8466 (mt) REVERT: Q 121 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8475 (mt) REVERT: R 3 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7339 (tmm) REVERT: R 105 LEU cc_start: 0.9056 (OUTLIER) cc_final: 0.8778 (tp) REVERT: R 148 ASP cc_start: 0.7731 (m-30) cc_final: 0.7513 (m-30) REVERT: S 51 LEU cc_start: 0.8751 (mt) cc_final: 0.8530 (mt) REVERT: S 108 GLN cc_start: 0.8849 (tt0) cc_final: 0.8463 (mt0) REVERT: U 95 ASN cc_start: 0.7502 (p0) cc_final: 0.7174 (p0) REVERT: U 96 LEU cc_start: 0.8190 (OUTLIER) cc_final: 0.7871 (mt) REVERT: V 16 ILE cc_start: 0.8145 (OUTLIER) cc_final: 0.7836 (pt) REVERT: V 18 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8576 (pp) REVERT: V 124 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.6527 (mm-30) REVERT: W 1 MET cc_start: 0.6601 (OUTLIER) cc_final: 0.5855 (pmm) REVERT: Y 75 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8583 (mtm180) REVERT: Z 81 MET cc_start: 0.8872 (tpt) cc_final: 0.8649 (tpt) REVERT: a 4 ARG cc_start: 0.8640 (OUTLIER) cc_final: 0.8372 (ttp80) REVERT: a 12 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7484 (mmp-170) REVERT: a 32 ARG cc_start: 0.8958 (OUTLIER) cc_final: 0.8357 (mtt-85) REVERT: b 52 LYS cc_start: 0.7676 (ttmt) cc_final: 0.7363 (mtpp) REVERT: c 37 MET cc_start: 0.7616 (tpp) cc_final: 0.7130 (mmt) REVERT: e 22 ARG cc_start: 0.8907 (OUTLIER) cc_final: 0.8155 (ttt180) REVERT: e 86 GLU cc_start: 0.7746 (mt-10) cc_final: 0.7425 (mt-10) REVERT: f 5 LEU cc_start: 0.8996 (OUTLIER) cc_final: 0.8692 (mt) REVERT: f 100 ARG cc_start: 0.8739 (OUTLIER) cc_final: 0.8167 (tpp80) REVERT: g 5 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8701 (pp) REVERT: h 23 ASP cc_start: 0.7639 (OUTLIER) cc_final: 0.7361 (m-30) REVERT: h 69 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8261 (mm) REVERT: h 96 ASN cc_start: 0.7494 (t0) cc_final: 0.6851 (t0) REVERT: i 4 ARG cc_start: 0.6953 (OUTLIER) cc_final: 0.6089 (tpt-90) REVERT: n 11 ARG cc_start: 0.6915 (mtm180) cc_final: 0.5887 (tpt-90) REVERT: n 14 LYS cc_start: 0.8667 (mtpt) cc_final: 0.7486 (mmtt) REVERT: o 89 LYS cc_start: 0.8438 (OUTLIER) cc_final: 0.8121 (ptmm) REVERT: p 29 ILE cc_start: 0.9222 (mm) cc_final: 0.8901 (mt) REVERT: r 28 GLU cc_start: 0.8297 (pm20) cc_final: 0.8003 (pm20) REVERT: r 71 ARG cc_start: 0.8139 (OUTLIER) cc_final: 0.7844 (ptt-90) REVERT: r 103 HIS cc_start: 0.7534 (OUTLIER) cc_final: 0.6845 (m-70) REVERT: r 107 ARG cc_start: 0.8362 (tmm-80) cc_final: 0.8103 (ttp80) REVERT: t 10 LEU cc_start: 0.6936 (mt) cc_final: 0.6572 (pp) REVERT: u 154 HIS cc_start: 0.2280 (OUTLIER) cc_final: 0.1834 (m-70) REVERT: x 82 GLU cc_start: 0.5168 (OUTLIER) cc_final: 0.4564 (mm-30) REVERT: x 86 LEU cc_start: 0.4361 (OUTLIER) cc_final: 0.4019 (mp) REVERT: x 150 GLN cc_start: 0.4566 (OUTLIER) cc_final: 0.4190 (pm20) REVERT: x 185 GLU cc_start: 0.1794 (OUTLIER) cc_final: 0.0976 (pt0) REVERT: x 295 LEU cc_start: 0.4926 (tp) cc_final: 0.4612 (tt) REVERT: x 342 MET cc_start: 0.4225 (mtp) cc_final: 0.3825 (tmm) REVERT: x 369 MET cc_start: 0.2386 (mtm) cc_final: 0.1963 (tpt) REVERT: x 430 MET cc_start: 0.1974 (ptm) cc_final: 0.1155 (ttm) REVERT: y 73 ILE cc_start: -0.0451 (OUTLIER) cc_final: -0.0744 (tp) REVERT: z 580 MET cc_start: 0.3309 (OUTLIER) cc_final: 0.2951 (tmm) outliers start: 345 outliers final: 247 residues processed: 1256 average time/residue: 1.3734 time to fit residues: 2994.8205 Evaluate side-chains 1286 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 290 poor density : 996 time to evaluate : 7.705 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 162 ASN Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 146 LEU Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 18 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 202 ASN Chi-restraints excluded: chain I residue 210 ARG Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 55 TYR Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain J residue 150 CYS Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 103 ARG Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 155 MET Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain L residue 198 ARG Chi-restraints excluded: chain M residue 8 GLU Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain M residue 108 ASP Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 32 GLN Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 174 LEU Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain P residue 25 HIS Chi-restraints excluded: chain P residue 69 ARG Chi-restraints excluded: chain P residue 104 LEU Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 125 MET Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 111 SER Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain R residue 3 MET Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 74 ARG Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 130 ASN Chi-restraints excluded: chain R residue 139 MET Chi-restraints excluded: chain R residue 149 LYS Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 49 SER Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain S residue 169 THR Chi-restraints excluded: chain S residue 174 THR Chi-restraints excluded: chain T residue 32 ARG Chi-restraints excluded: chain T residue 33 ILE Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 79 SER Chi-restraints excluded: chain U residue 96 LEU Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 111 GLU Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain V residue 124 GLU Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 153 ILE Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 52 ASP Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 75 ARG Chi-restraints excluded: chain Y residue 79 VAL Chi-restraints excluded: chain Y residue 102 SER Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Z residue 35 ASP Chi-restraints excluded: chain Z residue 42 LEU Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 57 MET Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain a residue 4 ARG Chi-restraints excluded: chain a residue 12 ARG Chi-restraints excluded: chain a residue 32 ARG Chi-restraints excluded: chain a residue 38 MET Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 135 GLU Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 92 CYS Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain d residue 21 VAL Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 97 ASP Chi-restraints excluded: chain d residue 102 LEU Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain d residue 112 THR Chi-restraints excluded: chain d residue 113 THR Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 13 VAL Chi-restraints excluded: chain e residue 22 ARG Chi-restraints excluded: chain e residue 41 ILE Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 81 ASN Chi-restraints excluded: chain e residue 123 THR Chi-restraints excluded: chain f residue 5 LEU Chi-restraints excluded: chain f residue 31 GLU Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain f residue 47 CYS Chi-restraints excluded: chain f residue 100 ARG Chi-restraints excluded: chain f residue 108 SER Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 32 TYR Chi-restraints excluded: chain g residue 35 THR Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 30 GLN Chi-restraints excluded: chain h residue 67 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 82 ASP Chi-restraints excluded: chain h residue 88 THR Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain i residue 4 ARG Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain i residue 81 ILE Chi-restraints excluded: chain j residue 61 THR Chi-restraints excluded: chain k residue 30 ASP Chi-restraints excluded: chain l residue 11 ARG Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 66 ILE Chi-restraints excluded: chain o residue 77 CYS Chi-restraints excluded: chain o residue 89 LYS Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain r residue 58 LYS Chi-restraints excluded: chain r residue 60 VAL Chi-restraints excluded: chain r residue 71 ARG Chi-restraints excluded: chain r residue 78 VAL Chi-restraints excluded: chain r residue 80 THR Chi-restraints excluded: chain r residue 89 THR Chi-restraints excluded: chain r residue 103 HIS Chi-restraints excluded: chain r residue 105 ASP Chi-restraints excluded: chain u residue 94 LEU Chi-restraints excluded: chain u residue 127 VAL Chi-restraints excluded: chain u residue 141 LEU Chi-restraints excluded: chain u residue 154 HIS Chi-restraints excluded: chain u residue 169 LEU Chi-restraints excluded: chain u residue 184 LEU Chi-restraints excluded: chain v residue 68 LEU Chi-restraints excluded: chain v residue 88 LEU Chi-restraints excluded: chain v residue 114 THR Chi-restraints excluded: chain v residue 162 VAL Chi-restraints excluded: chain w residue 53 THR Chi-restraints excluded: chain w residue 62 ILE Chi-restraints excluded: chain x residue 12 SER Chi-restraints excluded: chain x residue 36 CYS Chi-restraints excluded: chain x residue 82 GLU Chi-restraints excluded: chain x residue 86 LEU Chi-restraints excluded: chain x residue 97 THR Chi-restraints excluded: chain x residue 150 GLN Chi-restraints excluded: chain x residue 166 MET Chi-restraints excluded: chain x residue 169 VAL Chi-restraints excluded: chain x residue 185 GLU Chi-restraints excluded: chain x residue 220 VAL Chi-restraints excluded: chain x residue 222 ASP Chi-restraints excluded: chain x residue 240 VAL Chi-restraints excluded: chain x residue 245 VAL Chi-restraints excluded: chain x residue 260 LEU Chi-restraints excluded: chain x residue 279 ILE Chi-restraints excluded: chain x residue 307 VAL Chi-restraints excluded: chain x residue 315 ASN Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 73 ILE Chi-restraints excluded: chain z residue 580 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 372 optimal weight: 9.9990 chunk 996 optimal weight: 20.0000 chunk 218 optimal weight: 10.0000 chunk 649 optimal weight: 4.9990 chunk 273 optimal weight: 10.0000 chunk 1107 optimal weight: 9.9990 chunk 919 optimal weight: 10.0000 chunk 512 optimal weight: 8.9990 chunk 92 optimal weight: 30.0000 chunk 366 optimal weight: 10.0000 chunk 581 optimal weight: 0.6980 overall best weight: 6.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN E 246 GLN ** E 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 GLN G 64 GLN J 104 ASN L 104 ASN M 125 ASN N 37 HIS Q 125 GLN S 92 ASN T 114 GLN X 105 ASN X 111 GLN ** a 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 73 HIS e 57 ASN ** e 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 ASN m 117 HIS ** m 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 45 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.3782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.100 159521 Z= 0.384 Angle : 0.730 14.575 234784 Z= 0.370 Chirality : 0.043 0.354 29216 Planarity : 0.006 0.092 14749 Dihedral : 24.669 179.754 72595 Min Nonbonded Distance : 1.917 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.73 % Favored : 93.16 % Rotamer: Outliers : 5.83 % Allowed : 18.01 % Favored : 76.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.09), residues: 7563 helix: 1.11 (0.10), residues: 2787 sheet: -0.48 (0.16), residues: 1027 loop : -1.39 (0.10), residues: 3749 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP N 120 HIS 0.013 0.002 HIS E 124 PHE 0.025 0.002 PHE S 176 TYR 0.025 0.002 TYR f 106 ARG 0.010 0.001 ARG E 119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1390 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 384 poor density : 1006 time to evaluate : 7.934 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: B 4 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.7953 (ttt180) REVERT: B 71 GLU cc_start: 0.6915 (OUTLIER) cc_final: 0.6273 (tt0) REVERT: B 204 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7732 (mt0) REVERT: B 314 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8118 (pp) REVERT: C 49 ARG cc_start: 0.8639 (OUTLIER) cc_final: 0.7959 (ttp-170) REVERT: D 51 MET cc_start: 0.8380 (OUTLIER) cc_final: 0.8130 (tmm) REVERT: E 108 MET cc_start: 0.7089 (mmt) cc_final: 0.6352 (mmt) REVERT: E 203 LYS cc_start: 0.8466 (tmmt) cc_final: 0.7490 (ptpt) REVERT: E 241 GLN cc_start: 0.8300 (tp40) cc_final: 0.7965 (tp-100) REVERT: E 282 LEU cc_start: 0.8786 (OUTLIER) cc_final: 0.8529 (pt) REVERT: F 32 ILE cc_start: 0.7937 (OUTLIER) cc_final: 0.7567 (mp) REVERT: F 38 LYS cc_start: 0.8134 (mmtm) cc_final: 0.7822 (ttpt) REVERT: F 139 GLU cc_start: 0.8116 (tt0) cc_final: 0.7784 (tt0) REVERT: G 253 LEU cc_start: 0.7557 (OUTLIER) cc_final: 0.7064 (mm) REVERT: I 184 MET cc_start: 0.7757 (mtt) cc_final: 0.7418 (mtt) REVERT: I 210 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6524 (mtt90) REVERT: J 18 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7545 (mtp85) REVERT: L 9 ILE cc_start: 0.7891 (OUTLIER) cc_final: 0.7593 (tp) REVERT: L 103 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7563 (ptp-110) REVERT: L 155 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.8300 (mtm) REVERT: L 198 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7522 (mpt-90) REVERT: M 8 GLU cc_start: 0.7183 (OUTLIER) cc_final: 0.6257 (tm-30) REVERT: M 81 ASP cc_start: 0.8048 (OUTLIER) cc_final: 0.7534 (m-30) REVERT: M 93 LYS cc_start: 0.8072 (OUTLIER) cc_final: 0.7669 (mttt) REVERT: N 15 GLN cc_start: 0.8447 (mm-40) cc_final: 0.8064 (mt0) REVERT: N 32 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7430 (mp10) REVERT: N 174 LEU cc_start: 0.8818 (OUTLIER) cc_final: 0.8443 (pp) REVERT: O 87 MET cc_start: 0.9240 (mtt) cc_final: 0.8894 (mtt) REVERT: O 196 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8496 (mt) REVERT: Q 121 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8506 (mt) REVERT: R 3 MET cc_start: 0.8364 (OUTLIER) cc_final: 0.7499 (tmm) REVERT: R 6 LEU cc_start: 0.8067 (OUTLIER) cc_final: 0.7806 (tp) REVERT: R 47 ASP cc_start: 0.7984 (t70) cc_final: 0.7740 (t0) REVERT: R 148 ASP cc_start: 0.7766 (m-30) cc_final: 0.7403 (m-30) REVERT: S 51 LEU cc_start: 0.8749 (mt) cc_final: 0.8511 (mt) REVERT: S 92 ASN cc_start: 0.8204 (OUTLIER) cc_final: 0.7927 (m-40) REVERT: S 108 GLN cc_start: 0.8985 (tt0) cc_final: 0.8705 (mt0) REVERT: U 50 ASN cc_start: 0.8299 (m110) cc_final: 0.8080 (m110) REVERT: U 95 ASN cc_start: 0.7683 (p0) cc_final: 0.7342 (p0) REVERT: U 96 LEU cc_start: 0.8260 (OUTLIER) cc_final: 0.7970 (mt) REVERT: U 99 TRP cc_start: 0.6886 (OUTLIER) cc_final: 0.4962 (m-90) REVERT: V 16 ILE cc_start: 0.8279 (OUTLIER) cc_final: 0.7966 (pt) REVERT: V 18 LEU cc_start: 0.8825 (OUTLIER) cc_final: 0.8607 (pp) REVERT: V 124 GLU cc_start: 0.7872 (OUTLIER) cc_final: 0.6623 (mm-30) REVERT: W 15 PRO cc_start: 0.7743 (Cg_endo) cc_final: 0.7522 (Cg_exo) REVERT: Y 75 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8593 (mtt180) REVERT: Z 81 MET cc_start: 0.8762 (tpt) cc_final: 0.8518 (tpt) REVERT: a 12 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.8302 (mmp-170) REVERT: a 32 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8379 (mtt-85) REVERT: b 52 LYS cc_start: 0.7700 (ttmt) cc_final: 0.7364 (mtpp) REVERT: c 37 MET cc_start: 0.7645 (tpp) cc_final: 0.7184 (mmt) REVERT: e 22 ARG cc_start: 0.8923 (OUTLIER) cc_final: 0.8099 (ttt180) REVERT: e 86 GLU cc_start: 0.7761 (mt-10) cc_final: 0.7470 (mt-10) REVERT: f 5 LEU cc_start: 0.9055 (OUTLIER) cc_final: 0.8758 (mt) REVERT: f 100 ARG cc_start: 0.8825 (OUTLIER) cc_final: 0.8483 (tpp80) REVERT: g 5 LEU cc_start: 0.8923 (OUTLIER) cc_final: 0.8702 (pp) REVERT: h 23 ASP cc_start: 0.7657 (OUTLIER) cc_final: 0.7449 (m-30) REVERT: h 63 GLN cc_start: 0.8219 (mt0) cc_final: 0.7996 (mt0) REVERT: h 69 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8438 (mm) REVERT: h 96 ASN cc_start: 0.7662 (t0) cc_final: 0.6968 (t0) REVERT: h 107 GLN cc_start: 0.7926 (OUTLIER) cc_final: 0.7138 (tm-30) REVERT: i 4 ARG cc_start: 0.7032 (OUTLIER) cc_final: 0.5856 (tpt-90) REVERT: n 10 MET cc_start: 0.5376 (ttt) cc_final: 0.4963 (ttt) REVERT: n 11 ARG cc_start: 0.7188 (mtm180) cc_final: 0.6060 (tpt-90) REVERT: n 14 LYS cc_start: 0.8744 (mtpt) cc_final: 0.7501 (mmtt) REVERT: o 89 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8209 (ptmm) REVERT: p 29 ILE cc_start: 0.9242 (mm) cc_final: 0.8896 (mt) REVERT: r 71 ARG cc_start: 0.8187 (OUTLIER) cc_final: 0.7771 (ptt-90) REVERT: r 103 HIS cc_start: 0.7623 (OUTLIER) cc_final: 0.6964 (m-70) REVERT: r 107 ARG cc_start: 0.8334 (tmm-80) cc_final: 0.7980 (ttp80) REVERT: t 10 LEU cc_start: 0.7068 (mt) cc_final: 0.6637 (pp) REVERT: u 124 LEU cc_start: 0.1131 (OUTLIER) cc_final: 0.0862 (mm) REVERT: v 184 ILE cc_start: 0.1182 (OUTLIER) cc_final: 0.0651 (mt) REVERT: w 9 GLU cc_start: 0.5354 (OUTLIER) cc_final: 0.4098 (tp30) REVERT: x 82 GLU cc_start: 0.5354 (OUTLIER) cc_final: 0.4659 (mm-30) REVERT: x 86 LEU cc_start: 0.4537 (OUTLIER) cc_final: 0.4175 (mp) REVERT: x 120 LYS cc_start: 0.4821 (OUTLIER) cc_final: 0.4171 (mttt) REVERT: x 150 GLN cc_start: 0.4742 (pm20) cc_final: 0.4328 (pm20) REVERT: x 185 GLU cc_start: 0.1649 (OUTLIER) cc_final: 0.0940 (pt0) REVERT: x 342 MET cc_start: 0.4453 (mtp) cc_final: 0.3817 (tmm) REVERT: x 430 MET cc_start: 0.2582 (ptm) cc_final: 0.1634 (ttm) REVERT: y 73 ILE cc_start: -0.0481 (OUTLIER) cc_final: -0.0762 (tp) REVERT: z 580 MET cc_start: 0.3311 (OUTLIER) cc_final: 0.1115 (ptt) outliers start: 384 outliers final: 270 residues processed: 1278 average time/residue: 1.3411 time to fit residues: 2971.5481 Evaluate side-chains 1299 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 323 poor density : 976 time to evaluate : 7.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 158 ILE Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain B residue 4 ARG Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 49 ARG Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 262 ASP Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 18 ILE Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain H residue 147 GLU Chi-restraints excluded: chain H residue 186 THR Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 183 ASP Chi-restraints excluded: chain I residue 202 ASN Chi-restraints excluded: chain I residue 210 ARG Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 55 TYR Chi-restraints excluded: chain J residue 98 ASN Chi-restraints excluded: chain J residue 150 CYS Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 42 ARG Chi-restraints excluded: chain L residue 99 ASP Chi-restraints excluded: chain L residue 103 ARG Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 155 MET Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain L residue 198 ARG Chi-restraints excluded: chain M residue 8 GLU Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain M residue 93 LYS Chi-restraints excluded: chain M residue 108 ASP Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 32 GLN Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 174 LEU Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain P residue 12 THR Chi-restraints excluded: chain P residue 25 HIS Chi-restraints excluded: chain P residue 104 LEU Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 125 MET Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain Q residue 75 ARG Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 111 SER Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain R residue 3 MET Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 74 ARG Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 139 MET Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 49 SER Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 92 ASN Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain S residue 169 THR Chi-restraints excluded: chain S residue 174 THR Chi-restraints excluded: chain T residue 25 VAL Chi-restraints excluded: chain T residue 32 ARG Chi-restraints excluded: chain T residue 33 ILE Chi-restraints excluded: chain T residue 48 VAL Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 79 SER Chi-restraints excluded: chain U residue 96 LEU Chi-restraints excluded: chain U residue 99 TRP Chi-restraints excluded: chain U residue 111 GLU Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 60 MET Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain V residue 124 GLU Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 127 LEU Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 52 ASP Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 75 ARG Chi-restraints excluded: chain Y residue 79 VAL Chi-restraints excluded: chain Y residue 102 SER Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 57 MET Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain a residue 12 ARG Chi-restraints excluded: chain a residue 32 ARG Chi-restraints excluded: chain a residue 38 MET Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 22 LYS Chi-restraints excluded: chain c residue 15 ASN Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 90 ARG Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain d residue 21 VAL Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 97 ASP Chi-restraints excluded: chain d residue 102 LEU Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain d residue 112 THR Chi-restraints excluded: chain d residue 113 THR Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 13 VAL Chi-restraints excluded: chain e residue 22 ARG Chi-restraints excluded: chain e residue 41 ILE Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 81 ASN Chi-restraints excluded: chain e residue 123 THR Chi-restraints excluded: chain f residue 5 LEU Chi-restraints excluded: chain f residue 31 GLU Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain f residue 47 CYS Chi-restraints excluded: chain f residue 100 ARG Chi-restraints excluded: chain f residue 108 SER Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 32 TYR Chi-restraints excluded: chain g residue 35 THR Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 67 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 82 ASP Chi-restraints excluded: chain h residue 88 THR Chi-restraints excluded: chain h residue 107 GLN Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain i residue 4 ARG Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain i residue 81 ILE Chi-restraints excluded: chain j residue 13 ASN Chi-restraints excluded: chain j residue 61 THR Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain k residue 30 ASP Chi-restraints excluded: chain l residue 11 ARG Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 66 ILE Chi-restraints excluded: chain o residue 77 CYS Chi-restraints excluded: chain o residue 89 LYS Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 89 LEU Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain r residue 58 LYS Chi-restraints excluded: chain r residue 60 VAL Chi-restraints excluded: chain r residue 71 ARG Chi-restraints excluded: chain r residue 78 VAL Chi-restraints excluded: chain r residue 80 THR Chi-restraints excluded: chain r residue 89 THR Chi-restraints excluded: chain r residue 103 HIS Chi-restraints excluded: chain r residue 105 ASP Chi-restraints excluded: chain t residue 4 LEU Chi-restraints excluded: chain t residue 40 ILE Chi-restraints excluded: chain u residue 94 LEU Chi-restraints excluded: chain u residue 124 LEU Chi-restraints excluded: chain u residue 127 VAL Chi-restraints excluded: chain u residue 141 LEU Chi-restraints excluded: chain u residue 154 HIS Chi-restraints excluded: chain u residue 169 LEU Chi-restraints excluded: chain v residue 68 LEU Chi-restraints excluded: chain v residue 88 LEU Chi-restraints excluded: chain v residue 114 THR Chi-restraints excluded: chain v residue 162 VAL Chi-restraints excluded: chain v residue 184 ILE Chi-restraints excluded: chain w residue 9 GLU Chi-restraints excluded: chain w residue 53 THR Chi-restraints excluded: chain w residue 62 ILE Chi-restraints excluded: chain x residue 12 SER Chi-restraints excluded: chain x residue 31 MET Chi-restraints excluded: chain x residue 36 CYS Chi-restraints excluded: chain x residue 43 ASP Chi-restraints excluded: chain x residue 82 GLU Chi-restraints excluded: chain x residue 86 LEU Chi-restraints excluded: chain x residue 97 THR Chi-restraints excluded: chain x residue 116 THR Chi-restraints excluded: chain x residue 120 LYS Chi-restraints excluded: chain x residue 141 ARG Chi-restraints excluded: chain x residue 169 VAL Chi-restraints excluded: chain x residue 185 GLU Chi-restraints excluded: chain x residue 222 ASP Chi-restraints excluded: chain x residue 240 VAL Chi-restraints excluded: chain x residue 245 VAL Chi-restraints excluded: chain x residue 279 ILE Chi-restraints excluded: chain x residue 307 VAL Chi-restraints excluded: chain x residue 315 ASN Chi-restraints excluded: chain x residue 379 MET Chi-restraints excluded: chain y residue 29 VAL Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 73 ILE Chi-restraints excluded: chain z residue 580 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 1068 optimal weight: 9.9990 chunk 124 optimal weight: 10.0000 chunk 631 optimal weight: 10.0000 chunk 809 optimal weight: 10.0000 chunk 626 optimal weight: 10.0000 chunk 932 optimal weight: 7.9990 chunk 618 optimal weight: 0.7980 chunk 1103 optimal weight: 10.0000 chunk 690 optimal weight: 7.9990 chunk 672 optimal weight: 0.9990 chunk 509 optimal weight: 9.9990 overall best weight: 5.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 122 GLN ** E 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 GLN N 37 HIS Q 125 GLN R 130 ASN S 92 ASN T 114 GLN ** X 93 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 ASN X 111 GLN ** a 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 57 ASN g 28 ASN h 30 GLN l 33 ASN ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 44 ASN y 45 ASN y 87 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 159521 Z= 0.308 Angle : 0.668 15.051 234784 Z= 0.340 Chirality : 0.040 0.338 29216 Planarity : 0.005 0.089 14749 Dihedral : 24.654 179.959 72589 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.24 % Favored : 93.65 % Rotamer: Outliers : 5.92 % Allowed : 18.63 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.10), residues: 7563 helix: 1.21 (0.10), residues: 2782 sheet: -0.42 (0.16), residues: 1012 loop : -1.37 (0.10), residues: 3769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP N 120 HIS 0.021 0.001 HIS S 91 PHE 0.022 0.002 PHE S 176 TYR 0.025 0.002 TYR E 212 ARG 0.009 0.001 ARG I 203 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1402 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 390 poor density : 1012 time to evaluate : 7.908 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: B 4 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.7851 (ttt180) REVERT: B 71 GLU cc_start: 0.6860 (OUTLIER) cc_final: 0.6332 (tt0) REVERT: B 204 GLN cc_start: 0.8462 (OUTLIER) cc_final: 0.7636 (mt0) REVERT: B 314 ILE cc_start: 0.8302 (OUTLIER) cc_final: 0.8078 (pp) REVERT: C 178 ASN cc_start: 0.7799 (m-40) cc_final: 0.7540 (t0) REVERT: D 51 MET cc_start: 0.8384 (OUTLIER) cc_final: 0.8134 (tmm) REVERT: E 59 TYR cc_start: 0.8503 (t80) cc_final: 0.8223 (t80) REVERT: E 108 MET cc_start: 0.7067 (mmt) cc_final: 0.6335 (mmt) REVERT: E 203 LYS cc_start: 0.8426 (tmmt) cc_final: 0.7465 (ptpt) REVERT: E 241 GLN cc_start: 0.8257 (tp40) cc_final: 0.7940 (tp-100) REVERT: E 282 LEU cc_start: 0.8722 (OUTLIER) cc_final: 0.8487 (pt) REVERT: F 32 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7660 (mp) REVERT: F 38 LYS cc_start: 0.8135 (mmtm) cc_final: 0.7824 (ttpt) REVERT: F 139 GLU cc_start: 0.8115 (tt0) cc_final: 0.7902 (tt0) REVERT: G 253 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7000 (mm) REVERT: I 184 MET cc_start: 0.7771 (mtt) cc_final: 0.7441 (mtt) REVERT: I 210 ARG cc_start: 0.7142 (OUTLIER) cc_final: 0.6580 (mtt90) REVERT: J 18 ARG cc_start: 0.8375 (OUTLIER) cc_final: 0.7639 (mtp85) REVERT: L 9 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7523 (tp) REVERT: L 103 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7468 (ptp-110) REVERT: L 155 MET cc_start: 0.8756 (OUTLIER) cc_final: 0.8311 (mtm) REVERT: L 198 ARG cc_start: 0.7864 (OUTLIER) cc_final: 0.7427 (mpt-90) REVERT: M 8 GLU cc_start: 0.7147 (OUTLIER) cc_final: 0.6248 (tm-30) REVERT: M 81 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7578 (m-30) REVERT: N 32 GLN cc_start: 0.8201 (OUTLIER) cc_final: 0.7382 (mp10) REVERT: N 174 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8510 (pp) REVERT: O 87 MET cc_start: 0.9167 (mtt) cc_final: 0.8844 (mtt) REVERT: O 196 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8499 (mt) REVERT: P 115 GLU cc_start: 0.6885 (pt0) cc_final: 0.6640 (pt0) REVERT: Q 121 LEU cc_start: 0.8774 (OUTLIER) cc_final: 0.8492 (mt) REVERT: R 3 MET cc_start: 0.8359 (OUTLIER) cc_final: 0.7497 (tmm) REVERT: R 6 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7797 (tp) REVERT: R 47 ASP cc_start: 0.7965 (t70) cc_final: 0.7708 (t0) REVERT: R 105 LEU cc_start: 0.9084 (OUTLIER) cc_final: 0.8765 (tp) REVERT: R 148 ASP cc_start: 0.7749 (m-30) cc_final: 0.7410 (m-30) REVERT: S 51 LEU cc_start: 0.8804 (mt) cc_final: 0.8553 (mt) REVERT: S 108 GLN cc_start: 0.8932 (tt0) cc_final: 0.8609 (mt0) REVERT: U 22 THR cc_start: 0.8400 (p) cc_final: 0.8075 (m) REVERT: U 95 ASN cc_start: 0.7624 (p0) cc_final: 0.7288 (p0) REVERT: U 96 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7929 (mt) REVERT: U 99 TRP cc_start: 0.6880 (OUTLIER) cc_final: 0.4967 (m-90) REVERT: V 16 ILE cc_start: 0.8196 (OUTLIER) cc_final: 0.7858 (pt) REVERT: V 18 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8600 (pp) REVERT: V 124 GLU cc_start: 0.7845 (OUTLIER) cc_final: 0.6700 (mm-30) REVERT: W 1 MET cc_start: 0.6327 (OUTLIER) cc_final: 0.5468 (pmm) REVERT: W 15 PRO cc_start: 0.7686 (Cg_endo) cc_final: 0.7446 (Cg_exo) REVERT: Y 75 ARG cc_start: 0.9048 (OUTLIER) cc_final: 0.8584 (mtm180) REVERT: Z 81 MET cc_start: 0.8780 (tpt) cc_final: 0.8539 (tpt) REVERT: a 4 ARG cc_start: 0.8652 (OUTLIER) cc_final: 0.8359 (ttp80) REVERT: a 12 ARG cc_start: 0.8749 (OUTLIER) cc_final: 0.8061 (mmp-170) REVERT: a 32 ARG cc_start: 0.9017 (OUTLIER) cc_final: 0.8389 (mtt-85) REVERT: c 37 MET cc_start: 0.7636 (tpp) cc_final: 0.7195 (mmt) REVERT: e 22 ARG cc_start: 0.8941 (OUTLIER) cc_final: 0.8177 (ttt180) REVERT: e 86 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7439 (mt-10) REVERT: f 5 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8730 (mt) REVERT: f 100 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8143 (tpp80) REVERT: g 5 LEU cc_start: 0.8901 (OUTLIER) cc_final: 0.8678 (pp) REVERT: h 23 ASP cc_start: 0.7680 (OUTLIER) cc_final: 0.7424 (m-30) REVERT: h 69 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8349 (mm) REVERT: h 96 ASN cc_start: 0.7563 (OUTLIER) cc_final: 0.6870 (t0) REVERT: i 4 ARG cc_start: 0.7040 (OUTLIER) cc_final: 0.5914 (tpt-90) REVERT: j 67 LEU cc_start: 0.8910 (OUTLIER) cc_final: 0.8668 (mp) REVERT: n 10 MET cc_start: 0.5021 (ttt) cc_final: 0.4630 (ttt) REVERT: n 11 ARG cc_start: 0.7150 (mtm180) cc_final: 0.5988 (tpt-90) REVERT: n 14 LYS cc_start: 0.8736 (mtpt) cc_final: 0.7566 (mmtt) REVERT: o 58 LYS cc_start: 0.8481 (OUTLIER) cc_final: 0.8124 (mtpt) REVERT: o 89 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8031 (ptmm) REVERT: p 29 ILE cc_start: 0.9225 (mm) cc_final: 0.8898 (mt) REVERT: r 71 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7832 (ptt-90) REVERT: r 103 HIS cc_start: 0.7566 (OUTLIER) cc_final: 0.6952 (m-70) REVERT: t 10 LEU cc_start: 0.7065 (mt) cc_final: 0.6639 (pp) REVERT: u 124 LEU cc_start: 0.1136 (OUTLIER) cc_final: 0.0872 (mm) REVERT: u 243 ASN cc_start: -0.0981 (OUTLIER) cc_final: -0.1237 (m-40) REVERT: v 184 ILE cc_start: 0.1075 (OUTLIER) cc_final: 0.0611 (mt) REVERT: w 9 GLU cc_start: 0.5302 (OUTLIER) cc_final: 0.4554 (tp30) REVERT: x 82 GLU cc_start: 0.5342 (OUTLIER) cc_final: 0.4653 (mm-30) REVERT: x 86 LEU cc_start: 0.4555 (OUTLIER) cc_final: 0.4191 (mp) REVERT: x 120 LYS cc_start: 0.4745 (OUTLIER) cc_final: 0.3967 (mttt) REVERT: x 342 MET cc_start: 0.4301 (mtp) cc_final: 0.4016 (tmm) REVERT: x 430 MET cc_start: 0.2689 (ptm) cc_final: 0.1806 (ttm) REVERT: z 580 MET cc_start: 0.3624 (OUTLIER) cc_final: 0.1522 (ptt) outliers start: 390 outliers final: 285 residues processed: 1281 average time/residue: 1.3270 time to fit residues: 2940.8329 Evaluate side-chains 1321 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 339 poor density : 982 time to evaluate : 7.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain B residue 4 ARG Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 136 LYS Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 42 LYS Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 232 GLU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 18 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 183 ASP Chi-restraints excluded: chain I residue 202 ASN Chi-restraints excluded: chain I residue 210 ARG Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 55 TYR Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 143 ASP Chi-restraints excluded: chain J residue 150 CYS Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 42 ARG Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 103 ARG Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 155 MET Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain L residue 198 ARG Chi-restraints excluded: chain M residue 8 GLU Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 50 MET Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain M residue 108 ASP Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 32 GLN Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 174 LEU Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain P residue 25 HIS Chi-restraints excluded: chain P residue 69 ARG Chi-restraints excluded: chain P residue 104 LEU Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain Q residue 75 ARG Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 111 SER Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain R residue 3 MET Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 74 ARG Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 130 ASN Chi-restraints excluded: chain R residue 139 MET Chi-restraints excluded: chain R residue 149 LYS Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 49 SER Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain S residue 169 THR Chi-restraints excluded: chain S residue 174 THR Chi-restraints excluded: chain T residue 25 VAL Chi-restraints excluded: chain T residue 32 ARG Chi-restraints excluded: chain T residue 33 ILE Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain U residue 18 VAL Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 79 SER Chi-restraints excluded: chain U residue 96 LEU Chi-restraints excluded: chain U residue 99 TRP Chi-restraints excluded: chain U residue 111 GLU Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain V residue 124 GLU Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 127 LEU Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 52 ASP Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 75 ARG Chi-restraints excluded: chain Y residue 79 VAL Chi-restraints excluded: chain Y residue 102 SER Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Z residue 10 VAL Chi-restraints excluded: chain Z residue 35 ASP Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 57 MET Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain a residue 4 ARG Chi-restraints excluded: chain a residue 12 ARG Chi-restraints excluded: chain a residue 32 ARG Chi-restraints excluded: chain a residue 38 MET Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 22 LYS Chi-restraints excluded: chain b residue 54 LEU Chi-restraints excluded: chain c residue 15 ASN Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 92 CYS Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain d residue 21 VAL Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain d residue 112 THR Chi-restraints excluded: chain d residue 113 THR Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 13 VAL Chi-restraints excluded: chain e residue 22 ARG Chi-restraints excluded: chain e residue 41 ILE Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 81 ASN Chi-restraints excluded: chain e residue 85 LEU Chi-restraints excluded: chain e residue 123 THR Chi-restraints excluded: chain f residue 5 LEU Chi-restraints excluded: chain f residue 31 GLU Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain f residue 47 CYS Chi-restraints excluded: chain f residue 100 ARG Chi-restraints excluded: chain f residue 108 SER Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 32 TYR Chi-restraints excluded: chain g residue 35 THR Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain h residue 22 ASP Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 30 GLN Chi-restraints excluded: chain h residue 67 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 82 ASP Chi-restraints excluded: chain h residue 88 THR Chi-restraints excluded: chain h residue 96 ASN Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain i residue 4 ARG Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain i residue 81 ILE Chi-restraints excluded: chain j residue 13 ASN Chi-restraints excluded: chain j residue 61 THR Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain k residue 30 ASP Chi-restraints excluded: chain l residue 11 ARG Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 58 LYS Chi-restraints excluded: chain o residue 66 ILE Chi-restraints excluded: chain o residue 77 CYS Chi-restraints excluded: chain o residue 89 LYS Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 89 LEU Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain r residue 17 LEU Chi-restraints excluded: chain r residue 58 LYS Chi-restraints excluded: chain r residue 60 VAL Chi-restraints excluded: chain r residue 71 ARG Chi-restraints excluded: chain r residue 78 VAL Chi-restraints excluded: chain r residue 80 THR Chi-restraints excluded: chain r residue 89 THR Chi-restraints excluded: chain r residue 103 HIS Chi-restraints excluded: chain r residue 105 ASP Chi-restraints excluded: chain t residue 4 LEU Chi-restraints excluded: chain t residue 40 ILE Chi-restraints excluded: chain u residue 94 LEU Chi-restraints excluded: chain u residue 124 LEU Chi-restraints excluded: chain u residue 127 VAL Chi-restraints excluded: chain u residue 141 LEU Chi-restraints excluded: chain u residue 154 HIS Chi-restraints excluded: chain u residue 169 LEU Chi-restraints excluded: chain u residue 243 ASN Chi-restraints excluded: chain v residue 68 LEU Chi-restraints excluded: chain v residue 88 LEU Chi-restraints excluded: chain v residue 114 THR Chi-restraints excluded: chain v residue 162 VAL Chi-restraints excluded: chain v residue 184 ILE Chi-restraints excluded: chain w residue 9 GLU Chi-restraints excluded: chain w residue 53 THR Chi-restraints excluded: chain w residue 62 ILE Chi-restraints excluded: chain x residue 12 SER Chi-restraints excluded: chain x residue 36 CYS Chi-restraints excluded: chain x residue 71 LYS Chi-restraints excluded: chain x residue 82 GLU Chi-restraints excluded: chain x residue 86 LEU Chi-restraints excluded: chain x residue 97 THR Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain x residue 116 THR Chi-restraints excluded: chain x residue 120 LYS Chi-restraints excluded: chain x residue 141 ARG Chi-restraints excluded: chain x residue 169 VAL Chi-restraints excluded: chain x residue 185 GLU Chi-restraints excluded: chain x residue 222 ASP Chi-restraints excluded: chain x residue 230 GLU Chi-restraints excluded: chain x residue 240 VAL Chi-restraints excluded: chain x residue 245 VAL Chi-restraints excluded: chain x residue 279 ILE Chi-restraints excluded: chain x residue 307 VAL Chi-restraints excluded: chain x residue 315 ASN Chi-restraints excluded: chain x residue 379 MET Chi-restraints excluded: chain y residue 52 LEU Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain z residue 580 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 682 optimal weight: 4.9990 chunk 440 optimal weight: 8.9990 chunk 659 optimal weight: 10.0000 chunk 332 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 213 optimal weight: 10.0000 chunk 701 optimal weight: 3.9990 chunk 751 optimal weight: 1.9990 chunk 545 optimal weight: 20.0000 chunk 102 optimal weight: 20.0000 chunk 867 optimal weight: 3.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 205 ASN ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN ** E 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 GLN G 64 GLN M 125 ASN N 37 HIS O 5 GLN Q 125 GLN T 114 GLN X 105 ASN X 111 GLN ** a 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 30 GLN l 33 ASN ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 45 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 159521 Z= 0.279 Angle : 0.651 14.720 234784 Z= 0.332 Chirality : 0.039 0.328 29216 Planarity : 0.005 0.107 14749 Dihedral : 24.624 179.923 72589 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 6.53 % Favored : 93.37 % Rotamer: Outliers : 5.82 % Allowed : 18.95 % Favored : 75.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.10), residues: 7563 helix: 1.29 (0.10), residues: 2776 sheet: -0.42 (0.16), residues: 1018 loop : -1.34 (0.10), residues: 3769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP N 120 HIS 0.010 0.001 HIS E 124 PHE 0.026 0.002 PHE x 285 TYR 0.025 0.002 TYR E 212 ARG 0.009 0.000 ARG I 203 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1378 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 383 poor density : 995 time to evaluate : 7.835 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: B 4 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.7857 (ttt180) REVERT: B 71 GLU cc_start: 0.6877 (OUTLIER) cc_final: 0.6339 (tt0) REVERT: B 204 GLN cc_start: 0.8434 (OUTLIER) cc_final: 0.7626 (mt0) REVERT: B 314 ILE cc_start: 0.8312 (OUTLIER) cc_final: 0.8069 (pp) REVERT: C 178 ASN cc_start: 0.7700 (m-40) cc_final: 0.7427 (t0) REVERT: D 51 MET cc_start: 0.8407 (OUTLIER) cc_final: 0.7843 (tmm) REVERT: E 108 MET cc_start: 0.6996 (mmt) cc_final: 0.6287 (mmt) REVERT: E 203 LYS cc_start: 0.8431 (tmmt) cc_final: 0.7473 (ptpt) REVERT: E 241 GLN cc_start: 0.8248 (tp40) cc_final: 0.7923 (tp-100) REVERT: E 282 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8443 (pt) REVERT: F 32 ILE cc_start: 0.7985 (OUTLIER) cc_final: 0.7623 (mp) REVERT: F 38 LYS cc_start: 0.8136 (mmtm) cc_final: 0.7824 (ttpt) REVERT: F 139 GLU cc_start: 0.8094 (tt0) cc_final: 0.7794 (tt0) REVERT: G 253 LEU cc_start: 0.7495 (OUTLIER) cc_final: 0.6985 (mm) REVERT: I 116 ARG cc_start: 0.9012 (OUTLIER) cc_final: 0.8513 (ptp90) REVERT: I 184 MET cc_start: 0.7764 (mtt) cc_final: 0.7430 (mtt) REVERT: I 210 ARG cc_start: 0.7153 (OUTLIER) cc_final: 0.6514 (mtt90) REVERT: J 18 ARG cc_start: 0.8303 (OUTLIER) cc_final: 0.7576 (mtp85) REVERT: L 9 ILE cc_start: 0.7837 (OUTLIER) cc_final: 0.7504 (tp) REVERT: L 103 ARG cc_start: 0.7901 (OUTLIER) cc_final: 0.7443 (ptp-110) REVERT: L 142 GLU cc_start: 0.6647 (pt0) cc_final: 0.6427 (pt0) REVERT: L 155 MET cc_start: 0.8753 (OUTLIER) cc_final: 0.8303 (mtm) REVERT: L 198 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7367 (mpt-90) REVERT: M 8 GLU cc_start: 0.7143 (OUTLIER) cc_final: 0.6211 (tm-30) REVERT: M 81 ASP cc_start: 0.8063 (OUTLIER) cc_final: 0.7571 (m-30) REVERT: M 93 LYS cc_start: 0.8043 (OUTLIER) cc_final: 0.7649 (mttt) REVERT: N 32 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7385 (mp10) REVERT: N 162 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.7187 (mtp85) REVERT: N 174 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8487 (pp) REVERT: O 87 MET cc_start: 0.9175 (mtt) cc_final: 0.8829 (mtt) REVERT: O 196 LEU cc_start: 0.8840 (OUTLIER) cc_final: 0.8490 (mt) REVERT: Q 121 LEU cc_start: 0.8776 (OUTLIER) cc_final: 0.8493 (mt) REVERT: R 3 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.7549 (tmm) REVERT: R 6 LEU cc_start: 0.8080 (OUTLIER) cc_final: 0.7791 (tp) REVERT: R 47 ASP cc_start: 0.7975 (t70) cc_final: 0.7702 (t0) REVERT: R 105 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8767 (tp) REVERT: R 148 ASP cc_start: 0.7737 (m-30) cc_final: 0.7489 (m-30) REVERT: S 51 LEU cc_start: 0.8727 (mt) cc_final: 0.8498 (mt) REVERT: S 108 GLN cc_start: 0.8916 (tt0) cc_final: 0.8611 (mt0) REVERT: U 22 THR cc_start: 0.8311 (OUTLIER) cc_final: 0.8061 (m) REVERT: U 95 ASN cc_start: 0.7642 (p0) cc_final: 0.7336 (p0) REVERT: U 96 LEU cc_start: 0.8204 (OUTLIER) cc_final: 0.7981 (mt) REVERT: U 99 TRP cc_start: 0.6871 (OUTLIER) cc_final: 0.4967 (m-90) REVERT: V 16 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7845 (pt) REVERT: V 18 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8580 (pp) REVERT: V 71 GLU cc_start: 0.6678 (mp0) cc_final: 0.6191 (mp0) REVERT: V 124 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.6687 (mm-30) REVERT: W 1 MET cc_start: 0.6386 (OUTLIER) cc_final: 0.5549 (pmm) REVERT: W 47 ARG cc_start: 0.7916 (OUTLIER) cc_final: 0.7713 (mtm180) REVERT: Y 75 ARG cc_start: 0.9044 (OUTLIER) cc_final: 0.8580 (mtm180) REVERT: Z 81 MET cc_start: 0.8859 (tpt) cc_final: 0.8622 (tpt) REVERT: a 4 ARG cc_start: 0.8656 (OUTLIER) cc_final: 0.8369 (ttp80) REVERT: a 12 ARG cc_start: 0.8726 (OUTLIER) cc_final: 0.7711 (mmp-170) REVERT: a 32 ARG cc_start: 0.9014 (OUTLIER) cc_final: 0.8428 (mtt-85) REVERT: d 97 ASP cc_start: 0.4040 (OUTLIER) cc_final: 0.3597 (p0) REVERT: e 22 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8171 (ttt180) REVERT: e 86 GLU cc_start: 0.7762 (mt-10) cc_final: 0.7419 (mt-10) REVERT: f 5 LEU cc_start: 0.8991 (OUTLIER) cc_final: 0.8673 (mt) REVERT: f 100 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8186 (tpp80) REVERT: g 5 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8671 (pp) REVERT: h 23 ASP cc_start: 0.7667 (OUTLIER) cc_final: 0.7379 (m-30) REVERT: h 69 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8305 (mm) REVERT: h 96 ASN cc_start: 0.7492 (OUTLIER) cc_final: 0.6839 (t0) REVERT: h 107 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.6984 (tm-30) REVERT: i 4 ARG cc_start: 0.7041 (OUTLIER) cc_final: 0.5904 (tpt-90) REVERT: j 67 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8650 (mp) REVERT: n 10 MET cc_start: 0.5130 (ttt) cc_final: 0.4645 (ttt) REVERT: n 11 ARG cc_start: 0.7150 (mtm180) cc_final: 0.5986 (tpt-90) REVERT: n 14 LYS cc_start: 0.8727 (mtpt) cc_final: 0.7567 (mmtt) REVERT: o 58 LYS cc_start: 0.8478 (OUTLIER) cc_final: 0.8049 (mtpt) REVERT: o 82 MET cc_start: 0.7450 (mmm) cc_final: 0.6981 (mmt) REVERT: o 89 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8077 (ptmm) REVERT: p 29 ILE cc_start: 0.9248 (mm) cc_final: 0.8935 (mt) REVERT: r 71 ARG cc_start: 0.8183 (OUTLIER) cc_final: 0.7847 (ptt-90) REVERT: r 103 HIS cc_start: 0.7559 (OUTLIER) cc_final: 0.6860 (m-70) REVERT: t 10 LEU cc_start: 0.7050 (mt) cc_final: 0.6637 (pp) REVERT: u 124 LEU cc_start: 0.1386 (OUTLIER) cc_final: 0.1163 (mm) REVERT: u 228 GLU cc_start: 0.0697 (OUTLIER) cc_final: 0.0328 (mt-10) REVERT: v 184 ILE cc_start: 0.0884 (OUTLIER) cc_final: 0.0434 (mt) REVERT: x 6 LEU cc_start: 0.5001 (tt) cc_final: 0.4750 (mm) REVERT: x 82 GLU cc_start: 0.5168 (OUTLIER) cc_final: 0.4472 (mm-30) REVERT: x 86 LEU cc_start: 0.4516 (OUTLIER) cc_final: 0.4201 (mp) REVERT: x 342 MET cc_start: 0.4210 (mtp) cc_final: 0.3869 (tmm) REVERT: x 430 MET cc_start: 0.2759 (ptm) cc_final: 0.1854 (ttm) REVERT: y 116 ASP cc_start: 0.3099 (OUTLIER) cc_final: 0.1507 (p0) REVERT: z 580 MET cc_start: 0.3589 (OUTLIER) cc_final: 0.1574 (ptt) outliers start: 383 outliers final: 284 residues processed: 1262 average time/residue: 1.3790 time to fit residues: 3012.5545 Evaluate side-chains 1321 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 344 poor density : 977 time to evaluate : 7.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain A residue 227 ARG Chi-restraints excluded: chain B residue 4 ARG Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 231 VAL Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 306 ASP Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain B residue 382 VAL Chi-restraints excluded: chain C residue 22 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 228 THR Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 9 ASN Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 51 MET Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 42 LYS Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 169 ILE Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 161 VAL Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 205 THR Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 222 ILE Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 18 ILE Chi-restraints excluded: chain H residue 20 LEU Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 116 ARG Chi-restraints excluded: chain I residue 125 THR Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 183 ASP Chi-restraints excluded: chain I residue 202 ASN Chi-restraints excluded: chain I residue 210 ARG Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 55 TYR Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain L residue 9 ILE Chi-restraints excluded: chain L residue 22 VAL Chi-restraints excluded: chain L residue 33 ILE Chi-restraints excluded: chain L residue 42 ARG Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 103 ARG Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 151 THR Chi-restraints excluded: chain L residue 155 MET Chi-restraints excluded: chain L residue 160 VAL Chi-restraints excluded: chain L residue 169 ILE Chi-restraints excluded: chain L residue 198 ARG Chi-restraints excluded: chain M residue 8 GLU Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 58 THR Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain M residue 93 LYS Chi-restraints excluded: chain M residue 108 ASP Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 32 GLN Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 162 ARG Chi-restraints excluded: chain N residue 174 LEU Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 43 ILE Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 25 HIS Chi-restraints excluded: chain P residue 69 ARG Chi-restraints excluded: chain P residue 104 LEU Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain Q residue 75 ARG Chi-restraints excluded: chain Q residue 83 VAL Chi-restraints excluded: chain Q residue 111 SER Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain R residue 3 MET Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 74 ARG Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 139 MET Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 38 VAL Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 49 SER Chi-restraints excluded: chain S residue 57 SER Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 82 LEU Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 169 THR Chi-restraints excluded: chain S residue 174 THR Chi-restraints excluded: chain T residue 25 VAL Chi-restraints excluded: chain T residue 32 ARG Chi-restraints excluded: chain T residue 52 MET Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 75 VAL Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain U residue 18 VAL Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 66 SER Chi-restraints excluded: chain U residue 79 SER Chi-restraints excluded: chain U residue 96 LEU Chi-restraints excluded: chain U residue 99 TRP Chi-restraints excluded: chain U residue 111 GLU Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 41 SER Chi-restraints excluded: chain V residue 60 MET Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain V residue 124 GLU Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain W residue 47 ARG Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 85 SER Chi-restraints excluded: chain X residue 127 LEU Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 52 ASP Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 75 ARG Chi-restraints excluded: chain Y residue 79 VAL Chi-restraints excluded: chain Y residue 102 SER Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Z residue 10 VAL Chi-restraints excluded: chain Z residue 35 ASP Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 57 MET Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain Z residue 86 SER Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 95 VAL Chi-restraints excluded: chain a residue 4 ARG Chi-restraints excluded: chain a residue 12 ARG Chi-restraints excluded: chain a residue 32 ARG Chi-restraints excluded: chain a residue 38 MET Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 64 LYS Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 22 LYS Chi-restraints excluded: chain c residue 15 ASN Chi-restraints excluded: chain c residue 69 THR Chi-restraints excluded: chain c residue 92 CYS Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain d residue 21 VAL Chi-restraints excluded: chain d residue 33 ILE Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 54 MET Chi-restraints excluded: chain d residue 72 VAL Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 97 ASP Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain d residue 112 THR Chi-restraints excluded: chain d residue 113 THR Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 13 VAL Chi-restraints excluded: chain e residue 22 ARG Chi-restraints excluded: chain e residue 41 ILE Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 81 ASN Chi-restraints excluded: chain e residue 123 THR Chi-restraints excluded: chain f residue 5 LEU Chi-restraints excluded: chain f residue 31 GLU Chi-restraints excluded: chain f residue 47 CYS Chi-restraints excluded: chain f residue 100 ARG Chi-restraints excluded: chain f residue 108 SER Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 32 TYR Chi-restraints excluded: chain g residue 35 THR Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain h residue 22 ASP Chi-restraints excluded: chain h residue 23 ASP Chi-restraints excluded: chain h residue 67 GLU Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 82 ASP Chi-restraints excluded: chain h residue 88 THR Chi-restraints excluded: chain h residue 96 ASN Chi-restraints excluded: chain h residue 107 GLN Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain i residue 4 ARG Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain i residue 81 ILE Chi-restraints excluded: chain j residue 13 ASN Chi-restraints excluded: chain j residue 61 THR Chi-restraints excluded: chain j residue 67 LEU Chi-restraints excluded: chain k residue 30 ASP Chi-restraints excluded: chain l residue 11 ARG Chi-restraints excluded: chain m residue 103 LEU Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 58 LYS Chi-restraints excluded: chain o residue 66 ILE Chi-restraints excluded: chain o residue 77 CYS Chi-restraints excluded: chain o residue 89 LYS Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 52 VAL Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 89 LEU Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain r residue 58 LYS Chi-restraints excluded: chain r residue 60 VAL Chi-restraints excluded: chain r residue 71 ARG Chi-restraints excluded: chain r residue 78 VAL Chi-restraints excluded: chain r residue 80 THR Chi-restraints excluded: chain r residue 89 THR Chi-restraints excluded: chain r residue 103 HIS Chi-restraints excluded: chain r residue 105 ASP Chi-restraints excluded: chain t residue 4 LEU Chi-restraints excluded: chain t residue 40 ILE Chi-restraints excluded: chain u residue 94 LEU Chi-restraints excluded: chain u residue 124 LEU Chi-restraints excluded: chain u residue 127 VAL Chi-restraints excluded: chain u residue 141 LEU Chi-restraints excluded: chain u residue 154 HIS Chi-restraints excluded: chain u residue 169 LEU Chi-restraints excluded: chain u residue 228 GLU Chi-restraints excluded: chain v residue 68 LEU Chi-restraints excluded: chain v residue 88 LEU Chi-restraints excluded: chain v residue 114 THR Chi-restraints excluded: chain v residue 162 VAL Chi-restraints excluded: chain v residue 184 ILE Chi-restraints excluded: chain w residue 53 THR Chi-restraints excluded: chain w residue 62 ILE Chi-restraints excluded: chain x residue 12 SER Chi-restraints excluded: chain x residue 36 CYS Chi-restraints excluded: chain x residue 43 ASP Chi-restraints excluded: chain x residue 71 LYS Chi-restraints excluded: chain x residue 82 GLU Chi-restraints excluded: chain x residue 86 LEU Chi-restraints excluded: chain x residue 97 THR Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain x residue 116 THR Chi-restraints excluded: chain x residue 141 ARG Chi-restraints excluded: chain x residue 169 VAL Chi-restraints excluded: chain x residue 222 ASP Chi-restraints excluded: chain x residue 230 GLU Chi-restraints excluded: chain x residue 240 VAL Chi-restraints excluded: chain x residue 245 VAL Chi-restraints excluded: chain x residue 279 ILE Chi-restraints excluded: chain x residue 307 VAL Chi-restraints excluded: chain x residue 315 ASN Chi-restraints excluded: chain x residue 379 MET Chi-restraints excluded: chain y residue 52 LEU Chi-restraints excluded: chain y residue 68 VAL Chi-restraints excluded: chain y residue 116 ASP Chi-restraints excluded: chain z residue 580 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 1003 optimal weight: 1.9990 chunk 1057 optimal weight: 20.0000 chunk 964 optimal weight: 1.9990 chunk 1028 optimal weight: 0.8980 chunk 1056 optimal weight: 6.9990 chunk 618 optimal weight: 0.0870 chunk 448 optimal weight: 2.9990 chunk 807 optimal weight: 7.9990 chunk 315 optimal weight: 10.0000 chunk 929 optimal weight: 7.9990 chunk 972 optimal weight: 4.9990 overall best weight: 1.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 64 GLN J 104 ASN M 125 ASN N 37 HIS O 5 GLN P 118 GLN Q 125 GLN T 114 GLN T 127 GLN X 105 ASN X 111 GLN ** a 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 100 ASN e 57 ASN e 101 HIS j 66 HIS ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 ASN ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7992 moved from start: 0.3708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 159521 Z= 0.151 Angle : 0.572 15.745 234784 Z= 0.293 Chirality : 0.035 0.287 29216 Planarity : 0.004 0.106 14749 Dihedral : 24.545 179.956 72586 Min Nonbonded Distance : 2.019 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.74 % Favored : 94.19 % Rotamer: Outliers : 4.37 % Allowed : 20.53 % Favored : 75.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.03 (0.10), residues: 7563 helix: 1.62 (0.10), residues: 2766 sheet: -0.30 (0.16), residues: 1022 loop : -1.22 (0.10), residues: 3775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 120 HIS 0.007 0.001 HIS S 163 PHE 0.019 0.001 PHE S 176 TYR 0.024 0.001 TYR E 212 ARG 0.008 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1309 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 288 poor density : 1021 time to evaluate : 8.129 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: B 204 GLN cc_start: 0.8369 (OUTLIER) cc_final: 0.7715 (mt0) REVERT: B 314 ILE cc_start: 0.8286 (OUTLIER) cc_final: 0.8064 (pp) REVERT: C 178 ASN cc_start: 0.7509 (m-40) cc_final: 0.7255 (t0) REVERT: D 33 ARG cc_start: 0.8564 (OUTLIER) cc_final: 0.6905 (ttt180) REVERT: E 108 MET cc_start: 0.6809 (mmt) cc_final: 0.6264 (mmt) REVERT: E 282 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8300 (pt) REVERT: F 32 ILE cc_start: 0.7930 (OUTLIER) cc_final: 0.7545 (mp) REVERT: F 139 GLU cc_start: 0.7945 (tt0) cc_final: 0.7611 (tt0) REVERT: G 253 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.6981 (mm) REVERT: I 102 MET cc_start: 0.8189 (mmt) cc_final: 0.7648 (mmt) REVERT: I 116 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8471 (ptp90) REVERT: I 184 MET cc_start: 0.7700 (mtt) cc_final: 0.7385 (mtt) REVERT: I 198 LYS cc_start: 0.8454 (ttmm) cc_final: 0.8106 (tppt) REVERT: I 210 ARG cc_start: 0.6964 (OUTLIER) cc_final: 0.6350 (mtt90) REVERT: I 214 SER cc_start: 0.7618 (OUTLIER) cc_final: 0.7320 (m) REVERT: J 18 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.7755 (mtp85) REVERT: L 103 ARG cc_start: 0.7825 (OUTLIER) cc_final: 0.7395 (ptp-110) REVERT: L 155 MET cc_start: 0.8774 (OUTLIER) cc_final: 0.8250 (mtm) REVERT: M 8 GLU cc_start: 0.7062 (OUTLIER) cc_final: 0.6249 (tm-30) REVERT: M 81 ASP cc_start: 0.7982 (OUTLIER) cc_final: 0.7532 (m-30) REVERT: M 93 LYS cc_start: 0.7957 (OUTLIER) cc_final: 0.7607 (mttt) REVERT: N 5 LYS cc_start: 0.8024 (ttmm) cc_final: 0.7765 (mmmm) REVERT: N 32 GLN cc_start: 0.8119 (OUTLIER) cc_final: 0.7288 (mp10) REVERT: N 174 LEU cc_start: 0.8707 (OUTLIER) cc_final: 0.8486 (pp) REVERT: O 87 MET cc_start: 0.8988 (mtt) cc_final: 0.8727 (mtt) REVERT: P 91 LEU cc_start: 0.8335 (pp) cc_final: 0.8022 (mt) REVERT: Q 121 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8479 (mt) REVERT: R 3 MET cc_start: 0.8330 (OUTLIER) cc_final: 0.7446 (tmm) REVERT: R 105 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8814 (tp) REVERT: U 22 THR cc_start: 0.8174 (OUTLIER) cc_final: 0.7929 (m) REVERT: U 50 ASN cc_start: 0.8310 (m110) cc_final: 0.8072 (m110) REVERT: U 95 ASN cc_start: 0.7621 (p0) cc_final: 0.7297 (p0) REVERT: U 96 LEU cc_start: 0.8174 (OUTLIER) cc_final: 0.7971 (mt) REVERT: U 99 TRP cc_start: 0.6856 (OUTLIER) cc_final: 0.4939 (m-90) REVERT: V 16 ILE cc_start: 0.8012 (OUTLIER) cc_final: 0.7684 (pt) REVERT: V 18 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8541 (pp) REVERT: V 71 GLU cc_start: 0.6709 (mp0) cc_final: 0.6249 (mp0) REVERT: W 1 MET cc_start: 0.6346 (OUTLIER) cc_final: 0.5884 (pmm) REVERT: X 71 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8392 (tt) REVERT: X 111 GLN cc_start: 0.6750 (mp-120) cc_final: 0.6527 (mp10) REVERT: Y 75 ARG cc_start: 0.8977 (OUTLIER) cc_final: 0.8512 (mtm180) REVERT: Z 81 MET cc_start: 0.8903 (tpt) cc_final: 0.8674 (tpt) REVERT: a 32 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8322 (mtt-85) REVERT: d 97 ASP cc_start: 0.3912 (OUTLIER) cc_final: 0.3502 (p0) REVERT: e 22 ARG cc_start: 0.8904 (OUTLIER) cc_final: 0.8069 (ttt90) REVERT: e 58 ILE cc_start: 0.8475 (tp) cc_final: 0.8245 (tp) REVERT: e 86 GLU cc_start: 0.7744 (mt-10) cc_final: 0.7402 (mt-10) REVERT: f 5 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8649 (mt) REVERT: f 100 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8252 (tpp80) REVERT: g 5 LEU cc_start: 0.8843 (OUTLIER) cc_final: 0.8597 (pp) REVERT: h 23 ASP cc_start: 0.7516 (m-30) cc_final: 0.7274 (m-30) REVERT: h 69 LEU cc_start: 0.8569 (OUTLIER) cc_final: 0.8157 (mm) REVERT: h 96 ASN cc_start: 0.7326 (OUTLIER) cc_final: 0.6664 (t0) REVERT: h 107 GLN cc_start: 0.7758 (OUTLIER) cc_final: 0.6956 (tm-30) REVERT: i 4 ARG cc_start: 0.7033 (OUTLIER) cc_final: 0.5997 (tpt-90) REVERT: l 11 ARG cc_start: 0.7895 (OUTLIER) cc_final: 0.6552 (mtp-110) REVERT: n 11 ARG cc_start: 0.7068 (mtm180) cc_final: 0.5802 (tpt-90) REVERT: n 14 LYS cc_start: 0.8614 (mtpt) cc_final: 0.7404 (mmtt) REVERT: o 58 LYS cc_start: 0.8422 (OUTLIER) cc_final: 0.8058 (mtpt) REVERT: o 89 LYS cc_start: 0.8341 (OUTLIER) cc_final: 0.7970 (ptmm) REVERT: p 29 ILE cc_start: 0.9237 (mm) cc_final: 0.8966 (mt) REVERT: r 71 ARG cc_start: 0.8127 (OUTLIER) cc_final: 0.7862 (ptt-90) REVERT: r 103 HIS cc_start: 0.7498 (OUTLIER) cc_final: 0.6770 (m-70) REVERT: t 10 LEU cc_start: 0.6995 (mt) cc_final: 0.6520 (pp) REVERT: u 124 LEU cc_start: 0.1346 (OUTLIER) cc_final: 0.1108 (mm) REVERT: u 243 ASN cc_start: -0.1074 (OUTLIER) cc_final: -0.1319 (m-40) REVERT: w 9 GLU cc_start: 0.5291 (OUTLIER) cc_final: 0.4870 (tm-30) REVERT: x 6 LEU cc_start: 0.5029 (tt) cc_final: 0.4818 (mm) REVERT: x 82 GLU cc_start: 0.4816 (OUTLIER) cc_final: 0.4490 (mm-30) REVERT: x 194 ARG cc_start: 0.2318 (mmt180) cc_final: 0.1231 (mmt90) REVERT: x 342 MET cc_start: 0.4184 (mtp) cc_final: 0.3960 (tmm) REVERT: x 430 MET cc_start: 0.2581 (ptm) cc_final: 0.1761 (ttm) REVERT: y 116 ASP cc_start: 0.2922 (OUTLIER) cc_final: 0.1403 (p0) REVERT: z 580 MET cc_start: 0.3573 (ppp) cc_final: 0.1584 (ptt) outliers start: 288 outliers final: 200 residues processed: 1214 average time/residue: 1.5161 time to fit residues: 3215.8483 Evaluate side-chains 1233 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 248 poor density : 985 time to evaluate : 7.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 9 ASN Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 165 SER Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 32 ILE Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 18 ILE Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 116 ARG Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 183 ASP Chi-restraints excluded: chain I residue 210 ARG Chi-restraints excluded: chain I residue 214 SER Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 55 TYR Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 42 ARG Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 103 ARG Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 155 MET Chi-restraints excluded: chain L residue 169 ILE Chi-restraints excluded: chain M residue 8 GLU Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain M residue 93 LYS Chi-restraints excluded: chain M residue 108 ASP Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 32 GLN Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 174 LEU Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 69 ARG Chi-restraints excluded: chain P residue 104 LEU Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain Q residue 111 SER Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain R residue 3 MET Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 74 ARG Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 131 VAL Chi-restraints excluded: chain R residue 139 MET Chi-restraints excluded: chain R residue 149 LYS Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain S residue 174 THR Chi-restraints excluded: chain T residue 32 ARG Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 79 SER Chi-restraints excluded: chain U residue 96 LEU Chi-restraints excluded: chain U residue 99 TRP Chi-restraints excluded: chain U residue 102 VAL Chi-restraints excluded: chain U residue 111 GLU Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 60 MET Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 27 LYS Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 127 LEU Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 52 ASP Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 75 ARG Chi-restraints excluded: chain Y residue 79 VAL Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Z residue 35 ASP Chi-restraints excluded: chain Z residue 57 MET Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain a residue 32 ARG Chi-restraints excluded: chain a residue 38 MET Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 22 LYS Chi-restraints excluded: chain c residue 92 CYS Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 97 ASP Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 13 VAL Chi-restraints excluded: chain e residue 22 ARG Chi-restraints excluded: chain e residue 41 ILE Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 81 ASN Chi-restraints excluded: chain f residue 5 LEU Chi-restraints excluded: chain f residue 31 GLU Chi-restraints excluded: chain f residue 47 CYS Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 100 ARG Chi-restraints excluded: chain f residue 108 SER Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 32 TYR Chi-restraints excluded: chain g residue 35 THR Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain h residue 69 LEU Chi-restraints excluded: chain h residue 82 ASP Chi-restraints excluded: chain h residue 88 THR Chi-restraints excluded: chain h residue 96 ASN Chi-restraints excluded: chain h residue 107 GLN Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain i residue 4 ARG Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain j residue 13 ASN Chi-restraints excluded: chain k residue 30 ASP Chi-restraints excluded: chain l residue 11 ARG Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 58 LYS Chi-restraints excluded: chain o residue 66 ILE Chi-restraints excluded: chain o residue 77 CYS Chi-restraints excluded: chain o residue 89 LYS Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 89 LEU Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain r residue 58 LYS Chi-restraints excluded: chain r residue 60 VAL Chi-restraints excluded: chain r residue 71 ARG Chi-restraints excluded: chain r residue 78 VAL Chi-restraints excluded: chain r residue 80 THR Chi-restraints excluded: chain r residue 103 HIS Chi-restraints excluded: chain r residue 105 ASP Chi-restraints excluded: chain t residue 4 LEU Chi-restraints excluded: chain u residue 94 LEU Chi-restraints excluded: chain u residue 124 LEU Chi-restraints excluded: chain u residue 127 VAL Chi-restraints excluded: chain u residue 154 HIS Chi-restraints excluded: chain u residue 169 LEU Chi-restraints excluded: chain u residue 243 ASN Chi-restraints excluded: chain v residue 68 LEU Chi-restraints excluded: chain v residue 88 LEU Chi-restraints excluded: chain w residue 9 GLU Chi-restraints excluded: chain w residue 53 THR Chi-restraints excluded: chain w residue 62 ILE Chi-restraints excluded: chain x residue 36 CYS Chi-restraints excluded: chain x residue 82 GLU Chi-restraints excluded: chain x residue 116 THR Chi-restraints excluded: chain x residue 169 VAL Chi-restraints excluded: chain x residue 198 GLU Chi-restraints excluded: chain x residue 222 ASP Chi-restraints excluded: chain x residue 230 GLU Chi-restraints excluded: chain x residue 240 VAL Chi-restraints excluded: chain x residue 245 VAL Chi-restraints excluded: chain x residue 279 ILE Chi-restraints excluded: chain x residue 307 VAL Chi-restraints excluded: chain y residue 52 LEU Chi-restraints excluded: chain y residue 116 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 1024 optimal weight: 0.4980 chunk 675 optimal weight: 9.9990 chunk 1087 optimal weight: 30.0000 chunk 663 optimal weight: 0.7980 chunk 515 optimal weight: 5.9990 chunk 755 optimal weight: 2.9990 chunk 1140 optimal weight: 6.9990 chunk 1049 optimal weight: 10.0000 chunk 908 optimal weight: 2.9990 chunk 94 optimal weight: 30.0000 chunk 701 optimal weight: 5.9990 overall best weight: 2.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN G 64 GLN J 104 ASN L 104 ASN N 37 HIS ** O 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 GLN T 114 GLN X 69 ASN X 105 ASN ** a 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 57 ASN ** k 28 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** l 33 ASN ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.3730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 159521 Z= 0.184 Angle : 0.576 15.953 234784 Z= 0.294 Chirality : 0.035 0.283 29216 Planarity : 0.004 0.107 14749 Dihedral : 24.493 179.915 72581 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.86 % Favored : 94.06 % Rotamer: Outliers : 3.96 % Allowed : 21.12 % Favored : 74.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.01 (0.10), residues: 7563 helix: 1.63 (0.10), residues: 2782 sheet: -0.31 (0.16), residues: 1046 loop : -1.18 (0.10), residues: 3735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP N 120 HIS 0.009 0.001 HIS e 101 PHE 0.018 0.001 PHE S 176 TYR 0.026 0.001 TYR V 88 ARG 0.010 0.000 ARG B 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15126 Ramachandran restraints generated. 7563 Oldfield, 0 Emsley, 7563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1269 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 261 poor density : 1008 time to evaluate : 7.979 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: B 71 GLU cc_start: 0.6676 (OUTLIER) cc_final: 0.6193 (tt0) REVERT: B 204 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7730 (mt0) REVERT: B 314 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8069 (pp) REVERT: C 178 ASN cc_start: 0.7491 (m-40) cc_final: 0.7214 (t0) REVERT: C 352 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7224 (mm-30) REVERT: D 33 ARG cc_start: 0.8546 (OUTLIER) cc_final: 0.6702 (ttt180) REVERT: E 108 MET cc_start: 0.6873 (mmt) cc_final: 0.6310 (mmt) REVERT: E 282 LEU cc_start: 0.8532 (OUTLIER) cc_final: 0.8263 (pt) REVERT: F 139 GLU cc_start: 0.7900 (tt0) cc_final: 0.7550 (tt0) REVERT: F 202 ARG cc_start: 0.8168 (mmm160) cc_final: 0.7937 (mmm160) REVERT: G 253 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.6996 (mm) REVERT: I 102 MET cc_start: 0.8188 (mmt) cc_final: 0.7634 (mmt) REVERT: I 116 ARG cc_start: 0.8935 (OUTLIER) cc_final: 0.8437 (ptp90) REVERT: I 184 MET cc_start: 0.7720 (mtt) cc_final: 0.7357 (mtt) REVERT: I 198 LYS cc_start: 0.8516 (ttmm) cc_final: 0.8092 (tppt) REVERT: I 210 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6353 (mtt90) REVERT: I 214 SER cc_start: 0.7658 (p) cc_final: 0.7358 (m) REVERT: J 18 ARG cc_start: 0.8322 (OUTLIER) cc_final: 0.7653 (mtp85) REVERT: L 103 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7411 (ptp-110) REVERT: L 155 MET cc_start: 0.8795 (OUTLIER) cc_final: 0.8253 (mtm) REVERT: M 8 GLU cc_start: 0.7088 (OUTLIER) cc_final: 0.6259 (tm-30) REVERT: M 81 ASP cc_start: 0.7999 (OUTLIER) cc_final: 0.7545 (m-30) REVERT: M 93 LYS cc_start: 0.7949 (OUTLIER) cc_final: 0.7577 (mttt) REVERT: N 32 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7284 (mp10) REVERT: N 174 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8448 (pp) REVERT: O 87 MET cc_start: 0.9082 (mtt) cc_final: 0.8803 (mtt) REVERT: O 196 LEU cc_start: 0.8824 (OUTLIER) cc_final: 0.8525 (mt) REVERT: P 91 LEU cc_start: 0.8354 (pp) cc_final: 0.7977 (mt) REVERT: Q 121 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8497 (mt) REVERT: R 3 MET cc_start: 0.8354 (OUTLIER) cc_final: 0.7452 (tmm) REVERT: R 105 LEU cc_start: 0.9044 (OUTLIER) cc_final: 0.8828 (tp) REVERT: S 108 GLN cc_start: 0.8726 (tt0) cc_final: 0.8411 (mt0) REVERT: T 57 TYR cc_start: 0.8903 (m-80) cc_final: 0.8418 (m-80) REVERT: T 94 GLU cc_start: 0.7329 (pt0) cc_final: 0.7021 (pt0) REVERT: U 22 THR cc_start: 0.8131 (OUTLIER) cc_final: 0.7892 (m) REVERT: U 50 ASN cc_start: 0.8302 (m110) cc_final: 0.8079 (m-40) REVERT: U 95 ASN cc_start: 0.7686 (p0) cc_final: 0.7364 (p0) REVERT: U 99 TRP cc_start: 0.6797 (OUTLIER) cc_final: 0.4823 (m-90) REVERT: V 16 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7660 (pt) REVERT: V 18 LEU cc_start: 0.8813 (OUTLIER) cc_final: 0.8558 (pp) REVERT: V 71 GLU cc_start: 0.6718 (mp0) cc_final: 0.6269 (mp0) REVERT: W 1 MET cc_start: 0.6144 (OUTLIER) cc_final: 0.5372 (pmm) REVERT: X 71 LEU cc_start: 0.8666 (OUTLIER) cc_final: 0.8444 (tt) REVERT: Y 75 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8575 (mtm180) REVERT: Z 81 MET cc_start: 0.8906 (tpt) cc_final: 0.8679 (tpt) REVERT: a 32 ARG cc_start: 0.8953 (OUTLIER) cc_final: 0.8339 (mtt-85) REVERT: d 97 ASP cc_start: 0.3820 (OUTLIER) cc_final: 0.3422 (p0) REVERT: e 22 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8140 (ttt180) REVERT: e 58 ILE cc_start: 0.8466 (tp) cc_final: 0.8224 (tp) REVERT: e 86 GLU cc_start: 0.7750 (mt-10) cc_final: 0.7409 (mt-10) REVERT: f 5 LEU cc_start: 0.8968 (OUTLIER) cc_final: 0.8662 (mt) REVERT: f 100 ARG cc_start: 0.8580 (OUTLIER) cc_final: 0.8272 (tpp80) REVERT: g 5 LEU cc_start: 0.8849 (OUTLIER) cc_final: 0.8621 (pp) REVERT: h 91 MET cc_start: 0.8416 (mtp) cc_final: 0.8016 (mtp) REVERT: h 96 ASN cc_start: 0.7317 (t0) cc_final: 0.6664 (t0) REVERT: h 107 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.6972 (tm-30) REVERT: i 4 ARG cc_start: 0.7107 (OUTLIER) cc_final: 0.6100 (tpt-90) REVERT: l 11 ARG cc_start: 0.7879 (OUTLIER) cc_final: 0.6513 (mtp-110) REVERT: n 11 ARG cc_start: 0.7082 (mtm180) cc_final: 0.5819 (tpt-90) REVERT: n 14 LYS cc_start: 0.8617 (mtpt) cc_final: 0.7403 (mmtt) REVERT: o 58 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8123 (mtpt) REVERT: o 89 LYS cc_start: 0.8418 (OUTLIER) cc_final: 0.8024 (ptmm) REVERT: p 29 ILE cc_start: 0.9243 (mm) cc_final: 0.8965 (mt) REVERT: r 71 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7841 (ptt-90) REVERT: r 103 HIS cc_start: 0.7504 (OUTLIER) cc_final: 0.6767 (m-70) REVERT: t 10 LEU cc_start: 0.6995 (mt) cc_final: 0.6513 (pp) REVERT: u 124 LEU cc_start: 0.1356 (OUTLIER) cc_final: 0.1133 (mm) REVERT: u 243 ASN cc_start: -0.1042 (OUTLIER) cc_final: -0.1292 (m-40) REVERT: w 9 GLU cc_start: 0.5385 (OUTLIER) cc_final: 0.4241 (tp30) REVERT: x 6 LEU cc_start: 0.5016 (tt) cc_final: 0.4786 (mm) REVERT: x 86 LEU cc_start: 0.4483 (OUTLIER) cc_final: 0.4211 (mp) REVERT: x 194 ARG cc_start: 0.2258 (mmt180) cc_final: 0.1164 (mmt90) REVERT: x 430 MET cc_start: 0.2558 (ptm) cc_final: 0.1777 (ttm) REVERT: y 116 ASP cc_start: 0.3055 (OUTLIER) cc_final: 0.1476 (p0) REVERT: z 580 MET cc_start: 0.3557 (ppp) cc_final: 0.1582 (ptt) outliers start: 261 outliers final: 202 residues processed: 1185 average time/residue: 1.3435 time to fit residues: 2757.1817 Evaluate side-chains 1237 residues out of total 6608 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 247 poor density : 990 time to evaluate : 7.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 207 VAL Chi-restraints excluded: chain A residue 208 GLU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 29 VAL Chi-restraints excluded: chain B residue 53 MET Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 71 GLU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 175 GLN Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 204 GLN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 268 ARG Chi-restraints excluded: chain B residue 309 LEU Chi-restraints excluded: chain B residue 314 ILE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 125 CYS Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 9 ASN Chi-restraints excluded: chain D residue 18 VAL Chi-restraints excluded: chain D residue 33 ARG Chi-restraints excluded: chain D residue 55 VAL Chi-restraints excluded: chain D residue 117 LYS Chi-restraints excluded: chain D residue 118 ILE Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 252 VAL Chi-restraints excluded: chain E residue 47 VAL Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 124 HIS Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 171 VAL Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 191 ILE Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 76 MET Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain G residue 52 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 202 VAL Chi-restraints excluded: chain G residue 210 GLU Chi-restraints excluded: chain G residue 215 LEU Chi-restraints excluded: chain G residue 253 LEU Chi-restraints excluded: chain H residue 1 MET Chi-restraints excluded: chain H residue 4 ILE Chi-restraints excluded: chain H residue 17 ASP Chi-restraints excluded: chain H residue 18 ILE Chi-restraints excluded: chain H residue 48 LEU Chi-restraints excluded: chain H residue 111 LEU Chi-restraints excluded: chain H residue 145 VAL Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 113 THR Chi-restraints excluded: chain I residue 116 ARG Chi-restraints excluded: chain I residue 126 VAL Chi-restraints excluded: chain I residue 163 GLN Chi-restraints excluded: chain I residue 169 LYS Chi-restraints excluded: chain I residue 183 ASP Chi-restraints excluded: chain I residue 210 ARG Chi-restraints excluded: chain J residue 18 ARG Chi-restraints excluded: chain J residue 47 THR Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 55 TYR Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain L residue 10 LEU Chi-restraints excluded: chain L residue 42 ARG Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 103 ARG Chi-restraints excluded: chain L residue 124 LEU Chi-restraints excluded: chain L residue 125 VAL Chi-restraints excluded: chain L residue 155 MET Chi-restraints excluded: chain L residue 169 ILE Chi-restraints excluded: chain M residue 8 GLU Chi-restraints excluded: chain M residue 34 ASN Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 73 VAL Chi-restraints excluded: chain M residue 81 ASP Chi-restraints excluded: chain M residue 93 LYS Chi-restraints excluded: chain N residue 18 VAL Chi-restraints excluded: chain N residue 32 GLN Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 77 LYS Chi-restraints excluded: chain N residue 89 VAL Chi-restraints excluded: chain N residue 126 THR Chi-restraints excluded: chain N residue 151 ILE Chi-restraints excluded: chain N residue 174 LEU Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 104 VAL Chi-restraints excluded: chain O residue 132 THR Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 196 LEU Chi-restraints excluded: chain P residue 7 ASP Chi-restraints excluded: chain P residue 69 ARG Chi-restraints excluded: chain P residue 104 LEU Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 150 LEU Chi-restraints excluded: chain P residue 151 THR Chi-restraints excluded: chain Q residue 111 SER Chi-restraints excluded: chain Q residue 121 LEU Chi-restraints excluded: chain Q residue 128 LEU Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain R residue 3 MET Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 74 ARG Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 139 MET Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain S residue 19 THR Chi-restraints excluded: chain S residue 24 THR Chi-restraints excluded: chain S residue 42 SER Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 132 ILE Chi-restraints excluded: chain S residue 158 VAL Chi-restraints excluded: chain S residue 174 THR Chi-restraints excluded: chain T residue 32 ARG Chi-restraints excluded: chain T residue 42 ILE Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 72 VAL Chi-restraints excluded: chain T residue 85 LEU Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 79 SER Chi-restraints excluded: chain U residue 99 TRP Chi-restraints excluded: chain U residue 111 GLU Chi-restraints excluded: chain V residue 16 ILE Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 60 MET Chi-restraints excluded: chain V residue 106 VAL Chi-restraints excluded: chain W residue 1 MET Chi-restraints excluded: chain W residue 27 LYS Chi-restraints excluded: chain W residue 38 SER Chi-restraints excluded: chain X residue 64 SER Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 52 ASP Chi-restraints excluded: chain Y residue 55 VAL Chi-restraints excluded: chain Y residue 75 ARG Chi-restraints excluded: chain Y residue 79 VAL Chi-restraints excluded: chain Y residue 102 SER Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Z residue 35 ASP Chi-restraints excluded: chain Z residue 57 MET Chi-restraints excluded: chain Z residue 62 ILE Chi-restraints excluded: chain a residue 32 ARG Chi-restraints excluded: chain a residue 58 MET Chi-restraints excluded: chain a residue 82 VAL Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 22 LYS Chi-restraints excluded: chain c residue 92 CYS Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain c residue 94 LEU Chi-restraints excluded: chain c residue 98 ASP Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 72 VAL Chi-restraints excluded: chain d residue 80 VAL Chi-restraints excluded: chain d residue 97 ASP Chi-restraints excluded: chain d residue 111 VAL Chi-restraints excluded: chain d residue 113 THR Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 13 VAL Chi-restraints excluded: chain e residue 22 ARG Chi-restraints excluded: chain e residue 41 ILE Chi-restraints excluded: chain e residue 66 THR Chi-restraints excluded: chain e residue 81 ASN Chi-restraints excluded: chain f residue 5 LEU Chi-restraints excluded: chain f residue 31 GLU Chi-restraints excluded: chain f residue 47 CYS Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 100 ARG Chi-restraints excluded: chain f residue 108 SER Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 32 TYR Chi-restraints excluded: chain g residue 35 THR Chi-restraints excluded: chain g residue 53 LEU Chi-restraints excluded: chain g residue 59 VAL Chi-restraints excluded: chain g residue 76 ARG Chi-restraints excluded: chain h residue 82 ASP Chi-restraints excluded: chain h residue 88 THR Chi-restraints excluded: chain h residue 107 GLN Chi-restraints excluded: chain h residue 116 LEU Chi-restraints excluded: chain i residue 4 ARG Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 46 GLU Chi-restraints excluded: chain j residue 13 ASN Chi-restraints excluded: chain k residue 30 ASP Chi-restraints excluded: chain l residue 11 ARG Chi-restraints excluded: chain m residue 127 VAL Chi-restraints excluded: chain o residue 2 VAL Chi-restraints excluded: chain o residue 58 LYS Chi-restraints excluded: chain o residue 66 ILE Chi-restraints excluded: chain o residue 77 CYS Chi-restraints excluded: chain o residue 89 LYS Chi-restraints excluded: chain o residue 103 VAL Chi-restraints excluded: chain p residue 16 THR Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 89 LEU Chi-restraints excluded: chain q residue 41 VAL Chi-restraints excluded: chain r residue 58 LYS Chi-restraints excluded: chain r residue 60 VAL Chi-restraints excluded: chain r residue 71 ARG Chi-restraints excluded: chain r residue 78 VAL Chi-restraints excluded: chain r residue 80 THR Chi-restraints excluded: chain r residue 103 HIS Chi-restraints excluded: chain r residue 105 ASP Chi-restraints excluded: chain t residue 4 LEU Chi-restraints excluded: chain u residue 94 LEU Chi-restraints excluded: chain u residue 124 LEU Chi-restraints excluded: chain u residue 127 VAL Chi-restraints excluded: chain u residue 154 HIS Chi-restraints excluded: chain u residue 169 LEU Chi-restraints excluded: chain u residue 243 ASN Chi-restraints excluded: chain v residue 68 LEU Chi-restraints excluded: chain v residue 88 LEU Chi-restraints excluded: chain w residue 9 GLU Chi-restraints excluded: chain w residue 53 THR Chi-restraints excluded: chain w residue 62 ILE Chi-restraints excluded: chain x residue 36 CYS Chi-restraints excluded: chain x residue 86 LEU Chi-restraints excluded: chain x residue 97 THR Chi-restraints excluded: chain x residue 103 VAL Chi-restraints excluded: chain x residue 116 THR Chi-restraints excluded: chain x residue 169 VAL Chi-restraints excluded: chain x residue 198 GLU Chi-restraints excluded: chain x residue 222 ASP Chi-restraints excluded: chain x residue 230 GLU Chi-restraints excluded: chain x residue 240 VAL Chi-restraints excluded: chain x residue 245 VAL Chi-restraints excluded: chain x residue 307 VAL Chi-restraints excluded: chain x residue 315 ASN Chi-restraints excluded: chain y residue 116 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 556 optimal weight: 8.9990 chunk 721 optimal weight: 10.0000 chunk 967 optimal weight: 0.0370 chunk 278 optimal weight: 10.0000 chunk 837 optimal weight: 7.9990 chunk 134 optimal weight: 10.0000 chunk 252 optimal weight: 10.0000 chunk 909 optimal weight: 9.9990 chunk 380 optimal weight: 10.0000 chunk 934 optimal weight: 4.9990 chunk 115 optimal weight: 10.0000 overall best weight: 6.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 167 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 204 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN ** E 280 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 118 GLN G 64 GLN ** J 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 37 HIS ** O 5 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 GLN ** T 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 105 ASN X 111 GLN ** a 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 57 ASN g 28 ASN i 36 HIS ** m 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 165 HIS ** w 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.150240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.118199 restraints weight = 251371.930| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.14 r_work: 0.3232 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3138 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3103 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3103 r_free = 0.3103 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3103 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.4138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.084 159521 Z= 0.353 Angle : 0.703 15.387 234784 Z= 0.356 Chirality : 0.042 0.338 29216 Planarity : 0.006 0.109 14749 Dihedral : 24.589 179.735 72576 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.75 % Favored : 93.13 % Rotamer: Outliers : 4.34 % Allowed : 20.96 % Favored : 74.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 1.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.10), residues: 7563 helix: 1.30 (0.10), residues: 2778 sheet: -0.47 (0.16), residues: 1050 loop : -1.34 (0.10), residues: 3735 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP N 120 HIS 0.014 0.002 HIS E 124 PHE 0.021 0.002 PHE S 176 TYR 0.032 0.002 TYR O 168 ARG 0.010 0.001 ARG I 203 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 46010.85 seconds wall clock time: 801 minutes 6.82 seconds (48066.82 seconds total)