Starting phenix.real_space_refine on Fri Dec 15 21:59:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7y_2762/12_2023/3j7y_2762.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7y_2762/12_2023/3j7y_2762.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7y_2762/12_2023/3j7y_2762.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7y_2762/12_2023/3j7y_2762.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7y_2762/12_2023/3j7y_2762.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/3j7y_2762/12_2023/3j7y_2762.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.028 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 3 6.06 5 P 1530 5.49 5 Mg 66 5.21 5 S 256 5.16 5 C 53844 2.51 5 N 17169 2.21 5 O 21253 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 103": "NH1" <-> "NH2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "D GLU 115": "OE1" <-> "OE2" Residue "D GLU 123": "OE1" <-> "OE2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "D ARG 284": "NH1" <-> "NH2" Residue "E GLU 51": "OE1" <-> "OE2" Residue "E ASP 82": "OD1" <-> "OD2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "E PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 239": "NH1" <-> "NH2" Residue "E GLU 325": "OE1" <-> "OE2" Residue "E GLU 327": "OE1" <-> "OE2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F TYR 162": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 194": "OE1" <-> "OE2" Residue "F GLU 225": "OE1" <-> "OE2" Residue "F GLU 232": "OE1" <-> "OE2" Residue "H ARG 76": "NH1" <-> "NH2" Residue "H GLU 103": "OE1" <-> "OE2" Residue "J GLU 55": "OE1" <-> "OE2" Residue "K ARG 118": "NH1" <-> "NH2" Residue "K GLU 135": "OE1" <-> "OE2" Residue "K GLU 144": "OE1" <-> "OE2" Residue "K GLU 162": "OE1" <-> "OE2" Residue "K ARG 177": "NH1" <-> "NH2" Residue "L ARG 37": "NH1" <-> "NH2" Residue "L ARG 95": "NH1" <-> "NH2" Residue "L ARG 99": "NH1" <-> "NH2" Residue "L GLU 109": "OE1" <-> "OE2" Residue "L GLU 131": "OE1" <-> "OE2" Residue "M ARG 38": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 47": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M GLU 56": "OE1" <-> "OE2" Residue "M ARG 57": "NH1" <-> "NH2" Residue "M ARG 62": "NH1" <-> "NH2" Residue "M ARG 134": "NH1" <-> "NH2" Residue "M ARG 182": "NH1" <-> "NH2" Residue "M ASP 185": "OD1" <-> "OD2" Residue "M GLU 209": "OE1" <-> "OE2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N ARG 55": "NH1" <-> "NH2" Residue "N GLU 103": "OE1" <-> "OE2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "N GLU 168": "OE1" <-> "OE2" Residue "N GLU 170": "OE1" <-> "OE2" Residue "N GLU 196": "OE1" <-> "OE2" Residue "N PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "O ARG 106": "NH1" <-> "NH2" Residue "O GLU 124": "OE1" <-> "OE2" Residue "O ARG 137": "NH1" <-> "NH2" Residue "O ARG 138": "NH1" <-> "NH2" Residue "O ARG 153": "NH1" <-> "NH2" Residue "P ARG 50": "NH1" <-> "NH2" Residue "P ARG 53": "NH1" <-> "NH2" Residue "P GLU 56": "OE1" <-> "OE2" Residue "P ARG 62": "NH1" <-> "NH2" Residue "P ARG 74": "NH1" <-> "NH2" Residue "P GLU 75": "OE1" <-> "OE2" Residue "P PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P ARG 79": "NH1" <-> "NH2" Residue "P GLU 94": "OE1" <-> "OE2" Residue "P ARG 107": "NH1" <-> "NH2" Residue "P GLU 151": "OE1" <-> "OE2" Residue "P GLU 173": "OE1" <-> "OE2" Residue "P ARG 176": "NH1" <-> "NH2" Residue "Q ARG 83": "NH1" <-> "NH2" Residue "Q PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 156": "OE1" <-> "OE2" Residue "Q GLU 165": "OE1" <-> "OE2" Residue "Q GLU 251": "OE1" <-> "OE2" Residue "Q GLU 256": "OE1" <-> "OE2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R ARG 32": "NH1" <-> "NH2" Residue "R GLU 78": "OE1" <-> "OE2" Residue "R ARG 122": "NH1" <-> "NH2" Residue "R ARG 123": "NH1" <-> "NH2" Residue "S ARG 104": "NH1" <-> "NH2" Residue "S GLU 131": "OE1" <-> "OE2" Residue "S ARG 155": "NH1" <-> "NH2" Residue "S GLU 162": "OE1" <-> "OE2" Residue "S ARG 184": "NH1" <-> "NH2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T ARG 130": "NH1" <-> "NH2" Residue "T ARG 149": "NH1" <-> "NH2" Residue "T ARG 157": "NH1" <-> "NH2" Residue "T GLU 180": "OE1" <-> "OE2" Residue "T GLU 187": "OE1" <-> "OE2" Residue "U ARG 11": "NH1" <-> "NH2" Residue "U ARG 30": "NH1" <-> "NH2" Residue "U ARG 71": "NH1" <-> "NH2" Residue "U ARG 80": "NH1" <-> "NH2" Residue "U ARG 83": "NH1" <-> "NH2" Residue "V ARG 20": "NH1" <-> "NH2" Residue "V ARG 40": "NH1" <-> "NH2" Residue "V GLU 52": "OE1" <-> "OE2" Residue "V ARG 96": "NH1" <-> "NH2" Residue "V ARG 118": "NH1" <-> "NH2" Residue "V GLU 132": "OE1" <-> "OE2" Residue "V GLU 142": "OE1" <-> "OE2" Residue "V ARG 145": "NH1" <-> "NH2" Residue "V ARG 185": "NH1" <-> "NH2" Residue "V GLU 196": "OE1" <-> "OE2" Residue "V GLU 206": "OE1" <-> "OE2" Residue "W ARG 49": "NH1" <-> "NH2" Residue "W GLU 57": "OE1" <-> "OE2" Residue "W ARG 74": "NH1" <-> "NH2" Residue "W GLU 94": "OE1" <-> "OE2" Residue "W ARG 109": "NH1" <-> "NH2" Residue "X ARG 23": "NH1" <-> "NH2" Residue "X GLU 35": "OE1" <-> "OE2" Residue "X ARG 59": "NH1" <-> "NH2" Residue "X GLU 60": "OE1" <-> "OE2" Residue "X ARG 77": "NH1" <-> "NH2" Residue "X GLU 113": "OE1" <-> "OE2" Residue "X GLU 117": "OE1" <-> "OE2" Residue "X ASP 152": "OD1" <-> "OD2" Residue "X ARG 163": "NH1" <-> "NH2" Residue "X GLU 179": "OE1" <-> "OE2" Residue "X ARG 184": "NH1" <-> "NH2" Residue "X GLU 193": "OE1" <-> "OE2" Residue "X GLU 198": "OE1" <-> "OE2" Residue "X GLU 213": "OE1" <-> "OE2" Residue "X ARG 216": "NH1" <-> "NH2" Residue "X GLU 219": "OE1" <-> "OE2" Residue "X PHE 227": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 233": "OE1" <-> "OE2" Residue "Y GLU 65": "OE1" <-> "OE2" Residue "Y GLU 66": "OE1" <-> "OE2" Residue "Y GLU 77": "OE1" <-> "OE2" Residue "Y ARG 91": "NH1" <-> "NH2" Residue "Y ARG 109": "NH1" <-> "NH2" Residue "Y GLU 118": "OE1" <-> "OE2" Residue "Y GLU 150": "OE1" <-> "OE2" Residue "Y ARG 162": "NH1" <-> "NH2" Residue "Y ARG 175": "NH1" <-> "NH2" Residue "Y ARG 196": "NH1" <-> "NH2" Residue "Y ARG 210": "NH1" <-> "NH2" Residue "Z GLU 43": "OE1" <-> "OE2" Residue "0 TYR 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "0 GLU 136": "OE1" <-> "OE2" Residue "0 GLU 176": "OE1" <-> "OE2" Residue "1 ARG 19": "NH1" <-> "NH2" Residue "1 ARG 34": "NH1" <-> "NH2" Residue "1 GLU 58": "OE1" <-> "OE2" Residue "1 ARG 63": "NH1" <-> "NH2" Residue "2 ARG 69": "NH1" <-> "NH2" Residue "3 ARG 104": "NH1" <-> "NH2" Residue "3 ARG 116": "NH1" <-> "NH2" Residue "3 ARG 125": "NH1" <-> "NH2" Residue "3 ARG 168": "NH1" <-> "NH2" Residue "3 ARG 183": "NH1" <-> "NH2" Residue "5 ARG 80": "NH1" <-> "NH2" Residue "5 GLU 95": "OE1" <-> "OE2" Residue "5 ARG 110": "NH1" <-> "NH2" Residue "5 GLU 152": "OE1" <-> "OE2" Residue "5 ARG 162": "NH1" <-> "NH2" Residue "5 GLU 168": "OE1" <-> "OE2" Residue "5 ARG 223": "NH1" <-> "NH2" Residue "5 GLU 244": "OE1" <-> "OE2" Residue "5 GLU 254": "OE1" <-> "OE2" Residue "5 GLU 267": "OE1" <-> "OE2" Residue "5 ARG 303": "NH1" <-> "NH2" Residue "5 ARG 350": "NH1" <-> "NH2" Residue "5 GLU 399": "OE1" <-> "OE2" Residue "5 GLU 409": "OE1" <-> "OE2" Residue "6 ARG 27": "NH1" <-> "NH2" Residue "6 ARG 28": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Residue "6 ARG 58": "NH1" <-> "NH2" Residue "6 ARG 60": "NH1" <-> "NH2" Residue "6 ARG 136": "NH1" <-> "NH2" Residue "6 ARG 159": "NH1" <-> "NH2" Residue "6 GLU 197": "OE1" <-> "OE2" Residue "6 GLU 207": "OE1" <-> "OE2" Residue "6 ARG 261": "NH1" <-> "NH2" Residue "6 ARG 296": "NH1" <-> "NH2" Residue "6 ARG 299": "NH1" <-> "NH2" Residue "6 ARG 322": "NH1" <-> "NH2" Residue "6 GLU 343": "OE1" <-> "OE2" Residue "6 ARG 364": "NH1" <-> "NH2" Residue "6 GLU 374": "OE1" <-> "OE2" Residue "7 GLU 66": "OE1" <-> "OE2" Residue "7 GLU 97": "OE1" <-> "OE2" Residue "7 ARG 168": "NH1" <-> "NH2" Residue "7 GLU 171": "OE1" <-> "OE2" Residue "7 GLU 220": "OE1" <-> "OE2" Residue "7 GLU 228": "OE1" <-> "OE2" Residue "7 GLU 242": "OE1" <-> "OE2" Residue "7 ARG 250": "NH1" <-> "NH2" Residue "7 ARG 271": "NH1" <-> "NH2" Residue "8 GLU 88": "OE1" <-> "OE2" Residue "8 ARG 93": "NH1" <-> "NH2" Residue "9 ARG 25": "NH1" <-> "NH2" Residue "9 ARG 28": "NH1" <-> "NH2" Residue "9 ARG 49": "NH1" <-> "NH2" Residue "9 GLU 55": "OE1" <-> "OE2" Residue "9 GLU 82": "OE1" <-> "OE2" Residue "9 GLU 124": "OE1" <-> "OE2" Residue "a GLU 104": "OE1" <-> "OE2" Residue "a GLU 110": "OE1" <-> "OE2" Residue "a ARG 122": "NH1" <-> "NH2" Residue "a ARG 128": "NH1" <-> "NH2" Residue "a ARG 133": "NH1" <-> "NH2" Residue "a ARG 142": "NH1" <-> "NH2" Residue "b ARG 28": "NH1" <-> "NH2" Residue "b ARG 41": "NH1" <-> "NH2" Residue "b ARG 49": "NH1" <-> "NH2" Residue "b GLU 50": "OE1" <-> "OE2" Residue "b GLU 95": "OE1" <-> "OE2" Residue "b ARG 114": "NH1" <-> "NH2" Residue "b ARG 144": "NH1" <-> "NH2" Residue "b ARG 146": "NH1" <-> "NH2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c GLU 81": "OE1" <-> "OE2" Residue "c GLU 176": "OE1" <-> "OE2" Residue "c GLU 182": "OE1" <-> "OE2" Residue "c ARG 216": "NH1" <-> "NH2" Residue "c GLU 227": "OE1" <-> "OE2" Residue "c GLU 287": "OE1" <-> "OE2" Residue "d ARG 159": "NH1" <-> "NH2" Residue "d GLU 166": "OE1" <-> "OE2" Residue "d GLU 249": "OE1" <-> "OE2" Residue "e GLU 133": "OE1" <-> "OE2" Residue "e PHE 173": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 214": "OD1" <-> "OD2" Residue "f ARG 155": "NH1" <-> "NH2" Residue "g GLU 40": "OE1" <-> "OE2" Residue "g ARG 90": "NH1" <-> "NH2" Residue "g ARG 105": "NH1" <-> "NH2" Residue "h GLU 71": "OE1" <-> "OE2" Residue "h GLU 92": "OE1" <-> "OE2" Residue "h ARG 116": "NH1" <-> "NH2" Residue "i ARG 46": "NH1" <-> "NH2" Residue "i GLU 49": "OE1" <-> "OE2" Residue "i GLU 67": "OE1" <-> "OE2" Residue "i ARG 75": "NH1" <-> "NH2" Residue "i GLU 87": "OE1" <-> "OE2" Residue "i ARG 93": "NH1" <-> "NH2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "j ARG 28": "NH1" <-> "NH2" Residue "j TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "j GLU 45": "OE1" <-> "OE2" Residue "j ARG 55": "NH1" <-> "NH2" Residue "j ARG 65": "NH1" <-> "NH2" Residue "j ARG 66": "NH1" <-> "NH2" Residue "j GLU 71": "OE1" <-> "OE2" Residue "j ARG 76": "NH1" <-> "NH2" Residue "j ARG 94": "NH1" <-> "NH2" Residue "j ARG 103": "NH1" <-> "NH2" Residue "k GLU 28": "OE1" <-> "OE2" Residue "k ARG 31": "NH1" <-> "NH2" Residue "k ARG 77": "NH1" <-> "NH2" Residue "o ARG 23": "NH1" <-> "NH2" Residue "o GLU 44": "OE1" <-> "OE2" Residue "o GLU 59": "OE1" <-> "OE2" Residue "o ARG 60": "NH1" <-> "NH2" Residue "o ARG 68": "NH1" <-> "NH2" Residue "o GLU 69": "OE1" <-> "OE2" Residue "o GLU 72": "OE1" <-> "OE2" Residue "p PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "p GLU 132": "OE1" <-> "OE2" Residue "q ARG 33": "NH1" <-> "NH2" Residue "q ARG 38": "NH1" <-> "NH2" Residue "q GLU 43": "OE1" <-> "OE2" Residue "q ARG 63": "NH1" <-> "NH2" Residue "q GLU 84": "OE1" <-> "OE2" Residue "q GLU 88": "OE1" <-> "OE2" Residue "q GLU 89": "OE1" <-> "OE2" Residue "q GLU 101": "OE1" <-> "OE2" Residue "q GLU 110": "OE1" <-> "OE2" Residue "q ARG 114": "NH1" <-> "NH2" Residue "q GLU 118": "OE1" <-> "OE2" Residue "r GLU 40": "OE1" <-> "OE2" Residue "r GLU 59": "OE1" <-> "OE2" Residue "r ARG 132": "NH1" <-> "NH2" Residue "r ARG 153": "NH1" <-> "NH2" Residue "r ARG 171": "NH1" <-> "NH2" Residue "s TYR 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 59": "NH1" <-> "NH2" Residue "s ARG 81": "NH1" <-> "NH2" Residue "s ASP 103": "OD1" <-> "OD2" Residue "s ARG 158": "NH1" <-> "NH2" Residue "s ARG 160": "NH1" <-> "NH2" Residue "s ARG 162": "NH1" <-> "NH2" Residue "s GLU 167": "OE1" <-> "OE2" Residue "s GLU 168": "OE1" <-> "OE2" Residue "s GLU 170": "OE1" <-> "OE2" Residue "s ARG 212": "NH1" <-> "NH2" Residue "s GLU 214": "OE1" <-> "OE2" Residue "s GLU 215": "OE1" <-> "OE2" Residue "s ARG 219": "NH1" <-> "NH2" Residue "s ARG 222": "NH1" <-> "NH2" Residue "s ARG 223": "NH1" <-> "NH2" Residue "s ARG 242": "NH1" <-> "NH2" Residue "s GLU 249": "OE1" <-> "OE2" Residue "s GLU 260": "OE1" <-> "OE2" Residue "s ARG 276": "NH1" <-> "NH2" Residue "s GLU 279": "OE1" <-> "OE2" Residue "s ARG 308": "NH1" <-> "NH2" Residue "s GLU 309": "OE1" <-> "OE2" Residue "s ARG 389": "NH1" <-> "NH2" Time to flip residues: 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 94121 Number of models: 1 Model: "" Number of chains: 56 Chain: "A" Number of atoms: 31261 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1472, 31261 Classifications: {'RNA': 1472} Modifications used: {'rna2p_pur': 155, 'rna2p_pyr': 103, 'rna3p_pur': 622, 'rna3p_pyr': 592} Link IDs: {'rna2p': 257, 'rna3p': 1214} Chain breaks: 14 Chain: "B" Number of atoms: 1211 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 1211 Classifications: {'RNA': 57} Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 29, 'rna3p_pyr': 27} Link IDs: {'rna2p': 1, 'rna3p': 55} Chain breaks: 5 Chain: "D" Number of atoms: 1842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1842 Classifications: {'peptide': 236} Link IDs: {'PTRANS': 12, 'TRANS': 223} Chain: "E" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2365 Classifications: {'peptide': 300} Link IDs: {'CIS': 2, 'PTRANS': 24, 'TRANS': 273} Chain breaks: 1 Chain: "F" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2013 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 21, 'TRANS': 228} Chain: "H" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "I" Number of atoms: 1283 Number of conformers: 1 Conformer: "" Number of residues, atoms: 158, 1283 Classifications: {'peptide': 158} Link IDs: {'PTRANS': 11, 'TRANS': 146} Chain breaks: 1 Chain: "J" Number of atoms: 1061 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1061 Classifications: {'peptide': 140} Link IDs: {'CIS': 1, 'PTRANS': 9, 'TRANS': 129} Chain: "K" Number of atoms: 1451 Number of conformers: 1 Conformer: "" Number of residues, atoms: 177, 1451 Classifications: {'peptide': 177} Link IDs: {'PTRANS': 15, 'TRANS': 161} Chain: "L" Number of atoms: 889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 889 Classifications: {'peptide': 115} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 105} Chain: "M" Number of atoms: 2305 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2305 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 26, 'TRANS': 260} Chain: "N" Number of atoms: 1654 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1654 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 14, 'TRANS': 190} Chain: "O" Number of atoms: 1245 Number of conformers: 1 Conformer: "" Number of residues, atoms: 152, 1245 Classifications: {'peptide': 152} Link IDs: {'PTRANS': 9, 'TRANS': 142} Chain: "P" Number of atoms: 1080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 133, 1080 Classifications: {'peptide': 133} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 126} Chain breaks: 1 Chain: "Q" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 204, 1704 Classifications: {'peptide': 204} Link IDs: {'PTRANS': 12, 'TRANS': 191} Chain breaks: 1 Chain: "R" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1153 Classifications: {'peptide': 140} Link IDs: {'CIS': 1, 'PTRANS': 3, 'TRANS': 135} Chain: "S" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1251 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "T" Number of atoms: 1368 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1368 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 12, 'TRANS': 153} Chain: "U" Number of atoms: 922 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 922 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 9, 'TRANS': 101} Chain: "V" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1551 Classifications: {'peptide': 189} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 172} Chain breaks: 2 Chain: "W" Number of atoms: 842 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 842 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 6, 'TRANS': 100} Chain: "X" Number of atoms: 2027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2027 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 17, 'TRANS': 225} Chain: "Y" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 176, 1517 Classifications: {'peptide': 176} Link IDs: {'PTRANS': 7, 'TRANS': 168} Chain: "Z" Number of atoms: 978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 978 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 11, 'TRANS': 108} Chain: "0" Number of atoms: 803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 803 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 6, 'TRANS': 91} Chain breaks: 1 Chain: "1" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 433 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "2" Number of atoms: 351 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 351 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 2, 'TRANS': 40} Chain: "3" Number of atoms: 831 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 831 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "4" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 36, 322 Classifications: {'peptide': 36} Link IDs: {'PTRANS': 1, 'TRANS': 34} Chain: "5" Number of atoms: 3064 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 3064 Classifications: {'peptide': 376} Link IDs: {'CIS': 4, 'PCIS': 1, 'PTRANS': 30, 'TRANS': 340} Chain breaks: 3 Chain: "6" Number of atoms: 2636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2636 Classifications: {'peptide': 325} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'CIS': 3, 'PTRANS': 30, 'TRANS': 291} Chain breaks: 5 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 105 Unresolved non-hydrogen dihedrals: 65 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 4, 'ARG:plan': 5, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 60 Chain: "7" Number of atoms: 2158 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2158 Classifications: {'peptide': 266} Link IDs: {'CIS': 1, 'PTRANS': 15, 'TRANS': 249} Chain breaks: 3 Chain: "8" Number of atoms: 482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 482 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 1, 'TRANS': 55} Chain: "9" Number of atoms: 873 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 873 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 9, 'TRANS': 99} Chain breaks: 1 Chain: "a" Number of atoms: 343 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 343 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 4, 'TRANS': 34} Chain: "b" Number of atoms: 1178 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1178 Classifications: {'peptide': 148} Link IDs: {'PTRANS': 9, 'TRANS': 138} Chain: "c" Number of atoms: 2217 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2217 Classifications: {'peptide': 275} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 258} Chain breaks: 1 Chain: "d" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1347 Classifications: {'peptide': 162} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 11, 'TRANS': 148} Chain breaks: 2 Chain: "e" Number of atoms: 1082 Number of conformers: 1 Conformer: "" Number of residues, atoms: 134, 1082 Classifications: {'peptide': 134} Link IDs: {'PTRANS': 5, 'TRANS': 128} Chain: "f" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 703 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain breaks: 5 Unresolved non-hydrogen bonds: 32 Unresolved non-hydrogen angles: 48 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'UNK:plan-1': 16} Unresolved non-hydrogen planarities: 16 Chain: "g" Number of atoms: 1067 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1067 Classifications: {'peptide': 129} Link IDs: {'PCIS': 2, 'PTRANS': 13, 'TRANS': 113} Chain: "h" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 827 Classifications: {'peptide': 100} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 91} Chain breaks: 1 Chain: "i" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 816 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 5, 'TRANS': 90} Chain: "j" Number of atoms: 684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 684 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Chain: "k" Number of atoms: 655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 655 Classifications: {'peptide': 84} Link IDs: {'CIS': 1, 'PTRANS': 2, 'TRANS': 80} Chain: "o" Number of atoms: 797 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 797 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 5, 'TRANS': 88} Chain: "p" Number of atoms: 674 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 674 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain breaks: 1 Chain: "q" Number of atoms: 1076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 1076 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 14, 'TRANS': 113} Chain: "r" Number of atoms: 1203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1203 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 16, 'TRANS': 129} Chain breaks: 2 Chain: "s" Number of atoms: 3036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 3036 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Chain breaks: 1 Chain: "t" Number of atoms: 615 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 615 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 123} Link IDs: {'CIS': 1, 'TRANS': 121} Chain breaks: 4 Unresolved non-hydrogen bonds: 246 Unresolved non-hydrogen angles: 369 Unresolved non-hydrogen dihedrals: 123 Planarities with less than four sites: {'UNK:plan-1': 123} Unresolved non-hydrogen planarities: 123 Chain: "A" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 66, 87 Unusual residues: {' MG': 65} Classifications: {'RNA': 1, 'undetermined': 65} Modifications used: {'rna2p_pur': 1} Link IDs: {None: 65} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 64021 SG CYS 0 110 172.224 142.604 167.301 1.00 48.90 S ATOM 64043 SG CYS 0 113 173.174 144.646 165.029 1.00 49.06 S ATOM 64123 SG CYS 0 123 171.955 141.132 164.079 1.00 48.84 S ATOM 64146 SG CYS 0 126 175.011 141.984 165.961 1.00 49.80 S ATOM 66258 SG CYS 4 76 96.156 59.121 154.876 1.00 65.14 S ATOM 66281 SG CYS 4 79 96.212 62.172 156.414 1.00 49.93 S ATOM 66405 SG CYS 4 92 96.883 60.639 158.924 1.00 51.04 S ATOM 89411 SG CYS r 70 70.051 87.465 167.088 1.00 62.48 S ATOM 89726 SG CYS r 108 72.363 86.540 164.616 1.00 61.00 S Time building chain proxies: 36.97, per 1000 atoms: 0.39 Number of scatterers: 94121 At special positions: 0 Unit cell: (253.26, 222.44, 219.76, 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 3 29.99 S 256 16.00 P 1530 15.00 Mg 66 11.99 O 21253 8.00 N 17169 7.00 C 53844 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 35.31 Conformation dependent library (CDL) restraints added in 9.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 0 200 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 110 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 126 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 123 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 113 " pdb=" ZN 4 200 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 79 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 76 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 92 " pdb=" ZN r 200 " pdb="ZN ZN r 200 " - pdb=" SG CYS r 70 " pdb="ZN ZN r 200 " - pdb=" SG CYS r 108 " Number of angles added : 6 14626 Ramachandran restraints generated. 7313 Oldfield, 0 Emsley, 7313 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14330 Finding SS restraints... Secondary structure from input PDB file: 248 helices and 74 sheets defined 39.0% alpha, 13.3% beta 389 base pairs and 623 stacking pairs defined. Time for finding SS restraints: 26.53 Creating SS restraints... Processing helix chain 'D' and resid 185 through 187 No H-bonds generated for 'chain 'D' and resid 185 through 187' Processing helix chain 'D' and resid 251 through 255 Processing helix chain 'D' and resid 259 through 266 removed outlier: 3.666A pdb=" N ASN D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 76 removed outlier: 4.315A pdb=" N PHE E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 83 removed outlier: 4.011A pdb=" N ASP E 82 " --> pdb=" O CYS E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 157 Processing helix chain 'E' and resid 158 through 168 Processing helix chain 'E' and resid 194 through 198 Processing helix chain 'E' and resid 217 through 222 Processing helix chain 'E' and resid 304 through 308 removed outlier: 3.714A pdb=" N LYS E 308 " --> pdb=" O PRO E 305 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 89 Processing helix chain 'F' and resid 92 through 107 removed outlier: 4.658A pdb=" N LYS F 107 " --> pdb=" O GLN F 103 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 184 Processing helix chain 'F' and resid 199 through 211 Processing helix chain 'F' and resid 227 through 237 removed outlier: 4.272A pdb=" N ARG F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 244 through 248 Processing helix chain 'F' and resid 249 through 256 Processing helix chain 'F' and resid 263 through 275 removed outlier: 3.733A pdb=" N TRP F 275 " --> pdb=" O ASP F 271 " (cutoff:3.500A) Processing helix chain 'H' and resid 116 through 122 Processing helix chain 'H' and resid 123 through 127 Processing helix chain 'H' and resid 133 through 147 removed outlier: 3.823A pdb=" N LYS H 138 " --> pdb=" O PRO H 134 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N LEU H 139 " --> pdb=" O GLU H 135 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 51 Processing helix chain 'I' and resid 78 through 93 Processing helix chain 'I' and resid 105 through 119 Processing helix chain 'I' and resid 127 through 139 Proline residue: I 133 - end of helix Processing helix chain 'I' and resid 160 through 171 removed outlier: 3.757A pdb=" N MET I 164 " --> pdb=" O LYS I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 197 Processing helix chain 'J' and resid 35 through 40 removed outlier: 3.515A pdb=" N GLY J 40 " --> pdb=" O GLY J 36 " (cutoff:3.500A) Processing helix chain 'J' and resid 46 through 60 Processing helix chain 'J' and resid 86 through 95 Processing helix chain 'J' and resid 113 through 126 removed outlier: 4.184A pdb=" N GLN J 126 " --> pdb=" O ARG J 122 " (cutoff:3.500A) Processing helix chain 'J' and resid 136 through 151 removed outlier: 4.050A pdb=" N VAL J 140 " --> pdb=" O PRO J 136 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N SER J 143 " --> pdb=" O SER J 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 14 Processing helix chain 'K' and resid 29 through 41 removed outlier: 4.086A pdb=" N MET K 34 " --> pdb=" O LYS K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 70 through 75 Processing helix chain 'K' and resid 92 through 99 Processing helix chain 'K' and resid 101 through 112 Processing helix chain 'K' and resid 116 through 124 removed outlier: 4.257A pdb=" N THR K 120 " --> pdb=" O LEU K 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 134 through 141 Processing helix chain 'K' and resid 159 through 166 removed outlier: 3.581A pdb=" N ILE K 163 " --> pdb=" O THR K 159 " (cutoff:3.500A) Processing helix chain 'L' and resid 44 through 49 removed outlier: 3.747A pdb=" N ASN L 48 " --> pdb=" O SER L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 124 through 130 removed outlier: 3.556A pdb=" N LEU L 127 " --> pdb=" O PRO L 124 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ARG L 130 " --> pdb=" O LEU L 127 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 140 removed outlier: 3.672A pdb=" N LEU L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 16 Processing helix chain 'M' and resid 73 through 78 removed outlier: 3.791A pdb=" N ILE M 78 " --> pdb=" O PHE M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 90 removed outlier: 3.708A pdb=" N ARG M 90 " --> pdb=" O HIS M 87 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 108 Processing helix chain 'M' and resid 117 through 125 Processing helix chain 'M' and resid 160 through 170 Processing helix chain 'M' and resid 180 through 189 Processing helix chain 'M' and resid 189 through 197 removed outlier: 3.761A pdb=" N PHE M 193 " --> pdb=" O LYS M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 210 through 215 Processing helix chain 'M' and resid 216 through 220 removed outlier: 3.951A pdb=" N ASN M 219 " --> pdb=" O ASP M 216 " (cutoff:3.500A) Processing helix chain 'M' and resid 228 through 241 Processing helix chain 'M' and resid 252 through 257 Processing helix chain 'M' and resid 287 through 296 Processing helix chain 'N' and resid 68 through 72 removed outlier: 3.523A pdb=" N ASP N 71 " --> pdb=" O ASN N 68 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 112 Processing helix chain 'N' and resid 168 through 183 removed outlier: 4.014A pdb=" N PHE N 175 " --> pdb=" O GLU N 171 " (cutoff:3.500A) Processing helix chain 'N' and resid 192 through 209 Processing helix chain 'N' and resid 214 through 221 removed outlier: 3.541A pdb=" N ILE N 218 " --> pdb=" O THR N 214 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 229 Processing helix chain 'O' and resid 21 through 40 Processing helix chain 'O' and resid 46 through 65 removed outlier: 3.502A pdb=" N ASP O 50 " --> pdb=" O TRP O 46 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU O 51 " --> pdb=" O ALA O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 80 Processing helix chain 'O' and resid 84 through 92 removed outlier: 3.794A pdb=" N LYS O 88 " --> pdb=" O ASP O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 97 Processing helix chain 'O' and resid 143 through 160 Processing helix chain 'P' and resid 53 through 58 Processing helix chain 'P' and resid 105 through 109 removed outlier: 3.672A pdb=" N TRP P 109 " --> pdb=" O THR P 106 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 139 Processing helix chain 'P' and resid 148 through 154 Processing helix chain 'P' and resid 154 through 168 Processing helix chain 'Q' and resid 88 through 106 removed outlier: 3.884A pdb=" N PHE Q 92 " --> pdb=" O ASP Q 88 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL Q 105 " --> pdb=" O GLU Q 101 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 146 Processing helix chain 'Q' and resid 187 through 193 Processing helix chain 'Q' and resid 244 through 249 removed outlier: 4.223A pdb=" N CYS Q 248 " --> pdb=" O ARG Q 244 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 259 Processing helix chain 'Q' and resid 275 through 292 Processing helix chain 'R' and resid 16 through 29 removed outlier: 3.736A pdb=" N ARG R 20 " --> pdb=" O ASP R 16 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL R 24 " --> pdb=" O ARG R 20 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N HIS R 27 " --> pdb=" O GLU R 23 " (cutoff:3.500A) Processing helix chain 'R' and resid 32 through 37 removed outlier: 3.841A pdb=" N LYS R 35 " --> pdb=" O ARG R 32 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 78 removed outlier: 3.724A pdb=" N ARG R 44 " --> pdb=" O ARG R 40 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 94 Processing helix chain 'R' and resid 98 through 109 Processing helix chain 'R' and resid 109 through 133 removed outlier: 3.571A pdb=" N GLY R 133 " --> pdb=" O ALA R 129 " (cutoff:3.500A) Processing helix chain 'S' and resid 68 through 90 Processing helix chain 'T' and resid 49 through 55 removed outlier: 4.062A pdb=" N LYS T 53 " --> pdb=" O ARG T 49 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ASN T 55 " --> pdb=" O TRP T 51 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 95 removed outlier: 3.726A pdb=" N LEU T 90 " --> pdb=" O LYS T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 98 through 109 Processing helix chain 'T' and resid 111 through 131 removed outlier: 3.859A pdb=" N LYS T 115 " --> pdb=" O LYS T 111 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ILE T 116 " --> pdb=" O LYS T 112 " (cutoff:3.500A) Processing helix chain 'T' and resid 136 through 138 No H-bonds generated for 'chain 'T' and resid 136 through 138' Processing helix chain 'T' and resid 191 through 206 removed outlier: 3.543A pdb=" N ARG T 206 " --> pdb=" O GLN T 202 " (cutoff:3.500A) Processing helix chain 'U' and resid 49 through 61 Processing helix chain 'V' and resid 28 through 35 Processing helix chain 'V' and resid 178 through 183 Processing helix chain 'V' and resid 192 through 203 removed outlier: 3.901A pdb=" N GLU V 196 " --> pdb=" O LYS V 192 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLU V 197 " --> pdb=" O THR V 193 " (cutoff:3.500A) Processing helix chain 'W' and resid 110 through 120 removed outlier: 3.666A pdb=" N VAL W 114 " --> pdb=" O ASN W 110 " (cutoff:3.500A) Processing helix chain 'X' and resid 7 through 9 No H-bonds generated for 'chain 'X' and resid 7 through 9' Processing helix chain 'X' and resid 10 through 19 removed outlier: 3.512A pdb=" N ARG X 17 " --> pdb=" O ARG X 13 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N GLY X 19 " --> pdb=" O GLN X 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 19 through 24 removed outlier: 3.668A pdb=" N ARG X 23 " --> pdb=" O GLY X 19 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 35 removed outlier: 3.961A pdb=" N SER X 31 " --> pdb=" O HIS X 27 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N GLU X 35 " --> pdb=" O SER X 31 " (cutoff:3.500A) Processing helix chain 'X' and resid 128 through 138 Processing helix chain 'X' and resid 140 through 148 Processing helix chain 'X' and resid 149 through 154 removed outlier: 3.739A pdb=" N CYS X 154 " --> pdb=" O GLY X 150 " (cutoff:3.500A) Processing helix chain 'X' and resid 155 through 172 Processing helix chain 'X' and resid 180 through 191 removed outlier: 3.575A pdb=" N TYR X 191 " --> pdb=" O ILE X 187 " (cutoff:3.500A) Processing helix chain 'X' and resid 197 through 204 removed outlier: 4.021A pdb=" N TRP X 203 " --> pdb=" O GLU X 199 " (cutoff:3.500A) Processing helix chain 'X' and resid 207 through 219 Processing helix chain 'X' and resid 225 through 244 removed outlier: 3.678A pdb=" N ILE X 229 " --> pdb=" O PRO X 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 63 through 68 Processing helix chain 'Y' and resid 70 through 74 Processing helix chain 'Y' and resid 86 through 93 Processing helix chain 'Y' and resid 94 through 123 Processing helix chain 'Y' and resid 129 through 158 removed outlier: 3.577A pdb=" N ASP Y 133 " --> pdb=" O PRO Y 129 " (cutoff:3.500A) Processing helix chain 'Y' and resid 187 through 190 Processing helix chain 'Y' and resid 191 through 196 removed outlier: 3.622A pdb=" N ASN Y 195 " --> pdb=" O ASN Y 191 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ARG Y 196 " --> pdb=" O LYS Y 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'Y' and resid 191 through 196' Processing helix chain 'Y' and resid 203 through 238 removed outlier: 4.298A pdb=" N HIS Y 207 " --> pdb=" O PRO Y 203 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N PHE Y 208 " --> pdb=" O TYR Y 204 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 56 Processing helix chain 'Z' and resid 79 through 90 Processing helix chain 'Z' and resid 103 through 113 removed outlier: 3.698A pdb=" N LYS Z 109 " --> pdb=" O SER Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 130 through 134 removed outlier: 3.989A pdb=" N MET Z 134 " --> pdb=" O GLU Z 131 " (cutoff:3.500A) Processing helix chain '0' and resid 86 through 95 Processing helix chain '0' and resid 123 through 145 removed outlier: 3.631A pdb=" N LYS 0 129 " --> pdb=" O TYR 0 125 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL 0 130 " --> pdb=" O CYS 0 126 " (cutoff:3.500A) Processing helix chain '2' and resid 56 through 65 Processing helix chain '2' and resid 65 through 72 removed outlier: 3.861A pdb=" N THR 2 72 " --> pdb=" O ARG 2 68 " (cutoff:3.500A) Processing helix chain '2' and resid 72 through 86 Processing helix chain '3' and resid 107 through 113 removed outlier: 3.839A pdb=" N ILE 3 111 " --> pdb=" O VAL 3 107 " (cutoff:3.500A) Processing helix chain '3' and resid 137 through 145 Processing helix chain '3' and resid 151 through 162 Processing helix chain '3' and resid 163 through 168 Processing helix chain '3' and resid 177 through 181 Processing helix chain '4' and resid 95 through 99 Processing helix chain '5' and resid 47 through 52 Processing helix chain '5' and resid 84 through 88 removed outlier: 3.506A pdb=" N TYR 5 88 " --> pdb=" O PRO 5 85 " (cutoff:3.500A) Processing helix chain '5' and resid 116 through 125 Processing helix chain '5' and resid 133 through 139 Processing helix chain '5' and resid 151 through 163 Processing helix chain '5' and resid 172 through 190 Proline residue: 5 178 - end of helix Processing helix chain '5' and resid 191 through 193 No H-bonds generated for 'chain '5' and resid 191 through 193' Processing helix chain '5' and resid 195 through 199 removed outlier: 3.572A pdb=" N ALA 5 199 " --> pdb=" O PRO 5 196 " (cutoff:3.500A) Processing helix chain '5' and resid 241 through 249 removed outlier: 4.085A pdb=" N LYS 5 249 " --> pdb=" O ILE 5 245 " (cutoff:3.500A) Processing helix chain '5' and resid 305 through 329 Processing helix chain '5' and resid 407 through 420 removed outlier: 4.489A pdb=" N PHE 5 411 " --> pdb=" O LYS 5 407 " (cutoff:3.500A) Processing helix chain '6' and resid 54 through 67 Processing helix chain '6' and resid 73 through 78 removed outlier: 4.276A pdb=" N TYR 6 77 " --> pdb=" O THR 6 73 " (cutoff:3.500A) Processing helix chain '6' and resid 100 through 118 Processing helix chain '6' and resid 131 through 142 removed outlier: 3.708A pdb=" N VAL 6 135 " --> pdb=" O PRO 6 131 " (cutoff:3.500A) Processing helix chain '6' and resid 143 through 156 removed outlier: 3.576A pdb=" N GLN 6 149 " --> pdb=" O PRO 6 145 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N ARG 6 150 " --> pdb=" O TYR 6 146 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU 6 151 " --> pdb=" O HIS 6 147 " (cutoff:3.500A) Processing helix chain '6' and resid 156 through 161 Processing helix chain '6' and resid 292 through 297 removed outlier: 4.055A pdb=" N ARG 6 296 " --> pdb=" O GLN 6 292 " (cutoff:3.500A) Processing helix chain '6' and resid 299 through 306 removed outlier: 3.691A pdb=" N PHE 6 303 " --> pdb=" O ARG 6 299 " (cutoff:3.500A) Processing helix chain '6' and resid 324 through 334 removed outlier: 4.026A pdb=" N THR 6 328 " --> pdb=" O ASP 6 324 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N TYR 6 329 " --> pdb=" O ASP 6 325 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU 6 334 " --> pdb=" O ILE 6 330 " (cutoff:3.500A) Processing helix chain '6' and resid 362 through 369 removed outlier: 3.724A pdb=" N LEU 6 366 " --> pdb=" O LEU 6 363 " (cutoff:3.500A) Processing helix chain '7' and resid 37 through 58 removed outlier: 3.888A pdb=" N THR 7 41 " --> pdb=" O PRO 7 37 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU 7 42 " --> pdb=" O THR 7 38 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU 7 58 " --> pdb=" O ARG 7 54 " (cutoff:3.500A) Processing helix chain '7' and resid 87 through 96 removed outlier: 3.742A pdb=" N CYS 7 91 " --> pdb=" O THR 7 87 " (cutoff:3.500A) Processing helix chain '7' and resid 97 through 103 Processing helix chain '7' and resid 135 through 158 removed outlier: 4.112A pdb=" N PHE 7 158 " --> pdb=" O ILE 7 154 " (cutoff:3.500A) Processing helix chain '7' and resid 195 through 213 Processing helix chain '7' and resid 222 through 231 Processing helix chain '7' and resid 233 through 247 Processing helix chain '7' and resid 271 through 273 No H-bonds generated for 'chain '7' and resid 271 through 273' Processing helix chain '7' and resid 309 through 322 Processing helix chain '8' and resid 64 through 110 removed outlier: 3.504A pdb=" N GLN 8 83 " --> pdb=" O LEU 8 79 " (cutoff:3.500A) Processing helix chain '8' and resid 110 through 119 removed outlier: 3.506A pdb=" N HIS 8 114 " --> pdb=" O SER 8 110 " (cutoff:3.500A) Processing helix chain '9' and resid 27 through 34 removed outlier: 3.677A pdb=" N ARG 9 33 " --> pdb=" O SER 9 29 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N LYS 9 34 " --> pdb=" O PHE 9 30 " (cutoff:3.500A) Processing helix chain '9' and resid 87 through 94 Processing helix chain '9' and resid 96 through 103 Processing helix chain 'a' and resid 105 through 117 Processing helix chain 'a' and resid 119 through 123 removed outlier: 4.123A pdb=" N ARG a 122 " --> pdb=" O THR a 119 " (cutoff:3.500A) Processing helix chain 'a' and resid 127 through 134 Processing helix chain 'b' and resid 37 through 40 Processing helix chain 'b' and resid 41 through 58 removed outlier: 4.655A pdb=" N VAL b 51 " --> pdb=" O VAL b 47 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE b 52 " --> pdb=" O GLU b 48 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N ASP b 53 " --> pdb=" O ARG b 49 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE b 54 " --> pdb=" O GLU b 50 " (cutoff:3.500A) Processing helix chain 'b' and resid 93 through 107 Processing helix chain 'b' and resid 139 through 143 Processing helix chain 'c' and resid 35 through 53 Processing helix chain 'c' and resid 67 through 79 removed outlier: 3.536A pdb=" N LEU c 79 " --> pdb=" O PHE c 75 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 93 removed outlier: 3.627A pdb=" N THR c 90 " --> pdb=" O ASP c 86 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ALA c 91 " --> pdb=" O LEU c 87 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE c 92 " --> pdb=" O LEU c 88 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL c 93 " --> pdb=" O LYS c 89 " (cutoff:3.500A) Processing helix chain 'c' and resid 94 through 107 Processing helix chain 'c' and resid 122 through 145 removed outlier: 4.027A pdb=" N GLN c 128 " --> pdb=" O GLU c 124 " (cutoff:3.500A) Processing helix chain 'c' and resid 149 through 162 Processing helix chain 'c' and resid 164 through 174 Processing helix chain 'c' and resid 174 through 179 removed outlier: 4.132A pdb=" N LEU c 178 " --> pdb=" O ALA c 174 " (cutoff:3.500A) Processing helix chain 'c' and resid 187 through 206 Processing helix chain 'c' and resid 207 through 219 Processing helix chain 'c' and resid 220 through 223 Processing helix chain 'c' and resid 236 through 249 removed outlier: 3.994A pdb=" N LEU c 240 " --> pdb=" O ASN c 236 " (cutoff:3.500A) Processing helix chain 'c' and resid 288 through 305 Processing helix chain 'd' and resid 118 through 130 removed outlier: 4.244A pdb=" N ALA d 130 " --> pdb=" O LYS d 126 " (cutoff:3.500A) Processing helix chain 'd' and resid 136 through 155 removed outlier: 3.535A pdb=" N LYS d 140 " --> pdb=" O ASP d 136 " (cutoff:3.500A) Processing helix chain 'd' and resid 156 through 161 Processing helix chain 'd' and resid 167 through 174 removed outlier: 3.971A pdb=" N ASP d 171 " --> pdb=" O HIS d 167 " (cutoff:3.500A) Processing helix chain 'e' and resid 139 through 153 Processing helix chain 'e' and resid 225 through 234 Processing helix chain 'f' and resid 100 through 118 Processing helix chain 'f' and resid 163 through 176 Processing helix chain 'g' and resid 44 through 52 removed outlier: 4.384A pdb=" N VAL g 48 " --> pdb=" O GLU g 44 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU g 51 " --> pdb=" O PHE g 47 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU g 52 " --> pdb=" O VAL g 48 " (cutoff:3.500A) Processing helix chain 'g' and resid 116 through 133 Proline residue: g 130 - end of helix Processing helix chain 'g' and resid 153 through 165 Processing helix chain 'h' and resid 66 through 78 removed outlier: 3.559A pdb=" N GLU h 71 " --> pdb=" O GLN h 67 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 109 Processing helix chain 'h' and resid 122 through 132 removed outlier: 3.668A pdb=" N VAL h 126 " --> pdb=" O ARG h 122 " (cutoff:3.500A) Processing helix chain 'h' and resid 138 through 146 Processing helix chain 'i' and resid 48 through 53 removed outlier: 3.710A pdb=" N MET i 53 " --> pdb=" O GLU i 49 " (cutoff:3.500A) Processing helix chain 'i' and resid 69 through 73 Processing helix chain 'i' and resid 77 through 81 removed outlier: 3.793A pdb=" N ARG i 81 " --> pdb=" O ILE i 78 " (cutoff:3.500A) Processing helix chain 'i' and resid 86 through 98 Processing helix chain 'i' and resid 99 through 102 Processing helix chain 'i' and resid 103 through 123 removed outlier: 3.792A pdb=" N ASN i 109 " --> pdb=" O ASP i 105 " (cutoff:3.500A) Processing helix chain 'j' and resid 26 through 31 removed outlier: 3.781A pdb=" N GLN j 30 " --> pdb=" O GLN j 26 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLN j 31 " --> pdb=" O TRP j 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'j' and resid 26 through 31' Processing helix chain 'j' and resid 60 through 107 Processing helix chain 'k' and resid 27 through 36 removed outlier: 3.526A pdb=" N ARG k 31 " --> pdb=" O VAL k 27 " (cutoff:3.500A) Processing helix chain 'k' and resid 41 through 46 Processing helix chain 'k' and resid 82 through 96 Processing helix chain 'o' and resid 28 through 50 Processing helix chain 'o' and resid 56 through 60 removed outlier: 3.975A pdb=" N ARG o 60 " --> pdb=" O GLU o 57 " (cutoff:3.500A) Processing helix chain 'o' and resid 63 through 80 Processing helix chain 'o' and resid 87 through 95 removed outlier: 4.051A pdb=" N GLN o 91 " --> pdb=" O PHE o 87 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU o 95 " --> pdb=" O GLN o 91 " (cutoff:3.500A) Processing helix chain 'o' and resid 96 through 99 Processing helix chain 'p' and resid 112 through 123 Processing helix chain 'p' and resid 142 through 163 removed outlier: 3.736A pdb=" N ASN p 146 " --> pdb=" O TYR p 142 " (cutoff:3.500A) Processing helix chain 'q' and resid 48 through 53 removed outlier: 3.556A pdb=" N LEU q 52 " --> pdb=" O PRO q 48 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY q 53 " --> pdb=" O ARG q 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 48 through 53' Processing helix chain 'q' and resid 53 through 64 removed outlier: 3.583A pdb=" N ALA q 57 " --> pdb=" O GLY q 53 " (cutoff:3.500A) Processing helix chain 'q' and resid 71 through 75 removed outlier: 3.589A pdb=" N SER q 74 " --> pdb=" O VAL q 71 " (cutoff:3.500A) Processing helix chain 'q' and resid 78 through 93 Processing helix chain 'q' and resid 95 through 152 Proline residue: q 129 - end of helix Processing helix chain 'r' and resid 70 through 76 removed outlier: 4.092A pdb=" N TRP r 75 " --> pdb=" O PRO r 71 " (cutoff:3.500A) Processing helix chain 'r' and resid 85 through 90 removed outlier: 3.740A pdb=" N LEU r 89 " --> pdb=" O ASP r 85 " (cutoff:3.500A) Processing helix chain 'r' and resid 91 through 93 No H-bonds generated for 'chain 'r' and resid 91 through 93' Processing helix chain 'r' and resid 101 through 106 Processing helix chain 'r' and resid 108 through 126 removed outlier: 3.520A pdb=" N LYS r 114 " --> pdb=" O GLU r 110 " (cutoff:3.500A) Processing helix chain 'r' and resid 167 through 171 removed outlier: 3.968A pdb=" N ARG r 171 " --> pdb=" O ARG r 168 " (cutoff:3.500A) Processing helix chain 's' and resid 55 through 73 Processing helix chain 's' and resid 75 through 85 Processing helix chain 's' and resid 101 through 111 removed outlier: 3.955A pdb=" N TRP s 105 " --> pdb=" O ASN s 101 " (cutoff:3.500A) Processing helix chain 's' and resid 141 through 155 removed outlier: 3.872A pdb=" N GLU s 153 " --> pdb=" O CYS s 149 " (cutoff:3.500A) Processing helix chain 's' and resid 167 through 172 Processing helix chain 's' and resid 172 through 189 removed outlier: 3.639A pdb=" N PHE s 176 " --> pdb=" O ILE s 172 " (cutoff:3.500A) Processing helix chain 's' and resid 193 through 198 removed outlier: 3.591A pdb=" N ALA s 197 " --> pdb=" O PRO s 193 " (cutoff:3.500A) Processing helix chain 's' and resid 267 through 271 removed outlier: 3.555A pdb=" N LEU s 271 " --> pdb=" O PRO s 268 " (cutoff:3.500A) Processing helix chain 's' and resid 307 through 314 Processing helix chain 's' and resid 318 through 343 removed outlier: 4.210A pdb=" N VAL s 322 " --> pdb=" O ASP s 318 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N PHE s 324 " --> pdb=" O ILE s 320 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LEU s 332 " --> pdb=" O ALA s 328 " (cutoff:3.500A) Processing helix chain 's' and resid 380 through 385 removed outlier: 3.855A pdb=" N GLN s 385 " --> pdb=" O THR s 381 " (cutoff:3.500A) Processing helix chain 's' and resid 414 through 427 removed outlier: 3.908A pdb=" N LEU s 418 " --> pdb=" O ASN s 414 " (cutoff:3.500A) Processing helix chain 't' and resid 101 through 127 Processing helix chain 't' and resid 201 through 217 Processing helix chain 't' and resid 306 through 311 Processing helix chain 't' and resid 401 through 414 Processing sheet with id= A, first strand: chain 'D' and resid 77 through 78 Processing sheet with id= B, first strand: chain 'D' and resid 147 through 152 removed outlier: 6.307A pdb=" N ILE D 139 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N VAL D 129 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU D 141 " --> pdb=" O ILE D 127 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 181 through 183 removed outlier: 5.803A pdb=" N LEU D 216 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLN D 227 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N ARG D 218 " --> pdb=" O ILE D 225 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 196 through 197 Processing sheet with id= E, first strand: chain 'E' and resid 332 through 333 removed outlier: 6.814A pdb=" N VAL E 273 " --> pdb=" O ASN E 286 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N ASN E 286 " --> pdb=" O VAL E 273 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ARG E 275 " --> pdb=" O TYR E 284 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N HIS E 117 " --> pdb=" O PRO E 108 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL E 119 " --> pdb=" O MET E 106 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N MET E 106 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N LEU E 121 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N LEU E 296 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 5.082A pdb=" N LYS E 209 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N VAL E 204 " --> pdb=" O GLY E 270 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'E' and resid 129 through 133 removed outlier: 3.535A pdb=" N LYS E 131 " --> pdb=" O SER E 146 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ALA E 143 " --> pdb=" O ILE E 181 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'E' and resid 215 through 216 Processing sheet with id= H, first strand: chain 'F' and resid 48 through 49 removed outlier: 6.446A pdb=" N ARG F 49 " --> pdb=" O ASP F 81 " (cutoff:3.500A) removed outlier: 10.234A pdb=" N LEU F 187 " --> pdb=" O GLN F 63 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N TRP F 65 " --> pdb=" O LEU F 187 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ILE F 189 " --> pdb=" O TRP F 65 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'F' and resid 109 through 110 Processing sheet with id= J, first strand: chain 'H' and resid 54 through 58 removed outlier: 7.148A pdb=" N ILE H 55 " --> pdb=" O VAL H 83 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'H' and resid 111 through 115 Processing sheet with id= L, first strand: chain 'I' and resid 121 through 124 Processing sheet with id= M, first strand: chain 'J' and resid 71 through 72 Processing sheet with id= N, first strand: chain 'K' and resid 18 through 22 removed outlier: 6.205A pdb=" N TYR K 19 " --> pdb=" O VAL K 58 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N MET K 60 " --> pdb=" O TYR K 19 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N LEU K 21 " --> pdb=" O MET K 60 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'K' and resid 66 through 68 removed outlier: 3.755A pdb=" N PHE K 67 " --> pdb=" O ASN r 148 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR r 150 " --> pdb=" O PHE K 67 " (cutoff:3.500A) No H-bonds generated for sheet with id= O Processing sheet with id= P, first strand: chain 'K' and resid 76 through 80 Processing sheet with id= Q, first strand: chain 'L' and resid 39 through 40 removed outlier: 6.201A pdb=" N ARG L 39 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 7.542A pdb=" N LEU L 107 " --> pdb=" O ARG L 39 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LYS L 83 " --> pdb=" O ILE L 108 " (cutoff:3.500A) removed outlier: 7.388A pdb=" N GLN L 72 " --> pdb=" O VAL L 60 " (cutoff:3.500A) removed outlier: 5.148A pdb=" N VAL L 60 " --> pdb=" O GLN L 72 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU L 74 " --> pdb=" O ILE L 58 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ARG L 56 " --> pdb=" O ALA L 76 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'L' and resid 98 through 100 removed outlier: 6.635A pdb=" N THR Q 148 " --> pdb=" O ARG Q 140 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ARG Q 140 " --> pdb=" O THR Q 148 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N ILE Q 150 " --> pdb=" O ILE Q 138 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N VAL Q 154 " --> pdb=" O LEU Q 134 " (cutoff:3.500A) removed outlier: 9.122A pdb=" N LEU Q 134 " --> pdb=" O VAL Q 154 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLU Q 173 " --> pdb=" O THR Q 120 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'L' and resid 119 through 123 removed outlier: 8.308A pdb=" N ILE L 119 " --> pdb=" O GLN L 142 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N PHE L 144 " --> pdb=" O ILE L 119 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N THR L 121 " --> pdb=" O PHE L 144 " (cutoff:3.500A) No H-bonds generated for sheet with id= S Processing sheet with id= T, first strand: chain 'M' and resid 92 through 97 removed outlier: 6.058A pdb=" N GLN M 92 " --> pdb=" O ASP M 135 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N GLY M 137 " --> pdb=" O GLN M 92 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'M' and resid 153 through 156 removed outlier: 5.913A pdb=" N ILE M 154 " --> pdb=" O THR M 175 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'M' and resid 274 through 276 Processing sheet with id= W, first strand: chain 'N' and resid 118 through 122 removed outlier: 6.121A pdb=" N LEU N 159 " --> pdb=" O ALA N 91 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA N 91 " --> pdb=" O LEU N 159 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL N 161 " --> pdb=" O ILE N 89 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'N' and resid 95 through 97 removed outlier: 5.499A pdb=" N ILE N 147 " --> pdb=" O ARG N 133 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N ARG N 133 " --> pdb=" O ILE N 147 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'O' and resid 43 through 45 removed outlier: 4.215A pdb=" N MET O 120 " --> pdb=" O ILE O 110 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'P' and resid 82 through 84 removed outlier: 6.694A pdb=" N ALA P 91 " --> pdb=" O SER P 103 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N SER P 103 " --> pdb=" O ALA P 91 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N VAL P 93 " --> pdb=" O VAL P 101 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'S' and resid 104 through 109 removed outlier: 7.256A pdb=" N HIS S 100 " --> pdb=" O VAL S 133 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N VAL S 133 " --> pdb=" O HIS S 100 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N ASN S 140 " --> pdb=" O UNK t 28 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N UNK t 29 " --> pdb=" O UNK t 12 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'b' and resid 119 through 120 removed outlier: 6.680A pdb=" N GLN S 190 " --> pdb=" O LYS S 163 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LYS S 163 " --> pdb=" O GLN S 190 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N VAL S 192 " --> pdb=" O ILE S 161 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N GLU S 157 " --> pdb=" O ASN S 196 " (cutoff:3.500A) removed outlier: 4.493A pdb=" N ILE S 198 " --> pdb=" O ARG S 155 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ARG S 155 " --> pdb=" O ILE S 198 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL S 156 " --> pdb=" O LEU S 130 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'S' and resid 169 through 175 removed outlier: 4.404A pdb=" N PHE S 180 " --> pdb=" O ARG S 175 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'T' and resid 72 through 80 removed outlier: 5.377A pdb=" N CYS T 172 " --> pdb=" O GLN T 79 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL T 179 " --> pdb=" O ILE T 142 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ILE T 142 " --> pdb=" O VAL T 179 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'T' and resid 153 through 156 Processing sheet with id= AF, first strand: chain 'U' and resid 18 through 19 Processing sheet with id= AG, first strand: chain 'U' and resid 27 through 29 removed outlier: 4.496A pdb=" N GLN U 41 " --> pdb=" O VAL U 29 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LYS U 93 " --> pdb=" O ILE U 44 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'V' and resid 115 through 116 removed outlier: 6.084A pdb=" N THR V 61 " --> pdb=" O VAL V 123 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N LEU V 122 " --> pdb=" O THR V 131 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'V' and resid 93 through 98 Processing sheet with id= AJ, first strand: chain 'V' and resid 133 through 137 removed outlier: 4.215A pdb=" N ARG V 145 " --> pdb=" O ILE V 154 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'W' and resid 52 through 53 removed outlier: 6.410A pdb=" N ILE W 66 " --> pdb=" O ALA W 91 " (cutoff:3.500A) removed outlier: 6.080A pdb=" N ALA W 91 " --> pdb=" O ILE W 66 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'W' and resid 60 through 61 removed outlier: 6.637A pdb=" N HIS W 76 " --> pdb=" O VAL W 131 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N VAL W 133 " --> pdb=" O HIS W 76 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'W' and resid 144 through 148 removed outlier: 4.041A pdb=" N ALA W 146 " --> pdb=" O VAL 6 341 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'X' and resid 86 through 91 Processing sheet with id= AO, first strand: chain 'X' and resid 112 through 116 removed outlier: 3.812A pdb=" N LYS X 121 " --> pdb=" O SER X 116 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'Y' and resid 169 through 170 Processing sheet with id= AQ, first strand: chain 'Z' and resid 97 through 101 Processing sheet with id= AR, first strand: chain '0' and resid 107 through 108 Processing sheet with id= AS, first strand: chain '0' and resid 157 through 159 Processing sheet with id= AT, first strand: chain '1' and resid 29 through 35 removed outlier: 8.133A pdb=" N ASN 1 15 " --> pdb=" O ARG 1 63 " (cutoff:3.500A) removed outlier: 8.113A pdb=" N ARG 1 63 " --> pdb=" O ASN 1 15 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N LEU 1 17 " --> pdb=" O LYS 1 61 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N LYS 1 61 " --> pdb=" O LEU 1 17 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ARG 1 19 " --> pdb=" O LYS 1 59 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain '3' and resid 114 through 116 Processing sheet with id= AV, first strand: chain '4' and resid 80 through 84 Processing sheet with id= AW, first strand: chain '5' and resid 211 through 213 removed outlier: 6.348A pdb=" N TYR 5 105 " --> pdb=" O GLN 5 221 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain '5' and resid 126 through 129 removed outlier: 5.489A pdb=" N LYS 5 127 " --> pdb=" O ALA 5 374 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N VAL 5 376 " --> pdb=" O LYS 5 127 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N ILE 5 129 " --> pdb=" O VAL 5 376 " (cutoff:3.500A) removed outlier: 8.665A pdb=" N GLN 5 343 " --> pdb=" O TYR 5 287 " (cutoff:3.500A) removed outlier: 6.173A pdb=" N HIS 5 289 " --> pdb=" O GLN 5 343 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N VAL 5 345 " --> pdb=" O HIS 5 289 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N LEU 5 291 " --> pdb=" O VAL 5 345 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N THR 5 232 " --> pdb=" O PRO 5 288 " (cutoff:3.500A) Processing sheet with id= AY, first strand: chain '6' and resid 185 through 186 Processing sheet with id= AZ, first strand: chain '6' and resid 191 through 192 removed outlier: 6.568A pdb=" N ASN 6 191 " --> pdb=" O GLN 6 320 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LYS 6 274 " --> pdb=" O PRO 6 313 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N PHE 6 273 " --> pdb=" O THR 6 215 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N THR 6 215 " --> pdb=" O PHE 6 273 " (cutoff:3.500A) removed outlier: 7.230A pdb=" N TRP 6 214 " --> pdb=" O THR 6 238 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N THR 6 238 " --> pdb=" O TRP 6 214 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N LEU 6 216 " --> pdb=" O LEU 6 236 " (cutoff:3.500A) removed outlier: 4.811A pdb=" N LEU 6 236 " --> pdb=" O LEU 6 216 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU 6 218 " --> pdb=" O HIS 6 234 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain '7' and resid 112 through 114 removed outlier: 3.547A pdb=" N LEU 7 105 " --> pdb=" O LEU 7 128 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N ILE 7 125 " --> pdb=" O GLU 7 66 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N LYS 7 68 " --> pdb=" O ILE 7 125 " (cutoff:3.500A) removed outlier: 8.476A pdb=" N PHE 7 127 " --> pdb=" O LYS 7 68 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL 7 78 " --> pdb=" O ILE d 282 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain '7' and resid 166 through 168 removed outlier: 3.748A pdb=" N ARG 7 168 " --> pdb=" O ASP 7 182 " (cutoff:3.500A) Processing sheet with id= BC, first strand: chain '7' and resid 166 through 168 removed outlier: 3.748A pdb=" N ARG 7 168 " --> pdb=" O ASP 7 182 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain '7' and resid 217 through 221 Processing sheet with id= BE, first strand: chain '9' and resid 42 through 45 removed outlier: 3.603A pdb=" N PHE 9 43 " --> pdb=" O VAL 9 51 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'b' and resid 84 through 88 Processing sheet with id= BG, first strand: chain 'c' and resid 257 through 261 removed outlier: 5.669A pdb=" N LEU c 257 " --> pdb=" O GLY c 273 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N GLY c 273 " --> pdb=" O LEU c 257 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N SER c 261 " --> pdb=" O LEU c 269 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA c 282 " --> pdb=" O LEU c 274 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'd' and resid 180 through 181 Processing sheet with id= BI, first strand: chain 'd' and resid 184 through 188 removed outlier: 3.710A pdb=" N SER d 184 " --> pdb=" O THR d 221 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL d 186 " --> pdb=" O ARG d 219 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG d 219 " --> pdb=" O VAL d 186 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N SER d 188 " --> pdb=" O HIS d 217 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N HIS d 217 " --> pdb=" O SER d 188 " (cutoff:3.500A) removed outlier: 4.069A pdb=" N GLN d 196 " --> pdb=" O THR d 213 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG d 215 " --> pdb=" O VAL d 194 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N VAL d 194 " --> pdb=" O ARG d 215 " (cutoff:3.500A) Processing sheet with id= BJ, first strand: chain 'd' and resid 184 through 188 removed outlier: 3.710A pdb=" N SER d 184 " --> pdb=" O THR d 221 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL d 186 " --> pdb=" O ARG d 219 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N ARG d 219 " --> pdb=" O VAL d 186 " (cutoff:3.500A) removed outlier: 5.300A pdb=" N SER d 188 " --> pdb=" O HIS d 217 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N HIS d 217 " --> pdb=" O SER d 188 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LYS d 250 " --> pdb=" O GLY d 210 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N TYR d 245 " --> pdb=" O LYS d 264 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N LYS d 264 " --> pdb=" O TYR d 245 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL d 247 " --> pdb=" O HIS d 262 " (cutoff:3.500A) Processing sheet with id= BK, first strand: chain 'e' and resid 102 through 104 removed outlier: 6.487A pdb=" N THR e 103 " --> pdb=" O PHE e 188 " (cutoff:3.500A) No H-bonds generated for sheet with id= BK Processing sheet with id= BL, first strand: chain 'e' and resid 157 through 160 removed outlier: 7.275A pdb=" N LYS e 191 " --> pdb=" O LYS e 159 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N ALA e 192 " --> pdb=" O ARG e 107 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N LEU e 109 " --> pdb=" O ALA e 192 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N LYS e 108 " --> pdb=" O LEU e 115 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU e 115 " --> pdb=" O LYS e 108 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ASP e 110 " --> pdb=" O LEU e 113 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N VAL e 209 " --> pdb=" O LEU e 116 " (cutoff:3.500A) Processing sheet with id= BM, first strand: chain 'f' and resid 120 through 121 removed outlier: 4.149A pdb=" N LYS f 120 " --> pdb=" O SER f 160 " (cutoff:3.500A) Processing sheet with id= BN, first strand: chain 'f' and resid 126 through 127 removed outlier: 3.754A pdb=" N GLU f 154 " --> pdb=" O MET f 127 " (cutoff:3.500A) Processing sheet with id= BO, first strand: chain 'f' and resid 183 through 184 removed outlier: 3.899A pdb=" N UNK f 264 " --> pdb=" O LEU f 184 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'g' and resid 84 through 86 Processing sheet with id= BQ, first strand: chain 'g' and resid 96 through 100 Processing sheet with id= BR, first strand: chain 'k' and resid 65 through 66 removed outlier: 3.621A pdb=" N LEU k 74 " --> pdb=" O VAL k 66 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE k 75 " --> pdb=" O ILE r 49 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N GLY r 51 " --> pdb=" O ILE k 75 " (cutoff:3.500A) Processing sheet with id= BS, first strand: chain 'p' and resid 77 through 81 Processing sheet with id= BT, first strand: chain 's' and resid 206 through 216 removed outlier: 5.210A pdb=" N LEU s 229 " --> pdb=" O ARG s 212 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLU s 214 " --> pdb=" O ASP s 227 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASP s 227 " --> pdb=" O GLU s 214 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ASP s 234 " --> pdb=" O VAL s 93 " (cutoff:3.500A) removed outlier: 4.643A pdb=" N PHE s 274 " --> pdb=" O MET s 92 " (cutoff:3.500A) Processing sheet with id= BU, first strand: chain 's' and resid 112 through 116 removed outlier: 6.153A pdb=" N VAL s 113 " --> pdb=" O CYS s 393 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N GLY s 395 " --> pdb=" O VAL s 113 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU s 115 " --> pdb=" O GLY s 395 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER s 368 " --> pdb=" O ILE s 361 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE s 361 " --> pdb=" O SER s 368 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N TYR s 294 " --> pdb=" O VAL s 356 " (cutoff:3.500A) removed outlier: 9.389A pdb=" N GLN s 358 " --> pdb=" O TYR s 294 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N HIS s 296 " --> pdb=" O GLN s 358 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N VAL s 360 " --> pdb=" O HIS s 296 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLN s 298 " --> pdb=" O VAL s 360 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N THR s 362 " --> pdb=" O GLN s 298 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N GLY s 295 " --> pdb=" O ILE s 243 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N ILE s 243 " --> pdb=" O GLY s 295 " (cutoff:3.500A) removed outlier: 4.238A pdb=" N THR s 297 " --> pdb=" O ILE s 241 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE s 241 " --> pdb=" O THR s 297 " (cutoff:3.500A) Processing sheet with id= BV, first strand: chain 's' and resid 112 through 116 removed outlier: 6.153A pdb=" N VAL s 113 " --> pdb=" O CYS s 393 " (cutoff:3.500A) removed outlier: 7.933A pdb=" N GLY s 395 " --> pdb=" O VAL s 113 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU s 115 " --> pdb=" O GLY s 395 " (cutoff:3.500A) 2371 hydrogen bonds defined for protein. 6651 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 955 hydrogen bonds 1676 hydrogen bond angles 0 basepair planarities 389 basepair parallelities 623 stacking parallelities Total time for adding SS restraints: 58.98 Time building geometry restraints manager: 38.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 11375 1.31 - 1.44: 35499 1.44 - 1.57: 49024 1.57 - 1.70: 3060 1.70 - 1.83: 404 Bond restraints: 99362 Sorted by residual: bond pdb=" CD GLU R 23 " pdb=" OE2 GLU R 23 " ideal model delta sigma weight residual 1.249 1.458 -0.209 1.90e-02 2.77e+03 1.21e+02 bond pdb=" CD GLU P 151 " pdb=" OE1 GLU P 151 " ideal model delta sigma weight residual 1.249 1.451 -0.202 1.90e-02 2.77e+03 1.14e+02 bond pdb=" CG ASP s 318 " pdb=" OD2 ASP s 318 " ideal model delta sigma weight residual 1.249 1.447 -0.198 1.90e-02 2.77e+03 1.09e+02 bond pdb=" CG ASN 6 191 " pdb=" OD1 ASN 6 191 " ideal model delta sigma weight residual 1.231 1.426 -0.195 1.90e-02 2.77e+03 1.05e+02 bond pdb=" CG ASP 0 108 " pdb=" OD2 ASP 0 108 " ideal model delta sigma weight residual 1.249 1.420 -0.171 1.90e-02 2.77e+03 8.13e+01 ... (remaining 99357 not shown) Histogram of bond angle deviations from ideal: 96.00 - 104.75: 7874 104.75 - 113.50: 56086 113.50 - 122.25: 54401 122.25 - 131.00: 22453 131.00 - 139.75: 842 Bond angle restraints: 141656 Sorted by residual: angle pdb=" O3' A A2374 " pdb=" C3' A A2374 " pdb=" C2' A A2374 " ideal model delta sigma weight residual 109.50 124.93 -15.43 1.50e+00 4.44e-01 1.06e+02 angle pdb=" N HIS i 124 " pdb=" CA HIS i 124 " pdb=" C HIS i 124 " ideal model delta sigma weight residual 111.36 121.27 -9.91 1.09e+00 8.42e-01 8.26e+01 angle pdb=" O3' A A1823 " pdb=" C3' A A1823 " pdb=" C2' A A1823 " ideal model delta sigma weight residual 109.50 122.18 -12.68 1.50e+00 4.44e-01 7.15e+01 angle pdb=" O3' U A1806 " pdb=" C3' U A1806 " pdb=" C2' U A1806 " ideal model delta sigma weight residual 109.50 121.80 -12.30 1.50e+00 4.44e-01 6.72e+01 angle pdb=" O3' A A1772 " pdb=" C3' A A1772 " pdb=" C2' A A1772 " ideal model delta sigma weight residual 113.70 125.93 -12.23 1.50e+00 4.44e-01 6.64e+01 ... (remaining 141651 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.95: 55184 35.95 - 71.90: 4121 71.90 - 107.85: 552 107.85 - 143.81: 24 143.81 - 179.76: 77 Dihedral angle restraints: 59958 sinusoidal: 37844 harmonic: 22114 Sorted by residual: dihedral pdb=" C5' C A1901 " pdb=" C4' C A1901 " pdb=" C3' C A1901 " pdb=" O3' C A1901 " ideal model delta sinusoidal sigma weight residual 147.00 62.65 84.35 1 8.00e+00 1.56e-02 1.35e+02 dihedral pdb=" C5' A A2231 " pdb=" C4' A A2231 " pdb=" C3' A A2231 " pdb=" O3' A A2231 " ideal model delta sinusoidal sigma weight residual 147.00 69.34 77.66 1 8.00e+00 1.56e-02 1.18e+02 dihedral pdb=" C5' C A1677 " pdb=" C4' C A1677 " pdb=" C3' C A1677 " pdb=" O3' C A1677 " ideal model delta sinusoidal sigma weight residual 147.00 72.41 74.59 1 8.00e+00 1.56e-02 1.10e+02 ... (remaining 59955 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.131: 13843 0.131 - 0.263: 2766 0.263 - 0.394: 142 0.394 - 0.526: 19 0.526 - 0.657: 8 Chirality restraints: 16778 Sorted by residual: chirality pdb=" C3' C A1901 " pdb=" C4' C A1901 " pdb=" O3' C A1901 " pdb=" C2' C A1901 " both_signs ideal model delta sigma weight residual False -2.74 -2.09 -0.66 2.00e-01 2.50e+01 1.08e+01 chirality pdb=" CA HIS i 124 " pdb=" N HIS i 124 " pdb=" C HIS i 124 " pdb=" CB HIS i 124 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.58e+00 chirality pdb=" C3' A A2530 " pdb=" C4' A A2530 " pdb=" O3' A A2530 " pdb=" C2' A A2530 " both_signs ideal model delta sigma weight residual False -2.74 -2.14 -0.60 2.00e-01 2.50e+01 9.09e+00 ... (remaining 16775 not shown) Planarity restraints: 12503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN 6 191 " -0.036 2.00e-02 2.50e+03 6.95e-02 4.83e+01 pdb=" CG ASN 6 191 " 0.120 2.00e-02 2.50e+03 pdb=" OD1 ASN 6 191 " -0.045 2.00e-02 2.50e+03 pdb=" ND2 ASN 6 191 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU e 180 " 0.034 2.00e-02 2.50e+03 6.46e-02 4.18e+01 pdb=" CD GLU e 180 " -0.112 2.00e-02 2.50e+03 pdb=" OE1 GLU e 180 " 0.044 2.00e-02 2.50e+03 pdb=" OE2 GLU e 180 " 0.034 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A2321 " 0.087 2.00e-02 2.50e+03 3.85e-02 4.08e+01 pdb=" N9 A A2321 " -0.087 2.00e-02 2.50e+03 pdb=" C8 A A2321 " -0.011 2.00e-02 2.50e+03 pdb=" N7 A A2321 " 0.002 2.00e-02 2.50e+03 pdb=" C5 A A2321 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A A2321 " 0.016 2.00e-02 2.50e+03 pdb=" N6 A A2321 " 0.018 2.00e-02 2.50e+03 pdb=" N1 A A2321 " 0.009 2.00e-02 2.50e+03 pdb=" C2 A A2321 " -0.007 2.00e-02 2.50e+03 pdb=" N3 A A2321 " -0.020 2.00e-02 2.50e+03 pdb=" C4 A A2321 " -0.007 2.00e-02 2.50e+03 ... (remaining 12500 not shown) Histogram of nonbonded interaction distances: 1.71 - 2.35: 142 2.35 - 2.98: 44029 2.98 - 3.62: 153530 3.62 - 4.26: 240128 4.26 - 4.90: 364601 Nonbonded interactions: 802430 Sorted by model distance: nonbonded pdb=" CG2 THR H 53 " pdb=" CG2 THR H 86 " model vdw 1.708 3.880 nonbonded pdb=" CE MET k 76 " pdb=" CG MET k 86 " model vdw 1.714 3.860 nonbonded pdb=" OP2 U A2115 " pdb="MG MG A3365 " model vdw 1.786 2.170 nonbonded pdb=" O2' U A2559 " pdb=" O4' G A2560 " model vdw 1.853 2.440 nonbonded pdb=" NH1 ARG K 154 " pdb=" OE2 GLU K 157 " model vdw 1.857 2.520 ... (remaining 802425 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.490 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 11.210 Check model and map are aligned: 1.060 Set scattering table: 0.710 Process input model: 245.820 Find NCS groups from input model: 2.540 Set up NCS constraints: 0.240 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: 0.020 Load rotamer database and sin/cos tables:2.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 268.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 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 : 0.008 0.209 99362 Z= 0.534 Angle : 1.343 15.426 141656 Z= 0.926 Chirality : 0.096 0.657 16778 Planarity : 0.008 0.104 12503 Dihedral : 22.522 179.756 45628 Min Nonbonded Distance : 1.708 Molprobity Statistics. All-atom Clashscore : 8.61 Ramachandran Plot: Outliers : 2.20 % Allowed : 7.93 % Favored : 89.87 % Rotamer: Outliers : 8.93 % Allowed : 11.69 % Favored : 79.37 % Cbeta Deviations : 0.43 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.25 % Twisted Proline : 0.20 % 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: -1.78 (0.09), residues: 7313 helix: 0.78 (0.08), residues: 2471 sheet: -2.15 (0.15), residues: 886 loop : -2.34 (0.09), residues: 3956 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.004 TRP D 66 HIS 0.017 0.003 HIS i 124 PHE 0.062 0.005 PHE 6 303 TYR 0.044 0.004 TYR 6 365 ARG 0.024 0.001 ARG D 90 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14626 Ramachandran restraints generated. 7313 Oldfield, 0 Emsley, 7313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14626 Ramachandran restraints generated. 7313 Oldfield, 0 Emsley, 7313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 2695 residues out of total 6571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 585 poor density : 2110 time to evaluate : 7.053 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 outliers start: 585 outliers final: 127 residues processed: 2488 average time/residue: 1.0558 time to fit residues: 4286.2270 Evaluate side-chains 1533 residues out of total 6571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1406 time to evaluate : 6.224 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 127 outliers final: 2 residues processed: 127 average time/residue: 0.8807 time to fit residues: 206.7110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 751 optimal weight: 5.9990 chunk 674 optimal weight: 1.9990 chunk 374 optimal weight: 5.9990 chunk 230 optimal weight: 1.9990 chunk 455 optimal weight: 8.9990 chunk 360 optimal weight: 0.9980 chunk 697 optimal weight: 0.2980 chunk 269 optimal weight: 3.9990 chunk 424 optimal weight: 0.8980 chunk 519 optimal weight: 0.0970 chunk 808 optimal weight: 0.7980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 ASN D 276 HIS ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 180 ASN E 184 ASN E 231 HIS F 58 HIS F 97 HIS F 98 GLN F 103 GLN F 184 GLN F 249 ASN I 61 HIS I 189 GLN K 117 HIS ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 64 ASN L 142 GLN ** M 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 130 GLN O 112 ASN P 120 ASN Q 139 GLN R 30 HIS R 89 ASN S 196 ASN T 109 ASN T 125 GLN T 132 HIS T 133 ASN U 35 GLN U 55 ASN V 94 HIS V 117 HIS V 119 GLN X 15 GLN X 27 HIS X 177 HIS Y 88 GLN Y 122 GLN Y 157 GLN Z 47 GLN 1 15 ASN 5 94 HIS 5 102 GLN ** 5 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 251 HIS ** 5 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 380 GLN 5 384 GLN ** 5 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 147 HIS 6 163 HIS 7 55 GLN 7 246 GLN 8 114 HIS b 17 ASN b 123 ASN ** b 131 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 172 ASN c 192 GLN c 193 GLN d 149 HIS d 235 GLN d 251 GLN d 286 GLN e 154 ASN e 182 ASN e 208 HIS f 61 HIS ** f 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 65 HIS ** g 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 110 HIS h 151 ASN i 59 ASN j 36 ASN k 26 ASN o 62 HIS o 85 HIS q 137 GLN s 67 GLN s 238 ASN s 382 GLN ** s 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 75 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8073 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 99362 Z= 0.213 Angle : 0.757 16.190 141656 Z= 0.387 Chirality : 0.043 0.377 16778 Planarity : 0.006 0.082 12503 Dihedral : 22.006 179.953 29933 Min Nonbonded Distance : 1.858 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.86 % Allowed : 6.14 % Favored : 93.00 % Rotamer: Outliers : 4.20 % Allowed : 17.37 % Favored : 78.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.23 % Twisted Proline : 0.40 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.10), residues: 7313 helix: 2.59 (0.10), residues: 2499 sheet: -1.65 (0.15), residues: 903 loop : -1.86 (0.09), residues: 3911 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP E 90 HIS 0.010 0.001 HIS 6 163 PHE 0.027 0.002 PHE s 283 TYR 0.033 0.002 TYR 6 51 ARG 0.009 0.001 ARG M 182 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14626 Ramachandran restraints generated. 7313 Oldfield, 0 Emsley, 7313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14626 Ramachandran restraints generated. 7313 Oldfield, 0 Emsley, 7313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1818 residues out of total 6571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 275 poor density : 1543 time to evaluate : 6.315 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 275 outliers final: 122 residues processed: 1720 average time/residue: 0.9639 time to fit residues: 2782.4741 Evaluate side-chains 1436 residues out of total 6571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 122 poor density : 1314 time to evaluate : 6.168 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 122 outliers final: 1 residues processed: 122 average time/residue: 0.7056 time to fit residues: 170.1699 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 449 optimal weight: 8.9990 chunk 250 optimal weight: 6.9990 chunk 672 optimal weight: 7.9990 chunk 550 optimal weight: 3.9990 chunk 222 optimal weight: 2.9990 chunk 809 optimal weight: 1.9990 chunk 874 optimal weight: 5.9990 chunk 721 optimal weight: 5.9990 chunk 802 optimal weight: 5.9990 chunk 276 optimal weight: 4.9990 chunk 649 optimal weight: 0.9980 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 195 ASN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 48 HIS K 74 GLN ** K 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 142 GLN M 123 ASN N 208 ASN O 91 GLN Q 253 GLN R 77 GLN R 89 ASN S 118 ASN S 140 ASN T 125 GLN T 151 GLN Y 183 GLN Y 225 ASN 5 119 GLN ** 5 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 224 HIS 6 320 GLN 6 354 GLN a 137 ASN b 131 HIS d 154 ASN d 207 ASN ** f 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 65 HIS ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 59 ASN ** k 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 60 GLN q 100 GLN q 107 GLN ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 382 GLN s 420 GLN Total number of N/Q/H flips: 31 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 moved from start: 0.3540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.073 99362 Z= 0.375 Angle : 0.785 17.632 141656 Z= 0.401 Chirality : 0.047 0.378 16778 Planarity : 0.007 0.080 12503 Dihedral : 21.684 179.688 29933 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.77 % Allowed : 7.12 % Favored : 92.11 % Rotamer: Outliers : 4.23 % Allowed : 19.62 % Favored : 76.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.23 % Twisted Proline : 0.20 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.51 (0.10), residues: 7313 helix: 2.06 (0.10), residues: 2500 sheet: -1.43 (0.16), residues: 923 loop : -1.77 (0.10), residues: 3890 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP V 170 HIS 0.013 0.002 HIS s 296 PHE 0.036 0.002 PHE 7 260 TYR 0.036 0.002 TYR 6 51 ARG 0.017 0.001 ARG D 149 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14626 Ramachandran restraints generated. 7313 Oldfield, 0 Emsley, 7313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14626 Ramachandran restraints generated. 7313 Oldfield, 0 Emsley, 7313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1696 residues out of total 6571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 277 poor density : 1419 time to evaluate : 6.522 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: 277 outliers final: 154 residues processed: 1594 average time/residue: 0.9289 time to fit residues: 2493.3882 Evaluate side-chains 1447 residues out of total 6571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 154 poor density : 1293 time to evaluate : 6.271 Switching outliers to nearest non-outliers outliers start: 154 outliers final: 0 residues processed: 154 average time/residue: 0.6956 time to fit residues: 211.2338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 799 optimal weight: 0.5980 chunk 608 optimal weight: 0.5980 chunk 420 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 386 optimal weight: 3.9990 chunk 543 optimal weight: 3.9990 chunk 812 optimal weight: 10.0000 chunk 860 optimal weight: 0.0030 chunk 424 optimal weight: 0.9980 chunk 770 optimal weight: 10.0000 chunk 231 optimal weight: 2.9990 overall best weight: 0.8392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 115 GLN E 184 ASN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 101 ASN I 114 HIS I 119 HIS K 9 GLN ** K 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 GLN N 138 HIS N 178 GLN N 208 ASN N 210 GLN N 222 ASN T 109 ASN V 117 HIS V 119 GLN Y 183 GLN ** 5 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 266 HIS 5 353 HIS ** 5 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 163 HIS ** 9 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 154 ASN ** e 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 115 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 65 HIS g 73 GLN ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** j 30 GLN k 15 GLN q 60 GLN q 107 GLN ** s 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 373 GLN s 375 ASN s 382 GLN s 420 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 99362 Z= 0.183 Angle : 0.660 15.412 141656 Z= 0.336 Chirality : 0.040 0.363 16778 Planarity : 0.005 0.079 12503 Dihedral : 21.535 179.655 29933 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.72 % Allowed : 6.25 % Favored : 93.03 % Rotamer: Outliers : 2.61 % Allowed : 21.22 % Favored : 76.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.23 % Twisted Proline : 0.20 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.10), residues: 7313 helix: 2.05 (0.10), residues: 2506 sheet: -1.14 (0.16), residues: 919 loop : -1.60 (0.10), residues: 3888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP Y 178 HIS 0.015 0.001 HIS s 71 PHE 0.028 0.002 PHE 6 319 TYR 0.035 0.002 TYR 6 51 ARG 0.009 0.000 ARG I 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14626 Ramachandran restraints generated. 7313 Oldfield, 0 Emsley, 7313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14626 Ramachandran restraints generated. 7313 Oldfield, 0 Emsley, 7313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1606 residues out of total 6571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 171 poor density : 1435 time to evaluate : 7.915 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: 171 outliers final: 67 residues processed: 1540 average time/residue: 0.9583 time to fit residues: 2477.9023 Evaluate side-chains 1384 residues out of total 6571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 1317 time to evaluate : 6.388 Switching outliers to nearest non-outliers outliers start: 67 outliers final: 0 residues processed: 67 average time/residue: 0.7240 time to fit residues: 99.1443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 716 optimal weight: 5.9990 chunk 488 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 640 optimal weight: 10.0000 chunk 354 optimal weight: 4.9990 chunk 734 optimal weight: 7.9990 chunk 594 optimal weight: 7.9990 chunk 1 optimal weight: 6.9990 chunk 439 optimal weight: 0.8980 chunk 772 optimal weight: 6.9990 chunk 217 optimal weight: 3.9990 overall best weight: 4.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 233 GLN E 184 ASN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 93 ASN I 101 ASN K 140 ASN ** K 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 GLN ** L 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 114 GLN N 138 HIS N 208 ASN N 209 ASN N 222 ASN O 91 GLN ** O 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 87 HIS P 141 ASN R 77 GLN R 94 GLN S 118 ASN T 195 HIS V 119 GLN 5 94 HIS 5 108 HIS 5 156 ASN 5 385 HIS 6 147 HIS a 137 ASN b 17 ASN d 207 ASN ** e 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 111 HIS g 65 HIS ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 87 GLN i 108 HIS ** k 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** k 19 GLN o 21 HIS o 62 HIS ** q 60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 107 GLN r 112 HIS r 170 ASN ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 314 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 375 ASN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.109 99362 Z= 0.513 Angle : 0.849 17.694 141656 Z= 0.427 Chirality : 0.050 0.372 16778 Planarity : 0.007 0.082 12503 Dihedral : 21.524 179.732 29933 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.72 % Allowed : 7.53 % Favored : 91.74 % Rotamer: Outliers : 4.15 % Allowed : 21.69 % Favored : 74.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.23 % Twisted Proline : 0.20 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.10), residues: 7313 helix: 1.30 (0.10), residues: 2520 sheet: -1.19 (0.16), residues: 923 loop : -1.77 (0.10), residues: 3870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP s 346 HIS 0.011 0.002 HIS i 120 PHE 0.027 0.003 PHE 5 60 TYR 0.050 0.003 TYR r 187 ARG 0.015 0.001 ARG M 59 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14626 Ramachandran restraints generated. 7313 Oldfield, 0 Emsley, 7313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14626 Ramachandran restraints generated. 7313 Oldfield, 0 Emsley, 7313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1609 residues out of total 6571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 272 poor density : 1337 time to evaluate : 6.193 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 outliers start: 272 outliers final: 170 residues processed: 1491 average time/residue: 0.9592 time to fit residues: 2398.1327 Evaluate side-chains 1434 residues out of total 6571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 1264 time to evaluate : 6.210 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 170 outliers final: 1 residues processed: 170 average time/residue: 0.7202 time to fit residues: 238.1033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 289 optimal weight: 0.9980 chunk 774 optimal weight: 0.9980 chunk 170 optimal weight: 0.0970 chunk 505 optimal weight: 1.9990 chunk 212 optimal weight: 0.3980 chunk 861 optimal weight: 1.9990 chunk 714 optimal weight: 0.5980 chunk 398 optimal weight: 0.8980 chunk 71 optimal weight: 6.9990 chunk 284 optimal weight: 4.9990 chunk 452 optimal weight: 0.7980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 ASN F 63 GLN I 101 ASN K 147 GLN K 160 GLN N 138 HIS O 91 GLN O 112 ASN S 100 HIS T 109 ASN U 74 HIS V 119 GLN Y 183 GLN ** 5 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 149 GLN 6 354 GLN ** 9 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 123 ASN ** e 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 115 ASN g 104 ASN ** g 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 15 GLN q 107 GLN s 71 HIS ** s 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 373 GLN s 375 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 99362 Z= 0.173 Angle : 0.661 14.057 141656 Z= 0.334 Chirality : 0.040 0.338 16778 Planarity : 0.005 0.087 12503 Dihedral : 21.394 179.627 29933 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.67 % Allowed : 6.21 % Favored : 93.12 % Rotamer: Outliers : 1.68 % Allowed : 22.96 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.23 % Twisted Proline : 0.20 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.10), residues: 7313 helix: 1.71 (0.10), residues: 2493 sheet: -0.92 (0.17), residues: 906 loop : -1.52 (0.10), residues: 3914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP s 346 HIS 0.011 0.001 HIS s 71 PHE 0.022 0.001 PHE 5 279 TYR 0.039 0.001 TYR 5 383 ARG 0.013 0.001 ARG Y 175 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14626 Ramachandran restraints generated. 7313 Oldfield, 0 Emsley, 7313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14626 Ramachandran restraints generated. 7313 Oldfield, 0 Emsley, 7313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1499 residues out of total 6571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 110 poor density : 1389 time to evaluate : 6.281 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 outliers start: 110 outliers final: 39 residues processed: 1453 average time/residue: 0.9458 time to fit residues: 2311.7269 Evaluate side-chains 1326 residues out of total 6571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 1287 time to evaluate : 6.249 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 39 outliers final: 1 residues processed: 39 average time/residue: 0.7319 time to fit residues: 61.9098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 830 optimal weight: 5.9990 chunk 97 optimal weight: 6.9990 chunk 490 optimal weight: 0.9990 chunk 628 optimal weight: 20.0000 chunk 487 optimal weight: 2.9990 chunk 724 optimal weight: 0.0670 chunk 480 optimal weight: 7.9990 chunk 857 optimal weight: 5.9990 chunk 536 optimal weight: 5.9990 chunk 522 optimal weight: 0.6980 chunk 396 optimal weight: 2.9990 overall best weight: 1.5524 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 ASN F 63 GLN I 101 ASN J 84 GLN K 9 GLN K 160 GLN ** L 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 117 ASN N 208 ASN N 209 ASN O 91 GLN ** O 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 118 ASN T 109 ASN V 119 GLN 5 94 HIS ** 5 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 163 HIS 9 129 GLN 9 134 ASN b 27 GLN b 123 ASN d 207 ASN ** e 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** f 115 ASN g 104 ASN ** g 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 59 ASN o 46 HIS ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 373 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 375 ASN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 99362 Z= 0.231 Angle : 0.666 16.923 141656 Z= 0.335 Chirality : 0.040 0.323 16778 Planarity : 0.005 0.082 12503 Dihedral : 21.272 179.717 29933 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 11.72 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.78 % Favored : 92.56 % Rotamer: Outliers : 1.82 % Allowed : 24.14 % Favored : 74.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.23 % Twisted Proline : 0.20 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.10), residues: 7313 helix: 1.68 (0.10), residues: 2482 sheet: -0.90 (0.17), residues: 909 loop : -1.46 (0.10), residues: 3922 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP s 346 HIS 0.005 0.001 HIS o 94 PHE 0.049 0.002 PHE 7 260 TYR 0.035 0.002 TYR 6 51 ARG 0.012 0.001 ARG Y 175 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14626 Ramachandran restraints generated. 7313 Oldfield, 0 Emsley, 7313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14626 Ramachandran restraints generated. 7313 Oldfield, 0 Emsley, 7313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1428 residues out of total 6571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 119 poor density : 1309 time to evaluate : 6.307 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 outliers start: 119 outliers final: 66 residues processed: 1362 average time/residue: 0.9706 time to fit residues: 2216.0666 Evaluate side-chains 1333 residues out of total 6571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 1267 time to evaluate : 6.350 Switching outliers to nearest non-outliers outliers start: 66 outliers final: 0 residues processed: 66 average time/residue: 0.7786 time to fit residues: 101.8606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 530 optimal weight: 0.0980 chunk 342 optimal weight: 0.0870 chunk 512 optimal weight: 0.9990 chunk 258 optimal weight: 4.9990 chunk 168 optimal weight: 4.9990 chunk 166 optimal weight: 0.8980 chunk 545 optimal weight: 0.8980 chunk 584 optimal weight: 2.9990 chunk 424 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 674 optimal weight: 1.9990 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 ASN F 241 ASN ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 160 GLN N 117 ASN N 208 ASN ** O 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 35 GLN U 84 ASN ** 5 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 84 ASN ** 8 99 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 137 ASN ** g 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 19 GLN q 60 GLN q 107 GLN ** s 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 373 GLN s 375 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 99362 Z= 0.162 Angle : 0.636 16.833 141656 Z= 0.319 Chirality : 0.038 0.315 16778 Planarity : 0.005 0.081 12503 Dihedral : 21.200 179.738 29933 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 11.43 Ramachandran Plot: Outliers : 0.66 % Allowed : 6.47 % Favored : 92.88 % Rotamer: Outliers : 1.11 % Allowed : 24.60 % Favored : 74.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.23 % Twisted Proline : 0.20 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.23 (0.10), residues: 7313 helix: 1.81 (0.11), residues: 2479 sheet: -0.81 (0.17), residues: 911 loop : -1.34 (0.10), residues: 3923 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP s 346 HIS 0.036 0.001 HIS s 71 PHE 0.042 0.001 PHE 6 318 TYR 0.037 0.001 TYR 5 383 ARG 0.010 0.000 ARG Y 175 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14626 Ramachandran restraints generated. 7313 Oldfield, 0 Emsley, 7313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14626 Ramachandran restraints generated. 7313 Oldfield, 0 Emsley, 7313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1442 residues out of total 6571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 1369 time to evaluate : 6.166 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 outliers start: 73 outliers final: 28 residues processed: 1407 average time/residue: 1.0013 time to fit residues: 2370.8460 Evaluate side-chains 1308 residues out of total 6571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 1280 time to evaluate : 6.203 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 0 residues processed: 28 average time/residue: 0.7177 time to fit residues: 46.0204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 780 optimal weight: 0.9980 chunk 821 optimal weight: 8.9990 chunk 749 optimal weight: 4.9990 chunk 799 optimal weight: 3.9990 chunk 481 optimal weight: 4.9990 chunk 348 optimal weight: 0.8980 chunk 627 optimal weight: 4.9990 chunk 245 optimal weight: 0.0040 chunk 722 optimal weight: 6.9990 chunk 756 optimal weight: 2.9990 chunk 796 optimal weight: 10.0000 overall best weight: 1.7796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 ASN I 150 HIS ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 9 GLN P 161 GLN S 118 ASN U 35 GLN V 119 GLN ** Y 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 94 HIS ** 5 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 84 ASN 7 277 GLN a 137 ASN d 207 ASN f 115 ASN g 104 ASN ** g 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** k 19 GLN q 60 GLN ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 375 ASN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.4824 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 99362 Z= 0.251 Angle : 0.672 17.753 141656 Z= 0.336 Chirality : 0.041 0.313 16778 Planarity : 0.005 0.083 12503 Dihedral : 21.143 179.701 29933 Min Nonbonded Distance : 1.823 Molprobity Statistics. All-atom Clashscore : 11.76 Ramachandran Plot: Outliers : 0.67 % Allowed : 6.91 % Favored : 92.42 % Rotamer: Outliers : 0.84 % Allowed : 25.65 % Favored : 73.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.23 % Twisted Proline : 0.20 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.30 (0.10), residues: 7313 helix: 1.68 (0.11), residues: 2497 sheet: -0.78 (0.17), residues: 928 loop : -1.36 (0.10), residues: 3888 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.001 TRP s 346 HIS 0.012 0.001 HIS 5 251 PHE 0.057 0.002 PHE 7 260 TYR 0.033 0.002 TYR 6 51 ARG 0.010 0.001 ARG 6 261 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14626 Ramachandran restraints generated. 7313 Oldfield, 0 Emsley, 7313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14626 Ramachandran restraints generated. 7313 Oldfield, 0 Emsley, 7313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1338 residues out of total 6571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1283 time to evaluate : 6.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 55 outliers final: 35 residues processed: 1310 average time/residue: 0.9645 time to fit residues: 2129.2010 Evaluate side-chains 1287 residues out of total 6571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1252 time to evaluate : 6.286 Switching outliers to nearest non-outliers outliers start: 35 outliers final: 0 residues processed: 35 average time/residue: 0.7063 time to fit residues: 55.1723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 524 optimal weight: 4.9990 chunk 845 optimal weight: 4.9990 chunk 515 optimal weight: 3.9990 chunk 401 optimal weight: 0.8980 chunk 587 optimal weight: 5.9990 chunk 886 optimal weight: 20.0000 chunk 816 optimal weight: 0.3980 chunk 706 optimal weight: 6.9990 chunk 73 optimal weight: 7.9990 chunk 545 optimal weight: 0.9990 chunk 432 optimal weight: 2.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 ASN I 150 HIS ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 161 GLN ** Y 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 207 HIS ** 5 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 84 ASN a 137 ASN g 92 HIS ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 107 GLN s 71 HIS ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 427 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8142 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 99362 Z= 0.252 Angle : 0.676 17.392 141656 Z= 0.338 Chirality : 0.041 0.312 16778 Planarity : 0.005 0.083 12503 Dihedral : 21.149 179.707 29933 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 11.84 Ramachandran Plot: Outliers : 0.64 % Allowed : 6.99 % Favored : 92.37 % Rotamer: Outliers : 0.46 % Allowed : 26.06 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.23 % Twisted Proline : 0.20 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.10), residues: 7313 helix: 1.59 (0.10), residues: 2495 sheet: -0.79 (0.16), residues: 929 loop : -1.36 (0.10), residues: 3889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP s 346 HIS 0.019 0.001 HIS d 161 PHE 0.042 0.002 PHE 7 260 TYR 0.032 0.002 TYR 6 51 ARG 0.014 0.001 ARG Y 175 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 14626 Ramachandran restraints generated. 7313 Oldfield, 0 Emsley, 7313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 14626 Ramachandran restraints generated. 7313 Oldfield, 0 Emsley, 7313 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1308 residues out of total 6571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 1278 time to evaluate : 6.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 25 residues processed: 1293 average time/residue: 0.9883 time to fit residues: 2159.6032 Evaluate side-chains 1274 residues out of total 6571 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 1249 time to evaluate : 6.317 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 0 residues processed: 25 average time/residue: 0.8192 time to fit residues: 45.0517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 890 random chunks: chunk 560 optimal weight: 0.6980 chunk 752 optimal weight: 0.9990 chunk 216 optimal weight: 2.9990 chunk 651 optimal weight: 6.9990 chunk 104 optimal weight: 10.0000 chunk 196 optimal weight: 0.8980 chunk 707 optimal weight: 3.9990 chunk 295 optimal weight: 5.9990 chunk 726 optimal weight: 10.0000 chunk 89 optimal weight: 9.9990 chunk 130 optimal weight: 7.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 184 ASN I 150 HIS ** I 151 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 161 GLN S 118 ASN U 16 GLN V 119 GLN W 86 ASN ** Y 183 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 94 HIS ** 5 251 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 147 HIS 7 84 ASN a 137 ASN d 207 ASN f 115 ASN ** g 104 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 141 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** q 107 GLN ** s 240 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.151198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.129170 restraints weight = 132093.654| |-----------------------------------------------------------------------------| r_work (start): 0.3343 rms_B_bonded: 1.27 r_work: 0.3102 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3102 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.4982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 99362 Z= 0.261 Angle : 0.682 17.543 141656 Z= 0.341 Chirality : 0.041 0.411 16778 Planarity : 0.005 0.083 12503 Dihedral : 21.151 179.756 29933 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.66 % Allowed : 7.14 % Favored : 92.21 % Rotamer: Outliers : 0.63 % Allowed : 25.98 % Favored : 73.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.40 % Cis-general : 0.23 % Twisted Proline : 0.20 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.10), residues: 7313 helix: 1.56 (0.10), residues: 2483 sheet: -0.83 (0.16), residues: 928 loop : -1.36 (0.10), residues: 3902 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP s 346 HIS 0.013 0.001 HIS d 161 PHE 0.038 0.002 PHE 7 260 TYR 0.033 0.002 TYR 6 51 ARG 0.017 0.001 ARG Y 175 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33560.18 seconds wall clock time: 583 minutes 43.51 seconds (35023.51 seconds total)