Starting phenix.real_space_refine on Mon Mar 18 10:05:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh7_13967/03_2024/7qh7_13967.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh7_13967/03_2024/7qh7_13967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh7_13967/03_2024/7qh7_13967.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh7_13967/03_2024/7qh7_13967.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh7_13967/03_2024/7qh7_13967.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7qh7_13967/03_2024/7qh7_13967.pdb" } resolution = 2.89 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: 7 Type Number sf(0) Gaussians Zn 3 6.06 5 P 1312 5.49 5 Mg 50 5.21 5 S 247 5.16 5 C 49189 2.51 5 N 15531 2.21 5 O 19065 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D ARG 80": "NH1" <-> "NH2" Residue "D ARG 92": "NH1" <-> "NH2" Residue "D ARG 103": "NH1" <-> "NH2" Residue "D ARG 113": "NH1" <-> "NH2" Residue "D ARG 147": "NH1" <-> "NH2" Residue "D GLU 199": "OE1" <-> "OE2" Residue "D ARG 232": "NH1" <-> "NH2" Residue "D ARG 274": "NH1" <-> "NH2" Residue "E ARG 154": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E ARG 166": "NH1" <-> "NH2" Residue "E ARG 239": "NH1" <-> "NH2" Residue "E GLU 268": "OE1" <-> "OE2" Residue "F ARG 49": "NH1" <-> "NH2" Residue "F ARG 59": "NH1" <-> "NH2" Residue "F ARG 70": "NH1" <-> "NH2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F ARG 108": "NH1" <-> "NH2" Residue "F ARG 121": "NH1" <-> "NH2" Residue "F ARG 156": "NH1" <-> "NH2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F ARG 210": "NH1" <-> "NH2" Residue "H ARG 76": "NH1" <-> "NH2" Residue "I ARG 44": "NH1" <-> "NH2" Residue "K ARG 16": "NH1" <-> "NH2" Residue "K ARG 118": "NH1" <-> "NH2" Residue "K ARG 124": "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 ARG 128": "NH1" <-> "NH2" Residue "L ARG 130": "NH1" <-> "NH2" Residue "M GLU 37": "OE1" <-> "OE2" 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 GLU 68": "OE1" <-> "OE2" Residue "M ARG 91": "NH1" <-> "NH2" Residue "M ARG 134": "NH1" <-> "NH2" Residue "M GLU 155": "OE1" <-> "OE2" Residue "M GLU 161": "OE1" <-> "OE2" Residue "M ARG 182": "NH1" <-> "NH2" Residue "M GLU 231": "OE1" <-> "OE2" Residue "M GLU 235": "OE1" <-> "OE2" Residue "M ARG 259": "NH1" <-> "NH2" Residue "M GLU 288": "OE1" <-> "OE2" Residue "N ARG 51": "NH1" <-> "NH2" Residue "N ARG 123": "NH1" <-> "NH2" Residue "N GLU 203": "OE1" <-> "OE2" Residue "N GLU 206": "OE1" <-> "OE2" Residue "O ARG 38": "NH1" <-> "NH2" Residue "O ARG 106": "NH1" <-> "NH2" Residue "O GLU 124": "OE1" <-> "OE2" Residue "O ARG 137": "NH1" <-> "NH2" Residue "O ARG 138": "NH1" <-> "NH2" Residue "O ARG 153": "NH1" <-> "NH2" Residue "P ARG 54": "NH1" <-> "NH2" 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 GLU 167": "OE1" <-> "OE2" Residue "P ARG 177": "NH1" <-> "NH2" Residue "Q ARG 74": "NH1" <-> "NH2" 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 "R ARG 11": "NH1" <-> "NH2" Residue "R ARG 13": "NH1" <-> "NH2" Residue "R ARG 32": "NH1" <-> "NH2" Residue "R ARG 122": "NH1" <-> "NH2" Residue "R ARG 123": "NH1" <-> "NH2" Residue "S ARG 155": "NH1" <-> "NH2" Residue "S ARG 184": "NH1" <-> "NH2" Residue "S GLU 199": "OE1" <-> "OE2" Residue "T ARG 49": "NH1" <-> "NH2" Residue "T ARG 77": "NH1" <-> "NH2" Residue "T GLU 107": "OE1" <-> "OE2" Residue "T ARG 130": "NH1" <-> "NH2" Residue "T ARG 137": "NH1" <-> "NH2" Residue "T ARG 149": "NH1" <-> "NH2" Residue "U ARG 11": "NH1" <-> "NH2" Residue "U ARG 69": "NH1" <-> "NH2" Residue "U ARG 71": "NH1" <-> "NH2" Residue "U ARG 80": "NH1" <-> "NH2" Residue "U ARG 83": "NH1" <-> "NH2" Residue "U ARG 143": "NH1" <-> "NH2" Residue "V ARG 185": "NH1" <-> "NH2" Residue "W ARG 49": "NH1" <-> "NH2" Residue "W ARG 74": "NH1" <-> "NH2" Residue "W ARG 109": "NH1" <-> "NH2" Residue "X GLU 18": "OE1" <-> "OE2" Residue "X ARG 23": "NH1" <-> "NH2" Residue "X ARG 59": "NH1" <-> "NH2" Residue "X ARG 77": "NH1" <-> "NH2" Residue "X GLU 137": "OE1" <-> "OE2" Residue "X ARG 163": "NH1" <-> "NH2" Residue "X ARG 183": "NH1" <-> "NH2" Residue "X ARG 184": "NH1" <-> "NH2" Residue "X ARG 216": "NH1" <-> "NH2" Residue "Y ARG 91": "NH1" <-> "NH2" Residue "Y GLU 96": "OE1" <-> "OE2" Residue "Y ARG 109": "NH1" <-> "NH2" Residue "Y ARG 131": "NH1" <-> "NH2" Residue "Y GLU 148": "OE1" <-> "OE2" Residue "Y ARG 162": "NH1" <-> "NH2" Residue "Y ARG 175": "NH1" <-> "NH2" Residue "Y ARG 196": "NH1" <-> "NH2" Residue "Y ARG 210": "NH1" <-> "NH2" Residue "Y GLU 212": "OE1" <-> "OE2" Residue "Y ARG 213": "NH1" <-> "NH2" Residue "0 GLU 133": "OE1" <-> "OE2" Residue "1 ARG 19": "NH1" <-> "NH2" 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 ARG 116": "NH1" <-> "NH2" Residue "3 ARG 125": "NH1" <-> "NH2" Residue "3 ARG 145": "NH1" <-> "NH2" Residue "3 ARG 168": "NH1" <-> "NH2" Residue "3 ARG 183": "NH1" <-> "NH2" Residue "5 ARG 48": "NH1" <-> "NH2" Residue "5 ARG 80": "NH1" <-> "NH2" Residue "5 ARG 86": "NH1" <-> "NH2" Residue "5 GLU 130": "OE1" <-> "OE2" Residue "5 ARG 223": "NH1" <-> "NH2" Residue "5 GLU 246": "OE1" <-> "OE2" Residue "5 ARG 303": "NH1" <-> "NH2" Residue "5 ARG 350": "NH1" <-> "NH2" Residue "6 ARG 56": "NH1" <-> "NH2" Residue "6 ARG 58": "NH1" <-> "NH2" Residue "6 ARG 60": "NH1" <-> "NH2" Residue "6 GLU 62": "OE1" <-> "OE2" Residue "6 ARG 72": "NH1" <-> "NH2" Residue "6 ARG 75": "NH1" <-> "NH2" Residue "6 ARG 136": "NH1" <-> "NH2" Residue "6 GLU 138": "OE1" <-> "OE2" Residue "6 ARG 159": "NH1" <-> "NH2" Residue "6 ARG 244": "NH1" <-> "NH2" Residue "6 ARG 261": "NH1" <-> "NH2" Residue "6 ARG 296": "NH1" <-> "NH2" Residue "6 ARG 299": "NH1" <-> "NH2" Residue "6 ARG 322": "NH1" <-> "NH2" Residue "6 ARG 360": "NH1" <-> "NH2" Residue "6 ARG 364": "NH1" <-> "NH2" Residue "7 ARG 168": "NH1" <-> "NH2" Residue "7 GLU 171": "OE1" <-> "OE2" Residue "7 GLU 220": "OE1" <-> "OE2" Residue "7 ARG 271": "NH1" <-> "NH2" Residue "9 ARG 17": "NH1" <-> "NH2" Residue "9 ARG 28": "NH1" <-> "NH2" Residue "9 ARG 49": "NH1" <-> "NH2" Residue "9 GLU 115": "OE1" <-> "OE2" Residue "9 GLU 120": "OE1" <-> "OE2" Residue "a GLU 104": "OE1" <-> "OE2" Residue "a GLU 110": "OE1" <-> "OE2" Residue "a ARG 128": "NH1" <-> "NH2" Residue "a ARG 131": "NH1" <-> "NH2" Residue "a ARG 142": "NH1" <-> "NH2" Residue "b ARG 28": "NH1" <-> "NH2" Residue "b ARG 35": "NH1" <-> "NH2" Residue "b ARG 41": "NH1" <-> "NH2" Residue "b PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b ARG 49": "NH1" <-> "NH2" Residue "b GLU 87": "OE1" <-> "OE2" Residue "b GLU 95": "OE1" <-> "OE2" Residue "b ARG 114": "NH1" <-> "NH2" Residue "b ARG 144": "NH1" <-> "NH2" Residue "b ARG 146": "NH1" <-> "NH2" Residue "c GLU 46": "OE1" <-> "OE2" Residue "c ARG 52": "NH1" <-> "NH2" Residue "c GLU 71": "OE1" <-> "OE2" Residue "c GLU 124": "OE1" <-> "OE2" Residue "c GLU 209": "OE1" <-> "OE2" Residue "c ARG 210": "NH1" <-> "NH2" Residue "c ARG 216": "NH1" <-> "NH2" Residue "c GLU 227": "OE1" <-> "OE2" Residue "c GLU 287": "OE1" <-> "OE2" Residue "c ARG 312": "NH1" <-> "NH2" Residue "d ARG 159": "NH1" <-> "NH2" Residue "d GLU 244": "OE1" <-> "OE2" Residue "d GLU 249": "OE1" <-> "OE2" 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 ARG 75": "NH1" <-> "NH2" Residue "i GLU 87": "OE1" <-> "OE2" Residue "i ARG 93": "NH1" <-> "NH2" Residue "i ARG 123": "NH1" <-> "NH2" Residue "j ARG 28": "NH1" <-> "NH2" Residue "j 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 ARG 103": "NH1" <-> "NH2" Residue "o ARG 38": "NH1" <-> "NH2" Residue "o ARG 60": "NH1" <-> "NH2" Residue "o ARG 68": "NH1" <-> "NH2" Residue "o ARG 86": "NH1" <-> "NH2" 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 ARG 132": "NH1" <-> "NH2" 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 GLU 78": "OE1" <-> "OE2" Residue "s ARG 81": "NH1" <-> "NH2" Residue "s ARG 143": "NH1" <-> "NH2" 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 GLU 214": "OE1" <-> "OE2" Residue "s ARG 219": "NH1" <-> "NH2" Residue "s ARG 222": "NH1" <-> "NH2" Residue "s ARG 223": "NH1" <-> "NH2" Residue "s ARG 242": "NH1" <-> "NH2" Residue "s ARG 276": "NH1" <-> "NH2" Residue "s ARG 308": "NH1" <-> "NH2" Residue "s ARG 389": "NH1" <-> "NH2" Residue "u TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "v ARG 6": "NH1" <-> "NH2" Residue "v ARG 14": "NH1" <-> "NH2" Residue "v ARG 24": "NH1" <-> "NH2" Residue "v ARG 28": "NH1" <-> "NH2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 85397 Number of models: 1 Model: "" Number of chains: 59 Chain: "D" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1671 Classifications: {'peptide': 215} Link IDs: {'PTRANS': 9, 'TRANS': 205} Chain: "E" Number of atoms: 2396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2396 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 24, 'TRANS': 279} Chain: "F" Number of atoms: 2013 Number of conformers: 1 Conformer: "" Number of residues, atoms: 250, 2013 Classifications: {'peptide': 250} Link IDs: {'PTRANS': 21, 'TRANS': 228} Chain: "H" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 5, 'TRANS': 89} Chain: "I" Number of atoms: 247 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 247 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 5, 'TRANS': 24} 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: 1621 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1621 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 13, 'TRANS': 187} 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: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 139, 1143 Classifications: {'peptide': 139} Link IDs: {'PTRANS': 3, 'TRANS': 135} Chain: "S" Number of atoms: 1251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 156, 1251 Classifications: {'peptide': 156} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 145} Chain: "T" Number of atoms: 1274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 1274 Classifications: {'peptide': 155} Link IDs: {'PTRANS': 12, 'TRANS': 142} Chain breaks: 1 Chain: "U" Number of atoms: 1030 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1030 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 11, 'TRANS': 113} Chain breaks: 1 Chain: "V" Number of atoms: 402 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 402 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "W" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 801 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 6, 'TRANS': 93} 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: 1506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1506 Classifications: {'peptide': 175} Link IDs: {'PTRANS': 7, 'TRANS': 167} Chain: "Z" Number of atoms: 937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 937 Classifications: {'peptide': 115} Link IDs: {'PTRANS': 10, 'TRANS': 104} 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: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 408 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 1, 'TRANS': 47} 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: 3199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 392, 3199 Classifications: {'peptide': 392} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 359} Chain: "6" Number of atoms: 2460 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 2460 Classifications: {'peptide': 292} Link IDs: {'PTRANS': 28, 'TRANS': 263} Chain breaks: 3 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: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 672 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 9, 'TRANS': 70} 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: 2214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 275, 2214 Classifications: {'peptide': 275} Link IDs: {'PCIS': 1, 'PTRANS': 15, 'TRANS': 258} Chain breaks: 1 Chain: "d" Number of atoms: 1308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 157, 1308 Classifications: {'peptide': 157} Link IDs: {'PTRANS': 11, 'TRANS': 145} Chain breaks: 3 Chain: "f" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 142 Classifications: {'peptide': 17} Link IDs: {'PTRANS': 1, 'TRANS': 15} 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: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 829 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 8, '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: 689 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 689 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 6, 'TRANS': 79} Chain: "o" Number of atoms: 687 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 687 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 4, 'TRANS': 76} Chain: "p" Number of atoms: 1045 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 1045 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain breaks: 3 Chain: "q" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 841 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 13, 'TRANS': 87} Chain: "r" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 1068 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 15, '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: 26670 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1256, 26670 Classifications: {'RNA': 1256} Modifications used: {'rna2p_pur': 125, 'rna2p_pyr': 94, 'rna3p_pur': 537, 'rna3p_pyr': 500} Link IDs: {'rna2p': 218, 'rna3p': 1037} Chain breaks: 25 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: "4" Number of atoms: 333 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 333 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "0" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "r" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 49 Unusual residues: {' MG': 49} Classifications: {'undetermined': 49} Link IDs: {None: 48} Chain: "4" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "i" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 28218 SG CYS 0 110 148.266 153.428 188.036 1.00 11.84 S ATOM 28320 SG CYS 0 123 148.209 149.444 186.976 1.00 6.73 S ATOM 28343 SG CYS 0 126 148.950 149.220 189.639 1.00 8.72 S ATOM 7096 SG CYS I 64 79.278 186.961 101.039 1.00 21.41 S ATOM 50979 SG CYS r 70 78.141 188.171 101.638 1.00 21.46 S ATOM 51294 SG CYS r 108 75.668 186.515 102.886 1.00 20.21 S ATOM 85091 SG CYS 4 76 53.800 171.720 127.895 1.00 26.75 S ATOM 85114 SG CYS 4 79 57.237 171.558 126.612 1.00 23.68 S ATOM 85238 SG CYS 4 92 56.536 172.780 130.202 1.00 22.02 S Time building chain proxies: 32.87, per 1000 atoms: 0.38 Number of scatterers: 85397 At special positions: 0 Unit cell: (222.6, 219.42, 243.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 3 29.99 S 247 16.00 P 1312 15.00 Mg 50 11.99 O 19065 8.00 N 15531 7.00 C 49189 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: 30.90 Conformation dependent library (CDL) restraints added in 9.1 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 0 126 " pdb="ZN ZN 0 200 " - pdb=" SG CYS 0 110 " pdb=" ZN 4 200 " pdb="ZN ZN 4 200 " - pdb=" NE2 HIS 4 98 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 76 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 79 " pdb="ZN ZN 4 200 " - pdb=" SG CYS 4 92 " pdb=" ZN r 301 " pdb="ZN ZN r 301 " - pdb=" SG CYS I 64 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 70 " pdb="ZN ZN r 301 " - pdb=" SG CYS r 108 " Number of angles added : 3 13778 Ramachandran restraints generated. 6889 Oldfield, 0 Emsley, 6889 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 13238 Finding SS restraints... Secondary structure from input PDB file: 255 helices and 64 sheets defined 37.7% alpha, 13.4% beta 335 base pairs and 619 stacking pairs defined. Time for finding SS restraints: 24.38 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 267 removed outlier: 3.781A pdb=" N ASN D 263 " --> pdb=" O LYS D 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 48 through 52 removed outlier: 4.547A pdb=" N HIS E 52 " --> pdb=" O TRP E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 57 through 75 Processing helix chain 'E' and resid 158 through 169 Processing helix chain 'E' and resid 182 through 186 Processing helix chain 'E' and resid 194 through 198 Processing helix chain 'E' and resid 217 through 223 Processing helix chain 'E' and resid 320 through 324 removed outlier: 3.746A pdb=" N ASP E 324 " --> pdb=" O PRO E 321 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 88 Processing helix chain 'F' and resid 92 through 106 removed outlier: 3.602A pdb=" N LEU F 96 " --> pdb=" O ARG F 92 " (cutoff:3.500A) Processing helix chain 'F' and resid 166 through 184 Processing helix chain 'F' and resid 199 through 210 removed outlier: 3.799A pdb=" N LEU F 203 " --> pdb=" O ASP F 199 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ARG F 210 " --> pdb=" O LEU F 206 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 237 removed outlier: 4.174A pdb=" N ARG F 236 " --> pdb=" O GLU F 232 " (cutoff:3.500A) removed outlier: 3.720A 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: 3.719A pdb=" N HIS F 256 " --> pdb=" O SER F 252 " (cutoff:3.500A) Processing helix chain 'F' and resid 263 through 275 Processing helix chain 'H' and resid 74 through 77 Processing helix chain 'H' and resid 116 through 122 Processing helix chain 'H' and resid 123 through 127 removed outlier: 4.221A pdb=" N GLN H 126 " --> pdb=" O LEU H 123 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY H 127 " --> pdb=" O LEU H 124 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 123 through 127' Processing helix chain 'H' and resid 136 through 146 removed outlier: 3.552A pdb=" N GLU H 141 " --> pdb=" O LYS H 137 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N GLU H 142 " --> pdb=" O LYS H 138 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLU H 143 " --> pdb=" O LEU H 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 41 through 51 Processing helix chain 'I' and resid 61 through 65 Processing helix chain 'K' and resid 5 through 15 Processing helix chain 'K' and resid 27 through 41 Processing helix chain 'K' and resid 48 through 52 removed outlier: 3.728A pdb=" N SER K 51 " --> pdb=" O HIS K 48 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ASP K 52 " --> pdb=" O ALA K 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 48 through 52' Processing helix chain 'K' and resid 61 through 64 Processing helix chain 'K' and resid 70 through 75 Processing helix chain 'K' and resid 92 through 99 Processing helix chain 'K' and resid 101 through 112 Processing helix chain 'K' and resid 116 through 123 removed outlier: 4.452A pdb=" N THR K 120 " --> pdb=" O LEU K 116 " (cutoff:3.500A) 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 removed outlier: 3.831A pdb=" N PHE K 166 " --> pdb=" O GLU K 162 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 141 removed outlier: 3.694A pdb=" N ALA L 141 " --> pdb=" O VAL L 137 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 16 Processing helix chain 'M' and resid 17 through 19 No H-bonds generated for 'chain 'M' and resid 17 through 19' Processing helix chain 'M' and resid 55 through 60 removed outlier: 3.515A pdb=" N GLY M 60 " --> pdb=" O GLU M 56 " (cutoff:3.500A) Processing helix chain 'M' and resid 98 through 107 Processing helix chain 'M' and resid 117 through 123 Processing helix chain 'M' and resid 130 through 133 Processing helix chain 'M' and resid 160 through 169 Processing helix chain 'M' and resid 180 through 189 removed outlier: 3.948A pdb=" N ASP M 185 " --> pdb=" O PRO M 181 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ILE M 186 " --> pdb=" O ARG M 182 " (cutoff:3.500A) Processing helix chain 'M' and resid 189 through 197 removed outlier: 3.826A pdb=" N PHE M 193 " --> pdb=" O LYS M 189 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N GLY M 197 " --> pdb=" O PHE M 193 " (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 228 through 241 Processing helix chain 'M' and resid 246 through 250 removed outlier: 3.716A pdb=" N LYS M 249 " --> pdb=" O ASP M 246 " (cutoff:3.500A) Processing helix chain 'M' and resid 252 through 258 removed outlier: 3.672A pdb=" N THR M 258 " --> pdb=" O LYS M 254 " (cutoff:3.500A) Processing helix chain 'M' and resid 287 through 296 removed outlier: 3.621A pdb=" N SER M 296 " --> pdb=" O LYS M 292 " (cutoff:3.500A) Processing helix chain 'N' and resid 98 through 111 removed outlier: 3.774A pdb=" N ARG N 111 " --> pdb=" O LEU N 107 " (cutoff:3.500A) Processing helix chain 'N' and resid 170 through 183 removed outlier: 4.886A pdb=" N ASP N 177 " --> pdb=" O GLN N 173 " (cutoff:3.500A) removed outlier: 4.819A pdb=" N GLN N 178 " --> pdb=" O GLY N 174 " (cutoff:3.500A) Processing helix chain 'N' and resid 192 through 208 Processing helix chain 'N' and resid 214 through 221 Processing helix chain 'N' and resid 225 through 230 removed outlier: 3.789A pdb=" N LEU N 230 " --> pdb=" O ARG N 227 " (cutoff:3.500A) Processing helix chain 'N' and resid 231 through 238 removed outlier: 3.912A pdb=" N LEU N 235 " --> pdb=" O SER N 231 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N THR N 236 " --> pdb=" O PRO N 232 " (cutoff:3.500A) Processing helix chain 'O' and resid 21 through 40 Processing helix chain 'O' and resid 46 through 65 removed outlier: 4.603A pdb=" N GLY O 54 " --> pdb=" O ASP O 50 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N TYR O 55 " --> pdb=" O GLU O 51 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU O 65 " --> pdb=" O ASP O 61 " (cutoff:3.500A) Processing helix chain 'O' and resid 69 through 80 removed outlier: 3.546A pdb=" N MET O 73 " --> pdb=" O ASN O 69 " (cutoff:3.500A) Processing helix chain 'O' and resid 84 through 92 removed outlier: 4.059A pdb=" N LYS O 88 " --> pdb=" O ASP O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 92 through 97 Processing helix chain 'O' and resid 143 through 160 Processing helix chain 'P' and resid 39 through 43 Processing helix chain 'P' and resid 54 through 59 Processing helix chain 'P' and resid 109 through 114 removed outlier: 4.091A pdb=" N LYS P 114 " --> pdb=" O TRP P 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 121 through 139 Processing helix chain 'P' and resid 149 through 155 Processing helix chain 'P' and resid 155 through 169 removed outlier: 3.665A pdb=" N LEU P 161 " --> pdb=" O SER P 157 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLY P 169 " --> pdb=" O MET P 165 " (cutoff:3.500A) Processing helix chain 'Q' and resid 77 through 81 Processing helix chain 'Q' and resid 88 through 104 removed outlier: 3.743A pdb=" N PHE Q 92 " --> pdb=" O ASP Q 88 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS Q 104 " --> pdb=" O LEU Q 100 " (cutoff:3.500A) Processing helix chain 'Q' and resid 143 through 146 removed outlier: 3.866A 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 188 through 192 Processing helix chain 'Q' and resid 194 through 198 Processing helix chain 'Q' and resid 244 through 249 removed outlier: 3.875A pdb=" N CYS Q 248 " --> pdb=" O ARG Q 244 " (cutoff:3.500A) Processing helix chain 'Q' and resid 252 through 257 removed outlier: 3.541A pdb=" N GLU Q 256 " --> pdb=" O GLN Q 252 " (cutoff:3.500A) Processing helix chain 'Q' and resid 268 through 272 removed outlier: 3.844A pdb=" N GLU Q 272 " --> pdb=" O MET Q 269 " (cutoff:3.500A) Processing helix chain 'Q' and resid 275 through 289 removed outlier: 3.828A pdb=" N ALA Q 281 " --> pdb=" O LYS Q 277 " (cutoff:3.500A) Processing helix chain 'R' and resid 16 through 26 removed outlier: 3.769A pdb=" N ARG R 20 " --> pdb=" O ASP R 16 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N VAL R 24 " --> pdb=" O ARG R 20 " (cutoff:3.500A) Processing helix chain 'R' and resid 33 through 37 removed outlier: 3.812A pdb=" N ASN R 36 " --> pdb=" O GLY R 33 " (cutoff:3.500A) Processing helix chain 'R' and resid 38 through 79 removed outlier: 4.421A pdb=" N ARG R 44 " --> pdb=" O ARG R 40 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N ARG R 57 " --> pdb=" O CYS R 53 " (cutoff:3.500A) removed outlier: 4.924A pdb=" N TYR R 58 " --> pdb=" O THR R 54 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N LEU R 59 " --> pdb=" O LYS R 55 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N HIS R 79 " --> pdb=" O ALA R 75 " (cutoff:3.500A) Processing helix chain 'R' and resid 82 through 91 Processing helix chain 'R' and resid 92 through 94 No H-bonds generated for 'chain 'R' and resid 92 through 94' 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 89 removed outlier: 3.781A pdb=" N ARG S 74 " --> pdb=" O VAL S 70 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR S 89 " --> pdb=" O GLU S 85 " (cutoff:3.500A) Processing helix chain 'T' and resid 50 through 54 Processing helix chain 'T' and resid 83 through 94 removed outlier: 4.858A pdb=" N TYR T 89 " --> pdb=" O ASP T 85 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU T 90 " --> pdb=" O LYS T 86 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N ILE T 94 " --> pdb=" O LEU T 90 " (cutoff:3.500A) Processing helix chain 'T' and resid 98 through 108 removed outlier: 3.834A pdb=" N PHE T 108 " --> pdb=" O ALA T 104 " (cutoff:3.500A) Processing helix chain 'T' and resid 112 through 131 removed outlier: 4.313A pdb=" N ILE T 116 " --> pdb=" O LYS T 112 " (cutoff:3.500A) Processing helix chain 'T' and resid 191 through 204 Processing helix chain 'U' and resid 49 through 62 Processing helix chain 'V' and resid 178 through 183 Processing helix chain 'V' and resid 193 through 202 removed outlier: 3.525A pdb=" N GLU V 200 " --> pdb=" O GLU V 196 " (cutoff:3.500A) Processing helix chain 'X' and resid 10 through 19 removed outlier: 3.806A pdb=" N ARG X 17 " --> pdb=" O ARG X 13 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLU X 18 " --> pdb=" O LEU X 14 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N GLY X 19 " --> pdb=" O GLN X 15 " (cutoff:3.500A) Processing helix chain 'X' and resid 20 through 24 removed outlier: 3.603A pdb=" N LEU X 24 " --> pdb=" O CYS X 21 " (cutoff:3.500A) Processing helix chain 'X' and resid 25 through 34 Processing helix chain 'X' and resid 72 through 78 Processing helix chain 'X' and resid 129 through 139 Processing helix chain 'X' and resid 140 through 148 Processing helix chain 'X' and resid 149 through 154 Processing helix chain 'X' and resid 155 through 172 Processing helix chain 'X' and resid 180 through 191 removed outlier: 3.583A pdb=" N TYR X 191 " --> pdb=" O ILE X 187 " (cutoff:3.500A) Processing helix chain 'X' and resid 192 through 195 removed outlier: 3.730A pdb=" N ALA X 195 " --> pdb=" O LYS X 192 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 192 through 195' Processing helix chain 'X' and resid 197 through 202 Processing helix chain 'X' and resid 207 through 220 Processing helix chain 'X' and resid 225 through 244 removed outlier: 3.671A pdb=" N ILE X 229 " --> pdb=" O PRO X 225 " (cutoff:3.500A) Processing helix chain 'Y' and resid 63 through 68 Processing helix chain 'Y' and resid 70 through 74 Processing helix chain 'Y' and resid 86 through 92 removed outlier: 3.907A pdb=" N ASN Y 92 " --> pdb=" O GLN Y 88 " (cutoff:3.500A) Processing helix chain 'Y' and resid 94 through 123 Processing helix chain 'Y' and resid 129 through 159 removed outlier: 3.997A pdb=" N ASP Y 133 " --> pdb=" O PRO Y 129 " (cutoff:3.500A) Processing helix chain 'Y' and resid 187 through 191 removed outlier: 3.655A pdb=" N ASN Y 191 " --> pdb=" O TRP Y 188 " (cutoff:3.500A) Processing helix chain 'Y' and resid 204 through 234 removed outlier: 4.585A pdb=" N PHE Y 208 " --> pdb=" O TYR Y 204 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE Y 219 " --> pdb=" O LYS Y 215 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LYS Y 220 " --> pdb=" O ARG Y 216 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N ALA Y 231 " --> pdb=" O GLU Y 227 " (cutoff:3.500A) Processing helix chain 'Z' and resid 42 through 46 Processing helix chain 'Z' and resid 49 through 54 removed outlier: 4.331A pdb=" N GLU Z 54 " --> pdb=" O PRO Z 50 " (cutoff:3.500A) Processing helix chain 'Z' and resid 79 through 89 removed outlier: 4.369A pdb=" N ILE Z 85 " --> pdb=" O TRP Z 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 103 through 111 removed outlier: 4.232A pdb=" N LYS Z 109 " --> pdb=" O SER Z 105 " (cutoff:3.500A) Processing helix chain '0' and resid 86 through 95 Processing helix chain '0' and resid 96 through 100 Processing helix chain '0' and resid 123 through 146 removed outlier: 3.793A pdb=" N GLU 0 133 " --> pdb=" O LYS 0 129 " (cutoff:3.500A) Processing helix chain '2' and resid 56 through 64 Processing helix chain '2' and resid 65 through 71 Processing helix chain '2' and resid 72 through 85 Processing helix chain '3' and resid 107 through 112 removed outlier: 4.076A pdb=" N ILE 3 111 " --> pdb=" O VAL 3 107 " (cutoff:3.500A) removed outlier: 3.598A 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 145 Processing helix chain '3' and resid 151 through 161 Processing helix chain '3' and resid 164 through 168 removed outlier: 3.566A pdb=" N ARG 3 168 " --> pdb=" O PHE 3 165 " (cutoff:3.500A) Processing helix chain '3' and resid 177 through 181 removed outlier: 3.672A pdb=" N HIS 3 181 " --> pdb=" O GLN 3 178 " (cutoff:3.500A) Processing helix chain '5' and resid 35 through 39 Processing helix chain '5' and resid 47 through 52 removed outlier: 3.568A pdb=" N ILE 5 52 " --> pdb=" O VAL 5 49 " (cutoff:3.500A) Processing helix chain '5' and resid 84 through 88 Processing helix chain '5' and resid 92 through 96 removed outlier: 3.660A pdb=" N HIS 5 96 " --> pdb=" O LEU 5 93 " (cutoff:3.500A) Processing helix chain '5' and resid 116 through 125 Processing helix chain '5' and resid 133 through 138 Processing helix chain '5' and resid 149 through 163 Processing helix chain '5' and resid 172 through 189 Proline residue: 5 178 - end of helix removed outlier: 3.878A pdb=" N VAL 5 181 " --> pdb=" O CYS 5 177 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLN 5 186 " --> pdb=" O ASP 5 182 " (cutoff:3.500A) Processing helix chain '5' and resid 241 through 246 removed outlier: 3.847A pdb=" N GLU 5 246 " --> pdb=" O ARG 5 242 " (cutoff:3.500A) Processing helix chain '5' and resid 247 through 249 No H-bonds generated for 'chain '5' and resid 247 through 249' Processing helix chain '5' and resid 299 through 303 Processing helix chain '5' and resid 305 through 329 Processing helix chain '5' and resid 408 through 420 Processing helix chain '6' and resid 53 through 65 Processing helix chain '6' and resid 73 through 78 removed outlier: 4.320A pdb=" N TYR 6 77 " --> pdb=" O THR 6 73 " (cutoff:3.500A) Processing helix chain '6' and resid 132 through 155 Proline residue: 6 145 - end of helix Processing helix chain '6' and resid 157 through 162 Processing helix chain '6' and resid 194 through 199 removed outlier: 3.919A pdb=" N ALA 6 199 " --> pdb=" O THR 6 196 " (cutoff:3.500A) Processing helix chain '6' and resid 292 through 295 Processing helix chain '6' and resid 299 through 307 Processing helix chain '6' and resid 327 through 333 removed outlier: 3.916A pdb=" N PHE 6 331 " --> pdb=" O VAL 6 327 " (cutoff:3.500A) Processing helix chain '6' and resid 364 through 369 removed outlier: 3.920A pdb=" N TYR 6 369 " --> pdb=" O TYR 6 365 " (cutoff:3.500A) Processing helix chain '7' and resid 37 through 57 removed outlier: 4.399A pdb=" N GLU 7 42 " --> pdb=" O THR 7 38 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N LEU 7 47 " --> pdb=" O MET 7 43 " (cutoff:3.500A) Processing helix chain '7' and resid 87 through 96 removed outlier: 3.943A pdb=" N HIS 7 94 " --> pdb=" O SER 7 90 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU 7 95 " --> pdb=" O CYS 7 91 " (cutoff:3.500A) Processing helix chain '7' and resid 96 through 103 Processing helix chain '7' and resid 135 through 155 Processing helix chain '7' and resid 173 through 177 removed outlier: 3.593A pdb=" N GLY 7 177 " --> pdb=" O VAL 7 174 " (cutoff:3.500A) Processing helix chain '7' and resid 186 through 190 removed outlier: 3.501A pdb=" N ASP 7 190 " --> pdb=" O SER 7 187 " (cutoff:3.500A) Processing helix chain '7' and resid 195 through 213 removed outlier: 3.529A pdb=" N ASP 7 213 " --> pdb=" O LEU 7 209 " (cutoff:3.500A) Processing helix chain '7' and resid 224 through 229 Processing helix chain '7' and resid 238 through 245 removed outlier: 3.522A pdb=" N GLU 7 242 " --> pdb=" O ASP 7 238 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ALA 7 244 " --> pdb=" O ILE 7 240 " (cutoff:3.500A) Processing helix chain '7' and resid 309 through 319 Processing helix chain '9' and resid 27 through 34 Processing helix chain '9' and resid 46 through 48 No H-bonds generated for 'chain '9' and resid 46 through 48' Processing helix chain '9' and resid 54 through 57 removed outlier: 3.835A 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 96 removed outlier: 3.733A pdb=" N GLU 9 94 " --> pdb=" O GLN 9 90 " (cutoff:3.500A) Processing helix chain '9' and resid 96 through 105 removed outlier: 3.784A pdb=" N LYS 9 105 " --> pdb=" O GLU 9 101 " (cutoff:3.500A) Processing helix chain '9' and resid 114 through 118 Processing helix chain 'a' and resid 68 through 72 Processing helix chain 'a' and resid 104 through 116 Processing helix chain 'a' and resid 127 through 134 Processing helix chain 'b' and resid 40 through 50 Processing helix chain 'b' and resid 50 through 58 Processing helix chain 'b' and resid 93 through 106 Processing helix chain 'b' and resid 139 through 143 removed outlier: 3.539A pdb=" N LEU b 143 " --> pdb=" O PHE b 140 " (cutoff:3.500A) Processing helix chain 'c' and resid 35 through 50 Processing helix chain 'c' and resid 67 through 79 removed outlier: 3.735A pdb=" N LEU c 79 " --> pdb=" O PHE c 75 " (cutoff:3.500A) Processing helix chain 'c' and resid 84 through 92 removed outlier: 3.525A pdb=" N PHE c 92 " --> pdb=" O LEU c 88 " (cutoff:3.500A) 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 removed outlier: 3.997A pdb=" N HIS c 168 " --> pdb=" O GLU c 164 " (cutoff:3.500A) Processing helix chain 'c' and resid 174 through 179 removed outlier: 3.860A 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 removed outlier: 3.528A pdb=" N THR c 211 " --> pdb=" O GLY c 207 " (cutoff:3.500A) Processing helix chain 'c' and resid 220 through 224 Processing helix chain 'c' and resid 227 through 231 Processing helix chain 'c' and resid 236 through 248 removed outlier: 3.668A pdb=" N LEU c 240 " --> pdb=" O ASN c 236 " (cutoff:3.500A) Processing helix chain 'c' and resid 288 through 306 Processing helix chain 'd' and resid 118 through 130 removed outlier: 4.287A pdb=" N ARG d 124 " --> pdb=" O VAL d 120 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ILE d 125 " --> pdb=" O SER d 121 " (cutoff:3.500A) Processing helix chain 'd' and resid 135 through 151 removed outlier: 4.484A pdb=" N GLU d 139 " --> pdb=" O LYS d 135 " (cutoff:3.500A) Processing helix chain 'd' and resid 156 through 164 removed outlier: 4.226A pdb=" N LEU d 160 " --> pdb=" O ASP d 156 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N THR d 162 " --> pdb=" O ASP d 158 " (cutoff:3.500A) Processing helix chain 'd' and resid 168 through 175 removed outlier: 3.593A pdb=" N MET d 172 " --> pdb=" O CYS d 168 " (cutoff:3.500A) Processing helix chain 'f' and resid 59 through 63 Processing helix chain 'g' and resid 45 through 50 removed outlier: 3.782A pdb=" N GLU g 49 " --> pdb=" O TYR g 45 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N ARG g 50 " --> pdb=" O GLN g 46 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 45 through 50' Processing helix chain 'g' and resid 116 through 133 removed outlier: 3.836A pdb=" N LEU g 120 " --> pdb=" O ASP g 116 " (cutoff:3.500A) Proline residue: g 130 - end of helix Processing helix chain 'g' and resid 153 through 164 Processing helix chain 'h' and resid 65 through 78 removed outlier: 3.956A pdb=" N GLU h 71 " --> pdb=" O GLN h 67 " (cutoff:3.500A) Processing helix chain 'h' and resid 85 through 89 Processing helix chain 'h' and resid 94 through 109 Processing helix chain 'h' and resid 113 through 117 removed outlier: 3.752A pdb=" N LEU h 117 " --> pdb=" O ASN h 114 " (cutoff:3.500A) Processing helix chain 'h' and resid 122 through 130 Processing helix chain 'h' and resid 138 through 144 removed outlier: 3.804A pdb=" N SER h 144 " --> pdb=" O PHE h 140 " (cutoff:3.500A) Processing helix chain 'i' and resid 48 through 53 Processing helix chain 'i' and resid 69 through 74 Processing helix chain 'i' and resid 86 through 99 Processing helix chain 'i' and resid 100 through 102 No H-bonds generated for 'chain 'i' and resid 100 through 102' Processing helix chain 'i' and resid 103 through 124 Processing helix chain 'j' and resid 24 through 31 Processing helix chain 'j' and resid 41 through 46 removed outlier: 3.510A pdb=" N LEU j 46 " --> pdb=" O PRO j 42 " (cutoff:3.500A) Processing helix chain 'j' and resid 60 through 100 Processing helix chain 'j' and resid 102 through 106 Processing helix chain 'o' and resid 28 through 48 removed outlier: 3.633A pdb=" N LYS o 32 " --> pdb=" O SER o 28 " (cutoff:3.500A) Processing helix chain 'o' and resid 55 through 60 removed outlier: 3.790A pdb=" N ARG o 60 " --> pdb=" O ARG o 56 " (cutoff:3.500A) Processing helix chain 'o' and resid 63 through 79 Processing helix chain 'o' and resid 87 through 94 removed outlier: 3.600A pdb=" N GLN o 91 " --> pdb=" O PHE o 87 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N HIS o 94 " --> pdb=" O ASP o 90 " (cutoff:3.500A) Processing helix chain 'o' and resid 95 through 99 Processing helix chain 'p' and resid 44 through 49 removed outlier: 3.627A pdb=" N TYR p 49 " --> pdb=" O LEU p 45 " (cutoff:3.500A) Processing helix chain 'p' and resid 50 through 53 removed outlier: 3.737A pdb=" N GLN p 53 " --> pdb=" O PRO p 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'p' and resid 50 through 53' Processing helix chain 'p' and resid 112 through 123 Processing helix chain 'p' and resid 142 through 162 removed outlier: 3.554A pdb=" N ASN p 146 " --> pdb=" O TYR p 142 " (cutoff:3.500A) Processing helix chain 'p' and resid 177 through 185 removed outlier: 4.265A pdb=" N MET p 183 " --> pdb=" O ARG p 179 " (cutoff:3.500A) Processing helix chain 'q' and resid 48 through 52 removed outlier: 3.741A pdb=" N LEU q 52 " --> pdb=" O ARG q 49 " (cutoff:3.500A) Processing helix chain 'q' and resid 53 through 65 removed outlier: 3.907A pdb=" N ALA q 57 " --> pdb=" O GLY q 53 " (cutoff:3.500A) Processing helix chain 'q' and resid 66 through 69 Processing helix chain 'q' and resid 71 through 76 removed outlier: 3.739A pdb=" N TRP q 76 " --> pdb=" O GLY q 73 " (cutoff:3.500A) Processing helix chain 'q' and resid 78 through 93 removed outlier: 3.865A pdb=" N GLU q 84 " --> pdb=" O GLU q 80 " (cutoff:3.500A) Processing helix chain 'q' and resid 95 through 118 removed outlier: 4.132A pdb=" N GLU q 118 " --> pdb=" O ARG q 114 " (cutoff:3.500A) Processing helix chain 'q' and resid 119 through 121 No H-bonds generated for 'chain 'q' and resid 119 through 121' Processing helix chain 'r' and resid 85 through 90 Processing helix chain 'r' and resid 101 through 106 Processing helix chain 'r' and resid 108 through 125 removed outlier: 3.842A pdb=" N LYS r 114 " --> pdb=" O GLU r 110 " (cutoff:3.500A) Processing helix chain 'r' and resid 167 through 171 removed outlier: 3.679A pdb=" N ARG r 171 " --> pdb=" O ARG r 168 " (cutoff:3.500A) Processing helix chain 'r' and resid 178 through 182 removed outlier: 3.571A pdb=" N LEU r 181 " --> pdb=" O SER r 178 " (cutoff:3.500A) Processing helix chain 's' and resid 55 through 72 removed outlier: 3.559A pdb=" N ARG s 59 " --> pdb=" O SER s 55 " (cutoff:3.500A) Processing helix chain 's' and resid 75 through 85 Processing helix chain 's' and resid 101 through 109 removed outlier: 3.822A pdb=" N TRP s 105 " --> pdb=" O ASN s 101 " (cutoff:3.500A) Processing helix chain 's' and resid 141 through 155 Processing helix chain 's' and resid 167 through 172 Processing helix chain 's' and resid 173 through 189 Processing helix chain 's' and resid 192 through 197 removed outlier: 4.056A pdb=" N ALA s 196 " --> pdb=" O ASN s 192 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ALA s 197 " --> pdb=" O PRO s 193 " (cutoff:3.500A) No H-bonds generated for 'chain 's' and resid 192 through 197' Processing helix chain 's' and resid 267 through 271 Processing helix chain 's' and resid 309 through 314 removed outlier: 3.699A pdb=" N GLN s 314 " --> pdb=" O ARG s 310 " (cutoff:3.500A) Processing helix chain 's' and resid 319 through 343 removed outlier: 3.922A pdb=" N VAL s 323 " --> pdb=" O GLN s 319 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N PHE s 324 " --> pdb=" O ILE s 320 " (cutoff:3.500A) Processing helix chain 's' and resid 415 through 426 Processing helix chain 'u' and resid 93 through 104 removed outlier: 3.708A pdb=" N MET u 97 " --> pdb=" O ASP u 93 " (cutoff:3.500A) Processing helix chain 'u' and resid 131 through 150 removed outlier: 4.091A pdb=" N LYS u 150 " --> pdb=" O TYR u 146 " (cutoff:3.500A) Processing helix chain 'u' and resid 181 through 188 Processing helix chain 'u' and resid 189 through 196 removed outlier: 3.537A pdb=" N LEU u 193 " --> pdb=" O GLU u 189 " (cutoff:3.500A) Processing helix chain 'v' and resid 7 through 21 Processing helix chain 'v' and resid 27 through 41 removed outlier: 3.808A pdb=" N PHE v 39 " --> pdb=" O ILE v 35 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LYS v 41 " --> pdb=" O ARG v 37 " (cutoff:3.500A) Processing helix chain 'v' and resid 49 through 64 removed outlier: 4.491A pdb=" N ARG v 53 " --> pdb=" O GLU v 49 " (cutoff:3.500A) Processing helix chain 'w' and resid 75 through 90 removed outlier: 3.560A pdb=" N TYR w 90 " --> pdb=" O VAL w 86 " (cutoff:3.500A) Processing helix chain 'w' and resid 111 through 123 Processing helix chain 'w' and resid 131 through 136 removed outlier: 3.785A pdb=" N ALA w 135 " --> pdb=" O PRO w 131 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLU w 136 " --> pdb=" O ASP w 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'w' and resid 131 through 136' Processing helix chain 'w' and resid 140 through 152 removed outlier: 4.004A pdb=" N LYS w 152 " --> pdb=" O ILE w 148 " (cutoff:3.500A) Processing helix chain '4' and resid 95 through 98 removed outlier: 3.799A pdb=" N HIS 4 98 " --> pdb=" O HIS 4 95 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 95 through 98' Processing sheet with id=AA1, first strand: chain 'D' and resid 77 through 78 Processing sheet with id=AA2, first strand: chain 'D' and resid 147 through 152 removed outlier: 6.814A pdb=" N LEU D 141 " --> pdb=" O ILE D 127 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 181 through 183 removed outlier: 6.660A pdb=" N ILE D 225 " --> pdb=" O LEU D 217 " (cutoff:3.500A) removed outlier: 4.855A pdb=" N LYS D 219 " --> pdb=" O THR D 223 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR D 223 " --> pdb=" O LYS D 219 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG D 232 " --> pdb=" O LEU D 228 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 331 through 333 removed outlier: 5.081A pdb=" N LYS E 272 " --> pdb=" O ASN E 286 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N TYR E 284 " --> pdb=" O TRP E 274 " (cutoff:3.500A) removed outlier: 4.473A pdb=" N ILE E 276 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N ILE E 282 " --> pdb=" O ILE E 276 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N VAL E 119 " --> pdb=" O MET E 106 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N MET E 106 " --> pdb=" O VAL E 119 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N LEU E 121 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 7.739A pdb=" N LEU E 296 " --> pdb=" O LYS E 209 " (cutoff:3.500A) removed outlier: 5.265A pdb=" N LYS E 209 " --> pdb=" O LEU E 296 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N VAL E 206 " --> pdb=" O TYR E 269 " (cutoff:3.500A) removed outlier: 5.415A pdb=" N TYR E 269 " --> pdb=" O VAL E 206 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N ALA E 208 " --> pdb=" O THR E 267 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N THR E 267 " --> pdb=" O ALA E 208 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 128 through 133 removed outlier: 6.290A pdb=" N SER E 146 " --> pdb=" O LEU E 130 " (cutoff:3.500A) removed outlier: 4.491A pdb=" N TYR E 132 " --> pdb=" O THR E 144 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR E 144 " --> pdb=" O TYR E 132 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N THR E 175 " --> pdb=" O GLY E 149 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 214 through 216 removed outlier: 3.988A pdb=" N GLY E 214 " --> pdb=" O MET E 261 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'F' and resid 62 through 66 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 190 removed outlier: 3.593A pdb=" N LEU F 261 " --> pdb=" O HIS F 188 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU F 217 " --> pdb=" O VAL F 260 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N THR F 262 " --> pdb=" O LEU F 217 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL F 219 " --> pdb=" O THR F 262 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N VAL F 216 " --> pdb=" O ASN F 241 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N ILE F 243 " --> pdb=" O VAL F 216 " (cutoff:3.500A) removed outlier: 6.244A 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: 6.616A pdb=" N GLU H 57 " --> pdb=" O LEU H 82 " (cutoff:3.500A) removed outlier: 5.503A pdb=" N LEU H 82 " --> pdb=" O GLU H 57 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N TYR X 91 " --> pdb=" O TYR H 80 " (cutoff:3.500A) removed outlier: 8.354A pdb=" N LEU H 82 " --> pdb=" O TYR X 91 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'H' and resid 111 through 115 Processing sheet with id=AB3, first strand: chain 'K' and resid 125 through 127 removed outlier: 6.437A pdb=" N VAL K 57 " --> pdb=" O HIS K 126 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N TRP K 18 " --> pdb=" O VAL K 142 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N GLU K 144 " --> pdb=" O TRP K 18 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LEU K 20 " --> pdb=" O GLU K 144 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 66 through 68 removed outlier: 3.788A pdb=" N TYR r 150 " --> pdb=" O PHE K 67 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 76 through 80 Processing sheet with id=AB6, first strand: chain 'L' and resid 39 through 40 removed outlier: 6.297A pdb=" N ARG L 39 " --> pdb=" O VAL L 105 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N LEU L 107 " --> pdb=" O ARG L 39 " (cutoff:3.500A) removed outlier: 5.852A pdb=" N ASN L 104 " --> pdb=" O VAL L 87 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N HIS L 59 " --> pdb=" O LEU L 74 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N ALA L 76 " --> pdb=" O CYS L 57 " (cutoff:3.500A) removed outlier: 6.077A pdb=" N CYS L 57 " --> pdb=" O ALA L 76 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'M' and resid 92 through 97 removed outlier: 7.871A pdb=" N GLN M 92 " --> pdb=" O TYR M 136 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N VAL M 138 " --> pdb=" O GLN M 92 " (cutoff:3.500A) removed outlier: 5.674A pdb=" N LYS M 94 " --> pdb=" O VAL M 138 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N LEU M 140 " --> pdb=" O LYS M 94 " (cutoff:3.500A) removed outlier: 5.992A 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 156 removed outlier: 6.590A pdb=" N ILE M 154 " --> pdb=" O THR M 175 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 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 118 through 122 removed outlier: 6.403A pdb=" N LEU N 159 " --> pdb=" O ALA N 91 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N ALA N 91 " --> pdb=" O LEU N 159 " (cutoff:3.500A) removed outlier: 4.702A pdb=" N VAL N 161 " --> pdb=" O ILE N 89 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ILE N 89 " --> pdb=" O VAL N 161 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'N' and resid 95 through 97 removed outlier: 4.121A pdb=" N ILE N 131 " --> pdb=" O ASP N 148 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N TYR N 150 " --> pdb=" O LYS N 129 " (cutoff:3.500A) removed outlier: 5.634A pdb=" N LYS N 129 " --> pdb=" O TYR N 150 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'O' and resid 41 through 45 Processing sheet with id=AC4, first strand: chain 'P' and resid 47 through 48 removed outlier: 4.268A pdb=" N PHE W 142 " --> pdb=" O PHE P 48 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N PHE W 142 " --> pdb=" O VAL 6 345 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N VAL 6 345 " --> pdb=" O PHE W 142 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N LEU W 144 " --> pdb=" O GLU 6 343 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N GLU 6 343 " --> pdb=" O LEU W 144 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N ALA W 146 " --> pdb=" O VAL 6 341 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'P' and resid 79 through 85 removed outlier: 6.152A pdb=" N HIS P 96 " --> pdb=" O VAL P 101 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N VAL P 101 " --> pdb=" O HIS P 96 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'Q' and resid 158 through 165 removed outlier: 7.144A pdb=" N THR Q 148 " --> pdb=" O ARG Q 140 " (cutoff:3.500A) removed outlier: 4.935A pdb=" N ARG Q 140 " --> pdb=" O THR Q 148 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N ILE Q 150 " --> pdb=" O ILE Q 138 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL Q 154 " --> pdb=" O LEU Q 134 " (cutoff:3.500A) removed outlier: 9.199A pdb=" N LEU Q 134 " --> pdb=" O VAL Q 154 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ILE Q 116 " --> pdb=" O VAL Q 177 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N ALA Q 122 " --> pdb=" O VAL Q 171 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N VAL Q 171 " --> pdb=" O ALA Q 122 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'S' and resid 105 through 109 removed outlier: 6.544A pdb=" N PHE S 96 " --> pdb=" O VAL S 136 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N VAL S 136 " --> pdb=" O PHE S 96 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N VAL S 98 " --> pdb=" O LEU S 134 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N LEU S 134 " --> pdb=" O GLY S 145 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'b' and resid 119 through 120 removed outlier: 6.955A pdb=" N GLN S 190 " --> pdb=" O LYS S 163 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYS S 163 " --> pdb=" O GLN S 190 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N VAL S 192 " --> pdb=" O ILE S 161 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N GLU S 157 " --> pdb=" O ASN S 196 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE S 198 " --> pdb=" O ARG S 155 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ARG S 155 " --> pdb=" O ILE S 198 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N VAL S 156 " --> pdb=" O LEU S 130 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'S' and resid 169 through 175 removed outlier: 4.046A pdb=" N PHE S 180 " --> pdb=" O ARG S 175 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'T' and resid 72 through 80 removed outlier: 6.852A pdb=" N GLU T 72 " --> pdb=" O GLU T 180 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N GLU T 180 " --> pdb=" O GLU T 72 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N TYR T 74 " --> pdb=" O LEU T 178 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N LEU T 178 " --> pdb=" O TYR T 74 " (cutoff:3.500A) removed outlier: 5.236A pdb=" N CYS T 76 " --> pdb=" O VAL T 176 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL T 176 " --> pdb=" O CYS T 76 " (cutoff:3.500A) removed outlier: 5.589A pdb=" N ARG T 78 " --> pdb=" O TYR T 174 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR T 174 " --> pdb=" O ARG T 78 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N VAL T 179 " --> pdb=" O ILE T 142 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ILE T 142 " --> pdb=" O VAL T 179 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'U' and resid 18 through 19 removed outlier: 3.611A pdb=" N VAL U 19 " --> pdb=" O GLU 9 59 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'U' and resid 27 through 28 removed outlier: 3.768A pdb=" N LYS U 93 " --> pdb=" O ILE U 44 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'V' and resid 176 through 177 Processing sheet with id=AD5, first strand: chain 'W' and resid 60 through 61 Processing sheet with id=AD6, first strand: chain 'W' and resid 66 through 68 removed outlier: 6.665A pdb=" N LEU W 89 " --> pdb=" O ILE W 67 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'X' and resid 50 through 52 Processing sheet with id=AD8, first strand: chain 'X' and resid 109 through 116 Processing sheet with id=AD9, first strand: chain 'Y' and resid 166 through 170 Processing sheet with id=AE1, first strand: chain 'Z' and resid 98 through 101 Processing sheet with id=AE2, first strand: chain 'Z' and resid 137 through 139 Processing sheet with id=AE3, first strand: chain '0' and resid 107 through 109 Processing sheet with id=AE4, first strand: chain '0' and resid 156 through 159 removed outlier: 3.509A pdb=" N LEU 0 159 " --> pdb=" O ILE 0 175 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain '1' and resid 30 through 35 removed outlier: 3.503A pdb=" N PHE 1 30 " --> pdb=" O MET 1 20 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU 1 17 " --> pdb=" O LYS 1 61 " (cutoff:3.500A) removed outlier: 5.425A pdb=" N LYS 1 61 " --> pdb=" O LEU 1 17 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ARG 1 19 " --> pdb=" O LYS 1 59 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N LYS 1 59 " --> pdb=" O ARG 1 19 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain '3' and resid 115 through 116 Processing sheet with id=AE7, first strand: chain '5' and resid 207 through 215 removed outlier: 6.126A pdb=" N TYR 5 105 " --> pdb=" O GLN 5 221 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N ARG 5 223 " --> pdb=" O TYR 5 105 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N PHE 5 107 " --> pdb=" O ARG 5 223 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER 5 225 " --> pdb=" O PHE 5 107 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain '5' and resid 126 through 130 removed outlier: 7.119A pdb=" N ASN 5 372 " --> pdb=" O ASN 5 360 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N ASN 5 360 " --> pdb=" O ASN 5 372 " (cutoff:3.500A) removed outlier: 5.494A pdb=" N ALA 5 374 " --> pdb=" O GLN 5 358 " (cutoff:3.500A) removed outlier: 7.354A pdb=" N GLN 5 358 " --> pdb=" O ALA 5 374 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N VAL 5 376 " --> pdb=" O VAL 5 356 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N VAL 5 356 " --> pdb=" O VAL 5 376 " (cutoff:3.500A) removed outlier: 5.417A pdb=" N SER 5 378 " --> pdb=" O PHE 5 354 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N PHE 5 354 " --> pdb=" O SER 5 378 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N THR 5 361 " --> pdb=" O GLN 5 338 " (cutoff:3.500A) removed outlier: 10.390A pdb=" N GLN 5 338 " --> pdb=" O THR 5 361 " (cutoff:3.500A) removed outlier: 9.317A pdb=" N TYR 5 287 " --> pdb=" O VAL 5 341 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N GLN 5 343 " --> pdb=" O TYR 5 287 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N HIS 5 289 " --> pdb=" O GLN 5 343 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N VAL 5 345 " --> pdb=" O HIS 5 289 " (cutoff:3.500A) removed outlier: 6.235A pdb=" N LEU 5 291 " --> pdb=" O VAL 5 345 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N THR 5 347 " --> pdb=" O LEU 5 291 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N LEU 5 293 " --> pdb=" O THR 5 347 " (cutoff:3.500A) removed outlier: 7.053A pdb=" N LEU 5 230 " --> pdb=" O HIS 5 289 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ILE 5 202 " --> pdb=" O SER 5 231 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain '5' and resid 383 through 387 removed outlier: 6.565A pdb=" N TYR 5 383 " --> pdb=" O PHE 5 406 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N PHE 5 406 " --> pdb=" O TYR 5 383 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain '6' and resid 177 through 178 removed outlier: 3.509A pdb=" N TYR 6 177 " --> pdb=" O MET 6 185 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain '6' and resid 191 through 192 removed outlier: 6.027A pdb=" N ASN 6 191 " --> pdb=" O GLN 6 320 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU 6 272 " --> pdb=" O ALA 6 314 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N LEU 6 316 " --> pdb=" O PHE 6 270 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N PHE 6 270 " --> pdb=" O LEU 6 316 " (cutoff:3.500A) removed outlier: 4.528A pdb=" N PHE 6 318 " --> pdb=" O LEU 6 268 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N LEU 6 268 " --> pdb=" O PHE 6 318 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N GLN 6 320 " --> pdb=" O HIS 6 266 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N HIS 6 266 " --> pdb=" O GLN 6 320 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N TRP 6 214 " --> pdb=" O ASN 6 239 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N ASN 6 239 " --> pdb=" O TRP 6 214 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TRP 6 235 " --> pdb=" O LEU 6 218 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N SER 6 220 " --> pdb=" O LEU 6 233 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N LEU 6 233 " --> pdb=" O SER 6 220 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain '7' and resid 112 through 113 removed outlier: 8.830A pdb=" N CYS 7 123 " --> pdb=" O LYS 7 64 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N GLU 7 66 " --> pdb=" O CYS 7 123 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N ILE 7 125 " --> pdb=" O GLU 7 66 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N LYS 7 68 " --> pdb=" O ILE 7 125 " (cutoff:3.500A) removed outlier: 8.644A pdb=" N PHE 7 127 " --> pdb=" O LYS 7 68 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain '7' and resid 165 through 168 removed outlier: 5.516A pdb=" N LEU 7 166 " --> pdb=" O VAL 7 184 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N VAL 7 184 " --> pdb=" O LEU 7 166 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ILE 7 294 " --> pdb=" O HIS 7 284 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N HIS 7 284 " --> pdb=" O ILE 7 294 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ARG 7 296 " --> pdb=" O ALA 7 282 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N ALA 7 282 " --> pdb=" O ARG 7 296 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLN 7 298 " --> pdb=" O VAL 7 280 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N VAL 7 280 " --> pdb=" O GLN 7 298 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N VAL 7 300 " --> pdb=" O TYR 7 278 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N TYR 7 278 " --> pdb=" O VAL 7 300 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N LEU 7 302 " --> pdb=" O PHE 7 276 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain '7' and resid 217 through 222 Processing sheet with id=AF6, first strand: chain '9' and resid 42 through 44 Processing sheet with id=AF7, first strand: chain 'a' and resid 73 through 74 removed outlier: 5.561A pdb=" N SER c 255 " --> pdb=" O TYR c 275 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N TYR c 275 " --> pdb=" O SER c 255 " (cutoff:3.500A) removed outlier: 5.218A pdb=" N LEU c 257 " --> pdb=" O GLY c 273 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N GLY c 273 " --> pdb=" O LEU c 257 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'b' and resid 8 through 9 Processing sheet with id=AF9, first strand: chain 'b' and resid 84 through 87 removed outlier: 6.822A pdb=" N ARG b 74 " --> pdb=" O PHE b 31 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N PHE b 31 " --> pdb=" O ARG b 74 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL b 76 " --> pdb=" O LEU b 29 " (cutoff:3.500A) removed outlier: 4.360A pdb=" N LEU b 29 " --> pdb=" O VAL b 76 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLU b 78 " --> pdb=" O GLN b 27 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ILE b 63 " --> pdb=" O LYS h 153 " (cutoff:3.500A) removed outlier: 8.143A pdb=" N THR h 155 " --> pdb=" O ILE b 63 " (cutoff:3.500A) removed outlier: 7.144A pdb=" N VAL b 65 " --> pdb=" O THR h 155 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'd' and resid 184 through 188 removed outlier: 6.748A pdb=" N ARG d 219 " --> pdb=" O VAL d 186 " (cutoff:3.500A) removed outlier: 5.178A pdb=" N SER d 188 " --> pdb=" O HIS d 217 " (cutoff:3.500A) removed outlier: 7.639A pdb=" N HIS d 217 " --> pdb=" O SER d 188 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL d 247 " --> pdb=" O HIS d 262 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'd' and resid 224 through 225 removed outlier: 6.532A pdb=" N ILE d 224 " --> pdb=" O MET d 232 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'g' and resid 84 through 86 Processing sheet with id=AG4, first strand: chain 'g' and resid 96 through 101 Processing sheet with id=AG5, first strand: chain 'p' and resid 97 through 104 removed outlier: 7.541A pdb=" N SER p 97 " --> pdb=" O SER p 139 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER p 139 " --> pdb=" O SER p 97 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 's' and resid 206 through 216 removed outlier: 5.372A pdb=" N HIS s 207 " --> pdb=" O ASP s 235 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N ASP s 235 " --> pdb=" O HIS s 207 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N TYR s 209 " --> pdb=" O ILE s 233 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N ILE s 233 " --> pdb=" O TYR s 209 " (cutoff:3.500A) removed outlier: 5.654A pdb=" N VAL s 211 " --> pdb=" O TYR s 231 " (cutoff:3.500A) removed outlier: 6.855A pdb=" N TYR s 231 " --> pdb=" O VAL s 211 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N GLY s 213 " --> pdb=" O LEU s 229 " (cutoff:3.500A) removed outlier: 4.224A pdb=" N ASP s 234 " --> pdb=" O VAL s 93 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 's' and resid 112 through 113 Processing sheet with id=AG8, first strand: chain 's' and resid 199 through 202 removed outlier: 6.366A pdb=" N GLN s 298 " --> pdb=" O VAL s 360 " (cutoff:3.500A) removed outlier: 7.741A pdb=" N THR s 362 " --> pdb=" O GLN s 298 " (cutoff:3.500A) removed outlier: 6.070A pdb=" N HIS s 300 " --> pdb=" O THR s 362 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'u' and resid 159 through 160 Processing sheet with id=AH1, first strand: chain '4' and resid 67 through 68 removed outlier: 5.929A pdb=" N LYS 4 67 " --> pdb=" O ARG 4 101 " (cutoff:3.500A) 2018 hydrogen bonds defined for protein. 5589 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 822 hydrogen bonds 1448 hydrogen bond angles 0 basepair planarities 335 basepair parallelities 619 stacking parallelities Total time for adding SS restraints: 58.01 Time building geometry restraints manager: 33.64 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: 17023 1.33 - 1.45: 28174 1.45 - 1.57: 41859 1.57 - 1.70: 2593 1.70 - 1.82: 388 Bond restraints: 90037 Sorted by residual: bond pdb=" C LYS i 68 " pdb=" N HIS i 69 " ideal model delta sigma weight residual 1.329 1.284 0.044 1.35e-02 5.49e+03 1.08e+01 bond pdb=" C ALA Y 163 " pdb=" N ARG Y 164 " ideal model delta sigma weight residual 1.331 1.284 0.047 1.63e-02 3.76e+03 8.41e+00 bond pdb=" CA SER D 272 " pdb=" CB SER D 272 " ideal model delta sigma weight residual 1.530 1.487 0.043 1.55e-02 4.16e+03 7.61e+00 bond pdb=" C HIS K 43 " pdb=" N LYS K 44 " ideal model delta sigma weight residual 1.332 1.294 0.039 1.44e-02 4.82e+03 7.18e+00 bond pdb=" C ARG D 269 " pdb=" N PRO D 270 " ideal model delta sigma weight residual 1.335 1.312 0.023 8.70e-03 1.32e+04 6.91e+00 ... (remaining 90032 not shown) Histogram of bond angle deviations from ideal: 98.69 - 105.77: 8247 105.77 - 112.85: 49205 112.85 - 119.93: 32702 119.93 - 127.02: 33889 127.02 - 134.10: 3919 Bond angle restraints: 127962 Sorted by residual: angle pdb=" C2' C A2713 " pdb=" C1' C A2713 " pdb=" N1 C A2713 " ideal model delta sigma weight residual 112.00 117.56 -5.56 1.50e+00 4.44e-01 1.37e+01 angle pdb=" N VAL P 61 " pdb=" CA VAL P 61 " pdb=" C VAL P 61 " ideal model delta sigma weight residual 113.47 109.81 3.66 1.01e+00 9.80e-01 1.31e+01 angle pdb=" N ARG M 47 " pdb=" CA ARG M 47 " pdb=" C ARG M 47 " ideal model delta sigma weight residual 113.43 109.01 4.42 1.26e+00 6.30e-01 1.23e+01 angle pdb=" CA VAL s 251 " pdb=" C VAL s 251 " pdb=" N PRO s 252 " ideal model delta sigma weight residual 116.57 119.98 -3.41 9.80e-01 1.04e+00 1.21e+01 angle pdb=" C4' C A2718 " pdb=" C3' C A2718 " pdb=" O3' C A2718 " ideal model delta sigma weight residual 109.40 114.47 -5.07 1.50e+00 4.44e-01 1.14e+01 ... (remaining 127957 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.76: 52029 35.76 - 71.52: 3055 71.52 - 107.27: 429 107.27 - 143.03: 10 143.03 - 178.79: 11 Dihedral angle restraints: 55534 sinusoidal: 35082 harmonic: 20452 Sorted by residual: dihedral pdb=" O4' C A2474 " pdb=" C1' C A2474 " pdb=" N1 C A2474 " pdb=" C2 C A2474 " ideal model delta sinusoidal sigma weight residual -160.00 13.04 -173.04 1 1.50e+01 4.44e-03 8.50e+01 dihedral pdb=" O4' C A2511 " pdb=" C1' C A2511 " pdb=" N1 C A2511 " pdb=" C2 C A2511 " ideal model delta sinusoidal sigma weight residual 200.00 34.79 165.21 1 1.50e+01 4.44e-03 8.39e+01 dihedral pdb=" O4' C A3009 " pdb=" C1' C A3009 " pdb=" N1 C A3009 " pdb=" C2 C A3009 " ideal model delta sinusoidal sigma weight residual 200.00 39.18 160.82 1 1.50e+01 4.44e-03 8.30e+01 ... (remaining 55531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 11277 0.048 - 0.096: 3040 0.096 - 0.144: 632 0.144 - 0.192: 48 0.192 - 0.239: 10 Chirality restraints: 15007 Sorted by residual: chirality pdb=" C3' A A1986 " pdb=" C4' A A1986 " pdb=" O3' A A1986 " pdb=" C2' A A1986 " both_signs ideal model delta sigma weight residual False -2.74 -2.51 -0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" C1' A A2245 " pdb=" O4' A A2245 " pdb=" C2' A A2245 " pdb=" N9 A A2245 " both_signs ideal model delta sigma weight residual False 2.44 2.20 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" C1' A A2444 " pdb=" O4' A A2444 " pdb=" C2' A A2444 " pdb=" N9 A A2444 " both_signs ideal model delta sigma weight residual False 2.44 2.21 0.23 2.00e-01 2.50e+01 1.34e+00 ... (remaining 15004 not shown) Planarity restraints: 11567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C A2713 " 0.050 2.00e-02 2.50e+03 2.60e-02 1.53e+01 pdb=" N1 C A2713 " -0.057 2.00e-02 2.50e+03 pdb=" C2 C A2713 " -0.004 2.00e-02 2.50e+03 pdb=" O2 C A2713 " -0.004 2.00e-02 2.50e+03 pdb=" N3 C A2713 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C A2713 " 0.005 2.00e-02 2.50e+03 pdb=" N4 C A2713 " 0.016 2.00e-02 2.50e+03 pdb=" C5 C A2713 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C A2713 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY a 106 " -0.059 5.00e-02 4.00e+02 8.99e-02 1.29e+01 pdb=" N PRO a 107 " 0.155 5.00e-02 4.00e+02 pdb=" CA PRO a 107 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO a 107 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' G A3163 " -0.023 2.00e-02 2.50e+03 1.82e-02 9.99e+00 pdb=" N9 G A3163 " 0.018 2.00e-02 2.50e+03 pdb=" C8 G A3163 " -0.002 2.00e-02 2.50e+03 pdb=" N7 G A3163 " 0.002 2.00e-02 2.50e+03 pdb=" C5 G A3163 " 0.002 2.00e-02 2.50e+03 pdb=" C6 G A3163 " 0.023 2.00e-02 2.50e+03 pdb=" O6 G A3163 " -0.024 2.00e-02 2.50e+03 pdb=" N1 G A3163 " -0.014 2.00e-02 2.50e+03 pdb=" C2 G A3163 " 0.038 2.00e-02 2.50e+03 pdb=" N2 G A3163 " -0.019 2.00e-02 2.50e+03 pdb=" N3 G A3163 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G A3163 " 0.000 2.00e-02 2.50e+03 ... (remaining 11564 not shown) Histogram of nonbonded interaction distances: 1.15 - 1.90: 7 1.90 - 2.65: 2889 2.65 - 3.40: 112578 3.40 - 4.15: 228367 4.15 - 4.90: 374211 Nonbonded interactions: 718052 Sorted by model distance: nonbonded pdb="MG MG A3342 " pdb="MG MG A3343 " model vdw 1.147 1.300 nonbonded pdb=" OP1 U A3102 " pdb="MG MG A3322 " model vdw 1.829 2.170 nonbonded pdb=" OP2 G A2496 " pdb="MG MG A3348 " model vdw 1.843 2.170 nonbonded pdb=" OP1 U A2035 " pdb="MG MG A3331 " model vdw 1.848 2.170 nonbonded pdb=" O4 U A2422 " pdb="MG MG A3340 " model vdw 1.852 2.170 ... (remaining 718047 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: 3.120 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: 0.100 Extract box with map and model: 12.740 Check model and map are aligned: 0.950 Set scattering table: 0.590 Process input model: 227.640 Find NCS groups from input model: 2.300 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.030 Load rotamer database and sin/cos tables:10.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 258.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5838 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 : 0.007 0.072 90037 Z= 0.468 Angle : 0.715 9.101 127962 Z= 0.385 Chirality : 0.045 0.239 15007 Planarity : 0.005 0.090 11567 Dihedral : 19.370 178.791 42296 Min Nonbonded Distance : 1.147 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.09 % Allowed : 7.62 % Favored : 92.29 % Rotamer: Outliers : 3.11 % Allowed : 8.87 % Favored : 88.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.65 (0.10), residues: 6889 helix: -0.32 (0.11), residues: 2202 sheet: -1.23 (0.16), residues: 845 loop : -1.54 (0.10), residues: 3842 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP s 210 HIS 0.008 0.001 HIS L 52 PHE 0.025 0.002 PHE 5 60 TYR 0.027 0.002 TYR 5 176 ARG 0.008 0.001 ARG u 119 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13778 Ramachandran restraints generated. 6889 Oldfield, 0 Emsley, 6889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13778 Ramachandran restraints generated. 6889 Oldfield, 0 Emsley, 6889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1285 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 193 poor density : 1092 time to evaluate : 5.802 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: F 117 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.6783 (ptt180) REVERT: S 86 MET cc_start: 0.4093 (mtp) cc_final: 0.3721 (mtp) REVERT: T 152 CYS cc_start: 0.5288 (OUTLIER) cc_final: 0.5087 (t) REVERT: 1 31 ASN cc_start: 0.0081 (OUTLIER) cc_final: -0.1675 (t0) REVERT: 6 194 THR cc_start: 0.6459 (OUTLIER) cc_final: 0.6032 (t) outliers start: 193 outliers final: 51 residues processed: 1259 average time/residue: 1.7739 time to fit residues: 2941.9701 Evaluate side-chains 680 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 625 time to evaluate : 5.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 248 ILE Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 110 SER Chi-restraints excluded: chain F residue 117 ARG Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 239 THR Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 105 VAL Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 108 ILE Chi-restraints excluded: chain K residue 112 LEU Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 188 CYS Chi-restraints excluded: chain N residue 206 GLU Chi-restraints excluded: chain O residue 10 SER Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain S residue 124 CYS Chi-restraints excluded: chain T residue 152 CYS Chi-restraints excluded: chain U residue 29 VAL Chi-restraints excluded: chain V residue 211 LYS Chi-restraints excluded: chain W residue 112 GLU Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Y residue 205 VAL Chi-restraints excluded: chain Z residue 80 TYR Chi-restraints excluded: chain 0 residue 131 CYS Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 1 residue 31 ASN Chi-restraints excluded: chain 2 residue 92 HIS Chi-restraints excluded: chain 3 residue 106 THR Chi-restraints excluded: chain 5 residue 84 ASP Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain 6 residue 194 THR Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 233 LEU Chi-restraints excluded: chain 7 residue 108 VAL Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 9 residue 29 SER Chi-restraints excluded: chain 9 residue 39 LYS Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain h residue 142 GLU Chi-restraints excluded: chain j residue 45 GLU Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain s residue 156 TYR Chi-restraints excluded: chain s residue 174 LEU Chi-restraints excluded: chain s residue 331 SER Chi-restraints excluded: chain s residue 404 THR Chi-restraints excluded: chain 4 residue 79 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 809 random chunks: chunk 683 optimal weight: 10.0000 chunk 613 optimal weight: 1.9990 chunk 340 optimal weight: 9.9990 chunk 209 optimal weight: 8.9990 chunk 413 optimal weight: 3.9990 chunk 327 optimal weight: 10.0000 chunk 634 optimal weight: 20.0000 chunk 245 optimal weight: 6.9990 chunk 385 optimal weight: 0.0970 chunk 471 optimal weight: 6.9990 chunk 734 optimal weight: 10.0000 overall best weight: 4.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 271 ASN E 128 HIS F 130 GLN F 201 GLN K 74 GLN ** N 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 91 GLN ** R 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 35 ASN ** 2 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 108 HIS ** 7 198 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 287 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 111 GLN c 77 HIS g 63 HIS o 96 ASN ** p 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 81 GLN r 79 HIS ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 154 HIS s 382 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5862 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 90037 Z= 0.237 Angle : 0.691 14.847 127962 Z= 0.350 Chirality : 0.041 0.306 15007 Planarity : 0.005 0.073 11567 Dihedral : 20.291 178.558 27489 Min Nonbonded Distance : 1.127 Molprobity Statistics. All-atom Clashscore : 11.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.11 % Favored : 94.86 % Rotamer: Outliers : 3.35 % Allowed : 16.91 % Favored : 79.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.10), residues: 6889 helix: 0.15 (0.11), residues: 2221 sheet: -0.85 (0.17), residues: 849 loop : -1.05 (0.10), residues: 3819 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP 2 66 HIS 0.011 0.001 HIS F 138 PHE 0.024 0.002 PHE v 30 TYR 0.025 0.002 TYR D 206 ARG 0.012 0.001 ARG 4 87 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13778 Ramachandran restraints generated. 6889 Oldfield, 0 Emsley, 6889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13778 Ramachandran restraints generated. 6889 Oldfield, 0 Emsley, 6889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 945 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 737 time to evaluate : 6.485 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: K 67 PHE cc_start: 0.6384 (OUTLIER) cc_final: 0.5912 (t80) REVERT: 1 31 ASN cc_start: -0.0072 (OUTLIER) cc_final: -0.1601 (t0) outliers start: 208 outliers final: 78 residues processed: 885 average time/residue: 1.6996 time to fit residues: 2008.3014 Evaluate side-chains 659 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 579 time to evaluate : 6.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 93 VAL Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain L residue 134 TYR Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 72 PHE Chi-restraints excluded: chain Q residue 250 THR Chi-restraints excluded: chain R residue 18 TYR Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 112 GLU Chi-restraints excluded: chain X residue 21 CYS Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain Y residue 73 ASN Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Z residue 45 VAL Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 1 residue 31 ASN Chi-restraints excluded: chain 2 residue 77 GLN Chi-restraints excluded: chain 2 residue 92 HIS Chi-restraints excluded: chain 3 residue 115 LEU Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 5 residue 84 ASP Chi-restraints excluded: chain 5 residue 94 HIS Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain 6 residue 194 THR Chi-restraints excluded: chain 7 residue 96 SER Chi-restraints excluded: chain 7 residue 108 VAL Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 9 residue 19 SER Chi-restraints excluded: chain 9 residue 29 SER Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 134 LYS Chi-restraints excluded: chain b residue 53 ASP Chi-restraints excluded: chain b residue 92 LYS Chi-restraints excluded: chain b residue 93 SER Chi-restraints excluded: chain c residue 69 HIS Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 181 SER Chi-restraints excluded: chain d residue 127 ASP Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain d residue 181 VAL Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 68 THR Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain g residue 154 ASP Chi-restraints excluded: chain h residue 141 ASP Chi-restraints excluded: chain i residue 98 VAL Chi-restraints excluded: chain i residue 114 ILE Chi-restraints excluded: chain j residue 29 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain p residue 77 THR Chi-restraints excluded: chain p residue 150 CYS Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 76 ASN Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain s residue 156 TYR Chi-restraints excluded: chain u residue 110 CYS Chi-restraints excluded: chain u residue 122 ASP Chi-restraints excluded: chain u residue 130 THR Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 184 THR Chi-restraints excluded: chain v residue 61 PHE Chi-restraints excluded: chain v residue 63 ASN Chi-restraints excluded: chain 4 residue 74 LYS Chi-restraints excluded: chain 4 residue 79 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 809 random chunks: chunk 408 optimal weight: 8.9990 chunk 228 optimal weight: 20.0000 chunk 611 optimal weight: 1.9990 chunk 500 optimal weight: 6.9990 chunk 202 optimal weight: 0.3980 chunk 735 optimal weight: 30.0000 chunk 795 optimal weight: 10.0000 chunk 655 optimal weight: 8.9990 chunk 729 optimal weight: 10.0000 chunk 250 optimal weight: 5.9990 chunk 590 optimal weight: 6.9990 overall best weight: 4.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 271 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 100 GLN ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 GLN ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 241 GLN 1 35 ASN ** 2 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 45 ASN 7 69 HIS 7 198 ASN ** 9 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 GLN h 147 ASN o 96 ASN r 146 GLN ** r 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 67 GLN ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 382 GLN ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5890 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 90037 Z= 0.240 Angle : 0.648 12.085 127962 Z= 0.327 Chirality : 0.039 0.244 15007 Planarity : 0.005 0.064 11567 Dihedral : 20.182 179.618 27433 Min Nonbonded Distance : 1.125 Molprobity Statistics. All-atom Clashscore : 12.46 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.21 % Favored : 94.76 % Rotamer: Outliers : 3.30 % Allowed : 18.46 % Favored : 78.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.10), residues: 6889 helix: 0.27 (0.11), residues: 2228 sheet: -0.66 (0.17), residues: 852 loop : -0.86 (0.10), residues: 3809 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP 2 66 HIS 0.008 0.001 HIS F 138 PHE 0.030 0.001 PHE v 39 TYR 0.025 0.002 TYR R 18 ARG 0.010 0.000 ARG 4 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13778 Ramachandran restraints generated. 6889 Oldfield, 0 Emsley, 6889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13778 Ramachandran restraints generated. 6889 Oldfield, 0 Emsley, 6889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 861 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 205 poor density : 656 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 67 PHE cc_start: 0.6530 (OUTLIER) cc_final: 0.6138 (t80) REVERT: 1 31 ASN cc_start: -0.0022 (OUTLIER) cc_final: -0.1542 (t0) REVERT: 2 92 HIS cc_start: 0.5850 (OUTLIER) cc_final: 0.4421 (t70) REVERT: 4 98 HIS cc_start: 0.5809 (OUTLIER) cc_final: 0.5132 (p-80) outliers start: 205 outliers final: 93 residues processed: 802 average time/residue: 1.6192 time to fit residues: 1759.1248 Evaluate side-chains 663 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 566 time to evaluate : 5.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain H residue 147 ARG Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 134 TYR Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 126 LYS Chi-restraints excluded: chain P residue 72 PHE Chi-restraints excluded: chain P residue 142 ASN Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain P residue 162 GLN Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain S residue 124 CYS Chi-restraints excluded: chain T residue 119 GLU Chi-restraints excluded: chain T residue 152 CYS Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 97 VAL Chi-restraints excluded: chain V residue 181 ASP Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain X residue 21 CYS Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain Y residue 73 ASN Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Z residue 39 SER Chi-restraints excluded: chain Z residue 45 VAL Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 110 LEU Chi-restraints excluded: chain 0 residue 101 ILE Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 1 residue 31 ASN Chi-restraints excluded: chain 2 residue 77 GLN Chi-restraints excluded: chain 2 residue 92 HIS Chi-restraints excluded: chain 3 residue 106 THR Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 3 residue 115 LEU Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 5 residue 94 HIS Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 5 residue 307 ASP Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain 6 residue 194 THR Chi-restraints excluded: chain 7 residue 108 VAL Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 9 residue 19 SER Chi-restraints excluded: chain 9 residue 29 SER Chi-restraints excluded: chain 9 residue 39 LYS Chi-restraints excluded: chain a residue 108 MET Chi-restraints excluded: chain a residue 134 LYS Chi-restraints excluded: chain a residue 136 LEU Chi-restraints excluded: chain b residue 53 ASP Chi-restraints excluded: chain c residue 69 HIS Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 181 SER Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain h residue 141 ASP Chi-restraints excluded: chain i residue 98 VAL Chi-restraints excluded: chain j residue 29 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain p residue 77 THR Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain r residue 146 GLN Chi-restraints excluded: chain s residue 41 VAL Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain s residue 156 TYR Chi-restraints excluded: chain s residue 323 VAL Chi-restraints excluded: chain s residue 331 SER Chi-restraints excluded: chain u residue 112 ILE Chi-restraints excluded: chain u residue 114 VAL Chi-restraints excluded: chain u residue 130 THR Chi-restraints excluded: chain u residue 184 THR Chi-restraints excluded: chain v residue 35 ILE Chi-restraints excluded: chain v residue 63 ASN Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain 4 residue 74 LYS Chi-restraints excluded: chain 4 residue 79 CYS Chi-restraints excluded: chain 4 residue 98 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 809 random chunks: chunk 727 optimal weight: 10.0000 chunk 553 optimal weight: 0.0370 chunk 381 optimal weight: 40.0000 chunk 81 optimal weight: 7.9990 chunk 351 optimal weight: 1.9990 chunk 494 optimal weight: 5.9990 chunk 738 optimal weight: 20.0000 chunk 781 optimal weight: 20.0000 chunk 385 optimal weight: 7.9990 chunk 700 optimal weight: 20.0000 chunk 210 optimal weight: 3.9990 overall best weight: 4.0066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 271 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 GLN ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 64 HIS ** Q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 147 GLN U 74 HIS ** Z 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 96 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 77 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 6 277 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 9 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 67 GLN ** r 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** s 67 GLN ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 382 GLN ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5891 moved from start: 0.2753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 90037 Z= 0.223 Angle : 0.640 13.680 127962 Z= 0.320 Chirality : 0.039 0.237 15007 Planarity : 0.005 0.060 11567 Dihedral : 20.152 179.726 27422 Min Nonbonded Distance : 1.136 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.21 % Favored : 94.77 % Rotamer: Outliers : 3.38 % Allowed : 19.44 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.10), residues: 6889 helix: 0.49 (0.11), residues: 2205 sheet: -0.49 (0.17), residues: 825 loop : -0.77 (0.10), residues: 3859 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP 2 66 HIS 0.008 0.001 HIS b 90 PHE 0.048 0.001 PHE v 32 TYR 0.024 0.001 TYR F 162 ARG 0.009 0.000 ARG 7 61 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13778 Ramachandran restraints generated. 6889 Oldfield, 0 Emsley, 6889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13778 Ramachandran restraints generated. 6889 Oldfield, 0 Emsley, 6889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 845 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 635 time to evaluate : 5.925 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: K 67 PHE cc_start: 0.6480 (OUTLIER) cc_final: 0.6153 (t80) REVERT: L 96 MET cc_start: 0.6066 (mmt) cc_final: 0.5853 (mpm) REVERT: 1 31 ASN cc_start: -0.0262 (OUTLIER) cc_final: -0.1620 (t0) REVERT: 2 92 HIS cc_start: 0.5736 (OUTLIER) cc_final: 0.4274 (t70) outliers start: 210 outliers final: 98 residues processed: 778 average time/residue: 1.6057 time to fit residues: 1701.5415 Evaluate side-chains 654 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 101 poor density : 553 time to evaluate : 5.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain H residue 91 LYS Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain L residue 71 ASP Chi-restraints excluded: chain L residue 86 ILE Chi-restraints excluded: chain L residue 134 TYR Chi-restraints excluded: chain L residue 140 ILE Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 98 LYS Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 72 PHE Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 142 ASN Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain S residue 124 CYS Chi-restraints excluded: chain T residue 119 GLU Chi-restraints excluded: chain U residue 12 LEU Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 97 VAL Chi-restraints excluded: chain V residue 181 ASP Chi-restraints excluded: chain V residue 194 LEU Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain X residue 21 CYS Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain Y residue 73 ASN Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 110 LEU Chi-restraints excluded: chain 0 residue 101 ILE Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 1 residue 31 ASN Chi-restraints excluded: chain 2 residue 92 HIS Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 3 residue 112 ASP Chi-restraints excluded: chain 3 residue 115 LEU Chi-restraints excluded: chain 3 residue 153 THR Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 5 residue 94 HIS Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 5 residue 232 THR Chi-restraints excluded: chain 5 residue 307 ASP Chi-restraints excluded: chain 5 residue 351 VAL Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain 6 residue 194 THR Chi-restraints excluded: chain 7 residue 108 VAL Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 9 residue 29 SER Chi-restraints excluded: chain 9 residue 39 LYS Chi-restraints excluded: chain 9 residue 93 SER Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 134 LYS Chi-restraints excluded: chain a residue 136 LEU Chi-restraints excluded: chain b residue 53 ASP Chi-restraints excluded: chain c residue 69 HIS Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 167 CYS Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain d residue 243 LEU Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain h residue 141 ASP Chi-restraints excluded: chain i residue 98 VAL Chi-restraints excluded: chain j residue 29 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 90 ASP Chi-restraints excluded: chain p residue 77 THR Chi-restraints excluded: chain p residue 150 CYS Chi-restraints excluded: chain r residue 70 CYS Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 156 TYR Chi-restraints excluded: chain s residue 323 VAL Chi-restraints excluded: chain s residue 331 SER Chi-restraints excluded: chain u residue 114 VAL Chi-restraints excluded: chain u residue 122 ASP Chi-restraints excluded: chain u residue 141 TYR Chi-restraints excluded: chain u residue 184 THR Chi-restraints excluded: chain v residue 63 ASN Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain 4 residue 79 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 809 random chunks: chunk 651 optimal weight: 10.0000 chunk 443 optimal weight: 5.9990 chunk 11 optimal weight: 10.0000 chunk 582 optimal weight: 5.9990 chunk 322 optimal weight: 7.9990 chunk 667 optimal weight: 40.0000 chunk 540 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 399 optimal weight: 20.0000 chunk 701 optimal weight: 20.0000 chunk 197 optimal weight: 20.0000 overall best weight: 7.9992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 271 ASN ** E 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 130 GLN ** I 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 74 GLN ** N 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 79 GLN T 109 ASN ** Y 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 5 108 HIS ** 5 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 385 HIS d 217 HIS f 61 HIS h 110 HIS h 147 ASN o 46 HIS ** r 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** v 43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5978 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.111 90037 Z= 0.356 Angle : 0.692 14.429 127962 Z= 0.347 Chirality : 0.040 0.235 15007 Planarity : 0.005 0.063 11567 Dihedral : 20.246 179.693 27418 Min Nonbonded Distance : 1.081 Molprobity Statistics. All-atom Clashscore : 16.33 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.60 % Favored : 94.38 % Rotamer: Outliers : 3.82 % Allowed : 20.15 % Favored : 76.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.10), residues: 6889 helix: 0.41 (0.11), residues: 2203 sheet: -0.56 (0.17), residues: 840 loop : -0.76 (0.10), residues: 3846 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP N 213 HIS 0.005 0.001 HIS 4 98 PHE 0.018 0.002 PHE b 46 TYR 0.032 0.002 TYR F 162 ARG 0.013 0.001 ARG j 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13778 Ramachandran restraints generated. 6889 Oldfield, 0 Emsley, 6889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13778 Ramachandran restraints generated. 6889 Oldfield, 0 Emsley, 6889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 824 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 237 poor density : 587 time to evaluate : 5.884 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: E 310 LEU cc_start: 0.6660 (pp) cc_final: 0.6459 (pt) REVERT: K 67 PHE cc_start: 0.6454 (OUTLIER) cc_final: 0.6042 (t80) REVERT: 1 31 ASN cc_start: -0.0105 (OUTLIER) cc_final: -0.1547 (t0) REVERT: 2 92 HIS cc_start: 0.5620 (OUTLIER) cc_final: 0.3827 (t70) REVERT: q 41 ASP cc_start: 0.6037 (t0) cc_final: 0.5501 (t0) outliers start: 237 outliers final: 125 residues processed: 754 average time/residue: 1.6280 time to fit residues: 1670.7361 Evaluate side-chains 653 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 128 poor density : 525 time to evaluate : 5.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 289 ASN Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 126 LYS Chi-restraints excluded: chain P residue 72 PHE Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 142 ASN Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 145 LEU Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain S residue 124 CYS Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain T residue 85 ASP Chi-restraints excluded: chain T residue 119 GLU Chi-restraints excluded: chain T residue 205 SER Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 97 VAL Chi-restraints excluded: chain V residue 181 ASP Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain W residue 111 THR Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 141 THR Chi-restraints excluded: chain X residue 21 CYS Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain Y residue 73 ASN Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 76 ARG Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 110 LEU Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 1 residue 31 ASN Chi-restraints excluded: chain 2 residue 79 ILE Chi-restraints excluded: chain 2 residue 92 HIS Chi-restraints excluded: chain 3 residue 106 THR Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 3 residue 112 ASP Chi-restraints excluded: chain 3 residue 115 LEU Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 5 residue 94 HIS Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 5 residue 160 HIS Chi-restraints excluded: chain 5 residue 232 THR Chi-restraints excluded: chain 5 residue 307 ASP Chi-restraints excluded: chain 5 residue 351 VAL Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain 6 residue 161 LEU Chi-restraints excluded: chain 6 residue 194 THR Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 376 THR Chi-restraints excluded: chain 7 residue 96 SER Chi-restraints excluded: chain 7 residue 108 VAL Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 9 residue 29 SER Chi-restraints excluded: chain 9 residue 39 LYS Chi-restraints excluded: chain 9 residue 59 GLU Chi-restraints excluded: chain 9 residue 93 SER Chi-restraints excluded: chain a residue 108 MET Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 134 LYS Chi-restraints excluded: chain b residue 53 ASP Chi-restraints excluded: chain b residue 62 VAL Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain c residue 69 HIS Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 167 CYS Chi-restraints excluded: chain c residue 181 SER Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain d residue 181 VAL Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain h residue 76 GLU Chi-restraints excluded: chain i residue 98 VAL Chi-restraints excluded: chain j residue 29 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 90 ASP Chi-restraints excluded: chain p residue 77 THR Chi-restraints excluded: chain p residue 150 CYS Chi-restraints excluded: chain r residue 76 ASN Chi-restraints excluded: chain s residue 41 VAL Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 100 LEU Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain s residue 156 TYR Chi-restraints excluded: chain s residue 229 LEU Chi-restraints excluded: chain s residue 323 VAL Chi-restraints excluded: chain s residue 331 SER Chi-restraints excluded: chain u residue 122 ASP Chi-restraints excluded: chain u residue 130 THR Chi-restraints excluded: chain u residue 184 THR Chi-restraints excluded: chain v residue 5 SER Chi-restraints excluded: chain v residue 63 ASN Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain w residue 114 ASP Chi-restraints excluded: chain w residue 134 ASP Chi-restraints excluded: chain 4 residue 95 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 809 random chunks: chunk 263 optimal weight: 9.9990 chunk 704 optimal weight: 10.0000 chunk 154 optimal weight: 20.0000 chunk 459 optimal weight: 0.9990 chunk 193 optimal weight: 0.8980 chunk 782 optimal weight: 30.0000 chunk 649 optimal weight: 7.9990 chunk 362 optimal weight: 20.0000 chunk 65 optimal weight: 10.0000 chunk 258 optimal weight: 9.9990 chunk 410 optimal weight: 30.0000 overall best weight: 5.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 271 ASN E 57 ASN I 41 HIS ** I 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN ** P 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 147 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 ASN ** Y 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 280 GLN 7 298 GLN q 81 GLN q 119 GLN r 196 HIS ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 103 HIS ** 4 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5957 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 90037 Z= 0.283 Angle : 0.668 15.199 127962 Z= 0.333 Chirality : 0.039 0.226 15007 Planarity : 0.005 0.065 11567 Dihedral : 20.274 179.358 27416 Min Nonbonded Distance : 1.129 Molprobity Statistics. All-atom Clashscore : 15.68 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.41 % Favored : 94.57 % Rotamer: Outliers : 3.24 % Allowed : 21.68 % Favored : 75.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.10), residues: 6889 helix: 0.48 (0.11), residues: 2209 sheet: -0.53 (0.17), residues: 852 loop : -0.71 (0.10), residues: 3828 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP 7 143 HIS 0.009 0.001 HIS K 48 PHE 0.049 0.001 PHE v 32 TYR 0.026 0.001 TYR F 162 ARG 0.009 0.000 ARG W 119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13778 Ramachandran restraints generated. 6889 Oldfield, 0 Emsley, 6889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13778 Ramachandran restraints generated. 6889 Oldfield, 0 Emsley, 6889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 787 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 586 time to evaluate : 6.040 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: K 67 PHE cc_start: 0.6429 (OUTLIER) cc_final: 0.5983 (t80) REVERT: L 96 MET cc_start: 0.6058 (mmt) cc_final: 0.5837 (mpm) REVERT: N 113 MET cc_start: 0.6754 (OUTLIER) cc_final: 0.6234 (mpt) REVERT: N 140 MET cc_start: -0.0206 (mtt) cc_final: -0.0487 (ttt) REVERT: S 182 LYS cc_start: 0.7752 (OUTLIER) cc_final: 0.6940 (ptmt) REVERT: 1 31 ASN cc_start: -0.0298 (OUTLIER) cc_final: -0.1158 (t0) REVERT: 2 92 HIS cc_start: 0.5684 (OUTLIER) cc_final: 0.4025 (t70) REVERT: 7 193 MET cc_start: 0.5601 (tpp) cc_final: 0.5394 (tpt) REVERT: p 74 ASP cc_start: 0.5571 (p0) cc_final: 0.5204 (p0) outliers start: 201 outliers final: 120 residues processed: 732 average time/residue: 1.6248 time to fit residues: 1623.0372 Evaluate side-chains 653 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 125 poor density : 528 time to evaluate : 5.804 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 107 MET Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain I residue 48 MET Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 113 MET Chi-restraints excluded: chain N residue 201 ASP Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain O residue 126 LYS Chi-restraints excluded: chain P residue 72 PHE Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 142 ASN Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 145 LEU Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain S residue 65 VAL Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain S residue 182 LYS Chi-restraints excluded: chain T residue 119 GLU Chi-restraints excluded: chain T residue 152 CYS Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 74 HIS Chi-restraints excluded: chain U residue 97 VAL Chi-restraints excluded: chain V residue 181 ASP Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain W residue 116 LEU Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 141 THR Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain Y residue 73 ASN Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 76 ARG Chi-restraints excluded: chain Z residue 84 ASP Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 110 LEU Chi-restraints excluded: chain 0 residue 101 ILE Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 1 residue 31 ASN Chi-restraints excluded: chain 2 residue 90 LEU Chi-restraints excluded: chain 2 residue 92 HIS Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 3 residue 112 ASP Chi-restraints excluded: chain 3 residue 115 LEU Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 5 residue 94 HIS Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 5 residue 160 HIS Chi-restraints excluded: chain 5 residue 232 THR Chi-restraints excluded: chain 5 residue 307 ASP Chi-restraints excluded: chain 5 residue 351 VAL Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain 6 residue 194 THR Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 265 ILE Chi-restraints excluded: chain 7 residue 96 SER Chi-restraints excluded: chain 7 residue 108 VAL Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 9 residue 19 SER Chi-restraints excluded: chain 9 residue 29 SER Chi-restraints excluded: chain 9 residue 93 SER Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 134 LYS Chi-restraints excluded: chain b residue 53 ASP Chi-restraints excluded: chain c residue 69 HIS Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 167 CYS Chi-restraints excluded: chain c residue 181 SER Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain d residue 181 VAL Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 98 VAL Chi-restraints excluded: chain j residue 29 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 90 ASP Chi-restraints excluded: chain p residue 77 THR Chi-restraints excluded: chain p residue 150 CYS Chi-restraints excluded: chain s residue 41 VAL Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 100 LEU Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain s residue 156 TYR Chi-restraints excluded: chain s residue 323 VAL Chi-restraints excluded: chain s residue 331 SER Chi-restraints excluded: chain u residue 112 ILE Chi-restraints excluded: chain u residue 122 ASP Chi-restraints excluded: chain u residue 141 TYR Chi-restraints excluded: chain u residue 184 THR Chi-restraints excluded: chain v residue 5 SER Chi-restraints excluded: chain v residue 63 ASN Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain w residue 111 ASP Chi-restraints excluded: chain w residue 114 ASP Chi-restraints excluded: chain w residue 134 ASP Chi-restraints excluded: chain 4 residue 95 HIS Chi-restraints excluded: chain 4 residue 98 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 809 random chunks: chunk 754 optimal weight: 10.0000 chunk 88 optimal weight: 0.9980 chunk 445 optimal weight: 6.9990 chunk 571 optimal weight: 7.9990 chunk 442 optimal weight: 30.0000 chunk 658 optimal weight: 50.0000 chunk 437 optimal weight: 0.6980 chunk 779 optimal weight: 20.0000 chunk 487 optimal weight: 10.0000 chunk 475 optimal weight: 5.9990 chunk 359 optimal weight: 5.9990 overall best weight: 4.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 271 ASN ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 96 HIS ** P 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 63 ASN R 147 GLN ** S 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 ASN ** Y 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 298 GLN a 137 ASN ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 148 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** w 103 HIS ** 4 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5934 moved from start: 0.3485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.136 90037 Z= 0.231 Angle : 0.657 17.304 127962 Z= 0.328 Chirality : 0.039 0.268 15007 Planarity : 0.004 0.064 11567 Dihedral : 20.252 179.048 27416 Min Nonbonded Distance : 1.143 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.28 % Favored : 94.70 % Rotamer: Outliers : 2.95 % Allowed : 22.37 % Favored : 74.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.10), residues: 6889 helix: 0.55 (0.11), residues: 2200 sheet: -0.53 (0.17), residues: 856 loop : -0.66 (0.10), residues: 3833 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP Q 260 HIS 0.007 0.001 HIS 7 255 PHE 0.017 0.001 PHE u 124 TYR 0.031 0.001 TYR F 162 ARG 0.008 0.000 ARG a 122 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13778 Ramachandran restraints generated. 6889 Oldfield, 0 Emsley, 6889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13778 Ramachandran restraints generated. 6889 Oldfield, 0 Emsley, 6889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 774 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 591 time to evaluate : 5.906 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: K 67 PHE cc_start: 0.6563 (OUTLIER) cc_final: 0.6181 (t80) REVERT: L 96 MET cc_start: 0.6152 (mmt) cc_final: 0.5943 (mpm) REVERT: S 182 LYS cc_start: 0.7645 (OUTLIER) cc_final: 0.6833 (ptmt) REVERT: 1 31 ASN cc_start: -0.0289 (OUTLIER) cc_final: -0.1292 (t0) REVERT: 2 92 HIS cc_start: 0.5555 (OUTLIER) cc_final: 0.3977 (t70) REVERT: p 74 ASP cc_start: 0.5714 (p0) cc_final: 0.5380 (p0) outliers start: 183 outliers final: 117 residues processed: 725 average time/residue: 1.5620 time to fit residues: 1555.2719 Evaluate side-chains 655 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 121 poor density : 534 time to evaluate : 5.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain H residue 136 ASN Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 289 ASN Chi-restraints excluded: chain N residue 83 THR Chi-restraints excluded: chain N residue 84 GLU Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain O residue 18 MET Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 72 PHE Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 142 ASN Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 145 LEU Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain S residue 65 VAL Chi-restraints excluded: chain S residue 143 LEU Chi-restraints excluded: chain S residue 182 LYS Chi-restraints excluded: chain T residue 119 GLU Chi-restraints excluded: chain T residue 152 CYS Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 74 HIS Chi-restraints excluded: chain U residue 97 VAL Chi-restraints excluded: chain V residue 181 ASP Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 141 THR Chi-restraints excluded: chain X residue 21 CYS Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain Y residue 73 ASN Chi-restraints excluded: chain Y residue 153 LEU Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 76 ARG Chi-restraints excluded: chain Z residue 84 ASP Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 110 LEU Chi-restraints excluded: chain 0 residue 101 ILE Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 1 residue 31 ASN Chi-restraints excluded: chain 2 residue 92 HIS Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 3 residue 112 ASP Chi-restraints excluded: chain 3 residue 115 LEU Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 5 residue 94 HIS Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 5 residue 160 HIS Chi-restraints excluded: chain 5 residue 232 THR Chi-restraints excluded: chain 5 residue 307 ASP Chi-restraints excluded: chain 5 residue 351 VAL Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain 6 residue 194 THR Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 265 ILE Chi-restraints excluded: chain 7 residue 96 SER Chi-restraints excluded: chain 7 residue 108 VAL Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 7 residue 220 GLU Chi-restraints excluded: chain 9 residue 29 SER Chi-restraints excluded: chain 9 residue 93 SER Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 134 LYS Chi-restraints excluded: chain b residue 53 ASP Chi-restraints excluded: chain c residue 69 HIS Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 167 CYS Chi-restraints excluded: chain c residue 181 SER Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain d residue 181 VAL Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain i residue 98 VAL Chi-restraints excluded: chain j residue 29 LEU Chi-restraints excluded: chain o residue 27 VAL Chi-restraints excluded: chain o residue 90 ASP Chi-restraints excluded: chain p residue 77 THR Chi-restraints excluded: chain p residue 150 CYS Chi-restraints excluded: chain s residue 41 VAL Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 100 LEU Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain s residue 156 TYR Chi-restraints excluded: chain s residue 323 VAL Chi-restraints excluded: chain s residue 331 SER Chi-restraints excluded: chain s residue 356 VAL Chi-restraints excluded: chain u residue 122 ASP Chi-restraints excluded: chain u residue 130 THR Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain u residue 184 THR Chi-restraints excluded: chain v residue 63 ASN Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain w residue 134 ASP Chi-restraints excluded: chain 4 residue 95 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 809 random chunks: chunk 482 optimal weight: 2.9990 chunk 311 optimal weight: 9.9990 chunk 465 optimal weight: 2.9990 chunk 234 optimal weight: 9.9990 chunk 153 optimal weight: 40.0000 chunk 151 optimal weight: 20.0000 chunk 495 optimal weight: 6.9990 chunk 531 optimal weight: 50.0000 chunk 385 optimal weight: 10.0000 chunk 72 optimal weight: 8.9990 chunk 612 optimal weight: 8.9990 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 271 ASN I 45 GLN K 74 GLN ** N 178 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 ASN ** Y 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 150 GLN ** 5 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 7 94 HIS ** 7 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** o 94 HIS ** q 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5966 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.127 90037 Z= 0.297 Angle : 0.690 15.624 127962 Z= 0.343 Chirality : 0.040 0.232 15007 Planarity : 0.005 0.082 11567 Dihedral : 20.258 179.215 27416 Min Nonbonded Distance : 1.120 Molprobity Statistics. All-atom Clashscore : 16.80 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.53 % Favored : 94.45 % Rotamer: Outliers : 2.88 % Allowed : 22.85 % Favored : 74.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.10), residues: 6889 helix: 0.50 (0.11), residues: 2216 sheet: -0.51 (0.17), residues: 857 loop : -0.64 (0.11), residues: 3816 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 213 HIS 0.008 0.001 HIS K 48 PHE 0.052 0.001 PHE v 32 TYR 0.036 0.002 TYR 6 154 ARG 0.018 0.000 ARG W 119 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13778 Ramachandran restraints generated. 6889 Oldfield, 0 Emsley, 6889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13778 Ramachandran restraints generated. 6889 Oldfield, 0 Emsley, 6889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 748 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 179 poor density : 569 time to evaluate : 5.936 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: K 67 PHE cc_start: 0.6575 (OUTLIER) cc_final: 0.6165 (t80) REVERT: L 96 MET cc_start: 0.6085 (mmt) cc_final: 0.5837 (mpm) REVERT: N 140 MET cc_start: -0.0444 (mtt) cc_final: -0.0670 (ttt) REVERT: P 86 THR cc_start: 0.4373 (OUTLIER) cc_final: 0.4121 (t) REVERT: S 182 LYS cc_start: 0.7618 (OUTLIER) cc_final: 0.6814 (ptmt) REVERT: 1 31 ASN cc_start: -0.0184 (OUTLIER) cc_final: -0.1216 (t0) REVERT: 2 92 HIS cc_start: 0.5661 (OUTLIER) cc_final: 0.3961 (t70) REVERT: b 71 CYS cc_start: 0.4079 (OUTLIER) cc_final: 0.3324 (m) REVERT: p 74 ASP cc_start: 0.5672 (p0) cc_final: 0.5360 (p0) outliers start: 179 outliers final: 133 residues processed: 702 average time/residue: 1.5891 time to fit residues: 1526.6264 Evaluate side-chains 665 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 526 time to evaluate : 5.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 121 ARG Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain H residue 136 ASN Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 135 GLU Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 289 ASN Chi-restraints excluded: chain N residue 201 ASP Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain P residue 142 ASN Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 145 LEU Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain R residue 20 ARG Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 66 THR Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain S residue 65 VAL Chi-restraints excluded: chain S residue 182 LYS Chi-restraints excluded: chain T residue 119 GLU Chi-restraints excluded: chain T residue 152 CYS Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 74 HIS Chi-restraints excluded: chain U residue 97 VAL Chi-restraints excluded: chain V residue 181 ASP Chi-restraints excluded: chain V residue 191 LEU Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain W residue 116 LEU Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 141 THR Chi-restraints excluded: chain X residue 21 CYS Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain Y residue 73 ASN Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 76 ARG Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 110 LEU Chi-restraints excluded: chain Z residue 142 THR Chi-restraints excluded: chain 0 residue 101 ILE Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 1 residue 31 ASN Chi-restraints excluded: chain 2 residue 79 ILE Chi-restraints excluded: chain 2 residue 90 LEU Chi-restraints excluded: chain 2 residue 92 HIS Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 3 residue 112 ASP Chi-restraints excluded: chain 3 residue 115 LEU Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 5 residue 39 ARG Chi-restraints excluded: chain 5 residue 94 HIS Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 5 residue 160 HIS Chi-restraints excluded: chain 5 residue 212 THR Chi-restraints excluded: chain 5 residue 232 THR Chi-restraints excluded: chain 5 residue 307 ASP Chi-restraints excluded: chain 5 residue 351 VAL Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain 6 residue 194 THR Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 265 ILE Chi-restraints excluded: chain 7 residue 96 SER Chi-restraints excluded: chain 7 residue 108 VAL Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 9 residue 29 SER Chi-restraints excluded: chain 9 residue 93 SER Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 134 LYS Chi-restraints excluded: chain b residue 53 ASP Chi-restraints excluded: chain b residue 71 CYS Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain c residue 69 HIS Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 100 SER Chi-restraints excluded: chain c residue 167 CYS Chi-restraints excluded: chain c residue 181 SER Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain d residue 181 VAL Chi-restraints excluded: chain d residue 277 LEU Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain g residue 143 VAL Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 98 VAL 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 77 THR Chi-restraints excluded: chain p residue 150 CYS Chi-restraints excluded: chain s residue 41 VAL Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 100 LEU Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain s residue 156 TYR Chi-restraints excluded: chain s residue 323 VAL Chi-restraints excluded: chain s residue 331 SER Chi-restraints excluded: chain s residue 356 VAL Chi-restraints excluded: chain s residue 376 THR Chi-restraints excluded: chain u residue 110 CYS Chi-restraints excluded: chain u residue 112 ILE Chi-restraints excluded: chain u residue 122 ASP Chi-restraints excluded: chain u residue 130 THR Chi-restraints excluded: chain u residue 141 TYR Chi-restraints excluded: chain v residue 5 SER Chi-restraints excluded: chain v residue 63 ASN Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain w residue 111 ASP Chi-restraints excluded: chain w residue 134 ASP Chi-restraints excluded: chain 4 residue 95 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 809 random chunks: chunk 709 optimal weight: 20.0000 chunk 747 optimal weight: 20.0000 chunk 681 optimal weight: 20.0000 chunk 726 optimal weight: 10.0000 chunk 746 optimal weight: 20.0000 chunk 437 optimal weight: 0.3980 chunk 316 optimal weight: 8.9990 chunk 570 optimal weight: 5.9990 chunk 222 optimal weight: 10.0000 chunk 656 optimal weight: 6.9990 chunk 687 optimal weight: 10.0000 overall best weight: 6.4790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 271 ASN ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 ASN ** Y 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** q 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** w 103 HIS ** 4 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5974 moved from start: 0.3762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.126 90037 Z= 0.305 Angle : 0.712 19.304 127962 Z= 0.354 Chirality : 0.040 0.310 15007 Planarity : 0.005 0.072 11567 Dihedral : 20.278 178.972 27414 Min Nonbonded Distance : 1.126 Molprobity Statistics. All-atom Clashscore : 17.58 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.62 % Favored : 94.37 % Rotamer: Outliers : 2.83 % Allowed : 23.34 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.10), residues: 6889 helix: 0.49 (0.11), residues: 2211 sheet: -0.53 (0.17), residues: 858 loop : -0.63 (0.11), residues: 3820 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 213 HIS 0.007 0.001 HIS 7 255 PHE 0.021 0.001 PHE u 124 TYR 0.037 0.002 TYR c 97 ARG 0.015 0.000 ARG W 119 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13778 Ramachandran restraints generated. 6889 Oldfield, 0 Emsley, 6889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13778 Ramachandran restraints generated. 6889 Oldfield, 0 Emsley, 6889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 176 poor density : 556 time to evaluate : 6.052 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: K 67 PHE cc_start: 0.6412 (OUTLIER) cc_final: 0.6035 (t80) REVERT: L 96 MET cc_start: 0.6171 (OUTLIER) cc_final: 0.5948 (mpm) REVERT: N 118 MET cc_start: 0.3500 (ppp) cc_final: 0.3215 (ppp) REVERT: N 140 MET cc_start: -0.0310 (mtt) cc_final: -0.0534 (ttt) REVERT: P 86 THR cc_start: 0.4188 (OUTLIER) cc_final: 0.3970 (t) REVERT: P 108 ARG cc_start: 0.4325 (OUTLIER) cc_final: 0.2752 (tmt170) REVERT: R 39 TYR cc_start: 0.6343 (t80) cc_final: 0.6090 (t80) REVERT: S 182 LYS cc_start: 0.7635 (OUTLIER) cc_final: 0.6794 (ptmt) REVERT: 1 31 ASN cc_start: -0.0122 (OUTLIER) cc_final: -0.1186 (t0) REVERT: 2 92 HIS cc_start: 0.5707 (OUTLIER) cc_final: 0.4016 (t70) REVERT: b 71 CYS cc_start: 0.3903 (OUTLIER) cc_final: 0.3330 (m) REVERT: p 74 ASP cc_start: 0.5696 (p0) cc_final: 0.5395 (p0) outliers start: 176 outliers final: 132 residues processed: 682 average time/residue: 1.6234 time to fit residues: 1518.4600 Evaluate side-chains 666 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 526 time to evaluate : 5.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain E residue 106 MET Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain F residue 250 VAL Chi-restraints excluded: chain H residue 136 ASN Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 289 ASN Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain O residue 61 ASP Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 72 PHE Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain P residue 108 ARG Chi-restraints excluded: chain P residue 142 ASN Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain R residue 18 TYR Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain S residue 182 LYS Chi-restraints excluded: chain T residue 119 GLU Chi-restraints excluded: chain T residue 152 CYS Chi-restraints excluded: chain U residue 52 ASP Chi-restraints excluded: chain U residue 74 HIS Chi-restraints excluded: chain U residue 97 VAL Chi-restraints excluded: chain V residue 181 ASP Chi-restraints excluded: chain V residue 194 LEU Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain W residue 116 LEU Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 141 THR Chi-restraints excluded: chain X residue 21 CYS Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain Y residue 73 ASN Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 76 ARG Chi-restraints excluded: chain Z residue 84 ASP Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 110 LEU Chi-restraints excluded: chain Z residue 142 THR Chi-restraints excluded: chain 0 residue 101 ILE Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 1 residue 31 ASN Chi-restraints excluded: chain 2 residue 79 ILE Chi-restraints excluded: chain 2 residue 92 HIS Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 3 residue 112 ASP Chi-restraints excluded: chain 3 residue 115 LEU Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 5 residue 39 ARG Chi-restraints excluded: chain 5 residue 94 HIS Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 5 residue 160 HIS Chi-restraints excluded: chain 5 residue 212 THR Chi-restraints excluded: chain 5 residue 232 THR Chi-restraints excluded: chain 5 residue 307 ASP Chi-restraints excluded: chain 5 residue 351 VAL Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain 6 residue 194 THR Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 6 residue 265 ILE Chi-restraints excluded: chain 7 residue 96 SER Chi-restraints excluded: chain 7 residue 108 VAL Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 9 residue 19 SER Chi-restraints excluded: chain 9 residue 29 SER Chi-restraints excluded: chain 9 residue 93 SER Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 134 LYS Chi-restraints excluded: chain b residue 53 ASP Chi-restraints excluded: chain b residue 66 ASN Chi-restraints excluded: chain b residue 71 CYS Chi-restraints excluded: chain b residue 100 LEU Chi-restraints excluded: chain c residue 69 HIS Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 100 SER Chi-restraints excluded: chain c residue 167 CYS Chi-restraints excluded: chain c residue 181 SER Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain d residue 181 VAL Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain g residue 143 VAL Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain i residue 98 VAL 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 p residue 77 THR Chi-restraints excluded: chain p residue 160 GLU Chi-restraints excluded: chain s residue 41 VAL Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 100 LEU Chi-restraints excluded: chain s residue 113 VAL Chi-restraints excluded: chain s residue 156 TYR Chi-restraints excluded: chain s residue 323 VAL Chi-restraints excluded: chain s residue 331 SER Chi-restraints excluded: chain s residue 356 VAL Chi-restraints excluded: chain s residue 376 THR Chi-restraints excluded: chain u residue 110 CYS Chi-restraints excluded: chain u residue 112 ILE Chi-restraints excluded: chain u residue 122 ASP Chi-restraints excluded: chain u residue 141 TYR Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain v residue 5 SER Chi-restraints excluded: chain v residue 9 VAL Chi-restraints excluded: chain v residue 63 ASN Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain w residue 111 ASP Chi-restraints excluded: chain 4 residue 95 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 809 random chunks: chunk 724 optimal weight: 20.0000 chunk 477 optimal weight: 9.9990 chunk 768 optimal weight: 40.0000 chunk 468 optimal weight: 0.2980 chunk 364 optimal weight: 0.0980 chunk 534 optimal weight: 20.0000 chunk 805 optimal weight: 50.0000 chunk 741 optimal weight: 20.0000 chunk 641 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 495 optimal weight: 2.9990 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 271 ASN ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 ASN ** Y 95 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 385 HIS ** 7 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 298 GLN b 25 GLN p 123 HIS ** q 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 102 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5945 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.128 90037 Z= 0.242 Angle : 0.711 19.718 127962 Z= 0.352 Chirality : 0.039 0.287 15007 Planarity : 0.005 0.070 11567 Dihedral : 20.268 178.567 27414 Min Nonbonded Distance : 1.152 Molprobity Statistics. All-atom Clashscore : 16.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.27 % Allowed : 23.98 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.10), residues: 6889 helix: 0.53 (0.11), residues: 2196 sheet: -0.42 (0.17), residues: 843 loop : -0.63 (0.10), residues: 3850 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP u 167 HIS 0.007 0.001 HIS 7 255 PHE 0.057 0.001 PHE v 32 TYR 0.043 0.001 TYR 7 211 ARG 0.016 0.000 ARG W 119 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13778 Ramachandran restraints generated. 6889 Oldfield, 0 Emsley, 6889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13778 Ramachandran restraints generated. 6889 Oldfield, 0 Emsley, 6889 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 702 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 561 time to evaluate : 6.214 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: K 67 PHE cc_start: 0.6541 (OUTLIER) cc_final: 0.6233 (t80) REVERT: L 96 MET cc_start: 0.6119 (OUTLIER) cc_final: 0.5892 (mpm) REVERT: N 140 MET cc_start: -0.0320 (mtt) cc_final: -0.0931 (ttt) REVERT: P 86 THR cc_start: 0.4289 (OUTLIER) cc_final: 0.4078 (t) REVERT: P 108 ARG cc_start: 0.4325 (OUTLIER) cc_final: 0.2754 (tmt170) REVERT: R 22 GLN cc_start: 0.5266 (pp30) cc_final: 0.5008 (pp30) REVERT: S 182 LYS cc_start: 0.7624 (OUTLIER) cc_final: 0.6788 (ptmt) REVERT: 1 31 ASN cc_start: -0.0267 (OUTLIER) cc_final: -0.0899 (t0) REVERT: 2 92 HIS cc_start: 0.5578 (OUTLIER) cc_final: 0.3910 (t70) REVERT: b 71 CYS cc_start: 0.4210 (OUTLIER) cc_final: 0.3735 (m) REVERT: p 74 ASP cc_start: 0.5690 (p0) cc_final: 0.5406 (p0) outliers start: 141 outliers final: 118 residues processed: 665 average time/residue: 1.6129 time to fit residues: 1480.5051 Evaluate side-chains 663 residues out of total 6209 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 537 time to evaluate : 6.509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 68 SER Chi-restraints excluded: chain D residue 126 VAL Chi-restraints excluded: chain D residue 199 GLU Chi-restraints excluded: chain D residue 236 VAL Chi-restraints excluded: chain D residue 244 VAL Chi-restraints excluded: chain E residue 144 THR Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 289 VAL Chi-restraints excluded: chain E residue 295 CYS Chi-restraints excluded: chain E residue 297 VAL Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 145 LEU Chi-restraints excluded: chain F residue 174 LEU Chi-restraints excluded: chain F residue 216 VAL Chi-restraints excluded: chain H residue 136 ASN Chi-restraints excluded: chain K residue 67 PHE Chi-restraints excluded: chain K residue 101 VAL Chi-restraints excluded: chain K residue 122 MET Chi-restraints excluded: chain K residue 159 THR Chi-restraints excluded: chain L residue 75 LEU Chi-restraints excluded: chain L residue 96 MET Chi-restraints excluded: chain M residue 116 ILE Chi-restraints excluded: chain M residue 146 ASP Chi-restraints excluded: chain M residue 160 SER Chi-restraints excluded: chain M residue 274 VAL Chi-restraints excluded: chain M residue 289 ASN Chi-restraints excluded: chain N residue 236 THR Chi-restraints excluded: chain O residue 42 ILE Chi-restraints excluded: chain O residue 99 ASP Chi-restraints excluded: chain P residue 70 THR Chi-restraints excluded: chain P residue 72 PHE Chi-restraints excluded: chain P residue 83 VAL Chi-restraints excluded: chain P residue 86 THR Chi-restraints excluded: chain P residue 108 ARG Chi-restraints excluded: chain P residue 149 THR Chi-restraints excluded: chain Q residue 115 SER Chi-restraints excluded: chain Q residue 160 VAL Chi-restraints excluded: chain R residue 18 TYR Chi-restraints excluded: chain R residue 41 LEU Chi-restraints excluded: chain R residue 145 VAL Chi-restraints excluded: chain S residue 154 VAL Chi-restraints excluded: chain S residue 182 LYS Chi-restraints excluded: chain T residue 119 GLU Chi-restraints excluded: chain T residue 152 CYS Chi-restraints excluded: chain U residue 74 HIS Chi-restraints excluded: chain U residue 97 VAL Chi-restraints excluded: chain V residue 181 ASP Chi-restraints excluded: chain V residue 213 VAL Chi-restraints excluded: chain W residue 116 LEU Chi-restraints excluded: chain W residue 118 THR Chi-restraints excluded: chain W residue 141 THR Chi-restraints excluded: chain X residue 21 CYS Chi-restraints excluded: chain X residue 22 SER Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 124 THR Chi-restraints excluded: chain X residue 131 THR Chi-restraints excluded: chain Y residue 73 ASN Chi-restraints excluded: chain Z residue 52 ASP Chi-restraints excluded: chain Z residue 75 THR Chi-restraints excluded: chain Z residue 76 ARG Chi-restraints excluded: chain Z residue 84 ASP Chi-restraints excluded: chain Z residue 85 ILE Chi-restraints excluded: chain Z residue 110 LEU Chi-restraints excluded: chain Z residue 142 THR Chi-restraints excluded: chain 0 residue 101 ILE Chi-restraints excluded: chain 0 residue 158 VAL Chi-restraints excluded: chain 0 residue 186 THR Chi-restraints excluded: chain 1 residue 31 ASN Chi-restraints excluded: chain 2 residue 79 ILE Chi-restraints excluded: chain 2 residue 92 HIS Chi-restraints excluded: chain 3 residue 107 VAL Chi-restraints excluded: chain 3 residue 112 ASP Chi-restraints excluded: chain 3 residue 115 LEU Chi-restraints excluded: chain 3 residue 186 LEU Chi-restraints excluded: chain 5 residue 94 HIS Chi-restraints excluded: chain 5 residue 101 ASP Chi-restraints excluded: chain 5 residue 160 HIS Chi-restraints excluded: chain 5 residue 212 THR Chi-restraints excluded: chain 5 residue 232 THR Chi-restraints excluded: chain 5 residue 307 ASP Chi-restraints excluded: chain 5 residue 351 VAL Chi-restraints excluded: chain 5 residue 361 THR Chi-restraints excluded: chain 6 residue 194 THR Chi-restraints excluded: chain 6 residue 222 ASP Chi-restraints excluded: chain 7 residue 96 SER Chi-restraints excluded: chain 7 residue 108 VAL Chi-restraints excluded: chain 7 residue 129 THR Chi-restraints excluded: chain 9 residue 19 SER Chi-restraints excluded: chain 9 residue 29 SER Chi-restraints excluded: chain a residue 113 SER Chi-restraints excluded: chain a residue 134 LYS Chi-restraints excluded: chain b residue 53 ASP Chi-restraints excluded: chain b residue 71 CYS Chi-restraints excluded: chain b residue 88 SER Chi-restraints excluded: chain c residue 69 HIS Chi-restraints excluded: chain c residue 82 ASN Chi-restraints excluded: chain c residue 167 CYS Chi-restraints excluded: chain c residue 181 SER Chi-restraints excluded: chain d residue 153 ASN Chi-restraints excluded: chain f residue 60 LYS Chi-restraints excluded: chain g residue 129 SER Chi-restraints excluded: chain g residue 143 VAL Chi-restraints excluded: chain i residue 98 VAL 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 36 ILE Chi-restraints excluded: chain p residue 77 THR Chi-restraints excluded: chain p residue 160 GLU Chi-restraints excluded: chain s residue 41 VAL Chi-restraints excluded: chain s residue 77 ASP Chi-restraints excluded: chain s residue 100 LEU Chi-restraints excluded: chain s residue 156 TYR Chi-restraints excluded: chain s residue 323 VAL Chi-restraints excluded: chain s residue 331 SER Chi-restraints excluded: chain s residue 356 VAL Chi-restraints excluded: chain s residue 376 THR Chi-restraints excluded: chain u residue 110 CYS Chi-restraints excluded: chain u residue 122 ASP Chi-restraints excluded: chain u residue 141 TYR Chi-restraints excluded: chain u residue 148 HIS Chi-restraints excluded: chain v residue 5 SER Chi-restraints excluded: chain v residue 9 VAL Chi-restraints excluded: chain v residue 63 ASN Chi-restraints excluded: chain v residue 70 ILE Chi-restraints excluded: chain 4 residue 95 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 809 random chunks: chunk 393 optimal weight: 20.0000 chunk 509 optimal weight: 0.0060 chunk 683 optimal weight: 10.0000 chunk 196 optimal weight: 1.9990 chunk 591 optimal weight: 5.9990 chunk 94 optimal weight: 10.0000 chunk 178 optimal weight: 3.9990 chunk 642 optimal weight: 10.0000 chunk 269 optimal weight: 7.9990 chunk 660 optimal weight: 7.9990 chunk 81 optimal weight: 0.6980 overall best weight: 2.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 271 ASN O 91 GLN ** O 158 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 209 GLN ** R 22 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 109 ASN ** Z 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 165 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 385 HIS ** 7 255 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 7 298 GLN b 25 GLN g 73 GLN i 65 ASN ** q 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 314 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.046180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.035195 restraints weight = 658275.252| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.99 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.145 90037 Z= 0.200 Angle : 0.701 18.906 127962 Z= 0.347 Chirality : 0.038 0.239 15007 Planarity : 0.005 0.069 11567 Dihedral : 20.228 178.446 27414 Min Nonbonded Distance : 1.173 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.18 % Favored : 94.82 % Rotamer: Outliers : 1.96 % Allowed : 24.40 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.48 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.10), residues: 6889 helix: 0.56 (0.12), residues: 2190 sheet: -0.40 (0.17), residues: 841 loop : -0.60 (0.10), residues: 3858 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP u 167 HIS 0.011 0.001 HIS F 97 PHE 0.021 0.001 PHE u 124 TYR 0.035 0.001 TYR u 120 ARG 0.017 0.000 ARG X 44 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25946.04 seconds wall clock time: 455 minutes 24.96 seconds (27324.96 seconds total)