Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 21 10:47:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j92_2832/07_2023/3j92_2832_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j92_2832/07_2023/3j92_2832.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j92_2832/07_2023/3j92_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_2832/07_2023/3j92_2832_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j92_2832/07_2023/3j92_2832_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j92_2832/07_2023/3j92_2832.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j92_2832/07_2023/3j92_2832.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j92_2832/07_2023/3j92_2832_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j92_2832/07_2023/3j92_2832_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/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: 20 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: 49.61, per 1000 atoms: 0.34 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: 62.01 Conformation dependent library (CDL) restraints added in 7.8 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 forstructures with more than 99999 atoms! 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 1219 base pairs and 1869 stacking pairs defined. Time for finding SS restraints: 61.93 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: 3209 hydrogen bonds 5602 hydrogen bond angles 0 basepair planarities 1219 basepair parallelities 1869 stacking parallelities Total time for adding SS restraints: 300.10 Time building geometry restraints manager: 67.09 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: 79732 35.98 - 71.96: 5773 71.96 - 107.94: 456 107.94 - 143.93: 103 143.93 - 179.91: 140 Dihedral angle restraints: 86204 sinusoidal: 63992 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 86201 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: 201890 3.41 - 4.16: 468137 4.16 - 4.90: 661503 Nonbonded interactions: 1340718 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 1340713 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: 3.290 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: 16.370 Check model and map are aligned: 1.650 Set scattering table: 0.980 Process input model: 597.060 Find NCS groups from input model: 3.550 Set up NCS constraints: 0.450 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 626.020 ------------------------------------------------------------------------------- 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= 0.619 Angle : 1.595 36.793 232053 Z= 1.059 Chirality : 0.114 1.028 29042 Planarity : 0.011 0.437 14451 Dihedral : 21.533 179.908 71819 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 % 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 *********************** 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 : 6.379 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 outliers start: 1152 outliers final: 208 residues processed: 2900 average time/residue: 1.5930 time to fit residues: 7735.3265 Evaluate side-chains 1584 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1376 time to evaluate : 6.943 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 208 outliers final: 3 residues processed: 208 average time/residue: 1.2945 time to fit residues: 503.1630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 966 optimal weight: 10.0000 chunk 867 optimal weight: 10.0000 chunk 481 optimal weight: 0.9980 chunk 296 optimal weight: 0.6980 chunk 585 optimal weight: 0.9990 chunk 463 optimal weight: 1.9990 chunk 897 optimal weight: 7.9990 chunk 347 optimal weight: 0.9980 chunk 545 optimal weight: 2.9990 chunk 667 optimal weight: 40.0000 chunk 1039 optimal weight: 7.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- 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 167 GLN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 258 HIS ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 61 GLN C 142 HIS ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 329 ASN D 42 ASN D 81 HIS ** E 43 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 246 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 262 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 ASN G 82 GLN G 236 HIS G 240 ASN ** I 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 168 GLN L 13 HIS L 104 ASN 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 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 50 ASN O 72 HIS O 96 GLN O 199 HIS P 75 GLN Q 125 GLN R 58 HIS R 130 ASN S 50 GLN S 108 GLN S 122 HIS S 144 GLN ** S 163 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 3 ASN T 70 HIS T 79 GLN ** U 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 95 ASN ** V 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 24 HIS Y 100 HIS Z 28 ASN Z 127 ASN b 11 ASN ** b 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 78 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 30 HIS d 100 ASN 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 p 33 GLN r 36 ASN r 83 ASN ** s 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 70 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7469 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.120 157414 Z= 0.247 Angle : 0.885 14.724 232053 Z= 0.446 Chirality : 0.046 0.460 29042 Planarity : 0.007 0.144 14451 Dihedral : 19.075 179.654 56683 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 1.02 % Allowed : 6.16 % Favored : 92.82 % Rotamer Outliers : 5.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.04 % Twisted Proline : 2.71 % 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: -1.84 (0.10), residues: 7132 helix: 0.89 (0.11), residues: 2421 sheet: -2.43 (0.14), residues: 965 loop : -2.42 (0.09), residues: 3746 *********************** 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 1929 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 320 poor density : 1609 time to evaluate : 7.017 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 outliers start: 320 outliers final: 130 residues processed: 1811 average time/residue: 1.3842 time to fit residues: 4370.2050 Evaluate side-chains 1393 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 1263 time to evaluate : 6.905 Switching outliers to nearest non-outliers outliers start: 130 outliers final: 0 residues processed: 130 average time/residue: 1.1923 time to fit residues: 301.7460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 577 optimal weight: 2.9990 chunk 322 optimal weight: 0.7980 chunk 865 optimal weight: 8.9990 chunk 708 optimal weight: 40.0000 chunk 286 optimal weight: 0.9980 chunk 1041 optimal weight: 10.0000 chunk 1125 optimal weight: 10.0000 chunk 927 optimal weight: 10.0000 chunk 1032 optimal weight: 10.0000 chunk 355 optimal weight: 8.9990 chunk 835 optimal weight: 9.9990 overall best weight: 4.5586 ------------------------------------------------------------------------------- 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 68 ASN ** B 175 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 204 GLN B 301 ASN B 376 HIS C 47 ASN D 42 ASN ** D 157 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** ** D 229 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** 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 73 ASN I 123 GLN I 213 HIS L 19 GLN ** L 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 ASN M 33 GLN N 29 GLN N 196 ASN P 21 ASN P 56 GLN ** Q 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 21 GLN ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 122 HIS S 163 HIS T 139 HIS ** V 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 93 ASN X 107 HIS X 111 GLN ** Y 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 96 HIS Y 100 HIS Z 28 ASN Z 127 ASN a 28 HIS a 44 ASN a 93 ASN ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 100 ASN f 24 HIS k 28 ASN k 31 ASN p 33 GLN ** r 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.6120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.206 157414 Z= 0.440 Angle : 0.949 21.035 232053 Z= 0.480 Chirality : 0.050 0.522 29042 Planarity : 0.009 0.236 14451 Dihedral : 18.574 179.780 56683 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 16.11 Ramachandran Plot: Outliers : 0.86 % Allowed : 8.57 % Favored : 90.58 % Rotamer Outliers : 6.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.04 % Twisted Proline : 2.03 % Twisted General : 0.13 % 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: -2.12 (0.09), residues: 7132 helix: 0.04 (0.10), residues: 2445 sheet: -2.05 (0.15), residues: 960 loop : -2.29 (0.09), residues: 3727 *********************** 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 1945 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 399 poor density : 1546 time to evaluate : 7.139 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 outliers start: 399 outliers final: 156 residues processed: 1787 average time/residue: 1.3533 time to fit residues: 4234.0520 Evaluate side-chains 1375 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 156 poor density : 1219 time to evaluate : 7.069 Switching outliers to nearest non-outliers outliers start: 156 outliers final: 0 residues processed: 156 average time/residue: 1.1269 time to fit residues: 338.4710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 497 optimal weight: 10.0000 chunk 699 optimal weight: 30.0000 chunk 1045 optimal weight: 10.0000 chunk 1106 optimal weight: 10.0000 chunk 546 optimal weight: 3.9990 chunk 990 optimal weight: 30.0000 chunk 298 optimal weight: 5.9990 overall best weight: 5.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 50 HIS ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 175 GLN B 322 HIS ** C 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 57 ASN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 GLN E 264 GLN F 41 GLN G 81 ASN ** G 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 140 GLN ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 98 ASN L 19 GLN ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 188 ASN M 83 ASN M 131 GLN ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 182 HIS N 201 HIS O 50 ASN P 28 ASN Q 44 ASN R 58 HIS ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 95 HIS U 44 GLN U 95 ASN V 135 ASN Y 24 HIS Y 43 ASN Y 127 GLN ** a 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 17 HIS b 50 ASN ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 18 ASN e 24 GLN f 21 GLN f 24 HIS g 28 ASN g 73 HIS h 65 GLN h 108 GLN i 15 HIS i 26 HIS j 66 HIS k 28 ASN k 31 ASN l 25 GLN m 120 ASN r 36 ASN s 41 GLN ** s 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** t 65 GLN v 325 ASN v 363 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 moved from start: 0.7709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.155 157414 Z= 0.439 Angle : 0.877 16.327 232053 Z= 0.441 Chirality : 0.047 0.390 29042 Planarity : 0.007 0.134 14451 Dihedral : 18.421 179.919 56683 Min Nonbonded Distance : 1.688 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.76 % Allowed : 7.38 % Favored : 91.87 % Rotamer Outliers : 6.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.04 % Twisted Proline : 2.37 % 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: -2.00 (0.09), residues: 7132 helix: 0.14 (0.10), residues: 2454 sheet: -2.00 (0.15), residues: 997 loop : -2.21 (0.09), residues: 3681 *********************** 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 1782 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 389 poor density : 1393 time to evaluate : 7.116 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 outliers start: 389 outliers final: 169 residues processed: 1650 average time/residue: 1.3526 time to fit residues: 3920.8825 Evaluate side-chains 1370 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1201 time to evaluate : 7.031 Switching outliers to nearest non-outliers outliers start: 169 outliers final: 0 residues processed: 169 average time/residue: 1.0798 time to fit residues: 361.5812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 16 optimal weight: 0.9990 chunk 824 optimal weight: 30.0000 chunk 456 optimal weight: 6.9990 chunk 944 optimal weight: 7.9990 chunk 765 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 565 optimal weight: 2.9990 chunk 993 optimal weight: 10.0000 chunk 279 optimal weight: 3.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 HIS ** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 322 HIS C 116 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 252 GLN ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 66 GLN I 133 GLN ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 159 ASN L 188 ASN N 87 HIS N 196 ASN O 143 HIS ** P 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 44 ASN R 40 GLN R 58 HIS ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 117 HIS T 77 ASN T 90 ASN U 44 GLN X 111 GLN Z 127 ASN ** a 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 50 ASN ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 100 ASN e 24 GLN e 80 HIS ** f 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 3 GLN g 28 ASN ** i 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 48 ASN j 66 HIS ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 120 ASN ** o 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 46 HIS r 85 ASN r 121 GLN ** s 81 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** v 363 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.8176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.112 157414 Z= 0.334 Angle : 0.773 16.986 232053 Z= 0.391 Chirality : 0.042 0.400 29042 Planarity : 0.006 0.169 14451 Dihedral : 18.180 179.635 56683 Min Nonbonded Distance : 1.237 Molprobity Statistics. All-atom Clashscore : 15.28 Ramachandran Plot: Outliers : 0.64 % Allowed : 7.80 % Favored : 91.56 % Rotamer Outliers : 3.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.04 % Twisted Proline : 2.37 % 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: -1.70 (0.09), residues: 7132 helix: 0.48 (0.10), residues: 2460 sheet: -1.90 (0.15), residues: 944 loop : -2.10 (0.09), residues: 3728 *********************** 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 1521 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1320 time to evaluate : 7.304 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 outliers start: 201 outliers final: 101 residues processed: 1433 average time/residue: 1.3774 time to fit residues: 3477.8204 Evaluate side-chains 1299 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 1198 time to evaluate : 6.355 Switching outliers to nearest non-outliers outliers start: 101 outliers final: 0 residues processed: 101 average time/residue: 1.1195 time to fit residues: 222.7335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 372 optimal weight: 4.9990 chunk 996 optimal weight: 8.9990 chunk 218 optimal weight: 0.4980 chunk 649 optimal weight: 0.9990 chunk 273 optimal weight: 8.9990 chunk 1107 optimal weight: 20.0000 chunk 919 optimal weight: 20.0000 chunk 512 optimal weight: 8.9990 chunk 92 optimal weight: 3.9990 chunk 366 optimal weight: 6.9990 chunk 581 optimal weight: 6.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 HIS ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 HIS ** 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** ** I 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 133 GLN ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 167 GLN ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 87 HIS N 196 ASN ** P 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 7 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 111 GLN Y 56 GLN ** a 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 19 GLN ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 24 GLN g 3 GLN g 28 ASN j 66 HIS l 38 ASN m 84 GLN ** o 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 30 ASN t 68 GLN v 363 GLN ** z1609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8454 moved from start: 0.8613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.128 157414 Z= 0.300 Angle : 0.742 18.180 232053 Z= 0.375 Chirality : 0.041 0.394 29042 Planarity : 0.006 0.150 14451 Dihedral : 18.023 179.615 56683 Min Nonbonded Distance : 1.031 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.60 % Allowed : 7.38 % Favored : 92.02 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.04 % Twisted Proline : 1.69 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.10), residues: 7132 helix: 0.65 (0.11), residues: 2431 sheet: -1.78 (0.16), residues: 948 loop : -1.95 (0.09), residues: 3753 *********************** 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 1459 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 1280 time to evaluate : 7.121 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 outliers start: 179 outliers final: 81 residues processed: 1373 average time/residue: 1.3386 time to fit residues: 3238.7392 Evaluate side-chains 1287 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 81 poor density : 1206 time to evaluate : 7.062 Switching outliers to nearest non-outliers outliers start: 81 outliers final: 0 residues processed: 81 average time/residue: 1.0006 time to fit residues: 163.4135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 631 optimal weight: 20.0000 chunk 809 optimal weight: 20.0000 chunk 626 optimal weight: 20.0000 chunk 932 optimal weight: 10.0000 chunk 618 optimal weight: 2.9990 chunk 1103 optimal weight: 20.0000 chunk 690 optimal weight: 20.0000 chunk 672 optimal weight: 20.0000 chunk 509 optimal weight: 0.9980 overall best weight: 6.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 3 HIS ** 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 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 124 HIS ** 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 100 HIS H 98 HIS ** I 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 117 ASN ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 196 ASN ** O 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 40 ASN ** R 130 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 144 GLN ** W 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 HIS X 111 GLN Y 56 GLN ** a 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 50 ASN ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 24 GLN g 28 ASN h 96 ASN j 66 HIS m 84 GLN ** o 51 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** r 46 HIS ** t 65 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** v 363 GLN v 479 HIS w 17 ASN ** z1592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z1609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.9036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.116 157414 Z= 0.520 Angle : 0.890 16.805 232053 Z= 0.445 Chirality : 0.047 0.454 29042 Planarity : 0.007 0.145 14451 Dihedral : 18.204 179.243 56683 Min Nonbonded Distance : 1.012 Molprobity Statistics. All-atom Clashscore : 17.11 Ramachandran Plot: Outliers : 0.62 % Allowed : 8.65 % Favored : 90.73 % Rotamer Outliers : 3.21 % Cbeta Deviations : 0.00 % 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: -1.87 (0.09), residues: 7132 helix: 0.27 (0.10), residues: 2458 sheet: -1.94 (0.15), residues: 977 loop : -2.15 (0.09), residues: 3697 *********************** 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 1426 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1230 time to evaluate : 7.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 196 outliers final: 108 residues processed: 1334 average time/residue: 1.4020 time to fit residues: 3297.4905 Evaluate side-chains 1276 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 1168 time to evaluate : 7.041 Switching outliers to nearest non-outliers outliers start: 108 outliers final: 0 residues processed: 108 average time/residue: 1.1405 time to fit residues: 243.8422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 682 optimal weight: 5.9990 chunk 440 optimal weight: 2.9990 chunk 659 optimal weight: 40.0000 chunk 332 optimal weight: 4.9990 chunk 216 optimal weight: 3.9990 chunk 213 optimal weight: 5.9990 chunk 701 optimal weight: 40.0000 chunk 751 optimal weight: 50.0000 chunk 545 optimal weight: 3.9990 chunk 102 optimal weight: 1.9990 chunk 867 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 215 ASN C 347 HIS ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 202 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 GLN ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 195 HIS ** I 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 115 GLN ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 196 ASN ** P 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 44 GLN V 36 ASN ** W 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 59 HIS ** a 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 19 GLN ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 24 GLN g 28 ASN k 31 ASN ** l 33 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 84 GLN r 46 HIS v 363 GLN ** v 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 479 HIS ** z1592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z1609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.9223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.077 157414 Z= 0.299 Angle : 0.748 16.776 232053 Z= 0.378 Chirality : 0.041 0.389 29042 Planarity : 0.006 0.141 14451 Dihedral : 18.012 179.775 56683 Min Nonbonded Distance : 1.066 Molprobity Statistics. All-atom Clashscore : 15.46 Ramachandran Plot: Outliers : 0.59 % Allowed : 7.21 % Favored : 92.20 % Rotamer Outliers : 1.70 % 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: -1.59 (0.10), residues: 7132 helix: 0.58 (0.11), residues: 2435 sheet: -1.84 (0.16), residues: 969 loop : -2.01 (0.09), residues: 3728 *********************** 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 1334 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 1230 time to evaluate : 7.111 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 outliers start: 104 outliers final: 53 residues processed: 1288 average time/residue: 1.3616 time to fit residues: 3094.5880 Evaluate side-chains 1231 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 1178 time to evaluate : 6.999 Switching outliers to nearest non-outliers outliers start: 53 outliers final: 0 residues processed: 53 average time/residue: 1.1484 time to fit residues: 123.1512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 9.9990 chunk 964 optimal weight: 10.0000 chunk 1028 optimal weight: 10.0000 chunk 1056 optimal weight: 9.9990 chunk 618 optimal weight: 0.8980 chunk 448 optimal weight: 0.0000 chunk 807 optimal weight: 10.0000 chunk 315 optimal weight: 0.5980 chunk 929 optimal weight: 10.0000 chunk 972 optimal weight: 10.0000 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 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** C 215 ASN D 131 ASN ** D 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 195 HIS ** 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 241 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 115 GLN N 57 GLN ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 36 ASN W 48 GLN W 59 HIS Z 127 ASN ** a 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 85 GLN ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 24 GLN ** g 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 28 ASN m 84 GLN r 45 HIS v 363 GLN ** v 404 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** v 479 HIS w 17 ASN z1569 HIS ** z1592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z1609 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.9365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.078 157414 Z= 0.347 Angle : 0.767 18.806 232053 Z= 0.386 Chirality : 0.042 0.401 29042 Planarity : 0.006 0.140 14451 Dihedral : 17.953 179.596 56683 Min Nonbonded Distance : 1.073 Molprobity Statistics. All-atom Clashscore : 15.84 Ramachandran Plot: Outliers : 0.57 % Allowed : 8.38 % Favored : 91.04 % Rotamer Outliers : 1.21 % 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: -1.61 (0.10), residues: 7132 helix: 0.55 (0.11), residues: 2448 sheet: -1.84 (0.16), residues: 963 loop : -2.03 (0.10), residues: 3721 *********************** 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 1275 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 1201 time to evaluate : 7.163 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 outliers start: 74 outliers final: 32 residues processed: 1237 average time/residue: 1.3098 time to fit residues: 2867.7369 Evaluate side-chains 1213 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 1181 time to evaluate : 6.253 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 0 residues processed: 32 average time/residue: 1.0955 time to fit residues: 74.2667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 663 optimal weight: 4.9990 chunk 515 optimal weight: 5.9990 chunk 755 optimal weight: 7.9990 chunk 1140 optimal weight: 10.0000 chunk 1049 optimal weight: 8.9990 chunk 908 optimal weight: 30.0000 chunk 94 optimal weight: 3.9990 chunk 701 optimal weight: 40.0000 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 162 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 186 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 ASN ** C 187 GLN ** 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** ** E 97 ASN ** 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 ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 HIS ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 115 GLN ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 196 ASN ** P 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 36 ASN ** a 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 60 ASN ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 24 GLN g 28 ASN k 31 ASN m 84 GLN v 363 GLN v 402 GLN v 479 HIS ** z1592 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z1609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.9613 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= 0.494 Angle : 0.880 18.302 232053 Z= 0.440 Chirality : 0.046 0.426 29042 Planarity : 0.007 0.143 14451 Dihedral : 18.099 179.969 56683 Min Nonbonded Distance : 1.029 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.50 % Allowed : 9.00 % Favored : 90.49 % Rotamer Outliers : 0.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.04 % Twisted Proline : 2.03 % 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: -1.90 (0.10), residues: 7132 helix: 0.28 (0.10), residues: 2442 sheet: -1.95 (0.16), residues: 972 loop : -2.19 (0.09), residues: 3718 ********************** 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 1259 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 1199 time to evaluate : 7.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 60 outliers final: 39 residues processed: 1225 average time/residue: 1.3872 time to fit residues: 3008.9069 Evaluate side-chains 1205 residues out of total 6223 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1166 time to evaluate : 7.098 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 0 residues processed: 39 average time/residue: 1.1965 time to fit residues: 97.1633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 1145 random chunks: chunk 556 optimal weight: 5.9990 chunk 721 optimal weight: 20.0000 chunk 967 optimal weight: 10.0000 chunk 278 optimal weight: 0.9990 chunk 837 optimal weight: 40.0000 chunk 134 optimal weight: 2.9990 chunk 252 optimal weight: 3.9990 chunk 909 optimal weight: 20.0000 chunk 380 optimal weight: 0.8980 chunk 934 optimal weight: 7.9990 chunk 115 optimal weight: 0.7980 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 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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** C 215 ASN D 122 GLN ** D 195 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 222 GLN ** E 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 132 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 165 ASN G 66 GLN ** I 59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 144 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 97 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 133 HIS ** P 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 36 ASN W 48 GLN W 59 HIS X 111 GLN Z 127 ASN ** a 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** m 84 GLN r 36 ASN v 363 GLN v 479 HIS w 17 ASN z1592 ASN ** z1609 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.117753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.089536 restraints weight = 291920.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.090104 restraints weight = 192524.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.091042 restraints weight = 148607.714| |-----------------------------------------------------------------------------| r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.9730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.083 157414 Z= 0.212 Angle : 0.711 19.161 232053 Z= 0.360 Chirality : 0.038 0.359 29042 Planarity : 0.006 0.139 14451 Dihedral : 17.841 179.896 56683 Min Nonbonded Distance : 1.122 Molprobity Statistics. All-atom Clashscore : 15.15 Ramachandran Plot: Outliers : 0.46 % Allowed : 7.16 % Favored : 92.37 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.34 % Cis-general : 0.04 % Twisted Proline : 1.69 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.51 (0.10), residues: 7132 helix: 0.66 (0.11), residues: 2443 sheet: -1.80 (0.16), residues: 969 loop : -1.97 (0.10), residues: 3720 =============================================================================== Job complete usr+sys time: 49343.06 seconds wall clock time: 858 minutes 7.32 seconds (51487.32 seconds total)