Starting phenix.real_space_refine on Tue Feb 20 04:48:21 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh6_13965/02_2024/7qh6_13965.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh6_13965/02_2024/7qh6_13965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh6_13965/02_2024/7qh6_13965.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh6_13965/02_2024/7qh6_13965.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh6_13965/02_2024/7qh6_13965.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh6_13965/02_2024/7qh6_13965.pdb" } resolution = 3.08 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 1189 5.49 5 S 248 5.16 5 C 48460 2.51 5 N 15185 2.21 5 O 18342 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 103": "NH1" <-> "NH2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "E GLU 83": "OE1" <-> "OE2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "E TYR 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 327": "OE1" <-> "OE2" Residue "E GLU 330": "OE1" <-> "OE2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F GLU 75": "OE1" <-> "OE2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" 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 TYR 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ARG 76": "NH1" <-> "NH2" Residue "H GLU 92": "OE1" <-> "OE2" Residue "K ARG 16": "NH1" <-> "NH2" Residue "K ASP 22": "OD1" <-> "OD2" Residue "K ARG 118": "NH1" <-> "NH2" 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 ASP 110": "OD1" <-> "OD2" Residue "L ARG 118": "NH1" <-> "NH2" Residue "L ARG 128": "NH1" <-> "NH2" Residue "L ARG 130": "NH1" <-> "NH2" Residue "M ARG 38": "NH1" <-> "NH2" Residue "M ARG 44": "NH1" <-> "NH2" Residue "M ARG 51": "NH1" <-> "NH2" Residue "M ARG 57": "NH1" <-> "NH2" Residue "M ARG 62": "NH1" <-> "NH2" Residue "M TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 134": "NH1" <-> "NH2" Residue "M PHE 148": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ARG 182": "NH1" <-> "NH2" Residue "M GLU 251": "OE1" <-> "OE2" Residue "M ARG 259": "NH1" <-> "NH2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "O ASP 84": "OD1" <-> "OD2" Residue "O TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 106": "NH1" <-> "NH2" Residue "O ARG 137": "NH1" <-> "NH2" Residue "O ARG 138": "NH1" <-> "NH2" Residue "O ARG 153": "NH1" <-> "NH2" Residue "P ARG 51": "NH1" <-> "NH2" Residue "P ARG 54": "NH1" <-> "NH2" Residue "P GLU 57": "OE1" <-> "OE2" Residue "P ARG 63": "NH1" <-> "NH2" Residue "P ARG 75": "NH1" <-> "NH2" Residue "P ARG 80": "NH1" <-> "NH2" Residue "P ARG 108": "NH1" <-> "NH2" Residue "P ARG 177": "NH1" <-> "NH2" Residue "Q ARG 74": "NH1" <-> "NH2" Residue "Q ARG 86": "NH1" <-> "NH2" Residue "Q PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ARG 143": "NH1" <-> "NH2" Residue "Q ARG 191": "NH1" <-> "NH2" Residue "Q ARG 244": "NH1" <-> "NH2" Residue "Q ARG 271": "NH1" <-> "NH2" Residue "Q GLU 279": "OE1" <-> "OE2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 32": "NH1" <-> "NH2" Residue "R TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 122": "NH1" <-> "NH2" Residue "R ARG 123": "NH1" <-> "NH2" Residue "R PHE 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 104": "NH1" <-> "NH2" Residue "S ARG 155": "NH1" <-> "NH2" Residue "S PHE 174": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S ARG 184": "NH1" <-> "NH2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T GLU 107": "OE1" <-> "OE2" Residue "T ARG 130": "NH1" <-> "NH2" Residue "T ARG 149": "NH1" <-> "NH2" Residue "T ARG 157": "NH1" <-> "NH2" Residue "T PHE 175": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 30": "NH1" <-> "NH2" Residue "U PHE 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 47": "OE1" <-> "OE2" Residue "U TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 71": "NH1" <-> "NH2" Residue "U ARG 80": "NH1" <-> "NH2" Residue "U ARG 83": "NH1" <-> "NH2" Residue "U PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U ARG 143": "NH1" <-> "NH2" Residue "V ARG 96": "NH1" <-> "NH2" Residue "V ARG 118": "NH1" <-> "NH2" Residue "V ARG 145": "NH1" <-> "NH2" Residue "V ARG 185": "NH1" <-> "NH2" Residue "V TYR 216": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 49": "NH1" <-> "NH2" Residue "W ARG 74": "NH1" <-> "NH2" Residue "W ARG 109": "NH1" <-> "NH2" Residue "W ARG 119": "NH1" <-> "NH2" Residue "X ARG 23": "NH1" <-> "NH2" Residue "X ARG 59": "NH1" <-> "NH2" Residue "X GLU 74": "OE1" <-> "OE2" Residue "X ARG 77": "NH1" <-> "NH2" Residue "X ARG 163": "NH1" <-> "NH2" Residue "X ARG 184": "NH1" <-> "NH2" Residue "X GLU 198": "OE1" <-> "OE2" Residue "X ARG 216": "NH1" <-> "NH2" Residue "Y ARG 91": "NH1" <-> "NH2" Residue "Y ARG 109": "NH1" <-> "NH2" Residue "Y ARG 175": "NH1" <-> "NH2" Residue "Y ARG 196": "NH1" <-> "NH2" Residue "Y PHE 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ARG 210": "NH1" <-> "NH2" Residue "Z TYR 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 19": "NH1" <-> "NH2" Residue "1 PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "1 ARG 34": "NH1" <-> "NH2" Residue "2 ARG 49": "NH1" <-> "NH2" Residue "2 ARG 69": "NH1" <-> "NH2" Residue "3 ARG 104": "NH1" <-> "NH2" Residue "3 PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "3 ARG 116": "NH1" <-> "NH2" Residue "3 ARG 125": "NH1" <-> "NH2" Residue "3 ARG 168": "NH1" <-> "NH2" Residue "3 ASP 182": "OD1" <-> "OD2" Residue "3 ARG 183": "NH1" <-> "NH2" Residue "5 ARG 162": "NH1" <-> "NH2" Residue "5 PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 223": "NH1" <-> "NH2" Residue "5 TYR 257": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "5 ARG 303": "NH1" <-> "NH2" Residue "5 ARG 350": "NH1" <-> "NH2" Residue "5 GLU 409": "OE1" <-> "OE2" Residue "5 PHE 414": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 27": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Residue "6 ARG 58": "NH1" <-> "NH2" Residue "6 ARG 60": "NH1" <-> "NH2" Residue "6 ARG 72": "NH1" <-> "NH2" Residue "6 TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 124": "NH1" <-> "NH2" Residue "6 ARG 136": "NH1" <-> "NH2" Residue "6 ARG 159": "NH1" <-> "NH2" Residue "6 PHE 167": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 188": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 TYR 206": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 261": "NH1" <-> "NH2" Residue "6 PHE 273": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 296": "NH1" <-> "NH2" Residue "6 ARG 299": "NH1" <-> "NH2" Residue "6 PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 322": "NH1" <-> "NH2" Residue "6 TYR 329": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "6 ARG 364": "NH1" <-> "NH2" Residue "6 TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 GLU 124": "OE1" <-> "OE2" Residue "7 ARG 168": "NH1" <-> "NH2" Residue "7 TYR 235": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "7 ARG 250": "NH1" <-> "NH2" Residue "7 ARG 271": "NH1" <-> "NH2" Residue "9 ARG 25": "NH1" <-> "NH2" Residue "9 ARG 28": "NH1" <-> "NH2" Residue "9 PHE 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 ARG 49": "NH1" <-> "NH2" Residue "9 TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "9 PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "a ARG 122": "NH1" <-> "NH2" Residue "a ARG 128": "NH1" <-> "NH2" Residue "a ARG 131": "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 ARG 114": "NH1" <-> "NH2" Residue "b ARG 144": "NH1" <-> "NH2" Residue "b ARG 146": "NH1" <-> "NH2" Residue "b GLU 147": "OE1" <-> "OE2" Residue "c PHE 35": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c PHE 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c PHE 184": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c ARG 216": "NH1" <-> "NH2" Residue "d PHE 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "d ARG 159": "NH1" <-> "NH2" Residue "d PHE 185": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g ARG 90": "NH1" <-> "NH2" Residue "g ARG 105": "NH1" <-> "NH2" Residue "h ARG 69": "NH1" <-> "NH2" Residue "h ARG 116": "NH1" <-> "NH2" Residue "i ARG 46": "NH1" <-> "NH2" Residue "i GLU 49": "OE1" <-> "OE2" Residue "i ARG 75": "NH1" <-> "NH2" 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 ARG 55": "NH1" <-> "NH2" Residue "j ARG 65": "NH1" <-> "NH2" Residue "j ARG 66": "NH1" <-> "NH2" Residue "j ARG 76": "NH1" <-> "NH2" Residue "j ARG 94": "NH1" <-> "NH2" Residue "j GLU 106": "OE1" <-> "OE2" Residue "o ARG 23": "NH1" <-> "NH2" Residue "o GLU 42": "OE1" <-> "OE2" Residue "o ARG 60": "NH1" <-> "NH2" Residue "o ARG 68": "NH1" <-> "NH2" Residue "p TYR 142": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "q ARG 33": "NH1" <-> "NH2" Residue "q ARG 38": "NH1" <-> "NH2" Residue "q ARG 63": "NH1" <-> "NH2" Residue "q ARG 114": "NH1" <-> "NH2" Residue "r TYR 81": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 132": "NH1" <-> "NH2" Residue "r TYR 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "r ARG 153": "NH1" <-> "NH2" Residue "r ARG 168": "NH1" <-> "NH2" Residue "r ARG 171": "NH1" <-> "NH2" Residue "s ARG 59": "NH1" <-> "NH2" Residue "s ARG 81": "NH1" <-> "NH2" Residue "s TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 158": "NH1" <-> "NH2" Residue "s ARG 160": "NH1" <-> "NH2" Residue "s ARG 162": "NH1" <-> "NH2" Residue "s ARG 212": "NH1" <-> "NH2" Residue "s ARG 219": "NH1" <-> "NH2" Residue "s ARG 222": "NH1" <-> "NH2" Residue "s ARG 223": "NH1" <-> "NH2" Residue "s TYR 231": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ARG 242": "NH1" <-> "NH2" Residue "s ARG 276": "NH1" <-> "NH2" Residue "s ARG 308": "NH1" <-> "NH2" Residue "s ASP 318": "OD1" <-> "OD2" Residue "s PHE 333": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s TYR 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "s ASP 384": "OD1" <-> "OD2" Residue "s ARG 389": "NH1" <-> "NH2" Residue "u TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 6": "NH1" <-> "NH2" Residue "v ARG 14": "NH1" <-> "NH2" Residue "v ARG 24": "NH1" <-> "NH2" Residue "v TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 28": "NH1" <-> "NH2" Residue "w PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "w GLU 143": "OE1" <-> "OE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 83425 Number of models: 1 Model: "" Number of chains: 47 Chain: "D" Number of atoms: 1349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1349 Classifications: {'peptide': 174} Link IDs: {'PTRANS': 8, 'TRANS': 165} Chain: "E" Number of atoms: 2249 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2249 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 22, 'TRANS': 261} 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: "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: {'PTRANS': 8, 'TRANS': 106} 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: 1148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1148 Classifications: {'peptide': 141} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 134} Chain: "Q" Number of atoms: 1805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1805 Classifications: {'peptide': 217} Link IDs: {'PTRANS': 14, 'TRANS': 202} Chain: "R" Number of atoms: 1153 Number of conformers: 1 Conformer: "" Number of residues, atoms: 140, 1153 Classifications: {'peptide': 140} Link IDs: {'PTRANS': 3, 'TRANS': 136} 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: 1154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1154 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 11, 'TRANS': 127} Chain breaks: 1 Chain: "V" Number of atoms: 1333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1333 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 9, 'TRANS': 153} Chain breaks: 1 Chain: "W" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 859 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 6, 'TRANS': 102} Chain: "X" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 243, 2035 Classifications: {'peptide': 243} Link IDs: {'PTRANS': 18, 'TRANS': 224} 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: 955 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 955 Classifications: {'peptide': 117} Link IDs: {'PTRANS': 10, 'TRANS': 106} Chain: "0" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 880 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 7, 'TRANS': 100} 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: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 367 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} 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: "5" Number of atoms: 3037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 3037 Classifications: {'peptide': 373} Link IDs: {'PCIS': 1, 'PTRANS': 28, 'TRANS': 343} Chain breaks: 1 Chain: "6" Number of atoms: 2640 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2640 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 21} Link IDs: {'PTRANS': 28, 'TRANS': 295} Chain breaks: 3 Unresolved non-hydrogen bonds: 83 Unresolved non-hydrogen angles: 103 Unresolved non-hydrogen dihedrals: 63 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 4, 'GLU:plan': 5, 'ARG:plan': 4, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 59 Chain: "7" Number of atoms: 2334 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2334 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 17, 'TRANS': 269} Chain: "9" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 117, 947 Classifications: {'peptide': 117} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 107} Chain breaks: 1 Chain: "a" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 686 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 10, 'TRANS': 71} Chain breaks: 1 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: 1529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1529 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 15, 'TRANS': 169} Chain breaks: 3 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: {'PTRANS': 7, 'TRANS': 92} Chain breaks: 1 Chain: "i" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 827 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 5, 'TRANS': 91} 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: "o" Number of atoms: 771 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 771 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 5, 'TRANS': 85} Chain: "p" Number of atoms: 1058 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1058 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain breaks: 3 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: 1075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 1075 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 16, 'TRANS': 113} Chain breaks: 1 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: "u" Number of atoms: 927 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 927 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 4, 'TRANS': 106} Chain: "v" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 588 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 1, 'TRANS': 67} Chain: "w" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 638 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 3, 'TRANS': 75} Chain: "A" Number of atoms: 24063 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 24063 Classifications: {'RNA': 1133} Modifications used: {'rna2p_pur': 131, 'rna2p_pyr': 94, 'rna3p_pur': 473, 'rna3p_pyr': 435} Link IDs: {'rna2p': 224, 'rna3p': 908} Chain breaks: 20 Chain: "B" Number of atoms: 1191 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 1191 Classifications: {'RNA': 56} Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 1, 'rna3p_pur': 29, 'rna3p_pyr': 25} Link IDs: {'rna2p': 2, 'rna3p': 53} Chain breaks: 4 Chain: "0" 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 28781 SG CYS 0 110 145.771 152.643 190.025 1.00 25.72 S ATOM 28803 SG CYS 0 113 148.347 149.877 190.275 1.00 36.56 S ATOM 28883 SG CYS 0 123 144.861 149.106 188.858 1.00 19.24 S ATOM 28906 SG CYS 0 126 145.701 149.183 192.382 1.00 22.32 S Time building chain proxies: 31.75, per 1000 atoms: 0.38 Number of scatterers: 83425 At special positions: 0 Unit cell: (220.48, 218.36, 243.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 248 16.00 P 1189 15.00 O 18342 8.00 N 15185 7.00 C 48460 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: 28.96 Conformation dependent library (CDL) restraints added in 7.9 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN 0 200 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 123 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 113 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 126 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 110 " Number of angles added : 6 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13420 Finding SS restraints... Secondary structure from input PDB file: 260 helices and 74 sheets defined 38.6% alpha, 13.9% beta 303 base pairs and 546 stacking pairs defined. Time for finding SS restraints: 21.76 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 259 through 266 removed outlier: 4.228A pdb=" N ASN D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU D 266 " --> pdb=" O ARG D 262 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 52 removed outlier: 4.126A pdb=" N HIS E 52 " --> pdb=" O TRP E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 76 removed outlier: 3.808A pdb=" N PHE E 60 " --> pdb=" O GLU E 56 " (cutoff:3.500A) Processing helix chain 'E' and resid 134 through 139 removed outlier: 3.849A pdb=" N CYS E 138 " --> pdb=" O LYS E 135 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN E 139 " --> pdb=" O GLU E 136 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 157 removed outlier: 3.836A pdb=" N ARG E 156 " --> pdb=" O SER E 153 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LYS E 157 " --> pdb=" O ARG E 154 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 153 through 157' Processing helix chain 'E' and resid 158 through 169 Processing helix chain 'E' and resid 194 through 198 removed outlier: 3.585A pdb=" N PHE E 198 " --> pdb=" O ALA E 195 " (cutoff:3.500A) Processing helix chain 'E' and resid 217 through 222 Processing helix chain 'E' and resid 304 through 308 removed outlier: 3.822A pdb=" N LYS E 308 " --> pdb=" O PRO E 305 " (cutoff:3.500A) Processing helix chain 'E' and resid 320 through 324 Processing helix chain 'F' and resid 83 through 88 Processing helix chain 'F' and resid 92 through 105 Processing helix chain 'F' and resid 166 through 184 Processing helix chain 'F' and resid 199 through 210 removed outlier: 3.982A pdb=" N LEU F 203 " --> pdb=" O ASP F 199 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 237 removed outlier: 3.934A pdb=" N ARG F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N LEU F 237 " --> pdb=" O ALA F 233 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 248 No H-bonds generated for 'chain 'F' and resid 246 through 248' Processing helix chain 'F' and resid 249 through 256 removed outlier: 3.823A pdb=" N HIS F 256 " --> pdb=" O SER F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 262 through 276 Processing helix chain 'H' and resid 74 through 78 removed outlier: 3.997A pdb=" N ARG H 78 " --> pdb=" O ARG H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 89 No H-bonds generated for 'chain 'H' and resid 87 through 89' Processing helix chain 'H' and resid 115 through 122 Processing helix chain 'H' and resid 136 through 146 Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 27 through 40 removed outlier: 3.606A pdb=" N LEU K 31 " --> pdb=" O PRO K 27 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N GLN K 40 " --> pdb=" O SER K 36 " (cutoff:3.500A) Processing helix chain 'K' and resid 48 through 52 removed outlier: 3.536A pdb=" N ASP K 52 " --> pdb=" O ALA K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.645A pdb=" N ILE K 65 " --> pdb=" O THR K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' 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 removed outlier: 3.558A pdb=" N LYS K 105 " --> pdb=" O VAL K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 117 through 124 Processing helix chain 'K' and resid 134 through 139 Processing helix chain 'K' and resid 154 through 158 Processing helix chain 'K' and resid 159 through 166 Processing helix chain 'L' and resid 44 through 48 removed outlier: 3.553A pdb=" N GLY L 47 " --> pdb=" O SER L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 129 removed outlier: 3.680A pdb=" N LYS L 129 " --> pdb=" O SER L 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 126 through 129' Processing helix chain 'L' and resid 134 through 138 removed outlier: 3.685A pdb=" N VAL L 137 " --> pdb=" O TYR L 134 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 19 removed outlier: 3.905A pdb=" N GLY M 18 " --> pdb=" O ASP M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 73 through 78 removed outlier: 3.950A pdb=" N ILE M 78 " --> pdb=" O PHE M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 107 Processing helix chain 'M' and resid 117 through 124 Processing helix chain 'M' and resid 131 through 133 No H-bonds generated for 'chain 'M' and resid 131 through 133' Processing helix chain 'M' and resid 160 through 170 removed outlier: 4.273A pdb=" N ASN M 170 " --> pdb=" O ALA M 166 " (cutoff:3.500A) Processing helix chain 'M' and resid 180 through 189 removed outlier: 3.736A pdb=" N LYS M 189 " --> pdb=" O ASP M 185 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 195 removed outlier: 3.590A pdb=" N PHE M 193 " --> pdb=" O LYS M 189 " (cutoff:3.500A) Processing helix chain 'M' and resid 207 through 209 No H-bonds generated for 'chain 'M' and resid 207 through 209' Processing helix chain 'M' and resid 210 through 215 Processing helix chain 'M' and resid 216 through 220 Processing helix chain 'M' and resid 225 through 227 No H-bonds generated for 'chain 'M' and resid 225 through 227' Processing helix chain 'M' and resid 228 through 241 removed outlier: 4.094A pdb=" N ALA M 232 " --> pdb=" O LYS M 228 " (cutoff:3.500A) Processing helix chain 'M' and resid 246 through 250 removed outlier: 3.896A pdb=" N LYS M 249 " --> pdb=" O ASP M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 258 Processing helix chain 'M' and resid 287 through 295 Processing helix chain 'N' and resid 68 through 72 Processing helix chain 'N' and resid 98 through 112 removed outlier: 3.897A pdb=" N SER N 112 " --> pdb=" O THR N 108 " (cutoff:3.500A) Processing helix chain 'N' and resid 172 through 183 removed outlier: 3.696A pdb=" N LEU N 176 " --> pdb=" O VAL N 172 " (cutoff:3.500A) Processing helix chain 'N' and resid 192 through 209 removed outlier: 3.693A pdb=" N GLU N 196 " --> pdb=" O ARG N 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 215 through 220 Processing helix chain 'N' and resid 225 through 229 Processing helix chain 'N' and resid 233 through 238 Processing helix chain 'O' and resid 21 through 40 Processing helix chain 'O' and resid 46 through 64 removed outlier: 4.115A pdb=" N LYS O 58 " --> pdb=" O GLY O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 80 removed outlier: 3.757A pdb=" N MET O 73 " --> pdb=" O ASN O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 82 through 84 No H-bonds generated for 'chain 'O' and resid 82 through 84' Processing helix chain 'O' and resid 85 through 91 Processing helix chain 'O' and resid 92 through 97 Processing helix chain 'O' and resid 143 through 158 Processing helix chain 'P' and resid 39 through 43 removed outlier: 3.582A pdb=" N GLU P 42 " --> pdb=" O VAL P 39 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA P 43 " --> pdb=" O GLU P 40 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 39 through 43' Processing helix chain 'P' and resid 54 through 59 Processing helix chain 'P' and resid 109 through 115 removed outlier: 3.830A pdb=" N HIS P 115 " --> pdb=" O ALA P 111 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 138 Processing helix chain 'P' and resid 149 through 154 removed outlier: 3.695A pdb=" N ALA P 154 " --> pdb=" O PRO P 150 " (cutoff:3.500A) Processing helix chain 'P' and resid 155 through 169 removed outlier: 3.673A pdb=" N GLY P 169 " --> pdb=" O MET P 165 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 81 removed outlier: 3.652A pdb=" N ILE Q 81 " --> pdb=" O PRO Q 78 " (cutoff:3.500A) Processing helix chain 'Q' and resid 88 through 104 removed outlier: 4.187A pdb=" N PHE Q 92 " --> pdb=" O ASP Q 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 146 removed outlier: 4.264A pdb=" N GLY Q 146 " --> pdb=" O ARG Q 143 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 143 through 146' Processing helix chain 'Q' and resid 187 through 193 removed outlier: 3.918A pdb=" N LEU Q 190 " --> pdb=" O LEU Q 187 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N ARG Q 191 " --> pdb=" O LEU Q 188 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ALA Q 193 " --> pdb=" O LEU Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 194 through 199 removed outlier: 3.752A pdb=" N THR Q 199 " --> pdb=" O GLU Q 196 " (cutoff:3.500A) Processing helix chain 'Q' and resid 250 through 258 removed outlier: 3.593A pdb=" N MET Q 254 " --> pdb=" O THR Q 250 " (cutoff:3.500A) Processing helix chain 'Q' and resid 262 through 267 removed outlier: 4.189A pdb=" N GLU Q 266 " --> pdb=" O GLN Q 262 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE Q 267 " --> pdb=" O PRO Q 263 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 262 through 267' Processing helix chain 'Q' and resid 276 through 288 Processing helix chain 'R' and resid 16 through 26 removed outlier: 3.954A pdb=" N ARG R 20 " --> pdb=" O ASP R 16 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N VAL R 24 " --> pdb=" O ARG R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 37 removed outlier: 4.125A pdb=" N ASN R 36 " --> pdb=" O GLY R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 79 removed outlier: 4.433A pdb=" N ARG R 44 " --> pdb=" O ARG R 40 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N ARG R 57 " --> pdb=" O CYS R 53 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N LEU R 59 " --> pdb=" O LYS R 55 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 92 Processing helix chain 'R' and resid 98 through 109 Processing helix chain 'R' and resid 109 through 133 Processing helix chain 'S' and resid 68 through 90 Processing helix chain 'T' and resid 53 through 57 removed outlier: 3.664A pdb=" N ILE T 57 " --> pdb=" O LYS T 54 " (cutoff:3.500A) Processing helix chain 'T' and resid 83 through 94 removed outlier: 5.297A pdb=" N TYR T 89 " --> pdb=" O ASP T 85 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N LEU T 90 " --> pdb=" O LYS T 86 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE T 94 " --> pdb=" O LEU T 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 98 through 107 Processing helix chain 'T' and resid 113 through 131 Processing helix chain 'T' and resid 191 through 205 Processing helix chain 'U' and resid 49 through 61 Processing helix chain 'U' and resid 127 through 136 Processing helix chain 'V' and resid 178 through 182 Processing helix chain 'V' and resid 193 through 203 Processing helix chain 'W' and resid 110 through 120 removed outlier: 3.526A pdb=" N LEU W 120 " --> pdb=" O LEU W 116 " (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 16 Processing helix chain 'X' and resid 25 through 34 Processing helix chain 'X' and resid 72 through 77 Processing helix chain 'X' and resid 128 through 139 Processing helix chain 'X' and resid 140 through 148 Processing helix chain 'X' and resid 149 through 154 removed outlier: 3.698A pdb=" N LEU X 153 " --> pdb=" O PRO X 149 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N CYS X 154 " --> pdb=" O LYS X 150 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 149 through 154' Processing helix chain 'X' and resid 155 through 172 Processing helix chain 'X' and resid 173 through 177 removed outlier: 3.583A pdb=" N HIS X 177 " --> pdb=" O PRO X 174 " (cutoff:3.500A) Processing helix chain 'X' and resid 180 through 191 removed outlier: 3.602A pdb=" N ARG X 184 " --> pdb=" O ASP X 180 " (cutoff:3.500A) Processing helix chain 'X' and resid 192 through 195 Processing helix chain 'X' and resid 197 through 203 removed outlier: 3.728A pdb=" N GLU X 202 " --> pdb=" O GLU X 198 " (cutoff:3.500A) removed outlier: 4.641A 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 243 removed outlier: 3.732A pdb=" N ILE X 229 " --> pdb=" O PRO X 225 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N LEU X 243 " --> pdb=" O GLN X 239 " (cutoff:3.500A) Processing helix chain 'X' and resid 244 through 244 No H-bonds generated for 'chain 'X' and resid 244 through 244' Processing helix chain 'Y' and resid 63 through 68 removed outlier: 3.618A pdb=" N GLU Y 66 " --> pdb=" O GLY Y 63 " (cutoff:3.500A) Processing helix chain 'Y' and resid 70 through 74 Processing helix chain 'Y' and resid 86 through 92 Processing helix chain 'Y' and resid 95 through 123 Processing helix chain 'Y' and resid 129 through 159 removed outlier: 3.628A pdb=" N ASP Y 133 " --> pdb=" O PRO Y 129 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N LEU Y 156 " --> pdb=" O ALA Y 152 " (cutoff:3.500A) Processing helix chain 'Y' and resid 187 through 191 removed outlier: 3.539A pdb=" N ASN Y 191 " --> pdb=" O TRP Y 188 " (cutoff:3.500A) Processing helix chain 'Y' and resid 204 through 236 removed outlier: 4.558A pdb=" N PHE Y 208 " --> pdb=" O TYR Y 204 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 47 removed outlier: 3.669A pdb=" N GLN Z 47 " --> pdb=" O LYS Z 44 " (cutoff:3.500A) Processing helix chain 'Z' and resid 49 through 56 Processing helix chain 'Z' and resid 79 through 89 Processing helix chain 'Z' and resid 103 through 111 Processing helix chain 'Z' and resid 112 through 115 removed outlier: 5.530A pdb=" N HIS Z 115 " --> pdb=" O VAL Z 112 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 112 through 115' Processing helix chain '0' and resid 88 through 95 Processing helix chain '0' and resid 123 through 146 Processing helix chain '2' and resid 56 through 62 Processing helix chain '2' and resid 65 through 70 Processing helix chain '2' and resid 72 through 85 Processing helix chain '3' and resid 107 through 112 removed outlier: 3.771A pdb=" N ILE 3 111 " --> pdb=" O VAL 3 107 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ASP 3 112 " --> pdb=" O LYS 3 108 " (cutoff:3.500A) No H-bonds generated for 'chain '3' and resid 107 through 112' Processing helix chain '3' and resid 137 through 146 Processing helix chain '3' and resid 151 through 162 Processing helix chain '3' and resid 177 through 181 Processing helix chain '5' and resid 47 through 52 removed outlier: 3.611A pdb=" N TYR 5 50 " --> pdb=" O ASP 5 47 " (cutoff:3.500A) Processing helix chain '5' and resid 59 through 63 removed outlier: 3.771A pdb=" N GLY 5 62 " --> pdb=" O THR 5 59 " (cutoff:3.500A) Processing helix chain '5' and resid 84 through 88 removed outlier: 3.669A pdb=" N TYR 5 88 " --> pdb=" O PRO 5 85 " (cutoff:3.500A) Processing helix chain '5' and resid 116 through 125 removed outlier: 3.582A pdb=" N ALA 5 120 " --> pdb=" O GLY 5 116 " (cutoff:3.500A) Processing helix chain '5' and resid 133 through 138 removed outlier: 3.509A pdb=" N LEU 5 137 " --> pdb=" O PRO 5 133 " (cutoff:3.500A) Processing helix chain '5' and resid 139 through 141 No H-bonds generated for 'chain '5' and resid 139 through 141' Processing helix chain '5' and resid 149 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 194 Processing helix chain '5' and resid 195 through 199 removed outlier: 3.508A pdb=" N LEU 5 198 " --> pdb=" O HIS 5 195 " (cutoff:3.500A) Processing helix chain '5' and resid 241 through 248 Processing helix chain '5' and resid 249 through 251 No H-bonds generated for 'chain '5' and resid 249 through 251' Processing helix chain '5' and resid 299 through 303 Processing helix chain '5' and resid 305 through 330 Processing helix chain '5' and resid 408 through 420 Processing helix chain '6' and resid 54 through 67 Processing helix chain '6' and resid 74 through 79 Processing helix chain '6' and resid 100 through 116 Processing helix chain '6' and resid 116 through 125 Processing helix chain '6' and resid 132 through 155 removed outlier: 3.710A pdb=" N GLY 6 144 " --> pdb=" O GLU 6 140 " (cutoff:3.500A) Proline residue: 6 145 - end of helix Processing helix chain '6' and resid 156 through 163 removed outlier: 3.696A pdb=" N ASP 6 160 " --> pdb=" O GLY 6 156 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS 6 163 " --> pdb=" O ARG 6 159 " (cutoff:3.500A) Processing helix chain '6' and resid 195 through 199 removed outlier: 3.657A pdb=" N ALA 6 199 " --> pdb=" O THR 6 196 " (cutoff:3.500A) Processing helix chain '6' and resid 299 through 307 removed outlier: 4.142A pdb=" N HIS 6 307 " --> pdb=" O PHE 6 303 " (cutoff:3.500A) Processing helix chain '6' and resid 324 through 334 removed outlier: 3.601A pdb=" N THR 6 328 " --> pdb=" O ASP 6 324 " (cutoff:3.500A) Processing helix chain '6' and resid 362 through 368 Processing helix chain '7' and resid 37 through 58 removed outlier: 3.651A pdb=" N LEU 7 58 " --> pdb=" O ARG 7 54 " (cutoff:3.500A) Processing helix chain '7' and resid 87 through 96 Processing helix chain '7' and resid 96 through 103 Processing helix chain '7' and resid 135 through 155 removed outlier: 4.165A pdb=" N ASN 7 139 " --> pdb=" O PRO 7 135 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LYS 7 140 " --> pdb=" O GLY 7 136 " (cutoff:3.500A) Processing helix chain '7' and resid 173 through 177 removed outlier: 4.075A pdb=" N GLY 7 177 " --> pdb=" O VAL 7 174 " (cutoff:3.500A) Processing helix chain '7' and resid 187 through 190 Processing helix chain '7' and resid 195 through 213 removed outlier: 3.708A pdb=" N LEU 7 199 " --> pdb=" O THR 7 195 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ASP 7 213 " --> pdb=" O LEU 7 209 " (cutoff:3.500A) Processing helix chain '7' and resid 223 through 230 Processing helix chain '7' and resid 233 through 247 Processing helix chain '7' and resid 309 through 320 Processing helix chain '9' and resid 27 through 34 Processing helix chain '9' and resid 54 through 57 removed outlier: 3.786A pdb=" N VAL 9 57 " --> pdb=" O LYS 9 54 " (cutoff:3.500A) No H-bonds generated for 'chain '9' and resid 54 through 57' Processing helix chain '9' and resid 87 through 104 Proline residue: 9 98 - end of helix Processing helix chain 'a' and resid 106 through 116 Processing helix chain 'a' and resid 119 through 124 removed outlier: 4.031A pdb=" N ARG a 122 " --> pdb=" O THR a 119 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N TYR a 124 " --> pdb=" O HIS a 121 " (cutoff:3.500A) Processing helix chain 'a' and resid 128 through 133 removed outlier: 3.747A pdb=" N ARG a 133 " --> pdb=" O TYR a 129 " (cutoff:3.500A) Processing helix chain 'b' and resid 37 through 39 No H-bonds generated for 'chain 'b' and resid 37 through 39' Processing helix chain 'b' and resid 40 through 49 removed outlier: 3.759A pdb=" N PHE b 46 " --> pdb=" O GLY b 42 " (cutoff:3.500A) Processing helix chain 'b' and resid 50 through 58 removed outlier: 3.511A pdb=" N ASN b 58 " --> pdb=" O PHE b 54 " (cutoff:3.500A) Processing helix chain 'b' and resid 93 through 105 Processing helix chain 'b' and resid 139 through 143 removed outlier: 3.558A pdb=" N LEU b 143 " --> pdb=" O PHE b 140 " (cutoff:3.500A) Processing helix chain 'c' and resid 35 through 53 removed outlier: 3.518A pdb=" N PHE c 39 " --> pdb=" O PHE c 35 " (cutoff:3.500A) Processing helix chain 'c' and resid 67 through 79 removed outlier: 3.720A pdb=" N LEU c 79 " --> pdb=" O PHE c 75 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 91 Processing helix chain 'c' and resid 94 through 105 Processing helix chain 'c' and resid 122 through 145 Processing helix chain 'c' and resid 149 through 161 Processing helix chain 'c' and resid 162 through 172 Processing helix chain 'c' and resid 174 through 179 removed outlier: 4.057A pdb=" N LEU c 178 " --> pdb=" O ALA c 174 " (cutoff:3.500A) Processing helix chain 'c' and resid 187 through 219 Proline residue: c 208 - end of helix Processing helix chain 'c' and resid 220 through 224 removed outlier: 3.568A pdb=" N MET c 223 " --> pdb=" O ILE c 220 " (cutoff:3.500A) Processing helix chain 'c' and resid 227 through 231 removed outlier: 3.544A pdb=" N GLU c 230 " --> pdb=" O GLU c 227 " (cutoff:3.500A) Processing helix chain 'c' and resid 236 through 248 removed outlier: 3.892A 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 127 removed outlier: 3.692A pdb=" N ASP d 127 " --> pdb=" O ARG d 123 " (cutoff:3.500A) Processing helix chain 'd' and resid 133 through 135 No H-bonds generated for 'chain 'd' and resid 133 through 135' Processing helix chain 'd' and resid 136 through 155 removed outlier: 3.717A pdb=" N LYS d 140 " --> pdb=" O ASP d 136 " (cutoff:3.500A) Processing helix chain 'd' and resid 156 through 164 Processing helix chain 'd' and resid 168 through 177 removed outlier: 3.832A pdb=" N MET d 172 " --> pdb=" O CYS d 168 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ASP d 175 " --> pdb=" O ASP d 171 " (cutoff:3.500A) Processing helix chain 'g' and resid 45 through 50 Processing helix chain 'g' and resid 116 through 133 Proline residue: g 130 - end of helix Processing helix chain 'g' and resid 153 through 164 Processing helix chain 'h' and resid 65 through 77 removed outlier: 3.509A pdb=" N VAL h 77 " --> pdb=" O TYR h 73 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 89 Processing helix chain 'h' and resid 93 through 109 Processing helix chain 'h' and resid 113 through 117 Processing helix chain 'h' and resid 122 through 131 Processing helix chain 'h' and resid 138 through 146 removed outlier: 3.585A pdb=" N GLU h 142 " --> pdb=" O SER h 138 " (cutoff:3.500A) Processing helix chain 'i' and resid 69 through 74 removed outlier: 3.584A pdb=" N ILE i 74 " --> pdb=" O LYS i 71 " (cutoff:3.500A) Processing helix chain 'i' and resid 77 through 81 removed outlier: 4.085A pdb=" N ARG i 81 " --> pdb=" O ILE i 78 " (cutoff:3.500A) Processing helix chain 'i' and resid 86 through 99 Processing helix chain 'i' and resid 103 through 124 Processing helix chain 'j' and resid 25 through 30 Processing helix chain 'j' and resid 41 through 46 removed outlier: 3.560A pdb=" N LEU j 46 " --> pdb=" O PRO j 42 " (cutoff:3.500A) Processing helix chain 'j' and resid 60 through 101 Processing helix chain 'o' and resid 28 through 49 Processing helix chain 'o' and resid 55 through 60 removed outlier: 3.735A pdb=" N ARG o 60 " --> pdb=" O ARG o 56 " (cutoff:3.500A) Processing helix chain 'o' and resid 63 through 80 Processing helix chain 'o' and resid 87 through 94 removed outlier: 4.049A pdb=" N GLN o 91 " --> pdb=" O PHE o 87 " (cutoff:3.500A) Processing helix chain 'o' and resid 95 through 97 No H-bonds generated for 'chain 'o' and resid 95 through 97' Processing helix chain 'p' and resid 44 through 49 removed outlier: 3.628A pdb=" N TYR p 49 " --> pdb=" O LEU p 45 " (cutoff:3.500A) Processing helix chain 'p' and resid 54 through 59 Processing helix chain 'p' and resid 112 through 123 Processing helix chain 'p' and resid 142 through 163 removed outlier: 3.506A pdb=" N ASN p 146 " --> pdb=" O TYR p 142 " (cutoff:3.500A) Processing helix chain 'p' and resid 175 through 188 Processing helix chain 'q' and resid 48 through 52 Processing helix chain 'q' and resid 53 through 65 removed outlier: 4.007A pdb=" N ALA q 57 " --> pdb=" O GLY q 53 " (cutoff:3.500A) Processing helix chain 'q' and resid 66 through 68 No H-bonds generated for 'chain 'q' and resid 66 through 68' Processing helix chain 'q' and resid 71 through 76 Processing helix chain 'q' and resid 78 through 93 Processing helix chain 'q' and resid 95 through 150 Proline residue: q 129 - end of helix removed outlier: 3.759A pdb=" N LYS q 150 " --> pdb=" O ALA q 146 " (cutoff:3.500A) Processing helix chain 'r' and resid 72 through 76 Processing helix chain 'r' and resid 85 through 91 Processing helix chain 'r' and resid 101 through 106 Processing helix chain 'r' and resid 108 through 125 Processing helix chain 'r' and resid 128 through 132 removed outlier: 3.839A pdb=" N ARG r 132 " --> pdb=" O PRO r 129 " (cutoff:3.500A) Processing helix chain 'r' and resid 155 through 159 removed outlier: 4.124A pdb=" N VAL r 159 " --> pdb=" O PRO r 156 " (cutoff:3.500A) Processing helix chain 'r' and resid 178 through 182 removed outlier: 3.765A pdb=" N ARG r 182 " --> pdb=" O PRO r 179 " (cutoff:3.500A) Processing helix chain 's' and resid 55 through 72 Processing helix chain 's' and resid 75 through 84 Processing helix chain 's' and resid 101 through 111 removed outlier: 4.090A pdb=" N TRP s 105 " --> pdb=" O ASN s 101 " (cutoff:3.500A) Processing helix chain 's' and resid 141 through 155 removed outlier: 4.243A pdb=" N GLU s 153 " --> pdb=" O CYS s 149 " (cutoff:3.500A) Processing helix chain 's' and resid 164 through 166 No H-bonds generated for 'chain 's' and resid 164 through 166' Processing helix chain 's' and resid 167 through 172 Processing helix chain 's' and resid 172 through 188 removed outlier: 3.735A pdb=" N PHE s 176 " --> pdb=" O ILE s 172 " (cutoff:3.500A) Processing helix chain 's' and resid 193 through 198 removed outlier: 4.228A pdb=" N ALA s 197 " --> pdb=" O PRO s 193 " (cutoff:3.500A) Processing helix chain 's' and resid 219 through 223 removed outlier: 4.306A pdb=" N ARG s 222 " --> pdb=" O ARG s 219 " (cutoff:3.500A) Processing helix chain 's' and resid 303 through 306 Processing helix chain 's' and resid 307 through 313 removed outlier: 3.548A pdb=" N LEU s 311 " --> pdb=" O ARG s 307 " (cutoff:3.500A) Processing helix chain 's' and resid 319 through 343 removed outlier: 4.296A pdb=" N VAL s 323 " --> pdb=" O GLN s 319 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N PHE s 324 " --> pdb=" O ILE s 320 " (cutoff:3.500A) Processing helix chain 's' and resid 414 through 427 removed outlier: 4.249A pdb=" N LEU s 418 " --> pdb=" O ASN s 414 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ASN s 427 " --> pdb=" O HIS s 423 " (cutoff:3.500A) Processing helix chain 'u' and resid 93 through 105 Processing helix chain 'u' and resid 131 through 150 removed outlier: 3.659A pdb=" N LYS u 150 " --> pdb=" O TYR u 146 " (cutoff:3.500A) Processing helix chain 'u' and resid 181 through 189 Processing helix chain 'u' and resid 189 through 196 removed outlier: 3.741A pdb=" N LEU u 193 " --> pdb=" O GLU u 189 " (cutoff:3.500A) Processing helix chain 'v' and resid 5 through 22 removed outlier: 4.058A pdb=" N GLN v 22 " --> pdb=" O ARG v 18 " (cutoff:3.500A) Processing helix chain 'v' and resid 27 through 40 Processing helix chain 'v' and resid 47 through 64 Processing helix chain 'w' and resid 75 through 90 Processing helix chain 'w' and resid 111 through 124 Processing helix chain 'w' and resid 140 through 152 removed outlier: 3.871A pdb=" N LYS w 152 " --> pdb=" O ILE w 148 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 147 through 152 removed outlier: 6.798A pdb=" N ILE D 139 " --> pdb=" O VAL D 129 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N VAL D 129 " --> pdb=" O ILE D 139 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N LEU D 141 " --> pdb=" O ILE D 127 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 181 through 183 Processing sheet with id=AA3, first strand: chain 'D' and resid 216 through 220 removed outlier: 6.294A pdb=" N LEU D 216 " --> pdb=" O GLN D 227 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLN D 227 " --> pdb=" O LEU D 216 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG D 218 " --> pdb=" O ILE D 225 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 331 through 332 removed outlier: 5.187A pdb=" N LYS E 272 " --> pdb=" O ASN E 286 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N TYR E 284 " --> pdb=" O TRP E 274 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N ILE E 276 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N ILE E 282 " --> pdb=" O ILE E 276 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N HIS E 117 " --> pdb=" O PRO E 108 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL E 119 " --> pdb=" O MET E 106 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N MET E 106 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N LEU E 121 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N GLN E 202 " --> pdb=" O LYS E 272 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS E 272 " --> pdb=" O GLN E 202 " (cutoff:3.500A) removed outlier: 5.360A pdb=" N VAL E 204 " --> pdb=" O GLY E 270 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 128 through 133 removed outlier: 6.493A pdb=" N SER E 146 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 4.592A pdb=" N TYR E 132 " --> pdb=" O THR E 144 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR E 144 " --> pdb=" O TYR E 132 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N THR E 151 " --> pdb=" O LYS E 173 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N LYS E 173 " --> pdb=" O THR E 151 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 214 through 216 Processing sheet with id=AA7, first strand: chain 'F' and resid 62 through 65 Processing sheet with id=AA8, first strand: chain 'F' and resid 109 through 111 Processing sheet with id=AA9, first strand: chain 'F' and resid 187 through 188 removed outlier: 6.713A pdb=" N VAL F 216 " --> pdb=" O ASN F 241 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N ILE F 243 " --> pdb=" O VAL F 216 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU F 218 " --> pdb=" O ILE F 243 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'H' and resid 54 through 58 removed outlier: 6.829A pdb=" N GLU H 57 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 5.365A pdb=" N LEU H 82 " --> pdb=" O GLU H 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 111 through 114 Processing sheet with id=AB3, first strand: chain 'K' and resid 125 through 128 removed outlier: 6.318A pdb=" N VAL K 57 " --> pdb=" O HIS K 126 " (cutoff:3.500A) removed outlier: 7.996A pdb=" N PHE K 128 " --> pdb=" O VAL K 57 " (cutoff:3.500A) removed outlier: 6.684A pdb=" N ILE K 59 " --> pdb=" O PHE K 128 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N TYR K 19 " --> pdb=" O VAL K 58 " (cutoff:3.500A) removed outlier: 7.765A pdb=" N MET K 60 " --> pdb=" O TYR K 19 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LEU K 21 " --> pdb=" O MET K 60 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 76 through 80 Processing sheet with id=AB5, first strand: chain 'L' and resid 39 through 40 removed outlier: 6.769A pdb=" N ARG L 39 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 8.617A pdb=" N LEU L 107 " --> pdb=" O ARG L 39 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS L 83 " --> pdb=" O ILE L 108 " (cutoff:3.500A) removed outlier: 7.880A pdb=" N GLN L 72 " --> pdb=" O VAL L 60 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N VAL L 60 " --> pdb=" O GLN L 72 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N LEU L 74 " --> pdb=" O ILE L 58 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG L 56 " --> pdb=" O ALA L 76 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 123 through 124 removed outlier: 6.716A pdb=" N ILE L 123 " --> pdb=" O VAL L 145 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain 'M' and resid 92 through 97 removed outlier: 7.748A pdb=" N GLN M 92 " --> pdb=" O TYR M 136 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL M 138 " --> pdb=" O GLN M 92 " (cutoff:3.500A) removed outlier: 5.384A pdb=" N LYS M 94 " --> pdb=" O VAL M 138 " (cutoff:3.500A) removed outlier: 5.930A pdb=" N LEU M 140 " --> pdb=" O LYS M 94 " (cutoff:3.500A) removed outlier: 5.980A pdb=" N LEU M 96 " --> pdb=" O LEU M 140 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'M' and resid 153 through 154 Processing sheet with id=AB9, first strand: chain 'M' and resid 274 through 276 Processing sheet with id=AC1, first strand: chain 'N' and resid 119 through 122 removed outlier: 6.710A pdb=" N ILE N 89 " --> pdb=" O VAL N 160 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N GLU N 162 " --> pdb=" O PHE N 87 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N PHE N 87 " --> pdb=" O GLU N 162 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 95 through 97 removed outlier: 5.387A pdb=" N ILE N 147 " --> pdb=" O ARG N 133 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ARG N 133 " --> pdb=" O ILE N 147 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N HIS N 149 " --> pdb=" O ILE N 131 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'N' and resid 241 through 242 Processing sheet with id=AC4, first strand: chain 'O' and resid 41 through 45 removed outlier: 4.668A pdb=" N MET O 120 " --> pdb=" O ILE O 110 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE O 110 " --> pdb=" O MET O 120 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 47 through 48 removed outlier: 4.227A pdb=" N PHE W 142 " --> pdb=" O PHE P 48 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N PHE W 142 " --> pdb=" O VAL 6 345 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N VAL 6 345 " --> pdb=" O PHE W 142 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N LEU W 144 " --> pdb=" O GLU 6 343 " (cutoff:3.500A) removed outlier: 7.526A pdb=" N GLU 6 343 " --> pdb=" O LEU W 144 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ALA W 146 " --> pdb=" O VAL 6 341 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'P' and resid 79 through 85 removed outlier: 6.612A pdb=" N HIS P 96 " --> pdb=" O VAL P 101 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N VAL P 101 " --> pdb=" O HIS P 96 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'Q' and resid 158 through 165 removed outlier: 7.092A pdb=" N THR Q 148 " --> pdb=" O ARG Q 140 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ARG Q 140 " --> pdb=" O THR Q 148 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE Q 150 " --> pdb=" O ILE Q 138 " (cutoff:3.500A) removed outlier: 6.265A pdb=" N VAL Q 154 " --> pdb=" O LEU Q 134 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N LEU Q 134 " --> pdb=" O VAL Q 154 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ARG Q 118 " --> pdb=" O VAL Q 176 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N VAL Q 176 " --> pdb=" O ARG Q 118 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N THR Q 120 " --> pdb=" O ILE Q 174 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N ILE Q 174 " --> pdb=" O THR Q 120 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'S' and resid 106 through 109 removed outlier: 7.579A pdb=" N LEU S 134 " --> pdb=" O GLY S 145 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'S' and resid 113 through 116 removed outlier: 3.789A pdb=" N GLU S 162 " --> pdb=" O VAL S 192 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ARG S 194 " --> pdb=" O VAL S 160 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VAL S 160 " --> pdb=" O ARG S 194 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'S' and resid 113 through 116 removed outlier: 3.789A pdb=" N GLU S 162 " --> pdb=" O VAL S 192 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ARG S 194 " --> pdb=" O VAL S 160 " (cutoff:3.500A) removed outlier: 5.471A pdb=" N VAL S 160 " --> pdb=" O ARG S 194 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'S' and resid 169 through 175 removed outlier: 4.232A pdb=" N PHE S 180 " --> pdb=" O ARG S 175 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'T' and resid 72 through 77 removed outlier: 6.409A pdb=" N HIS T 173 " --> pdb=" O SER T 147 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N SER T 147 " --> pdb=" O HIS T 173 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N PHE T 175 " --> pdb=" O SER T 145 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER T 145 " --> pdb=" O PHE T 175 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LYS T 177 " --> pdb=" O ALA T 143 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 153 through 158 Processing sheet with id=AD5, first strand: chain 'U' and resid 18 through 19 removed outlier: 3.762A pdb=" N VAL U 19 " --> pdb=" O GLU 9 59 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'U' and resid 27 through 28 removed outlier: 3.743A pdb=" N LYS U 93 " --> pdb=" O ILE U 44 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'V' and resid 85 through 88 removed outlier: 3.746A pdb=" N VAL V 87 " --> pdb=" O GLN V 78 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N GLN V 78 " --> pdb=" O VAL V 87 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'V' and resid 93 through 98 Processing sheet with id=AD9, first strand: chain 'V' and resid 145 through 146 removed outlier: 3.947A pdb=" N ARG V 145 " --> pdb=" O ILE V 154 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'V' and resid 176 through 177 Processing sheet with id=AE2, first strand: chain 'V' and resid 214 through 215 Processing sheet with id=AE3, first strand: chain 'W' and resid 65 through 68 removed outlier: 3.593A pdb=" N ASN W 65 " --> pdb=" O ALA W 91 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N LEU W 89 " --> pdb=" O ILE W 67 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'W' and resid 76 through 77 Processing sheet with id=AE5, first strand: chain 'X' and resid 50 through 51 Processing sheet with id=AE6, first strand: chain 'X' and resid 86 through 91 Processing sheet with id=AE7, first strand: chain 'X' and resid 110 through 116 Processing sheet with id=AE8, first strand: chain 'Y' and resid 166 through 170 Processing sheet with id=AE9, first strand: chain 'Z' and resid 98 through 101 Processing sheet with id=AF1, first strand: chain 'Z' and resid 138 through 139 Processing sheet with id=AF2, first strand: chain '0' and resid 107 through 110 Processing sheet with id=AF3, first strand: chain '0' and resid 156 through 159 removed outlier: 3.608A pdb=" N ILE 0 175 " --> pdb=" O VAL 0 157 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain '1' and resid 30 through 35 removed outlier: 5.862A pdb=" N ARG 1 19 " --> pdb=" O LYS 1 61 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N LYS 1 61 " --> pdb=" O ARG 1 19 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain '1' and resid 42 through 47 Processing sheet with id=AF6, first strand: chain '3' and resid 115 through 116 Processing sheet with id=AF7, first strand: chain '5' and resid 104 through 106 Processing sheet with id=AF8, first strand: chain '5' and resid 126 through 130 removed outlier: 5.397A pdb=" N LYS 5 127 " --> pdb=" O ALA 5 374 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N VAL 5 376 " --> pdb=" O LYS 5 127 " (cutoff:3.500A) removed outlier: 5.750A pdb=" N ILE 5 129 " --> pdb=" O VAL 5 376 " (cutoff:3.500A) removed outlier: 8.162A pdb=" N THR 5 361 " --> pdb=" O GLN 5 338 " (cutoff:3.500A) removed outlier: 10.662A pdb=" N GLN 5 338 " --> pdb=" O THR 5 361 " (cutoff:3.500A) removed outlier: 12.632A pdb=" N TYR 5 287 " --> pdb=" O PRO 5 339 " (cutoff:3.500A) removed outlier: 9.793A pdb=" N VAL 5 341 " --> pdb=" O TYR 5 287 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N HIS 5 289 " --> pdb=" O VAL 5 341 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLN 5 343 " --> pdb=" O HIS 5 289 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N LEU 5 230 " --> pdb=" O HIS 5 289 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain '5' and resid 207 through 215 Processing sheet with id=AG1, first strand: chain '5' and resid 385 through 387 Processing sheet with id=AG2, first strand: chain '6' and resid 184 through 187 removed outlier: 4.314A pdb=" N VAL 6 175 " --> pdb=" O VAL 6 187 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain '6' and resid 191 through 192 removed outlier: 6.798A pdb=" N ASN 6 191 " --> pdb=" O GLN 6 320 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR 6 312 " --> pdb=" O LYS 6 274 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N LEU 6 272 " --> pdb=" O ALA 6 314 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N LEU 6 316 " --> pdb=" O PHE 6 270 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N PHE 6 270 " --> pdb=" O LEU 6 316 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N PHE 6 318 " --> pdb=" O LEU 6 268 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N LEU 6 268 " --> pdb=" O PHE 6 318 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLN 6 320 " --> pdb=" O HIS 6 266 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N HIS 6 266 " --> pdb=" O GLN 6 320 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N LEU 6 216 " --> pdb=" O LEU 6 236 " (cutoff:3.500A) removed outlier: 4.406A pdb=" N LEU 6 236 " --> pdb=" O LEU 6 216 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N LEU 6 218 " --> pdb=" O HIS 6 234 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR 6 232 " --> pdb=" O SER 6 220 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain '7' and resid 111 through 114 removed outlier: 8.102A pdb=" N ILE 7 125 " --> pdb=" O GLU 7 66 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N LYS 7 68 " --> pdb=" O ILE 7 125 " (cutoff:3.500A) removed outlier: 8.671A pdb=" N PHE 7 127 " --> pdb=" O LYS 7 68 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL 7 78 " --> pdb=" O ILE d 282 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain '7' and resid 164 through 168 removed outlier: 7.252A pdb=" N ASP 7 182 " --> pdb=" O VAL 7 167 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL 7 300 " --> pdb=" O VAL 7 280 " (cutoff:3.500A) removed outlier: 5.079A pdb=" N VAL 7 280 " --> pdb=" O VAL 7 300 " (cutoff:3.500A) removed outlier: 7.497A pdb=" N LEU 7 302 " --> pdb=" O TYR 7 278 " (cutoff:3.500A) removed outlier: 5.530A pdb=" N TYR 7 278 " --> pdb=" O LEU 7 302 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain '7' and resid 217 through 222 Processing sheet with id=AG7, first strand: chain '9' and resid 42 through 45 Processing sheet with id=AG8, first strand: chain 'a' and resid 73 through 74 removed outlier: 5.477A pdb=" N SER c 255 " --> pdb=" O TYR c 275 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TYR c 275 " --> pdb=" O SER c 255 " (cutoff:3.500A) removed outlier: 5.245A pdb=" N LEU c 257 " --> pdb=" O GLY c 273 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N GLY c 273 " --> pdb=" O LEU c 257 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ARG c 259 " --> pdb=" O PHE c 271 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N TYR c 270 " --> pdb=" O PRO c 285 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N VAL c 272 " --> pdb=" O GLU c 283 " (cutoff:3.500A) removed outlier: 4.461A pdb=" N GLU c 283 " --> pdb=" O VAL c 272 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU c 274 " --> pdb=" O ILE c 281 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE c 281 " --> pdb=" O LEU c 274 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LYS c 279 " --> pdb=" O CYS c 276 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 8 through 9 Processing sheet with id=AH1, first strand: chain 'b' and resid 84 through 87 removed outlier: 3.559A pdb=" N ARG b 74 " --> pdb=" O SER b 32 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ILE b 63 " --> pdb=" O LYS h 153 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'd' and resid 184 through 198 removed outlier: 12.626A pdb=" N SER d 188 " --> pdb=" O THR d 221 " (cutoff:3.500A) removed outlier: 12.845A pdb=" N THR d 221 " --> pdb=" O SER d 188 " (cutoff:3.500A) removed outlier: 9.531A pdb=" N GLU d 190 " --> pdb=" O ARG d 219 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ARG d 219 " --> pdb=" O GLU d 190 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N SER d 192 " --> pdb=" O HIS d 217 " (cutoff:3.500A) removed outlier: 7.678A pdb=" N HIS d 217 " --> pdb=" O SER d 192 " (cutoff:3.500A) removed outlier: 5.662A pdb=" N VAL d 194 " --> pdb=" O ARG d 215 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N ARG d 215 " --> pdb=" O VAL d 194 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N GLN d 196 " --> pdb=" O THR d 213 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR d 213 " --> pdb=" O GLN d 196 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N TYR d 245 " --> pdb=" O ILE d 265 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N GLU d 249 " --> pdb=" O MET d 261 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N MET d 261 " --> pdb=" O GLU d 249 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'd' and resid 224 through 225 removed outlier: 7.211A pdb=" N ILE d 224 " --> pdb=" O MET d 232 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'g' and resid 96 through 101 Processing sheet with id=AH5, first strand: chain 'p' and resid 77 through 81 removed outlier: 3.971A pdb=" N LYS p 98 " --> pdb=" O CYS p 81 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N SER p 97 " --> pdb=" O SER p 139 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N SER p 139 " --> pdb=" O SER p 97 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 's' and resid 206 through 210 removed outlier: 6.371A pdb=" N TYR s 91 " --> pdb=" O GLN s 232 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N ASP s 234 " --> pdb=" O TYR s 91 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 's' and resid 112 through 116 removed outlier: 6.425A pdb=" N HIS s 296 " --> pdb=" O GLN s 358 " (cutoff:3.500A) removed outlier: 8.188A pdb=" N VAL s 360 " --> pdb=" O HIS s 296 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLN s 298 " --> pdb=" O VAL s 360 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N THR s 362 " --> pdb=" O GLN s 298 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N HIS s 300 " --> pdb=" O THR s 362 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N ILE s 241 " --> pdb=" O HIS s 296 " (cutoff:3.500A) removed outlier: 4.985A pdb=" N GLN s 298 " --> pdb=" O ASN s 239 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N ASN s 239 " --> pdb=" O GLN s 298 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 's' and resid 112 through 116 Processing sheet with id=AH9, first strand: chain 's' and resid 215 through 216 Processing sheet with id=AI1, first strand: chain 's' and resid 404 through 405 Processing sheet with id=AI2, first strand: chain 'u' and resid 108 through 113 2179 hydrogen bonds defined for protein. 6045 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 738 hydrogen bonds 1288 hydrogen bond angles 0 basepair planarities 303 basepair parallelities 546 stacking parallelities Total time for adding SS restraints: 46.03 Time building geometry restraints manager: 31.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 19475 1.33 - 1.46: 26332 1.46 - 1.58: 39292 1.58 - 1.70: 2348 1.70 - 1.83: 392 Bond restraints: 87839 Sorted by residual: bond pdb=" C HIS 6 373 " pdb=" N GLU 6 374 " ideal model delta sigma weight residual 1.330 1.264 0.066 1.47e-02 4.63e+03 2.03e+01 bond pdb=" C MET M 204 " pdb=" N LEU M 205 " ideal model delta sigma weight residual 1.331 1.289 0.042 1.48e-02 4.57e+03 7.98e+00 bond pdb=" C HIS 2 64 " pdb=" N GLY 2 65 " ideal model delta sigma weight residual 1.334 1.299 0.035 1.52e-02 4.33e+03 5.38e+00 bond pdb=" C PRO 5 76 " pdb=" N PRO 5 77 " ideal model delta sigma weight residual 1.332 1.357 -0.025 1.12e-02 7.97e+03 4.99e+00 bond pdb=" C GLU D 199 " pdb=" N PRO D 200 " ideal model delta sigma weight residual 1.332 1.355 -0.023 1.12e-02 7.97e+03 4.31e+00 ... (remaining 87834 not shown) Histogram of bond angle deviations from ideal: 98.06 - 105.48: 7155 105.48 - 112.90: 48128 112.90 - 120.32: 35714 120.32 - 127.75: 30484 127.75 - 135.17: 2948 Bond angle restraints: 124429 Sorted by residual: angle pdb=" N ILE g 57 " pdb=" CA ILE g 57 " pdb=" C ILE g 57 " ideal model delta sigma weight residual 109.02 105.34 3.68 9.30e-01 1.16e+00 1.56e+01 angle pdb=" C3' C A3168 " pdb=" O3' C A3168 " pdb=" P C A3169 " ideal model delta sigma weight residual 120.20 126.05 -5.85 1.50e+00 4.44e-01 1.52e+01 angle pdb=" C4' C A3168 " pdb=" C3' C A3168 " pdb=" O3' C A3168 " ideal model delta sigma weight residual 109.40 114.85 -5.45 1.50e+00 4.44e-01 1.32e+01 angle pdb=" N GLY 5 116 " pdb=" CA GLY 5 116 " pdb=" C GLY 5 116 " ideal model delta sigma weight residual 111.21 114.95 -3.74 1.04e+00 9.25e-01 1.29e+01 angle pdb=" C3' C A2414 " pdb=" O3' C A2414 " pdb=" P C A2415 " ideal model delta sigma weight residual 120.20 125.50 -5.30 1.50e+00 4.44e-01 1.25e+01 ... (remaining 124424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.98: 50630 35.98 - 71.96: 2996 71.96 - 107.94: 384 107.94 - 143.92: 15 143.92 - 179.90: 23 Dihedral angle restraints: 54048 sinusoidal: 33315 harmonic: 20733 Sorted by residual: dihedral pdb=" O4' C A2379 " pdb=" C1' C A2379 " pdb=" N1 C A2379 " pdb=" C2 C A2379 " ideal model delta sinusoidal sigma weight residual -160.00 19.61 -179.61 1 1.50e+01 4.44e-03 8.53e+01 dihedral pdb=" O4' C A1689 " pdb=" C1' C A1689 " pdb=" N1 C A1689 " pdb=" C2 C A1689 " ideal model delta sinusoidal sigma weight residual 200.00 27.19 172.81 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' C A3169 " pdb=" C1' C A3169 " pdb=" N1 C A3169 " pdb=" C2 C A3169 " ideal model delta sinusoidal sigma weight residual 200.00 29.21 170.79 1 1.50e+01 4.44e-03 8.48e+01 ... (remaining 54045 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 11650 0.051 - 0.103: 2294 0.103 - 0.154: 524 0.154 - 0.205: 31 0.205 - 0.257: 7 Chirality restraints: 14506 Sorted by residual: chirality pdb=" C1' A A1853 " pdb=" O4' A A1853 " pdb=" C2' A A1853 " pdb=" N9 A A1853 " both_signs ideal model delta sigma weight residual False 2.46 2.20 0.26 2.00e-01 2.50e+01 1.65e+00 chirality pdb=" C3' A A2457 " pdb=" C4' A A2457 " pdb=" O3' A A2457 " pdb=" C2' A A2457 " both_signs ideal model delta sigma weight residual False -2.74 -2.50 -0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" C3' C A3168 " pdb=" C4' C A3168 " pdb=" O3' C A3168 " pdb=" C2' C A3168 " both_signs ideal model delta sigma weight residual False -2.74 -2.50 -0.25 2.00e-01 2.50e+01 1.52e+00 ... (remaining 14503 not shown) Planarity restraints: 11588 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS Q 225 " -0.055 5.00e-02 4.00e+02 8.27e-02 1.09e+01 pdb=" N PRO Q 226 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO Q 226 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO Q 226 " -0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G A2697 " 0.042 2.00e-02 2.50e+03 1.89e-02 1.07e+01 pdb=" N9 G A2697 " -0.048 2.00e-02 2.50e+03 pdb=" C8 G A2697 " -0.005 2.00e-02 2.50e+03 pdb=" N7 G A2697 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G A2697 " -0.002 2.00e-02 2.50e+03 pdb=" C6 G A2697 " 0.005 2.00e-02 2.50e+03 pdb=" O6 G A2697 " 0.011 2.00e-02 2.50e+03 pdb=" N1 G A2697 " 0.005 2.00e-02 2.50e+03 pdb=" C2 G A2697 " 0.001 2.00e-02 2.50e+03 pdb=" N2 G A2697 " -0.004 2.00e-02 2.50e+03 pdb=" N3 G A2697 " -0.005 2.00e-02 2.50e+03 pdb=" C4 G A2697 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A A2239 " 0.042 2.00e-02 2.50e+03 1.97e-02 1.06e+01 pdb=" N9 A A2239 " -0.047 2.00e-02 2.50e+03 pdb=" C8 A A2239 " -0.004 2.00e-02 2.50e+03 pdb=" N7 A A2239 " -0.000 2.00e-02 2.50e+03 pdb=" C5 A A2239 " 0.001 2.00e-02 2.50e+03 pdb=" C6 A A2239 " 0.006 2.00e-02 2.50e+03 pdb=" N6 A A2239 " 0.011 2.00e-02 2.50e+03 pdb=" N1 A A2239 " 0.004 2.00e-02 2.50e+03 pdb=" C2 A A2239 " -0.011 2.00e-02 2.50e+03 pdb=" N3 A A2239 " -0.002 2.00e-02 2.50e+03 pdb=" C4 A A2239 " -0.001 2.00e-02 2.50e+03 ... (remaining 11585 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 916 2.54 - 3.13: 64969 3.13 - 3.72: 138268 3.72 - 4.31: 188136 4.31 - 4.90: 294333 Nonbonded interactions: 686622 Sorted by model distance: nonbonded pdb=" O LYS X 96 " pdb=" O2' U A1728 " model vdw 1.954 2.440 nonbonded pdb=" O2' A A1718 " pdb=" O2' C A1911 " model vdw 1.988 2.440 nonbonded pdb=" O2 U A2093 " pdb=" O2' U A2266 " model vdw 1.988 2.440 nonbonded pdb=" OD1 ASN j 36 " pdb=" OG SER j 38 " model vdw 1.989 2.440 nonbonded pdb=" OE2 GLU W 57 " pdb=" O2' G A2063 " model vdw 1.990 2.440 ... (remaining 686617 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: 4.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 13.220 Check model and map are aligned: 0.940 Set scattering table: 0.580 Process input model: 206.270 Find NCS groups from input model: 2.360 Set up NCS constraints: 0.260 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 230.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5652 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 : 0.006 0.072 87839 Z= 0.370 Angle : 0.776 11.936 124429 Z= 0.409 Chirality : 0.044 0.257 14506 Planarity : 0.006 0.083 11588 Dihedral : 19.925 179.901 40628 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 4.29 % Allowed : 10.01 % Favored : 85.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.10), residues: 6987 helix: -0.56 (0.10), residues: 2258 sheet: -1.21 (0.17), residues: 815 loop : -1.71 (0.10), residues: 3914 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP s 210 HIS 0.008 0.001 HIS o 62 PHE 0.023 0.002 PHE 5 60 TYR 0.027 0.002 TYR 5 176 ARG 0.007 0.001 ARG 9 25 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1149 residues out of total 6293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 269 poor density : 880 time to evaluate : 6.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 140 PHE cc_start: 0.5646 (OUTLIER) cc_final: 0.5206 (m-10) REVERT: L 74 LEU cc_start: 0.6480 (mt) cc_final: 0.6070 (mt) REVERT: L 130 ARG cc_start: 0.3075 (OUTLIER) cc_final: 0.2402 (tpt170) REVERT: V 102 MET cc_start: -0.0143 (mmt) cc_final: -0.2745 (ttt) REVERT: V 108 MET cc_start: 0.3375 (ttt) cc_final: 0.2748 (ttp) REVERT: V 126 MET cc_start: 0.6780 (tmm) cc_final: 0.6531 (tmm) REVERT: 2 56 SER cc_start: 0.7636 (OUTLIER) cc_final: 0.6664 (p) REVERT: b 48 GLU cc_start: 0.5039 (OUTLIER) cc_final: 0.4597 (mm-30) REVERT: i 80 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6538 (pp) outliers start: 269 outliers final: 88 residues processed: 1108 average time/residue: 0.8377 time to fit residues: 1548.7673 Evaluate side-chains 614 residues out of total 6293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 521 time to evaluate : 7.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 45 SER Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 242 LEU Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 130 VAL Chi-restraints excluded: chain H residue 140 PHE Chi-restraints excluded: chain K residue 115 ASN Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain L residue 130 ARG Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 183 SER Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain O residue 158 GLN Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain S residue 124 CYS Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 162 GLU Chi-restraints excluded: chain S residue 171 ILE Chi-restraints excluded: chain S residue 197 SER Chi-restraints excluded: chain U residue 94 VAL Chi-restraints excluded: chain V residue 200 GLU Chi-restraints excluded: chain X residue 11 TRP Chi-restraints excluded: chain X residue 95 ASP Chi-restraints excluded: chain X residue 137 GLU Chi-restraints excluded: chain X residue 220 GLU Chi-restraints excluded: chain Z residue 119 ILE Chi-restraints excluded: chain 0 residue 96 ASN Chi-restraints excluded: chain 0 residue 110 CYS Chi-restraints excluded: chain 2 residue 56 SER Chi-restraints excluded: chain 3 residue 146 GLU Chi-restraints excluded: chain 3 residue 162 THR Chi-restraints excluded: chain 3 residue 164 SER Chi-restraints excluded: chain 5 residue 175 THR Chi-restraints excluded: chain 5 residue 272 ASP Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 5 residue 324 GLN Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 6 residue 50 LYS Chi-restraints excluded: chain 6 residue 64 GLU Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 192 GLU Chi-restraints excluded: chain 6 residue 298 PHE Chi-restraints excluded: chain 6 residue 322 ARG Chi-restraints excluded: chain 6 residue 334 LEU Chi-restraints excluded: chain 7 residue 96 SER Chi-restraints excluded: chain 9 residue 29 SER Chi-restraints excluded: chain 9 residue 39 LYS Chi-restraints excluded: chain a residue 53 SER Chi-restraints excluded: chain a residue 64 SER Chi-restraints excluded: chain b residue 48 GLU Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain b residue 58 ASN Chi-restraints excluded: chain b residue 119 PHE Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 198 VAL Chi-restraints excluded: chain g residue 89 SER Chi-restraints excluded: chain g residue 105 ARG Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain h residue 91 LEU Chi-restraints excluded: chain h residue 146 SER Chi-restraints excluded: chain h residue 158 TYR Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain o residue 28 SER Chi-restraints excluded: chain o residue 54 MET Chi-restraints excluded: chain o residue 74 ILE Chi-restraints excluded: chain p residue 185 ARG Chi-restraints excluded: chain p residue 187 ARG Chi-restraints excluded: chain q residue 74 SER Chi-restraints excluded: chain r residue 56 THR Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 87 LEU Chi-restraints excluded: chain r residue 196 HIS Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 229 LEU Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 371 CYS Chi-restraints excluded: chain s residue 376 THR Chi-restraints excluded: chain s residue 401 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 682 optimal weight: 50.0000 chunk 612 optimal weight: 9.9990 chunk 339 optimal weight: 8.9990 chunk 209 optimal weight: 9.9990 chunk 413 optimal weight: 7.9990 chunk 327 optimal weight: 7.9990 chunk 633 optimal weight: 7.9990 chunk 245 optimal weight: 7.9990 chunk 385 optimal weight: 40.0000 chunk 471 optimal weight: 10.0000 chunk 733 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 235 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 117 HIS E 174 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 26 ASN N 173 GLN N 237 HIS ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 239 ASN R 22 GLN R 27 HIS R 77 GLN ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 ASN ** V 78 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 80 HIS X 94 ASN Y 89 GLN Y 183 GLN ** 0 170 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 45 HIS 2 57 ASN ** 6 191 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 359 HIS ** a 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 90 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 123 GLN h 135 GLN i 59 ASN ** o 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 46 HIS o 91 GLN ** p 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 296 HIS u 105 ASN ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** w 115 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5831 moved from start: 0.2142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 87839 Z= 0.332 Angle : 0.739 12.813 124429 Z= 0.376 Chirality : 0.042 0.307 14506 Planarity : 0.006 0.075 11588 Dihedral : 21.028 178.755 25767 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.58 % Favored : 94.42 % Rotamer: Outliers : 3.33 % Allowed : 15.74 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.10), residues: 6987 helix: -0.05 (0.10), residues: 2338 sheet: -0.96 (0.17), residues: 858 loop : -1.31 (0.10), residues: 3791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP u 167 HIS 0.019 0.001 HIS u 148 PHE 0.022 0.002 PHE K 166 TYR 0.028 0.002 TYR R 39 ARG 0.015 0.001 ARG M 91 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 6293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 209 poor density : 523 time to evaluate : 6.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: V 102 MET cc_start: -0.0491 (mmt) cc_final: -0.2901 (ttt) REVERT: V 108 MET cc_start: 0.3425 (ttt) cc_final: 0.2866 (ttp) REVERT: a 75 ILE cc_start: 0.6057 (OUTLIER) cc_final: 0.4847 (mm) REVERT: i 128 ARG cc_start: 0.4188 (OUTLIER) cc_final: 0.3738 (ptp90) REVERT: q 131 MET cc_start: 0.5949 (ppp) cc_final: 0.5184 (ppp) REVERT: s 89 MET cc_start: 0.5940 (tpp) cc_final: 0.5628 (mmm) outliers start: 209 outliers final: 110 residues processed: 691 average time/residue: 0.8204 time to fit residues: 971.2017 Evaluate side-chains 567 residues out of total 6293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 112 poor density : 455 time to evaluate : 6.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 96 LEU Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 133 THR Chi-restraints excluded: chain F residue 159 THR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain N residue 173 GLN Chi-restraints excluded: chain O residue 33 LEU Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 98 LYS Chi-restraints excluded: chain P residue 49 THR Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 18 TYR Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 91 GLN Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 162 GLU Chi-restraints excluded: chain T residue 98 SER Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 193 VAL Chi-restraints excluded: chain U residue 89 LYS Chi-restraints excluded: chain V residue 194 LEU Chi-restraints excluded: chain V residue 200 GLU Chi-restraints excluded: chain W residue 73 PHE Chi-restraints excluded: chain X residue 95 ASP Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 124 LEU Chi-restraints excluded: chain 0 residue 96 ASN Chi-restraints excluded: chain 0 residue 110 CYS Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 1 residue 41 LEU Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 3 residue 162 THR Chi-restraints excluded: chain 3 residue 164 SER Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 5 residue 175 THR Chi-restraints excluded: chain 5 residue 272 ASP Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 5 residue 324 GLN Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain 6 residue 50 LYS Chi-restraints excluded: chain 6 residue 64 GLU Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 322 ARG Chi-restraints excluded: chain 6 residue 334 LEU Chi-restraints excluded: chain 7 residue 161 GLU Chi-restraints excluded: chain 7 residue 287 GLN Chi-restraints excluded: chain 9 residue 29 SER Chi-restraints excluded: chain a residue 53 SER Chi-restraints excluded: chain a residue 75 ILE Chi-restraints excluded: chain b residue 50 GLU Chi-restraints excluded: chain b residue 58 ASN Chi-restraints excluded: chain b residue 76 VAL Chi-restraints excluded: chain b residue 119 PHE Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain c residue 32 LYS Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 100 SER Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 246 LYS Chi-restraints excluded: chain c residue 249 ASN Chi-restraints excluded: chain g residue 89 SER Chi-restraints excluded: chain g residue 105 ARG Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain h residue 93 ASP Chi-restraints excluded: chain h residue 158 TYR Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain i residue 80 LEU Chi-restraints excluded: chain i residue 128 ARG Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 54 MET Chi-restraints excluded: chain o residue 90 ASP Chi-restraints excluded: chain p residue 74 ASP Chi-restraints excluded: chain q residue 102 SER Chi-restraints excluded: chain r residue 56 THR Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 87 LEU Chi-restraints excluded: chain r residue 172 VAL Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 182 SER Chi-restraints excluded: chain s residue 229 LEU Chi-restraints excluded: chain s residue 234 ASP Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 371 CYS Chi-restraints excluded: chain s residue 376 THR Chi-restraints excluded: chain s residue 401 LEU Chi-restraints excluded: chain u residue 136 HIS Chi-restraints excluded: chain v residue 49 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 407 optimal weight: 20.0000 chunk 227 optimal weight: 7.9990 chunk 610 optimal weight: 10.0000 chunk 499 optimal weight: 20.0000 chunk 202 optimal weight: 10.0000 chunk 735 optimal weight: 20.0000 chunk 794 optimal weight: 50.0000 chunk 654 optimal weight: 40.0000 chunk 728 optimal weight: 20.0000 chunk 250 optimal weight: 8.9990 chunk 589 optimal weight: 20.0000 overall best weight: 11.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 227 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 294 ASN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 276 GLN K 40 GLN ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 173 GLN N 210 GLN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 239 ASN ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 23 ASN ** V 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 41 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 108 HIS ** 6 292 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 26 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 105 GLN ** o 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5985 moved from start: 0.3345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.114 87839 Z= 0.419 Angle : 0.766 12.942 124429 Z= 0.389 Chirality : 0.043 0.407 14506 Planarity : 0.006 0.075 11588 Dihedral : 21.214 178.682 25692 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 22.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.53 % Favored : 93.47 % Rotamer: Outliers : 4.56 % Allowed : 16.31 % Favored : 79.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.10), residues: 6987 helix: -0.06 (0.10), residues: 2367 sheet: -1.17 (0.16), residues: 934 loop : -1.16 (0.10), residues: 3686 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP V 85 HIS 0.013 0.002 HIS u 148 PHE 0.035 0.002 PHE N 169 TYR 0.037 0.002 TYR R 39 ARG 0.014 0.001 ARG V 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 743 residues out of total 6293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 286 poor density : 457 time to evaluate : 6.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 220 LYS cc_start: 0.4950 (mtmt) cc_final: 0.4592 (mtmt) REVERT: H 97 ILE cc_start: 0.6740 (OUTLIER) cc_final: 0.6443 (mt) REVERT: N 118 MET cc_start: 0.7317 (mmt) cc_final: 0.6813 (mmt) REVERT: N 251 VAL cc_start: 0.5578 (OUTLIER) cc_final: 0.5286 (t) REVERT: V 102 MET cc_start: -0.0647 (mmt) cc_final: -0.3150 (ttt) REVERT: 0 185 PHE cc_start: 0.5461 (OUTLIER) cc_final: 0.5131 (t80) REVERT: d 129 ASP cc_start: 0.3997 (OUTLIER) cc_final: 0.3567 (p0) REVERT: q 131 MET cc_start: 0.6115 (ppp) cc_final: 0.5652 (ppp) REVERT: u 177 ILE cc_start: 0.7886 (OUTLIER) cc_final: 0.7644 (tp) REVERT: v 10 LEU cc_start: 0.7924 (mt) cc_final: 0.7703 (mt) REVERT: w 120 MET cc_start: 0.5763 (mmt) cc_final: 0.5490 (mmp) outliers start: 286 outliers final: 145 residues processed: 705 average time/residue: 0.7613 time to fit residues: 937.2813 Evaluate side-chains 560 residues out of total 6293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 410 time to evaluate : 5.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 208 ARG Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 204 VAL Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 318 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain H residue 96 LEU Chi-restraints excluded: chain H residue 97 ILE Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 115 ASN Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 251 VAL Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 98 LYS Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 127 SER Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 196 GLU Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 18 TYR Chi-restraints excluded: chain R residue 73 THR Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 112 THR Chi-restraints excluded: chain R residue 143 SER Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 91 GLN Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain S residue 162 GLU Chi-restraints excluded: chain T residue 167 MET Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 193 VAL Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 89 LYS Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain V residue 194 LEU Chi-restraints excluded: chain V residue 200 GLU Chi-restraints excluded: chain W residue 73 PHE Chi-restraints excluded: chain W residue 97 VAL Chi-restraints excluded: chain X residue 95 ASP Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 97 ASP Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain 0 residue 96 ASN Chi-restraints excluded: chain 0 residue 110 CYS Chi-restraints excluded: chain 0 residue 112 GLU Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 185 PHE Chi-restraints excluded: chain 1 residue 41 LEU Chi-restraints excluded: chain 3 residue 94 LEU Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 3 residue 113 ARG Chi-restraints excluded: chain 3 residue 151 ASN Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 5 residue 272 ASP Chi-restraints excluded: chain 5 residue 324 GLN Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain 6 residue 64 GLU Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 197 GLU Chi-restraints excluded: chain 6 residue 322 ARG Chi-restraints excluded: chain 6 residue 334 LEU Chi-restraints excluded: chain 6 residue 376 THR Chi-restraints excluded: chain 7 residue 100 CYS Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 132 ASP Chi-restraints excluded: chain 7 residue 211 TYR Chi-restraints excluded: chain 9 residue 29 SER Chi-restraints excluded: chain 9 residue 66 THR Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 58 ASN Chi-restraints excluded: chain b residue 119 PHE Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain c residue 32 LYS Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 100 SER Chi-restraints excluded: chain c residue 138 THR Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 198 VAL Chi-restraints excluded: chain c residue 211 THR Chi-restraints excluded: chain c residue 249 ASN Chi-restraints excluded: chain d residue 129 ASP Chi-restraints excluded: chain d residue 164 VAL Chi-restraints excluded: chain d residue 181 VAL Chi-restraints excluded: chain g residue 89 SER Chi-restraints excluded: chain g residue 105 ARG Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain g residue 143 VAL Chi-restraints excluded: chain h residue 91 LEU Chi-restraints excluded: chain h residue 93 ASP Chi-restraints excluded: chain h residue 118 HIS Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain j residue 97 LYS Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 54 MET Chi-restraints excluded: chain o residue 59 GLU Chi-restraints excluded: chain o residue 90 ASP Chi-restraints excluded: chain p residue 74 ASP Chi-restraints excluded: chain p residue 183 MET Chi-restraints excluded: chain q residue 102 SER Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 87 LEU Chi-restraints excluded: chain r residue 117 GLU Chi-restraints excluded: chain r residue 148 ASN Chi-restraints excluded: chain r residue 196 HIS Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 181 VAL Chi-restraints excluded: chain s residue 182 SER Chi-restraints excluded: chain s residue 229 LEU Chi-restraints excluded: chain s residue 234 ASP Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 331 SER Chi-restraints excluded: chain s residue 371 CYS Chi-restraints excluded: chain s residue 376 THR Chi-restraints excluded: chain u residue 136 HIS Chi-restraints excluded: chain u residue 177 ILE Chi-restraints excluded: chain v residue 65 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 726 optimal weight: 20.0000 chunk 552 optimal weight: 0.9990 chunk 381 optimal weight: 5.9990 chunk 81 optimal weight: 10.0000 chunk 350 optimal weight: 9.9990 chunk 493 optimal weight: 20.0000 chunk 737 optimal weight: 10.0000 chunk 781 optimal weight: 40.0000 chunk 385 optimal weight: 9.9990 chunk 699 optimal weight: 10.0000 chunk 210 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 113 ASN M 53 HIS N 173 GLN ** N 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 239 ASN ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 41 ASN W 72 HIS Y 189 HIS Z 126 GLN ** Z 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 165 GLN ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 292 GLN ** 6 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 361 GLN a 71 HIS ** a 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 129 GLN ** b 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 87 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5945 moved from start: 0.3632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 87839 Z= 0.283 Angle : 0.669 12.698 124429 Z= 0.338 Chirality : 0.040 0.347 14506 Planarity : 0.005 0.078 11588 Dihedral : 21.190 179.080 25661 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 19.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 3.48 % Allowed : 18.32 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.91 (0.10), residues: 6987 helix: 0.29 (0.11), residues: 2361 sheet: -1.07 (0.17), residues: 910 loop : -1.03 (0.10), residues: 3716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP i 47 HIS 0.009 0.001 HIS W 72 PHE 0.024 0.002 PHE Q 164 TYR 0.027 0.002 TYR R 39 ARG 0.013 0.000 ARG j 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 663 residues out of total 6293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 445 time to evaluate : 6.045 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 220 LYS cc_start: 0.4642 (mtmt) cc_final: 0.4353 (mtmt) REVERT: L 130 ARG cc_start: 0.4152 (OUTLIER) cc_final: 0.1980 (tpt170) REVERT: N 118 MET cc_start: 0.7296 (mmt) cc_final: 0.6924 (mmt) REVERT: V 102 MET cc_start: -0.0645 (mmt) cc_final: -0.3216 (ttt) REVERT: 0 185 PHE cc_start: 0.5157 (OUTLIER) cc_final: 0.4882 (t80) REVERT: 3 113 ARG cc_start: 0.6408 (OUTLIER) cc_final: 0.4314 (mpt-90) REVERT: 5 362 THR cc_start: 0.7382 (OUTLIER) cc_final: 0.7060 (m) REVERT: i 128 ARG cc_start: 0.4462 (OUTLIER) cc_final: 0.3499 (ptt-90) REVERT: q 131 MET cc_start: 0.5963 (ppp) cc_final: 0.5243 (ppp) REVERT: r 123 HIS cc_start: 0.5986 (OUTLIER) cc_final: 0.5518 (m-70) REVERT: v 66 LEU cc_start: 0.6250 (tp) cc_final: 0.5967 (tp) outliers start: 218 outliers final: 152 residues processed: 627 average time/residue: 0.8436 time to fit residues: 925.4615 Evaluate side-chains 572 residues out of total 6293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 158 poor density : 414 time to evaluate : 6.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 208 ARG Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain H residue 64 LEU Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain L residue 130 ARG Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain M residue 248 THR Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 280 LYS Chi-restraints excluded: chain N residue 226 ILE Chi-restraints excluded: chain N residue 247 MET Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 98 LYS Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 127 SER Chi-restraints excluded: chain Q residue 196 GLU Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 18 TYR Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 91 GLN Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain S residue 135 LEU Chi-restraints excluded: chain S residue 162 GLU Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 193 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 74 HIS Chi-restraints excluded: chain U residue 89 LYS Chi-restraints excluded: chain V residue 85 TRP Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 126 LEU Chi-restraints excluded: chain X residue 65 VAL Chi-restraints excluded: chain X residue 95 ASP Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 141 LEU Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 97 ASP Chi-restraints excluded: chain Y residue 133 ASP Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain 0 residue 96 ASN Chi-restraints excluded: chain 0 residue 110 CYS Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 0 residue 185 PHE Chi-restraints excluded: chain 1 residue 41 LEU Chi-restraints excluded: chain 2 residue 60 ARG Chi-restraints excluded: chain 2 residue 91 SER Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 3 residue 113 ARG Chi-restraints excluded: chain 3 residue 151 ASN Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 5 residue 272 ASP Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 5 residue 324 GLN Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain 5 residue 362 THR Chi-restraints excluded: chain 6 residue 64 GLU Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 322 ARG Chi-restraints excluded: chain 6 residue 334 LEU Chi-restraints excluded: chain 6 residue 376 THR Chi-restraints excluded: chain 7 residue 100 CYS Chi-restraints excluded: chain 7 residue 211 TYR Chi-restraints excluded: chain 7 residue 287 GLN Chi-restraints excluded: chain 9 residue 29 SER Chi-restraints excluded: chain a residue 115 MET Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 58 ASN Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain b residue 119 PHE Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain c residue 32 LYS Chi-restraints excluded: chain c residue 58 VAL Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 198 VAL Chi-restraints excluded: chain c residue 211 THR Chi-restraints excluded: chain c residue 249 ASN Chi-restraints excluded: chain d residue 164 VAL Chi-restraints excluded: chain d residue 175 ASP Chi-restraints excluded: chain d residue 181 VAL Chi-restraints excluded: chain d residue 263 THR Chi-restraints excluded: chain g residue 89 SER Chi-restraints excluded: chain g residue 105 ARG Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain g residue 143 VAL Chi-restraints excluded: chain g residue 154 ASP Chi-restraints excluded: chain h residue 91 LEU Chi-restraints excluded: chain h residue 93 ASP Chi-restraints excluded: chain h residue 118 HIS Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain i residue 128 ARG Chi-restraints excluded: chain j residue 97 LYS Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 54 MET Chi-restraints excluded: chain o residue 90 ASP Chi-restraints excluded: chain p residue 74 ASP Chi-restraints excluded: chain p residue 105 LEU Chi-restraints excluded: chain p residue 183 MET Chi-restraints excluded: chain q residue 46 LEU Chi-restraints excluded: chain q residue 102 SER Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 87 LEU Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain r residue 196 HIS Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 181 VAL Chi-restraints excluded: chain s residue 182 SER Chi-restraints excluded: chain s residue 229 LEU Chi-restraints excluded: chain s residue 234 ASP Chi-restraints excluded: chain s residue 239 ASN Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 331 SER Chi-restraints excluded: chain s residue 371 CYS Chi-restraints excluded: chain s residue 376 THR Chi-restraints excluded: chain s residue 401 LEU Chi-restraints excluded: chain u residue 136 HIS Chi-restraints excluded: chain u residue 141 TYR Chi-restraints excluded: chain u residue 168 LEU Chi-restraints excluded: chain u residue 193 LEU Chi-restraints excluded: chain v residue 69 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 650 optimal weight: 7.9990 chunk 443 optimal weight: 20.0000 chunk 11 optimal weight: 0.0770 chunk 581 optimal weight: 8.9990 chunk 322 optimal weight: 3.9990 chunk 666 optimal weight: 7.9990 chunk 539 optimal weight: 50.0000 chunk 0 optimal weight: 40.0000 chunk 398 optimal weight: 9.9990 chunk 701 optimal weight: 30.0000 chunk 197 optimal weight: 50.0000 overall best weight: 5.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 103 ASN ** N 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 142 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 239 ASN ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 HIS ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 176 HIS ** p 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5935 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.078 87839 Z= 0.242 Angle : 0.641 10.423 124429 Z= 0.323 Chirality : 0.039 0.319 14506 Planarity : 0.005 0.073 11588 Dihedral : 21.133 179.176 25651 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 18.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.79 % Allowed : 18.54 % Favored : 77.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.10), residues: 6987 helix: 0.51 (0.11), residues: 2339 sheet: -0.96 (0.17), residues: 910 loop : -0.85 (0.11), residues: 3738 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP i 47 HIS 0.011 0.001 HIS Y 99 PHE 0.020 0.001 PHE c 214 TYR 0.022 0.001 TYR R 108 ARG 0.008 0.000 ARG s 223 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 680 residues out of total 6293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 442 time to evaluate : 6.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 220 LYS cc_start: 0.4725 (mtmt) cc_final: 0.4500 (mtmt) REVERT: L 130 ARG cc_start: 0.4339 (OUTLIER) cc_final: 0.2094 (tpt170) REVERT: N 118 MET cc_start: 0.7214 (OUTLIER) cc_final: 0.7008 (mmt) REVERT: T 167 MET cc_start: -0.2894 (tpt) cc_final: -0.3157 (tpt) REVERT: V 102 MET cc_start: -0.0673 (mmt) cc_final: -0.2779 (ttt) REVERT: 0 185 PHE cc_start: 0.5198 (OUTLIER) cc_final: 0.4974 (t80) REVERT: 3 113 ARG cc_start: 0.6322 (OUTLIER) cc_final: 0.4276 (mpt-90) REVERT: 5 362 THR cc_start: 0.7354 (OUTLIER) cc_final: 0.6962 (m) REVERT: d 129 ASP cc_start: 0.3973 (OUTLIER) cc_final: 0.3477 (p0) REVERT: d 131 ASN cc_start: 0.5514 (p0) cc_final: 0.5114 (p0) REVERT: i 128 ARG cc_start: 0.4140 (OUTLIER) cc_final: 0.3360 (ptt-90) REVERT: r 123 HIS cc_start: 0.5932 (OUTLIER) cc_final: 0.5461 (m-70) outliers start: 238 outliers final: 165 residues processed: 641 average time/residue: 0.7782 time to fit residues: 867.5525 Evaluate side-chains 578 residues out of total 6293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 173 poor density : 405 time to evaluate : 5.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 208 ARG Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 133 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 115 ASN Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain L residue 107 LEU Chi-restraints excluded: chain L residue 129 LYS Chi-restraints excluded: chain L residue 130 ARG Chi-restraints excluded: chain L residue 134 TYR Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 280 LYS Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 118 MET Chi-restraints excluded: chain N residue 163 MET Chi-restraints excluded: chain N residue 247 MET Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 98 LYS Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 127 SER Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 196 GLU Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 18 TYR Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 91 GLN Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain S residue 135 LEU Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain S residue 144 LEU Chi-restraints excluded: chain S residue 162 GLU Chi-restraints excluded: chain T residue 98 SER Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 193 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 55 ASN Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 74 HIS Chi-restraints excluded: chain U residue 89 LYS Chi-restraints excluded: chain V residue 85 TRP Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 126 LEU Chi-restraints excluded: chain W residue 141 THR Chi-restraints excluded: chain X residue 65 VAL Chi-restraints excluded: chain X residue 95 ASP Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 141 LEU Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 97 ASP Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain Z residue 119 ILE Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain 0 residue 96 ASN Chi-restraints excluded: chain 0 residue 110 CYS Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 159 LEU Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 0 residue 185 PHE Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 41 LEU Chi-restraints excluded: chain 2 residue 60 ARG Chi-restraints excluded: chain 2 residue 91 SER Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 3 residue 113 ARG Chi-restraints excluded: chain 3 residue 151 ASN Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 5 residue 324 GLN Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain 5 residue 362 THR Chi-restraints excluded: chain 6 residue 64 GLU Chi-restraints excluded: chain 6 residue 322 ARG Chi-restraints excluded: chain 6 residue 334 LEU Chi-restraints excluded: chain 6 residue 376 THR Chi-restraints excluded: chain 7 residue 100 CYS Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 132 ASP Chi-restraints excluded: chain 7 residue 138 VAL Chi-restraints excluded: chain 7 residue 139 ASN Chi-restraints excluded: chain 7 residue 211 TYR Chi-restraints excluded: chain 9 residue 66 THR Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain a residue 115 MET Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 58 ASN Chi-restraints excluded: chain b residue 119 PHE Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain c residue 32 LYS Chi-restraints excluded: chain c residue 58 VAL Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 198 VAL Chi-restraints excluded: chain c residue 211 THR Chi-restraints excluded: chain c residue 235 ILE Chi-restraints excluded: chain c residue 249 ASN Chi-restraints excluded: chain d residue 129 ASP Chi-restraints excluded: chain d residue 164 VAL Chi-restraints excluded: chain d residue 181 VAL Chi-restraints excluded: chain g residue 89 SER Chi-restraints excluded: chain g residue 91 MET Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain g residue 154 ASP Chi-restraints excluded: chain h residue 91 LEU Chi-restraints excluded: chain h residue 93 ASP Chi-restraints excluded: chain h residue 118 HIS Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain i residue 128 ARG Chi-restraints excluded: chain j residue 97 LYS Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 90 ASP Chi-restraints excluded: chain p residue 105 LEU Chi-restraints excluded: chain p residue 183 MET Chi-restraints excluded: chain q residue 46 LEU Chi-restraints excluded: chain q residue 102 SER Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 87 LEU Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain r residue 148 ASN Chi-restraints excluded: chain r residue 196 HIS Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 176 PHE Chi-restraints excluded: chain s residue 181 VAL Chi-restraints excluded: chain s residue 182 SER Chi-restraints excluded: chain s residue 223 ARG Chi-restraints excluded: chain s residue 229 LEU Chi-restraints excluded: chain s residue 234 ASP Chi-restraints excluded: chain s residue 239 ASN Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 331 SER Chi-restraints excluded: chain s residue 371 CYS Chi-restraints excluded: chain s residue 376 THR Chi-restraints excluded: chain s residue 401 LEU Chi-restraints excluded: chain u residue 141 TYR Chi-restraints excluded: chain u residue 168 LEU Chi-restraints excluded: chain u residue 193 LEU Chi-restraints excluded: chain v residue 39 PHE Chi-restraints excluded: chain v residue 61 PHE Chi-restraints excluded: chain v residue 69 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 262 optimal weight: 5.9990 chunk 703 optimal weight: 20.0000 chunk 154 optimal weight: 9.9990 chunk 458 optimal weight: 20.0000 chunk 192 optimal weight: 20.0000 chunk 781 optimal weight: 40.0000 chunk 648 optimal weight: 6.9990 chunk 361 optimal weight: 10.0000 chunk 65 optimal weight: 6.9990 chunk 258 optimal weight: 0.9980 chunk 410 optimal weight: 30.0000 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 GLN ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 210 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 GLN ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 343 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 GLN ** h 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 58 GLN p 152 GLN ** p 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5947 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 87839 Z= 0.249 Angle : 0.643 18.508 124429 Z= 0.323 Chirality : 0.039 0.301 14506 Planarity : 0.005 0.061 11588 Dihedral : 21.126 179.755 25640 Min Nonbonded Distance : 1.980 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 3.64 % Allowed : 19.53 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.55 (0.10), residues: 6987 helix: 0.59 (0.11), residues: 2355 sheet: -0.90 (0.17), residues: 902 loop : -0.80 (0.11), residues: 3730 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP i 47 HIS 0.013 0.001 HIS F 97 PHE 0.019 0.001 PHE c 214 TYR 0.022 0.001 TYR R 108 ARG 0.011 0.000 ARG s 223 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 662 residues out of total 6293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 228 poor density : 434 time to evaluate : 6.082 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 130 ARG cc_start: 0.4282 (OUTLIER) cc_final: 0.1928 (tpt170) REVERT: Q 254 MET cc_start: 0.4424 (mpp) cc_final: 0.4158 (ptp) REVERT: V 102 MET cc_start: -0.0565 (mmt) cc_final: -0.2720 (ttt) REVERT: 0 185 PHE cc_start: 0.5234 (OUTLIER) cc_final: 0.5003 (t80) REVERT: 3 113 ARG cc_start: 0.6199 (OUTLIER) cc_final: 0.4179 (mpt-90) REVERT: 5 362 THR cc_start: 0.7328 (OUTLIER) cc_final: 0.6942 (m) REVERT: d 129 ASP cc_start: 0.3943 (OUTLIER) cc_final: 0.3490 (p0) REVERT: d 131 ASN cc_start: 0.5346 (p0) cc_final: 0.5122 (p0) REVERT: i 128 ARG cc_start: 0.4178 (OUTLIER) cc_final: 0.3319 (ptt-90) REVERT: p 182 ASN cc_start: 0.7633 (m-40) cc_final: 0.7165 (m-40) REVERT: r 123 HIS cc_start: 0.5950 (OUTLIER) cc_final: 0.5469 (m-70) outliers start: 228 outliers final: 176 residues processed: 620 average time/residue: 0.7776 time to fit residues: 836.3807 Evaluate side-chains 594 residues out of total 6293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 411 time to evaluate : 6.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 208 ARG Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 94 ASP Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 130 GLN Chi-restraints excluded: chain F residue 135 ARG Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 115 LYS Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain L residue 130 ARG Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 280 LYS Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 163 MET Chi-restraints excluded: chain N residue 178 GLN Chi-restraints excluded: chain N residue 247 MET Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 98 LYS Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 127 SER Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 196 GLU Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 18 TYR Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 105 LEU Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 91 GLN Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 135 LEU Chi-restraints excluded: chain S residue 162 GLU Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 193 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 55 ASN Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 74 HIS Chi-restraints excluded: chain U residue 89 LYS Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain W residue 97 VAL Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 126 LEU Chi-restraints excluded: chain W residue 141 THR Chi-restraints excluded: chain X residue 65 VAL Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 141 LEU Chi-restraints excluded: chain X residue 216 ARG Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 97 ASP Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain 0 residue 103 VAL Chi-restraints excluded: chain 0 residue 110 CYS Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 159 LEU Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 0 residue 185 PHE Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 2 residue 51 ASN Chi-restraints excluded: chain 2 residue 60 ARG Chi-restraints excluded: chain 2 residue 91 SER Chi-restraints excluded: chain 3 residue 94 LEU Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 3 residue 113 ARG Chi-restraints excluded: chain 3 residue 146 GLU Chi-restraints excluded: chain 3 residue 151 ASN Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 272 ASP Chi-restraints excluded: chain 5 residue 324 GLN Chi-restraints excluded: chain 5 residue 355 LEU Chi-restraints excluded: chain 5 residue 362 THR Chi-restraints excluded: chain 6 residue 64 GLU Chi-restraints excluded: chain 6 residue 225 LEU Chi-restraints excluded: chain 6 residue 334 LEU Chi-restraints excluded: chain 6 residue 376 THR Chi-restraints excluded: chain 7 residue 100 CYS Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 132 ASP Chi-restraints excluded: chain 7 residue 148 MET Chi-restraints excluded: chain 7 residue 211 TYR Chi-restraints excluded: chain 7 residue 287 GLN Chi-restraints excluded: chain 9 residue 66 THR Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain 9 residue 96 VAL Chi-restraints excluded: chain a residue 115 MET Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 58 ASN Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain c residue 58 VAL Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 198 VAL Chi-restraints excluded: chain c residue 211 THR Chi-restraints excluded: chain c residue 235 ILE Chi-restraints excluded: chain c residue 249 ASN Chi-restraints excluded: chain d residue 129 ASP Chi-restraints excluded: chain d residue 164 VAL Chi-restraints excluded: chain d residue 175 ASP Chi-restraints excluded: chain d residue 181 VAL Chi-restraints excluded: chain d residue 225 TYR Chi-restraints excluded: chain g residue 89 SER Chi-restraints excluded: chain g residue 91 MET Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain g residue 143 VAL Chi-restraints excluded: chain g residue 154 ASP Chi-restraints excluded: chain h residue 91 LEU Chi-restraints excluded: chain h residue 93 ASP Chi-restraints excluded: chain h residue 118 HIS Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain i residue 128 ARG Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 90 ASP Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain p residue 105 LEU Chi-restraints excluded: chain p residue 183 MET Chi-restraints excluded: chain q residue 46 LEU Chi-restraints excluded: chain q residue 102 SER Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 87 LEU Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain r residue 148 ASN Chi-restraints excluded: chain r residue 196 HIS Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 176 PHE Chi-restraints excluded: chain s residue 181 VAL Chi-restraints excluded: chain s residue 182 SER Chi-restraints excluded: chain s residue 223 ARG Chi-restraints excluded: chain s residue 229 LEU Chi-restraints excluded: chain s residue 234 ASP Chi-restraints excluded: chain s residue 239 ASN Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 331 SER Chi-restraints excluded: chain s residue 371 CYS Chi-restraints excluded: chain s residue 376 THR Chi-restraints excluded: chain s residue 401 LEU Chi-restraints excluded: chain u residue 141 TYR Chi-restraints excluded: chain u residue 170 VAL Chi-restraints excluded: chain u residue 193 LEU Chi-restraints excluded: chain v residue 61 PHE Chi-restraints excluded: chain v residue 69 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 753 optimal weight: 20.0000 chunk 88 optimal weight: 5.9990 chunk 445 optimal weight: 6.9990 chunk 570 optimal weight: 10.0000 chunk 442 optimal weight: 10.0000 chunk 658 optimal weight: 20.0000 chunk 436 optimal weight: 5.9990 chunk 778 optimal weight: 30.0000 chunk 487 optimal weight: 20.0000 chunk 474 optimal weight: 7.9990 chunk 359 optimal weight: 9.9990 overall best weight: 7.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 156 ASN ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 GLN ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 ASN N 173 GLN ** N 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 210 GLN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 332 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** o 58 GLN ** p 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5976 moved from start: 0.4347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 87839 Z= 0.284 Angle : 0.666 16.662 124429 Z= 0.333 Chirality : 0.039 0.291 14506 Planarity : 0.005 0.060 11588 Dihedral : 21.157 179.517 25626 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 3.68 % Allowed : 19.95 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.10), residues: 6987 helix: 0.56 (0.11), residues: 2366 sheet: -0.96 (0.17), residues: 909 loop : -0.80 (0.11), residues: 3712 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP V 135 HIS 0.007 0.001 HIS 6 332 PHE 0.020 0.002 PHE K 166 TYR 0.021 0.001 TYR U 7 ARG 0.011 0.000 ARG s 223 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 6293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 231 poor density : 411 time to evaluate : 6.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 91 MET cc_start: 0.4998 (mmp) cc_final: 0.3955 (mmp) REVERT: L 130 ARG cc_start: 0.4518 (OUTLIER) cc_final: 0.2078 (tpt170) REVERT: V 102 MET cc_start: -0.0664 (mmt) cc_final: -0.2974 (ttt) REVERT: 0 185 PHE cc_start: 0.5261 (OUTLIER) cc_final: 0.4979 (t80) REVERT: 5 313 MET cc_start: 0.5284 (mtp) cc_final: 0.4982 (mtp) REVERT: 5 362 THR cc_start: 0.7310 (OUTLIER) cc_final: 0.6934 (m) REVERT: 7 115 MET cc_start: 0.5088 (mmm) cc_final: 0.4457 (mmm) REVERT: i 128 ARG cc_start: 0.4272 (OUTLIER) cc_final: 0.3373 (ptt-90) REVERT: r 123 HIS cc_start: 0.6054 (OUTLIER) cc_final: 0.5543 (m-70) REVERT: w 120 MET cc_start: 0.5588 (mmt) cc_final: 0.5278 (mmp) outliers start: 231 outliers final: 184 residues processed: 604 average time/residue: 0.8546 time to fit residues: 900.2058 Evaluate side-chains 584 residues out of total 6293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 189 poor density : 395 time to evaluate : 6.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 157 MET Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain E residue 111 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 115 LYS Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain L residue 130 ARG Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 280 LYS Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 163 MET Chi-restraints excluded: chain N residue 178 GLN Chi-restraints excluded: chain N residue 210 GLN Chi-restraints excluded: chain N residue 226 ILE Chi-restraints excluded: chain N residue 247 MET Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 84 ASP Chi-restraints excluded: chain O residue 98 LYS Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 127 SER Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 196 GLU Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain Q residue 224 MET Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 18 TYR Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 91 GLN Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 135 LEU Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain S residue 162 GLU Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 193 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 55 ASN Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 74 HIS Chi-restraints excluded: chain U residue 89 LYS Chi-restraints excluded: chain V residue 57 PHE Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain W residue 71 ARG Chi-restraints excluded: chain W residue 97 VAL Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 126 LEU Chi-restraints excluded: chain W residue 141 THR Chi-restraints excluded: chain X residue 65 VAL Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 141 LEU Chi-restraints excluded: chain X residue 216 ARG Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 97 ASP Chi-restraints excluded: chain Y residue 133 ASP Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 119 ILE Chi-restraints excluded: chain Z residue 128 LEU Chi-restraints excluded: chain Z residue 147 VAL Chi-restraints excluded: chain 0 residue 103 VAL Chi-restraints excluded: chain 0 residue 110 CYS Chi-restraints excluded: chain 0 residue 112 GLU Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 0 residue 185 PHE Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 41 LEU Chi-restraints excluded: chain 2 residue 51 ASN Chi-restraints excluded: chain 2 residue 60 ARG Chi-restraints excluded: chain 3 residue 94 LEU Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 3 residue 113 ARG Chi-restraints excluded: chain 3 residue 146 GLU Chi-restraints excluded: chain 3 residue 151 ASN Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 272 ASP Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 5 residue 324 GLN Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain 5 residue 362 THR Chi-restraints excluded: chain 6 residue 64 GLU Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 225 LEU Chi-restraints excluded: chain 6 residue 334 LEU Chi-restraints excluded: chain 6 residue 376 THR Chi-restraints excluded: chain 7 residue 94 HIS Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 132 ASP Chi-restraints excluded: chain 7 residue 138 VAL Chi-restraints excluded: chain 7 residue 139 ASN Chi-restraints excluded: chain 7 residue 211 TYR Chi-restraints excluded: chain 7 residue 235 TYR Chi-restraints excluded: chain 9 residue 66 THR Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain 9 residue 96 VAL Chi-restraints excluded: chain a residue 115 MET Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 58 ASN Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain c residue 58 VAL Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 198 VAL Chi-restraints excluded: chain c residue 211 THR Chi-restraints excluded: chain c residue 249 ASN Chi-restraints excluded: chain d residue 164 VAL Chi-restraints excluded: chain d residue 175 ASP Chi-restraints excluded: chain d residue 181 VAL Chi-restraints excluded: chain d residue 225 TYR Chi-restraints excluded: chain g residue 89 SER Chi-restraints excluded: chain g residue 91 MET Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain g residue 143 VAL Chi-restraints excluded: chain g residue 154 ASP Chi-restraints excluded: chain h residue 93 ASP Chi-restraints excluded: chain h residue 118 HIS Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain i residue 128 ARG Chi-restraints excluded: chain j residue 98 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 90 ASP Chi-restraints excluded: chain p residue 105 LEU Chi-restraints excluded: chain q residue 46 LEU Chi-restraints excluded: chain q residue 102 SER Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 87 LEU Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain r residue 148 ASN Chi-restraints excluded: chain r residue 196 HIS Chi-restraints excluded: chain s residue 52 THR Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 176 PHE Chi-restraints excluded: chain s residue 181 VAL Chi-restraints excluded: chain s residue 182 SER Chi-restraints excluded: chain s residue 223 ARG Chi-restraints excluded: chain s residue 229 LEU Chi-restraints excluded: chain s residue 230 ARG Chi-restraints excluded: chain s residue 234 ASP Chi-restraints excluded: chain s residue 239 ASN Chi-restraints excluded: chain s residue 331 SER Chi-restraints excluded: chain s residue 371 CYS Chi-restraints excluded: chain s residue 376 THR Chi-restraints excluded: chain s residue 401 LEU Chi-restraints excluded: chain u residue 141 TYR Chi-restraints excluded: chain u residue 170 VAL Chi-restraints excluded: chain u residue 193 LEU Chi-restraints excluded: chain v residue 61 PHE Chi-restraints excluded: chain v residue 69 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 481 optimal weight: 8.9990 chunk 311 optimal weight: 3.9990 chunk 465 optimal weight: 8.9990 chunk 234 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 150 optimal weight: 2.9990 chunk 495 optimal weight: 9.9990 chunk 530 optimal weight: 20.0000 chunk 385 optimal weight: 30.0000 chunk 72 optimal weight: 10.0000 chunk 612 optimal weight: 2.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 173 GLN ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 332 HIS ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** s 387 ASN ** u 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5950 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 87839 Z= 0.228 Angle : 0.647 15.602 124429 Z= 0.323 Chirality : 0.039 0.287 14506 Planarity : 0.005 0.072 11588 Dihedral : 21.143 179.405 25624 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 19.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.38 % Allowed : 19.98 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.10), residues: 6987 helix: 0.64 (0.11), residues: 2376 sheet: -0.90 (0.17), residues: 918 loop : -0.70 (0.11), residues: 3693 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP i 47 HIS 0.007 0.001 HIS u 148 PHE 0.022 0.001 PHE c 214 TYR 0.024 0.001 TYR U 7 ARG 0.013 0.000 ARG a 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 6293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 421 time to evaluate : 6.161 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 91 MET cc_start: 0.5225 (OUTLIER) cc_final: 0.4271 (mmp) REVERT: L 127 LEU cc_start: 0.7031 (pt) cc_final: 0.6740 (pp) REVERT: L 130 ARG cc_start: 0.4294 (OUTLIER) cc_final: 0.2103 (tpt170) REVERT: N 118 MET cc_start: 0.7385 (mmt) cc_final: 0.7085 (mmt) REVERT: R 64 MET cc_start: 0.6686 (tpp) cc_final: 0.6345 (ttm) REVERT: V 102 MET cc_start: -0.0647 (mmt) cc_final: -0.3125 (ttt) REVERT: 0 185 PHE cc_start: 0.5127 (OUTLIER) cc_final: 0.4896 (t80) REVERT: 3 113 ARG cc_start: 0.6079 (OUTLIER) cc_final: 0.4183 (mpt-90) REVERT: 5 362 THR cc_start: 0.7220 (OUTLIER) cc_final: 0.6855 (m) REVERT: i 128 ARG cc_start: 0.4162 (OUTLIER) cc_final: 0.3302 (ptt-90) REVERT: r 123 HIS cc_start: 0.5987 (OUTLIER) cc_final: 0.5487 (m-70) REVERT: w 120 MET cc_start: 0.5441 (mmt) cc_final: 0.5049 (mmp) outliers start: 212 outliers final: 175 residues processed: 598 average time/residue: 0.7830 time to fit residues: 809.1740 Evaluate side-chains 586 residues out of total 6293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 182 poor density : 404 time to evaluate : 6.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 106 PHE Chi-restraints excluded: chain F residue 135 ARG Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 115 LYS Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain L residue 130 ARG Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 280 LYS Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 178 GLN Chi-restraints excluded: chain N residue 247 MET Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 98 LYS Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 196 GLU Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 18 TYR Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 91 GLN Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain S residue 134 LEU Chi-restraints excluded: chain S residue 135 LEU Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 193 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 55 ASN Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 74 HIS Chi-restraints excluded: chain U residue 89 LYS Chi-restraints excluded: chain U residue 111 PHE Chi-restraints excluded: chain V residue 57 PHE Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain W residue 71 ARG Chi-restraints excluded: chain W residue 97 VAL Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 126 LEU Chi-restraints excluded: chain W residue 141 THR Chi-restraints excluded: chain X residue 65 VAL Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 141 LEU Chi-restraints excluded: chain X residue 216 ARG Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 97 ASP Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 119 ILE Chi-restraints excluded: chain Z residue 147 VAL Chi-restraints excluded: chain 0 residue 103 VAL Chi-restraints excluded: chain 0 residue 110 CYS Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 0 residue 185 PHE Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 1 residue 41 LEU Chi-restraints excluded: chain 2 residue 51 ASN Chi-restraints excluded: chain 2 residue 60 ARG Chi-restraints excluded: chain 2 residue 91 SER Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 3 residue 113 ARG Chi-restraints excluded: chain 3 residue 146 GLU Chi-restraints excluded: chain 3 residue 151 ASN Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 272 ASP Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 5 residue 324 GLN Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain 5 residue 362 THR Chi-restraints excluded: chain 6 residue 64 GLU Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 225 LEU Chi-restraints excluded: chain 6 residue 334 LEU Chi-restraints excluded: chain 6 residue 376 THR Chi-restraints excluded: chain 7 residue 94 HIS Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 132 ASP Chi-restraints excluded: chain 7 residue 138 VAL Chi-restraints excluded: chain 7 residue 139 ASN Chi-restraints excluded: chain 7 residue 235 TYR Chi-restraints excluded: chain 9 residue 66 THR Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain 9 residue 96 VAL Chi-restraints excluded: chain a residue 115 MET Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 58 ASN Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain c residue 58 VAL Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 198 VAL Chi-restraints excluded: chain c residue 211 THR Chi-restraints excluded: chain c residue 249 ASN Chi-restraints excluded: chain d residue 164 VAL Chi-restraints excluded: chain d residue 175 ASP Chi-restraints excluded: chain d residue 181 VAL Chi-restraints excluded: chain d residue 225 TYR Chi-restraints excluded: chain g residue 89 SER Chi-restraints excluded: chain g residue 91 MET Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain g residue 143 VAL Chi-restraints excluded: chain g residue 154 ASP Chi-restraints excluded: chain h residue 91 LEU Chi-restraints excluded: chain h residue 93 ASP Chi-restraints excluded: chain h residue 118 HIS Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain i residue 128 ARG Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 90 ASP Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain p residue 105 LEU Chi-restraints excluded: chain p residue 183 MET Chi-restraints excluded: chain q residue 46 LEU Chi-restraints excluded: chain q residue 102 SER Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 87 LEU Chi-restraints excluded: chain r residue 100 LEU Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain r residue 148 ASN Chi-restraints excluded: chain r residue 196 HIS Chi-restraints excluded: chain s residue 52 THR Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 75 SER Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 176 PHE Chi-restraints excluded: chain s residue 181 VAL Chi-restraints excluded: chain s residue 182 SER Chi-restraints excluded: chain s residue 223 ARG Chi-restraints excluded: chain s residue 229 LEU Chi-restraints excluded: chain s residue 230 ARG Chi-restraints excluded: chain s residue 234 ASP Chi-restraints excluded: chain s residue 239 ASN Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 371 CYS Chi-restraints excluded: chain s residue 376 THR Chi-restraints excluded: chain s residue 401 LEU Chi-restraints excluded: chain u residue 141 TYR Chi-restraints excluded: chain u residue 170 VAL Chi-restraints excluded: chain v residue 69 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 708 optimal weight: 20.0000 chunk 746 optimal weight: 20.0000 chunk 680 optimal weight: 7.9990 chunk 725 optimal weight: 20.0000 chunk 745 optimal weight: 20.0000 chunk 436 optimal weight: 9.9990 chunk 316 optimal weight: 20.0000 chunk 569 optimal weight: 10.0000 chunk 222 optimal weight: 0.7980 chunk 655 optimal weight: 10.0000 chunk 686 optimal weight: 0.0170 overall best weight: 5.7626 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 59 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 173 GLN ** N 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 59 ASN ** p 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5958 moved from start: 0.4602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 87839 Z= 0.240 Angle : 0.655 15.239 124429 Z= 0.326 Chirality : 0.039 0.287 14506 Planarity : 0.005 0.060 11588 Dihedral : 21.131 179.195 25621 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.08 % Allowed : 20.38 % Favored : 76.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.10), residues: 6987 helix: 0.65 (0.11), residues: 2353 sheet: -0.88 (0.17), residues: 925 loop : -0.64 (0.11), residues: 3709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP U 150 HIS 0.008 0.001 HIS p 123 PHE 0.025 0.001 PHE c 214 TYR 0.050 0.001 TYR R 39 ARG 0.010 0.000 ARG s 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 6293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 413 time to evaluate : 6.498 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 91 MET cc_start: 0.5136 (OUTLIER) cc_final: 0.4428 (mmp) REVERT: L 127 LEU cc_start: 0.6753 (pt) cc_final: 0.6274 (pp) REVERT: L 130 ARG cc_start: 0.3889 (OUTLIER) cc_final: 0.2274 (tpt170) REVERT: R 64 MET cc_start: 0.6745 (tpp) cc_final: 0.6362 (ttm) REVERT: V 102 MET cc_start: -0.0526 (mmt) cc_final: -0.3107 (ttt) REVERT: 0 185 PHE cc_start: 0.5106 (OUTLIER) cc_final: 0.4891 (t80) REVERT: 5 362 THR cc_start: 0.7245 (OUTLIER) cc_final: 0.6909 (m) REVERT: 7 115 MET cc_start: 0.5180 (mmm) cc_final: 0.4467 (mmm) REVERT: i 128 ARG cc_start: 0.4093 (OUTLIER) cc_final: 0.3298 (ptt-90) REVERT: j 60 MET cc_start: 0.4208 (tpp) cc_final: 0.3877 (mmm) REVERT: r 123 HIS cc_start: 0.5958 (OUTLIER) cc_final: 0.5454 (m-70) REVERT: v 38 GLU cc_start: 0.7190 (pp20) cc_final: 0.6708 (tm-30) REVERT: w 120 MET cc_start: 0.5580 (mmt) cc_final: 0.5187 (mmp) outliers start: 193 outliers final: 172 residues processed: 576 average time/residue: 0.8285 time to fit residues: 830.8216 Evaluate side-chains 574 residues out of total 6293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 396 time to evaluate : 6.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain H residue 115 LYS Chi-restraints excluded: chain H residue 139 LEU Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain L residue 130 ARG Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain M residue 280 LYS Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 178 GLN Chi-restraints excluded: chain N residue 226 ILE Chi-restraints excluded: chain N residue 247 MET Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 98 LYS Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 196 GLU Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 18 TYR Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 91 GLN Chi-restraints excluded: chain S residue 120 LEU Chi-restraints excluded: chain S residue 135 LEU Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 193 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 21 ARG Chi-restraints excluded: chain U residue 55 ASN Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 74 HIS Chi-restraints excluded: chain U residue 89 LYS Chi-restraints excluded: chain U residue 111 PHE Chi-restraints excluded: chain V residue 57 PHE Chi-restraints excluded: chain V residue 107 THR Chi-restraints excluded: chain W residue 71 ARG Chi-restraints excluded: chain W residue 97 VAL Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 126 LEU Chi-restraints excluded: chain W residue 141 THR Chi-restraints excluded: chain X residue 65 VAL Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 141 LEU Chi-restraints excluded: chain X residue 216 ARG Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 97 ASP Chi-restraints excluded: chain Y residue 190 LEU Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 119 ILE Chi-restraints excluded: chain Z residue 147 VAL Chi-restraints excluded: chain 0 residue 103 VAL Chi-restraints excluded: chain 0 residue 112 GLU Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 0 residue 185 PHE Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 2 residue 51 ASN Chi-restraints excluded: chain 2 residue 60 ARG Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 3 residue 113 ARG Chi-restraints excluded: chain 3 residue 146 GLU Chi-restraints excluded: chain 3 residue 151 ASN Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 5 residue 324 GLN Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain 5 residue 362 THR Chi-restraints excluded: chain 6 residue 64 GLU Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 225 LEU Chi-restraints excluded: chain 6 residue 376 THR Chi-restraints excluded: chain 7 residue 94 HIS Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 132 ASP Chi-restraints excluded: chain 7 residue 138 VAL Chi-restraints excluded: chain 7 residue 139 ASN Chi-restraints excluded: chain 7 residue 211 TYR Chi-restraints excluded: chain 7 residue 235 TYR Chi-restraints excluded: chain 9 residue 66 THR Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain 9 residue 96 VAL Chi-restraints excluded: chain a residue 115 MET Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 58 ASN Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain c residue 58 VAL Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 211 THR Chi-restraints excluded: chain c residue 249 ASN Chi-restraints excluded: chain d residue 164 VAL Chi-restraints excluded: chain d residue 175 ASP Chi-restraints excluded: chain d residue 225 TYR Chi-restraints excluded: chain g residue 89 SER Chi-restraints excluded: chain g residue 91 MET Chi-restraints excluded: chain g residue 138 THR Chi-restraints excluded: chain g residue 143 VAL Chi-restraints excluded: chain g residue 154 ASP Chi-restraints excluded: chain h residue 91 LEU Chi-restraints excluded: chain h residue 93 ASP Chi-restraints excluded: chain h residue 118 HIS Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain i residue 128 ARG Chi-restraints excluded: chain j residue 29 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 90 ASP Chi-restraints excluded: chain p residue 105 LEU Chi-restraints excluded: chain p residue 183 MET Chi-restraints excluded: chain q residue 46 LEU Chi-restraints excluded: chain q residue 102 SER Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 87 LEU Chi-restraints excluded: chain r residue 100 LEU Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain r residue 148 ASN Chi-restraints excluded: chain r residue 196 HIS Chi-restraints excluded: chain s residue 52 THR Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 75 SER Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 176 PHE Chi-restraints excluded: chain s residue 181 VAL Chi-restraints excluded: chain s residue 182 SER Chi-restraints excluded: chain s residue 223 ARG Chi-restraints excluded: chain s residue 229 LEU Chi-restraints excluded: chain s residue 230 ARG Chi-restraints excluded: chain s residue 234 ASP Chi-restraints excluded: chain s residue 239 ASN Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 331 SER Chi-restraints excluded: chain s residue 371 CYS Chi-restraints excluded: chain s residue 376 THR Chi-restraints excluded: chain s residue 401 LEU Chi-restraints excluded: chain u residue 141 TYR Chi-restraints excluded: chain u residue 170 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 723 optimal weight: 20.0000 chunk 476 optimal weight: 7.9990 chunk 767 optimal weight: 20.0000 chunk 468 optimal weight: 2.9990 chunk 364 optimal weight: 6.9990 chunk 533 optimal weight: 3.9990 chunk 804 optimal weight: 30.0000 chunk 740 optimal weight: 20.0000 chunk 641 optimal weight: 7.9990 chunk 66 optimal weight: 4.9990 chunk 495 optimal weight: 7.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 235 GLN ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 59 HIS N 173 GLN ** N 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5952 moved from start: 0.4717 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 87839 Z= 0.230 Angle : 0.663 16.031 124429 Z= 0.329 Chirality : 0.039 0.406 14506 Planarity : 0.005 0.060 11588 Dihedral : 21.118 178.972 25615 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 20.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 2.84 % Allowed : 20.71 % Favored : 76.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.10), residues: 6987 helix: 0.64 (0.11), residues: 2361 sheet: -0.84 (0.17), residues: 922 loop : -0.61 (0.11), residues: 3704 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP o 17 HIS 0.007 0.001 HIS p 123 PHE 0.032 0.001 PHE v 32 TYR 0.049 0.001 TYR R 39 ARG 0.011 0.000 ARG p 179 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13974 Ramachandran restraints generated. 6987 Oldfield, 0 Emsley, 6987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 6293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 178 poor density : 413 time to evaluate : 6.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 235 GLN cc_start: 0.7096 (tm130) cc_final: 0.6851 (tm130) REVERT: L 35 MET cc_start: 0.4902 (ppp) cc_final: 0.4427 (ppp) REVERT: L 91 MET cc_start: 0.5009 (OUTLIER) cc_final: 0.4373 (mmp) REVERT: L 127 LEU cc_start: 0.6766 (pt) cc_final: 0.6345 (pp) REVERT: N 118 MET cc_start: 0.7284 (mmt) cc_final: 0.7011 (mmt) REVERT: R 64 MET cc_start: 0.6728 (tpp) cc_final: 0.6322 (ttm) REVERT: V 102 MET cc_start: -0.0652 (mmt) cc_final: -0.3266 (ttt) REVERT: V 108 MET cc_start: -0.2482 (ptt) cc_final: -0.3245 (ptt) REVERT: 3 113 ARG cc_start: 0.6030 (OUTLIER) cc_final: 0.4191 (mpt-90) REVERT: 5 362 THR cc_start: 0.7182 (OUTLIER) cc_final: 0.6854 (m) REVERT: 7 115 MET cc_start: 0.5030 (mmm) cc_final: 0.4361 (mmm) REVERT: i 128 ARG cc_start: 0.4086 (OUTLIER) cc_final: 0.3295 (ptt-90) REVERT: j 60 MET cc_start: 0.4070 (tpp) cc_final: 0.3682 (mmm) REVERT: o 17 TRP cc_start: -0.0234 (m100) cc_final: -0.0863 (m100) REVERT: r 123 HIS cc_start: 0.5931 (OUTLIER) cc_final: 0.5460 (m-70) REVERT: v 38 GLU cc_start: 0.7401 (pp20) cc_final: 0.6862 (tm-30) REVERT: w 120 MET cc_start: 0.5533 (mmt) cc_final: 0.5133 (mmp) outliers start: 178 outliers final: 162 residues processed: 561 average time/residue: 0.7861 time to fit residues: 766.8826 Evaluate side-chains 567 residues out of total 6293 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 167 poor density : 400 time to evaluate : 5.989 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 223 THR Chi-restraints excluded: chain E residue 113 ASP Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 126 ASP Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 95 ILE Chi-restraints excluded: chain F residue 179 THR Chi-restraints excluded: chain F residue 208 HIS Chi-restraints excluded: chain H residue 102 VAL Chi-restraints excluded: chain K residue 60 MET Chi-restraints excluded: chain K residue 81 THR Chi-restraints excluded: chain K residue 90 VAL Chi-restraints excluded: chain K residue 91 THR Chi-restraints excluded: chain K residue 156 ASP Chi-restraints excluded: chain L residue 59 HIS Chi-restraints excluded: chain L residue 74 LEU Chi-restraints excluded: chain L residue 91 MET Chi-restraints excluded: chain M residue 118 LEU Chi-restraints excluded: chain M residue 140 LEU Chi-restraints excluded: chain M residue 180 ASP Chi-restraints excluded: chain M residue 222 TYR Chi-restraints excluded: chain M residue 257 CYS Chi-restraints excluded: chain N residue 59 VAL Chi-restraints excluded: chain N residue 77 THR Chi-restraints excluded: chain N residue 178 GLN Chi-restraints excluded: chain N residue 226 ILE Chi-restraints excluded: chain N residue 247 MET Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 67 ASP Chi-restraints excluded: chain O residue 98 LYS Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 101 THR Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain P residue 93 LEU Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain Q residue 87 THR Chi-restraints excluded: chain Q residue 119 VAL Chi-restraints excluded: chain Q residue 186 SER Chi-restraints excluded: chain Q residue 196 GLU Chi-restraints excluded: chain Q residue 199 THR Chi-restraints excluded: chain Q residue 203 ASN Chi-restraints excluded: chain Q residue 275 THR Chi-restraints excluded: chain R residue 18 TYR Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 95 VAL Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain S residue 55 SER Chi-restraints excluded: chain S residue 58 SER Chi-restraints excluded: chain S residue 91 GLN Chi-restraints excluded: chain S residue 135 LEU Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain T residue 134 VAL Chi-restraints excluded: chain T residue 191 THR Chi-restraints excluded: chain T residue 193 VAL Chi-restraints excluded: chain U residue 19 VAL Chi-restraints excluded: chain U residue 55 ASN Chi-restraints excluded: chain U residue 63 VAL Chi-restraints excluded: chain U residue 74 HIS Chi-restraints excluded: chain U residue 89 LYS Chi-restraints excluded: chain V residue 57 PHE Chi-restraints excluded: chain W residue 71 ARG Chi-restraints excluded: chain W residue 97 VAL Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 126 LEU Chi-restraints excluded: chain W residue 141 THR Chi-restraints excluded: chain X residue 65 VAL Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain X residue 141 LEU Chi-restraints excluded: chain X residue 216 ARG Chi-restraints excluded: chain Y residue 86 THR Chi-restraints excluded: chain Y residue 97 ASP Chi-restraints excluded: chain Y residue 190 LEU Chi-restraints excluded: chain Z residue 37 THR Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 119 ILE Chi-restraints excluded: chain Z residue 147 VAL Chi-restraints excluded: chain 0 residue 103 VAL Chi-restraints excluded: chain 0 residue 112 GLU Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 169 ASP Chi-restraints excluded: chain 1 residue 17 LEU Chi-restraints excluded: chain 1 residue 18 VAL Chi-restraints excluded: chain 2 residue 51 ASN Chi-restraints excluded: chain 2 residue 60 ARG Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 3 residue 113 ARG Chi-restraints excluded: chain 3 residue 146 GLU Chi-restraints excluded: chain 3 residue 151 ASN Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 5 residue 252 VAL Chi-restraints excluded: chain 5 residue 294 LEU Chi-restraints excluded: chain 5 residue 324 GLN Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain 5 residue 362 THR Chi-restraints excluded: chain 6 residue 64 GLU Chi-restraints excluded: chain 6 residue 135 VAL Chi-restraints excluded: chain 6 residue 166 THR Chi-restraints excluded: chain 6 residue 225 LEU Chi-restraints excluded: chain 7 residue 94 HIS Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 132 ASP Chi-restraints excluded: chain 7 residue 138 VAL Chi-restraints excluded: chain 7 residue 139 ASN Chi-restraints excluded: chain 7 residue 211 TYR Chi-restraints excluded: chain 7 residue 235 TYR Chi-restraints excluded: chain 7 residue 259 ASP Chi-restraints excluded: chain 9 residue 66 THR Chi-restraints excluded: chain 9 residue 87 THR Chi-restraints excluded: chain 9 residue 96 VAL Chi-restraints excluded: chain a residue 115 MET Chi-restraints excluded: chain b residue 39 SER Chi-restraints excluded: chain b residue 58 ASN Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain b residue 119 PHE Chi-restraints excluded: chain b residue 121 THR Chi-restraints excluded: chain c residue 93 VAL Chi-restraints excluded: chain c residue 150 THR Chi-restraints excluded: chain c residue 178 LEU Chi-restraints excluded: chain c residue 211 THR Chi-restraints excluded: chain c residue 249 ASN Chi-restraints excluded: chain d residue 164 VAL Chi-restraints excluded: chain d residue 175 ASP Chi-restraints excluded: chain d residue 225 TYR Chi-restraints excluded: chain g residue 89 SER Chi-restraints excluded: chain g residue 91 MET Chi-restraints excluded: chain g residue 143 VAL Chi-restraints excluded: chain g residue 154 ASP Chi-restraints excluded: chain h residue 91 LEU Chi-restraints excluded: chain h residue 118 HIS Chi-restraints excluded: chain i residue 63 LEU Chi-restraints excluded: chain i residue 128 ARG Chi-restraints excluded: chain j residue 29 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 29 LEU Chi-restraints excluded: chain o residue 90 ASP Chi-restraints excluded: chain o residue 91 GLN Chi-restraints excluded: chain p residue 105 LEU Chi-restraints excluded: chain p residue 183 MET Chi-restraints excluded: chain q residue 46 LEU Chi-restraints excluded: chain q residue 102 SER Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 87 LEU Chi-restraints excluded: chain r residue 100 LEU Chi-restraints excluded: chain r residue 123 HIS Chi-restraints excluded: chain r residue 148 ASN Chi-restraints excluded: chain r residue 196 HIS Chi-restraints excluded: chain s residue 52 THR Chi-restraints excluded: chain s residue 66 TRP Chi-restraints excluded: chain s residue 75 SER Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 176 PHE Chi-restraints excluded: chain s residue 181 VAL Chi-restraints excluded: chain s residue 182 SER Chi-restraints excluded: chain s residue 223 ARG Chi-restraints excluded: chain s residue 229 LEU Chi-restraints excluded: chain s residue 230 ARG Chi-restraints excluded: chain s residue 234 ASP Chi-restraints excluded: chain s residue 239 ASN Chi-restraints excluded: chain s residue 243 ILE Chi-restraints excluded: chain s residue 331 SER Chi-restraints excluded: chain s residue 371 CYS Chi-restraints excluded: chain s residue 376 THR Chi-restraints excluded: chain s residue 401 LEU Chi-restraints excluded: chain u residue 141 TYR Chi-restraints excluded: chain u residue 167 TRP Chi-restraints excluded: chain u residue 170 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 808 random chunks: chunk 393 optimal weight: 40.0000 chunk 509 optimal weight: 10.0000 chunk 682 optimal weight: 50.0000 chunk 196 optimal weight: 6.9990 chunk 591 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 178 optimal weight: 40.0000 chunk 642 optimal weight: 6.9990 chunk 268 optimal weight: 50.0000 chunk 659 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 165 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 72 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 174 GLN ** F 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 105 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 173 GLN ** N 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 121 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 79 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 150 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 108 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 385 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 247 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 135 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 153 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 134 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** r 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.042815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 96)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.030306 restraints weight = 774850.794| |-----------------------------------------------------------------------------| r_work (start): 0.3318 rms_B_bonded: 5.23 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 87839 Z= 0.252 Angle : 0.670 15.649 124429 Z= 0.333 Chirality : 0.039 0.309 14506 Planarity : 0.005 0.072 11588 Dihedral : 21.128 179.190 25614 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 21.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 2.89 % Allowed : 20.79 % Favored : 76.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.46 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.10), residues: 6987 helix: 0.60 (0.11), residues: 2369 sheet: -0.83 (0.17), residues: 908 loop : -0.61 (0.11), residues: 3710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP Z 81 HIS 0.044 0.001 HIS L 59 PHE 0.032 0.002 PHE v 32 TYR 0.042 0.001 TYR Q 125 ARG 0.010 0.000 ARG Z 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17888.96 seconds wall clock time: 318 minutes 15.57 seconds (19095.57 seconds total)