Starting phenix.real_space_refine on Sat Mar 23 03:17:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j92_2832/03_2024/3j92_2832_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j92_2832/03_2024/3j92_2832.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j92_2832/03_2024/3j92_2832_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j92_2832/03_2024/3j92_2832_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j92_2832/03_2024/3j92_2832_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j92_2832/03_2024/3j92_2832.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j92_2832/03_2024/3j92_2832.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j92_2832/03_2024/3j92_2832_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j92_2832/03_2024/3j92_2832_updated.pdb" } resolution = 3.6 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= 0.003 sd= 0.019 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 4009 5.49 5 Mg 159 5.21 5 S 262 5.16 5 C 76305 2.51 5 N 27467 2.21 5 O 38179 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 109": "OE1" <-> "OE2" Residue "A GLU 118": "OE1" <-> "OE2" Residue "A GLU 208": "OE1" <-> "OE2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "B ARG 10": "NH1" <-> "NH2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B GLU 71": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "B ARG 97": "NH1" <-> "NH2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B ARG 268": "NH1" <-> "NH2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "B GLU 383": "OE1" <-> "OE2" Residue "C ARG 49": "NH1" <-> "NH2" Residue "C GLU 145": "OE1" <-> "OE2" Residue "C GLU 149": "OE1" <-> "OE2" Residue "C GLU 155": "OE1" <-> "OE2" Residue "C ARG 204": "NH1" <-> "NH2" Residue "C GLU 254": "OE1" <-> "OE2" 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 GLU 129": "OE1" <-> "OE2" Residue "D ARG 179": "NH1" <-> "NH2" Residue "D GLU 189": "OE1" <-> "OE2" Residue "D GLU 213": "OE1" <-> "OE2" Residue "D GLU 216": "OE1" <-> "OE2" Residue "D GLU 254": "OE1" <-> "OE2" Residue "D GLU 292": "OE1" <-> "OE2" Residue "E ARG 101": "NH1" <-> "NH2" Residue "E TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 115": "OE1" <-> "OE2" Residue "E ARG 157": "NH1" <-> "NH2" Residue "E ARG 184": "NH1" <-> "NH2" Residue "E GLU 234": "OE1" <-> "OE2" Residue "E GLU 240": "OE1" <-> "OE2" Residue "F GLU 29": "OE1" <-> "OE2" Residue "F ARG 48": "NH1" <-> "NH2" Residue "F GLU 54": "OE1" <-> "OE2" Residue "F GLU 70": "OE1" <-> "OE2" Residue "F ARG 96": "NH1" <-> "NH2" Residue "F GLU 139": "OE1" <-> "OE2" 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 GLU 105": "OE1" <-> "OE2" Residue "G GLU 109": "OE1" <-> "OE2" Residue "G ARG 113": "NH1" <-> "NH2" Residue "G GLU 165": "OE1" <-> "OE2" Residue "G ARG 189": "NH1" <-> "NH2" Residue "G GLU 210": "OE1" <-> "OE2" Residue "G GLU 220": "OE1" <-> "OE2" Residue "G ARG 234": "NH1" <-> "NH2" Residue "H GLU 14": "OE1" <-> "OE2" Residue "H ARG 23": "NH1" <-> "NH2" Residue "H GLU 44": "OE1" <-> "OE2" Residue "H ARG 89": "NH1" <-> "NH2" Residue "H GLU 107": "OE1" <-> "OE2" Residue "H GLU 113": "OE1" <-> "OE2" Residue "H GLU 143": "OE1" <-> "OE2" Residue "H GLU 147": "OE1" <-> "OE2" Residue "I ARG 4": "NH1" <-> "NH2" Residue "I GLU 45": "OE1" <-> "OE2" Residue "I ARG 69": "NH1" <-> "NH2" Residue "I ARG 98": "NH1" <-> "NH2" Residue "I ARG 116": "NH1" <-> "NH2" Residue "I GLU 145": "OE1" <-> "OE2" Residue "I GLU 146": "OE1" <-> "OE2" Residue "I ARG 153": "NH1" <-> "NH2" Residue "I ARG 162": "NH1" <-> "NH2" Residue "I GLU 182": "OE1" <-> "OE2" Residue "I TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ARG 210": "NH1" <-> "NH2" Residue "J GLU 9": "OE1" <-> "OE2" Residue "J GLU 41": "OE1" <-> "OE2" Residue "J ARG 64": "NH1" <-> "NH2" Residue "J GLU 66": "OE1" <-> "OE2" Residue "J GLU 91": "OE1" <-> "OE2" Residue "J GLU 93": "OE1" <-> "OE2" Residue "J GLU 111": "OE1" <-> "OE2" Residue "J ARG 146": "NH1" <-> "NH2" Residue "J GLU 161": "OE1" <-> "OE2" 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 GLU 142": "OE1" <-> "OE2" Residue "L ARG 158": "NH1" <-> "NH2" Residue "L GLU 164": "OE1" <-> "OE2" Residue "L GLU 201": "OE1" <-> "OE2" Residue "M GLU 8": "OE1" <-> "OE2" Residue "M ARG 11": "NH1" <-> "NH2" Residue "M TYR 14": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 78": "OE1" <-> "OE2" Residue "M ARG 98": "NH1" <-> "NH2" Residue "M GLU 99": "OE1" <-> "OE2" Residue "M ARG 109": "NH1" <-> "NH2" Residue "M ARG 119": "NH1" <-> "NH2" Residue "M ARG 121": "NH1" <-> "NH2" Residue "M GLU 126": "OE1" <-> "OE2" 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 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 "O GLU 157": "OE1" <-> "OE2" Residue "O GLU 158": "OE1" <-> "OE2" Residue "P GLU 9": "OE1" <-> "OE2" Residue "P GLU 31": "OE1" <-> "OE2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P GLU 115": "OE1" <-> "OE2" Residue "P GLU 147": "OE1" <-> "OE2" Residue "Q GLU 17": "OE1" <-> "OE2" Residue "Q ARG 37": "NH1" <-> "NH2" Residue "Q ARG 55": "NH1" <-> "NH2" Residue "Q GLU 76": "OE1" <-> "OE2" Residue "Q ARG 91": "NH1" <-> "NH2" Residue "Q GLU 94": "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 GLU 91": "OE1" <-> "OE2" Residue "R ARG 117": "NH1" <-> "NH2" Residue "R GLU 140": "OE1" <-> "OE2" Residue "R GLU 160": "OE1" <-> "OE2" Residue "R GLU 168": "OE1" <-> "OE2" 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 GLU 111": "OE1" <-> "OE2" Residue "T GLU 118": "OE1" <-> "OE2" Residue "T ARG 130": "NH1" <-> "NH2" Residue "T ARG 136": "NH1" <-> "NH2" Residue "T GLU 137": "OE1" <-> "OE2" Residue "T GLU 147": "OE1" <-> "OE2" Residue "T GLU 149": "OE1" <-> "OE2" Residue "T GLU 152": "OE1" <-> "OE2" Residue "T GLU 157": "OE1" <-> "OE2" Residue "U GLU 40": "OE1" <-> "OE2" Residue "V ARG 48": "NH1" <-> "NH2" Residue "V ARG 51": "NH1" <-> "NH2" Residue "V GLU 71": "OE1" <-> "OE2" Residue "V ARG 89": "NH1" <-> "NH2" Residue "V GLU 111": "OE1" <-> "OE2" Residue "V GLU 124": "OE1" <-> "OE2" 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 TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 91": "OE1" <-> "OE2" Residue "X ARG 129": "NH1" <-> "NH2" Residue "X GLU 133": "OE1" <-> "OE2" Residue "X ARG 139": "NH1" <-> "NH2" Residue "Y ARG 27": "NH1" <-> "NH2" Residue "Y GLU 83": "OE1" <-> "OE2" Residue "Y ARG 87": "NH1" <-> "NH2" Residue "Y GLU 120": "OE1" <-> "OE2" Residue "Y GLU 131": "OE1" <-> "OE2" Residue "Z ARG 65": "NH1" <-> "NH2" Residue "Z GLU 113": "OE1" <-> "OE2" Residue "Z GLU 119": "OE1" <-> "OE2" Residue "Z GLU 120": "OE1" <-> "OE2" 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 "b GLU 70": "OE1" <-> "OE2" Residue "c ARG 39": "NH1" <-> "NH2" Residue "c GLU 59": "OE1" <-> "OE2" Residue "c GLU 80": "OE1" <-> "OE2" Residue "d ARG 90": "NH1" <-> "NH2" Residue "d GLU 124": "OE1" <-> "OE2" Residue "e ARG 36": "NH1" <-> "NH2" Residue "e ARG 39": "NH1" <-> "NH2" Residue "e ARG 128": "NH1" <-> "NH2" Residue "f GLU 38": "OE1" <-> "OE2" Residue "f ARG 89": "NH1" <-> "NH2" Residue "g ARG 29": "NH1" <-> "NH2" Residue "g ARG 60": "NH1" <-> "NH2" Residue "g GLU 98": "OE1" <-> "OE2" Residue "h ARG 7": "NH1" <-> "NH2" Residue "h GLU 22": "OE1" <-> "OE2" Residue "h ARG 94": "NH1" <-> "NH2" Residue "h GLU 100": "OE1" <-> "OE2" Residue "i ARG 45": "NH1" <-> "NH2" Residue "i ARG 68": "NH1" <-> "NH2" Residue "i ARG 76": "NH1" <-> "NH2" Residue "i GLU 88": "OE1" <-> "OE2" 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 6": "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 "o ARG 40": "NH1" <-> "NH2" Residue "o ARG 43": "NH1" <-> "NH2" Residue "o ARG 78": "NH1" <-> "NH2" Residue "o GLU 92": "OE1" <-> "OE2" Residue "p ARG 17": "NH1" <-> "NH2" Residue "p ARG 49": "NH1" <-> "NH2" Residue "p ARG 84": "NH1" <-> "NH2" Residue "r GLU 28": "OE1" <-> "OE2" Residue "r ARG 35": "NH1" <-> "NH2" Residue "r GLU 52": "OE1" <-> "OE2" Residue "r ARG 112": "NH1" <-> "NH2" Residue "r ARG 113": "NH1" <-> "NH2" Residue "s GLU 93": "OE1" <-> "OE2" Residue "s GLU 171": "OE1" <-> "OE2" Residue "t GLU 21": "OE1" <-> "OE2" Residue "t GLU 87": "OE1" <-> "OE2" Residue "v GLU 316": "OE1" <-> "OE2" Residue "v ARG 360": "NH1" <-> "NH2" Residue "v ARG 411": "NH1" <-> "NH2" Residue "v GLU 492": "OE1" <-> "OE2" Residue "w ARG 14": "NH1" <-> "NH2" Residue "z ARG 1633": "NH1" <-> "NH2" Residue "0 PHE 1765": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 146386 Number of models: 1 Model: "" Number of chains: 65 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: 3147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3147 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 14, 'TRANS': 379} Chain: "C" Number of atoms: 2919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2919 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 18, 'TRANS': 348} Chain: "D" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2384 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 9, 'TRANS': 282} Chain: "E" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1904 Classifications: {'peptide': 236} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 222} Chain breaks: 1 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: 1939 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1939 Classifications: {'peptide': 241} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 227} Chain: "H" Number of atoms: 1518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1518 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 4, 'TRANS': 185} Chain: "I" Number of atoms: 1651 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1651 Classifications: {'peptide': 204} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 192} Chain breaks: 1 Chain: "J" Number of atoms: 1359 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1359 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 5, 'TRANS': 164} 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: 1131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 138, 1131 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: 1163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 1163 Classifications: {'peptide': 147} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 140} Chain: "b" Number of atoms: 610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 610 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: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 1015 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "i" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 832 Classifications: {'peptide': 102} Link IDs: {'PTRANS': 3, 'TRANS': 98} Chain: "j" Number of atoms: 706 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 706 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: "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: "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: 1522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 198, 1522 Classifications: {'peptide': 198} Link IDs: {'PTRANS': 9, 'TRANS': 188} Chain: "t" Number of atoms: 1238 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1238 Classifications: {'peptide': 163} Link IDs: {'CIS': 3, 'PCIS': 1, 'PTRANS': 10, 'TRANS': 148} Chain: "u" Number of atoms: 645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 645 Classifications: {'peptide': 130} Incomplete info: {'truncation_to_alanine': 117} Link IDs: {'PTRANS': 3, 'TRANS': 126} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 434 Unresolved non-hydrogen angles: 555 Unresolved non-hydrogen dihedrals: 359 Unresolved non-hydrogen chiralities: 42 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 3, 'TYR:plan': 6, 'ASN:plan1': 7, 'TRP:plan': 1, 'ASP:plan': 9, 'PHE:plan': 6, 'GLU:plan': 7, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 235 Chain: "v" Number of atoms: 1092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 1092 Classifications: {'peptide': 136} Link IDs: {'TRANS': 135} Chain breaks: 2 Chain: "w" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 110 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "x" Number of atoms: 1090 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1090 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 218} Link IDs: {'TRANS': 217} Chain breaks: 14 Unresolved non-hydrogen bonds: 436 Unresolved non-hydrogen angles: 654 Unresolved non-hydrogen dihedrals: 218 Planarities with less than four sites: {'UNK:plan-1': 218} Unresolved non-hydrogen planarities: 218 Chain: "y" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1055 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 211} Link IDs: {'TRANS': 210} Chain breaks: 12 Unresolved non-hydrogen bonds: 422 Unresolved non-hydrogen angles: 633 Unresolved non-hydrogen dihedrals: 211 Planarities with less than four sites: {'UNK:plan-1': 211} Unresolved non-hydrogen planarities: 211 Chain: "z" Number of atoms: 1057 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1057 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 2, 'TRANS': 127} Chain breaks: 4 Chain: "0" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 293 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "1" Number of atoms: 125 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 125 Classifications: {'peptide': 15} Link IDs: {'PTRANS': 1, 'TRANS': 13} Chain: "2" Number of atoms: 1601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 1601 Classifications: {'RNA': 75} Modifications used: {'5*END': 1, 'rna2p_pur': 7, 'rna2p_pyr': 3, 'rna3p': 1, 'rna3p_pur': 32, 'rna3p_pyr': 32} Link IDs: {'rna2p': 10, 'rna3p': 64} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Chain: "5" Number of atoms: 78486 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3662, 78486 Classifications: {'DNA': 1, 'RNA': 3661} Modifications used: {'5*END': 1, 'rna2p_pur': 327, 'rna2p_pyr': 215, 'rna3p_pur': 1674, 'rna3p_pyr': 1444} Link IDs: {'rna2p': 542, 'rna3p': 3119} Chain breaks: 11 Unresolved non-hydrogen bonds: 27 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 22 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {' U:plan': 1, ' C:plan': 1, ' C:plan2': 1} Unresolved non-hydrogen planarities: 20 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': 11, 'rna3p_pur': 62, 'rna3p_pyr': 69} Link IDs: {'rna2p': 24, 'rna3p': 131} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "g" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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: "5" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 150 Unusual residues: {' MG': 150} Classifications: {'undetermined': 150} Link IDs: {None: 149} Chain: "7" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Unusual residues: {' MG': 5} Classifications: {'undetermined': 5} Link IDs: {None: 4} Chain: "8" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 44941 SG CYS g 46 114.544 166.285 207.730 1.00 45.78 S ATOM 44958 SG CYS g 49 113.362 169.849 207.455 1.00 69.73 S ATOM 45221 SG CYS g 83 116.040 169.071 209.241 1.00 32.34 S ATOM 45241 SG CYS g 86 112.862 168.041 210.440 1.00 44.44 S ATOM 47468 SG CYS j 19 148.356 126.037 183.088 1.00 11.71 S ATOM 47496 SG CYS j 22 148.947 124.126 180.632 1.00 12.10 S ATOM 47587 SG CYS j 34 145.521 124.933 179.923 1.00 10.08 S ATOM 47606 SG CYS j 37 147.036 122.647 182.726 1.00 9.52 S ATOM 49209 SG CYS m 96 107.821 130.574 75.083 1.00 13.72 S ATOM 49235 SG CYS m 99 110.570 132.501 75.918 1.00 12.82 S ATOM 49325 SG CYS m 110 110.707 130.989 72.779 1.00 18.14 S ATOM 49369 SG CYS m 115 111.421 129.103 75.659 1.00 24.98 S ATOM 49567 SG CYS o 12 89.794 56.196 156.265 1.00 32.64 S ATOM 49591 SG CYS o 15 88.805 52.823 157.285 1.00 42.66 S ATOM 50060 SG CYS o 72 86.431 56.310 157.423 1.00 32.80 S ATOM 50097 SG CYS o 77 89.680 55.399 159.649 1.00 66.29 S ATOM 50627 SG CYS p 39 100.617 168.543 199.888 1.00 28.81 S ATOM 50650 SG CYS p 42 100.412 172.934 200.490 1.00 30.16 S ATOM 50772 SG CYS p 57 103.158 169.827 198.761 1.00 23.52 S ATOM 50788 SG CYS p 60 102.053 169.863 200.485 1.00 25.99 S Time building chain proxies: 54.44, per 1000 atoms: 0.37 Number of scatterers: 146386 At special positions: 0 Unit cell: (237.18, 268, 282.74, 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 262 16.00 P 4009 15.00 Mg 159 11.99 O 38179 8.00 N 27467 7.00 C 76305 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS 01734 " - pdb=" SG CYS 01758 " distance=2.04 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: 64.51 Conformation dependent library (CDL) restraints added in 8.1 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN g 201 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 83 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 46 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 49 " pdb="ZN ZN g 201 " - pdb=" SG CYS g 86 " pdb=" ZN j 101 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 22 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 37 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 34 " pdb="ZN ZN j 101 " - pdb=" SG CYS j 19 " pdb=" ZN m 201 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 96 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 115 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 99 " pdb="ZN ZN m 201 " - pdb=" SG CYS m 110 " pdb=" ZN o 201 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 12 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 77 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 15 " pdb="ZN ZN o 201 " - pdb=" SG CYS o 72 " pdb=" ZN p 100 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 60 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 39 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 42 " pdb="ZN ZN p 100 " - pdb=" SG CYS p 57 " Number of angles added : 30 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14382 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: 254 helices and 74 sheets defined 43.3% alpha, 14.4% beta 1220 base pairs and 1869 stacking pairs defined. Time for finding SS restraints: 78.20 Creating SS restraints... Processing helix chain 'A' and resid 5 through 13 removed outlier: 3.507A pdb=" N ARG A 9 " --> pdb=" O ILE A 5 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N LYS A 10 " --> pdb=" O ARG A 6 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N GLY A 11 " --> pdb=" O GLY A 7 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ALA A 12 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 4.119A 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 38 Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.683A 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: 3.897A pdb=" N ALA A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA A 191 " --> pdb=" O HIS A 187 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LYS A 192 " --> pdb=" O LYS A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 205 removed outlier: 4.056A pdb=" N MET A 204 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 5.934A pdb=" N ASN A 205 " --> pdb=" O GLY A 201 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 200 through 205' Processing helix chain 'B' and resid 13 through 18 removed outlier: 4.896A pdb=" N LEU B 17 " --> pdb=" O SER B 13 " (cutoff:3.500A) Proline residue: B 18 - end of helix No H-bonds generated for 'chain 'B' and resid 13 through 18' Processing helix chain 'B' and resid 111 through 120 removed outlier: 4.239A pdb=" N ARG B 117 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N PHE B 118 " --> pdb=" O CYS B 114 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N TYR B 119 " --> pdb=" O LYS B 115 " (cutoff:3.500A) removed outlier: 5.240A pdb=" N LYS B 120 " --> pdb=" O ARG B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 130 through 139 removed outlier: 3.590A pdb=" N LYS B 135 " --> pdb=" O THR B 131 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LYS B 136 " --> pdb=" O LYS B 132 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N TRP B 137 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 5.090A pdb=" N GLN B 138 " --> pdb=" O CYS B 134 " (cutoff:3.500A) removed outlier: 4.719A pdb=" N ASP B 139 " --> pdb=" O LYS B 135 " (cutoff:3.500A) Processing helix chain 'B' and resid 140 through 157 Processing helix chain 'B' and resid 167 through 172 removed outlier: 4.213A 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: 4.122A 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 356 through 361 removed outlier: 3.752A 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 'B' and resid 298 through 303 removed outlier: 3.877A pdb=" N ASN B 301 " --> pdb=" O LEU B 298 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA B 303 " --> pdb=" O LYS B 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 25 through 31 removed outlier: 4.400A pdb=" N LYS C 29 " --> pdb=" O PRO C 25 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ALA C 30 " --> pdb=" O ALA C 26 " (cutoff:3.500A) Proline residue: C 31 - end of helix No H-bonds generated for 'chain 'C' and resid 25 through 31' Processing helix chain 'C' and resid 33 through 49 removed outlier: 3.789A pdb=" N LYS C 46 " --> pdb=" O THR C 42 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ASN C 47 " --> pdb=" O ASN C 43 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ASN C 48 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ARG C 49 " --> pdb=" O ARG C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 116 through 134 removed outlier: 3.516A pdb=" N ALA C 132 " --> pdb=" O LEU C 128 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N LEU C 133 " --> pdb=" O ALA C 129 " (cutoff:3.500A) Proline residue: C 134 - end of helix Processing helix chain 'C' and resid 135 through 141 removed outlier: 3.599A pdb=" N GLY C 141 " --> pdb=" O VAL C 137 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 161 removed outlier: 5.155A pdb=" N SER C 160 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N TYR C 161 " --> pdb=" O LYS C 157 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 156 through 161' Processing helix chain 'C' and resid 163 through 175 removed outlier: 3.527A pdb=" N ALA C 167 " --> pdb=" O LYS C 163 " (cutoff:3.500A) Processing helix chain 'C' and resid 176 through 187 removed outlier: 3.746A pdb=" N ILE C 180 " --> pdb=" O ALA C 176 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLN C 187 " --> pdb=" O VAL C 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 193 through 198 removed outlier: 4.102A pdb=" N ARG C 197 " --> pdb=" O LYS C 193 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ASN C 198 " --> pdb=" O GLY C 194 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 193 through 198' Processing helix chain 'C' and resid 216 through 223 removed outlier: 3.818A pdb=" N ALA C 220 " --> pdb=" O GLY C 216 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N ARG C 222 " --> pdb=" O ILE C 218 " (cutoff:3.500A) removed outlier: 5.049A 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: 3.705A pdb=" N LYS C 259 " --> pdb=" O SER C 255 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N ASP C 261 " --> pdb=" O PHE C 257 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) Processing helix chain 'C' and resid 288 through 295 removed outlier: 4.500A pdb=" N ILE C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 296 through 303 removed outlier: 4.396A pdb=" N ALA C 301 " --> pdb=" O GLU C 297 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N LEU C 302 " --> pdb=" O ILE C 298 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N ARG C 303 " --> pdb=" O GLN C 299 " (cutoff:3.500A) Processing helix chain 'C' and resid 317 through 322 removed outlier: 4.757A 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 368 removed outlier: 4.356A pdb=" N THR C 334 " --> pdb=" O PRO C 330 " (cutoff:3.500A) removed outlier: 4.455A pdb=" N THR C 339 " --> pdb=" O MET C 335 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG C 342 " --> pdb=" O ASN C 338 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLN C 343 " --> pdb=" O THR C 339 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS C 368 " --> pdb=" O LYS C 364 " (cutoff:3.500A) 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: 4.012A pdb=" N ARG D 35 " --> pdb=" O TYR D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 79 through 87 removed outlier: 4.811A 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 removed outlier: 3.532A pdb=" N ARG D 112 " --> pdb=" O ARG D 108 " (cutoff:3.500A) Processing helix chain 'D' and resid 115 through 120 removed outlier: 4.433A pdb=" N TYR D 119 " --> pdb=" O MET D 115 " (cutoff:3.500A) removed outlier: 4.361A 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 removed outlier: 3.657A pdb=" N GLY D 161 " --> pdb=" O ASN D 157 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N LYS D 164 " --> pdb=" O PHE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 201 removed outlier: 6.375A pdb=" N HIS D 195 " --> pdb=" O ASN D 191 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG D 196 " --> pdb=" O ALA D 192 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 215 removed outlier: 3.987A pdb=" N ILE D 212 " --> pdb=" O MET D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 216 through 224 Processing helix chain 'D' and resid 225 through 230 removed outlier: 4.358A pdb=" N ASN D 229 " --> pdb=" O GLN D 225 " (cutoff:3.500A) removed outlier: 4.036A 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: 4.562A pdb=" N GLU D 237 " --> pdb=" O PRO D 233 " (cutoff:3.500A) removed outlier: 4.962A pdb=" N GLU D 238 " --> pdb=" O ASP D 234 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N MET D 239 " --> pdb=" O MET D 235 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N TYR D 240 " --> pdb=" O MET D 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 294 removed outlier: 4.717A pdb=" N ARG D 293 " --> pdb=" O ARG D 289 " (cutoff:3.500A) removed outlier: 4.345A pdb=" N ALA D 294 " --> pdb=" O ALA D 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 54 through 63 Processing helix chain 'E' and resid 186 through 191 removed outlier: 4.557A pdb=" N VAL E 190 " --> pdb=" O HIS E 186 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE E 191 " --> pdb=" O GLN E 187 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 186 through 191' Processing helix chain 'E' and resid 209 through 214 removed outlier: 4.158A pdb=" N LYS E 214 " --> pdb=" O ASP E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 239 through 261 removed outlier: 4.651A pdb=" N LYS E 243 " --> pdb=" O SER E 239 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS E 247 " --> pdb=" O LYS E 243 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA E 248 " --> pdb=" O VAL E 244 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ARG E 256 " --> pdb=" O GLN E 252 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ILE E 257 " --> pdb=" O ILE E 253 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS E 258 " --> pdb=" O LEU E 254 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA E 259 " --> pdb=" O ARG E 255 " (cutoff:3.500A) Proline residue: E 261 - end of helix Processing helix chain 'E' and resid 262 through 270 removed outlier: 5.001A pdb=" N VAL E 270 " --> pdb=" O TYR E 266 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 283 removed outlier: 5.305A pdb=" N VAL E 283 " --> pdb=" O PRO E 279 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 81 removed outlier: 4.117A pdb=" N LYS F 33 " --> pdb=" O GLU F 29 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE F 71 " --> pdb=" O TYR F 67 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N MET F 73 " --> pdb=" O THR F 69 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N GLY F 81 " --> pdb=" O ALA F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 115 removed outlier: 3.618A pdb=" N ARG F 108 " --> pdb=" O SER F 104 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 139 removed outlier: 3.832A pdb=" N ASN F 133 " --> pdb=" O LYS F 129 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N MET F 134 " --> pdb=" O ALA F 130 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N VAL F 138 " --> pdb=" O MET F 134 " (cutoff:3.500A) Processing helix chain 'F' and resid 148 through 158 removed outlier: 5.347A pdb=" N VAL F 152 " --> pdb=" O ASN F 148 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 181 removed outlier: 4.276A pdb=" N ILE F 177 " --> pdb=" O ASP F 173 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG F 179 " --> pdb=" O ALA F 175 " (cutoff:3.500A) Processing helix chain 'F' and resid 188 through 199 Processing helix chain 'F' and resid 202 through 211 removed outlier: 3.845A pdb=" N LEU F 210 " --> pdb=" O ALA F 206 " (cutoff:3.500A) removed outlier: 5.157A pdb=" N TRP F 211 " --> pdb=" O ASN F 207 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 250 removed outlier: 3.826A pdb=" N LEU F 245 " --> pdb=" O GLN F 241 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 74 removed outlier: 3.982A pdb=" N LEU G 70 " --> pdb=" O GLN G 66 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 86 removed outlier: 4.950A pdb=" N PHE G 83 " --> pdb=" O THR G 79 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N THR G 84 " --> pdb=" O ILE G 80 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N GLN G 85 " --> pdb=" O ASN G 81 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N ALA G 86 " --> pdb=" O GLN G 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 88 through 103 removed outlier: 3.768A pdb=" N LYS G 101 " --> pdb=" O LYS G 97 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N TYR G 102 " --> pdb=" O LEU G 98 " (cutoff:3.500A) Processing helix chain 'G' and resid 106 through 123 removed outlier: 5.819A pdb=" N LYS G 111 " --> pdb=" O LYS G 107 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG G 117 " --> pdb=" O ARG G 113 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N ALA G 122 " --> pdb=" O ALA G 118 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N ALA G 123 " --> pdb=" O GLU G 119 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 150 removed outlier: 5.153A pdb=" N THR G 145 " --> pdb=" O ASN G 141 " (cutoff:3.500A) removed outlier: 4.693A pdb=" N LYS G 150 " --> pdb=" O LEU G 146 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 178 removed outlier: 4.688A pdb=" N PHE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU G 170 " --> pdb=" O LEU G 166 " (cutoff:3.500A) Proline residue: G 171 - end of helix removed outlier: 3.572A pdb=" N ARG G 175 " --> pdb=" O PRO G 171 " (cutoff:3.500A) Processing helix chain 'G' and resid 186 through 195 removed outlier: 4.089A pdb=" N LEU G 193 " --> pdb=" O ARG G 189 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N VAL G 194 " --> pdb=" O LEU G 190 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N HIS G 195 " --> pdb=" O GLY G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 208 through 226 removed outlier: 4.455A pdb=" N GLY G 213 " --> pdb=" O SER G 209 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N ALA G 214 " --> pdb=" O GLU G 210 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ASN G 225 " --> pdb=" O ALA G 221 " (cutoff:3.500A) Processing helix chain 'G' and resid 229 through 237 removed outlier: 5.311A pdb=" N TRP G 237 " --> pdb=" O ILE G 233 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 265 removed outlier: 3.751A pdb=" N LYS G 257 " --> pdb=" O LEU G 253 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LEU G 261 " --> pdb=" O LYS G 257 " (cutoff:3.500A) removed outlier: 4.902A pdb=" N THR G 263 " --> pdb=" O LYS G 259 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N LYS G 264 " --> pdb=" O GLU G 260 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N LEU G 265 " --> pdb=" O LEU G 261 " (cutoff:3.500A) Processing helix chain 'H' and resid 63 through 86 removed outlier: 4.375A pdb=" N THR H 69 " --> pdb=" O LYS H 65 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N VAL H 70 " --> pdb=" O GLU H 66 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N ARG H 71 " --> pdb=" O LEU H 67 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N THR H 72 " --> pdb=" O ALA H 68 " (cutoff:3.500A) Processing helix chain 'H' and resid 150 through 166 removed outlier: 3.825A pdb=" N THR H 165 " --> pdb=" O ILE H 161 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N THR H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 176 removed outlier: 4.602A pdb=" N LEU H 176 " --> pdb=" O ILE H 172 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 11 removed outlier: 4.328A pdb=" N ARG I 10 " --> pdb=" O ALA I 6 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N TYR I 11 " --> pdb=" O ARG I 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 6 through 11' Processing helix chain 'I' and resid 42 through 47 removed outlier: 4.184A 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: 3.803A pdb=" N PHE I 157 " --> pdb=" O ARG I 153 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N LYS I 158 " --> pdb=" O ARG I 154 " (cutoff:3.500A) removed outlier: 4.139A 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: 4.613A pdb=" N GLU I 182 " --> pdb=" O ALA I 178 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N ASN I 183 " --> pdb=" O ASP I 179 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N LYS I 187 " --> pdb=" O ASN I 183 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS I 188 " --> pdb=" O MET I 184 " (cutoff:3.500A) Processing helix chain 'I' and resid 205 through 214 removed outlier: 4.676A pdb=" N TRP I 209 " --> pdb=" O PRO I 205 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG I 210 " --> pdb=" O LEU I 206 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N VAL I 211 " --> pdb=" O ASP I 207 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N LEU I 212 " --> pdb=" O LYS I 208 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N HIS I 213 " --> pdb=" O TRP I 209 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N SER I 214 " --> pdb=" O ARG I 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 205 through 214' Processing helix chain 'J' and resid 30 through 44 removed outlier: 3.884A pdb=" N LYS J 38 " --> pdb=" O THR J 34 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N VAL J 39 " --> pdb=" O ARG J 35 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 91 Processing helix chain 'J' and resid 152 through 157 removed outlier: 6.454A pdb=" N ARG J 156 " --> pdb=" O GLY J 152 " (cutoff:3.500A) removed outlier: 5.524A pdb=" N ILE J 157 " --> pdb=" O ALA J 153 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 152 through 157' Processing helix chain 'J' and resid 158 through 169 removed outlier: 3.569A pdb=" N ALA J 162 " --> pdb=" O SER J 158 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 116 removed outlier: 3.591A pdb=" N ASP J 114 " --> pdb=" O GLU J 111 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N GLY J 116 " --> pdb=" O ILE J 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 138 through 143 removed outlier: 3.707A pdb=" N ALA J 142 " --> pdb=" O PHE J 139 " (cutoff:3.500A) Processing helix chain 'L' and resid 17 through 22 removed outlier: 3.729A pdb=" N ARG L 21 " --> pdb=" O ASP L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 28 through 47 removed outlier: 3.785A pdb=" N ILE L 33 " --> pdb=" O PRO L 29 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG L 34 " --> pdb=" O ALA L 30 " (cutoff:3.500A) removed outlier: 4.041A 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: 3.935A pdb=" N ARG L 92 " --> pdb=" O LYS L 88 " (cutoff:3.500A) removed outlier: 4.656A pdb=" N THR L 93 " --> pdb=" O LYS L 89 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE L 94 " --> pdb=" O VAL L 90 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY L 95 " --> pdb=" O ALA L 91 " (cutoff:3.500A) Processing helix chain 'L' and resid 106 through 124 removed outlier: 3.544A pdb=" N LEU L 110 " --> pdb=" O CYS L 106 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASN L 113 " --> pdb=" O SER L 109 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU L 117 " --> pdb=" O ASN L 113 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 147 removed outlier: 4.207A pdb=" N GLU L 143 " --> pdb=" O SER L 139 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LYS L 145 " --> pdb=" O ALA L 141 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LEU L 146 " --> pdb=" O GLU L 142 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA L 147 " --> pdb=" O GLU L 143 " (cutoff:3.500A) Processing helix chain 'L' and resid 170 through 176 removed outlier: 3.584A pdb=" N LYS L 174 " --> pdb=" O THR L 170 " (cutoff:3.500A) removed outlier: 5.440A pdb=" N ASN L 175 " --> pdb=" O ASP L 171 " (cutoff:3.500A) Processing helix chain 'L' and resid 177 through 192 Processing helix chain 'L' and resid 193 through 211 removed outlier: 4.021A pdb=" N LYS L 210 " --> pdb=" O ASP L 206 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS L 211 " --> pdb=" O VAL L 207 " (cutoff:3.500A) Processing helix chain 'M' and resid 51 through 56 removed outlier: 3.857A pdb=" N MET M 55 " --> pdb=" O PRO M 51 " (cutoff:3.500A) removed outlier: 4.807A 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: 5.454A pdb=" N VAL M 73 " --> pdb=" O ARG M 69 " (cutoff:3.500A) Processing helix chain 'M' and resid 82 through 90 removed outlier: 3.528A pdb=" N ALA M 87 " --> pdb=" O ASN M 83 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA M 88 " --> pdb=" O ALA M 84 " (cutoff:3.500A) removed outlier: 5.933A 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 removed outlier: 3.657A pdb=" N ARG M 121 " --> pdb=" O LYS M 117 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 14 removed outlier: 3.802A pdb=" N TYR N 6 " --> pdb=" O GLY N 2 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N LYS N 13 " --> pdb=" O GLU N 9 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N LYS N 14 " --> pdb=" O LEU N 10 " (cutoff:3.500A) Processing helix chain 'N' and resid 16 through 34 removed outlier: 4.193A pdb=" N LEU N 33 " --> pdb=" O GLN N 29 " (cutoff:3.500A) removed outlier: 5.183A pdb=" N SER N 34 " --> pdb=" O TYR N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 44 through 52 removed outlier: 3.513A pdb=" N ALA N 48 " --> pdb=" O ARG N 44 " (cutoff:3.500A) Processing helix chain 'N' and resid 83 through 88 removed outlier: 3.941A pdb=" N HIS N 87 " --> pdb=" O LYS N 83 " (cutoff:3.500A) removed outlier: 6.159A 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 Processing helix chain 'N' and resid 139 through 146 removed outlier: 4.108A 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: 3.736A pdb=" N LYS N 170 " --> pdb=" O SER N 166 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N SER N 171 " --> pdb=" O ALA N 167 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ARG N 172 " --> pdb=" O GLY N 168 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLY N 173 " --> pdb=" O ARG N 169 " (cutoff:3.500A) Processing helix chain 'N' and resid 180 through 185 removed outlier: 6.574A pdb=" N ILE N 184 " --> pdb=" O PHE N 180 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLY N 185 " --> pdb=" O HIS N 181 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 180 through 185' Processing helix chain 'N' and resid 187 through 197 removed outlier: 3.753A pdb=" N TRP N 192 " --> pdb=" O ARG N 188 " (cutoff:3.500A) Processing helix chain 'O' and resid 15 through 30 removed outlier: 4.423A pdb=" N ALA O 21 " --> pdb=" O GLY O 17 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE O 22 " --> pdb=" O ARG O 18 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU O 28 " --> pdb=" O ALA O 24 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLY O 30 " --> pdb=" O GLN O 26 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 42 removed outlier: 4.204A pdb=" N ILE O 41 " --> pdb=" O ARG O 37 " (cutoff:3.500A) removed outlier: 5.385A pdb=" N ASN O 42 " --> pdb=" O CYS O 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 37 through 42' Processing helix chain 'O' and resid 46 through 61 removed outlier: 3.511A pdb=" N LYS O 60 " --> pdb=" O ALA O 56 " (cutoff:3.500A) removed outlier: 5.619A pdb=" N ARG O 61 " --> pdb=" O PHE O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 65 through 70 removed outlier: 3.936A 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: 3.654A pdb=" N MET O 87 " --> pdb=" O THR O 83 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU O 88 " --> pdb=" O VAL O 84 " (cutoff:3.500A) Proline residue: O 89 - end of helix Processing helix chain 'O' and resid 92 through 103 removed outlier: 5.261A 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 149 through 190 removed outlier: 3.641A pdb=" N THR O 153 " --> pdb=" O TYR O 149 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N LYS O 187 " --> pdb=" O LYS O 183 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LYS O 188 " --> pdb=" O ASN O 184 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ASP O 190 " --> pdb=" O GLU O 186 " (cutoff:3.500A) Processing helix chain 'O' and resid 191 through 200 removed outlier: 5.185A pdb=" N VAL O 195 " --> pdb=" O ARG O 191 " (cutoff:3.500A) removed outlier: 3.621A 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 removed outlier: 4.137A pdb=" N LYS P 46 " --> pdb=" O ARG P 42 " (cutoff:3.500A) Processing helix chain 'P' and resid 70 through 77 removed outlier: 4.380A pdb=" N LYS P 74 " --> pdb=" O CYS P 70 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N GLN P 75 " --> pdb=" O ALA P 71 " (cutoff:3.500A) removed outlier: 4.913A pdb=" N TRP P 76 " --> pdb=" O GLN P 72 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY P 77 " --> pdb=" O ALA P 73 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 70 through 77' Processing helix chain 'P' and resid 84 through 106 removed outlier: 4.313A pdb=" N LEU P 95 " --> pdb=" O LEU P 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 39 removed outlier: 3.815A pdb=" N ARG Q 26 " --> pdb=" O ASP Q 22 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE Q 34 " --> pdb=" O LYS Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 41 through 54 removed outlier: 3.924A pdb=" N GLN Q 45 " --> pdb=" O SER Q 41 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N MET Q 53 " --> pdb=" O LYS Q 49 " (cutoff:3.500A) removed outlier: 5.596A pdb=" N SER Q 54 " --> pdb=" O ARG Q 50 " (cutoff:3.500A) Processing helix chain 'Q' and resid 62 through 72 removed outlier: 3.983A pdb=" N MET Q 66 " --> pdb=" O SER Q 62 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LEU Q 72 " --> pdb=" O ARG Q 68 " (cutoff:3.500A) Processing helix chain 'Q' and resid 106 through 117 removed outlier: 3.592A pdb=" N GLY Q 117 " --> pdb=" O ILE Q 113 " (cutoff:3.500A) Processing helix chain 'Q' and resid 122 through 130 Processing helix chain 'Q' and resid 146 through 153 removed outlier: 4.413A pdb=" N ARG Q 150 " --> pdb=" O ARG Q 146 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N HIS Q 151 " --> pdb=" O GLU Q 147 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE Q 152 " --> pdb=" O VAL Q 148 " (cutoff:3.500A) removed outlier: 5.742A 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 'Q' and resid 171 through 176 removed outlier: 5.577A pdb=" N GLU Q 175 " --> pdb=" O GLY Q 171 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N ARG Q 176 " --> pdb=" O ARG Q 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 171 through 176' Processing helix chain 'R' and resid 4 through 16 Processing helix chain 'R' and resid 18 through 23 removed outlier: 6.467A pdb=" N VAL R 22 " --> pdb=" O GLY R 18 " (cutoff:3.500A) removed outlier: 5.997A 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: 3.940A pdb=" N ILE R 32 " --> pdb=" O GLU R 28 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ASN R 36 " --> pdb=" O ILE R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 48 removed outlier: 5.977A pdb=" N ARG R 42 " --> pdb=" O ARG R 38 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N LYS R 43 " --> pdb=" O GLN R 39 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N LEU R 44 " --> pdb=" O GLN R 40 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 73 Processing helix chain 'R' and resid 77 through 82 removed outlier: 3.671A pdb=" N ARG R 81 " --> pdb=" O GLY R 77 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N LYS R 82 " --> pdb=" O ILE R 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 77 through 82' Processing helix chain 'R' and resid 84 through 113 Proline residue: R 90 - end of helix removed outlier: 6.728A pdb=" N VAL R 93 " --> pdb=" O MET R 89 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR R 94 " --> pdb=" O PRO R 90 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N ARG R 97 " --> pdb=" O VAL R 93 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ARG R 98 " --> pdb=" O THR R 94 " (cutoff:3.500A) Processing helix chain 'R' and resid 116 through 130 Processing helix chain 'R' and resid 134 through 178 removed outlier: 3.603A pdb=" N GLU R 140 " --> pdb=" O ARG R 136 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N ARG R 173 " --> pdb=" O ALA R 169 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG R 176 " --> pdb=" O ARG R 172 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLN R 178 " --> pdb=" O GLU R 174 " (cutoff:3.500A) Processing helix chain 'S' and resid 36 through 52 Processing helix chain 'S' and resid 101 through 117 removed outlier: 3.941A pdb=" N THR S 107 " --> pdb=" O ALA S 103 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLN S 108 " --> pdb=" O GLY S 104 " (cutoff:3.500A) Processing helix chain 'S' and resid 120 through 125 removed outlier: 3.980A pdb=" N ILE S 124 " --> pdb=" O ARG S 120 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N GLN S 125 " --> pdb=" O ALA S 121 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 120 through 125' Processing helix chain 'S' and resid 139 through 147 removed outlier: 5.056A pdb=" N PHE S 145 " --> pdb=" O ALA S 141 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N HIS S 146 " --> pdb=" O VAL S 142 " (cutoff:3.500A) removed outlier: 4.957A 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: 3.747A pdb=" N PHE T 15 " --> pdb=" O THR T 11 " (cutoff:3.500A) removed outlier: 5.222A 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: 4.588A pdb=" N TYR T 30 " --> pdb=" O PRO T 26 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG T 32 " --> pdb=" O ALA T 28 " (cutoff:3.500A) Processing helix chain 'T' and resid 54 through 59 removed outlier: 3.635A pdb=" N HIS T 58 " --> pdb=" O HIS T 54 " (cutoff:3.500A) removed outlier: 6.232A 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: 4.844A pdb=" N ILE T 96 " --> pdb=" O ARG T 92 " (cutoff:3.500A) removed outlier: 5.421A 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 123 removed outlier: 4.152A pdb=" N ASP T 103 " --> pdb=" O SER T 99 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE T 105 " --> pdb=" O SER T 101 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU T 106 " --> pdb=" O ARG T 102 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N ALA T 119 " --> pdb=" O LYS T 115 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LYS T 120 " --> pdb=" O LYS T 116 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N GLU T 121 " --> pdb=" O LYS T 117 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N LYS T 122 " --> pdb=" O GLU T 118 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLY T 123 " --> pdb=" O ALA T 119 " (cutoff:3.500A) Processing helix chain 'U' and resid 25 through 32 removed outlier: 3.683A pdb=" N VAL U 29 " --> pdb=" O CYS U 25 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ASP U 31 " --> pdb=" O HIS U 27 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY U 32 " --> pdb=" O PRO U 28 " (cutoff:3.500A) Processing helix chain 'U' and resid 35 through 47 removed outlier: 3.870A pdb=" N PHE U 39 " --> pdb=" O ASP U 35 " (cutoff:3.500A) Processing helix chain 'U' and resid 53 through 60 removed outlier: 5.264A pdb=" N GLY U 57 " --> pdb=" O ALA U 53 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N GLY U 58 " --> pdb=" O GLY U 54 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N GLY U 59 " --> pdb=" O ASN U 55 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL U 60 " --> pdb=" O LEU U 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 53 through 60' Processing helix chain 'U' and resid 79 through 95 removed outlier: 5.004A pdb=" N LEU U 83 " --> pdb=" O SER U 79 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS U 84 " --> pdb=" O LYS U 80 " (cutoff:3.500A) Processing helix chain 'V' and resid 69 through 74 removed outlier: 6.430A pdb=" N LYS V 74 " --> pdb=" O PRO V 70 " (cutoff:3.500A) Processing helix chain 'V' and resid 122 through 130 removed outlier: 3.694A pdb=" N LEU V 128 " --> pdb=" O GLU V 124 " (cutoff:3.500A) Proline residue: V 130 - end of helix Processing helix chain 'V' and resid 131 through 137 removed outlier: 5.324A pdb=" N GLY V 137 " --> pdb=" O ALA V 133 " (cutoff:3.500A) Processing helix chain 'W' and resid 33 through 43 Processing helix chain 'W' and resid 45 through 50 removed outlier: 3.774A pdb=" N ILE W 49 " --> pdb=" O ASN W 45 " (cutoff:3.500A) removed outlier: 5.206A 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 removed outlier: 3.605A pdb=" N ARG W 56 " --> pdb=" O THR W 52 " (cutoff:3.500A) Processing helix chain 'X' and resid 72 through 78 removed outlier: 3.911A pdb=" N ILE X 76 " --> pdb=" O ASP X 72 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N ILE X 77 " --> pdb=" O HIS X 73 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N LYS X 78 " --> pdb=" O TYR X 74 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 72 through 78' Processing helix chain 'X' and resid 83 through 92 removed outlier: 3.532A pdb=" N GLU X 91 " --> pdb=" O MET X 87 " (cutoff:3.500A) Processing helix chain 'X' and resid 105 through 118 removed outlier: 3.767A pdb=" N LYS X 115 " --> pdb=" O GLN X 111 " (cutoff:3.500A) Processing helix chain 'X' and resid 145 through 154 removed outlier: 3.709A pdb=" N VAL X 149 " --> pdb=" O ASP X 145 " (cutoff:3.500A) Processing helix chain 'Y' and resid 10 through 21 removed outlier: 5.180A pdb=" N HIS Y 18 " --> pdb=" O ASN Y 14 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ALA Y 21 " --> pdb=" O ARG Y 17 " (cutoff:3.500A) Processing helix chain 'Y' and resid 22 through 31 removed outlier: 4.343A pdb=" N LYS Y 28 " --> pdb=" O HIS Y 24 " (cutoff:3.500A) removed outlier: 3.821A 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: 4.337A pdb=" N VAL Y 104 " --> pdb=" O HIS Y 100 " (cutoff:3.500A) removed outlier: 5.073A 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: 5.523A pdb=" N ILE Z 62 " --> pdb=" O GLY Z 58 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS Z 67 " --> pdb=" O ALA Z 63 " (cutoff:3.500A) Processing helix chain 'Z' and resid 76 through 81 removed outlier: 3.640A pdb=" N LEU Z 80 " --> pdb=" O ASN Z 76 " (cutoff:3.500A) removed outlier: 5.032A 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: 3.517A pdb=" N VAL Z 96 " --> pdb=" O ASP Z 92 " (cutoff:3.500A) removed outlier: 3.776A 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 99 through 104 removed outlier: 4.090A 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 99 through 104' Processing helix chain 'Z' and resid 105 through 125 removed outlier: 3.616A pdb=" N LYS Z 109 " --> pdb=" O ALA Z 105 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LYS Z 117 " --> pdb=" O GLU Z 113 " (cutoff:3.500A) removed outlier: 4.584A pdb=" N THR Z 124 " --> pdb=" O GLU Z 120 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N GLY Z 125 " --> pdb=" O ARG Z 121 " (cutoff:3.500A) Processing helix chain 'Z' and resid 127 through 133 removed outlier: 4.050A pdb=" N PHE Z 131 " --> pdb=" O ASN Z 127 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N GLN Z 132 " --> pdb=" O LYS Z 128 " (cutoff:3.500A) removed outlier: 5.656A 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: 3.965A pdb=" N ARG a 6 " --> pdb=" O PRO a 2 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N LYS a 7 " --> pdb=" O SER a 3 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 2 through 7' Processing helix chain 'a' and resid 41 through 49 Processing helix chain 'a' and resid 64 through 69 removed outlier: 4.519A pdb=" N SER a 68 " --> pdb=" O LYS a 64 " (cutoff:3.500A) Processing helix chain 'a' and resid 74 through 83 removed outlier: 3.584A pdb=" N LEU a 78 " --> pdb=" O ASN a 74 " (cutoff:3.500A) removed outlier: 5.144A pdb=" N TRP a 79 " --> pdb=" O LEU a 75 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N THR a 80 " --> pdb=" O ASP a 76 " (cutoff:3.500A) removed outlier: 4.921A pdb=" N LEU a 81 " --> pdb=" O LYS a 77 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N VAL a 82 " --> pdb=" O LEU a 78 " (cutoff:3.500A) removed outlier: 5.296A 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 93 removed outlier: 4.386A pdb=" N ALA a 90 " --> pdb=" O THR a 86 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N ALA a 91 " --> pdb=" O ARG a 87 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS a 92 " --> pdb=" O ILE a 88 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N ASN a 93 " --> pdb=" O ASN a 89 " (cutoff:3.500A) Processing helix chain 'a' and resid 102 through 107 removed outlier: 4.269A pdb=" N SER a 106 " --> pdb=" O ASP a 102 " (cutoff:3.500A) Processing helix chain 'a' and resid 130 through 141 Processing helix chain 'b' and resid 11 through 20 removed outlier: 4.484A pdb=" N ASN b 19 " --> pdb=" O LYS b 15 " (cutoff:3.500A) Processing helix chain 'b' and resid 36 through 55 removed outlier: 3.935A pdb=" N ARG b 41 " --> pdb=" O PRO b 37 " (cutoff:3.500A) removed outlier: 5.031A pdb=" N LYS b 51 " --> pdb=" O LYS b 47 " (cutoff:3.500A) removed outlier: 5.516A pdb=" N LYS b 52 " --> pdb=" O LYS b 48 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N GLY b 53 " --> pdb=" O HIS b 49 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N LEU b 54 " --> pdb=" O ASN b 50 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N LYS b 55 " --> pdb=" O LYS b 51 " (cutoff:3.500A) Processing helix chain 'b' and resid 56 through 76 removed outlier: 3.643A pdb=" N VAL b 76 " --> pdb=" O ILE b 72 " (cutoff:3.500A) Processing helix chain 'c' and resid 13 through 25 removed outlier: 4.020A pdb=" N LEU c 20 " --> pdb=" O SER c 16 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N VAL c 21 " --> pdb=" O ARG c 17 " (cutoff:3.500A) Processing helix chain 'c' and resid 30 through 41 removed outlier: 3.573A pdb=" N LYS c 36 " --> pdb=" O LYS c 32 " (cutoff:3.500A) Processing helix chain 'c' and resid 53 through 68 Processing helix chain 'c' and resid 77 through 86 removed outlier: 4.109A pdb=" N GLY c 86 " --> pdb=" O GLY c 82 " (cutoff:3.500A) Processing helix chain 'd' and resid 28 through 34 removed outlier: 4.125A pdb=" N ARG d 32 " --> pdb=" O ASN d 28 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N HIS d 34 " --> pdb=" O HIS d 30 " (cutoff:3.500A) Processing helix chain 'd' and resid 40 through 58 removed outlier: 3.699A pdb=" N GLY d 58 " --> pdb=" O MET d 54 " (cutoff:3.500A) Processing helix chain 'd' and resid 65 through 74 Processing helix chain 'e' and resid 24 through 29 removed outlier: 3.642A pdb=" N TYR e 28 " --> pdb=" O GLN e 24 " (cutoff:3.500A) removed outlier: 5.398A 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 removed outlier: 4.458A pdb=" N ARG e 48 " --> pdb=" O ARG e 44 " (cutoff:3.500A) Processing helix chain 'e' and resid 81 through 90 removed outlier: 3.647A pdb=" N LEU e 85 " --> pdb=" O ASN e 81 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLU e 86 " --> pdb=" O VAL e 82 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL e 87 " --> pdb=" O LYS e 83 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU e 88 " --> pdb=" O GLU e 84 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LEU e 89 " --> pdb=" O LEU e 85 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N MET e 90 " --> pdb=" O GLU e 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 81 through 90' Processing helix chain 'e' and resid 104 through 119 removed outlier: 3.777A pdb=" N LYS e 109 " --> pdb=" O SER e 105 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N ALA e 110 " --> pdb=" O LYS e 106 " (cutoff:3.500A) Processing helix chain 'f' and resid 35 through 40 removed outlier: 3.698A pdb=" N THR f 39 " --> pdb=" O ALA f 35 " (cutoff:3.500A) removed outlier: 6.203A 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 'f' and resid 93 through 98 removed outlier: 6.606A pdb=" N ILE f 97 " --> pdb=" O PRO f 93 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N GLY f 98 " --> pdb=" O ALA f 94 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 93 through 98' Processing helix chain 'g' and resid 60 through 67 removed outlier: 4.263A pdb=" N LEU g 64 " --> pdb=" O ARG g 60 " (cutoff:3.500A) removed outlier: 4.441A pdb=" N MET g 65 " --> pdb=" O PRO g 61 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N ARG g 66 " --> pdb=" O LYS g 62 " (cutoff:3.500A) Processing helix chain 'g' and resid 68 through 73 removed outlier: 3.757A pdb=" N LYS g 72 " --> pdb=" O SER g 68 " (cutoff:3.500A) Processing helix chain 'g' and resid 83 through 115 removed outlier: 4.428A pdb=" N VAL g 87 " --> pdb=" O CYS g 83 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LYS g 92 " --> pdb=" O ARG g 88 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU g 96 " --> pdb=" O LYS g 92 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU g 98 " --> pdb=" O ALA g 94 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 13 removed outlier: 3.872A pdb=" N LEU h 9 " --> pdb=" O LYS h 5 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG h 10 " --> pdb=" O ALA h 6 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N GLY h 11 " --> pdb=" O ARG h 7 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N LYS h 12 " --> pdb=" O ASP h 8 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N LYS h 13 " --> pdb=" O LEU h 9 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 5 through 13' Processing helix chain 'h' and resid 14 through 38 Processing helix chain 'h' and resid 40 through 74 removed outlier: 3.759A pdb=" N SER h 45 " --> pdb=" O ALA h 41 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N LYS h 46 " --> pdb=" O SER h 42 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE h 47 " --> pdb=" O LYS h 43 " (cutoff:3.500A) removed outlier: 5.961A pdb=" N ARG h 48 " --> pdb=" O LEU h 44 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL h 49 " --> pdb=" O SER h 45 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N LYS h 74 " --> pdb=" O ARG h 70 " (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: 3.611A pdb=" N ARG h 93 " --> pdb=" O ARG h 89 " (cutoff:3.500A) Processing helix chain 'h' and resid 96 through 102 removed outlier: 6.169A pdb=" N GLU h 100 " --> pdb=" O ASN h 96 " (cutoff:3.500A) removed outlier: 4.848A pdb=" N ASN h 101 " --> pdb=" O LYS h 97 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU h 102 " --> pdb=" O HIS h 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 96 through 102' Processing helix chain 'h' and resid 104 through 114 Processing helix chain 'i' and resid 25 through 30 removed outlier: 4.471A pdb=" N ARG i 29 " --> pdb=" O ARG i 25 " (cutoff:3.500A) removed outlier: 5.173A 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: 3.728A pdb=" N PHE i 39 " --> pdb=" O LYS i 35 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ARG i 45 " --> pdb=" O ARG i 41 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N GLU i 46 " --> pdb=" O ASP i 42 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL i 47 " --> pdb=" O MET i 43 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLY i 49 " --> pdb=" O ARG i 45 " (cutoff:3.500A) Processing helix chain 'i' and resid 51 through 64 removed outlier: 3.814A pdb=" N LEU i 60 " --> pdb=" O ARG i 56 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N SER i 64 " --> pdb=" O LEU i 60 " (cutoff:3.500A) Processing helix chain 'i' and resid 65 through 78 removed outlier: 3.552A pdb=" N ALA i 69 " --> pdb=" O LYS i 65 " (cutoff:3.500A) Processing helix chain 'i' and resid 79 through 103 removed outlier: 3.721A pdb=" N ALA i 83 " --> pdb=" O THR i 79 " (cutoff:3.500A) removed outlier: 4.517A pdb=" N LYS i 103 " --> pdb=" O LYS i 99 " (cutoff:3.500A) Processing helix chain 'j' and resid 4 through 11 removed outlier: 3.666A pdb=" N GLY j 9 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N LYS j 10 " --> pdb=" O SER j 6 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N ARG j 11 " --> pdb=" O SER j 7 " (cutoff:3.500A) Processing helix chain 'j' and resid 50 through 58 removed outlier: 4.565A pdb=" N ASN j 57 " --> pdb=" O ALA j 53 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N THR j 58 " --> pdb=" O LYS j 54 " (cutoff:3.500A) Processing helix chain 'j' and resid 65 through 77 removed outlier: 4.578A pdb=" N ILE j 69 " --> pdb=" O ARG j 65 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N ARG j 72 " --> pdb=" O LYS j 68 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N HIS j 76 " --> pdb=" O ARG j 72 " (cutoff:3.500A) Processing helix chain 'k' and resid 7 through 17 removed outlier: 3.736A pdb=" N ARG k 17 " --> pdb=" O LEU k 13 " (cutoff:3.500A) Processing helix chain 'k' and resid 49 through 60 removed outlier: 4.196A pdb=" N ALA k 53 " --> pdb=" O ASP k 49 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N GLN k 58 " --> pdb=" O GLU k 54 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N SER k 59 " --> pdb=" O LYS k 55 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU k 60 " --> pdb=" O LEU k 56 " (cutoff:3.500A) Processing helix chain 'l' and resid 6 through 21 removed outlier: 3.616A pdb=" N ASN l 20 " --> pdb=" O LYS l 16 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ARG l 21 " --> pdb=" O GLN l 17 " (cutoff:3.500A) Processing helix chain 'l' and resid 24 through 30 removed outlier: 4.177A pdb=" N ARG l 28 " --> pdb=" O PRO l 24 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N MET l 29 " --> pdb=" O GLN l 25 " (cutoff:3.500A) removed outlier: 4.046A 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: 3.524A pdb=" N TYR m 89 " --> pdb=" O LEU m 85 " (cutoff:3.500A) Processing helix chain 'o' and resid 35 through 46 Processing helix chain 'p' and resid 19 through 35 removed outlier: 3.549A pdb=" N LYS p 28 " --> pdb=" O LYS p 24 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE p 29 " --> pdb=" O MET p 25 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N HIS p 34 " --> pdb=" O GLU p 30 " (cutoff:3.500A) Processing helix chain 'p' and resid 73 through 92 removed outlier: 3.916A pdb=" N VAL p 77 " --> pdb=" O THR p 73 " (cutoff:3.500A) Processing helix chain 'r' and resid 2 through 11 Processing helix chain 'r' and resid 85 through 101 removed outlier: 4.957A pdb=" N THR r 89 " --> pdb=" O ASN r 85 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS r 101 " --> pdb=" O ILE r 97 " (cutoff:3.500A) Processing helix chain 'r' and resid 103 through 122 removed outlier: 3.645A pdb=" N ARG r 107 " --> pdb=" O ARG r 103 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N MET r 108 " --> pdb=" O PRO r 104 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ALA r 109 " --> pdb=" O ASP r 105 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LYS r 122 " --> pdb=" O LEU r 118 " (cutoff:3.500A) Processing helix chain 's' and resid 6 through 25 removed outlier: 4.630A pdb=" N LYS s 10 " --> pdb=" O ARG s 6 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU s 15 " --> pdb=" O SER s 11 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS s 16 " --> pdb=" O ASN s 12 " (cutoff:3.500A) Proline residue: s 25 - end of helix Processing helix chain 's' and resid 36 through 48 Processing helix chain 's' and resid 57 through 71 removed outlier: 4.505A pdb=" N MET s 61 " --> pdb=" O LYS s 57 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ARG s 62 " --> pdb=" O ASN s 58 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LYS s 63 " --> pdb=" O THR s 59 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N ALA s 64 " --> pdb=" O MET s 60 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ILE s 65 " --> pdb=" O MET s 61 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N GLU s 70 " --> pdb=" O ARG s 66 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ASN s 71 " --> pdb=" O GLY s 67 " (cutoff:3.500A) Processing helix chain 's' and resid 73 through 83 removed outlier: 6.576A pdb=" N LYS s 77 " --> pdb=" O PRO s 73 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N LEU s 78 " --> pdb=" O ALA s 74 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N LEU s 79 " --> pdb=" O LEU s 75 " (cutoff:3.500A) Proline residue: s 80 - end of helix removed outlier: 5.222A pdb=" N ARG s 83 " --> pdb=" O LEU s 79 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 73 through 83' Processing helix chain 's' and resid 94 through 106 removed outlier: 4.838A pdb=" N ILE s 98 " --> pdb=" O ASP s 94 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N LYS s 106 " --> pdb=" O LEU s 102 " (cutoff:3.500A) Processing helix chain 's' and resid 134 through 142 removed outlier: 4.736A pdb=" N PHE s 138 " --> pdb=" O LYS s 134 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LEU s 141 " --> pdb=" O PHE s 137 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N GLY s 142 " --> pdb=" O PHE s 138 " (cutoff:3.500A) Processing helix chain 's' and resid 168 through 179 Processing helix chain 't' and resid 30 through 37 Proline residue: t 34 - end of helix removed outlier: 4.087A pdb=" N LEU t 37 " --> pdb=" O GLY t 33 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 30 through 37' Processing helix chain 't' and resid 39 through 52 removed outlier: 5.999A pdb=" N GLY t 43 " --> pdb=" O PRO t 39 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ASP t 44 " --> pdb=" O LYS t 40 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N THR t 50 " --> pdb=" O ILE t 46 " (cutoff:3.500A) Processing helix chain 't' and resid 77 through 86 Processing helix chain 't' and resid 106 through 118 removed outlier: 4.816A pdb=" N VAL t 110 " --> pdb=" O PHE t 106 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ASN t 111 " --> pdb=" O ASP t 107 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ILE t 112 " --> pdb=" O GLU t 108 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ALA t 113 " --> pdb=" O ILE t 109 " (cutoff:3.500A) removed outlier: 5.763A pdb=" N HIS t 118 " --> pdb=" O ARG t 114 " (cutoff:3.500A) Processing helix chain 't' and resid 125 through 137 removed outlier: 3.593A pdb=" N ILE t 129 " --> pdb=" O LEU t 125 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N GLU t 131 " --> pdb=" O GLY t 127 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR t 135 " --> pdb=" O GLU t 131 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N GLN t 137 " --> pdb=" O LEU t 133 " (cutoff:3.500A) Processing helix chain 't' and resid 150 through 155 removed outlier: 4.581A pdb=" N ASP t 154 " --> pdb=" O ASP t 150 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ILE t 155 " --> pdb=" O ILE t 151 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 150 through 155' Processing helix chain 't' and resid 93 through 98 removed outlier: 6.306A pdb=" N LYS t 96 " --> pdb=" O LYS t 93 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N ASN t 97 " --> pdb=" O LYS t 94 " (cutoff:3.500A) removed outlier: 5.172A pdb=" N ILE t 98 " --> pdb=" O GLN t 95 " (cutoff:3.500A) No H-bonds generated for 'chain 't' and resid 93 through 98' Processing helix chain 'u' and resid 41 through 56 removed outlier: 5.076A pdb=" N ALA u 53 " --> pdb=" O ALA u 49 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N SER u 54 " --> pdb=" O GLU u 50 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N LEU u 55 " --> pdb=" O LEU u 51 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N LEU u 56 " --> pdb=" O ASN u 52 " (cutoff:3.500A) Processing helix chain 'u' and resid 106 through 116 removed outlier: 6.305A pdb=" N MET u 110 " --> pdb=" O SER u 106 " (cutoff:3.500A) Processing helix chain 'v' and resid 311 through 355 removed outlier: 4.649A pdb=" N LEU v 323 " --> pdb=" O ALA v 319 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N ASP v 324 " --> pdb=" O LEU v 320 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N ARG v 327 " --> pdb=" O LEU v 323 " (cutoff:3.500A) Processing helix chain 'v' and resid 356 through 372 removed outlier: 3.677A pdb=" N GLN v 372 " --> pdb=" O ALA v 368 " (cutoff:3.500A) Processing helix chain 'v' and resid 374 through 386 Processing helix chain 'v' and resid 394 through 400 removed outlier: 4.723A pdb=" N GLU v 398 " --> pdb=" O SER v 394 " (cutoff:3.500A) Processing helix chain 'v' and resid 468 through 501 removed outlier: 3.567A pdb=" N TYR v 476 " --> pdb=" O ASN v 472 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N HIS v 479 " --> pdb=" O LYS v 475 " (cutoff:3.500A) Processing helix chain 'w' and resid 17 through 27 Processing helix chain 'z' and resid 1561 through 1575 Processing helix chain 'z' and resid 1576 through 1586 removed outlier: 3.956A pdb=" N LEU z1581 " --> pdb=" O ALA z1577 " (cutoff:3.500A) Processing helix chain 'z' and resid 1587 through 1601 removed outlier: 3.594A pdb=" N PHE z1591 " --> pdb=" O GLU z1587 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N ASN z1592 " --> pdb=" O LYS z1588 " (cutoff:3.500A) Processing helix chain 'z' and resid 1602 through 1615 removed outlier: 4.773A pdb=" N LEU z1606 " --> pdb=" O VAL z1602 " (cutoff:3.500A) Processing helix chain 'z' and resid 1676 through 1688 Processing helix chain 'z' and resid 1694 through 1709 Processing helix chain '0' and resid 1742 through 1753 removed outlier: 6.639A pdb=" N LEU 01746 " --> pdb=" O HIS 01742 " (cutoff:3.500A) Processing sheet with id= 1, first strand: chain 'A' and resid 47 through 50 removed outlier: 3.539A pdb=" N ASP A 47 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N LEU A 58 " --> pdb=" O ILE A 49 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LYS A 60 " --> pdb=" O LYS A 46 " (cutoff:3.500A) removed outlier: 4.418A pdb=" N GLN A 86 " --> pdb=" O VAL A 45 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'A' and resid 135 through 139 removed outlier: 6.815A pdb=" N ARG A 147 " --> pdb=" O ILE A 137 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N HIS A 139 " --> pdb=" O LYS A 145 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LYS A 145 " --> pdb=" O HIS A 139 " (cutoff:3.500A) Processing sheet with id= 3, first strand: chain 'A' and resid 59 through 64 removed outlier: 3.565A pdb=" N GLU A 74 " --> pdb=" O VAL A 61 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ARG A 72 " --> pdb=" O PHE A 63 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'B' and resid 40 through 44 removed outlier: 4.874A pdb=" N GLY B 188 " --> pdb=" O PRO B 40 " (cutoff:3.500A) removed outlier: 4.931A pdb=" N HIS B 42 " --> pdb=" O ASN B 186 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N GLN B 184 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 5.108A pdb=" N HIS B 179 " --> pdb=" O THR B 166 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N ILE B 163 " --> pdb=" O VAL B 87 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N GLN B 203 " --> pdb=" O VAL B 86 " (cutoff:3.500A) Processing sheet with id= 5, first strand: chain 'B' and resid 53 through 59 removed outlier: 6.752A pdb=" N ILE B 78 " --> pdb=" O ALA B 51 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N ARG B 343 " --> pdb=" O LYS B 50 " (cutoff:3.500A) removed outlier: 7.458A pdb=" N VAL B 344 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N VAL B 222 " --> pdb=" O VAL B 344 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 98 through 102 removed outlier: 3.578A pdb=" N THR B 95 " --> pdb=" O GLY B 98 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N GLY B 91 " --> pdb=" O PHE B 102 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS B 103 " --> pdb=" O GLY B 91 " (cutoff:3.500A) Processing sheet with id= 7, first strand: chain 'B' and resid 286 through 290 removed outlier: 4.880A pdb=" N GLY B 290 " --> pdb=" O ASN B 328 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ASN B 328 " --> pdb=" O GLY B 290 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'B' and resid 76 through 80 No H-bonds generated for sheet with id= 8 Processing sheet with id= 9, first strand: chain 'B' and resid 88 through 93 Processing sheet with id= 10, first strand: chain 'B' and resid 215 through 218 removed outlier: 4.251A pdb=" N GLU B 215 " --> pdb=" O ILE B 284 " (cutoff:3.500A) Processing sheet with id= 11, first strand: chain 'C' and resid 7 through 10 removed outlier: 5.204A pdb=" N LYS C 20 " --> pdb=" O VAL C 10 " (cutoff:3.500A) Processing sheet with id= 12, first strand: chain 'C' and resid 226 through 232 removed outlier: 5.771A pdb=" N PHE C 249 " --> pdb=" O GLY C 206 " (cutoff:3.500A) Processing sheet with id= 13, first strand: chain 'D' and resid 60 through 66 Processing sheet with id= 14, first strand: chain 'E' and resid 143 through 149 removed outlier: 4.061A pdb=" N THR E 144 " --> pdb=" O PHE E 160 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS E 156 " --> pdb=" O ILE E 148 " (cutoff:3.500A) Processing sheet with id= 15, first strand: chain 'F' and resid 141 through 146 removed outlier: 7.803A pdb=" N TYR F 141 " --> pdb=" O ILE F 97 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLY F 145 " --> pdb=" O PHE F 93 " (cutoff:3.500A) removed outlier: 5.557A pdb=" N LYS F 90 " --> pdb=" O LEU F 127 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N ASN F 121 " --> pdb=" O ARG F 96 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N PHE F 120 " --> pdb=" O LEU F 215 " (cutoff:3.500A) Processing sheet with id= 16, first strand: chain 'F' and resid 160 through 163 removed outlier: 6.914A pdb=" N GLY F 160 " --> pdb=" O LEU F 171 " (cutoff:3.500A) Processing sheet with id= 17, first strand: chain 'G' and resid 179 through 185 removed outlier: 3.749A 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: 6.023A 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: 3.520A pdb=" N ASN H 102 " --> pdb=" O ARG H 115 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU H 111 " --> pdb=" O GLN H 106 " (cutoff:3.500A) removed outlier: 6.226A 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: 3.689A pdb=" N GLU H 147 " --> pdb=" O ALA H 133 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASP H 142 " --> pdb=" O SER H 94 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N SER H 94 " --> pdb=" O ASP H 142 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N LYS H 91 " --> pdb=" O SER H 182 " (cutoff:3.500A) Processing sheet with id= 22, first strand: chain 'H' and resid 88 through 91 Processing sheet with id= 23, first strand: chain 'I' and resid 34 through 37 removed outlier: 6.061A pdb=" N PHE I 34 " --> pdb=" O VAL I 89 " (cutoff:3.500A) removed outlier: 5.220A pdb=" N ILE I 135 " --> pdb=" O ARG I 90 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N MET I 136 " --> pdb=" O MET I 52 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N THR I 140 " --> pdb=" O LEU I 48 " (cutoff:3.500A) removed outlier: 5.888A pdb=" N GLY I 49 " --> pdb=" O SER I 168 " (cutoff:3.500A) Processing sheet with id= 24, first strand: chain 'I' and resid 95 through 98 removed outlier: 3.520A pdb=" N GLY I 124 " --> pdb=" O ILE I 97 " (cutoff:3.500A) Processing sheet with id= 25, first strand: chain 'I' and resid 189 through 192 removed outlier: 5.183A pdb=" N CYS I 189 " --> pdb=" O VAL I 200 " (cutoff:3.500A) Processing sheet with id= 26, first strand: chain 'J' and resid 48 through 52 removed outlier: 3.730A pdb=" N LEU J 22 " --> pdb=" O CYS J 72 " (cutoff:3.500A) removed outlier: 5.547A pdb=" N CYS J 25 " --> pdb=" O GLY J 127 " (cutoff:3.500A) removed outlier: 8.558A pdb=" N GLY J 127 " --> pdb=" O CYS J 25 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N PHE J 107 " --> pdb=" O PHE J 130 " (cutoff:3.500A) Processing sheet with id= 27, first strand: chain 'J' and resid 92 through 95 removed outlier: 6.738A pdb=" N LEU J 94 " --> pdb=" O ILE J 173 " (cutoff:3.500A) Processing sheet with id= 28, first strand: chain 'L' and resid 57 through 60 Processing sheet with id= 29, first strand: chain 'M' and resid 10 through 15 removed outlier: 4.342A pdb=" N ARG M 11 " --> pdb=" O ILE M 27 " (cutoff:3.500A) removed outlier: 4.273A 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) Processing sheet with id= 30, first strand: chain 'N' and resid 35 through 39 removed outlier: 7.004A pdb=" N ALA N 35 " --> pdb=" O ARG N 65 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ARG N 65 " --> pdb=" O ALA N 35 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS N 37 " --> pdb=" O ARG N 63 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N ILE N 61 " --> pdb=" O ALA N 39 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N ILE N 133 " --> pdb=" O LEU N 116 " (cutoff:3.500A) Processing sheet with id= 31, first strand: chain 'N' and resid 117 through 121 removed outlier: 3.722A pdb=" N ASN N 117 " --> pdb=" O ILE N 133 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N PHE N 129 " --> pdb=" O VAL N 121 " (cutoff:3.500A) Processing sheet with id= 32, first strand: chain 'O' and resid 6 through 10 removed outlier: 3.611A pdb=" N VAL O 34 " --> pdb=" O LEU O 7 " (cutoff:3.500A) Processing sheet with id= 33, first strand: chain 'P' and resid 14 through 20 removed outlier: 3.537A pdb=" N CYS P 15 " --> pdb=" O LEU P 150 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS P 116 " --> pdb=" O ILE P 149 " (cutoff:3.500A) Processing sheet with id= 34, first strand: chain 'P' and resid 57 through 60 removed outlier: 5.508A pdb=" N GLN P 80 " --> pdb=" O PHE P 60 " (cutoff:3.500A) Processing sheet with id= 35, first strand: chain 'P' and resid 124 through 131 removed outlier: 4.294A pdb=" N MET P 125 " --> pdb=" O SER P 141 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ARG P 127 " --> pdb=" O TYR P 139 " (cutoff:3.500A) Processing sheet with id= 36, first strand: chain 'Q' and resid 78 through 82 Processing sheet with id= 37, first strand: chain 'S' and resid 27 through 33 removed outlier: 6.815A pdb=" N VAL S 13 " --> pdb=" O VAL S 62 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N SER S 58 " --> pdb=" O LEU S 17 " (cutoff:3.500A) Processing sheet with id= 38, first strand: chain 'S' and resid 91 through 99 removed outlier: 3.834A pdb=" N MET S 93 " --> pdb=" O LEU S 82 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ASN S 77 " --> pdb=" O ILE S 132 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N LYS S 128 " --> pdb=" O TRP S 81 " (cutoff:3.500A) Processing sheet with id= 39, first strand: chain 'S' and resid 9 through 13 removed outlier: 4.208A pdb=" N GLU S 9 " --> pdb=" O VAL S 67 " (cutoff:3.500A) Processing sheet with id= 40, first strand: chain 'T' and resid 39 through 42 removed outlier: 4.559A pdb=" N LYS T 60 " --> pdb=" O ILE T 42 " (cutoff:3.500A) Processing sheet with id= 41, first strand: chain 'T' and resid 72 through 79 removed outlier: 3.882A pdb=" N ILE T 89 " --> pdb=" O ILE T 74 " (cutoff:3.500A) Processing sheet with id= 42, first strand: chain 'U' and resid 61 through 65 removed outlier: 4.072A pdb=" N THR U 71 " --> pdb=" O GLU U 64 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N ILE U 70 " --> pdb=" O LEU U 23 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LEU U 23 " --> pdb=" O ILE U 70 " (cutoff:3.500A) removed outlier: 5.511A pdb=" N GLU U 108 " --> pdb=" O LYS U 20 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP U 24 " --> pdb=" O TYR U 110 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N LEU U 112 " --> pdb=" O ASP U 24 " (cutoff:3.500A) Processing sheet with id= 43, first strand: chain 'V' and resid 35 through 40 removed outlier: 6.187A pdb=" N LYS V 35 " --> pdb=" O CYS V 28 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA V 24 " --> pdb=" O ILE V 39 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N ASN V 101 " --> pdb=" O VAL V 25 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE V 105 " --> pdb=" O ALA V 29 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N HIS V 77 " --> pdb=" O ALA V 63 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ASP V 59 " --> pdb=" O VAL V 81 " (cutoff:3.500A) Processing sheet with id= 44, first strand: chain 'V' and resid 82 through 85 removed outlier: 3.557A pdb=" N ARG V 83 " --> pdb=" O ALA V 102 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N ARG V 85 " --> pdb=" O ASP V 100 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N ASP V 100 " --> pdb=" O ARG V 85 " (cutoff:3.500A) Processing sheet with id= 45, first strand: chain 'W' and resid 3 through 6 removed outlier: 4.521A pdb=" N TYR W 11 " --> pdb=" O CYS W 6 " (cutoff:3.500A) Processing sheet with id= 46, first strand: chain 'W' and resid 18 through 22 Processing sheet with id= 47, first strand: chain 'X' and resid 94 through 100 removed outlier: 6.349A pdb=" N ASN X 94 " --> pdb=" O LEU X 140 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LYS X 134 " --> pdb=" O VAL X 100 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N TYR X 137 " --> pdb=" O ASN X 125 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS X 123 " --> pdb=" O ARG X 139 " (cutoff:3.500A) Processing sheet with id= 48, first strand: chain 'Y' and resid 53 through 56 removed outlier: 5.127A pdb=" N ASP Y 53 " --> pdb=" O VAL Y 70 " (cutoff:3.500A) Processing sheet with id= 49, first strand: chain 'Y' and resid 71 through 75 removed outlier: 3.648A pdb=" N GLN Y 72 " --> pdb=" O TYR Y 81 " (cutoff:3.500A) Processing sheet with id= 50, first strand: chain 'Y' and resid 85 through 89 removed outlier: 6.250A pdb=" N VAL Y 85 " --> pdb=" O VAL Y 97 " (cutoff:3.500A) removed outlier: 5.226A pdb=" N THR Y 93 " --> pdb=" O LYS Y 89 " (cutoff:3.500A) Processing sheet with id= 51, first strand: chain 'Z' and resid 10 through 13 removed outlier: 4.012A pdb=" N ARG Z 21 " --> pdb=" O VAL Z 13 " (cutoff:3.500A) Processing sheet with id= 52, first strand: chain 'Z' and resid 27 through 30 removed outlier: 5.843A pdb=" N HIS Z 40 " --> pdb=" O ILE Z 29 " (cutoff:3.500A) Processing sheet with id= 53, first strand: chain 'a' and resid 98 through 101 removed outlier: 3.522A pdb=" N ALA a 126 " --> pdb=" O VAL a 145 " (cutoff:3.500A) Processing sheet with id= 54, first strand: chain 'c' and resid 26 through 29 removed outlier: 6.519A pdb=" N LYS c 26 " --> pdb=" O ILE c 97 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLY c 70 " --> pdb=" O LYS c 44 " (cutoff:3.500A) Processing sheet with id= 55, first strand: chain 'd' and resid 20 through 27 removed outlier: 3.714A pdb=" N VAL d 21 " --> pdb=" O ARG d 90 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG d 90 " --> pdb=" O VAL d 21 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG d 23 " --> pdb=" O LEU d 88 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N ARG d 85 " --> pdb=" O VAL d 109 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ARG d 87 " --> pdb=" O THR d 107 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N TYR d 103 " --> pdb=" O LYS d 91 " (cutoff:3.500A) removed outlier: 4.973A pdb=" N ASP d 61 " --> pdb=" O LEU d 102 " (cutoff:3.500A) Processing sheet with id= 56, first strand: chain 'e' and resid 74 through 80 Processing sheet with id= 57, first strand: chain 'f' and resid 8 through 12 removed outlier: 6.208A pdb=" N LYS f 8 " --> pdb=" O GLU f 31 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N LEU f 27 " --> pdb=" O ALA f 12 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL f 84 " --> pdb=" O LEU f 28 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N ARG f 85 " --> pdb=" O THR f 75 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS f 73 " --> pdb=" O LYS f 87 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N LYS f 45 " --> pdb=" O VAL f 74 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ARG f 46 " --> pdb=" O MET f 104 " (cutoff:3.500A) Processing sheet with id= 58, first strand: chain 'f' and resid 6 through 11 removed outlier: 4.269A pdb=" N HIS f 99 " --> pdb=" O PHE f 11 " (cutoff:3.500A) Processing sheet with id= 59, first strand: chain 'g' and resid 20 through 24 Processing sheet with id= 60, first strand: chain 'j' and resid 26 through 29 removed outlier: 5.397A pdb=" N ALA j 26 " --> pdb=" O GLY j 35 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N GLY j 35 " --> pdb=" O ALA j 26 " (cutoff:3.500A) Processing sheet with id= 61, first strand: chain 'k' and resid 2 through 5 removed outlier: 4.517A pdb=" N VAL k 46 " --> pdb=" O ILE k 5 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ILE k 47 " --> pdb=" O VAL k 32 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N VAL k 32 " --> pdb=" O ILE k 47 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N LYS k 67 " --> pdb=" O VAL k 23 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N LYS k 27 " --> pdb=" O LEU k 69 " (cutoff:3.500A) Processing sheet with id= 62, first strand: chain 'm' and resid 100 through 104 removed outlier: 4.180A pdb=" N ALA m 101 " --> pdb=" O CYS m 96 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N LYS m 93 " --> pdb=" O LYS m 124 " (cutoff:3.500A) removed outlier: 8.092A pdb=" N ASN m 120 " --> pdb=" O ARG m 97 " (cutoff:3.500A) Processing sheet with id= 63, first strand: chain 'o' and resid 7 through 10 removed outlier: 3.733A pdb=" N THR o 10 " --> pdb=" O GLN o 19 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N THR o 24 " --> pdb=" O ARG o 69 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LYS o 64 " --> pdb=" O ARG o 87 " (cutoff:3.500A) removed outlier: 4.927A pdb=" N ARG o 87 " --> pdb=" O LYS o 64 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N ILE o 66 " --> pdb=" O ILE o 85 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N CYS o 72 " --> pdb=" O SER o 79 " (cutoff:3.500A) removed outlier: 4.996A pdb=" N SER o 79 " --> pdb=" O CYS o 72 " (cutoff:3.500A) Processing sheet with id= 64, first strand: chain 'p' and resid 47 through 50 removed outlier: 3.834A pdb=" N LYS p 48 " --> pdb=" O HIS p 56 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N ILE p 54 " --> pdb=" O ARG p 50 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N GLY p 53 " --> pdb=" O GLY p 66 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS p 62 " --> pdb=" O CYS p 57 " (cutoff:3.500A) Processing sheet with id= 65, first strand: chain 'r' and resid 16 through 19 removed outlier: 7.541A pdb=" N PHE r 16 " --> pdb=" O THR r 27 " (cutoff:3.500A) Processing sheet with id= 66, first strand: chain 'r' and resid 48 through 53 removed outlier: 5.268A pdb=" N THR r 48 " --> pdb=" O LYS r 65 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS r 65 " --> pdb=" O THR r 48 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLU r 52 " --> pdb=" O VAL r 61 " (cutoff:3.500A) removed outlier: 8.729A pdb=" N SER r 76 " --> pdb=" O ARG r 66 " (cutoff:3.500A) Processing sheet with id= 67, first strand: chain 's' and resid 51 through 55 removed outlier: 4.226A pdb=" N LYS s 26 " --> pdb=" O THR s 91 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N GLN s 191 " --> pdb=" O ILE s 29 " (cutoff:3.500A) Processing sheet with id= 68, first strand: chain 's' and resid 144 through 147 removed outlier: 7.267A pdb=" N THR s 144 " --> pdb=" O LEU s 155 " (cutoff:3.500A) Processing sheet with id= 69, first strand: chain 's' and resid 156 through 159 removed outlier: 7.126A pdb=" N CYS s 119 " --> pdb=" O THR s 163 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N THR s 163 " --> pdb=" O CYS s 119 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE s 161 " --> pdb=" O VAL s 121 " (cutoff:3.500A) Processing sheet with id= 70, first strand: chain 't' and resid 11 through 18 removed outlier: 4.830A pdb=" N THR t 59 " --> pdb=" O THR t 18 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N VAL t 60 " --> pdb=" O PRO t 75 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N LEU t 62 " --> pdb=" O VAL t 73 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N VAL t 73 " --> pdb=" O LEU t 62 " (cutoff:3.500A) Processing sheet with id= 71, first strand: chain 'u' and resid 62 through 66 removed outlier: 3.696A pdb=" N ASN u 62 " --> pdb=" O ARG u 74 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N VAL u 66 " --> pdb=" O THR u 70 " (cutoff:3.500A) removed outlier: 5.718A pdb=" N THR u 70 " --> pdb=" O VAL u 66 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N TYR u 71 " --> pdb=" O LEU u 86 " (cutoff:3.500A) Processing sheet with id= 72, first strand: chain 'u' and resid 123 through 126 removed outlier: 5.103A pdb=" N SER u 123 " --> pdb=" O GLN u 136 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLN u 136 " --> pdb=" O SER u 123 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N ARG u 131 " --> pdb=" O LEU u 150 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N PHE u 135 " --> pdb=" O LEU u 146 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU u 146 " --> pdb=" O PHE u 135 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N TYR u 144 " --> pdb=" O PHE u 137 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N HIS u 145 " --> pdb=" O THR u 159 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N THR u 159 " --> pdb=" O HIS u 145 " (cutoff:3.500A) Processing sheet with id= 73, first strand: chain 'v' and resid 408 through 411 removed outlier: 4.537A pdb=" N VAL v 461 " --> pdb=" O ARG v 411 " (cutoff:3.500A) Processing sheet with id= 74, first strand: chain 'z' and resid 1623 through 1629 removed outlier: 5.244A pdb=" N GLY z1623 " --> pdb=" O THR z1640 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N THR z1640 " --> pdb=" O GLY z1623 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N THR z1638 " --> pdb=" O THR z1625 " (cutoff:3.500A) removed outlier: 6.036A pdb=" N GLU z1634 " --> pdb=" O ARG z1629 " (cutoff:3.500A) removed outlier: 5.580A pdb=" N ARG z1633 " --> pdb=" O LEU z1652 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N LEU z1648 " --> pdb=" O ALA z1637 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N ILE z1649 " --> pdb=" O GLU z1664 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ILE z1662 " --> pdb=" O GLN z1651 " (cutoff:3.500A) 2161 hydrogen bonds defined for protein. 6399 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 3211 hydrogen bonds 5606 hydrogen bond angles 0 basepair planarities 1220 basepair parallelities 1869 stacking parallelities Total time for adding SS restraints: 279.76 Time building geometry restraints manager: 69.77 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.50: 107672 1.50 - 1.81: 49664 1.81 - 2.13: 74 2.13 - 2.44: 1 2.44 - 2.75: 3 Bond restraints: 157414 Sorted by residual: bond pdb=" O3' C 54942 " pdb=" P C 54944 " ideal model delta sigma weight residual 1.607 2.754 -1.147 1.50e-02 4.44e+03 5.85e+03 bond pdb=" O3' G 51840 " pdb=" P G 51842 " ideal model delta sigma weight residual 1.607 2.674 -1.067 1.50e-02 4.44e+03 5.06e+03 bond pdb=" O3' C 54939 " pdb=" P G 54941 " ideal model delta sigma weight residual 1.607 2.648 -1.041 1.50e-02 4.44e+03 4.82e+03 bond pdb=" O3' G 51823 " pdb=" P A 51825 " ideal model delta sigma weight residual 1.607 2.245 -0.638 1.50e-02 4.44e+03 1.81e+03 bond pdb=" C4 5MU 2 54 " pdb=" C5 5MU 2 54 " ideal model delta sigma weight residual 1.802 1.488 0.314 2.00e-02 2.50e+03 2.46e+02 ... (remaining 157409 not shown) Histogram of bond angle deviations from ideal: 67.21 - 82.20: 2 82.20 - 97.19: 18 97.19 - 112.18: 100601 112.18 - 127.17: 122076 127.17 - 142.16: 9356 Bond angle restraints: 232053 Sorted by residual: angle pdb=" O3' G 51840 " pdb=" P G 51842 " pdb=" O5' G 51842 " ideal model delta sigma weight residual 104.00 67.21 36.79 1.50e+00 4.44e-01 6.02e+02 angle pdb=" C3' G 51840 " pdb=" O3' G 51840 " pdb=" P G 51842 " ideal model delta sigma weight residual 120.20 89.98 30.22 1.50e+00 4.44e-01 4.06e+02 angle pdb=" N TYR a 61 " pdb=" CA TYR a 61 " pdb=" C TYR a 61 " ideal model delta sigma weight residual 111.07 131.89 -20.82 1.07e+00 8.73e-01 3.79e+02 angle pdb=" C3' C 54939 " pdb=" O3' C 54939 " pdb=" P G 54941 " ideal model delta sigma weight residual 120.20 96.03 24.17 1.50e+00 4.44e-01 2.60e+02 angle pdb=" C4' G 51358 " pdb=" C3' G 51358 " pdb=" O3' G 51358 " ideal model delta sigma weight residual 113.00 136.20 -23.20 1.50e+00 4.44e-01 2.39e+02 ... (remaining 232048 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 87404 35.98 - 71.96: 12760 71.96 - 107.94: 1403 107.94 - 143.93: 103 143.93 - 179.91: 140 Dihedral angle restraints: 101810 sinusoidal: 79598 harmonic: 22212 Sorted by residual: dihedral pdb=" CA LEU B 17 " pdb=" C LEU B 17 " pdb=" N PRO B 18 " pdb=" CA PRO B 18 " ideal model delta harmonic sigma weight residual 180.00 101.64 78.36 0 5.00e+00 4.00e-02 2.46e+02 dihedral pdb=" CA ARG 1 13 " pdb=" C ARG 1 13 " pdb=" N PHE 1 14 " pdb=" CA PHE 1 14 " ideal model delta harmonic sigma weight residual 180.00 124.54 55.46 0 5.00e+00 4.00e-02 1.23e+02 dihedral pdb=" C5' G 51380 " pdb=" C4' G 51380 " pdb=" C3' G 51380 " pdb=" O3' G 51380 " ideal model delta sinusoidal sigma weight residual 147.00 68.38 78.62 1 8.00e+00 1.56e-02 1.20e+02 ... (remaining 101807 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.206: 26900 0.206 - 0.411: 1999 0.411 - 0.617: 121 0.617 - 0.822: 19 0.822 - 1.028: 3 Chirality restraints: 29042 Sorted by residual: chirality pdb=" C3' G 51358 " pdb=" C4' G 51358 " pdb=" O3' G 51358 " pdb=" C2' G 51358 " both_signs ideal model delta sigma weight residual False -2.48 -1.45 -1.03 2.00e-01 2.50e+01 2.64e+01 chirality pdb=" CA HIS B 258 " pdb=" N HIS B 258 " pdb=" C HIS B 258 " pdb=" CB HIS B 258 " both_signs ideal model delta sigma weight residual False 2.51 1.50 1.01 2.00e-01 2.50e+01 2.57e+01 chirality pdb=" C3' G 51211 " pdb=" C4' G 51211 " pdb=" O3' G 51211 " pdb=" C2' G 51211 " both_signs ideal model delta sigma weight residual False -2.48 -1.63 -0.85 2.00e-01 2.50e+01 1.80e+01 ... (remaining 29039 not shown) Planarity restraints: 14451 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 5MU 2 54 " -0.136 2.00e-02 2.50e+03 4.37e-01 4.29e+03 pdb=" C4' 5MU 2 54 " 0.400 2.00e-02 2.50e+03 pdb=" O4' 5MU 2 54 " 0.549 2.00e-02 2.50e+03 pdb=" C3' 5MU 2 54 " -0.524 2.00e-02 2.50e+03 pdb=" O3' 5MU 2 54 " -0.229 2.00e-02 2.50e+03 pdb=" C2' 5MU 2 54 " -0.305 2.00e-02 2.50e+03 pdb=" O2' 5MU 2 54 " 0.587 2.00e-02 2.50e+03 pdb=" C1' 5MU 2 54 " 0.283 2.00e-02 2.50e+03 pdb=" N1 5MU 2 54 " -0.625 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C 52797 " 0.106 2.00e-02 2.50e+03 6.25e-02 8.80e+01 pdb=" N1 C 52797 " -0.084 2.00e-02 2.50e+03 pdb=" C2 C 52797 " -0.015 2.00e-02 2.50e+03 pdb=" O2 C 52797 " 0.023 2.00e-02 2.50e+03 pdb=" N3 C 52797 " -0.071 2.00e-02 2.50e+03 pdb=" C4 C 52797 " -0.016 2.00e-02 2.50e+03 pdb=" N4 C 52797 " 0.100 2.00e-02 2.50e+03 pdb=" C5 C 52797 " -0.018 2.00e-02 2.50e+03 pdb=" C6 C 52797 " -0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G 52793 " -0.096 2.00e-02 2.50e+03 5.41e-02 8.78e+01 pdb=" N9 G 52793 " 0.048 2.00e-02 2.50e+03 pdb=" C8 G 52793 " 0.010 2.00e-02 2.50e+03 pdb=" N7 G 52793 " 0.020 2.00e-02 2.50e+03 pdb=" C5 G 52793 " 0.051 2.00e-02 2.50e+03 pdb=" C6 G 52793 " 0.036 2.00e-02 2.50e+03 pdb=" O6 G 52793 " -0.124 2.00e-02 2.50e+03 pdb=" N1 G 52793 " 0.052 2.00e-02 2.50e+03 pdb=" C2 G 52793 " 0.003 2.00e-02 2.50e+03 pdb=" N2 G 52793 " -0.025 2.00e-02 2.50e+03 pdb=" N3 G 52793 " 0.013 2.00e-02 2.50e+03 pdb=" C4 G 52793 " 0.013 2.00e-02 2.50e+03 ... (remaining 14448 not shown) Histogram of nonbonded interaction distances: 1.19 - 1.93: 51 1.93 - 2.67: 9137 2.67 - 3.41: 201888 3.41 - 4.16: 468131 4.16 - 4.90: 661503 Nonbonded interactions: 1340710 Sorted by model distance: nonbonded pdb=" O4 U 5 43 " pdb=" N1 A 5 94 " model vdw 1.186 2.496 nonbonded pdb=" O TRP u 99 " pdb=" NZ LYS v 311 " model vdw 1.282 2.520 nonbonded pdb=" O VAL 1 24 " pdb=" O3' A 2 76 " model vdw 1.331 3.040 nonbonded pdb=" N1 A 53662 " pdb=" O4 U 53680 " model vdw 1.391 2.496 nonbonded pdb=" OG1 THR p 5 " pdb=" OP1 A 51554 " model vdw 1.488 2.440 ... (remaining 1340705 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'x' and resid 101 through 1413) selection = chain 'y' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.640 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: 0.140 Extract box with map and model: 12.350 Check model and map are aligned: 1.470 Set scattering table: 0.870 Process input model: 600.130 Find NCS groups from input model: 3.600 Set up NCS constraints: 0.430 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:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 623.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 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 : 0.010 1.147 157414 Z= 0.632 Angle : 1.595 36.793 232053 Z= 1.059 Chirality : 0.114 1.028 29042 Planarity : 0.011 0.437 14451 Dihedral : 26.719 179.908 87425 Min Nonbonded Distance : 1.186 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 3.21 % Allowed : 11.12 % Favored : 85.67 % Rotamer: Outliers : 18.87 % Allowed : 17.25 % Favored : 63.88 % Cbeta Deviations : 0.72 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.04 % Twisted Proline : 3.05 % Twisted General : 0.58 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.22 (0.09), residues: 7132 helix: -0.29 (0.09), residues: 2410 sheet: -3.26 (0.14), residues: 919 loop : -3.22 (0.08), residues: 3803 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.061 0.004 TRP A 196 HIS 0.040 0.004 HIS a 62 PHE 0.042 0.005 PHE S 145 TYR 0.051 0.005 TYR T 30 ARG 0.022 0.002 ARG L 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 3329 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1152 poor density : 2177 time to evaluate : 7.138 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8321 (tptp) cc_final: 0.7990 (ttpp) REVERT: A 63 PHE cc_start: 0.8599 (m-80) cc_final: 0.8351 (m-80) REVERT: A 163 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7281 (mtm180) REVERT: A 233 ARG cc_start: 0.7996 (OUTLIER) cc_final: 0.7710 (tpt90) REVERT: B 10 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8211 (ptm-80) REVERT: B 66 LYS cc_start: 0.7882 (OUTLIER) cc_final: 0.7639 (mtpt) REVERT: B 103 LYS cc_start: 0.7608 (OUTLIER) cc_final: 0.6986 (mmmt) REVERT: B 228 TYR cc_start: 0.7329 (t80) cc_final: 0.7120 (t80) REVERT: B 261 ARG cc_start: 0.6970 (OUTLIER) cc_final: 0.6515 (mtm-85) REVERT: B 292 LEU cc_start: 0.7707 (pt) cc_final: 0.7299 (pt) REVERT: B 294 LYS cc_start: 0.8146 (OUTLIER) cc_final: 0.7870 (mtmt) REVERT: B 306 ASP cc_start: 0.7356 (p0) cc_final: 0.7011 (p0) REVERT: B 332 MET cc_start: 0.8261 (ttp) cc_final: 0.7910 (ttm) REVERT: B 338 VAL cc_start: 0.9323 (p) cc_final: 0.9109 (m) REVERT: B 356 LYS cc_start: 0.8657 (OUTLIER) cc_final: 0.8263 (mtpt) REVERT: B 389 MET cc_start: 0.7998 (mmm) cc_final: 0.7608 (mtt) REVERT: C 13 GLU cc_start: 0.7337 (pt0) cc_final: 0.7069 (pp20) REVERT: D 217 ASP cc_start: 0.8595 (m-30) cc_final: 0.8271 (t0) REVERT: E 233 LYS cc_start: 0.5395 (OUTLIER) cc_final: 0.5019 (mmtm) REVERT: E 236 TYR cc_start: 0.6804 (OUTLIER) cc_final: 0.5973 (t80) REVERT: E 241 GLN cc_start: 0.6717 (tt0) cc_final: 0.6090 (tt0) REVERT: F 91 LEU cc_start: 0.6690 (OUTLIER) cc_final: 0.6458 (tp) REVERT: F 186 ILE cc_start: 0.6053 (mt) cc_final: 0.5667 (mt) REVERT: G 107 LYS cc_start: 0.8258 (tppt) cc_final: 0.7681 (mmtt) REVERT: G 117 ARG cc_start: 0.7689 (ttm-80) cc_final: 0.7354 (mtm180) REVERT: G 179 VAL cc_start: 0.6446 (t) cc_final: 0.6198 (p) REVERT: G 229 ARG cc_start: 0.7579 (OUTLIER) cc_final: 0.7280 (ptm-80) REVERT: G 240 ASN cc_start: 0.7231 (OUTLIER) cc_final: 0.6669 (t0) REVERT: H 50 LYS cc_start: 0.5926 (ttmt) cc_final: 0.5682 (ttmt) REVERT: H 63 ASN cc_start: 0.6278 (OUTLIER) cc_final: 0.5013 (p0) REVERT: H 116 ASN cc_start: 0.7753 (t0) cc_final: 0.7354 (t0) REVERT: I 11 TYR cc_start: 0.6440 (m-80) cc_final: 0.5325 (m-80) REVERT: I 60 LEU cc_start: 0.7579 (mt) cc_final: 0.7071 (mt) REVERT: I 79 SER cc_start: 0.7846 (OUTLIER) cc_final: 0.7560 (p) REVERT: I 99 ILE cc_start: 0.7621 (tp) cc_final: 0.7155 (tt) REVERT: I 147 HIS cc_start: 0.7436 (m-70) cc_final: 0.7126 (m170) REVERT: J 96 LYS cc_start: 0.7800 (OUTLIER) cc_final: 0.7474 (mttm) REVERT: J 171 ASP cc_start: 0.7218 (OUTLIER) cc_final: 0.6847 (t0) REVERT: L 35 ARG cc_start: 0.7706 (OUTLIER) cc_final: 0.5385 (mpt-90) REVERT: L 106 CYS cc_start: 0.6469 (p) cc_final: 0.6088 (p) REVERT: L 119 GLU cc_start: 0.6901 (OUTLIER) cc_final: 0.6646 (mm-30) REVERT: L 135 LYS cc_start: 0.8208 (mptp) cc_final: 0.7964 (mtpt) REVERT: N 44 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7291 (ttp-110) REVERT: N 123 GLU cc_start: 0.7350 (OUTLIER) cc_final: 0.7130 (pm20) REVERT: O 23 VAL cc_start: 0.8616 (t) cc_final: 0.8369 (t) REVERT: O 34 VAL cc_start: 0.8756 (t) cc_final: 0.7973 (p) REVERT: P 12 THR cc_start: 0.7479 (m) cc_final: 0.6879 (m) REVERT: P 25 HIS cc_start: 0.8130 (OUTLIER) cc_final: 0.7270 (m170) REVERT: P 31 GLU cc_start: 0.6498 (mm-30) cc_final: 0.6004 (mm-30) REVERT: P 110 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.6813 (t0) REVERT: P 142 SER cc_start: 0.8274 (m) cc_final: 0.8074 (p) REVERT: Q 49 LYS cc_start: 0.7195 (ttpp) cc_final: 0.6939 (tptt) REVERT: R 45 ILE cc_start: 0.9001 (mt) cc_final: 0.8499 (mt) REVERT: R 86 ASN cc_start: 0.8974 (t0) cc_final: 0.8730 (t0) REVERT: R 113 LYS cc_start: 0.8912 (OUTLIER) cc_final: 0.8572 (mmmt) REVERT: R 116 ASP cc_start: 0.8018 (p0) cc_final: 0.7811 (p0) REVERT: R 138 LEU cc_start: 0.8087 (OUTLIER) cc_final: 0.7818 (tp) REVERT: R 142 ILE cc_start: 0.9320 (mt) cc_final: 0.9074 (mt) REVERT: S 2 LYS cc_start: 0.4357 (OUTLIER) cc_final: 0.3510 (tttm) REVERT: S 67 VAL cc_start: 0.8659 (OUTLIER) cc_final: 0.8391 (t) REVERT: S 156 HIS cc_start: 0.6864 (OUTLIER) cc_final: 0.6580 (t70) REVERT: U 23 LEU cc_start: 0.8449 (OUTLIER) cc_final: 0.8230 (tt) REVERT: U 30 GLU cc_start: 0.8464 (mm-30) cc_final: 0.7557 (pp20) REVERT: U 40 GLU cc_start: 0.8937 (tt0) cc_final: 0.8689 (tt0) REVERT: U 62 THR cc_start: 0.7486 (m) cc_final: 0.6892 (p) REVERT: U 67 LYS cc_start: 0.7897 (OUTLIER) cc_final: 0.7636 (mmtm) REVERT: U 71 THR cc_start: 0.8528 (m) cc_final: 0.8297 (p) REVERT: U 73 THR cc_start: 0.7910 (m) cc_final: 0.7518 (m) REVERT: U 79 SER cc_start: 0.9082 (t) cc_final: 0.8541 (m) REVERT: U 100 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8360 (mt) REVERT: U 113 ARG cc_start: 0.7974 (OUTLIER) cc_final: 0.7656 (mtm-85) REVERT: V 18 LEU cc_start: 0.8662 (OUTLIER) cc_final: 0.8431 (pp) REVERT: V 69 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.8114 (pttt) REVERT: V 84 GLN cc_start: 0.8734 (OUTLIER) cc_final: 0.8525 (pt0) REVERT: V 109 LYS cc_start: 0.8212 (OUTLIER) cc_final: 0.8007 (tppt) REVERT: W 3 VAL cc_start: 0.8595 (m) cc_final: 0.8343 (m) REVERT: W 4 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7598 (mm-30) REVERT: W 13 ILE cc_start: 0.8304 (OUTLIER) cc_final: 0.7918 (tt) REVERT: W 25 ASP cc_start: 0.7898 (OUTLIER) cc_final: 0.7687 (p0) REVERT: W 32 LEU cc_start: 0.8969 (tp) cc_final: 0.8600 (tp) REVERT: W 47 ARG cc_start: 0.8926 (mtt-85) cc_final: 0.8645 (mpp80) REVERT: W 48 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8752 (tt0) REVERT: X 147 LEU cc_start: 0.7834 (OUTLIER) cc_final: 0.7550 (tp) REVERT: X 152 LYS cc_start: 0.8289 (OUTLIER) cc_final: 0.8086 (mttp) REVERT: Y 52 ASP cc_start: 0.7905 (p0) cc_final: 0.7694 (p0) REVERT: Y 87 ARG cc_start: 0.8067 (OUTLIER) cc_final: 0.7223 (ttm110) REVERT: Y 95 VAL cc_start: 0.8175 (t) cc_final: 0.7934 (m) REVERT: Y 128 VAL cc_start: 0.7697 (t) cc_final: 0.7456 (m) REVERT: Z 49 TYR cc_start: 0.7717 (m-80) cc_final: 0.7452 (m-80) REVERT: Z 81 MET cc_start: 0.8056 (OUTLIER) cc_final: 0.7729 (tpp) REVERT: c 14 ILE cc_start: 0.8433 (mt) cc_final: 0.8230 (tp) REVERT: c 59 GLU cc_start: 0.8707 (tp30) cc_final: 0.8167 (tp30) REVERT: c 61 GLU cc_start: 0.8515 (tt0) cc_final: 0.8149 (tm-30) REVERT: c 89 TYR cc_start: 0.8212 (OUTLIER) cc_final: 0.7780 (p90) REVERT: d 19 GLU cc_start: 0.7779 (OUTLIER) cc_final: 0.6811 (pm20) REVERT: d 48 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7412 (mm-30) REVERT: d 93 ASN cc_start: 0.7349 (t0) cc_final: 0.6635 (t0) REVERT: d 100 ASN cc_start: 0.8722 (m110) cc_final: 0.8092 (t0) REVERT: f 75 THR cc_start: 0.6877 (p) cc_final: 0.6585 (p) REVERT: g 7 TYR cc_start: 0.8600 (m-80) cc_final: 0.8061 (m-80) REVERT: g 19 LYS cc_start: 0.9202 (OUTLIER) cc_final: 0.8935 (mmtm) REVERT: g 102 ILE cc_start: 0.6906 (OUTLIER) cc_final: 0.6656 (mm) REVERT: g 112 GLN cc_start: 0.6377 (OUTLIER) cc_final: 0.6013 (pp30) REVERT: h 16 GLU cc_start: 0.8667 (tp30) cc_final: 0.8320 (tp30) REVERT: h 95 LEU cc_start: 0.8124 (mt) cc_final: 0.7823 (mm) REVERT: i 16 LYS cc_start: 0.8342 (tttt) cc_final: 0.7946 (mmtt) REVERT: i 18 THR cc_start: 0.6077 (OUTLIER) cc_final: 0.5293 (t) REVERT: i 98 ARG cc_start: 0.7175 (ttm-80) cc_final: 0.6962 (ttt180) REVERT: k 26 LYS cc_start: 0.7823 (tptp) cc_final: 0.7614 (tptp) REVERT: k 29 LYS cc_start: 0.8248 (ptpt) cc_final: 0.7934 (mmmt) REVERT: k 37 ARG cc_start: 0.7997 (OUTLIER) cc_final: 0.6122 (tpm-80) REVERT: k 67 LYS cc_start: 0.8013 (tmtt) cc_final: 0.7463 (ptpp) REVERT: l 4 HIS cc_start: 0.7673 (OUTLIER) cc_final: 0.7401 (m-70) REVERT: l 15 LYS cc_start: 0.7643 (tttp) cc_final: 0.7354 (tttp) REVERT: l 46 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8011 (ppt170) REVERT: o 73 VAL cc_start: 0.8156 (t) cc_final: 0.7937 (p) REVERT: o 100 LYS cc_start: 0.6973 (mmtp) cc_final: 0.6215 (mtmt) REVERT: p 70 THR cc_start: 0.8564 (p) cc_final: 0.8298 (p) REVERT: p 73 THR cc_start: 0.8134 (p) cc_final: 0.7897 (p) REVERT: r 24 THR cc_start: 0.6848 (OUTLIER) cc_final: 0.6607 (p) REVERT: r 102 TYR cc_start: 0.6392 (t80) cc_final: 0.6163 (t80) REVERT: s 18 ILE cc_start: 0.7285 (OUTLIER) cc_final: 0.7056 (tt) REVERT: s 83 ARG cc_start: 0.6056 (OUTLIER) cc_final: 0.4908 (mtp85) REVERT: t 14 TYR cc_start: 0.3776 (OUTLIER) cc_final: 0.3227 (p90) REVERT: t 41 LYS cc_start: 0.8208 (tmtp) cc_final: 0.7705 (mptt) REVERT: t 85 LEU cc_start: 0.7706 (mt) cc_final: 0.7482 (pp) REVERT: t 116 MET cc_start: 0.3782 (ptt) cc_final: 0.3156 (tpt) REVERT: v 346 LEU cc_start: 0.7361 (mt) cc_final: 0.7050 (mt) REVERT: v 347 LYS cc_start: 0.7569 (mttt) cc_final: 0.6882 (mmtt) REVERT: v 355 LEU cc_start: 0.8233 (OUTLIER) cc_final: 0.7893 (mt) REVERT: v 383 LYS cc_start: 0.7866 (OUTLIER) cc_final: 0.7602 (mmtp) REVERT: v 463 VAL cc_start: 0.6942 (OUTLIER) cc_final: 0.6707 (t) REVERT: v 482 TYR cc_start: 0.7157 (m-80) cc_final: 0.6930 (m-10) REVERT: z 1582 TRP cc_start: 0.6656 (OUTLIER) cc_final: 0.6111 (t-100) REVERT: z 1596 ARG cc_start: 0.8931 (mtt180) cc_final: 0.8551 (tpm170) REVERT: z 1677 ARG cc_start: 0.7146 (ttt90) cc_final: 0.6290 (ptp90) REVERT: 0 1765 PHE cc_start: 0.0894 (OUTLIER) cc_final: 0.0463 (t80) REVERT: 1 11 MET cc_start: 0.7471 (tpt) cc_final: 0.7018 (tpp) outliers start: 1152 outliers final: 208 residues processed: 2900 average time/residue: 1.6249 time to fit residues: 7836.4654 Evaluate side-chains 1659 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 271 poor density : 1388 time to evaluate : 7.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain B residue 10 ARG Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 67 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 167 GLN Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain B residue 261 ARG Chi-restraints excluded: chain B residue 294 LYS Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 328 ASN Chi-restraints excluded: chain B residue 344 VAL Chi-restraints excluded: chain B residue 356 LYS Chi-restraints excluded: chain B residue 379 PHE Chi-restraints excluded: chain C residue 20 LYS Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 76 ILE Chi-restraints excluded: chain C residue 150 LEU Chi-restraints excluded: chain C residue 193 LYS Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 237 ILE Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 73 MET Chi-restraints excluded: chain D residue 104 LEU Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 202 GLN Chi-restraints excluded: chain D residue 258 LYS Chi-restraints excluded: chain D residue 264 LYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 102 VAL Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 148 ILE Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 179 ARG Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 233 LYS Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 273 LEU Chi-restraints excluded: chain E residue 277 ILE Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain E residue 284 PHE Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 91 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 182 CYS Chi-restraints excluded: chain G residue 229 ARG Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain G residue 250 ILE Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain I residue 8 CYS Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 79 SER Chi-restraints excluded: chain I residue 116 ARG Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 187 LYS Chi-restraints excluded: chain I residue 189 CYS Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain J residue 96 LYS Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 151 ILE Chi-restraints excluded: chain J residue 164 ARG Chi-restraints excluded: chain J residue 171 ASP Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 113 ASN Chi-restraints excluded: chain L residue 119 GLU Chi-restraints excluded: chain M residue 29 ASP Chi-restraints excluded: chain M residue 37 LEU Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 98 ARG Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 44 ARG Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 123 GLU Chi-restraints excluded: chain N residue 131 GLU Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain O residue 22 ILE Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 58 LEU Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain P residue 24 VAL Chi-restraints excluded: chain P residue 25 HIS Chi-restraints excluded: chain P residue 105 LYS Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain Q residue 13 VAL Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 54 SER Chi-restraints excluded: chain Q residue 91 ARG Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain R residue 6 LEU Chi-restraints excluded: chain R residue 15 LEU Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 113 LYS Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain R residue 172 ARG Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain S residue 7 LEU Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 68 PHE Chi-restraints excluded: chain S residue 150 ILE Chi-restraints excluded: chain S residue 156 HIS Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 67 LYS Chi-restraints excluded: chain U residue 100 LEU Chi-restraints excluded: chain U residue 113 ARG Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 30 ASP Chi-restraints excluded: chain V residue 69 LYS Chi-restraints excluded: chain V residue 76 VAL Chi-restraints excluded: chain V residue 82 ILE Chi-restraints excluded: chain V residue 84 GLN Chi-restraints excluded: chain V residue 109 LYS Chi-restraints excluded: chain W residue 4 GLU Chi-restraints excluded: chain W residue 13 ILE Chi-restraints excluded: chain W residue 25 ASP Chi-restraints excluded: chain W residue 48 GLN Chi-restraints excluded: chain W residue 50 ASN Chi-restraints excluded: chain X residue 39 LYS Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain X residue 145 ASP Chi-restraints excluded: chain X residue 147 LEU Chi-restraints excluded: chain X residue 152 LYS Chi-restraints excluded: chain Y residue 7 VAL Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 38 LEU Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 87 ARG Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Y residue 117 LYS Chi-restraints excluded: chain Z residue 19 SER Chi-restraints excluded: chain Z residue 57 MET Chi-restraints excluded: chain Z residue 72 VAL Chi-restraints excluded: chain Z residue 81 MET Chi-restraints excluded: chain Z residue 83 THR Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 39 HIS Chi-restraints excluded: chain a residue 72 THR Chi-restraints excluded: chain a residue 84 GLU Chi-restraints excluded: chain a residue 122 VAL Chi-restraints excluded: chain a residue 134 GLU Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain b residue 27 GLN Chi-restraints excluded: chain c residue 16 SER Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 37 MET Chi-restraints excluded: chain c residue 50 ASN Chi-restraints excluded: chain c residue 51 ASN Chi-restraints excluded: chain c residue 78 ASN Chi-restraints excluded: chain c residue 89 TYR Chi-restraints excluded: chain c residue 91 VAL Chi-restraints excluded: chain d residue 19 GLU Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 28 ASN Chi-restraints excluded: chain d residue 31 LYS Chi-restraints excluded: chain d residue 34 HIS Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 38 PHE Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 102 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain e residue 58 ILE Chi-restraints excluded: chain e residue 79 VAL Chi-restraints excluded: chain e residue 104 SER Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain f residue 7 SER Chi-restraints excluded: chain f residue 21 GLN Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain f residue 60 PRO Chi-restraints excluded: chain f residue 106 TYR Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 19 LYS Chi-restraints excluded: chain g residue 64 LEU Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain g residue 112 GLN Chi-restraints excluded: chain h residue 88 THR Chi-restraints excluded: chain h residue 98 HIS Chi-restraints excluded: chain h residue 121 VAL Chi-restraints excluded: chain i residue 4 ARG Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 86 LYS Chi-restraints excluded: chain j residue 15 THR Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 69 ILE Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain k residue 37 ARG Chi-restraints excluded: chain k residue 56 LEU Chi-restraints excluded: chain l residue 4 HIS Chi-restraints excluded: chain l residue 46 ARG Chi-restraints excluded: chain m residue 85 LEU Chi-restraints excluded: chain m residue 119 ASN Chi-restraints excluded: chain o residue 55 ILE Chi-restraints excluded: chain o residue 61 LYS Chi-restraints excluded: chain o residue 63 THR Chi-restraints excluded: chain p residue 11 VAL Chi-restraints excluded: chain p residue 33 GLN Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 60 CYS Chi-restraints excluded: chain p residue 63 THR Chi-restraints excluded: chain p residue 87 LYS Chi-restraints excluded: chain r residue 17 LEU Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain r residue 28 GLU Chi-restraints excluded: chain r residue 67 ARG Chi-restraints excluded: chain s residue 18 ILE Chi-restraints excluded: chain s residue 83 ARG Chi-restraints excluded: chain s residue 149 ARG Chi-restraints excluded: chain t residue 14 TYR Chi-restraints excluded: chain t residue 44 ASP Chi-restraints excluded: chain t residue 106 PHE Chi-restraints excluded: chain t residue 114 ARG Chi-restraints excluded: chain v residue 310 LEU Chi-restraints excluded: chain v residue 316 GLU Chi-restraints excluded: chain v residue 324 ASP Chi-restraints excluded: chain v residue 355 LEU Chi-restraints excluded: chain v residue 373 ILE Chi-restraints excluded: chain v residue 383 LYS Chi-restraints excluded: chain v residue 463 VAL Chi-restraints excluded: chain z residue 1563 LEU Chi-restraints excluded: chain z residue 1571 THR Chi-restraints excluded: chain z residue 1582 TRP Chi-restraints excluded: chain z residue 1602 VAL Chi-restraints excluded: chain z residue 1632 THR Chi-restraints excluded: chain z residue 1668 ARG Chi-restraints excluded: chain z residue 1705 VAL Chi-restraints excluded: chain z residue 1709 PHE Chi-restraints excluded: chain 0 residue 1765 PHE Chi-restraints excluded: chain 1 residue 13 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 966 optimal weight: 9.9990 chunk 867 optimal weight: 10.0000 chunk 481 optimal weight: 0.0670 chunk 296 optimal weight: 0.6980 chunk 585 optimal weight: 0.9990 chunk 463 optimal weight: 0.8980 chunk 897 optimal weight: 7.9990 chunk 347 optimal weight: 0.9980 chunk 545 optimal weight: 5.9990 chunk 667 optimal weight: 40.0000 chunk 1039 optimal weight: 7.9990 overall best weight: 0.7320 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 HIS A 50 HIS A 132 ASN ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 217 GLN B 25 HIS B 167 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN C 61 GLN C 142 HIS ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 42 ASN D 81 HIS ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 GLN L 13 HIS L 104 ASN ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 33 GLN M 44 GLN N 29 GLN N 37 HIS N 91 GLN N 117 ASN ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 26 GLN O 50 ASN O 72 HIS O 96 GLN O 199 HIS P 40 HIS P 75 GLN ** Q 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 125 GLN S 50 GLN S 108 GLN S 122 HIS ** S 144 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 3 ASN T 79 GLN U 38 ASN U 95 ASN Y 24 HIS Y 100 HIS Z 28 ASN Z 127 ASN b 11 ASN ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 30 HIS e 24 GLN e 43 ASN e 52 GLN f 24 HIS ** f 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 99 HIS g 28 ASN g 110 GLN i 36 HIS j 16 HIS k 28 ASN k 31 ASN o 18 HIS r 36 ASN r 83 ASN ** s 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 65 GLN t 68 GLN t 115 GLN t 156 ASN v 325 ASN v 332 ASN v 363 GLN Total number of N/Q/H flips: 63 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.086 157414 Z= 0.223 Angle : 0.870 14.133 232053 Z= 0.444 Chirality : 0.045 0.450 29042 Planarity : 0.007 0.150 14451 Dihedral : 26.249 179.730 72880 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 1.04 % Allowed : 6.45 % Favored : 92.51 % Rotamer: Outliers : 8.03 % Allowed : 22.69 % Favored : 69.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.04 % Twisted Proline : 2.71 % Twisted General : 0.19 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.10), residues: 7132 helix: 0.84 (0.11), residues: 2413 sheet: -2.48 (0.14), residues: 964 loop : -2.41 (0.09), residues: 3755 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP J 165 HIS 0.013 0.002 HIS B 258 PHE 0.030 0.002 PHE I 22 TYR 0.026 0.002 TYR O 168 ARG 0.018 0.001 ARG k 3 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2091 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 490 poor density : 1601 time to evaluate : 7.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 LYS cc_start: 0.8306 (tptp) cc_final: 0.8017 (ttpt) REVERT: A 163 ARG cc_start: 0.7606 (OUTLIER) cc_final: 0.7292 (mtm180) REVERT: A 180 LEU cc_start: 0.9180 (mm) cc_final: 0.8948 (mt) REVERT: A 233 ARG cc_start: 0.7896 (OUTLIER) cc_final: 0.7622 (tpt90) REVERT: B 53 MET cc_start: 0.8331 (mtp) cc_final: 0.7866 (mtt) REVERT: B 300 LYS cc_start: 0.8769 (mttt) cc_final: 0.8470 (mptt) REVERT: C 94 ASN cc_start: 0.6735 (p0) cc_final: 0.6394 (p0) REVERT: C 95 MET cc_start: 0.7394 (pmm) cc_final: 0.6977 (pmm) REVERT: C 101 MET cc_start: 0.6734 (ptp) cc_final: 0.6320 (ptm) REVERT: C 122 TYR cc_start: 0.6867 (t80) cc_final: 0.6582 (t80) REVERT: D 214 GLU cc_start: 0.7525 (tp30) cc_final: 0.7311 (mm-30) REVERT: D 236 MET cc_start: 0.7107 (tpp) cc_final: 0.6857 (tpp) REVERT: E 95 ASP cc_start: 0.7084 (t0) cc_final: 0.6878 (t0) REVERT: E 236 TYR cc_start: 0.7089 (OUTLIER) cc_final: 0.5902 (t80) REVERT: E 241 GLN cc_start: 0.6244 (tt0) cc_final: 0.5714 (tt0) REVERT: F 245 LEU cc_start: 0.7979 (tt) cc_final: 0.7666 (tt) REVERT: G 46 GLN cc_start: 0.8465 (mm110) cc_final: 0.8255 (mm110) REVERT: G 71 TYR cc_start: 0.5919 (OUTLIER) cc_final: 0.5706 (m-80) REVERT: G 85 GLN cc_start: 0.7776 (tm-30) cc_final: 0.7534 (tm-30) REVERT: G 110 LYS cc_start: 0.5781 (tptp) cc_final: 0.4962 (mtmt) REVERT: G 117 ARG cc_start: 0.7446 (ttm-80) cc_final: 0.7119 (mtm180) REVERT: G 160 ASP cc_start: 0.7305 (p0) cc_final: 0.7096 (p0) REVERT: G 229 ARG cc_start: 0.7515 (OUTLIER) cc_final: 0.7228 (ptm-80) REVERT: G 240 ASN cc_start: 0.7448 (OUTLIER) cc_final: 0.6647 (t0) REVERT: H 50 LYS cc_start: 0.5856 (ttmt) cc_final: 0.5548 (ttmt) REVERT: I 11 TYR cc_start: 0.6130 (m-80) cc_final: 0.5127 (m-80) REVERT: I 60 LEU cc_start: 0.7865 (mt) cc_final: 0.7526 (mt) REVERT: I 115 MET cc_start: 0.6691 (tpp) cc_final: 0.6019 (tpp) REVERT: I 150 GLU cc_start: 0.7676 (tp30) cc_final: 0.7362 (tp30) REVERT: I 187 LYS cc_start: 0.7189 (OUTLIER) cc_final: 0.6474 (pttt) REVERT: J 12 MET cc_start: 0.6486 (ptp) cc_final: 0.5974 (ptp) REVERT: J 91 GLU cc_start: 0.7530 (pt0) cc_final: 0.7234 (pm20) REVERT: L 183 ARG cc_start: 0.7326 (mmm160) cc_final: 0.7068 (mmm-85) REVERT: O 79 ILE cc_start: 0.9158 (OUTLIER) cc_final: 0.8800 (mt) REVERT: O 173 GLN cc_start: 0.8336 (tm-30) cc_final: 0.7971 (tm-30) REVERT: P 54 GLN cc_start: 0.8350 (mp10) cc_final: 0.8086 (mt0) REVERT: P 87 SER cc_start: 0.8654 (m) cc_final: 0.8188 (p) REVERT: P 110 ASP cc_start: 0.7658 (OUTLIER) cc_final: 0.6372 (t0) REVERT: Q 8 ASN cc_start: 0.7587 (t0) cc_final: 0.7283 (t0) REVERT: Q 168 ARG cc_start: 0.8597 (ttp-170) cc_final: 0.7815 (ptm-80) REVERT: R 16 ARG cc_start: 0.8368 (mpp80) cc_final: 0.8047 (mtt90) REVERT: R 45 ILE cc_start: 0.8963 (mt) cc_final: 0.8503 (mt) REVERT: R 86 ASN cc_start: 0.8977 (t0) cc_final: 0.8611 (t0) REVERT: S 2 LYS cc_start: 0.4795 (OUTLIER) cc_final: 0.3532 (tmmm) REVERT: S 86 SER cc_start: 0.7702 (m) cc_final: 0.7440 (m) REVERT: U 30 GLU cc_start: 0.8535 (mm-30) cc_final: 0.7770 (pp20) REVERT: U 46 ARG cc_start: 0.8269 (tpp-160) cc_final: 0.7954 (tpp-160) REVERT: U 62 THR cc_start: 0.7293 (m) cc_final: 0.6714 (p) REVERT: U 67 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7700 (mmtm) REVERT: U 73 THR cc_start: 0.8133 (m) cc_final: 0.7737 (m) REVERT: U 90 TYR cc_start: 0.8844 (t80) cc_final: 0.8207 (t80) REVERT: V 15 ARG cc_start: 0.8084 (OUTLIER) cc_final: 0.7704 (tmm160) REVERT: V 18 LEU cc_start: 0.8955 (OUTLIER) cc_final: 0.8495 (pp) REVERT: V 88 TYR cc_start: 0.8561 (p90) cc_final: 0.8289 (p90) REVERT: W 47 ARG cc_start: 0.8990 (mtt-85) cc_final: 0.8748 (mpp80) REVERT: W 48 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8688 (tt0) REVERT: W 50 ASN cc_start: 0.7088 (OUTLIER) cc_final: 0.6748 (m-40) REVERT: X 111 GLN cc_start: 0.7682 (mm-40) cc_final: 0.7416 (tp-100) REVERT: X 152 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8035 (ttmt) REVERT: Z 5 MET cc_start: 0.8149 (mmt) cc_final: 0.7886 (mmt) REVERT: Z 49 TYR cc_start: 0.7785 (m-80) cc_final: 0.7575 (m-80) REVERT: c 29 LEU cc_start: 0.8997 (mp) cc_final: 0.8784 (mp) REVERT: c 35 LEU cc_start: 0.8675 (OUTLIER) cc_final: 0.8351 (mp) REVERT: c 36 LYS cc_start: 0.8345 (mttp) cc_final: 0.8120 (mtpt) REVERT: d 19 GLU cc_start: 0.7884 (OUTLIER) cc_final: 0.6923 (pm20) REVERT: d 31 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7863 (pttp) REVERT: d 48 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.6863 (mp0) REVERT: d 68 LEU cc_start: 0.8345 (tp) cc_final: 0.8138 (tp) REVERT: d 93 ASN cc_start: 0.7890 (t0) cc_final: 0.7479 (t0) REVERT: d 100 ASN cc_start: 0.8589 (m110) cc_final: 0.8141 (t0) REVERT: e 68 HIS cc_start: 0.7948 (OUTLIER) cc_final: 0.7506 (t-90) REVERT: g 5 LEU cc_start: 0.7995 (OUTLIER) cc_final: 0.7613 (pp) REVERT: i 16 LYS cc_start: 0.8402 (tttt) cc_final: 0.8047 (mmtm) REVERT: i 75 LYS cc_start: 0.7887 (tppt) cc_final: 0.7104 (ttpt) REVERT: i 86 LYS cc_start: 0.7894 (OUTLIER) cc_final: 0.7488 (tptm) REVERT: j 21 ARG cc_start: 0.6787 (ttp80) cc_final: 0.6343 (ttp80) REVERT: k 37 ARG cc_start: 0.7828 (OUTLIER) cc_final: 0.7608 (tpm-80) REVERT: k 50 LYS cc_start: 0.7944 (mmtt) cc_final: 0.7553 (ptmt) REVERT: k 52 LYS cc_start: 0.8535 (mmmt) cc_final: 0.7891 (mtmt) REVERT: l 4 HIS cc_start: 0.7306 (OUTLIER) cc_final: 0.6980 (m-70) REVERT: l 25 GLN cc_start: 0.6887 (pm20) cc_final: 0.6317 (mm110) REVERT: m 82 LEU cc_start: 0.8879 (tp) cc_final: 0.8552 (tp) REVERT: o 100 LYS cc_start: 0.7048 (mmtp) cc_final: 0.6761 (ttpp) REVERT: p 37 TYR cc_start: 0.8313 (m-80) cc_final: 0.8101 (m-80) REVERT: p 40 SER cc_start: 0.8772 (p) cc_final: 0.8473 (p) REVERT: p 47 MET cc_start: 0.8608 (mmt) cc_final: 0.8272 (tpt) REVERT: p 52 VAL cc_start: 0.8153 (m) cc_final: 0.7911 (m) REVERT: r 11 ARG cc_start: 0.8312 (ptm-80) cc_final: 0.7995 (ptm-80) REVERT: r 71 ARG cc_start: 0.5564 (mtt90) cc_final: 0.5154 (mtm180) REVERT: s 11 SER cc_start: 0.7729 (m) cc_final: 0.7504 (t) REVERT: t 41 LYS cc_start: 0.8281 (tmtp) cc_final: 0.7788 (mptt) REVERT: t 44 ASP cc_start: 0.5880 (OUTLIER) cc_final: 0.5492 (p0) REVERT: t 85 LEU cc_start: 0.7799 (mt) cc_final: 0.7504 (pp) REVERT: t 135 THR cc_start: 0.6792 (t) cc_final: 0.6540 (t) REVERT: v 347 LYS cc_start: 0.7271 (mttt) cc_final: 0.6806 (mmtt) REVERT: v 355 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.7979 (mt) REVERT: v 364 VAL cc_start: 0.9176 (t) cc_final: 0.8878 (m) REVERT: v 383 LYS cc_start: 0.7786 (OUTLIER) cc_final: 0.7563 (mmtp) REVERT: v 396 ILE cc_start: 0.5868 (OUTLIER) cc_final: 0.5224 (tp) REVERT: z 1572 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8569 (mp) REVERT: z 1582 TRP cc_start: 0.6896 (OUTLIER) cc_final: 0.6369 (t-100) REVERT: z 1596 ARG cc_start: 0.8902 (mtt180) cc_final: 0.8492 (tpm170) REVERT: z 1677 ARG cc_start: 0.6917 (ttt90) cc_final: 0.6187 (ptp90) outliers start: 490 outliers final: 208 residues processed: 1917 average time/residue: 1.3224 time to fit residues: 4355.8062 Evaluate side-chains 1543 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 239 poor density : 1304 time to evaluate : 7.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 101 THR Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 23 ARG Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 66 TYR Chi-restraints excluded: chain D residue 110 LEU Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 264 LYS Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 193 THR Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 282 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 164 ILE Chi-restraints excluded: chain F residue 217 SER Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 71 TYR Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 167 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 182 CYS Chi-restraints excluded: chain G residue 229 ARG Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 240 ASN Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 67 LEU Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 162 GLN Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain I residue 8 CYS Chi-restraints excluded: chain I residue 35 ASP Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 116 ARG Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 148 VAL Chi-restraints excluded: chain I residue 187 LYS Chi-restraints excluded: chain I residue 212 LEU Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 49 VAL Chi-restraints excluded: chain J residue 55 TYR Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 139 PHE Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 78 LEU Chi-restraints excluded: chain L residue 79 GLU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 113 MET Chi-restraints excluded: chain M residue 121 ARG Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 43 THR Chi-restraints excluded: chain N residue 61 ILE Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 81 TYR Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain N residue 100 SER Chi-restraints excluded: chain N residue 198 LEU Chi-restraints excluded: chain O residue 79 ILE Chi-restraints excluded: chain O residue 83 THR Chi-restraints excluded: chain O residue 126 VAL Chi-restraints excluded: chain P residue 5 SER Chi-restraints excluded: chain P residue 105 LYS Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 120 ASN Chi-restraints excluded: chain Q residue 31 LEU Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain R residue 30 ASN Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain S residue 7 LEU Chi-restraints excluded: chain S residue 17 LEU Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 68 PHE Chi-restraints excluded: chain S residue 84 TYR Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain T residue 49 GLN Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 74 ILE Chi-restraints excluded: chain T residue 95 HIS Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 67 LYS Chi-restraints excluded: chain U residue 99 TRP Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 27 ASN Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 42 SER Chi-restraints excluded: chain W residue 48 GLN Chi-restraints excluded: chain W residue 50 ASN Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 51 THR Chi-restraints excluded: chain X residue 77 ILE Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 133 GLU Chi-restraints excluded: chain X residue 152 LYS Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Y residue 130 LYS Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 57 MET Chi-restraints excluded: chain Z residue 72 VAL Chi-restraints excluded: chain Z residue 83 THR Chi-restraints excluded: chain Z residue 87 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 39 HIS Chi-restraints excluded: chain a residue 72 THR Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 84 GLU Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain c residue 37 MET Chi-restraints excluded: chain c residue 75 SER Chi-restraints excluded: chain c residue 83 THR Chi-restraints excluded: chain c residue 92 CYS Chi-restraints excluded: chain d residue 19 GLU Chi-restraints excluded: chain d residue 29 ILE Chi-restraints excluded: chain d residue 31 LYS Chi-restraints excluded: chain d residue 38 PHE Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 102 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 123 ASP Chi-restraints excluded: chain e residue 65 LYS Chi-restraints excluded: chain e residue 68 HIS Chi-restraints excluded: chain e residue 79 VAL Chi-restraints excluded: chain e residue 85 LEU Chi-restraints excluded: chain e residue 118 LEU Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain f residue 7 SER Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain g residue 5 LEU Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 64 LEU Chi-restraints excluded: chain h residue 88 THR Chi-restraints excluded: chain h residue 104 THR Chi-restraints excluded: chain h residue 121 VAL Chi-restraints excluded: chain i residue 20 ASN Chi-restraints excluded: chain i residue 34 THR Chi-restraints excluded: chain i residue 86 LYS Chi-restraints excluded: chain k residue 37 ARG Chi-restraints excluded: chain l residue 4 HIS Chi-restraints excluded: chain l residue 35 ILE Chi-restraints excluded: chain l residue 46 ARG Chi-restraints excluded: chain m residue 85 LEU Chi-restraints excluded: chain o residue 18 HIS Chi-restraints excluded: chain o residue 61 LYS Chi-restraints excluded: chain p residue 11 VAL Chi-restraints excluded: chain p residue 50 ARG Chi-restraints excluded: chain p residue 89 LEU Chi-restraints excluded: chain r residue 13 CYS Chi-restraints excluded: chain r residue 17 LEU Chi-restraints excluded: chain r residue 28 GLU Chi-restraints excluded: chain r residue 32 LEU Chi-restraints excluded: chain r residue 37 SER Chi-restraints excluded: chain r residue 64 ILE Chi-restraints excluded: chain r residue 67 ARG Chi-restraints excluded: chain r residue 68 SER Chi-restraints excluded: chain r residue 122 LYS Chi-restraints excluded: chain s residue 6 ARG Chi-restraints excluded: chain s residue 61 MET Chi-restraints excluded: chain s residue 83 ARG Chi-restraints excluded: chain t residue 44 ASP Chi-restraints excluded: chain t residue 106 PHE Chi-restraints excluded: chain v residue 324 ASP Chi-restraints excluded: chain v residue 355 LEU Chi-restraints excluded: chain v residue 373 ILE Chi-restraints excluded: chain v residue 383 LYS Chi-restraints excluded: chain v residue 396 ILE Chi-restraints excluded: chain v residue 399 LEU Chi-restraints excluded: chain v residue 401 LEU Chi-restraints excluded: chain v residue 407 THR Chi-restraints excluded: chain z residue 1572 LEU Chi-restraints excluded: chain z residue 1582 TRP Chi-restraints excluded: chain z residue 1602 VAL Chi-restraints excluded: chain z residue 1613 SER Chi-restraints excluded: chain z residue 1626 VAL Chi-restraints excluded: chain z residue 1696 GLU Chi-restraints excluded: chain 0 residue 1756 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 577 optimal weight: 4.9990 chunk 322 optimal weight: 2.9990 chunk 865 optimal weight: 8.9990 chunk 708 optimal weight: 40.0000 chunk 286 optimal weight: 0.9990 chunk 1041 optimal weight: 10.0000 chunk 1125 optimal weight: 9.9990 chunk 927 optimal weight: 10.0000 chunk 1032 optimal weight: 10.0000 chunk 355 optimal weight: 5.9990 chunk 835 optimal weight: 9.9990 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 140 ASN ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS B 68 ASN B 175 GLN ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 376 HIS C 43 ASN C 47 ASN C 116 ASN C 329 ASN D 42 ASN D 57 ASN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 246 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN F 241 GLN G 46 GLN I 123 GLN J 167 GLN L 159 ASN M 33 GLN ** M 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 29 GLN N 196 ASN P 21 ASN P 56 GLN R 58 HIS R 130 ASN S 122 HIS S 144 GLN S 163 HIS T 70 HIS T 79 GLN T 139 HIS U 50 ASN X 93 ASN X 107 HIS ** Y 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 96 HIS Z 28 ASN Z 76 ASN Z 127 ASN ** a 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 28 HIS a 44 ASN a 67 GLN a 93 ASN ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 24 HIS f 65 ASN k 31 ASN l 4 HIS p 33 GLN r 36 ASN t 65 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.6783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.207 157414 Z= 0.452 Angle : 0.991 17.125 232053 Z= 0.499 Chirality : 0.052 0.451 29042 Planarity : 0.009 0.185 14451 Dihedral : 25.889 179.870 72542 Min Nonbonded Distance : 1.769 Molprobity Statistics. All-atom Clashscore : 17.84 Ramachandran Plot: Outliers : 0.87 % Allowed : 8.99 % Favored : 90.14 % Rotamer: Outliers : 9.43 % Allowed : 23.65 % Favored : 66.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.04 % Twisted Proline : 1.69 % Twisted General : 0.17 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.09), residues: 7132 helix: -0.12 (0.10), residues: 2438 sheet: -2.12 (0.15), residues: 953 loop : -2.37 (0.09), residues: 3741 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.004 TRP O 81 HIS 0.086 0.003 HIS o 18 PHE 0.086 0.004 PHE b 45 TYR 0.046 0.004 TYR k 41 ARG 0.038 0.001 ARG X 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2170 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 576 poor density : 1594 time to evaluate : 6.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 36 GLU cc_start: 0.8068 (mt-10) cc_final: 0.7780 (mt-10) REVERT: A 145 LYS cc_start: 0.8811 (OUTLIER) cc_final: 0.8573 (mmmt) REVERT: A 163 ARG cc_start: 0.8645 (OUTLIER) cc_final: 0.8292 (ptt-90) REVERT: B 133 TYR cc_start: 0.8753 (t80) cc_final: 0.8324 (t80) REVERT: B 253 CYS cc_start: 0.9125 (t) cc_final: 0.8667 (t) REVERT: B 306 ASP cc_start: 0.8016 (p0) cc_final: 0.7599 (p0) REVERT: B 329 ASP cc_start: 0.8640 (OUTLIER) cc_final: 0.7982 (p0) REVERT: C 138 MET cc_start: 0.8451 (mmm) cc_final: 0.8115 (mmt) REVERT: C 139 SER cc_start: 0.9189 (m) cc_final: 0.8488 (p) REVERT: C 190 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8323 (ttm170) REVERT: C 218 ILE cc_start: 0.8670 (pp) cc_final: 0.8431 (pt) REVERT: C 288 ASP cc_start: 0.8431 (p0) cc_final: 0.8213 (p0) REVERT: D 68 ARG cc_start: 0.8649 (mmp80) cc_final: 0.7625 (mtp-110) REVERT: D 226 TYR cc_start: 0.7194 (OUTLIER) cc_final: 0.5235 (t80) REVERT: E 47 VAL cc_start: 0.8930 (p) cc_final: 0.8726 (m) REVERT: E 152 ARG cc_start: 0.8515 (OUTLIER) cc_final: 0.8190 (ptp90) REVERT: E 178 ASN cc_start: 0.7899 (m-40) cc_final: 0.7698 (m-40) REVERT: E 194 SER cc_start: 0.8699 (m) cc_final: 0.8415 (p) REVERT: E 212 TYR cc_start: 0.8648 (t80) cc_final: 0.8362 (t80) REVERT: E 236 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.5986 (t80) REVERT: E 264 GLN cc_start: 0.8603 (tt0) cc_final: 0.8335 (mt0) REVERT: F 41 GLN cc_start: 0.7828 (OUTLIER) cc_final: 0.7621 (mm-40) REVERT: F 111 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8598 (mt) REVERT: F 137 ILE cc_start: 0.8868 (OUTLIER) cc_final: 0.7685 (mt) REVERT: F 166 LYS cc_start: 0.8919 (mtpt) cc_final: 0.8474 (mttp) REVERT: F 195 GLU cc_start: 0.7704 (tp30) cc_final: 0.7460 (tp30) REVERT: F 227 THR cc_start: 0.8346 (p) cc_final: 0.8126 (p) REVERT: F 250 ASN cc_start: 0.8412 (OUTLIER) cc_final: 0.8171 (t0) REVERT: G 45 ILE cc_start: 0.7270 (pt) cc_final: 0.6867 (pt) REVERT: G 117 ARG cc_start: 0.7606 (ttm-80) cc_final: 0.7057 (tpp-160) REVERT: H 50 LYS cc_start: 0.5974 (ttmt) cc_final: 0.5267 (ttmt) REVERT: H 66 GLU cc_start: 0.7906 (mp0) cc_final: 0.7668 (mp0) REVERT: H 96 TYR cc_start: 0.8477 (p90) cc_final: 0.8231 (p90) REVERT: I 60 LEU cc_start: 0.9056 (mt) cc_final: 0.8731 (mt) REVERT: I 131 ILE cc_start: 0.8807 (OUTLIER) cc_final: 0.8596 (mp) REVERT: I 145 GLU cc_start: 0.8416 (tm-30) cc_final: 0.8099 (tm-30) REVERT: I 187 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.7863 (ptpt) REVERT: L 35 ARG cc_start: 0.8880 (OUTLIER) cc_final: 0.8581 (mtp85) REVERT: L 66 TYR cc_start: 0.8291 (m-80) cc_final: 0.7732 (m-80) REVERT: L 97 SER cc_start: 0.8693 (m) cc_final: 0.8322 (p) REVERT: L 164 GLU cc_start: 0.8420 (mp0) cc_final: 0.7935 (tp30) REVERT: L 188 ASN cc_start: 0.7960 (p0) cc_final: 0.7629 (m110) REVERT: M 95 ILE cc_start: 0.8825 (tt) cc_final: 0.8470 (mt) REVERT: M 96 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8340 (tm-30) REVERT: N 23 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8747 (mp) REVERT: N 30 TYR cc_start: 0.9173 (m-10) cc_final: 0.8904 (m-10) REVERT: N 51 LEU cc_start: 0.9077 (mp) cc_final: 0.8656 (mt) REVERT: N 116 LEU cc_start: 0.9022 (tp) cc_final: 0.8761 (tt) REVERT: N 117 ASN cc_start: 0.8900 (OUTLIER) cc_final: 0.8687 (m-40) REVERT: O 42 ASN cc_start: 0.9291 (OUTLIER) cc_final: 0.8898 (p0) REVERT: O 168 TYR cc_start: 0.8776 (t80) cc_final: 0.7708 (t80) REVERT: O 173 GLN cc_start: 0.8668 (tm-30) cc_final: 0.8361 (tm-30) REVERT: O 180 GLN cc_start: 0.8705 (tm-30) cc_final: 0.8443 (tm-30) REVERT: P 110 ASP cc_start: 0.7960 (OUTLIER) cc_final: 0.7568 (p0) REVERT: Q 16 LYS cc_start: 0.7389 (mmmt) cc_final: 0.7080 (mmtm) REVERT: Q 93 GLN cc_start: 0.8338 (mm-40) cc_final: 0.8113 (mm-40) REVERT: R 25 ASP cc_start: 0.8867 (t70) cc_final: 0.8037 (t0) REVERT: R 86 ASN cc_start: 0.8981 (t0) cc_final: 0.8638 (t0) REVERT: R 151 ARG cc_start: 0.6399 (mtm-85) cc_final: 0.6166 (mtp-110) REVERT: R 153 LYS cc_start: 0.7671 (OUTLIER) cc_final: 0.7386 (pptt) REVERT: S 2 LYS cc_start: 0.9018 (OUTLIER) cc_final: 0.8728 (tttt) REVERT: S 123 SER cc_start: 0.9078 (m) cc_final: 0.8336 (t) REVERT: S 127 MET cc_start: 0.8269 (mpp) cc_final: 0.8010 (mtm) REVERT: T 55 LYS cc_start: 0.9147 (OUTLIER) cc_final: 0.8808 (pttm) REVERT: T 110 LYS cc_start: 0.7845 (mptt) cc_final: 0.7621 (mtmm) REVERT: U 30 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8204 (pp20) REVERT: U 67 LYS cc_start: 0.8129 (OUTLIER) cc_final: 0.7811 (mttp) REVERT: U 73 THR cc_start: 0.8525 (m) cc_final: 0.8170 (m) REVERT: V 27 ASN cc_start: 0.8511 (OUTLIER) cc_final: 0.8218 (p0) REVERT: W 19 ARG cc_start: 0.7907 (ttt180) cc_final: 0.7530 (ttt90) REVERT: W 47 ARG cc_start: 0.8956 (mtt-85) cc_final: 0.8663 (mtm-85) REVERT: X 101 ASP cc_start: 0.8439 (t0) cc_final: 0.8013 (t0) REVERT: X 111 GLN cc_start: 0.8513 (mm-40) cc_final: 0.8225 (tp-100) REVERT: X 116 LEU cc_start: 0.9240 (mm) cc_final: 0.8949 (mm) REVERT: X 139 ARG cc_start: 0.8952 (tpt-90) cc_final: 0.8592 (tpt-90) REVERT: X 144 TYR cc_start: 0.8620 (m-80) cc_final: 0.8306 (m-80) REVERT: X 155 ILE cc_start: 0.9051 (OUTLIER) cc_final: 0.8833 (tp) REVERT: Y 1 MET cc_start: 0.7945 (tpp) cc_final: 0.7597 (tpt) REVERT: Y 30 MET cc_start: 0.8305 (ttm) cc_final: 0.7985 (mtm) REVERT: Y 36 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.7903 (mmtm) REVERT: Y 71 VAL cc_start: 0.8869 (OUTLIER) cc_final: 0.8375 (t) REVERT: Z 5 MET cc_start: 0.8625 (mmt) cc_final: 0.8284 (mmt) REVERT: Z 6 LYS cc_start: 0.9111 (mmmt) cc_final: 0.8869 (tppt) REVERT: Z 39 SER cc_start: 0.8825 (p) cc_final: 0.8503 (p) REVERT: Z 62 ILE cc_start: 0.9139 (mp) cc_final: 0.8848 (mp) REVERT: Z 64 LYS cc_start: 0.9079 (OUTLIER) cc_final: 0.8841 (tttm) REVERT: Z 97 ASN cc_start: 0.8757 (p0) cc_final: 0.8461 (p0) REVERT: a 5 LEU cc_start: 0.9273 (OUTLIER) cc_final: 0.9059 (mp) REVERT: a 42 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.8341 (ttm170) REVERT: a 46 ASP cc_start: 0.6823 (m-30) cc_final: 0.6566 (m-30) REVERT: c 35 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8781 (mp) REVERT: c 75 SER cc_start: 0.9321 (OUTLIER) cc_final: 0.9120 (t) REVERT: d 19 GLU cc_start: 0.8431 (OUTLIER) cc_final: 0.7430 (pm20) REVERT: d 31 LYS cc_start: 0.9198 (OUTLIER) cc_final: 0.8996 (ptmt) REVERT: d 46 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9228 (mp) REVERT: d 48 GLU cc_start: 0.7342 (OUTLIER) cc_final: 0.6827 (mp0) REVERT: d 117 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9096 (mm) REVERT: d 121 ASN cc_start: 0.8343 (t0) cc_final: 0.8036 (t0) REVERT: e 124 ASN cc_start: 0.9284 (p0) cc_final: 0.8884 (p0) REVERT: f 16 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7648 (ptp90) REVERT: f 108 SER cc_start: 0.8148 (p) cc_final: 0.7707 (p) REVERT: f 110 ILE cc_start: 0.7975 (OUTLIER) cc_final: 0.7772 (mp) REVERT: g 25 THR cc_start: 0.9430 (OUTLIER) cc_final: 0.9154 (p) REVERT: g 100 GLN cc_start: 0.8363 (mm-40) cc_final: 0.8055 (tp40) REVERT: g 102 ILE cc_start: 0.8401 (OUTLIER) cc_final: 0.7924 (mp) REVERT: h 16 GLU cc_start: 0.8970 (tp30) cc_final: 0.8296 (tp30) REVERT: h 23 ASP cc_start: 0.9015 (t0) cc_final: 0.8571 (t0) REVERT: h 27 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7848 (mm-30) REVERT: h 78 TYR cc_start: 0.8163 (m-10) cc_final: 0.7826 (m-10) REVERT: i 16 LYS cc_start: 0.8999 (tttt) cc_final: 0.8562 (mmtt) REVERT: j 85 LYS cc_start: 0.8441 (ttpt) cc_final: 0.7991 (ttmt) REVERT: k 10 ASP cc_start: 0.8905 (t0) cc_final: 0.8371 (m-30) REVERT: k 50 LYS cc_start: 0.8258 (mmtt) cc_final: 0.7039 (ttpt) REVERT: k 52 LYS cc_start: 0.8568 (mmmt) cc_final: 0.8266 (mtmt) REVERT: l 46 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8644 (ptt90) REVERT: o 82 MET cc_start: 0.8834 (mmm) cc_final: 0.8564 (mmt) REVERT: o 100 LYS cc_start: 0.8085 (mmtp) cc_final: 0.7728 (ttpp) REVERT: p 47 MET cc_start: 0.9092 (mmt) cc_final: 0.8784 (tpt) REVERT: r 90 LEU cc_start: 0.8573 (OUTLIER) cc_final: 0.8350 (mp) REVERT: r 93 ILE cc_start: 0.9342 (mm) cc_final: 0.9112 (mt) REVERT: s 60 MET cc_start: 0.8048 (mtp) cc_final: 0.7553 (mtp) REVERT: s 61 MET cc_start: 0.5938 (OUTLIER) cc_final: 0.5267 (mtm) REVERT: t 1 MET cc_start: 0.1503 (mpp) cc_final: 0.0931 (mmp) REVERT: t 41 LYS cc_start: 0.8230 (OUTLIER) cc_final: 0.7737 (mptt) REVERT: t 116 MET cc_start: 0.3383 (ptt) cc_final: 0.2701 (tpt) REVERT: v 347 LYS cc_start: 0.7332 (mttt) cc_final: 0.6864 (mmtt) REVERT: v 355 LEU cc_start: 0.8211 (mt) cc_final: 0.7695 (mt) REVERT: v 373 ILE cc_start: 0.8636 (OUTLIER) cc_final: 0.8275 (pt) REVERT: v 378 ILE cc_start: 0.8065 (mt) cc_final: 0.7402 (mm) REVERT: v 383 LYS cc_start: 0.8176 (OUTLIER) cc_final: 0.7784 (mmtp) REVERT: v 396 ILE cc_start: 0.6170 (OUTLIER) cc_final: 0.5569 (tp) REVERT: v 479 HIS cc_start: 0.7501 (t70) cc_final: 0.7187 (t70) REVERT: z 1583 TRP cc_start: 0.8672 (t60) cc_final: 0.8419 (t60) REVERT: z 1677 ARG cc_start: 0.7464 (ttt90) cc_final: 0.6496 (ptp90) REVERT: 1 11 MET cc_start: 0.6650 (tpp) cc_final: 0.6218 (tpp) outliers start: 576 outliers final: 238 residues processed: 1958 average time/residue: 1.3310 time to fit residues: 4490.0863 Evaluate side-chains 1553 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 285 poor density : 1268 time to evaluate : 7.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 ILE Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 88 VAL Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 163 ARG Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 163 ILE Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 207 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 370 THR Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain D residue 4 VAL Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 60 ILE Chi-restraints excluded: chain D residue 75 VAL Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 143 THR Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 159 VAL Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 221 LYS Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain D residue 264 LYS Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain E residue 274 THR Chi-restraints excluded: chain F residue 41 GLN Chi-restraints excluded: chain F residue 44 LEU Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 217 SER Chi-restraints excluded: chain F residue 250 ASN Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 76 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 81 ASN Chi-restraints excluded: chain G residue 84 THR Chi-restraints excluded: chain G residue 101 LYS Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 135 VAL Chi-restraints excluded: chain G residue 173 LEU Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain G residue 241 VAL Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 33 THR Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain I residue 8 CYS Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 71 CYS Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 180 GLU Chi-restraints excluded: chain I residue 187 LYS Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 139 PHE Chi-restraints excluded: chain J residue 167 GLN Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 111 GLN Chi-restraints excluded: chain L residue 157 ILE Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 42 CYS Chi-restraints excluded: chain M residue 45 VAL Chi-restraints excluded: chain M residue 59 ASP Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 121 ARG Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain N residue 23 LEU Chi-restraints excluded: chain N residue 25 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain N residue 101 VAL Chi-restraints excluded: chain N residue 117 ASN Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain O residue 26 GLN Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 42 ASN Chi-restraints excluded: chain O residue 100 ASP 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 P residue 105 LYS Chi-restraints excluded: chain P residue 110 ASP Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain Q residue 9 LYS Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 68 ARG Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 161 SER Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 56 THR Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 93 VAL Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain R residue 153 LYS Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 64 CYS Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 68 PHE Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain T residue 4 THR Chi-restraints excluded: chain T residue 55 LYS Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 118 GLU Chi-restraints excluded: chain T residue 126 VAL Chi-restraints excluded: chain T residue 143 THR Chi-restraints excluded: chain T residue 151 LEU Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 26 THR Chi-restraints excluded: chain U residue 50 ASN Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 67 LYS Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 27 ASN Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 51 THR Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain X residue 133 GLU Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 36 LYS Chi-restraints excluded: chain Y residue 57 VAL Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 71 VAL Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Y residue 130 LYS Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 30 ASP Chi-restraints excluded: chain Z residue 57 MET Chi-restraints excluded: chain Z residue 64 LYS Chi-restraints excluded: chain Z residue 72 VAL Chi-restraints excluded: chain Z residue 83 THR Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 127 ASN Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 39 HIS Chi-restraints excluded: chain a residue 42 ARG Chi-restraints excluded: chain a residue 72 THR Chi-restraints excluded: chain a residue 84 GLU Chi-restraints excluded: chain a residue 130 SER Chi-restraints excluded: chain b residue 51 LYS Chi-restraints excluded: chain c residue 21 VAL Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 34 THR Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain c residue 37 MET Chi-restraints excluded: chain c residue 75 SER Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 83 THR Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain d residue 19 GLU Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 31 LYS Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 102 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain e residue 42 ASP Chi-restraints excluded: chain e residue 65 LYS Chi-restraints excluded: chain e residue 79 VAL Chi-restraints excluded: chain e residue 80 HIS Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain f residue 16 ARG Chi-restraints excluded: chain f residue 33 VAL Chi-restraints excluded: chain f residue 110 ILE Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 64 LEU Chi-restraints excluded: chain g residue 86 CYS Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain h residue 67 GLU Chi-restraints excluded: chain h residue 88 THR Chi-restraints excluded: chain h residue 104 THR Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 18 THR Chi-restraints excluded: chain i residue 34 THR Chi-restraints excluded: chain i residue 92 ASN Chi-restraints excluded: chain j residue 68 LYS Chi-restraints excluded: chain j residue 69 ILE Chi-restraints excluded: chain k residue 48 THR Chi-restraints excluded: chain l residue 35 ILE Chi-restraints excluded: chain l residue 46 ARG Chi-restraints excluded: chain m residue 85 LEU Chi-restraints excluded: chain o residue 10 THR Chi-restraints excluded: chain o residue 46 SER Chi-restraints excluded: chain o residue 61 LYS Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain o residue 81 ARG Chi-restraints excluded: chain o residue 88 CYS Chi-restraints excluded: chain p residue 22 LEU Chi-restraints excluded: chain p residue 25 MET Chi-restraints excluded: chain p residue 26 VAL Chi-restraints excluded: chain p residue 33 GLN Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 89 LEU Chi-restraints excluded: chain r residue 13 CYS Chi-restraints excluded: chain r residue 17 LEU Chi-restraints excluded: chain r residue 32 LEU Chi-restraints excluded: chain r residue 90 LEU Chi-restraints excluded: chain s residue 6 ARG Chi-restraints excluded: chain s residue 61 MET Chi-restraints excluded: chain s residue 189 ILE Chi-restraints excluded: chain s residue 192 VAL Chi-restraints excluded: chain t residue 41 LYS Chi-restraints excluded: chain t residue 114 ARG Chi-restraints excluded: chain t residue 160 VAL Chi-restraints excluded: chain v residue 324 ASP Chi-restraints excluded: chain v residue 373 ILE Chi-restraints excluded: chain v residue 383 LYS Chi-restraints excluded: chain v residue 396 ILE Chi-restraints excluded: chain v residue 399 LEU Chi-restraints excluded: chain v residue 401 LEU Chi-restraints excluded: chain v residue 407 THR Chi-restraints excluded: chain v residue 466 SER Chi-restraints excluded: chain w residue 20 ARG Chi-restraints excluded: chain z residue 1571 THR Chi-restraints excluded: chain z residue 1582 TRP Chi-restraints excluded: chain z residue 1613 SER Chi-restraints excluded: chain z residue 1626 VAL Chi-restraints excluded: chain z residue 1694 ILE Chi-restraints excluded: chain z residue 1696 GLU Chi-restraints excluded: chain 0 residue 1756 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 1029 optimal weight: 30.0000 chunk 783 optimal weight: 10.0000 chunk 540 optimal weight: 6.9990 chunk 115 optimal weight: 0.9980 chunk 497 optimal weight: 1.9990 chunk 699 optimal weight: 30.0000 chunk 1045 optimal weight: 10.0000 chunk 1106 optimal weight: 10.0000 chunk 546 optimal weight: 5.9990 chunk 990 optimal weight: 30.0000 chunk 298 optimal weight: 0.8980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS ** B 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN C 38 ASN C 43 ASN D 45 ASN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 HIS ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 250 ASN G 66 GLN G 82 GLN G 141 ASN H 106 GLN H 140 GLN ** I 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 213 HIS J 98 ASN L 19 GLN L 104 ASN ** M 83 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 182 HIS ** O 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 143 HIS P 28 ASN Q 8 ASN R 40 GLN R 130 ASN U 50 ASN V 135 ASN Y 24 HIS ** Y 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 100 HIS ** Y 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 127 ASN a 14 HIS b 17 HIS b 50 ASN ** c 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 24 GLN g 28 ASN h 108 GLN i 15 HIS j 66 HIS j 76 HIS k 31 ASN m 120 ASN ** o 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 33 GLN r 30 ASN s 41 GLN ** t 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 325 ASN v 363 GLN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.7282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 157414 Z= 0.285 Angle : 0.763 16.041 232053 Z= 0.387 Chirality : 0.042 0.357 29042 Planarity : 0.006 0.133 14451 Dihedral : 25.661 179.782 72449 Min Nonbonded Distance : 1.829 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.76 % Allowed : 6.46 % Favored : 92.78 % Rotamer: Outliers : 6.80 % Allowed : 26.27 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.04 % Twisted Proline : 2.03 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.69 (0.10), residues: 7132 helix: 0.50 (0.11), residues: 2441 sheet: -1.88 (0.15), residues: 970 loop : -2.08 (0.09), residues: 3721 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP z1701 HIS 0.009 0.002 HIS R 143 PHE 0.032 0.002 PHE L 127 TYR 0.031 0.002 TYR E 266 ARG 0.036 0.001 ARG F 168 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1794 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 415 poor density : 1379 time to evaluate : 7.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ILE cc_start: 0.8539 (mm) cc_final: 0.8087 (mt) REVERT: A 180 LEU cc_start: 0.9385 (mt) cc_final: 0.9084 (mt) REVERT: A 204 MET cc_start: 0.8524 (mtt) cc_final: 0.8315 (mtt) REVERT: A 233 ARG cc_start: 0.8696 (OUTLIER) cc_final: 0.8271 (tpt90) REVERT: B 133 TYR cc_start: 0.8753 (t80) cc_final: 0.8482 (t80) REVERT: B 216 MET cc_start: 0.8329 (mmm) cc_final: 0.7994 (mmm) REVERT: B 253 CYS cc_start: 0.8421 (t) cc_final: 0.8204 (t) REVERT: C 44 LEU cc_start: 0.8998 (OUTLIER) cc_final: 0.8747 (mp) REVERT: C 139 SER cc_start: 0.9384 (m) cc_final: 0.8799 (p) REVERT: C 190 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8454 (ptm160) REVERT: C 254 GLU cc_start: 0.7830 (OUTLIER) cc_final: 0.7609 (pt0) REVERT: C 297 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8525 (mp0) REVERT: D 34 LYS cc_start: 0.8907 (tmtt) cc_final: 0.8568 (tttp) REVERT: D 42 ASN cc_start: 0.7627 (t0) cc_final: 0.7378 (t0) REVERT: D 68 ARG cc_start: 0.8852 (mmp80) cc_final: 0.8097 (mtp-110) REVERT: D 210 TYR cc_start: 0.7640 (t80) cc_final: 0.6656 (t80) REVERT: E 47 VAL cc_start: 0.9064 (p) cc_final: 0.8821 (m) REVERT: E 119 ARG cc_start: 0.7553 (mmm-85) cc_final: 0.7226 (ttm-80) REVERT: E 152 ARG cc_start: 0.8509 (OUTLIER) cc_final: 0.8212 (ttp-110) REVERT: E 194 SER cc_start: 0.8738 (m) cc_final: 0.8479 (p) REVERT: E 212 TYR cc_start: 0.8673 (t80) cc_final: 0.8420 (t80) REVERT: E 235 LYS cc_start: 0.8129 (mmmt) cc_final: 0.7710 (mmmm) REVERT: E 236 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.5825 (t80) REVERT: E 264 GLN cc_start: 0.8551 (tt0) cc_final: 0.8257 (mt0) REVERT: F 41 GLN cc_start: 0.7721 (mm110) cc_final: 0.7376 (mm110) REVERT: F 96 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8668 (ttt-90) REVERT: F 137 ILE cc_start: 0.9068 (OUTLIER) cc_final: 0.8011 (mt) REVERT: F 166 LYS cc_start: 0.8987 (mtpt) cc_final: 0.8533 (mttp) REVERT: F 227 THR cc_start: 0.8592 (OUTLIER) cc_final: 0.8217 (p) REVERT: G 32 PHE cc_start: 0.8243 (m-10) cc_final: 0.8025 (m-80) REVERT: G 45 ILE cc_start: 0.8058 (pt) cc_final: 0.7845 (pt) REVERT: G 82 GLN cc_start: 0.8896 (OUTLIER) cc_final: 0.8400 (pt0) REVERT: G 110 LYS cc_start: 0.7334 (tptp) cc_final: 0.6923 (mmmm) REVERT: G 117 ARG cc_start: 0.7481 (ttm-80) cc_final: 0.6988 (tpm170) REVERT: H 50 LYS cc_start: 0.5834 (ttmt) cc_final: 0.5078 (ttmt) REVERT: I 99 ILE cc_start: 0.9180 (tp) cc_final: 0.8764 (tt) REVERT: I 115 MET cc_start: 0.8851 (tpp) cc_final: 0.7906 (tpp) REVERT: I 145 GLU cc_start: 0.8254 (tm-30) cc_final: 0.7860 (tm-30) REVERT: J 163 MET cc_start: 0.8473 (mmm) cc_final: 0.8005 (mmm) REVERT: J 167 GLN cc_start: 0.9021 (tt0) cc_final: 0.8737 (mm-40) REVERT: L 35 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.8410 (mtp85) REVERT: L 66 TYR cc_start: 0.8589 (m-80) cc_final: 0.7974 (m-80) REVERT: L 103 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7751 (ptp90) REVERT: L 164 GLU cc_start: 0.8494 (mp0) cc_final: 0.8054 (tp30) REVERT: L 171 ASP cc_start: 0.9023 (p0) cc_final: 0.8743 (p0) REVERT: M 78 GLU cc_start: 0.7473 (mm-30) cc_final: 0.7049 (mm-30) REVERT: M 95 ILE cc_start: 0.8871 (tt) cc_final: 0.8630 (mt) REVERT: M 96 GLU cc_start: 0.8312 (tm-30) cc_final: 0.8015 (tm-30) REVERT: N 23 LEU cc_start: 0.9037 (mm) cc_final: 0.8572 (mp) REVERT: N 50 ARG cc_start: 0.7955 (mtm180) cc_final: 0.7657 (mtm180) REVERT: N 51 LEU cc_start: 0.9101 (mp) cc_final: 0.8622 (mt) REVERT: N 117 ASN cc_start: 0.8921 (OUTLIER) cc_final: 0.8670 (m-40) REVERT: N 181 HIS cc_start: 0.8019 (OUTLIER) cc_final: 0.7800 (m-70) REVERT: N 182 HIS cc_start: 0.7592 (OUTLIER) cc_final: 0.6841 (p90) REVERT: O 42 ASN cc_start: 0.9319 (p0) cc_final: 0.8989 (p0) REVERT: O 87 MET cc_start: 0.8126 (mtp) cc_final: 0.7850 (mtp) REVERT: O 108 ILE cc_start: 0.9249 (mt) cc_final: 0.9049 (mt) REVERT: O 113 ASP cc_start: 0.8367 (p0) cc_final: 0.7982 (t0) REVERT: O 168 TYR cc_start: 0.8878 (t80) cc_final: 0.8028 (t80) REVERT: O 173 GLN cc_start: 0.8831 (tm-30) cc_final: 0.8471 (tm-30) REVERT: O 186 GLU cc_start: 0.8313 (pt0) cc_final: 0.7762 (pm20) REVERT: P 110 ASP cc_start: 0.7760 (p0) cc_final: 0.7315 (t0) REVERT: R 20 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8747 (ttmm) REVERT: R 25 ASP cc_start: 0.8773 (t70) cc_final: 0.8159 (t0) REVERT: R 86 ASN cc_start: 0.8960 (t0) cc_final: 0.8549 (t0) REVERT: R 153 LYS cc_start: 0.7430 (pptt) cc_final: 0.7205 (pptt) REVERT: S 2 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8588 (tttt) REVERT: S 61 ILE cc_start: 0.9093 (mm) cc_final: 0.8831 (mm) REVERT: S 123 SER cc_start: 0.9088 (m) cc_final: 0.8371 (t) REVERT: S 127 MET cc_start: 0.8163 (mpp) cc_final: 0.7638 (mtm) REVERT: T 70 HIS cc_start: 0.8328 (OUTLIER) cc_final: 0.7666 (p90) REVERT: T 154 ILE cc_start: 0.9025 (OUTLIER) cc_final: 0.8815 (pp) REVERT: U 23 LEU cc_start: 0.8927 (OUTLIER) cc_final: 0.8712 (tt) REVERT: U 30 GLU cc_start: 0.8841 (mm-30) cc_final: 0.8195 (pp20) REVERT: U 73 THR cc_start: 0.8324 (m) cc_final: 0.8086 (m) REVERT: V 27 ASN cc_start: 0.8564 (OUTLIER) cc_final: 0.8265 (p0) REVERT: W 48 GLN cc_start: 0.8874 (mt0) cc_final: 0.8612 (tt0) REVERT: W 50 ASN cc_start: 0.7791 (t0) cc_final: 0.7443 (m110) REVERT: X 111 GLN cc_start: 0.8455 (mm-40) cc_final: 0.8116 (tp-100) REVERT: Y 30 MET cc_start: 0.8386 (ttm) cc_final: 0.8164 (ttp) REVERT: Y 106 ILE cc_start: 0.9056 (mt) cc_final: 0.8837 (mt) REVERT: Y 107 THR cc_start: 0.8992 (t) cc_final: 0.8723 (p) REVERT: Z 5 MET cc_start: 0.8572 (mmt) cc_final: 0.8216 (mmt) REVERT: Z 39 SER cc_start: 0.8684 (p) cc_final: 0.8395 (p) REVERT: Z 62 ILE cc_start: 0.9141 (mp) cc_final: 0.8814 (mp) REVERT: Z 64 LYS cc_start: 0.9139 (OUTLIER) cc_final: 0.8900 (tttm) REVERT: Z 97 ASN cc_start: 0.8724 (p0) cc_final: 0.8387 (p0) REVERT: a 32 ARG cc_start: 0.8928 (OUTLIER) cc_final: 0.8589 (mtt-85) REVERT: a 38 MET cc_start: 0.8557 (mmm) cc_final: 0.8036 (mtp) REVERT: a 46 ASP cc_start: 0.6736 (m-30) cc_final: 0.6498 (m-30) REVERT: a 84 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7510 (pp20) REVERT: c 35 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8735 (mp) REVERT: c 90 ARG cc_start: 0.8777 (ptt90) cc_final: 0.8233 (mtm-85) REVERT: d 19 GLU cc_start: 0.8429 (OUTLIER) cc_final: 0.7524 (pm20) REVERT: d 48 GLU cc_start: 0.7535 (OUTLIER) cc_final: 0.7018 (mm-30) REVERT: d 61 ASP cc_start: 0.8655 (t0) cc_final: 0.8428 (t70) REVERT: d 117 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.8980 (mm) REVERT: d 121 ASN cc_start: 0.8664 (t0) cc_final: 0.8359 (t0) REVERT: e 113 GLU cc_start: 0.8380 (pm20) cc_final: 0.7668 (pt0) REVERT: e 124 ASN cc_start: 0.9241 (p0) cc_final: 0.8899 (p0) REVERT: f 16 ARG cc_start: 0.9105 (OUTLIER) cc_final: 0.8888 (ptm160) REVERT: f 34 TYR cc_start: 0.8131 (m-80) cc_final: 0.7779 (m-80) REVERT: g 13 TYR cc_start: 0.8014 (m-80) cc_final: 0.7686 (m-80) REVERT: g 102 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.7787 (mp) REVERT: h 78 TYR cc_start: 0.8236 (m-10) cc_final: 0.7808 (m-10) REVERT: i 16 LYS cc_start: 0.9104 (tttt) cc_final: 0.8664 (mmtt) REVERT: j 85 LYS cc_start: 0.8381 (ttpt) cc_final: 0.7908 (ttmt) REVERT: k 10 ASP cc_start: 0.8790 (t0) cc_final: 0.8157 (m-30) REVERT: k 37 ARG cc_start: 0.8595 (OUTLIER) cc_final: 0.8361 (tpt170) REVERT: k 50 LYS cc_start: 0.8259 (mmtt) cc_final: 0.7732 (ttpt) REVERT: l 46 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8708 (ptt90) REVERT: o 100 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7519 (ttpp) REVERT: p 47 MET cc_start: 0.9005 (mmt) cc_final: 0.8749 (tpt) REVERT: r 30 ASN cc_start: 0.8475 (OUTLIER) cc_final: 0.7687 (m-40) REVERT: s 60 MET cc_start: 0.8102 (mtp) cc_final: 0.7746 (mtp) REVERT: t 1 MET cc_start: 0.1555 (mpp) cc_final: 0.0963 (mmp) REVERT: t 116 MET cc_start: 0.2428 (ptt) cc_final: 0.2052 (tpt) REVERT: v 342 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7150 (mm-30) REVERT: v 355 LEU cc_start: 0.8314 (mt) cc_final: 0.7754 (mt) REVERT: v 383 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7900 (mtpp) REVERT: v 396 ILE cc_start: 0.6656 (OUTLIER) cc_final: 0.6017 (tp) REVERT: z 1588 LYS cc_start: 0.8255 (tptm) cc_final: 0.7933 (tppt) REVERT: z 1627 LYS cc_start: 0.8019 (ptmm) cc_final: 0.7777 (ptmm) REVERT: z 1677 ARG cc_start: 0.7424 (ttt90) cc_final: 0.6412 (ptp90) REVERT: z 1701 TRP cc_start: 0.7878 (t60) cc_final: 0.7308 (t60) outliers start: 415 outliers final: 259 residues processed: 1651 average time/residue: 1.2890 time to fit residues: 3696.0437 Evaluate side-chains 1537 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 296 poor density : 1241 time to evaluate : 7.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain B residue 381 THR Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 254 GLU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 297 GLU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 129 GLU Chi-restraints excluded: chain D residue 144 CYS Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 217 ASP Chi-restraints excluded: chain D residue 264 LYS Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 217 SER Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain I residue 8 CYS Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 143 GLN Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 113 ILE Chi-restraints excluded: chain J residue 139 PHE Chi-restraints excluded: chain J residue 171 ASP Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 103 ARG Chi-restraints excluded: chain L residue 113 ASN Chi-restraints excluded: chain L residue 115 GLN Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 47 ARG Chi-restraints excluded: chain M residue 57 LEU Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 121 ARG Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 117 ASN Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 161 MET Chi-restraints excluded: chain N residue 181 HIS Chi-restraints excluded: chain N residue 182 HIS Chi-restraints excluded: chain N residue 193 ARG Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain P residue 5 SER Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 57 CYS Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 104 LEU Chi-restraints excluded: chain P residue 105 LYS Chi-restraints excluded: chain P residue 137 ASN Chi-restraints excluded: chain Q residue 9 LYS Chi-restraints excluded: chain Q residue 22 ASP Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 54 SER Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 68 ARG Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 126 LEU Chi-restraints excluded: chain Q residue 136 THR Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 167 VAL Chi-restraints excluded: chain R residue 20 LYS Chi-restraints excluded: chain R residue 37 SER Chi-restraints excluded: chain R residue 57 VAL Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 130 ASN Chi-restraints excluded: chain R residue 168 GLU Chi-restraints excluded: chain S residue 2 LYS Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 64 CYS Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 68 PHE Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 80 ILE Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 131 GLU Chi-restraints excluded: chain S residue 159 LEU Chi-restraints excluded: chain T residue 16 SER Chi-restraints excluded: chain T residue 45 MET Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 99 SER Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 49 VAL Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 62 THR Chi-restraints excluded: chain U residue 99 TRP Chi-restraints excluded: chain U residue 107 LYS Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 27 ASN Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 105 ILE Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 41 LEU Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 57 GLN Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 95 THR Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain X residue 119 ILE Chi-restraints excluded: chain X residue 127 LEU Chi-restraints excluded: chain X residue 133 GLU Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 67 ILE Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 64 LYS Chi-restraints excluded: chain Z residue 72 VAL Chi-restraints excluded: chain Z residue 78 ASN Chi-restraints excluded: chain Z residue 83 THR Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain a residue 32 ARG Chi-restraints excluded: chain a residue 34 ASN Chi-restraints excluded: chain a residue 39 HIS Chi-restraints excluded: chain a residue 81 LEU Chi-restraints excluded: chain a residue 84 GLU Chi-restraints excluded: chain a residue 86 THR Chi-restraints excluded: chain a residue 93 ASN Chi-restraints excluded: chain a residue 95 THR Chi-restraints excluded: chain a residue 130 SER Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 13 SER Chi-restraints excluded: chain b residue 50 ASN Chi-restraints excluded: chain c residue 16 SER Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain c residue 37 MET Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain d residue 19 GLU Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 31 LYS Chi-restraints excluded: chain d residue 32 ARG Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 100 ASN Chi-restraints excluded: chain d residue 102 LEU Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain e residue 25 SER Chi-restraints excluded: chain e residue 42 ASP Chi-restraints excluded: chain e residue 65 LYS Chi-restraints excluded: chain e residue 78 LEU Chi-restraints excluded: chain e residue 80 HIS Chi-restraints excluded: chain e residue 107 ASN Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain f residue 16 ARG Chi-restraints excluded: chain f residue 104 MET Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 12 SER Chi-restraints excluded: chain g residue 48 VAL Chi-restraints excluded: chain g residue 64 LEU Chi-restraints excluded: chain g residue 67 LEU Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain h residue 91 MET Chi-restraints excluded: chain h residue 104 THR Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 34 THR Chi-restraints excluded: chain i residue 79 THR Chi-restraints excluded: chain i residue 92 ASN Chi-restraints excluded: chain k residue 13 LEU Chi-restraints excluded: chain k residue 23 VAL Chi-restraints excluded: chain k residue 31 ASN Chi-restraints excluded: chain k residue 37 ARG Chi-restraints excluded: chain k residue 48 THR Chi-restraints excluded: chain k residue 60 LEU Chi-restraints excluded: chain l residue 35 ILE Chi-restraints excluded: chain l residue 46 ARG Chi-restraints excluded: chain m residue 102 ARG Chi-restraints excluded: chain o residue 46 SER Chi-restraints excluded: chain o residue 61 LYS Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain o residue 100 LYS Chi-restraints excluded: chain p residue 22 LEU Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 63 THR Chi-restraints excluded: chain p residue 89 LEU Chi-restraints excluded: chain r residue 13 CYS Chi-restraints excluded: chain r residue 17 LEU Chi-restraints excluded: chain r residue 30 ASN Chi-restraints excluded: chain r residue 33 LYS Chi-restraints excluded: chain r residue 124 VAL Chi-restraints excluded: chain s residue 59 THR Chi-restraints excluded: chain s residue 61 MET Chi-restraints excluded: chain s residue 192 VAL Chi-restraints excluded: chain t residue 62 LEU Chi-restraints excluded: chain t residue 114 ARG Chi-restraints excluded: chain v residue 324 ASP Chi-restraints excluded: chain v residue 362 ILE Chi-restraints excluded: chain v residue 383 LYS Chi-restraints excluded: chain v residue 396 ILE Chi-restraints excluded: chain v residue 399 LEU Chi-restraints excluded: chain v residue 401 LEU Chi-restraints excluded: chain v residue 407 THR Chi-restraints excluded: chain v residue 409 LEU Chi-restraints excluded: chain v residue 466 SER Chi-restraints excluded: chain z residue 1582 TRP Chi-restraints excluded: chain z residue 1599 SER Chi-restraints excluded: chain z residue 1608 PHE Chi-restraints excluded: chain z residue 1611 ILE Chi-restraints excluded: chain z residue 1613 SER Chi-restraints excluded: chain z residue 1650 ILE Chi-restraints excluded: chain z residue 1696 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 921 optimal weight: 20.0000 chunk 628 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 824 optimal weight: 30.0000 chunk 456 optimal weight: 6.9990 chunk 944 optimal weight: 8.9990 chunk 765 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 565 optimal weight: 7.9990 chunk 993 optimal weight: 10.0000 chunk 279 optimal weight: 1.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 55 HIS B 322 HIS ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 245 HIS ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 HIS ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 124 HIS ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 106 GLN ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 147 HIS J 97 ASN L 159 ASN L 188 ASN N 117 ASN N 182 HIS N 201 HIS O 50 ASN P 25 HIS S 144 GLN T 90 ASN U 50 ASN V 135 ASN W 59 HIS Z 76 ASN a 14 HIS b 50 ASN b 61 ASN ** c 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 24 GLN g 28 ASN i 26 HIS ** j 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 33 GLN r 46 HIS r 85 ASN ** t 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 363 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.8205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.246 157414 Z= 0.476 Angle : 0.887 19.865 232053 Z= 0.445 Chirality : 0.047 0.429 29042 Planarity : 0.007 0.179 14451 Dihedral : 25.590 179.897 72410 Min Nonbonded Distance : 1.100 Molprobity Statistics. All-atom Clashscore : 16.97 Ramachandran Plot: Outliers : 0.76 % Allowed : 8.67 % Favored : 90.58 % Rotamer: Outliers : 7.96 % Allowed : 26.27 % Favored : 65.77 % Cbeta Deviations : 0.01 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.04 % Twisted Proline : 2.03 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.92 (0.09), residues: 7132 helix: 0.23 (0.10), residues: 2453 sheet: -1.91 (0.15), residues: 980 loop : -2.20 (0.09), residues: 3699 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP z1701 HIS 0.026 0.002 HIS b 49 PHE 0.043 0.003 PHE b 45 TYR 0.036 0.003 TYR D 210 ARG 0.017 0.001 ARG t 16 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1795 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 486 poor density : 1309 time to evaluate : 7.313 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: A 107 MET cc_start: 0.8609 (mtm) cc_final: 0.8396 (mtm) REVERT: A 145 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8245 (mmmt) REVERT: A 179 ILE cc_start: 0.8617 (mm) cc_final: 0.8311 (mt) REVERT: A 204 MET cc_start: 0.8479 (mtt) cc_final: 0.8131 (mtt) REVERT: B 78 ILE cc_start: 0.9499 (OUTLIER) cc_final: 0.9228 (mp) REVERT: B 216 MET cc_start: 0.8343 (mmm) cc_final: 0.7820 (mmm) REVERT: B 253 CYS cc_start: 0.8985 (t) cc_final: 0.8513 (t) REVERT: C 89 GLN cc_start: 0.9214 (OUTLIER) cc_final: 0.8880 (mm-40) REVERT: C 190 ARG cc_start: 0.9224 (OUTLIER) cc_final: 0.8465 (ttm170) REVERT: C 268 ARG cc_start: 0.6900 (ptt180) cc_final: 0.6668 (ptp-170) REVERT: D 34 LYS cc_start: 0.8945 (tmtt) cc_final: 0.8633 (tttp) REVERT: D 68 ARG cc_start: 0.8975 (mmp80) cc_final: 0.8312 (mtp-110) REVERT: D 160 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.7671 (p90) REVERT: E 152 ARG cc_start: 0.8483 (OUTLIER) cc_final: 0.8194 (ttp-110) REVERT: E 194 SER cc_start: 0.8956 (m) cc_final: 0.8689 (p) REVERT: E 235 LYS cc_start: 0.8007 (mmmt) cc_final: 0.7676 (mmmt) REVERT: E 236 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.6304 (t80) REVERT: E 240 GLU cc_start: 0.7998 (tm-30) cc_final: 0.7299 (tm-30) REVERT: F 96 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8749 (ttt-90) REVERT: F 111 LEU cc_start: 0.9271 (OUTLIER) cc_final: 0.9006 (mt) REVERT: F 137 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8698 (mt) REVERT: F 166 LYS cc_start: 0.9036 (mtpt) cc_final: 0.8574 (mttp) REVERT: F 227 THR cc_start: 0.8559 (OUTLIER) cc_final: 0.8175 (p) REVERT: G 82 GLN cc_start: 0.8806 (OUTLIER) cc_final: 0.8512 (pp30) REVERT: G 110 LYS cc_start: 0.7096 (tptp) cc_final: 0.6787 (mmmm) REVERT: G 117 ARG cc_start: 0.7754 (ttm-80) cc_final: 0.7343 (tpm170) REVERT: G 220 GLU cc_start: 0.8830 (pp20) cc_final: 0.8602 (pp20) REVERT: G 230 TYR cc_start: 0.7881 (t80) cc_final: 0.7253 (t80) REVERT: H 50 LYS cc_start: 0.6041 (ttmt) cc_final: 0.5216 (ttmt) REVERT: I 115 MET cc_start: 0.8973 (tpp) cc_final: 0.8192 (tpp) REVERT: I 184 MET cc_start: 0.8203 (mmm) cc_final: 0.7615 (mmt) REVERT: L 35 ARG cc_start: 0.8912 (OUTLIER) cc_final: 0.8565 (mtp85) REVERT: L 113 ASN cc_start: 0.9274 (OUTLIER) cc_final: 0.9024 (m-40) REVERT: L 161 TYR cc_start: 0.7732 (OUTLIER) cc_final: 0.7209 (m-80) REVERT: L 164 GLU cc_start: 0.8725 (mp0) cc_final: 0.8168 (tp30) REVERT: L 197 LYS cc_start: 0.8833 (OUTLIER) cc_final: 0.8626 (tttm) REVERT: N 19 MET cc_start: 0.9006 (mmp) cc_final: 0.8770 (tpt) REVERT: N 23 LEU cc_start: 0.9142 (mm) cc_final: 0.8689 (mp) REVERT: N 50 ARG cc_start: 0.8138 (mtm180) cc_final: 0.7777 (mtm180) REVERT: N 51 LEU cc_start: 0.9149 (mp) cc_final: 0.8889 (mt) REVERT: N 145 ASN cc_start: 0.8241 (t0) cc_final: 0.7995 (t0) REVERT: N 182 HIS cc_start: 0.8103 (OUTLIER) cc_final: 0.7398 (p90) REVERT: O 42 ASN cc_start: 0.9380 (p0) cc_final: 0.8935 (p0) REVERT: O 113 ASP cc_start: 0.8415 (p0) cc_final: 0.7916 (t0) REVERT: O 141 LEU cc_start: 0.9249 (tp) cc_final: 0.8888 (tt) REVERT: O 155 THR cc_start: 0.9052 (p) cc_final: 0.8728 (t) REVERT: O 168 TYR cc_start: 0.9015 (t80) cc_final: 0.8293 (t80) REVERT: O 173 GLN cc_start: 0.8854 (tm-30) cc_final: 0.8324 (tm-30) REVERT: O 180 GLN cc_start: 0.8221 (tp40) cc_final: 0.7889 (tp-100) REVERT: R 25 ASP cc_start: 0.8878 (t70) cc_final: 0.8055 (t0) REVERT: R 45 ILE cc_start: 0.9029 (mm) cc_final: 0.8822 (mt) REVERT: R 86 ASN cc_start: 0.8910 (t0) cc_final: 0.8553 (t0) REVERT: S 10 TYR cc_start: 0.8777 (m-80) cc_final: 0.8455 (m-10) REVERT: S 17 LEU cc_start: 0.8858 (pt) cc_final: 0.8578 (tp) REVERT: S 61 ILE cc_start: 0.9280 (OUTLIER) cc_final: 0.8956 (mm) REVERT: S 96 GLU cc_start: 0.7826 (mt-10) cc_final: 0.7555 (mt-10) REVERT: S 127 MET cc_start: 0.8480 (mpp) cc_final: 0.8238 (mtp) REVERT: S 160 ARG cc_start: 0.8650 (mmm-85) cc_final: 0.8397 (mmm160) REVERT: T 70 HIS cc_start: 0.8584 (OUTLIER) cc_final: 0.8058 (p90) REVERT: T 151 LEU cc_start: 0.9304 (OUTLIER) cc_final: 0.9084 (mt) REVERT: T 154 ILE cc_start: 0.9018 (OUTLIER) cc_final: 0.8680 (pp) REVERT: U 30 GLU cc_start: 0.8908 (mm-30) cc_final: 0.8236 (tm-30) REVERT: U 83 LEU cc_start: 0.9156 (mp) cc_final: 0.8903 (mt) REVERT: V 27 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.8270 (p0) REVERT: W 19 ARG cc_start: 0.7686 (ttt180) cc_final: 0.7450 (ttt90) REVERT: W 50 ASN cc_start: 0.8271 (t0) cc_final: 0.7965 (t0) REVERT: X 101 ASP cc_start: 0.8622 (t0) cc_final: 0.8383 (t0) REVERT: X 111 GLN cc_start: 0.8390 (mm-40) cc_final: 0.8039 (tp-100) REVERT: Y 74 TYR cc_start: 0.8756 (OUTLIER) cc_final: 0.8227 (t80) REVERT: Y 75 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8471 (mtm180) REVERT: Z 5 MET cc_start: 0.8589 (mmt) cc_final: 0.8162 (mmt) REVERT: Z 6 LYS cc_start: 0.9082 (mmmt) cc_final: 0.8858 (tppt) REVERT: Z 62 ILE cc_start: 0.9100 (mp) cc_final: 0.8791 (mp) REVERT: Z 97 ASN cc_start: 0.8725 (p0) cc_final: 0.8365 (p0) REVERT: a 3 SER cc_start: 0.9100 (p) cc_final: 0.7947 (t) REVERT: a 32 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8315 (mtt-85) REVERT: a 38 MET cc_start: 0.8599 (mmm) cc_final: 0.8114 (mtp) REVERT: b 8 THR cc_start: 0.9254 (OUTLIER) cc_final: 0.8839 (m) REVERT: b 41 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8555 (ttt180) REVERT: c 35 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8776 (mp) REVERT: d 19 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7631 (pm20) REVERT: d 31 LYS cc_start: 0.9263 (OUTLIER) cc_final: 0.9021 (ptmt) REVERT: d 48 GLU cc_start: 0.7340 (OUTLIER) cc_final: 0.6983 (mp0) REVERT: d 61 ASP cc_start: 0.8765 (t0) cc_final: 0.8522 (t70) REVERT: d 117 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9059 (mm) REVERT: d 121 ASN cc_start: 0.8929 (t0) cc_final: 0.8659 (t0) REVERT: e 19 LYS cc_start: 0.8730 (OUTLIER) cc_final: 0.8054 (mmmm) REVERT: e 32 LYS cc_start: 0.8709 (mmmt) cc_final: 0.8454 (mmtp) REVERT: f 16 ARG cc_start: 0.9090 (OUTLIER) cc_final: 0.8488 (ptp90) REVERT: f 34 TYR cc_start: 0.8402 (m-80) cc_final: 0.8003 (m-80) REVERT: f 83 MET cc_start: 0.8583 (tpp) cc_final: 0.8362 (mmm) REVERT: f 85 ARG cc_start: 0.8774 (OUTLIER) cc_final: 0.8507 (ttm170) REVERT: g 13 TYR cc_start: 0.8655 (m-80) cc_final: 0.8152 (m-80) REVERT: g 102 ILE cc_start: 0.8443 (OUTLIER) cc_final: 0.7860 (mp) REVERT: i 12 ASN cc_start: 0.8233 (t0) cc_final: 0.7720 (p0) REVERT: k 10 ASP cc_start: 0.8884 (t0) cc_final: 0.8217 (m-30) REVERT: k 37 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.8463 (tpt170) REVERT: k 50 LYS cc_start: 0.8305 (mmtt) cc_final: 0.7691 (ttpt) REVERT: k 52 LYS cc_start: 0.8620 (mmmt) cc_final: 0.8365 (mtmt) REVERT: k 59 SER cc_start: 0.7180 (m) cc_final: 0.6555 (p) REVERT: o 26 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.8593 (t80) REVERT: o 45 GLN cc_start: 0.7530 (tp40) cc_final: 0.7086 (tt0) REVERT: o 100 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.7801 (ttpt) REVERT: o 102 GLN cc_start: 0.6701 (OUTLIER) cc_final: 0.6281 (mp10) REVERT: p 47 MET cc_start: 0.9081 (mmt) cc_final: 0.8802 (tpt) REVERT: r 5 LEU cc_start: 0.9071 (tp) cc_final: 0.8774 (tp) REVERT: r 14 SER cc_start: 0.9407 (t) cc_final: 0.9166 (p) REVERT: s 189 ILE cc_start: 0.5326 (OUTLIER) cc_final: 0.4815 (mp) REVERT: t 116 MET cc_start: 0.3186 (ptt) cc_final: 0.2843 (tpt) REVERT: v 355 LEU cc_start: 0.8397 (mt) cc_final: 0.7925 (mt) REVERT: v 383 LYS cc_start: 0.8447 (OUTLIER) cc_final: 0.7950 (mtpp) REVERT: v 470 TYR cc_start: 0.8242 (m-80) cc_final: 0.8019 (m-80) REVERT: z 1629 ARG cc_start: 0.7766 (mpt90) cc_final: 0.7061 (mmm-85) REVERT: z 1677 ARG cc_start: 0.7378 (ttt90) cc_final: 0.6453 (ptp90) outliers start: 486 outliers final: 307 residues processed: 1625 average time/residue: 1.3063 time to fit residues: 3705.5198 Evaluate side-chains 1561 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 349 poor density : 1212 time to evaluate : 7.132 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 73 THR Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 145 LYS Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain B residue 17 LEU Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 201 LEU Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain B residue 363 ILE Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 101 MET Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 246 VAL Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 314 LEU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 56 THR Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 221 LYS Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain D residue 232 THR Chi-restraints excluded: chain D residue 264 LYS Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain E residue 100 THR Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 141 THR Chi-restraints excluded: chain E residue 152 ARG Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 111 LEU Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 217 SER Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 82 GLN Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 108 GLN Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain H residue 3 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 134 CYS Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain I residue 8 CYS Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 71 CYS Chi-restraints excluded: chain I residue 142 LEU Chi-restraints excluded: chain I residue 143 GLN Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 83 LEU Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 139 PHE Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 171 ASP Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 113 ASN Chi-restraints excluded: chain L residue 115 GLN Chi-restraints excluded: chain L residue 125 ILE Chi-restraints excluded: chain L residue 157 ILE Chi-restraints excluded: chain L residue 161 TYR Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 197 LYS Chi-restraints excluded: chain L residue 208 GLU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 47 ARG Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain M residue 121 ARG Chi-restraints excluded: chain M residue 127 VAL Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 133 ILE Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 161 MET Chi-restraints excluded: chain N residue 182 HIS Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain O residue 26 GLN Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 145 VAL Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 57 CYS Chi-restraints excluded: chain P residue 94 MET Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 104 LEU Chi-restraints excluded: chain P residue 105 LYS Chi-restraints excluded: chain P residue 113 VAL Chi-restraints excluded: chain P residue 137 ASN Chi-restraints excluded: chain P residue 142 SER Chi-restraints excluded: chain P residue 152 GLU Chi-restraints excluded: chain Q residue 9 LYS Chi-restraints excluded: chain Q residue 22 ASP Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 54 SER Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 68 ARG Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 167 VAL Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 64 CYS Chi-restraints excluded: chain S residue 68 PHE Chi-restraints excluded: chain S residue 71 SER Chi-restraints excluded: chain S residue 80 ILE Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 131 GLU Chi-restraints excluded: chain S residue 148 SER Chi-restraints excluded: chain S residue 151 LYS Chi-restraints excluded: chain T residue 25 VAL Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 150 LEU Chi-restraints excluded: chain T residue 151 LEU Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain U residue 27 HIS Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 62 THR Chi-restraints excluded: chain U residue 99 TRP Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 22 VAL Chi-restraints excluded: chain V residue 27 ASN Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 105 ILE Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 25 ASP Chi-restraints excluded: chain W residue 53 VAL Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 51 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 113 VAL Chi-restraints excluded: chain X residue 127 LEU Chi-restraints excluded: chain X residue 133 GLU Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 67 ILE Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 75 ARG Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 72 VAL Chi-restraints excluded: chain Z residue 78 ASN Chi-restraints excluded: chain Z residue 83 THR Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain a residue 32 ARG Chi-restraints excluded: chain a residue 34 ASN Chi-restraints excluded: chain a residue 39 HIS Chi-restraints excluded: chain a residue 72 THR Chi-restraints excluded: chain a residue 81 LEU Chi-restraints excluded: chain a residue 86 THR Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 13 SER Chi-restraints excluded: chain b residue 41 ARG Chi-restraints excluded: chain c residue 16 SER Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain c residue 37 MET Chi-restraints excluded: chain c residue 50 ASN Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 81 LEU Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain d residue 19 GLU Chi-restraints excluded: chain d residue 21 VAL Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 31 LYS Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 100 ASN Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain e residue 19 LYS Chi-restraints excluded: chain e residue 25 SER Chi-restraints excluded: chain e residue 42 ASP Chi-restraints excluded: chain e residue 65 LYS Chi-restraints excluded: chain e residue 79 VAL Chi-restraints excluded: chain e residue 80 HIS Chi-restraints excluded: chain e residue 107 ASN Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain f residue 16 ARG Chi-restraints excluded: chain f residue 43 LEU Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 85 ARG Chi-restraints excluded: chain f residue 92 LEU Chi-restraints excluded: chain f residue 101 ILE Chi-restraints excluded: chain f residue 104 MET Chi-restraints excluded: chain g residue 6 THR Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 48 VAL Chi-restraints excluded: chain g residue 64 LEU Chi-restraints excluded: chain g residue 67 LEU Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain h residue 8 ASP Chi-restraints excluded: chain h residue 22 GLU Chi-restraints excluded: chain h residue 26 VAL Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 91 MET Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 34 THR Chi-restraints excluded: chain i residue 79 THR Chi-restraints excluded: chain j residue 68 LYS Chi-restraints excluded: chain k residue 13 LEU Chi-restraints excluded: chain k residue 23 VAL Chi-restraints excluded: chain k residue 37 ARG Chi-restraints excluded: chain k residue 48 THR Chi-restraints excluded: chain k residue 60 LEU Chi-restraints excluded: chain k residue 66 VAL Chi-restraints excluded: chain l residue 35 ILE Chi-restraints excluded: chain m residue 102 ARG Chi-restraints excluded: chain o residue 10 THR Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 26 TYR Chi-restraints excluded: chain o residue 46 SER Chi-restraints excluded: chain o residue 61 LYS Chi-restraints excluded: chain o residue 62 THR Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain o residue 81 ARG Chi-restraints excluded: chain o residue 100 LYS Chi-restraints excluded: chain o residue 102 GLN Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 63 THR Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain p residue 89 LEU Chi-restraints excluded: chain r residue 13 CYS Chi-restraints excluded: chain r residue 17 LEU Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain r residue 27 THR Chi-restraints excluded: chain r residue 30 ASN Chi-restraints excluded: chain r residue 33 LYS Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 124 VAL Chi-restraints excluded: chain s residue 30 VAL Chi-restraints excluded: chain s residue 61 MET Chi-restraints excluded: chain s residue 91 THR Chi-restraints excluded: chain s residue 189 ILE Chi-restraints excluded: chain s residue 192 VAL Chi-restraints excluded: chain t residue 13 VAL Chi-restraints excluded: chain t residue 62 LEU Chi-restraints excluded: chain t residue 96 LYS Chi-restraints excluded: chain t residue 131 GLU Chi-restraints excluded: chain t residue 139 VAL Chi-restraints excluded: chain v residue 324 ASP Chi-restraints excluded: chain v residue 383 LYS Chi-restraints excluded: chain v residue 396 ILE Chi-restraints excluded: chain v residue 399 LEU Chi-restraints excluded: chain v residue 401 LEU Chi-restraints excluded: chain v residue 407 THR Chi-restraints excluded: chain v residue 409 LEU Chi-restraints excluded: chain v residue 466 SER Chi-restraints excluded: chain z residue 1582 TRP Chi-restraints excluded: chain z residue 1599 SER Chi-restraints excluded: chain z residue 1608 PHE Chi-restraints excluded: chain z residue 1611 ILE Chi-restraints excluded: chain z residue 1613 SER Chi-restraints excluded: chain z residue 1650 ILE Chi-restraints excluded: chain z residue 1694 ILE Chi-restraints excluded: chain z residue 1696 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 372 optimal weight: 3.9990 chunk 996 optimal weight: 6.9990 chunk 218 optimal weight: 2.9990 chunk 649 optimal weight: 5.9990 chunk 273 optimal weight: 8.9990 chunk 1107 optimal weight: 20.0000 chunk 919 optimal weight: 20.0000 chunk 512 optimal weight: 3.9990 chunk 92 optimal weight: 0.9990 chunk 366 optimal weight: 0.3980 chunk 581 optimal weight: 0.9980 overall best weight: 1.8786 ------------------------------------------------------------------------------- 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 158 GLN B 322 HIS C 347 HIS D 45 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 ASN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 208 ASN ** I 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 158 HIS ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 108 GLN S 117 HIS Z 127 ASN b 50 ASN ** c 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 24 GLN g 28 ASN i 26 HIS j 48 ASN j 66 HIS m 120 ASN ** o 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 36 ASN r 46 HIS ** t 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 363 GLN z1704 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.8427 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 157414 Z= 0.202 Angle : 0.706 16.768 232053 Z= 0.358 Chirality : 0.039 0.360 29042 Planarity : 0.005 0.151 14451 Dihedral : 25.543 179.849 72382 Min Nonbonded Distance : 1.186 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.62 % Allowed : 6.58 % Favored : 92.81 % Rotamer: Outliers : 5.59 % Allowed : 28.80 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.04 % Twisted Proline : 1.69 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.10), residues: 7132 helix: 0.68 (0.11), residues: 2446 sheet: -1.73 (0.16), residues: 963 loop : -1.90 (0.10), residues: 3723 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP N 120 HIS 0.021 0.001 HIS N 182 PHE 0.020 0.002 PHE F 27 TYR 0.029 0.002 TYR z1639 ARG 0.013 0.001 ARG c 17 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1659 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 341 poor density : 1318 time to evaluate : 9.586 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: A 179 ILE cc_start: 0.8477 (mm) cc_final: 0.8086 (mt) REVERT: A 180 LEU cc_start: 0.9436 (mt) cc_final: 0.8939 (mt) REVERT: A 233 ARG cc_start: 0.8683 (OUTLIER) cc_final: 0.7815 (tpt170) REVERT: B 78 ILE cc_start: 0.9409 (OUTLIER) cc_final: 0.9166 (mp) REVERT: B 216 MET cc_start: 0.8312 (mmm) cc_final: 0.7891 (mmm) REVERT: B 253 CYS cc_start: 0.8308 (t) cc_final: 0.8083 (t) REVERT: C 89 GLN cc_start: 0.9119 (OUTLIER) cc_final: 0.8821 (mm-40) REVERT: C 139 SER cc_start: 0.9353 (m) cc_final: 0.8893 (t) REVERT: C 268 ARG cc_start: 0.6400 (ptt180) cc_final: 0.6192 (ptp-170) REVERT: D 34 LYS cc_start: 0.8871 (tmtt) cc_final: 0.8595 (tttp) REVERT: D 68 ARG cc_start: 0.8915 (mmp80) cc_final: 0.8308 (mtp-110) REVERT: D 89 LYS cc_start: 0.8661 (mmmt) cc_final: 0.8309 (mppt) REVERT: D 160 PHE cc_start: 0.8038 (OUTLIER) cc_final: 0.7416 (p90) REVERT: D 217 ASP cc_start: 0.8688 (m-30) cc_final: 0.8451 (p0) REVERT: E 194 SER cc_start: 0.8954 (m) cc_final: 0.8633 (p) REVERT: E 202 VAL cc_start: 0.8087 (OUTLIER) cc_final: 0.7883 (t) REVERT: E 235 LYS cc_start: 0.8084 (mmmt) cc_final: 0.7818 (mmmt) REVERT: E 236 TYR cc_start: 0.8274 (OUTLIER) cc_final: 0.6375 (t80) REVERT: E 240 GLU cc_start: 0.7656 (tm-30) cc_final: 0.6951 (tm-30) REVERT: F 96 ARG cc_start: 0.8973 (OUTLIER) cc_final: 0.8705 (ttt-90) REVERT: F 106 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8530 (mtpt) REVERT: F 112 GLN cc_start: 0.8417 (tp40) cc_final: 0.8210 (tp40) REVERT: F 137 ILE cc_start: 0.9324 (OUTLIER) cc_final: 0.8690 (mt) REVERT: F 138 VAL cc_start: 0.9092 (m) cc_final: 0.8747 (p) REVERT: F 166 LYS cc_start: 0.9013 (mtpt) cc_final: 0.8602 (mttp) REVERT: F 227 THR cc_start: 0.8539 (OUTLIER) cc_final: 0.8172 (p) REVERT: G 110 LYS cc_start: 0.7158 (tptp) cc_final: 0.6881 (mmmm) REVERT: G 117 ARG cc_start: 0.7658 (ttm-80) cc_final: 0.7266 (tpm170) REVERT: G 230 TYR cc_start: 0.7899 (t80) cc_final: 0.7067 (t80) REVERT: H 21 LYS cc_start: 0.8892 (OUTLIER) cc_final: 0.8305 (mmtt) REVERT: H 50 LYS cc_start: 0.5845 (ttmt) cc_final: 0.5088 (ttmt) REVERT: H 122 TYR cc_start: 0.9081 (t80) cc_final: 0.8827 (t80) REVERT: I 99 ILE cc_start: 0.9036 (tp) cc_final: 0.8747 (tt) REVERT: I 184 MET cc_start: 0.7925 (mmm) cc_final: 0.7390 (mmt) REVERT: J 42 GLN cc_start: 0.8524 (mt0) cc_final: 0.8316 (mp10) REVERT: J 163 MET cc_start: 0.8621 (mmm) cc_final: 0.8416 (mmm) REVERT: L 28 GLN cc_start: 0.9049 (OUTLIER) cc_final: 0.8824 (pt0) REVERT: L 35 ARG cc_start: 0.8918 (OUTLIER) cc_final: 0.8587 (mtt-85) REVERT: L 66 TYR cc_start: 0.8652 (m-80) cc_final: 0.8030 (m-80) REVERT: L 121 ARG cc_start: 0.9081 (mmm-85) cc_final: 0.8493 (mmm-85) REVERT: L 142 GLU cc_start: 0.7657 (pt0) cc_final: 0.7383 (pp20) REVERT: L 164 GLU cc_start: 0.8836 (mp0) cc_final: 0.8384 (tp30) REVERT: M 106 ASP cc_start: 0.8256 (t70) cc_final: 0.7985 (t70) REVERT: N 23 LEU cc_start: 0.9104 (mm) cc_final: 0.8726 (mp) REVERT: N 51 LEU cc_start: 0.9182 (mp) cc_final: 0.8974 (mt) REVERT: O 42 ASN cc_start: 0.9289 (OUTLIER) cc_final: 0.8816 (p0) REVERT: O 108 ILE cc_start: 0.9183 (mt) cc_final: 0.8831 (mt) REVERT: O 113 ASP cc_start: 0.8270 (p0) cc_final: 0.7658 (t0) REVERT: O 168 TYR cc_start: 0.8979 (t80) cc_final: 0.8115 (t80) REVERT: O 173 GLN cc_start: 0.8849 (tm-30) cc_final: 0.8478 (tm-30) REVERT: O 180 GLN cc_start: 0.8276 (tp40) cc_final: 0.7934 (tp-100) REVERT: O 191 ARG cc_start: 0.8840 (OUTLIER) cc_final: 0.8405 (tpp80) REVERT: P 99 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8654 (tt0) REVERT: R 25 ASP cc_start: 0.8873 (t70) cc_final: 0.8634 (t70) REVERT: R 28 GLU cc_start: 0.8154 (mp0) cc_final: 0.7490 (mm-30) REVERT: R 86 ASN cc_start: 0.8870 (t0) cc_final: 0.8462 (t0) REVERT: R 114 LYS cc_start: 0.9177 (tppp) cc_final: 0.8874 (mmtt) REVERT: R 148 ASP cc_start: 0.7438 (m-30) cc_final: 0.7177 (m-30) REVERT: S 61 ILE cc_start: 0.9127 (mm) cc_final: 0.8841 (mm) REVERT: S 127 MET cc_start: 0.8219 (mpp) cc_final: 0.7930 (mtp) REVERT: T 70 HIS cc_start: 0.8483 (OUTLIER) cc_final: 0.7756 (p90) REVERT: T 154 ILE cc_start: 0.9045 (OUTLIER) cc_final: 0.8649 (pp) REVERT: U 23 LEU cc_start: 0.8971 (OUTLIER) cc_final: 0.8608 (tt) REVERT: V 27 ASN cc_start: 0.8487 (OUTLIER) cc_final: 0.8122 (p0) REVERT: W 48 GLN cc_start: 0.8775 (mt0) cc_final: 0.8426 (tt0) REVERT: W 50 ASN cc_start: 0.7993 (t0) cc_final: 0.7633 (t0) REVERT: X 111 GLN cc_start: 0.8372 (mm-40) cc_final: 0.8018 (tp-100) REVERT: Y 75 ARG cc_start: 0.8978 (OUTLIER) cc_final: 0.8745 (mtt90) REVERT: Z 5 MET cc_start: 0.8578 (mmt) cc_final: 0.8369 (mmt) REVERT: Z 6 LYS cc_start: 0.9127 (mmmt) cc_final: 0.8872 (tppt) REVERT: Z 62 ILE cc_start: 0.9025 (mp) cc_final: 0.8728 (mp) REVERT: Z 97 ASN cc_start: 0.8767 (p0) cc_final: 0.8407 (p0) REVERT: Z 132 GLN cc_start: 0.8641 (mp10) cc_final: 0.8429 (mp10) REVERT: a 3 SER cc_start: 0.8967 (p) cc_final: 0.8260 (m) REVERT: a 12 ARG cc_start: 0.8276 (OUTLIER) cc_final: 0.7954 (mmt180) REVERT: a 38 MET cc_start: 0.8585 (mmm) cc_final: 0.8104 (mtp) REVERT: b 8 THR cc_start: 0.9073 (t) cc_final: 0.8574 (m) REVERT: c 35 LEU cc_start: 0.9163 (OUTLIER) cc_final: 0.8753 (mp) REVERT: c 90 ARG cc_start: 0.8777 (ptt90) cc_final: 0.8532 (mtm-85) REVERT: d 19 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7632 (pm20) REVERT: d 48 GLU cc_start: 0.7444 (OUTLIER) cc_final: 0.6924 (mm-30) REVERT: d 61 ASP cc_start: 0.8712 (t0) cc_final: 0.8372 (t70) REVERT: d 117 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9048 (mm) REVERT: d 121 ASN cc_start: 0.8846 (t0) cc_final: 0.8639 (t0) REVERT: e 113 GLU cc_start: 0.8475 (pm20) cc_final: 0.7871 (pt0) REVERT: f 16 ARG cc_start: 0.9153 (OUTLIER) cc_final: 0.8888 (ptm160) REVERT: f 34 TYR cc_start: 0.8348 (m-80) cc_final: 0.8000 (m-80) REVERT: g 7 TYR cc_start: 0.8958 (OUTLIER) cc_final: 0.7892 (m-80) REVERT: g 13 TYR cc_start: 0.8353 (m-80) cc_final: 0.8065 (m-80) REVERT: h 22 GLU cc_start: 0.8580 (pp20) cc_final: 0.8080 (pt0) REVERT: h 93 ARG cc_start: 0.9104 (mtt90) cc_final: 0.8372 (mtm-85) REVERT: h 113 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8607 (mm) REVERT: i 12 ASN cc_start: 0.8157 (t0) cc_final: 0.7828 (p0) REVERT: k 10 ASP cc_start: 0.8793 (t0) cc_final: 0.8256 (m-30) REVERT: k 50 LYS cc_start: 0.8271 (mmtt) cc_final: 0.7334 (ttpt) REVERT: k 52 LYS cc_start: 0.8586 (mmmt) cc_final: 0.8341 (mtmt) REVERT: k 59 SER cc_start: 0.7359 (m) cc_final: 0.6538 (p) REVERT: o 45 GLN cc_start: 0.7564 (tp40) cc_final: 0.7300 (tt0) REVERT: o 59 LYS cc_start: 0.8709 (mmmm) cc_final: 0.8467 (ptmt) REVERT: o 100 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7621 (ttpt) REVERT: p 47 MET cc_start: 0.9098 (mmt) cc_final: 0.8857 (tpt) REVERT: r 5 LEU cc_start: 0.8941 (tp) cc_final: 0.8722 (tp) REVERT: s 60 MET cc_start: 0.8031 (mtp) cc_final: 0.7660 (mtp) REVERT: s 192 VAL cc_start: 0.6441 (OUTLIER) cc_final: 0.5910 (t) REVERT: t 41 LYS cc_start: 0.8527 (tmtp) cc_final: 0.8057 (mptt) REVERT: t 96 LYS cc_start: 0.4440 (OUTLIER) cc_final: 0.4117 (mptt) REVERT: t 116 MET cc_start: 0.2417 (ptt) cc_final: 0.2099 (tpt) REVERT: v 355 LEU cc_start: 0.8407 (mt) cc_final: 0.7979 (mt) REVERT: v 383 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.7879 (mtpp) REVERT: v 396 ILE cc_start: 0.7275 (OUTLIER) cc_final: 0.6994 (mt) REVERT: v 470 TYR cc_start: 0.8237 (m-80) cc_final: 0.7995 (m-80) REVERT: z 1629 ARG cc_start: 0.7501 (mpt90) cc_final: 0.6953 (mmm-85) REVERT: z 1639 TYR cc_start: 0.6030 (m-80) cc_final: 0.5107 (m-80) REVERT: z 1677 ARG cc_start: 0.7393 (ttt90) cc_final: 0.6586 (ptp90) REVERT: z 1701 TRP cc_start: 0.7649 (t60) cc_final: 0.7418 (t60) outliers start: 341 outliers final: 219 residues processed: 1538 average time/residue: 1.2942 time to fit residues: 3446.5093 Evaluate side-chains 1491 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1239 time to evaluate : 7.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 95 GLN Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 233 ARG Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain B residue 56 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 208 ASN Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 90 VAL Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 221 LYS Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 264 LYS Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 106 LYS Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 217 SER Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 233 ILE Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 71 CYS Chi-restraints excluded: chain I residue 143 GLN Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 104 ASN Chi-restraints excluded: chain J residue 139 PHE Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 171 ASP Chi-restraints excluded: chain L residue 28 GLN Chi-restraints excluded: chain L residue 35 ARG Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 115 GLN Chi-restraints excluded: chain L residue 138 ASP Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 208 GLU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 56 GLN Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain N residue 110 CYS Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 131 GLU Chi-restraints excluded: chain N residue 161 MET Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain O residue 26 GLN Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 42 ASN Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 191 ARG Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 57 CYS Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 105 LYS Chi-restraints excluded: chain P residue 137 ASN Chi-restraints excluded: chain Q residue 9 LYS Chi-restraints excluded: chain Q residue 17 GLU Chi-restraints excluded: chain Q residue 22 ASP Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 122 THR Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 64 CYS Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 131 GLU Chi-restraints excluded: chain T residue 16 SER Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain U residue 23 LEU Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 61 VAL Chi-restraints excluded: chain U residue 99 TRP Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 27 ASN Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain Y residue 8 THR Chi-restraints excluded: chain Y residue 31 SER Chi-restraints excluded: chain Y residue 49 ILE Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 67 ILE Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 75 ARG Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 72 VAL Chi-restraints excluded: chain Z residue 78 ASN Chi-restraints excluded: chain Z residue 83 THR Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain a residue 12 ARG Chi-restraints excluded: chain a residue 39 HIS Chi-restraints excluded: chain a residue 81 LEU Chi-restraints excluded: chain a residue 86 THR Chi-restraints excluded: chain a residue 93 ASN Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain c residue 16 SER Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 34 THR Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain c residue 37 MET Chi-restraints excluded: chain c residue 50 ASN Chi-restraints excluded: chain c residue 65 MET Chi-restraints excluded: chain d residue 19 GLU Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 100 ASN Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain e residue 19 LYS Chi-restraints excluded: chain e residue 25 SER Chi-restraints excluded: chain e residue 42 ASP Chi-restraints excluded: chain e residue 65 LYS Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain f residue 16 ARG Chi-restraints excluded: chain f residue 101 ILE Chi-restraints excluded: chain f residue 104 MET Chi-restraints excluded: chain g residue 7 TYR Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 64 LEU Chi-restraints excluded: chain g residue 67 LEU Chi-restraints excluded: chain h residue 8 ASP Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain h residue 121 VAL Chi-restraints excluded: chain i residue 34 THR Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 48 ASN Chi-restraints excluded: chain j residue 66 HIS Chi-restraints excluded: chain j residue 68 LYS Chi-restraints excluded: chain j residue 69 ILE Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain k residue 13 LEU Chi-restraints excluded: chain k residue 23 VAL Chi-restraints excluded: chain k residue 48 THR Chi-restraints excluded: chain k residue 66 VAL Chi-restraints excluded: chain o residue 55 ILE Chi-restraints excluded: chain o residue 61 LYS Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain o residue 100 LYS Chi-restraints excluded: chain p residue 63 THR Chi-restraints excluded: chain p residue 89 LEU Chi-restraints excluded: chain r residue 13 CYS Chi-restraints excluded: chain r residue 17 LEU Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain r residue 68 SER Chi-restraints excluded: chain r residue 124 VAL Chi-restraints excluded: chain s residue 52 VAL Chi-restraints excluded: chain s residue 61 MET Chi-restraints excluded: chain s residue 91 THR Chi-restraints excluded: chain s residue 192 VAL Chi-restraints excluded: chain t residue 62 LEU Chi-restraints excluded: chain t residue 96 LYS Chi-restraints excluded: chain t residue 131 GLU Chi-restraints excluded: chain t residue 160 VAL Chi-restraints excluded: chain v residue 324 ASP Chi-restraints excluded: chain v residue 383 LYS Chi-restraints excluded: chain v residue 396 ILE Chi-restraints excluded: chain v residue 399 LEU Chi-restraints excluded: chain v residue 401 LEU Chi-restraints excluded: chain v residue 409 LEU Chi-restraints excluded: chain v residue 463 VAL Chi-restraints excluded: chain z residue 1582 TRP Chi-restraints excluded: chain z residue 1599 SER Chi-restraints excluded: chain z residue 1613 SER Chi-restraints excluded: chain z residue 1650 ILE Chi-restraints excluded: chain z residue 1696 GLU Chi-restraints excluded: chain 1 residue 16 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 1068 optimal weight: 10.0000 chunk 124 optimal weight: 8.9990 chunk 631 optimal weight: 20.0000 chunk 809 optimal weight: 20.0000 chunk 626 optimal weight: 9.9990 chunk 932 optimal weight: 10.0000 chunk 618 optimal weight: 7.9990 chunk 1103 optimal weight: 20.0000 chunk 690 optimal weight: 20.0000 chunk 672 optimal weight: 0.0370 chunk 509 optimal weight: 3.9990 overall best weight: 6.2066 ------------------------------------------------------------------------------- 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 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 158 GLN ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 100 HIS H 98 HIS I 147 HIS ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 57 GLN ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 182 HIS Q 188 ASN ** S 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 156 HIS U 44 GLN ** c 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 24 GLN g 3 GLN g 28 ASN h 96 ASN i 26 HIS j 66 HIS k 31 ASN m 84 GLN m 120 ASN r 46 HIS ** t 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 363 GLN w 17 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.8782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.114 157414 Z= 0.471 Angle : 0.857 17.535 232053 Z= 0.428 Chirality : 0.046 0.436 29042 Planarity : 0.007 0.147 14451 Dihedral : 25.478 179.759 72375 Min Nonbonded Distance : 1.072 Molprobity Statistics. All-atom Clashscore : 16.85 Ramachandran Plot: Outliers : 0.64 % Allowed : 8.68 % Favored : 90.68 % Rotamer: Outliers : 7.09 % Allowed : 27.91 % Favored : 65.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.04 % Twisted Proline : 1.69 % Twisted General : 0.10 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.10), residues: 7132 helix: 0.38 (0.10), residues: 2469 sheet: -1.86 (0.16), residues: 972 loop : -2.10 (0.09), residues: 3691 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP z1701 HIS 0.032 0.002 HIS j 66 PHE 0.025 0.003 PHE Q 123 TYR 0.028 0.003 TYR Z 49 ARG 0.012 0.001 ARG d 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1670 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 433 poor density : 1237 time to evaluate : 9.812 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: A 68 ARG cc_start: 0.7791 (ttm110) cc_final: 0.7161 (ttm-80) REVERT: A 179 ILE cc_start: 0.8456 (mm) cc_final: 0.8154 (mt) REVERT: A 204 MET cc_start: 0.8539 (mtt) cc_final: 0.8273 (mtt) REVERT: B 78 ILE cc_start: 0.9465 (OUTLIER) cc_final: 0.9213 (mp) REVERT: B 168 MET cc_start: 0.8615 (mmm) cc_final: 0.8372 (mmm) REVERT: B 216 MET cc_start: 0.8369 (mmm) cc_final: 0.7814 (mmm) REVERT: B 253 CYS cc_start: 0.8902 (t) cc_final: 0.8455 (t) REVERT: C 89 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8911 (mm-40) REVERT: C 268 ARG cc_start: 0.6923 (ptt180) cc_final: 0.6721 (ptp-170) REVERT: D 34 LYS cc_start: 0.8909 (tmtt) cc_final: 0.8672 (tttp) REVERT: D 68 ARG cc_start: 0.9077 (mmp80) cc_final: 0.8467 (mtp-110) REVERT: D 73 MET cc_start: 0.7742 (tpt) cc_final: 0.7485 (tpt) REVERT: D 89 LYS cc_start: 0.8742 (mmmt) cc_final: 0.8324 (mppt) REVERT: D 112 ARG cc_start: 0.8791 (OUTLIER) cc_final: 0.8436 (ttm-80) REVERT: D 160 PHE cc_start: 0.8345 (OUTLIER) cc_final: 0.7447 (p90) REVERT: E 194 SER cc_start: 0.9012 (m) cc_final: 0.8730 (p) REVERT: E 236 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.6727 (t80) REVERT: E 240 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7307 (tm-30) REVERT: F 96 ARG cc_start: 0.9006 (OUTLIER) cc_final: 0.8718 (ttt-90) REVERT: F 137 ILE cc_start: 0.9370 (OUTLIER) cc_final: 0.8845 (mt) REVERT: F 166 LYS cc_start: 0.9053 (mtpt) cc_final: 0.8622 (mttp) REVERT: F 227 THR cc_start: 0.8605 (OUTLIER) cc_final: 0.8231 (p) REVERT: G 110 LYS cc_start: 0.7325 (tptp) cc_final: 0.7073 (mmmm) REVERT: G 117 ARG cc_start: 0.7820 (ttm-80) cc_final: 0.7435 (tpm170) REVERT: G 230 TYR cc_start: 0.7886 (t80) cc_final: 0.6995 (t80) REVERT: H 21 LYS cc_start: 0.8956 (OUTLIER) cc_final: 0.8440 (mmtt) REVERT: H 50 LYS cc_start: 0.6095 (ttmt) cc_final: 0.5403 (ttmt) REVERT: H 66 GLU cc_start: 0.8083 (mp0) cc_final: 0.7848 (mp0) REVERT: I 99 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8986 (tt) REVERT: I 115 MET cc_start: 0.8942 (tpp) cc_final: 0.8206 (tpp) REVERT: I 184 MET cc_start: 0.7923 (mmm) cc_final: 0.7440 (mmt) REVERT: L 9 ILE cc_start: 0.8089 (tp) cc_final: 0.7883 (tp) REVERT: L 115 GLN cc_start: 0.8770 (OUTLIER) cc_final: 0.7817 (mp10) REVERT: L 164 GLU cc_start: 0.8764 (mp0) cc_final: 0.8290 (tp30) REVERT: L 200 LYS cc_start: 0.8800 (mptt) cc_final: 0.8584 (mptt) REVERT: N 23 LEU cc_start: 0.9189 (mm) cc_final: 0.8795 (mp) REVERT: N 182 HIS cc_start: 0.8241 (OUTLIER) cc_final: 0.7567 (p90) REVERT: O 42 ASN cc_start: 0.9295 (p0) cc_final: 0.8795 (p0) REVERT: O 113 ASP cc_start: 0.8382 (p0) cc_final: 0.7766 (t0) REVERT: O 155 THR cc_start: 0.9042 (p) cc_final: 0.8778 (t) REVERT: O 168 TYR cc_start: 0.9045 (t80) cc_final: 0.8386 (t80) REVERT: O 173 GLN cc_start: 0.8860 (tm-30) cc_final: 0.8393 (tm-30) REVERT: O 180 GLN cc_start: 0.8329 (tp40) cc_final: 0.7948 (tp-100) REVERT: O 191 ARG cc_start: 0.8820 (OUTLIER) cc_final: 0.8540 (tpp80) REVERT: P 99 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8701 (tt0) REVERT: R 25 ASP cc_start: 0.8936 (t70) cc_final: 0.8616 (t0) REVERT: R 28 GLU cc_start: 0.8354 (mp0) cc_final: 0.7696 (mm-30) REVERT: R 86 ASN cc_start: 0.8934 (t0) cc_final: 0.8568 (t0) REVERT: S 61 ILE cc_start: 0.9291 (OUTLIER) cc_final: 0.8970 (mm) REVERT: S 127 MET cc_start: 0.8374 (OUTLIER) cc_final: 0.8106 (mtp) REVERT: T 70 HIS cc_start: 0.8638 (OUTLIER) cc_final: 0.8055 (p90) REVERT: T 154 ILE cc_start: 0.9010 (OUTLIER) cc_final: 0.8644 (pp) REVERT: U 30 GLU cc_start: 0.8925 (mm-30) cc_final: 0.8502 (mt-10) REVERT: V 27 ASN cc_start: 0.8563 (OUTLIER) cc_final: 0.8265 (p0) REVERT: V 115 SER cc_start: 0.8483 (t) cc_final: 0.8168 (t) REVERT: W 50 ASN cc_start: 0.8295 (t0) cc_final: 0.7837 (t0) REVERT: X 101 ASP cc_start: 0.8613 (t0) cc_final: 0.8330 (t0) REVERT: X 111 GLN cc_start: 0.8414 (mm-40) cc_final: 0.8039 (tp-100) REVERT: Y 74 TYR cc_start: 0.8691 (OUTLIER) cc_final: 0.8263 (t80) REVERT: Y 75 ARG cc_start: 0.9004 (OUTLIER) cc_final: 0.8429 (mtm180) REVERT: Z 5 MET cc_start: 0.8461 (mmt) cc_final: 0.8193 (mmt) REVERT: Z 6 LYS cc_start: 0.9122 (mmmt) cc_final: 0.8857 (tppt) REVERT: Z 62 ILE cc_start: 0.9120 (mp) cc_final: 0.8826 (mp) REVERT: Z 97 ASN cc_start: 0.8806 (p0) cc_final: 0.8602 (p0) REVERT: a 3 SER cc_start: 0.8958 (p) cc_final: 0.7918 (t) REVERT: a 12 ARG cc_start: 0.8511 (OUTLIER) cc_final: 0.8101 (mmt180) REVERT: a 38 MET cc_start: 0.8577 (mmm) cc_final: 0.8082 (mtp) REVERT: a 84 GLU cc_start: 0.8476 (pp20) cc_final: 0.8027 (pp20) REVERT: b 8 THR cc_start: 0.9222 (t) cc_final: 0.8829 (m) REVERT: b 18 ARG cc_start: 0.8491 (ttm170) cc_final: 0.8276 (ttm170) REVERT: b 41 ARG cc_start: 0.8990 (OUTLIER) cc_final: 0.8598 (ttt180) REVERT: c 35 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8784 (mp) REVERT: c 92 CYS cc_start: 0.9396 (OUTLIER) cc_final: 0.9108 (t) REVERT: d 19 GLU cc_start: 0.8502 (OUTLIER) cc_final: 0.7708 (pm20) REVERT: d 48 GLU cc_start: 0.7292 (OUTLIER) cc_final: 0.6912 (mp0) REVERT: d 61 ASP cc_start: 0.8716 (t0) cc_final: 0.8349 (t70) REVERT: d 121 ASN cc_start: 0.8954 (t0) cc_final: 0.8665 (t0) REVERT: e 19 LYS cc_start: 0.8810 (OUTLIER) cc_final: 0.8151 (mmmm) REVERT: e 113 GLU cc_start: 0.8761 (pm20) cc_final: 0.7794 (pt0) REVERT: f 16 ARG cc_start: 0.9103 (OUTLIER) cc_final: 0.8532 (ptp90) REVERT: f 34 TYR cc_start: 0.8430 (m-80) cc_final: 0.8097 (m-80) REVERT: f 85 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8470 (ttp-170) REVERT: g 7 TYR cc_start: 0.9007 (OUTLIER) cc_final: 0.7956 (m-80) REVERT: g 13 TYR cc_start: 0.8416 (m-80) cc_final: 0.8158 (m-80) REVERT: g 102 ILE cc_start: 0.8456 (OUTLIER) cc_final: 0.7815 (mp) REVERT: h 22 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8172 (pt0) REVERT: h 113 LEU cc_start: 0.9068 (OUTLIER) cc_final: 0.8504 (mm) REVERT: i 12 ASN cc_start: 0.8163 (t0) cc_final: 0.7861 (p0) REVERT: i 43 MET cc_start: 0.8310 (tmm) cc_final: 0.7845 (tmm) REVERT: k 55 LYS cc_start: 0.9455 (ttmt) cc_final: 0.9080 (tmtt) REVERT: k 59 SER cc_start: 0.7599 (m) cc_final: 0.7235 (p) REVERT: k 67 LYS cc_start: 0.8355 (tppt) cc_final: 0.7936 (ptpp) REVERT: o 45 GLN cc_start: 0.7759 (tp40) cc_final: 0.7538 (tt0) REVERT: o 100 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7699 (ttpt) REVERT: p 47 MET cc_start: 0.9087 (mmt) cc_final: 0.8795 (tpt) REVERT: r 5 LEU cc_start: 0.9077 (tp) cc_final: 0.8723 (tp) REVERT: r 25 TYR cc_start: 0.8309 (m-80) cc_final: 0.7964 (m-80) REVERT: r 30 ASN cc_start: 0.8555 (OUTLIER) cc_final: 0.8131 (m110) REVERT: r 125 MET cc_start: 0.5700 (tpt) cc_final: 0.5413 (tmm) REVERT: s 101 MET cc_start: 0.5260 (ppp) cc_final: 0.5021 (ppp) REVERT: s 189 ILE cc_start: 0.5353 (OUTLIER) cc_final: 0.4849 (mp) REVERT: s 192 VAL cc_start: 0.6706 (OUTLIER) cc_final: 0.6122 (t) REVERT: t 41 LYS cc_start: 0.8602 (tmtp) cc_final: 0.8195 (mptt) REVERT: t 96 LYS cc_start: 0.4517 (OUTLIER) cc_final: 0.3980 (mptt) REVERT: t 116 MET cc_start: 0.2962 (ptt) cc_final: 0.2500 (tpt) REVERT: t 149 HIS cc_start: 0.4784 (m90) cc_final: 0.4437 (m90) REVERT: v 383 LYS cc_start: 0.8558 (OUTLIER) cc_final: 0.7901 (mtpp) REVERT: v 396 ILE cc_start: 0.7480 (OUTLIER) cc_final: 0.6983 (mt) REVERT: w 20 ARG cc_start: 0.7669 (OUTLIER) cc_final: 0.7177 (mpt-90) REVERT: z 1588 LYS cc_start: 0.8185 (tppt) cc_final: 0.7980 (tppt) REVERT: z 1624 MET cc_start: 0.6182 (tmm) cc_final: 0.5152 (ptp) REVERT: z 1636 MET cc_start: 0.8001 (tpt) cc_final: 0.7453 (mtt) REVERT: z 1639 TYR cc_start: 0.6597 (m-80) cc_final: 0.6239 (m-80) REVERT: z 1677 ARG cc_start: 0.6954 (ttt90) cc_final: 0.6447 (ptp90) outliers start: 433 outliers final: 307 residues processed: 1521 average time/residue: 1.2699 time to fit residues: 3357.7666 Evaluate side-chains 1535 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 348 poor density : 1187 time to evaluate : 6.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 157 VAL Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 226 ARG Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 222 VAL Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 292 LEU Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 125 VAL Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 235 MET Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 264 LYS Chi-restraints excluded: chain D residue 271 MET Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 105 LEU Chi-restraints excluded: chain E residue 108 MET Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 202 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 238 ILE Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 134 MET Chi-restraints excluded: chain F residue 135 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 217 SER Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 136 VAL Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 71 CYS Chi-restraints excluded: chain I residue 80 CYS Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 174 THR Chi-restraints excluded: chain I residue 180 GLU Chi-restraints excluded: chain I residue 197 VAL Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 26 VAL Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 102 THR Chi-restraints excluded: chain J residue 104 ASN Chi-restraints excluded: chain J residue 139 PHE Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 171 ASP Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 115 GLN Chi-restraints excluded: chain L residue 138 ASP Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 208 GLU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 56 GLN Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain N residue 110 CYS Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 131 GLU Chi-restraints excluded: chain N residue 148 THR Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 161 MET Chi-restraints excluded: chain N residue 182 HIS Chi-restraints excluded: chain N residue 184 ILE Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain O residue 26 GLN Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 185 VAL Chi-restraints excluded: chain O residue 191 ARG Chi-restraints excluded: chain P residue 2 VAL Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 30 ARG Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 57 CYS Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 104 LEU Chi-restraints excluded: chain P residue 105 LYS Chi-restraints excluded: chain P residue 137 ASN Chi-restraints excluded: chain Q residue 9 LYS Chi-restraints excluded: chain Q residue 17 GLU Chi-restraints excluded: chain Q residue 22 ASP Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain Q residue 188 ASN Chi-restraints excluded: chain R residue 51 ILE Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain R residue 137 ILE Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 48 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 64 CYS Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 80 ILE Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 127 MET Chi-restraints excluded: chain S residue 131 GLU Chi-restraints excluded: chain S residue 148 SER Chi-restraints excluded: chain S residue 174 THR Chi-restraints excluded: chain T residue 16 SER Chi-restraints excluded: chain T residue 25 VAL Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain U residue 27 HIS Chi-restraints excluded: chain U residue 62 THR Chi-restraints excluded: chain U residue 99 TRP Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 27 ASN Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 53 VAL Chi-restraints excluded: chain W residue 54 LEU Chi-restraints excluded: chain X residue 42 THR Chi-restraints excluded: chain X residue 43 SER Chi-restraints excluded: chain X residue 51 THR Chi-restraints excluded: chain X residue 57 GLN Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 113 VAL Chi-restraints excluded: chain X residue 120 ASP Chi-restraints excluded: chain X residue 127 LEU Chi-restraints excluded: chain X residue 133 GLU Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain Y residue 37 GLU Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 67 ILE Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 75 ARG Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Y residue 112 ASP Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 26 VAL Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 72 VAL Chi-restraints excluded: chain Z residue 78 ASN Chi-restraints excluded: chain Z residue 83 THR Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain Z residue 127 ASN Chi-restraints excluded: chain a residue 12 ARG Chi-restraints excluded: chain a residue 34 ASN Chi-restraints excluded: chain a residue 39 HIS Chi-restraints excluded: chain a residue 72 THR Chi-restraints excluded: chain a residue 81 LEU Chi-restraints excluded: chain a residue 93 ASN Chi-restraints excluded: chain a residue 100 ILE Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain b residue 41 ARG Chi-restraints excluded: chain c residue 16 SER Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain c residue 37 MET Chi-restraints excluded: chain c residue 50 ASN Chi-restraints excluded: chain c residue 65 MET Chi-restraints excluded: chain c residue 92 CYS Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain d residue 19 GLU Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 100 ASN Chi-restraints excluded: chain d residue 116 ASN Chi-restraints excluded: chain d residue 117 LEU Chi-restraints excluded: chain d residue 122 VAL Chi-restraints excluded: chain e residue 19 LYS Chi-restraints excluded: chain e residue 25 SER Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain e residue 42 ASP Chi-restraints excluded: chain e residue 65 LYS Chi-restraints excluded: chain e residue 79 VAL Chi-restraints excluded: chain e residue 80 HIS Chi-restraints excluded: chain e residue 90 MET Chi-restraints excluded: chain e residue 107 ASN Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain f residue 16 ARG Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 85 ARG Chi-restraints excluded: chain f residue 101 ILE Chi-restraints excluded: chain f residue 104 MET Chi-restraints excluded: chain g residue 7 TYR Chi-restraints excluded: chain g residue 12 SER Chi-restraints excluded: chain g residue 15 THR Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 64 LEU Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 106 VAL Chi-restraints excluded: chain h residue 8 ASP Chi-restraints excluded: chain h residue 22 GLU Chi-restraints excluded: chain h residue 26 VAL Chi-restraints excluded: chain h residue 36 VAL Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain h residue 121 VAL Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 34 THR Chi-restraints excluded: chain i residue 47 VAL Chi-restraints excluded: chain i residue 79 THR Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 48 ASN Chi-restraints excluded: chain j residue 66 HIS Chi-restraints excluded: chain j residue 69 ILE Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain k residue 13 LEU Chi-restraints excluded: chain k residue 23 VAL Chi-restraints excluded: chain k residue 31 ASN Chi-restraints excluded: chain k residue 66 VAL Chi-restraints excluded: chain l residue 35 ILE Chi-restraints excluded: chain o residue 24 THR Chi-restraints excluded: chain o residue 55 ILE Chi-restraints excluded: chain o residue 57 ARG Chi-restraints excluded: chain o residue 61 LYS Chi-restraints excluded: chain o residue 62 THR Chi-restraints excluded: chain o residue 68 LEU Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain o residue 81 ARG Chi-restraints excluded: chain o residue 100 LYS Chi-restraints excluded: chain p residue 22 LEU Chi-restraints excluded: chain p residue 25 MET Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 63 THR Chi-restraints excluded: chain p residue 86 LEU Chi-restraints excluded: chain p residue 89 LEU Chi-restraints excluded: chain r residue 13 CYS Chi-restraints excluded: chain r residue 17 LEU Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain r residue 30 ASN Chi-restraints excluded: chain r residue 33 LYS Chi-restraints excluded: chain r residue 48 THR Chi-restraints excluded: chain r residue 68 SER Chi-restraints excluded: chain r residue 83 ASN Chi-restraints excluded: chain r residue 93 ILE Chi-restraints excluded: chain r residue 117 ILE Chi-restraints excluded: chain r residue 124 VAL Chi-restraints excluded: chain s residue 35 VAL Chi-restraints excluded: chain s residue 52 VAL Chi-restraints excluded: chain s residue 61 MET Chi-restraints excluded: chain s residue 91 THR Chi-restraints excluded: chain s residue 189 ILE Chi-restraints excluded: chain s residue 192 VAL Chi-restraints excluded: chain t residue 38 SER Chi-restraints excluded: chain t residue 62 LEU Chi-restraints excluded: chain t residue 96 LYS Chi-restraints excluded: chain t residue 114 ARG Chi-restraints excluded: chain t residue 131 GLU Chi-restraints excluded: chain t residue 160 VAL Chi-restraints excluded: chain v residue 324 ASP Chi-restraints excluded: chain v residue 358 VAL Chi-restraints excluded: chain v residue 359 ASP Chi-restraints excluded: chain v residue 383 LYS Chi-restraints excluded: chain v residue 396 ILE Chi-restraints excluded: chain v residue 399 LEU Chi-restraints excluded: chain v residue 401 LEU Chi-restraints excluded: chain v residue 409 LEU Chi-restraints excluded: chain v residue 463 VAL Chi-restraints excluded: chain w residue 20 ARG Chi-restraints excluded: chain z residue 1582 TRP Chi-restraints excluded: chain z residue 1599 SER Chi-restraints excluded: chain z residue 1613 SER Chi-restraints excluded: chain z residue 1650 ILE Chi-restraints excluded: chain z residue 1694 ILE Chi-restraints excluded: chain z residue 1696 GLU Chi-restraints excluded: chain 1 residue 16 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 682 optimal weight: 8.9990 chunk 440 optimal weight: 6.9990 chunk 659 optimal weight: 40.0000 chunk 332 optimal weight: 2.9990 chunk 216 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 701 optimal weight: 40.0000 chunk 751 optimal weight: 50.0000 chunk 545 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 867 optimal weight: 10.0000 overall best weight: 1.9386 ------------------------------------------------------------------------------- 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 55 HIS ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 GLN ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 50 GLN ** T 95 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 GLN W 59 HIS b 49 HIS ** c 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 24 GLN g 3 GLN g 28 ASN h 96 ASN i 26 HIS j 48 ASN j 66 HIS k 31 ASN l 38 ASN m 84 GLN ** t 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 363 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.8960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 157414 Z= 0.202 Angle : 0.699 18.885 232053 Z= 0.353 Chirality : 0.038 0.353 29042 Planarity : 0.005 0.140 14451 Dihedral : 25.467 179.962 72366 Min Nonbonded Distance : 1.128 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.62 % Allowed : 6.21 % Favored : 93.17 % Rotamer: Outliers : 5.34 % Allowed : 29.63 % Favored : 65.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.04 % Twisted Proline : 1.69 % 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: -1.38 (0.10), residues: 7132 helix: 0.74 (0.11), residues: 2448 sheet: -1.68 (0.16), residues: 964 loop : -1.89 (0.10), residues: 3720 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP N 120 HIS 0.023 0.001 HIS j 66 PHE 0.020 0.002 PHE F 27 TYR 0.060 0.002 TYR v 470 ARG 0.020 0.001 ARG z1629 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1629 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 326 poor density : 1303 time to evaluate : 7.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 179 ILE cc_start: 0.8421 (mm) cc_final: 0.8033 (mt) REVERT: A 180 LEU cc_start: 0.9425 (mt) cc_final: 0.9089 (mt) REVERT: A 204 MET cc_start: 0.8556 (mtt) cc_final: 0.8324 (mtt) REVERT: B 78 ILE cc_start: 0.9368 (OUTLIER) cc_final: 0.9135 (mp) REVERT: B 79 VAL cc_start: 0.9595 (t) cc_final: 0.9372 (m) REVERT: B 216 MET cc_start: 0.8261 (mmm) cc_final: 0.7845 (mmm) REVERT: B 253 CYS cc_start: 0.8272 (t) cc_final: 0.8028 (t) REVERT: C 89 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.8866 (mm-40) REVERT: C 139 SER cc_start: 0.9338 (m) cc_final: 0.8889 (t) REVERT: D 15 ARG cc_start: 0.8232 (OUTLIER) cc_final: 0.7599 (mmp80) REVERT: D 34 LYS cc_start: 0.8854 (tmtt) cc_final: 0.8622 (tttp) REVERT: D 68 ARG cc_start: 0.9006 (mmp80) cc_final: 0.8439 (mtp-110) REVERT: D 89 LYS cc_start: 0.8723 (mmmt) cc_final: 0.8353 (mppt) REVERT: D 160 PHE cc_start: 0.7990 (OUTLIER) cc_final: 0.7196 (p90) REVERT: E 194 SER cc_start: 0.9005 (m) cc_final: 0.8678 (p) REVERT: E 235 LYS cc_start: 0.8058 (mmmt) cc_final: 0.7775 (mmmt) REVERT: E 236 TYR cc_start: 0.8335 (OUTLIER) cc_final: 0.6574 (t80) REVERT: E 255 ARG cc_start: 0.8597 (mmm-85) cc_final: 0.8294 (tpp80) REVERT: F 96 ARG cc_start: 0.8987 (OUTLIER) cc_final: 0.8759 (ttt-90) REVERT: F 137 ILE cc_start: 0.9371 (OUTLIER) cc_final: 0.8753 (mt) REVERT: F 138 VAL cc_start: 0.9031 (m) cc_final: 0.8731 (p) REVERT: F 154 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: F 166 LYS cc_start: 0.9006 (mtpt) cc_final: 0.8654 (mttp) REVERT: F 227 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8258 (p) REVERT: F 250 ASN cc_start: 0.7882 (t0) cc_final: 0.7591 (t0) REVERT: G 110 LYS cc_start: 0.7342 (tptp) cc_final: 0.7085 (mmmm) REVERT: G 117 ARG cc_start: 0.7708 (ttm-80) cc_final: 0.7346 (tpm170) REVERT: G 230 TYR cc_start: 0.7920 (t80) cc_final: 0.6998 (t80) REVERT: H 21 LYS cc_start: 0.8905 (OUTLIER) cc_final: 0.8333 (mttt) REVERT: H 50 LYS cc_start: 0.5666 (ttmt) cc_final: 0.4995 (ttmt) REVERT: H 108 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7868 (m110) REVERT: I 57 TYR cc_start: 0.8751 (t80) cc_final: 0.8364 (t80) REVERT: I 102 MET cc_start: 0.9086 (mmm) cc_final: 0.8856 (tpp) REVERT: I 115 MET cc_start: 0.8990 (tpp) cc_final: 0.8176 (tpp) REVERT: I 184 MET cc_start: 0.7801 (mmm) cc_final: 0.7411 (mmt) REVERT: J 12 MET cc_start: 0.8028 (OUTLIER) cc_final: 0.7561 (ttm) REVERT: L 20 ARG cc_start: 0.8423 (ttp-110) cc_final: 0.8221 (ttm-80) REVERT: L 121 ARG cc_start: 0.8973 (mmm-85) cc_final: 0.8540 (mmm-85) REVERT: L 164 GLU cc_start: 0.8764 (mp0) cc_final: 0.8347 (tp30) REVERT: L 200 LYS cc_start: 0.8680 (mptt) cc_final: 0.8477 (mptt) REVERT: M 78 GLU cc_start: 0.7369 (mm-30) cc_final: 0.7080 (mt-10) REVERT: N 23 LEU cc_start: 0.9089 (mm) cc_final: 0.8717 (mp) REVERT: N 182 HIS cc_start: 0.7650 (OUTLIER) cc_final: 0.7164 (p-80) REVERT: O 16 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9036 (tp) REVERT: O 42 ASN cc_start: 0.9223 (p0) cc_final: 0.8688 (p0) REVERT: O 108 ILE cc_start: 0.9102 (mt) cc_final: 0.8740 (mt) REVERT: O 113 ASP cc_start: 0.8233 (p0) cc_final: 0.7633 (t0) REVERT: O 168 TYR cc_start: 0.8966 (t80) cc_final: 0.8317 (t80) REVERT: O 173 GLN cc_start: 0.8858 (tm-30) cc_final: 0.8516 (tm-30) REVERT: O 180 GLN cc_start: 0.8299 (tp40) cc_final: 0.7946 (tp-100) REVERT: Q 53 MET cc_start: 0.8858 (mtt) cc_final: 0.8627 (mtt) REVERT: R 25 ASP cc_start: 0.8863 (t70) cc_final: 0.8601 (t70) REVERT: R 28 GLU cc_start: 0.8195 (mp0) cc_final: 0.7624 (mm-30) REVERT: R 86 ASN cc_start: 0.8864 (t0) cc_final: 0.8441 (t0) REVERT: S 61 ILE cc_start: 0.9162 (OUTLIER) cc_final: 0.8843 (mm) REVERT: T 70 HIS cc_start: 0.8551 (OUTLIER) cc_final: 0.8084 (p90) REVERT: T 154 ILE cc_start: 0.9020 (OUTLIER) cc_final: 0.8638 (pp) REVERT: T 157 GLU cc_start: 0.7493 (pp20) cc_final: 0.7132 (pp20) REVERT: U 111 GLU cc_start: 0.7941 (tt0) cc_final: 0.7589 (pt0) REVERT: V 27 ASN cc_start: 0.8453 (OUTLIER) cc_final: 0.8122 (p0) REVERT: W 48 GLN cc_start: 0.8698 (mt0) cc_final: 0.8496 (tt0) REVERT: W 50 ASN cc_start: 0.8120 (t0) cc_final: 0.7841 (m110) REVERT: X 101 ASP cc_start: 0.8510 (t0) cc_final: 0.8085 (t0) REVERT: X 111 GLN cc_start: 0.8314 (mm-40) cc_final: 0.7958 (tp-100) REVERT: Y 75 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8651 (mtt90) REVERT: Y 120 GLU cc_start: 0.8588 (mm-30) cc_final: 0.8355 (mm-30) REVERT: Z 5 MET cc_start: 0.8581 (mmt) cc_final: 0.8364 (mmt) REVERT: Z 6 LYS cc_start: 0.9116 (mmmt) cc_final: 0.8888 (tppt) REVERT: Z 28 ASN cc_start: 0.8388 (p0) cc_final: 0.8120 (p0) REVERT: Z 62 ILE cc_start: 0.9030 (mp) cc_final: 0.8758 (mp) REVERT: a 3 SER cc_start: 0.8807 (p) cc_final: 0.7751 (t) REVERT: a 12 ARG cc_start: 0.8289 (OUTLIER) cc_final: 0.7981 (mmt180) REVERT: a 38 MET cc_start: 0.8564 (mmm) cc_final: 0.8107 (mtp) REVERT: a 84 GLU cc_start: 0.8488 (pp20) cc_final: 0.8063 (pp20) REVERT: b 8 THR cc_start: 0.9089 (t) cc_final: 0.8603 (m) REVERT: b 18 ARG cc_start: 0.8267 (ttm170) cc_final: 0.8055 (ttm170) REVERT: b 41 ARG cc_start: 0.8875 (OUTLIER) cc_final: 0.8481 (ttt180) REVERT: c 35 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8760 (mp) REVERT: c 90 ARG cc_start: 0.8748 (ptt90) cc_final: 0.8273 (mtm-85) REVERT: c 92 CYS cc_start: 0.9337 (OUTLIER) cc_final: 0.8991 (t) REVERT: d 19 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.7650 (pm20) REVERT: d 48 GLU cc_start: 0.7293 (OUTLIER) cc_final: 0.6886 (mp0) REVERT: d 61 ASP cc_start: 0.8745 (t0) cc_final: 0.8356 (t70) REVERT: d 121 ASN cc_start: 0.8611 (t0) cc_final: 0.8356 (t0) REVERT: d 122 VAL cc_start: 0.8625 (p) cc_final: 0.8405 (p) REVERT: e 113 GLU cc_start: 0.8644 (pm20) cc_final: 0.7931 (pt0) REVERT: f 34 TYR cc_start: 0.8337 (m-80) cc_final: 0.8042 (m-80) REVERT: g 7 TYR cc_start: 0.8953 (OUTLIER) cc_final: 0.7865 (m-80) REVERT: h 15 GLU cc_start: 0.8795 (pp20) cc_final: 0.8277 (mm-30) REVERT: h 22 GLU cc_start: 0.8559 (pp20) cc_final: 0.8220 (pt0) REVERT: h 93 ARG cc_start: 0.9095 (mtt90) cc_final: 0.8666 (mtm-85) REVERT: h 113 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8457 (mm) REVERT: i 12 ASN cc_start: 0.8131 (t0) cc_final: 0.7823 (p0) REVERT: k 50 LYS cc_start: 0.8553 (mmtm) cc_final: 0.7795 (ttpt) REVERT: k 59 SER cc_start: 0.7766 (m) cc_final: 0.6855 (p) REVERT: k 67 LYS cc_start: 0.8436 (tppt) cc_final: 0.7916 (ptpp) REVERT: o 100 LYS cc_start: 0.8238 (OUTLIER) cc_final: 0.7742 (ttpt) REVERT: p 47 MET cc_start: 0.9060 (mmt) cc_final: 0.8768 (tpt) REVERT: r 25 TYR cc_start: 0.8110 (m-80) cc_final: 0.7636 (m-80) REVERT: r 30 ASN cc_start: 0.8422 (OUTLIER) cc_final: 0.7785 (m-40) REVERT: r 125 MET cc_start: 0.5703 (tpt) cc_final: 0.5409 (tmm) REVERT: s 101 MET cc_start: 0.5342 (ppp) cc_final: 0.4888 (ppp) REVERT: s 192 VAL cc_start: 0.6503 (OUTLIER) cc_final: 0.5912 (t) REVERT: t 41 LYS cc_start: 0.8531 (tmtp) cc_final: 0.8156 (mptt) REVERT: t 96 LYS cc_start: 0.4245 (OUTLIER) cc_final: 0.3806 (mptt) REVERT: t 116 MET cc_start: 0.2501 (ptt) cc_final: 0.2056 (tpt) REVERT: v 352 GLU cc_start: 0.7878 (tp30) cc_final: 0.7431 (tm-30) REVERT: v 383 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.7951 (mtpp) REVERT: v 396 ILE cc_start: 0.7806 (OUTLIER) cc_final: 0.7395 (mt) REVERT: z 1624 MET cc_start: 0.5830 (tmm) cc_final: 0.5150 (ptp) REVERT: z 1636 MET cc_start: 0.7899 (tpt) cc_final: 0.7561 (mtt) REVERT: z 1677 ARG cc_start: 0.7065 (ttt90) cc_final: 0.6506 (ptp90) REVERT: z 1701 TRP cc_start: 0.8171 (t60) cc_final: 0.7537 (t60) outliers start: 326 outliers final: 231 residues processed: 1517 average time/residue: 1.2931 time to fit residues: 3425.3540 Evaluate side-chains 1517 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 264 poor density : 1253 time to evaluate : 7.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 322 HIS Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain B residue 360 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 112 ARG Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 226 TYR Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 264 LYS Chi-restraints excluded: chain E residue 58 MET Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain E residue 257 ILE Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 217 SER Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 71 CYS Chi-restraints excluded: chain I residue 80 CYS Chi-restraints excluded: chain I residue 97 ILE Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 143 GLN Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain J residue 12 MET Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 55 TYR Chi-restraints excluded: chain J residue 104 ASN Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 139 PHE Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 171 ASP Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 115 GLN Chi-restraints excluded: chain L residue 138 ASP Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 208 GLU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 55 MET Chi-restraints excluded: chain M residue 56 GLN Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain N residue 110 CYS Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 116 LEU Chi-restraints excluded: chain N residue 131 GLU Chi-restraints excluded: chain N residue 161 MET Chi-restraints excluded: chain N residue 182 HIS Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 26 GLN Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 36 ILE Chi-restraints excluded: chain P residue 57 CYS Chi-restraints excluded: chain P residue 105 LYS Chi-restraints excluded: chain P residue 137 ASN Chi-restraints excluded: chain Q residue 9 LYS Chi-restraints excluded: chain Q residue 17 GLU Chi-restraints excluded: chain Q residue 22 ASP Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 50 GLN Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 64 CYS Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 77 ASN Chi-restraints excluded: chain S residue 131 GLU Chi-restraints excluded: chain T residue 16 SER Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 84 ILE Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 99 TRP Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 27 ASN Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain X residue 43 SER Chi-restraints excluded: chain X residue 51 THR Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 116 LEU Chi-restraints excluded: chain X residue 133 GLU Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 67 ILE Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 75 ARG Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 33 THR Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 72 VAL Chi-restraints excluded: chain Z residue 78 ASN Chi-restraints excluded: chain Z residue 83 THR Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain a residue 12 ARG Chi-restraints excluded: chain a residue 39 HIS Chi-restraints excluded: chain a residue 72 THR Chi-restraints excluded: chain a residue 100 ILE Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain b residue 41 ARG Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain c residue 37 MET Chi-restraints excluded: chain c residue 50 ASN Chi-restraints excluded: chain c residue 65 MET Chi-restraints excluded: chain c residue 92 CYS Chi-restraints excluded: chain d residue 19 GLU Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain e residue 19 LYS Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain e residue 42 ASP Chi-restraints excluded: chain e residue 65 LYS Chi-restraints excluded: chain e residue 80 HIS Chi-restraints excluded: chain e residue 107 ASN Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 101 ILE Chi-restraints excluded: chain f residue 104 MET Chi-restraints excluded: chain g residue 7 TYR Chi-restraints excluded: chain g residue 12 SER Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 64 LEU Chi-restraints excluded: chain g residue 67 LEU Chi-restraints excluded: chain h residue 8 ASP Chi-restraints excluded: chain h residue 16 GLU Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain h residue 121 VAL Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 34 THR Chi-restraints excluded: chain i residue 79 THR Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 48 ASN Chi-restraints excluded: chain j residue 66 HIS Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain k residue 13 LEU Chi-restraints excluded: chain k residue 23 VAL Chi-restraints excluded: chain k residue 31 ASN Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 66 VAL Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain o residue 10 THR Chi-restraints excluded: chain o residue 55 ILE Chi-restraints excluded: chain o residue 61 LYS Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain o residue 100 LYS Chi-restraints excluded: chain p residue 63 THR Chi-restraints excluded: chain p residue 89 LEU Chi-restraints excluded: chain r residue 10 VAL Chi-restraints excluded: chain r residue 17 LEU Chi-restraints excluded: chain r residue 30 ASN Chi-restraints excluded: chain r residue 68 SER Chi-restraints excluded: chain r residue 124 VAL Chi-restraints excluded: chain s residue 35 VAL Chi-restraints excluded: chain s residue 52 VAL Chi-restraints excluded: chain s residue 61 MET Chi-restraints excluded: chain s residue 91 THR Chi-restraints excluded: chain s residue 192 VAL Chi-restraints excluded: chain t residue 38 SER Chi-restraints excluded: chain t residue 62 LEU Chi-restraints excluded: chain t residue 96 LYS Chi-restraints excluded: chain t residue 131 GLU Chi-restraints excluded: chain t residue 160 VAL Chi-restraints excluded: chain v residue 383 LYS Chi-restraints excluded: chain v residue 396 ILE Chi-restraints excluded: chain v residue 399 LEU Chi-restraints excluded: chain v residue 401 LEU Chi-restraints excluded: chain v residue 409 LEU Chi-restraints excluded: chain v residue 463 VAL Chi-restraints excluded: chain z residue 1582 TRP Chi-restraints excluded: chain z residue 1613 SER Chi-restraints excluded: chain z residue 1645 VAL Chi-restraints excluded: chain z residue 1650 ILE Chi-restraints excluded: chain z residue 1696 GLU Chi-restraints excluded: chain z residue 1703 ASN Chi-restraints excluded: chain 1 residue 16 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 1003 optimal weight: 10.0000 chunk 1057 optimal weight: 10.0000 chunk 964 optimal weight: 10.0000 chunk 1028 optimal weight: 10.0000 chunk 1056 optimal weight: 10.0000 chunk 618 optimal weight: 8.9990 chunk 448 optimal weight: 1.9990 chunk 807 optimal weight: 10.0000 chunk 315 optimal weight: 0.0050 chunk 929 optimal weight: 10.0000 chunk 972 optimal weight: 10.0000 overall best weight: 6.2006 ------------------------------------------------------------------------------- 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 55 HIS ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 GLN ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 42 GLN ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 182 HIS Q 188 ASN ** S 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 GLN ** a 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 3 GLN g 28 ASN g 112 GLN ** h 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 26 HIS j 48 ASN j 66 HIS k 31 ASN m 84 GLN r 46 HIS ** t 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 363 GLN ** v 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 17 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z1704 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.9159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.105 157414 Z= 0.480 Angle : 0.852 18.057 232053 Z= 0.424 Chirality : 0.045 0.418 29042 Planarity : 0.007 0.142 14451 Dihedral : 25.401 179.585 72362 Min Nonbonded Distance : 1.041 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.55 % Allowed : 8.93 % Favored : 90.52 % Rotamer: Outliers : 5.73 % Allowed : 29.52 % Favored : 64.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.04 % Twisted Proline : 1.69 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.68 (0.10), residues: 7132 helix: 0.48 (0.11), residues: 2465 sheet: -1.83 (0.16), residues: 973 loop : -2.08 (0.09), residues: 3694 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP F 211 HIS 0.020 0.002 HIS j 66 PHE 0.026 0.003 PHE Q 123 TYR 0.039 0.003 TYR E 69 ARG 0.013 0.001 ARG Q 181 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1581 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 350 poor density : 1231 time to evaluate : 7.254 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: A 68 ARG cc_start: 0.7788 (ttm110) cc_final: 0.7076 (ttm-80) REVERT: A 179 ILE cc_start: 0.8513 (mm) cc_final: 0.8216 (mt) REVERT: B 78 ILE cc_start: 0.9431 (OUTLIER) cc_final: 0.9168 (mp) REVERT: B 216 MET cc_start: 0.8362 (mmm) cc_final: 0.7794 (mmm) REVERT: B 253 CYS cc_start: 0.8876 (t) cc_final: 0.8436 (t) REVERT: B 329 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.7902 (p0) REVERT: C 89 GLN cc_start: 0.9197 (OUTLIER) cc_final: 0.8917 (mm-40) REVERT: C 145 GLU cc_start: 0.8679 (pm20) cc_final: 0.8318 (pm20) REVERT: C 156 ASP cc_start: 0.7831 (t70) cc_final: 0.7579 (t70) REVERT: D 15 ARG cc_start: 0.8310 (OUTLIER) cc_final: 0.7623 (mmp80) REVERT: D 34 LYS cc_start: 0.8902 (tmtt) cc_final: 0.8680 (tttp) REVERT: D 68 ARG cc_start: 0.9100 (mmp80) cc_final: 0.8578 (mtp-110) REVERT: D 89 LYS cc_start: 0.8797 (mmmt) cc_final: 0.8419 (mptt) REVERT: D 160 PHE cc_start: 0.8321 (OUTLIER) cc_final: 0.7315 (p90) REVERT: E 194 SER cc_start: 0.9100 (m) cc_final: 0.8776 (p) REVERT: E 236 TYR cc_start: 0.8291 (OUTLIER) cc_final: 0.6849 (t80) REVERT: E 240 GLU cc_start: 0.7993 (tm-30) cc_final: 0.7713 (tm-30) REVERT: F 96 ARG cc_start: 0.8993 (OUTLIER) cc_final: 0.8685 (ttt-90) REVERT: F 137 ILE cc_start: 0.9390 (OUTLIER) cc_final: 0.8888 (mt) REVERT: F 166 LYS cc_start: 0.9012 (mtpt) cc_final: 0.8658 (mttp) REVERT: F 227 THR cc_start: 0.8636 (OUTLIER) cc_final: 0.8268 (p) REVERT: F 250 ASN cc_start: 0.8247 (t0) cc_final: 0.7983 (t0) REVERT: G 110 LYS cc_start: 0.7305 (tptp) cc_final: 0.7062 (mmmm) REVERT: G 117 ARG cc_start: 0.7784 (ttm-80) cc_final: 0.7384 (tpm170) REVERT: G 119 GLU cc_start: 0.5661 (OUTLIER) cc_final: 0.4701 (tm-30) REVERT: G 230 TYR cc_start: 0.8006 (t80) cc_final: 0.7285 (t80) REVERT: H 21 LYS cc_start: 0.8939 (OUTLIER) cc_final: 0.8365 (mttt) REVERT: H 50 LYS cc_start: 0.6082 (ttmt) cc_final: 0.5341 (ttmt) REVERT: I 57 TYR cc_start: 0.8844 (t80) cc_final: 0.8180 (t80) REVERT: I 99 ILE cc_start: 0.9242 (tp) cc_final: 0.9006 (tt) REVERT: I 115 MET cc_start: 0.8972 (tpp) cc_final: 0.8301 (tpp) REVERT: I 184 MET cc_start: 0.7764 (mmm) cc_final: 0.7287 (mmt) REVERT: L 115 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.7752 (mp10) REVERT: L 164 GLU cc_start: 0.8758 (mp0) cc_final: 0.8311 (tp30) REVERT: M 78 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7104 (mt-10) REVERT: N 23 LEU cc_start: 0.9168 (mm) cc_final: 0.8794 (mp) REVERT: N 62 TYR cc_start: 0.9242 (m-80) cc_final: 0.8957 (m-80) REVERT: N 182 HIS cc_start: 0.8019 (OUTLIER) cc_final: 0.7276 (p90) REVERT: O 16 LEU cc_start: 0.9363 (OUTLIER) cc_final: 0.9086 (tp) REVERT: O 42 ASN cc_start: 0.9263 (p0) cc_final: 0.8745 (p0) REVERT: O 82 ARG cc_start: 0.8377 (OUTLIER) cc_final: 0.8046 (ttt90) REVERT: O 113 ASP cc_start: 0.8356 (p0) cc_final: 0.7739 (t0) REVERT: O 168 TYR cc_start: 0.9061 (t80) cc_final: 0.8340 (t80) REVERT: O 173 GLN cc_start: 0.8891 (tm-30) cc_final: 0.8434 (tm-30) REVERT: O 180 GLN cc_start: 0.8374 (tp40) cc_final: 0.7960 (tp-100) REVERT: P 126 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7648 (ptp90) REVERT: Q 89 ASP cc_start: 0.8742 (t70) cc_final: 0.8230 (t0) REVERT: R 86 ASN cc_start: 0.8922 (t0) cc_final: 0.8537 (t0) REVERT: R 139 MET cc_start: 0.7951 (mtt) cc_final: 0.7744 (mtm) REVERT: S 61 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.8984 (mm) REVERT: T 70 HIS cc_start: 0.8657 (OUTLIER) cc_final: 0.8219 (p90) REVERT: T 154 ILE cc_start: 0.8982 (OUTLIER) cc_final: 0.8663 (pp) REVERT: T 157 GLU cc_start: 0.7930 (pp20) cc_final: 0.7592 (pp20) REVERT: U 30 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8527 (mt-10) REVERT: V 27 ASN cc_start: 0.8560 (OUTLIER) cc_final: 0.8243 (p0) REVERT: W 50 ASN cc_start: 0.8152 (t0) cc_final: 0.7897 (t0) REVERT: X 101 ASP cc_start: 0.8644 (t0) cc_final: 0.8331 (t0) REVERT: X 111 GLN cc_start: 0.8353 (mm-40) cc_final: 0.7988 (tp-100) REVERT: Y 74 TYR cc_start: 0.8762 (OUTLIER) cc_final: 0.8195 (t80) REVERT: Y 75 ARG cc_start: 0.8984 (OUTLIER) cc_final: 0.8411 (mtm180) REVERT: Y 120 GLU cc_start: 0.8576 (mm-30) cc_final: 0.8326 (mm-30) REVERT: Z 5 MET cc_start: 0.8574 (mmt) cc_final: 0.8192 (mmt) REVERT: Z 6 LYS cc_start: 0.9114 (mmmt) cc_final: 0.8887 (tppt) REVERT: a 3 SER cc_start: 0.8906 (p) cc_final: 0.7857 (t) REVERT: a 12 ARG cc_start: 0.8495 (OUTLIER) cc_final: 0.8080 (mmt180) REVERT: a 38 MET cc_start: 0.8568 (mmm) cc_final: 0.8077 (mtp) REVERT: b 8 THR cc_start: 0.9228 (OUTLIER) cc_final: 0.8840 (m) REVERT: b 41 ARG cc_start: 0.9059 (OUTLIER) cc_final: 0.8618 (ttt180) REVERT: c 35 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8714 (mp) REVERT: c 63 TYR cc_start: 0.8651 (m-80) cc_final: 0.7968 (m-80) REVERT: c 92 CYS cc_start: 0.9379 (OUTLIER) cc_final: 0.9024 (t) REVERT: d 19 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.7633 (pm20) REVERT: d 48 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6920 (mp0) REVERT: d 121 ASN cc_start: 0.8803 (t0) cc_final: 0.8537 (t0) REVERT: e 19 LYS cc_start: 0.8859 (OUTLIER) cc_final: 0.8183 (mmmm) REVERT: e 113 GLU cc_start: 0.8749 (pm20) cc_final: 0.7834 (pt0) REVERT: f 34 TYR cc_start: 0.8434 (m-80) cc_final: 0.8130 (m-80) REVERT: f 65 ASN cc_start: 0.7807 (p0) cc_final: 0.7129 (p0) REVERT: g 7 TYR cc_start: 0.8990 (OUTLIER) cc_final: 0.7944 (m-80) REVERT: g 102 ILE cc_start: 0.8315 (OUTLIER) cc_final: 0.7636 (mp) REVERT: h 15 GLU cc_start: 0.8841 (pp20) cc_final: 0.8348 (mm-30) REVERT: h 22 GLU cc_start: 0.8581 (pp20) cc_final: 0.8233 (pt0) REVERT: h 113 LEU cc_start: 0.9072 (OUTLIER) cc_final: 0.8527 (mm) REVERT: i 12 ASN cc_start: 0.8261 (t0) cc_final: 0.7976 (p0) REVERT: k 59 SER cc_start: 0.7830 (m) cc_final: 0.7044 (p) REVERT: k 67 LYS cc_start: 0.8424 (tppt) cc_final: 0.7930 (ptpp) REVERT: o 100 LYS cc_start: 0.8333 (OUTLIER) cc_final: 0.7744 (ttpt) REVERT: o 102 GLN cc_start: 0.7157 (mp10) cc_final: 0.6876 (mp10) REVERT: p 47 MET cc_start: 0.9094 (mmt) cc_final: 0.8856 (tpt) REVERT: r 25 TYR cc_start: 0.8242 (m-80) cc_final: 0.7712 (m-80) REVERT: r 30 ASN cc_start: 0.8543 (OUTLIER) cc_final: 0.8232 (m110) REVERT: s 61 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6953 (mtt) REVERT: s 192 VAL cc_start: 0.6620 (OUTLIER) cc_final: 0.6089 (t) REVERT: t 41 LYS cc_start: 0.8686 (tmtp) cc_final: 0.8277 (mptt) REVERT: t 116 MET cc_start: 0.2741 (ptt) cc_final: 0.2158 (tpt) REVERT: v 352 GLU cc_start: 0.7940 (tp30) cc_final: 0.7472 (tm-30) REVERT: v 377 GLU cc_start: 0.8126 (tm-30) cc_final: 0.7756 (mt-10) REVERT: v 383 LYS cc_start: 0.8595 (OUTLIER) cc_final: 0.7915 (mtpp) REVERT: v 396 ILE cc_start: 0.8062 (OUTLIER) cc_final: 0.7713 (mt) REVERT: z 1615 GLN cc_start: 0.5690 (tm-30) cc_final: 0.5376 (tm-30) REVERT: z 1624 MET cc_start: 0.5755 (tmm) cc_final: 0.4721 (ptp) REVERT: z 1629 ARG cc_start: 0.7080 (mmm160) cc_final: 0.6806 (mmm160) REVERT: z 1677 ARG cc_start: 0.6924 (ttt90) cc_final: 0.6455 (ptp90) REVERT: z 1701 TRP cc_start: 0.8130 (t60) cc_final: 0.7923 (t60) outliers start: 350 outliers final: 262 residues processed: 1467 average time/residue: 1.3363 time to fit residues: 3431.5417 Evaluate side-chains 1494 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 301 poor density : 1193 time to evaluate : 7.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 35 ASP Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 40 ASP Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 264 LYS Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 217 SER Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 48 LEU Chi-restraints excluded: chain I residue 71 CYS Chi-restraints excluded: chain I residue 80 CYS Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 143 GLN Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 104 ASN Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 139 PHE Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 171 ASP Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 115 GLN Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 208 GLU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 55 MET Chi-restraints excluded: chain M residue 56 GLN Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 104 MET Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain N residue 110 CYS Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 131 GLU Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 161 MET Chi-restraints excluded: chain N residue 182 HIS Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain O residue 6 VAL Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 26 GLN Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 60 LYS Chi-restraints excluded: chain O residue 82 ARG Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 57 CYS Chi-restraints excluded: chain P residue 95 LEU Chi-restraints excluded: chain P residue 105 LYS Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain P residue 137 ASN Chi-restraints excluded: chain Q residue 9 LYS Chi-restraints excluded: chain Q residue 17 GLU Chi-restraints excluded: chain Q residue 22 ASP Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 39 THR Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain R residue 127 VAL Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 51 LEU Chi-restraints excluded: chain S residue 54 MET Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 64 CYS Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 77 ASN Chi-restraints excluded: chain S residue 85 ASP Chi-restraints excluded: chain S residue 90 THR Chi-restraints excluded: chain S residue 131 GLU Chi-restraints excluded: chain T residue 16 SER Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 84 ILE Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain T residue 151 LEU Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 62 THR Chi-restraints excluded: chain U residue 99 TRP Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 27 ASN Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 105 ILE Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain X residue 43 SER Chi-restraints excluded: chain X residue 51 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 133 GLU Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain Y residue 37 GLU Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 67 ILE Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 75 ARG Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 46 ILE Chi-restraints excluded: chain Z residue 72 VAL Chi-restraints excluded: chain Z residue 78 ASN Chi-restraints excluded: chain Z residue 83 THR Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain a residue 12 ARG Chi-restraints excluded: chain a residue 34 ASN Chi-restraints excluded: chain a residue 39 HIS Chi-restraints excluded: chain a residue 72 THR Chi-restraints excluded: chain a residue 93 ASN Chi-restraints excluded: chain a residue 100 ILE Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain b residue 8 THR Chi-restraints excluded: chain b residue 41 ARG Chi-restraints excluded: chain c residue 24 SER Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain c residue 37 MET Chi-restraints excluded: chain c residue 50 ASN Chi-restraints excluded: chain c residue 65 MET Chi-restraints excluded: chain c residue 92 CYS Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain d residue 19 GLU Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 36 VAL Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 100 ASN Chi-restraints excluded: chain e residue 19 LYS Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain e residue 42 ASP Chi-restraints excluded: chain e residue 65 LYS Chi-restraints excluded: chain e residue 80 HIS Chi-restraints excluded: chain e residue 90 MET Chi-restraints excluded: chain e residue 107 ASN Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain f residue 43 LEU Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 101 ILE Chi-restraints excluded: chain f residue 104 MET Chi-restraints excluded: chain g residue 7 TYR Chi-restraints excluded: chain g residue 12 SER Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 64 LEU Chi-restraints excluded: chain g residue 86 CYS Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 103 VAL Chi-restraints excluded: chain h residue 8 ASP Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain h residue 121 VAL Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 34 THR Chi-restraints excluded: chain i residue 79 THR Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 66 HIS Chi-restraints excluded: chain j residue 68 LYS Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain k residue 13 LEU Chi-restraints excluded: chain k residue 23 VAL Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 66 VAL Chi-restraints excluded: chain l residue 35 ILE Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain o residue 10 THR Chi-restraints excluded: chain o residue 46 SER Chi-restraints excluded: chain o residue 55 ILE Chi-restraints excluded: chain o residue 61 LYS Chi-restraints excluded: chain o residue 62 THR Chi-restraints excluded: chain o residue 68 LEU Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain o residue 100 LYS Chi-restraints excluded: chain p residue 8 VAL Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 63 THR Chi-restraints excluded: chain p residue 89 LEU Chi-restraints excluded: chain r residue 13 CYS Chi-restraints excluded: chain r residue 17 LEU Chi-restraints excluded: chain r residue 24 THR Chi-restraints excluded: chain r residue 30 ASN Chi-restraints excluded: chain r residue 48 THR Chi-restraints excluded: chain r residue 68 SER Chi-restraints excluded: chain r residue 117 ILE Chi-restraints excluded: chain r residue 124 VAL Chi-restraints excluded: chain s residue 35 VAL Chi-restraints excluded: chain s residue 52 VAL Chi-restraints excluded: chain s residue 61 MET Chi-restraints excluded: chain s residue 91 THR Chi-restraints excluded: chain s residue 192 VAL Chi-restraints excluded: chain t residue 38 SER Chi-restraints excluded: chain t residue 62 LEU Chi-restraints excluded: chain t residue 131 GLU Chi-restraints excluded: chain t residue 160 VAL Chi-restraints excluded: chain v residue 383 LYS Chi-restraints excluded: chain v residue 396 ILE Chi-restraints excluded: chain v residue 399 LEU Chi-restraints excluded: chain v residue 401 LEU Chi-restraints excluded: chain v residue 409 LEU Chi-restraints excluded: chain w residue 16 SER Chi-restraints excluded: chain z residue 1582 TRP Chi-restraints excluded: chain z residue 1599 SER Chi-restraints excluded: chain z residue 1613 SER Chi-restraints excluded: chain z residue 1650 ILE Chi-restraints excluded: chain z residue 1696 GLU Chi-restraints excluded: chain z residue 1703 ASN Chi-restraints excluded: chain 1 residue 16 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 1024 optimal weight: 10.0000 chunk 675 optimal weight: 8.9990 chunk 1087 optimal weight: 8.9990 chunk 663 optimal weight: 0.0770 chunk 515 optimal weight: 3.9990 chunk 755 optimal weight: 6.9990 chunk 1140 optimal weight: 8.9990 chunk 1049 optimal weight: 7.9990 chunk 908 optimal weight: 20.0000 chunk 94 optimal weight: 7.9990 chunk 701 optimal weight: 40.0000 overall best weight: 5.4146 ------------------------------------------------------------------------------- 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 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 ASN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN ** R 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 50 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 85 GLN ** c 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 3 GLN g 28 ASN j 66 HIS m 84 GLN r 46 HIS ** t 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 363 GLN ** v 402 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z1704 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8509 moved from start: 0.9398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 157414 Z= 0.406 Angle : 0.804 17.894 232053 Z= 0.403 Chirality : 0.043 0.387 29042 Planarity : 0.006 0.142 14451 Dihedral : 25.422 179.954 72362 Min Nonbonded Distance : 1.027 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.52 % Allowed : 8.06 % Favored : 91.42 % Rotamer: Outliers : 5.37 % Allowed : 30.01 % Favored : 64.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.04 % Twisted Proline : 1.69 % Twisted General : 0.06 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.70 (0.10), residues: 7132 helix: 0.46 (0.11), residues: 2442 sheet: -1.85 (0.16), residues: 976 loop : -2.07 (0.09), residues: 3714 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP F 211 HIS 0.034 0.002 HIS j 66 PHE 0.028 0.002 PHE s 138 TYR 0.042 0.002 TYR v 470 ARG 0.015 0.001 ARG d 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14264 Ramachandran restraints generated. 7132 Oldfield, 0 Emsley, 7132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1565 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 328 poor density : 1237 time to evaluate : 7.094 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: A 68 ARG cc_start: 0.7787 (ttm110) cc_final: 0.7010 (ttm-80) REVERT: A 179 ILE cc_start: 0.8491 (mm) cc_final: 0.8189 (mt) REVERT: B 78 ILE cc_start: 0.9408 (OUTLIER) cc_final: 0.9140 (mp) REVERT: B 216 MET cc_start: 0.8353 (mmm) cc_final: 0.7797 (mmm) REVERT: B 253 CYS cc_start: 0.8587 (t) cc_final: 0.8258 (t) REVERT: B 329 ASP cc_start: 0.8563 (OUTLIER) cc_final: 0.7914 (p0) REVERT: C 89 GLN cc_start: 0.9208 (OUTLIER) cc_final: 0.8932 (mm-40) REVERT: C 145 GLU cc_start: 0.8633 (pm20) cc_final: 0.8324 (pm20) REVERT: C 156 ASP cc_start: 0.7795 (t70) cc_final: 0.7546 (t70) REVERT: D 15 ARG cc_start: 0.8287 (OUTLIER) cc_final: 0.7663 (mmp80) REVERT: D 68 ARG cc_start: 0.9022 (mmp80) cc_final: 0.8537 (mtp-110) REVERT: D 89 LYS cc_start: 0.8821 (mmmt) cc_final: 0.8471 (mptt) REVERT: D 122 GLN cc_start: 0.8924 (OUTLIER) cc_final: 0.8701 (tt0) REVERT: D 133 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8081 (pp20) REVERT: D 160 PHE cc_start: 0.8350 (OUTLIER) cc_final: 0.7298 (p90) REVERT: E 194 SER cc_start: 0.9154 (m) cc_final: 0.8815 (p) REVERT: E 236 TYR cc_start: 0.8312 (OUTLIER) cc_final: 0.6908 (t80) REVERT: E 240 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7653 (tm-30) REVERT: E 255 ARG cc_start: 0.8669 (mmm-85) cc_final: 0.8449 (tpp80) REVERT: F 96 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.8664 (ttt-90) REVERT: F 106 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8543 (mtpt) REVERT: F 137 ILE cc_start: 0.9426 (OUTLIER) cc_final: 0.8874 (mt) REVERT: F 138 VAL cc_start: 0.9112 (m) cc_final: 0.8804 (p) REVERT: F 166 LYS cc_start: 0.8924 (mtpt) cc_final: 0.8597 (mttp) REVERT: F 227 THR cc_start: 0.8646 (OUTLIER) cc_final: 0.8285 (p) REVERT: F 250 ASN cc_start: 0.8312 (t0) cc_final: 0.8066 (t0) REVERT: G 117 ARG cc_start: 0.7800 (ttm-80) cc_final: 0.7424 (tpm170) REVERT: G 119 GLU cc_start: 0.5825 (OUTLIER) cc_final: 0.4895 (tm-30) REVERT: G 230 TYR cc_start: 0.7948 (t80) cc_final: 0.7180 (t80) REVERT: H 21 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8346 (mttt) REVERT: H 50 LYS cc_start: 0.6104 (ttmt) cc_final: 0.5359 (ttmt) REVERT: I 57 TYR cc_start: 0.8775 (t80) cc_final: 0.8195 (t80) REVERT: I 115 MET cc_start: 0.8980 (tpp) cc_final: 0.8300 (tpp) REVERT: I 184 MET cc_start: 0.7703 (mmm) cc_final: 0.7308 (mmt) REVERT: L 115 GLN cc_start: 0.8728 (OUTLIER) cc_final: 0.7742 (mp10) REVERT: L 121 ARG cc_start: 0.9216 (mmm-85) cc_final: 0.8611 (mmm-85) REVERT: M 78 GLU cc_start: 0.7344 (mm-30) cc_final: 0.7102 (mt-10) REVERT: N 23 LEU cc_start: 0.9144 (mm) cc_final: 0.8786 (mp) REVERT: N 62 TYR cc_start: 0.9202 (m-80) cc_final: 0.8926 (m-80) REVERT: N 145 ASN cc_start: 0.8678 (t0) cc_final: 0.8243 (p0) REVERT: N 172 ARG cc_start: 0.8724 (mtp180) cc_final: 0.7311 (mtp180) REVERT: O 16 LEU cc_start: 0.9322 (OUTLIER) cc_final: 0.9037 (tp) REVERT: O 42 ASN cc_start: 0.9228 (p0) cc_final: 0.8705 (p0) REVERT: O 113 ASP cc_start: 0.8309 (p0) cc_final: 0.7707 (t0) REVERT: O 168 TYR cc_start: 0.9033 (t80) cc_final: 0.8453 (t80) REVERT: O 173 GLN cc_start: 0.8898 (tm-30) cc_final: 0.8433 (tm-30) REVERT: O 180 GLN cc_start: 0.8327 (tp40) cc_final: 0.7952 (tp-100) REVERT: P 126 ARG cc_start: 0.8295 (OUTLIER) cc_final: 0.7727 (ptp90) REVERT: R 3 MET cc_start: 0.8338 (tpt) cc_final: 0.7754 (tpt) REVERT: R 25 ASP cc_start: 0.8708 (t70) cc_final: 0.8271 (t0) REVERT: R 28 GLU cc_start: 0.8466 (pm20) cc_final: 0.8007 (pm20) REVERT: R 86 ASN cc_start: 0.8900 (t0) cc_final: 0.8497 (t0) REVERT: R 139 MET cc_start: 0.7913 (mtt) cc_final: 0.7681 (mtm) REVERT: S 21 LYS cc_start: 0.8598 (ptmm) cc_final: 0.8366 (mptt) REVERT: S 61 ILE cc_start: 0.9279 (OUTLIER) cc_final: 0.8958 (mm) REVERT: S 127 MET cc_start: 0.8475 (mtp) cc_final: 0.8081 (mtm) REVERT: T 70 HIS cc_start: 0.8600 (OUTLIER) cc_final: 0.8197 (p90) REVERT: T 151 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9120 (mt) REVERT: T 154 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8633 (pp) REVERT: T 157 GLU cc_start: 0.7928 (pp20) cc_final: 0.7511 (pp20) REVERT: U 30 GLU cc_start: 0.8951 (mm-30) cc_final: 0.8586 (mt-10) REVERT: U 90 TYR cc_start: 0.8679 (t80) cc_final: 0.8478 (t80) REVERT: V 27 ASN cc_start: 0.8534 (OUTLIER) cc_final: 0.8199 (p0) REVERT: W 50 ASN cc_start: 0.8153 (t0) cc_final: 0.7887 (t0) REVERT: X 101 ASP cc_start: 0.8658 (t0) cc_final: 0.8346 (t0) REVERT: X 111 GLN cc_start: 0.8345 (mm-40) cc_final: 0.7973 (tp-100) REVERT: Y 120 GLU cc_start: 0.8550 (mm-30) cc_final: 0.8280 (mm-30) REVERT: Z 5 MET cc_start: 0.8576 (mmt) cc_final: 0.8198 (mmt) REVERT: Z 6 LYS cc_start: 0.9133 (mmmt) cc_final: 0.8885 (tppt) REVERT: Z 88 ASP cc_start: 0.8409 (t0) cc_final: 0.8030 (p0) REVERT: a 3 SER cc_start: 0.8882 (p) cc_final: 0.7840 (t) REVERT: a 12 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.7970 (mmt180) REVERT: b 8 THR cc_start: 0.9121 (t) cc_final: 0.8710 (m) REVERT: b 41 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8670 (ttt180) REVERT: b 61 ASN cc_start: 0.8148 (m-40) cc_final: 0.7926 (m-40) REVERT: c 35 LEU cc_start: 0.9276 (OUTLIER) cc_final: 0.8766 (mp) REVERT: c 92 CYS cc_start: 0.9421 (OUTLIER) cc_final: 0.9089 (t) REVERT: d 19 GLU cc_start: 0.8381 (OUTLIER) cc_final: 0.7658 (pm20) REVERT: d 48 GLU cc_start: 0.7313 (OUTLIER) cc_final: 0.6726 (mp0) REVERT: d 121 ASN cc_start: 0.8800 (t0) cc_final: 0.8578 (t0) REVERT: e 19 LYS cc_start: 0.8898 (OUTLIER) cc_final: 0.8249 (mmmm) REVERT: e 113 GLU cc_start: 0.8705 (pm20) cc_final: 0.7878 (pt0) REVERT: f 34 TYR cc_start: 0.8414 (m-80) cc_final: 0.8111 (m-80) REVERT: g 7 TYR cc_start: 0.8989 (OUTLIER) cc_final: 0.7961 (m-80) REVERT: g 102 ILE cc_start: 0.8190 (OUTLIER) cc_final: 0.7460 (mp) REVERT: h 15 GLU cc_start: 0.8799 (pp20) cc_final: 0.8427 (mm-30) REVERT: h 22 GLU cc_start: 0.8602 (pp20) cc_final: 0.8336 (pt0) REVERT: h 113 LEU cc_start: 0.9035 (OUTLIER) cc_final: 0.8491 (mm) REVERT: i 12 ASN cc_start: 0.8378 (t0) cc_final: 0.8149 (p0) REVERT: k 52 LYS cc_start: 0.8578 (mmmt) cc_final: 0.8354 (mtmt) REVERT: k 59 SER cc_start: 0.8068 (m) cc_final: 0.7479 (p) REVERT: k 67 LYS cc_start: 0.8387 (tppt) cc_final: 0.7907 (ptpp) REVERT: o 81 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.7466 (mtm-85) REVERT: o 100 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.7745 (ttpt) REVERT: o 102 GLN cc_start: 0.7177 (mp10) cc_final: 0.6862 (mp10) REVERT: p 47 MET cc_start: 0.9107 (mmt) cc_final: 0.8862 (tpt) REVERT: r 30 ASN cc_start: 0.8590 (OUTLIER) cc_final: 0.8228 (m110) REVERT: s 60 MET cc_start: 0.7901 (mtp) cc_final: 0.7603 (mtp) REVERT: s 192 VAL cc_start: 0.6730 (OUTLIER) cc_final: 0.6188 (t) REVERT: t 116 MET cc_start: 0.2520 (ptt) cc_final: 0.1975 (tpt) REVERT: v 352 GLU cc_start: 0.7849 (tp30) cc_final: 0.7399 (tm-30) REVERT: v 377 GLU cc_start: 0.8315 (tm-30) cc_final: 0.7743 (mt-10) REVERT: v 383 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.7963 (mtpp) REVERT: v 396 ILE cc_start: 0.8225 (OUTLIER) cc_final: 0.7950 (mt) REVERT: z 1624 MET cc_start: 0.5642 (tmm) cc_final: 0.4873 (ptp) REVERT: z 1636 MET cc_start: 0.7910 (tpt) cc_final: 0.7457 (mtt) REVERT: z 1677 ARG cc_start: 0.6800 (ttt90) cc_final: 0.6403 (ptp90) REVERT: z 1701 TRP cc_start: 0.8223 (t60) cc_final: 0.7955 (t60) outliers start: 328 outliers final: 264 residues processed: 1461 average time/residue: 1.2752 time to fit residues: 3254.7479 Evaluate side-chains 1509 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 302 poor density : 1207 time to evaluate : 6.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 VAL Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 90 CYS Chi-restraints excluded: chain A residue 98 ILE Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 218 HIS Chi-restraints excluded: chain A residue 243 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 73 VAL Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 78 ILE Chi-restraints excluded: chain B residue 134 CYS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 251 VAL Chi-restraints excluded: chain B residue 258 HIS Chi-restraints excluded: chain B residue 289 GLN Chi-restraints excluded: chain B residue 299 ILE Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 345 LEU Chi-restraints excluded: chain C residue 10 VAL Chi-restraints excluded: chain C residue 13 GLU Chi-restraints excluded: chain C residue 23 THR Chi-restraints excluded: chain C residue 24 LEU Chi-restraints excluded: chain C residue 44 LEU Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 57 LEU Chi-restraints excluded: chain C residue 89 GLN Chi-restraints excluded: chain C residue 147 VAL Chi-restraints excluded: chain C residue 198 ASN Chi-restraints excluded: chain C residue 230 LEU Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 233 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 285 LEU Chi-restraints excluded: chain C residue 295 SER Chi-restraints excluded: chain C residue 335 MET Chi-restraints excluded: chain C residue 353 LYS Chi-restraints excluded: chain D residue 15 ARG Chi-restraints excluded: chain D residue 37 VAL Chi-restraints excluded: chain D residue 45 ASN Chi-restraints excluded: chain D residue 82 GLU Chi-restraints excluded: chain D residue 92 LEU Chi-restraints excluded: chain D residue 101 THR Chi-restraints excluded: chain D residue 122 GLN Chi-restraints excluded: chain D residue 133 GLU Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 163 LEU Chi-restraints excluded: chain D residue 187 SER Chi-restraints excluded: chain D residue 239 MET Chi-restraints excluded: chain D residue 264 LYS Chi-restraints excluded: chain E residue 116 ASP Chi-restraints excluded: chain E residue 159 ILE Chi-restraints excluded: chain E residue 197 ILE Chi-restraints excluded: chain E residue 199 ILE Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 236 TYR Chi-restraints excluded: chain F residue 37 LYS Chi-restraints excluded: chain F residue 51 LEU Chi-restraints excluded: chain F residue 96 ARG Chi-restraints excluded: chain F residue 106 LYS Chi-restraints excluded: chain F residue 113 LEU Chi-restraints excluded: chain F residue 127 LEU Chi-restraints excluded: chain F residue 132 ILE Chi-restraints excluded: chain F residue 137 ILE Chi-restraints excluded: chain F residue 154 GLU Chi-restraints excluded: chain F residue 180 SER Chi-restraints excluded: chain F residue 192 LEU Chi-restraints excluded: chain F residue 217 SER Chi-restraints excluded: chain F residue 227 THR Chi-restraints excluded: chain G residue 28 VAL Chi-restraints excluded: chain G residue 74 LEU Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 106 THR Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain G residue 140 VAL Chi-restraints excluded: chain G residue 194 VAL Chi-restraints excluded: chain G residue 201 THR Chi-restraints excluded: chain G residue 211 ASP Chi-restraints excluded: chain H residue 19 THR Chi-restraints excluded: chain H residue 21 LYS Chi-restraints excluded: chain H residue 25 VAL Chi-restraints excluded: chain H residue 26 ILE Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 63 ASN Chi-restraints excluded: chain H residue 92 MET Chi-restraints excluded: chain H residue 108 ASN Chi-restraints excluded: chain H residue 110 SER Chi-restraints excluded: chain H residue 132 VAL Chi-restraints excluded: chain H residue 151 ILE Chi-restraints excluded: chain H residue 157 SER Chi-restraints excluded: chain H residue 167 VAL Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 36 LEU Chi-restraints excluded: chain I residue 61 SER Chi-restraints excluded: chain I residue 71 CYS Chi-restraints excluded: chain I residue 80 CYS Chi-restraints excluded: chain I residue 131 ILE Chi-restraints excluded: chain I residue 143 GLN Chi-restraints excluded: chain I residue 206 LEU Chi-restraints excluded: chain J residue 17 ILE Chi-restraints excluded: chain J residue 100 SER Chi-restraints excluded: chain J residue 104 ASN Chi-restraints excluded: chain J residue 114 ASP Chi-restraints excluded: chain J residue 139 PHE Chi-restraints excluded: chain J residue 140 SER Chi-restraints excluded: chain J residue 141 ILE Chi-restraints excluded: chain J residue 148 THR Chi-restraints excluded: chain J residue 171 ASP Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 115 GLN Chi-restraints excluded: chain L residue 170 THR Chi-restraints excluded: chain L residue 208 GLU Chi-restraints excluded: chain M residue 15 VAL Chi-restraints excluded: chain M residue 56 GLN Chi-restraints excluded: chain M residue 62 LEU Chi-restraints excluded: chain M residue 104 MET Chi-restraints excluded: chain M residue 105 THR Chi-restraints excluded: chain N residue 17 ASP Chi-restraints excluded: chain N residue 60 VAL Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 75 VAL Chi-restraints excluded: chain N residue 87 HIS Chi-restraints excluded: chain N residue 110 CYS Chi-restraints excluded: chain N residue 113 LEU Chi-restraints excluded: chain N residue 115 VAL Chi-restraints excluded: chain N residue 131 GLU Chi-restraints excluded: chain N residue 155 VAL Chi-restraints excluded: chain N residue 161 MET Chi-restraints excluded: chain N residue 197 THR Chi-restraints excluded: chain O residue 16 LEU Chi-restraints excluded: chain O residue 26 GLN Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 60 LYS Chi-restraints excluded: chain P residue 20 SER Chi-restraints excluded: chain P residue 29 THR Chi-restraints excluded: chain P residue 57 CYS Chi-restraints excluded: chain P residue 105 LYS Chi-restraints excluded: chain P residue 126 ARG Chi-restraints excluded: chain P residue 137 ASN Chi-restraints excluded: chain P residue 152 GLU Chi-restraints excluded: chain Q residue 9 LYS Chi-restraints excluded: chain Q residue 17 GLU Chi-restraints excluded: chain Q residue 22 ASP Chi-restraints excluded: chain Q residue 27 LEU Chi-restraints excluded: chain Q residue 46 VAL Chi-restraints excluded: chain Q residue 47 VAL Chi-restraints excluded: chain Q residue 61 LEU Chi-restraints excluded: chain Q residue 82 VAL Chi-restraints excluded: chain Q residue 85 THR Chi-restraints excluded: chain Q residue 92 VAL Chi-restraints excluded: chain Q residue 120 ILE Chi-restraints excluded: chain Q residue 158 THR Chi-restraints excluded: chain R residue 84 THR Chi-restraints excluded: chain R residue 122 SER Chi-restraints excluded: chain S residue 39 VAL Chi-restraints excluded: chain S residue 54 MET Chi-restraints excluded: chain S residue 61 ILE Chi-restraints excluded: chain S residue 64 CYS Chi-restraints excluded: chain S residue 67 VAL Chi-restraints excluded: chain S residue 73 LEU Chi-restraints excluded: chain S residue 77 ASN Chi-restraints excluded: chain S residue 80 ILE Chi-restraints excluded: chain S residue 131 GLU Chi-restraints excluded: chain T residue 16 SER Chi-restraints excluded: chain T residue 70 HIS Chi-restraints excluded: chain T residue 84 ILE Chi-restraints excluded: chain T residue 96 ILE Chi-restraints excluded: chain T residue 128 LEU Chi-restraints excluded: chain T residue 151 LEU Chi-restraints excluded: chain T residue 154 ILE Chi-restraints excluded: chain U residue 22 THR Chi-restraints excluded: chain U residue 27 HIS Chi-restraints excluded: chain U residue 56 LEU Chi-restraints excluded: chain U residue 99 TRP Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain V residue 18 LEU Chi-restraints excluded: chain V residue 27 ASN Chi-restraints excluded: chain V residue 32 THR Chi-restraints excluded: chain V residue 64 THR Chi-restraints excluded: chain V residue 92 ASP Chi-restraints excluded: chain V residue 105 ILE Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain X residue 43 SER Chi-restraints excluded: chain X residue 51 THR Chi-restraints excluded: chain X residue 71 LEU Chi-restraints excluded: chain X residue 100 VAL Chi-restraints excluded: chain X residue 102 VAL Chi-restraints excluded: chain X residue 155 ILE Chi-restraints excluded: chain Y residue 37 GLU Chi-restraints excluded: chain Y residue 58 VAL Chi-restraints excluded: chain Y residue 67 ILE Chi-restraints excluded: chain Y residue 74 TYR Chi-restraints excluded: chain Y residue 104 VAL Chi-restraints excluded: chain Y residue 128 VAL Chi-restraints excluded: chain Z residue 24 VAL Chi-restraints excluded: chain Z residue 43 VAL Chi-restraints excluded: chain Z residue 72 VAL Chi-restraints excluded: chain Z residue 78 ASN Chi-restraints excluded: chain Z residue 83 THR Chi-restraints excluded: chain Z residue 94 THR Chi-restraints excluded: chain a residue 12 ARG Chi-restraints excluded: chain a residue 34 ASN Chi-restraints excluded: chain a residue 39 HIS Chi-restraints excluded: chain a residue 72 THR Chi-restraints excluded: chain a residue 100 ILE Chi-restraints excluded: chain a residue 140 VAL Chi-restraints excluded: chain a residue 147 VAL Chi-restraints excluded: chain b residue 41 ARG Chi-restraints excluded: chain c residue 28 VAL Chi-restraints excluded: chain c residue 35 LEU Chi-restraints excluded: chain c residue 37 MET Chi-restraints excluded: chain c residue 50 ASN Chi-restraints excluded: chain c residue 65 MET Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 92 CYS Chi-restraints excluded: chain c residue 93 THR Chi-restraints excluded: chain d residue 19 GLU Chi-restraints excluded: chain d residue 22 THR Chi-restraints excluded: chain d residue 46 LEU Chi-restraints excluded: chain d residue 48 GLU Chi-restraints excluded: chain d residue 77 ILE Chi-restraints excluded: chain d residue 84 ILE Chi-restraints excluded: chain d residue 100 ASN Chi-restraints excluded: chain e residue 19 LYS Chi-restraints excluded: chain e residue 25 SER Chi-restraints excluded: chain e residue 29 VAL Chi-restraints excluded: chain e residue 42 ASP Chi-restraints excluded: chain e residue 65 LYS Chi-restraints excluded: chain e residue 80 HIS Chi-restraints excluded: chain e residue 90 MET Chi-restraints excluded: chain e residue 107 ASN Chi-restraints excluded: chain e residue 122 VAL Chi-restraints excluded: chain f residue 43 LEU Chi-restraints excluded: chain f residue 84 VAL Chi-restraints excluded: chain f residue 101 ILE Chi-restraints excluded: chain f residue 104 MET Chi-restraints excluded: chain g residue 7 TYR Chi-restraints excluded: chain g residue 12 SER Chi-restraints excluded: chain g residue 25 THR Chi-restraints excluded: chain g residue 31 VAL Chi-restraints excluded: chain g residue 64 LEU Chi-restraints excluded: chain g residue 86 CYS Chi-restraints excluded: chain g residue 102 ILE Chi-restraints excluded: chain g residue 106 VAL Chi-restraints excluded: chain h residue 8 ASP Chi-restraints excluded: chain h residue 26 VAL Chi-restraints excluded: chain h residue 113 LEU Chi-restraints excluded: chain h residue 121 VAL Chi-restraints excluded: chain i residue 11 LEU Chi-restraints excluded: chain i residue 34 THR Chi-restraints excluded: chain i residue 79 THR Chi-restraints excluded: chain j residue 33 THR Chi-restraints excluded: chain j residue 66 HIS Chi-restraints excluded: chain j residue 68 LYS Chi-restraints excluded: chain j residue 83 THR Chi-restraints excluded: chain k residue 13 LEU Chi-restraints excluded: chain k residue 23 VAL Chi-restraints excluded: chain k residue 31 ASN Chi-restraints excluded: chain k residue 47 ILE Chi-restraints excluded: chain k residue 66 VAL Chi-restraints excluded: chain l residue 35 ILE Chi-restraints excluded: chain m residue 77 ILE Chi-restraints excluded: chain o residue 10 THR Chi-restraints excluded: chain o residue 55 ILE Chi-restraints excluded: chain o residue 61 LYS Chi-restraints excluded: chain o residue 62 THR Chi-restraints excluded: chain o residue 68 LEU Chi-restraints excluded: chain o residue 73 VAL Chi-restraints excluded: chain o residue 81 ARG Chi-restraints excluded: chain o residue 100 LYS Chi-restraints excluded: chain p residue 54 ILE Chi-restraints excluded: chain p residue 63 THR Chi-restraints excluded: chain p residue 89 LEU Chi-restraints excluded: chain r residue 13 CYS Chi-restraints excluded: chain r residue 17 LEU Chi-restraints excluded: chain r residue 30 ASN Chi-restraints excluded: chain r residue 48 THR Chi-restraints excluded: chain r residue 68 SER Chi-restraints excluded: chain r residue 124 VAL Chi-restraints excluded: chain s residue 35 VAL Chi-restraints excluded: chain s residue 52 VAL Chi-restraints excluded: chain s residue 61 MET Chi-restraints excluded: chain s residue 91 THR Chi-restraints excluded: chain s residue 192 VAL Chi-restraints excluded: chain t residue 38 SER Chi-restraints excluded: chain t residue 62 LEU Chi-restraints excluded: chain t residue 131 GLU Chi-restraints excluded: chain t residue 139 VAL Chi-restraints excluded: chain t residue 160 VAL Chi-restraints excluded: chain v residue 383 LYS Chi-restraints excluded: chain v residue 396 ILE Chi-restraints excluded: chain v residue 399 LEU Chi-restraints excluded: chain v residue 401 LEU Chi-restraints excluded: chain v residue 409 LEU Chi-restraints excluded: chain w residue 16 SER Chi-restraints excluded: chain z residue 1582 TRP Chi-restraints excluded: chain z residue 1599 SER Chi-restraints excluded: chain z residue 1613 SER Chi-restraints excluded: chain z residue 1650 ILE Chi-restraints excluded: chain z residue 1696 GLU Chi-restraints excluded: chain z residue 1703 ASN Chi-restraints excluded: chain 1 residue 16 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 556 optimal weight: 10.0000 chunk 721 optimal weight: 20.0000 chunk 967 optimal weight: 10.0000 chunk 278 optimal weight: 6.9990 chunk 837 optimal weight: 40.0000 chunk 134 optimal weight: 2.9990 chunk 252 optimal weight: 8.9990 chunk 909 optimal weight: 20.0000 chunk 380 optimal weight: 7.9990 chunk 934 optimal weight: 8.9990 chunk 115 optimal weight: 1.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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** ** B 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 264 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 HIS ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 ASN ** R 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 50 GLN V 36 ASN ** b 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 3 GLN g 28 ASN ** j 48 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 66 HIS m 84 GLN ** o 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** t 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 363 GLN v 479 HIS z1704 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.113481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.085119 restraints weight = 295238.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.085502 restraints weight = 208545.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.086884 restraints weight = 161250.180| |-----------------------------------------------------------------------------| r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.9587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.104 157414 Z= 0.448 Angle : 0.839 17.529 232053 Z= 0.419 Chirality : 0.045 0.408 29042 Planarity : 0.007 0.142 14451 Dihedral : 25.402 179.800 72361 Min Nonbonded Distance : 1.037 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.48 % Allowed : 8.96 % Favored : 90.56 % Rotamer: Outliers : 5.77 % Allowed : 29.68 % Favored : 64.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.04 % Twisted Proline : 1.69 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.78 (0.10), residues: 7132 helix: 0.40 (0.11), residues: 2439 sheet: -1.89 (0.16), residues: 977 loop : -2.12 (0.09), residues: 3716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP z1676 HIS 0.030 0.002 HIS j 66 PHE 0.025 0.002 PHE F 27 TYR 0.042 0.003 TYR v 470 ARG 0.027 0.001 ARG Z 84 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 50295.67 seconds wall clock time: 873 minutes 26.64 seconds (52406.64 seconds total)