Starting phenix.real_space_refine on Sun Mar 24 00:03:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fmg_3231/03_2024/5fmg_3231_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fmg_3231/03_2024/5fmg_3231.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fmg_3231/03_2024/5fmg_3231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fmg_3231/03_2024/5fmg_3231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fmg_3231/03_2024/5fmg_3231_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fmg_3231/03_2024/5fmg_3231_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 1.000 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: 4 Type Number sf(0) Gaussians S 192 5.16 5 C 25110 2.51 5 N 6640 2.21 5 O 7392 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b PHE 223": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 39334 Number of models: 1 Model: "" Number of chains: 30 Chain: "A" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1440 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 4, 'TRANS': 214} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 300 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 11, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 182 Chain: "B" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1381 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 7, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 202 Chain: "C" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1527 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 5, 'TRANS': 214} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 6, 'GLU:plan': 11, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 124 Chain: "D" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1409 Classifications: {'peptide': 215} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 74} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 14, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 169 Chain: "E" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1440 Classifications: {'peptide': 217} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 59} Link IDs: {'PTRANS': 4, 'TRANS': 212} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 291 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 152 Chain: "F" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1492 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 140 Chain: "G" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1542 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 9, 'ASN:plan1': 7, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 185 Chain: "H" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1316 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'TRANS': 190} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 211 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 115 Chain: "I" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1241 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 6, 'TRANS': 179} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 113 Chain: "J" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1273 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 299 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 175 Chain: "K" Number of atoms: 1452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1452 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 1, 'TRANS': 192} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 4, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 89 Chain: "L" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1355 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'TRANS': 188} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 5, 'ASN:plan1': 5, 'ASP:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 82 Chain: "M" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1413 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 4, 'TRANS': 194} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 109 Chain: "N" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1337 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 8, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 146 Chain: "O" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1440 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 73} Link IDs: {'PTRANS': 4, 'TRANS': 214} Chain breaks: 3 Unresolved chain link angles: 5 Unresolved non-hydrogen bonds: 300 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 241 Unresolved non-hydrogen chiralities: 16 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 5, 'ASN:plan1': 11, 'ASP:plan': 6, 'PHE:plan': 1, 'GLU:plan': 12, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 182 Chain: "P" Number of atoms: 1381 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1381 Classifications: {'peptide': 212} Incomplete info: {'truncation_to_alanine': 71} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain breaks: 2 Unresolved chain link angles: 6 Unresolved non-hydrogen bonds: 314 Unresolved non-hydrogen angles: 386 Unresolved non-hydrogen dihedrals: 262 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 6, 'ASN:plan1': 7, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 12, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 202 Chain: "Q" Number of atoms: 1527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1527 Classifications: {'peptide': 220} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 5, 'TRANS': 214} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 227 Unresolved non-hydrogen angles: 279 Unresolved non-hydrogen dihedrals: 184 Unresolved non-hydrogen chiralities: 13 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 4, 'ASP:plan': 6, 'GLU:plan': 11, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 124 Chain: "R" Number of atoms: 1409 Number of conformers: 1 Conformer: "" Number of residues, atoms: 215, 1409 Classifications: {'peptide': 215} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 74} Link IDs: {'PTRANS': 7, 'TRANS': 207} Chain breaks: 2 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 297 Unresolved non-hydrogen angles: 357 Unresolved non-hydrogen dihedrals: 250 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 6, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 4, 'PHE:plan': 3, 'GLU:plan': 14, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 169 Chain: "S" Number of atoms: 1440 Number of conformers: 1 Conformer: "" Number of residues, atoms: 217, 1440 Classifications: {'peptide': 217} Incomplete info: {'n_c_alpha_c_only': 1, 'truncation_to_alanine': 59} Link IDs: {'PTRANS': 4, 'TRANS': 212} Chain breaks: 1 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 239 Unresolved non-hydrogen angles: 291 Unresolved non-hydrogen dihedrals: 193 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 5, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 12, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 152 Chain: "T" Number of atoms: 1492 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1492 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 255 Unresolved non-hydrogen angles: 304 Unresolved non-hydrogen dihedrals: 214 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 2, 'ASN:plan1': 6, 'ASP:plan': 3, 'PHE:plan': 3, 'GLU:plan': 11, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 140 Chain: "U" Number of atoms: 1542 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1542 Classifications: {'peptide': 219} Incomplete info: {'truncation_to_alanine': 59} Link IDs: {'PTRANS': 5, 'TRANS': 213} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 270 Unresolved non-hydrogen angles: 336 Unresolved non-hydrogen dihedrals: 231 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 9, 'ASN:plan1': 7, 'ASP:plan': 8, 'PHE:plan': 2, 'GLU:plan': 9, 'ARG:plan': 5} Unresolved non-hydrogen planarities: 185 Chain: "V" Number of atoms: 1316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1316 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'TRANS': 190} Chain breaks: 1 Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 211 Unresolved non-hydrogen angles: 251 Unresolved non-hydrogen dihedrals: 182 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 3, 'ASP:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 3, 'HIS:plan': 3, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 115 Chain: "W" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 186, 1241 Classifications: {'peptide': 186} Incomplete info: {'truncation_to_alanine': 36} Link IDs: {'PTRANS': 6, 'TRANS': 179} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 167 Unresolved non-hydrogen angles: 211 Unresolved non-hydrogen dihedrals: 141 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'ARG:plan': 4, 'TYR:plan': 2, 'ASN:plan1': 6, 'TRP:plan': 1, 'HIS:plan': 2, 'PHE:plan': 2, 'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 113 Chain: "X" Number of atoms: 1273 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1273 Classifications: {'peptide': 191} Incomplete info: {'truncation_to_alanine': 50} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 236 Unresolved non-hydrogen angles: 299 Unresolved non-hydrogen dihedrals: 207 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 5, 'ASN:plan1': 5, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 175 Chain: "Y" Number of atoms: 1452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1452 Classifications: {'peptide': 194} Incomplete info: {'truncation_to_alanine': 35} Link IDs: {'PTRANS': 1, 'TRANS': 192} Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 193 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 4, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 89 Chain: "Z" Number of atoms: 1355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1355 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 29} Link IDs: {'TRANS': 188} Chain breaks: 1 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 120 Unresolved non-hydrogen angles: 148 Unresolved non-hydrogen dihedrals: 99 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'TYR:plan': 3, 'GLU:plan': 5, 'ASN:plan1': 5, 'ASP:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 82 Chain: "a" Number of atoms: 1413 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1413 Classifications: {'peptide': 199} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 4, 'TRANS': 194} Chain breaks: 2 Unresolved chain link angles: 3 Unresolved non-hydrogen bonds: 159 Unresolved non-hydrogen angles: 196 Unresolved non-hydrogen dihedrals: 133 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 109 Chain: "b" Number of atoms: 1337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 187, 1337 Classifications: {'peptide': 187} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 3, 'TRANS': 183} Chain breaks: 3 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 208 Unresolved non-hydrogen angles: 262 Unresolved non-hydrogen dihedrals: 187 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASP:plan': 4, 'TYR:plan': 8, 'ASN:plan1': 2, 'HIS:plan': 2, 'PHE:plan': 3, 'GLU:plan': 5, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 146 Chain: "I" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'7F1': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 49 Unusual residues: {'7F1': 1} Classifications: {'undetermined': 1} Time building chain proxies: 19.62, per 1000 atoms: 0.50 Number of scatterers: 39334 At special positions: 0 Unit cell: (140.4, 169.52, 135.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 192 16.00 O 7392 8.00 N 6640 7.00 C 25110 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS E 96 " - pdb=" SG CYS E 112 " distance=2.03 Simple disulfide: pdb=" SG CYS G 39 " - pdb=" SG CYS G 48 " distance=2.02 Simple disulfide: pdb=" SG CYS J 163 " - pdb=" SG CYS J 183 " distance=2.03 Simple disulfide: pdb=" SG CYS L 52 " - pdb=" SG CYS L 97 " distance=2.03 Simple disulfide: pdb=" SG CYS S 96 " - pdb=" SG CYS S 112 " distance=2.03 Simple disulfide: pdb=" SG CYS U 39 " - pdb=" SG CYS U 48 " distance=2.02 Simple disulfide: pdb=" SG CYS X 163 " - pdb=" SG CYS X 183 " distance=2.03 Simple disulfide: pdb=" SG CYS Z 52 " - pdb=" SG CYS Z 97 " distance=2.03 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 14.98 Conformation dependent library (CDL) restraints added in 7.8 seconds 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10692 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 158 helices and 58 sheets defined 35.4% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.51 Creating SS restraints... Processing helix chain 'A' and resid 10 through 12 No H-bonds generated for 'chain 'A' and resid 10 through 12' Processing helix chain 'A' and resid 24 through 33 Processing helix chain 'A' and resid 90 through 111 Processing helix chain 'A' and resid 117 through 133 removed outlier: 3.772A pdb=" N ASN A 123 " --> pdb=" O THR A 119 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR A 131 " --> pdb=" O LYS A 127 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR A 132 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN A 133 " --> pdb=" O GLN A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 182 through 187 removed outlier: 3.859A pdb=" N ARG A 187 " --> pdb=" O SER A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 216 removed outlier: 3.776A pdb=" N LEU A 211 " --> pdb=" O ASN A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 253 removed outlier: 3.609A pdb=" N LEU A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 249 through 253' Processing helix chain 'B' and resid 20 through 30 Processing helix chain 'B' and resid 59 through 61 No H-bonds generated for 'chain 'B' and resid 59 through 61' Processing helix chain 'B' and resid 80 through 100 Processing helix chain 'B' and resid 107 through 123 removed outlier: 3.873A pdb=" N PHE B 121 " --> pdb=" O ILE B 117 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR B 122 " --> pdb=" O VAL B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 167 through 172 removed outlier: 4.683A pdb=" N SER B 172 " --> pdb=" O GLN B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 180 removed outlier: 3.783A pdb=" N ARG B 177 " --> pdb=" O LEU B 174 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS B 180 " --> pdb=" O ARG B 177 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 195 removed outlier: 4.299A pdb=" N HIS B 189 " --> pdb=" O GLU B 185 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR B 190 " --> pdb=" O ASP B 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 227 No H-bonds generated for 'chain 'B' and resid 224 through 227' Processing helix chain 'C' and resid 19 through 30 removed outlier: 3.709A pdb=" N ASN C 30 " --> pdb=" O GLU C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 101 removed outlier: 4.507A pdb=" N ILE C 85 " --> pdb=" O ALA C 81 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU C 86 " --> pdb=" O ASP C 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 122 Processing helix chain 'C' and resid 141 through 143 No H-bonds generated for 'chain 'C' and resid 141 through 143' Processing helix chain 'C' and resid 168 through 177 removed outlier: 4.105A pdb=" N VAL C 174 " --> pdb=" O THR C 170 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU C 175 " --> pdb=" O ALA C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 185 through 199 removed outlier: 4.648A pdb=" N LEU C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR C 195 " --> pdb=" O LEU C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 204 through 207 No H-bonds generated for 'chain 'C' and resid 204 through 207' Processing helix chain 'C' and resid 227 through 233 Processing helix chain 'C' and resid 235 through 239 Processing helix chain 'D' and resid 17 through 27 removed outlier: 4.125A pdb=" N GLU D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA D 25 " --> pdb=" O HIS D 21 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL D 26 " --> pdb=" O ALA D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 77 through 97 removed outlier: 4.210A pdb=" N VAL D 82 " --> pdb=" O ALA D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 120 Processing helix chain 'D' and resid 165 through 173 Processing helix chain 'D' and resid 184 through 192 removed outlier: 4.003A pdb=" N LEU D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA D 189 " --> pdb=" O CYS D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 232 removed outlier: 4.270A pdb=" N SER D 224 " --> pdb=" O GLU D 221 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE D 229 " --> pdb=" O VAL D 226 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU D 232 " --> pdb=" O ILE D 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 31 removed outlier: 3.698A pdb=" N LEU E 28 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLY E 29 " --> pdb=" O GLU E 25 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ALA E 30 " --> pdb=" O TYR E 26 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE E 31 " --> pdb=" O ALA E 27 " (cutoff:3.500A) Processing helix chain 'E' and resid 82 through 100 removed outlier: 4.698A pdb=" N LYS E 100 " --> pdb=" O CYS E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 109 through 121 Processing helix chain 'E' and resid 174 through 186 removed outlier: 3.553A pdb=" N GLY E 178 " --> pdb=" O ALA E 175 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA E 179 " --> pdb=" O GLN E 176 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLU E 180 " --> pdb=" O GLU E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 193 through 207 removed outlier: 3.885A pdb=" N VAL E 207 " --> pdb=" O VAL E 203 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 240 Processing helix chain 'F' and resid 20 through 31 removed outlier: 3.607A pdb=" N ALA F 25 " --> pdb=" O GLN F 21 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER F 26 " --> pdb=" O VAL F 22 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU F 27 " --> pdb=" O GLU F 23 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLN F 31 " --> pdb=" O GLU F 27 " (cutoff:3.500A) Processing helix chain 'F' and resid 78 through 99 Processing helix chain 'F' and resid 105 through 121 Processing helix chain 'F' and resid 165 through 173 removed outlier: 3.959A pdb=" N GLU F 172 " --> pdb=" O LYS F 168 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS F 173 " --> pdb=" O THR F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 194 Processing helix chain 'F' and resid 226 through 235 removed outlier: 4.122A pdb=" N SER F 233 " --> pdb=" O GLU F 229 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS F 234 " --> pdb=" O GLU F 230 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL F 235 " --> pdb=" O TYR F 231 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 33 removed outlier: 4.056A pdb=" N ILE G 27 " --> pdb=" O GLN G 23 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR G 28 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS G 29 " --> pdb=" O GLU G 25 " (cutoff:3.500A) Processing helix chain 'G' and resid 84 through 105 Processing helix chain 'G' and resid 111 through 127 removed outlier: 4.087A pdb=" N TYR G 125 " --> pdb=" O TYR G 121 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR G 126 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU G 127 " --> pdb=" O HIS G 123 " (cutoff:3.500A) Processing helix chain 'G' and resid 172 through 175 No H-bonds generated for 'chain 'G' and resid 172 through 175' Processing helix chain 'G' and resid 182 through 187 Processing helix chain 'G' and resid 192 through 199 removed outlier: 3.963A pdb=" N LYS G 198 " --> pdb=" O GLU G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 242 Proline residue: G 239 - end of helix Processing helix chain 'H' and resid 49 through 69 Processing helix chain 'H' and resid 76 through 87 Processing helix chain 'H' and resid 184 through 196 removed outlier: 3.907A pdb=" N ILE H 187 " --> pdb=" O SER H 184 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR H 188 " --> pdb=" O GLY H 185 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN H 190 " --> pdb=" O ILE H 187 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER H 191 " --> pdb=" O TYR H 188 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU H 193 " --> pdb=" O GLN H 190 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN H 194 " --> pdb=" O SER H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 219 removed outlier: 4.538A pdb=" N ASN H 208 " --> pdb=" O LYS H 204 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU H 209 " --> pdb=" O GLU H 205 " (cutoff:3.500A) Processing helix chain 'I' and resid 49 through 69 Processing helix chain 'I' and resid 76 through 89 removed outlier: 3.661A pdb=" N VAL I 80 " --> pdb=" O VAL I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 141 removed outlier: 4.124A pdb=" N VAL I 137 " --> pdb=" O ASN I 133 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA I 140 " --> pdb=" O ALA I 136 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS I 141 " --> pdb=" O VAL I 137 " (cutoff:3.500A) Processing helix chain 'I' and resid 148 through 164 removed outlier: 4.175A pdb=" N CYS I 156 " --> pdb=" O LYS I 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 32 through 34 No H-bonds generated for 'chain 'J' and resid 32 through 34' Processing helix chain 'J' and resid 59 through 79 Processing helix chain 'J' and resid 86 through 98 Processing helix chain 'J' and resid 156 through 166 removed outlier: 4.291A pdb=" N SER J 165 " --> pdb=" O GLY J 161 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 187 Processing helix chain 'K' and resid 51 through 71 Processing helix chain 'K' and resid 78 through 91 Processing helix chain 'K' and resid 134 through 145 removed outlier: 3.627A pdb=" N TYR K 137 " --> pdb=" O TYR K 134 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL K 139 " --> pdb=" O ALA K 136 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER K 140 " --> pdb=" O TYR K 137 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA K 141 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU K 143 " --> pdb=" O SER K 140 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP K 144 " --> pdb=" O ALA K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 153 through 168 Processing helix chain 'L' and resid 49 through 70 Processing helix chain 'L' and resid 76 through 86 removed outlier: 3.796A pdb=" N LEU L 83 " --> pdb=" O ALA L 79 " (cutoff:3.500A) Processing helix chain 'L' and resid 132 through 141 removed outlier: 3.757A pdb=" N ILE L 138 " --> pdb=" O TYR L 134 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP L 140 " --> pdb=" O TYR L 136 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 165 Processing helix chain 'M' and resid 86 through 107 Processing helix chain 'M' and resid 113 through 130 removed outlier: 3.826A pdb=" N ARG M 127 " --> pdb=" O ILE M 123 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG M 128 " --> pdb=" O LEU M 124 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N PHE M 129 " --> pdb=" O TYR M 125 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE M 130 " --> pdb=" O SER M 126 " (cutoff:3.500A) Processing helix chain 'M' and resid 170 through 181 Proline residue: M 175 - end of helix removed outlier: 3.903A pdb=" N VAL M 181 " --> pdb=" O LEU M 177 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 212 removed outlier: 3.839A pdb=" N GLU M 211 " --> pdb=" O THR M 207 " (cutoff:3.500A) Processing helix chain 'N' and resid 58 through 73 Processing helix chain 'N' and resid 88 through 103 Processing helix chain 'N' and resid 179 through 184 Processing helix chain 'N' and resid 186 through 191 Processing helix chain 'N' and resid 199 through 216 removed outlier: 3.759A pdb=" N PHE N 215 " --> pdb=" O ARG N 211 " (cutoff:3.500A) Processing helix chain 'O' and resid 10 through 12 No H-bonds generated for 'chain 'O' and resid 10 through 12' Processing helix chain 'O' and resid 24 through 33 Processing helix chain 'O' and resid 90 through 111 Processing helix chain 'O' and resid 117 through 133 removed outlier: 3.772A pdb=" N ASN O 123 " --> pdb=" O THR O 119 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N TYR O 131 " --> pdb=" O LYS O 127 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N THR O 132 " --> pdb=" O ILE O 128 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLN O 133 " --> pdb=" O GLN O 129 " (cutoff:3.500A) Processing helix chain 'O' and resid 182 through 187 removed outlier: 3.859A pdb=" N ARG O 187 " --> pdb=" O SER O 183 " (cutoff:3.500A) Processing helix chain 'O' and resid 205 through 216 removed outlier: 3.776A pdb=" N LEU O 211 " --> pdb=" O ASN O 207 " (cutoff:3.500A) Processing helix chain 'O' and resid 249 through 253 removed outlier: 3.609A pdb=" N LEU O 253 " --> pdb=" O ILE O 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 249 through 253' Processing helix chain 'P' and resid 20 through 30 Processing helix chain 'P' and resid 59 through 61 No H-bonds generated for 'chain 'P' and resid 59 through 61' Processing helix chain 'P' and resid 80 through 100 Processing helix chain 'P' and resid 107 through 123 removed outlier: 3.873A pdb=" N PHE P 121 " --> pdb=" O ILE P 117 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N THR P 122 " --> pdb=" O VAL P 118 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 172 removed outlier: 4.683A pdb=" N SER P 172 " --> pdb=" O GLN P 168 " (cutoff:3.500A) Processing helix chain 'P' and resid 174 through 180 removed outlier: 3.783A pdb=" N ARG P 177 " --> pdb=" O LEU P 174 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N LYS P 180 " --> pdb=" O ARG P 177 " (cutoff:3.500A) Processing helix chain 'P' and resid 184 through 195 removed outlier: 4.299A pdb=" N HIS P 189 " --> pdb=" O GLU P 185 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N THR P 190 " --> pdb=" O ASP P 186 " (cutoff:3.500A) Processing helix chain 'P' and resid 224 through 227 No H-bonds generated for 'chain 'P' and resid 224 through 227' Processing helix chain 'Q' and resid 19 through 30 removed outlier: 3.709A pdb=" N ASN Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 80 through 101 removed outlier: 4.507A pdb=" N ILE Q 85 " --> pdb=" O ALA Q 81 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N LEU Q 86 " --> pdb=" O ASP Q 82 " (cutoff:3.500A) Processing helix chain 'Q' and resid 107 through 122 Processing helix chain 'Q' and resid 141 through 143 No H-bonds generated for 'chain 'Q' and resid 141 through 143' Processing helix chain 'Q' and resid 168 through 177 removed outlier: 4.105A pdb=" N VAL Q 174 " --> pdb=" O THR Q 170 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU Q 175 " --> pdb=" O ALA Q 171 " (cutoff:3.500A) Processing helix chain 'Q' and resid 185 through 199 removed outlier: 4.648A pdb=" N LEU Q 190 " --> pdb=" O GLU Q 186 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N THR Q 195 " --> pdb=" O LEU Q 191 " (cutoff:3.500A) Processing helix chain 'Q' and resid 204 through 207 No H-bonds generated for 'chain 'Q' and resid 204 through 207' Processing helix chain 'Q' and resid 227 through 233 Processing helix chain 'Q' and resid 235 through 239 Processing helix chain 'R' and resid 17 through 27 removed outlier: 4.125A pdb=" N GLU R 24 " --> pdb=" O GLU R 20 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N ALA R 25 " --> pdb=" O HIS R 21 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N VAL R 26 " --> pdb=" O ALA R 22 " (cutoff:3.500A) Processing helix chain 'R' and resid 77 through 97 removed outlier: 4.210A pdb=" N VAL R 82 " --> pdb=" O ALA R 78 " (cutoff:3.500A) Processing helix chain 'R' and resid 104 through 120 Processing helix chain 'R' and resid 165 through 173 Processing helix chain 'R' and resid 184 through 192 removed outlier: 4.003A pdb=" N LEU R 188 " --> pdb=" O ASP R 184 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N ALA R 189 " --> pdb=" O CYS R 185 " (cutoff:3.500A) Processing helix chain 'R' and resid 220 through 232 removed outlier: 4.270A pdb=" N SER R 224 " --> pdb=" O GLU R 221 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE R 229 " --> pdb=" O VAL R 226 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N GLU R 232 " --> pdb=" O ILE R 229 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 31 removed outlier: 3.698A pdb=" N LEU S 28 " --> pdb=" O VAL S 24 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N GLY S 29 " --> pdb=" O GLU S 25 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N ALA S 30 " --> pdb=" O TYR S 26 " (cutoff:3.500A) removed outlier: 4.803A pdb=" N ILE S 31 " --> pdb=" O ALA S 27 " (cutoff:3.500A) Processing helix chain 'S' and resid 82 through 100 removed outlier: 4.698A pdb=" N LYS S 100 " --> pdb=" O CYS S 96 " (cutoff:3.500A) Processing helix chain 'S' and resid 109 through 121 Processing helix chain 'S' and resid 174 through 186 removed outlier: 3.553A pdb=" N GLY S 178 " --> pdb=" O ALA S 175 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ALA S 179 " --> pdb=" O GLN S 176 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N GLU S 180 " --> pdb=" O GLU S 177 " (cutoff:3.500A) Processing helix chain 'S' and resid 193 through 207 removed outlier: 3.885A pdb=" N VAL S 207 " --> pdb=" O VAL S 203 " (cutoff:3.500A) Processing helix chain 'S' and resid 234 through 240 Processing helix chain 'T' and resid 20 through 31 removed outlier: 3.607A pdb=" N ALA T 25 " --> pdb=" O GLN T 21 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER T 26 " --> pdb=" O VAL T 22 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLU T 27 " --> pdb=" O GLU T 23 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N GLN T 31 " --> pdb=" O GLU T 27 " (cutoff:3.500A) Processing helix chain 'T' and resid 78 through 99 Processing helix chain 'T' and resid 105 through 121 Processing helix chain 'T' and resid 165 through 173 removed outlier: 3.959A pdb=" N GLU T 172 " --> pdb=" O LYS T 168 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N LYS T 173 " --> pdb=" O THR T 169 " (cutoff:3.500A) Processing helix chain 'T' and resid 183 through 194 Processing helix chain 'T' and resid 226 through 235 removed outlier: 4.122A pdb=" N SER T 233 " --> pdb=" O GLU T 229 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N LYS T 234 " --> pdb=" O GLU T 230 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N VAL T 235 " --> pdb=" O TYR T 231 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 33 removed outlier: 4.056A pdb=" N ILE U 27 " --> pdb=" O GLN U 23 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N TYR U 28 " --> pdb=" O VAL U 24 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS U 29 " --> pdb=" O GLU U 25 " (cutoff:3.500A) Processing helix chain 'U' and resid 84 through 105 Processing helix chain 'U' and resid 111 through 127 removed outlier: 4.087A pdb=" N TYR U 125 " --> pdb=" O TYR U 121 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR U 126 " --> pdb=" O ILE U 122 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU U 127 " --> pdb=" O HIS U 123 " (cutoff:3.500A) Processing helix chain 'U' and resid 172 through 175 No H-bonds generated for 'chain 'U' and resid 172 through 175' Processing helix chain 'U' and resid 182 through 187 Processing helix chain 'U' and resid 192 through 199 removed outlier: 3.963A pdb=" N LYS U 198 " --> pdb=" O GLU U 194 " (cutoff:3.500A) Processing helix chain 'U' and resid 234 through 242 Proline residue: U 239 - end of helix Processing helix chain 'V' and resid 49 through 69 Processing helix chain 'V' and resid 76 through 87 Processing helix chain 'V' and resid 184 through 196 removed outlier: 3.907A pdb=" N ILE V 187 " --> pdb=" O SER V 184 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N TYR V 188 " --> pdb=" O GLY V 185 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLN V 190 " --> pdb=" O ILE V 187 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N SER V 191 " --> pdb=" O TYR V 188 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU V 193 " --> pdb=" O GLN V 190 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLN V 194 " --> pdb=" O SER V 191 " (cutoff:3.500A) Processing helix chain 'V' and resid 203 through 219 removed outlier: 4.538A pdb=" N ASN V 208 " --> pdb=" O LYS V 204 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU V 209 " --> pdb=" O GLU V 205 " (cutoff:3.500A) Processing helix chain 'W' and resid 49 through 69 Processing helix chain 'W' and resid 76 through 89 removed outlier: 3.661A pdb=" N VAL W 80 " --> pdb=" O VAL W 76 " (cutoff:3.500A) Processing helix chain 'W' and resid 131 through 141 removed outlier: 4.124A pdb=" N VAL W 137 " --> pdb=" O ASN W 133 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N ALA W 140 " --> pdb=" O ALA W 136 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LYS W 141 " --> pdb=" O VAL W 137 " (cutoff:3.500A) Processing helix chain 'W' and resid 148 through 164 removed outlier: 4.175A pdb=" N CYS W 156 " --> pdb=" O LYS W 152 " (cutoff:3.500A) Processing helix chain 'X' and resid 32 through 34 No H-bonds generated for 'chain 'X' and resid 32 through 34' Processing helix chain 'X' and resid 59 through 79 Processing helix chain 'X' and resid 86 through 98 Processing helix chain 'X' and resid 156 through 166 removed outlier: 4.291A pdb=" N SER X 165 " --> pdb=" O GLY X 161 " (cutoff:3.500A) Processing helix chain 'X' and resid 173 through 187 Processing helix chain 'Y' and resid 51 through 71 Processing helix chain 'Y' and resid 78 through 91 Processing helix chain 'Y' and resid 134 through 145 removed outlier: 3.627A pdb=" N TYR Y 137 " --> pdb=" O TYR Y 134 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N VAL Y 139 " --> pdb=" O ALA Y 136 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N SER Y 140 " --> pdb=" O TYR Y 137 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ALA Y 141 " --> pdb=" O LEU Y 138 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N LEU Y 143 " --> pdb=" O SER Y 140 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP Y 144 " --> pdb=" O ALA Y 141 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 168 Processing helix chain 'Z' and resid 49 through 70 Processing helix chain 'Z' and resid 76 through 86 removed outlier: 3.796A pdb=" N LEU Z 83 " --> pdb=" O ALA Z 79 " (cutoff:3.500A) Processing helix chain 'Z' and resid 132 through 141 removed outlier: 3.757A pdb=" N ILE Z 138 " --> pdb=" O TYR Z 134 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N ASP Z 140 " --> pdb=" O TYR Z 136 " (cutoff:3.500A) Processing helix chain 'Z' and resid 149 through 165 Processing helix chain 'a' and resid 86 through 107 Processing helix chain 'a' and resid 113 through 130 removed outlier: 3.826A pdb=" N ARG a 127 " --> pdb=" O ILE a 123 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG a 128 " --> pdb=" O LEU a 124 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N PHE a 129 " --> pdb=" O TYR a 125 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N PHE a 130 " --> pdb=" O SER a 126 " (cutoff:3.500A) Processing helix chain 'a' and resid 170 through 181 Proline residue: a 175 - end of helix removed outlier: 3.903A pdb=" N VAL a 181 " --> pdb=" O LEU a 177 " (cutoff:3.500A) Processing helix chain 'a' and resid 195 through 212 removed outlier: 3.839A pdb=" N GLU a 211 " --> pdb=" O THR a 207 " (cutoff:3.500A) Processing helix chain 'b' and resid 58 through 73 Processing helix chain 'b' and resid 88 through 103 Processing helix chain 'b' and resid 179 through 184 Processing helix chain 'b' and resid 186 through 191 Processing helix chain 'b' and resid 199 through 216 removed outlier: 3.759A pdb=" N PHE b 215 " --> pdb=" O ARG b 211 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 171 through 174 Processing sheet with id= B, first strand: chain 'A' and resid 146 through 148 Processing sheet with id= C, first strand: chain 'B' and resid 37 through 40 removed outlier: 3.966A pdb=" N VAL B 212 " --> pdb=" O LYS B 220 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS B 220 " --> pdb=" O VAL B 212 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 134 through 138 Processing sheet with id= E, first strand: chain 'C' and resid 35 through 37 removed outlier: 3.696A pdb=" N ILE C 35 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'C' and resid 65 through 67 Processing sheet with id= G, first strand: chain 'D' and resid 158 through 161 Processing sheet with id= H, first strand: chain 'D' and resid 70 through 75 removed outlier: 4.302A pdb=" N ILE D 144 " --> pdb=" O TRP D 156 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'E' and resid 169 through 172 Processing sheet with id= J, first strand: chain 'E' and resid 75 through 78 removed outlier: 4.130A pdb=" N ALA E 77 " --> pdb=" O LEU E 144 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'F' and resid 157 through 160 Processing sheet with id= L, first strand: chain 'F' and resid 133 through 136 removed outlier: 4.048A pdb=" N ILE F 143 " --> pdb=" O TYR F 155 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'G' and resid 39 through 42 removed outlier: 3.665A pdb=" N GLY G 45 " --> pdb=" O CYS G 42 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'G' and resid 77 through 82 removed outlier: 3.604A pdb=" N SER G 142 " --> pdb=" O ASP G 150 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'H' and resid 179 through 182 Processing sheet with id= P, first strand: chain 'H' and resid 41 through 47 removed outlier: 4.073A pdb=" N GLY H 155 " --> pdb=" O GLN H 163 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN H 163 " --> pdb=" O GLY H 155 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'I' and resid 124 through 128 Processing sheet with id= R, first strand: chain 'I' and resid 41 through 47 Processing sheet with id= S, first strand: chain 'J' and resid 12 through 16 Processing sheet with id= T, first strand: chain 'J' and resid 143 through 146 removed outlier: 4.018A pdb=" N LEU J 134 " --> pdb=" O THR J 146 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL J 53 " --> pdb=" O LYS J 46 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LYS J 46 " --> pdb=" O VAL J 53 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'J' and resid 200 through 204 Processing sheet with id= V, first strand: chain 'K' and resid 129 through 132 Processing sheet with id= W, first strand: chain 'K' and resid 36 through 38 removed outlier: 3.758A pdb=" N CYS K 102 " --> pdb=" O CYS K 118 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'L' and resid 127 through 129 removed outlier: 3.626A pdb=" N GLY L 11 " --> pdb=" O PHE L 8 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'L' and resid 34 through 36 Processing sheet with id= Z, first strand: chain 'M' and resid 163 through 166 removed outlier: 3.931A pdb=" N VAL M 49 " --> pdb=" O ILE M 225 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'M' and resid 79 through 82 Processing sheet with id= AB, first strand: chain 'N' and resid 175 through 179 removed outlier: 6.847A pdb=" N SER N 11 " --> pdb=" O ASP N 26 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASP N 26 " --> pdb=" O SER N 11 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE N 226 " --> pdb=" O GLU N 237 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR N 230 " --> pdb=" O GLY N 233 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'N' and resid 50 through 53 Processing sheet with id= AD, first strand: chain 'O' and resid 171 through 174 Processing sheet with id= AE, first strand: chain 'O' and resid 146 through 148 Processing sheet with id= AF, first strand: chain 'P' and resid 37 through 40 removed outlier: 3.966A pdb=" N VAL P 212 " --> pdb=" O LYS P 220 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N LYS P 220 " --> pdb=" O VAL P 212 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'P' and resid 134 through 138 Processing sheet with id= AH, first strand: chain 'Q' and resid 35 through 37 removed outlier: 3.696A pdb=" N ILE Q 35 " --> pdb=" O GLY Q 46 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'Q' and resid 65 through 67 Processing sheet with id= AJ, first strand: chain 'R' and resid 158 through 161 Processing sheet with id= AK, first strand: chain 'R' and resid 70 through 75 removed outlier: 4.302A pdb=" N ILE R 144 " --> pdb=" O TRP R 156 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'S' and resid 169 through 172 Processing sheet with id= AM, first strand: chain 'S' and resid 75 through 78 removed outlier: 4.130A pdb=" N ALA S 77 " --> pdb=" O LEU S 144 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'T' and resid 157 through 160 Processing sheet with id= AO, first strand: chain 'T' and resid 133 through 136 removed outlier: 4.048A pdb=" N ILE T 143 " --> pdb=" O TYR T 155 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'U' and resid 39 through 42 removed outlier: 3.665A pdb=" N GLY U 45 " --> pdb=" O CYS U 42 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'U' and resid 77 through 82 removed outlier: 3.604A pdb=" N SER U 142 " --> pdb=" O ASP U 150 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'V' and resid 179 through 182 Processing sheet with id= AS, first strand: chain 'V' and resid 41 through 47 removed outlier: 4.073A pdb=" N GLY V 155 " --> pdb=" O GLN V 163 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N GLN V 163 " --> pdb=" O GLY V 155 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'W' and resid 124 through 128 Processing sheet with id= AU, first strand: chain 'W' and resid 41 through 47 Processing sheet with id= AV, first strand: chain 'X' and resid 12 through 16 Processing sheet with id= AW, first strand: chain 'X' and resid 143 through 146 removed outlier: 4.018A pdb=" N LEU X 134 " --> pdb=" O THR X 146 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL X 53 " --> pdb=" O LYS X 46 " (cutoff:3.500A) removed outlier: 5.355A pdb=" N LYS X 46 " --> pdb=" O VAL X 53 " (cutoff:3.500A) Processing sheet with id= AX, first strand: chain 'X' and resid 200 through 204 Processing sheet with id= AY, first strand: chain 'Y' and resid 129 through 132 Processing sheet with id= AZ, first strand: chain 'Y' and resid 36 through 38 removed outlier: 3.758A pdb=" N CYS Y 102 " --> pdb=" O CYS Y 118 " (cutoff:3.500A) Processing sheet with id= BA, first strand: chain 'Z' and resid 127 through 129 removed outlier: 3.626A pdb=" N GLY Z 11 " --> pdb=" O PHE Z 8 " (cutoff:3.500A) Processing sheet with id= BB, first strand: chain 'Z' and resid 34 through 36 Processing sheet with id= BC, first strand: chain 'a' and resid 163 through 166 removed outlier: 3.931A pdb=" N VAL a 49 " --> pdb=" O ILE a 225 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'a' and resid 79 through 82 Processing sheet with id= BE, first strand: chain 'b' and resid 175 through 179 removed outlier: 6.847A pdb=" N SER b 11 " --> pdb=" O ASP b 26 " (cutoff:3.500A) removed outlier: 4.589A pdb=" N ASP b 26 " --> pdb=" O SER b 11 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE b 226 " --> pdb=" O GLU b 237 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR b 230 " --> pdb=" O GLY b 233 " (cutoff:3.500A) Processing sheet with id= BF, first strand: chain 'b' and resid 50 through 53 1854 hydrogen bonds defined for protein. 5100 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 13.34 Time building geometry restraints manager: 16.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 6548 1.31 - 1.44: 10626 1.44 - 1.58: 22504 1.58 - 1.71: 2 1.71 - 1.85: 234 Bond restraints: 39914 Sorted by residual: bond pdb=" C THR W 1 " pdb=" N THR W 2 " ideal model delta sigma weight residual 1.331 1.688 -0.357 1.33e-02 5.65e+03 7.20e+02 bond pdb=" C THR I 1 " pdb=" N THR I 2 " ideal model delta sigma weight residual 1.331 1.688 -0.357 1.33e-02 5.65e+03 7.20e+02 bond pdb=" C02 7F1 I 300 " pdb=" C03 7F1 I 300 " ideal model delta sigma weight residual 1.325 1.551 -0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C02 7F1 W 300 " pdb=" C03 7F1 W 300 " ideal model delta sigma weight residual 1.325 1.551 -0.226 2.00e-02 2.50e+03 1.27e+02 bond pdb=" C14 7F1 W 300 " pdb=" N01 7F1 W 300 " ideal model delta sigma weight residual 1.345 1.493 -0.148 2.00e-02 2.50e+03 5.46e+01 ... (remaining 39909 not shown) Histogram of bond angle deviations from ideal: 98.26 - 106.08: 638 106.08 - 113.89: 23274 113.89 - 121.70: 21976 121.70 - 129.52: 8496 129.52 - 137.33: 168 Bond angle restraints: 54552 Sorted by residual: angle pdb=" O THR I 1 " pdb=" C THR I 1 " pdb=" N THR I 2 " ideal model delta sigma weight residual 123.00 101.81 21.19 1.60e+00 3.91e-01 1.75e+02 angle pdb=" O THR W 1 " pdb=" C THR W 1 " pdb=" N THR W 2 " ideal model delta sigma weight residual 123.00 101.81 21.19 1.60e+00 3.91e-01 1.75e+02 angle pdb=" CA LYS L 33 " pdb=" C LYS L 33 " pdb=" N ILE L 34 " ideal model delta sigma weight residual 118.47 104.82 13.65 1.26e+00 6.30e-01 1.17e+02 angle pdb=" CA LYS Z 33 " pdb=" C LYS Z 33 " pdb=" N ILE Z 34 " ideal model delta sigma weight residual 118.47 104.82 13.65 1.26e+00 6.30e-01 1.17e+02 angle pdb=" O GLU Z 32 " pdb=" C GLU Z 32 " pdb=" N LYS Z 33 " ideal model delta sigma weight residual 123.27 111.73 11.54 1.18e+00 7.18e-01 9.57e+01 ... (remaining 54547 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.99: 22938 19.99 - 39.98: 390 39.98 - 59.97: 72 59.97 - 79.97: 22 79.97 - 99.96: 8 Dihedral angle restraints: 23430 sinusoidal: 6846 harmonic: 16584 Sorted by residual: dihedral pdb=" CB CYS J 163 " pdb=" SG CYS J 163 " pdb=" SG CYS J 183 " pdb=" CB CYS J 183 " ideal model delta sinusoidal sigma weight residual 93.00 155.55 -62.55 1 1.00e+01 1.00e-02 5.17e+01 dihedral pdb=" CB CYS X 163 " pdb=" SG CYS X 163 " pdb=" SG CYS X 183 " pdb=" CB CYS X 183 " ideal model delta sinusoidal sigma weight residual 93.00 155.55 -62.55 1 1.00e+01 1.00e-02 5.17e+01 dihedral pdb=" CA PHE K 12 " pdb=" C PHE K 12 " pdb=" N VAL K 13 " pdb=" CA VAL K 13 " ideal model delta harmonic sigma weight residual 180.00 147.96 32.04 0 5.00e+00 4.00e-02 4.11e+01 ... (remaining 23427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 5036 0.068 - 0.136: 1612 0.136 - 0.204: 170 0.204 - 0.272: 14 0.272 - 0.340: 2 Chirality restraints: 6834 Sorted by residual: chirality pdb=" C01 7F1 I 300 " pdb=" C02 7F1 I 300 " pdb=" C05 7F1 I 300 " pdb=" N01 7F1 I 300 " both_signs ideal model delta sigma weight residual False 2.33 2.67 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" C01 7F1 W 300 " pdb=" C02 7F1 W 300 " pdb=" C05 7F1 W 300 " pdb=" N01 7F1 W 300 " both_signs ideal model delta sigma weight residual False 2.33 2.67 -0.34 2.00e-01 2.50e+01 2.88e+00 chirality pdb=" CA TYR M 152 " pdb=" N TYR M 152 " pdb=" C TYR M 152 " pdb=" CB TYR M 152 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.71e+00 ... (remaining 6831 not shown) Planarity restraints: 6918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C01 7F1 W 300 " 0.191 2.00e-02 2.50e+03 1.72e-01 2.97e+02 pdb=" C02 7F1 W 300 " -0.209 2.00e-02 2.50e+03 pdb=" C03 7F1 W 300 " -0.130 2.00e-02 2.50e+03 pdb=" S01 7F1 W 300 " 0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C01 7F1 I 300 " -0.191 2.00e-02 2.50e+03 1.72e-01 2.97e+02 pdb=" C02 7F1 I 300 " 0.209 2.00e-02 2.50e+03 pdb=" C03 7F1 I 300 " 0.130 2.00e-02 2.50e+03 pdb=" S01 7F1 I 300 " -0.148 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR W 1 " -0.071 2.00e-02 2.50e+03 1.12e-01 1.25e+02 pdb=" C THR W 1 " 0.194 2.00e-02 2.50e+03 pdb=" O THR W 1 " -0.069 2.00e-02 2.50e+03 pdb=" N THR W 2 " -0.054 2.00e-02 2.50e+03 ... (remaining 6915 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 1552 2.67 - 3.23: 42419 3.23 - 3.78: 60735 3.78 - 4.34: 83484 4.34 - 4.90: 136953 Nonbonded interactions: 325143 Sorted by model distance: nonbonded pdb=" OG SER H 31 " pdb=" NZ LYS H 33 " model vdw 2.110 2.520 nonbonded pdb=" OG SER V 31 " pdb=" NZ LYS V 33 " model vdw 2.110 2.520 nonbonded pdb=" OG SER B 9 " pdb=" O GLN B 123 " model vdw 2.116 2.440 nonbonded pdb=" OG SER P 9 " pdb=" O GLN P 123 " model vdw 2.116 2.440 nonbonded pdb=" ND1 HIS S 73 " pdb=" O GLN S 227 " model vdw 2.117 2.520 ... (remaining 325138 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'O' } ncs_group { reference = chain 'B' selection = chain 'P' } ncs_group { reference = chain 'C' selection = chain 'Q' } ncs_group { reference = chain 'D' selection = chain 'R' } ncs_group { reference = chain 'E' selection = chain 'S' } ncs_group { reference = chain 'F' selection = chain 'T' } ncs_group { reference = chain 'G' selection = chain 'U' } ncs_group { reference = chain 'H' selection = chain 'V' } ncs_group { reference = chain 'I' selection = chain 'W' } ncs_group { reference = chain 'J' selection = chain 'X' } ncs_group { reference = chain 'K' selection = chain 'Y' } ncs_group { reference = chain 'L' selection = chain 'Z' } ncs_group { reference = chain 'M' selection = chain 'a' } ncs_group { reference = chain 'N' selection = chain 'b' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.860 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 6.080 Check model and map are aligned: 0.460 Set scattering table: 0.320 Process input model: 99.720 Find NCS groups from input model: 4.510 Set up NCS constraints: 0.410 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: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 115.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 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 : 0.012 0.357 39914 Z= 0.798 Angle : 1.496 21.186 54552 Z= 0.975 Chirality : 0.062 0.340 6834 Planarity : 0.007 0.172 6918 Dihedral : 9.528 99.956 12714 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 1.11 % Allowed : 5.09 % Favored : 93.79 % Rotamer: Outliers : 0.29 % Allowed : 1.90 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.35 (0.10), residues: 5576 helix: -2.52 (0.08), residues: 1882 sheet: -2.41 (0.14), residues: 1028 loop : -0.17 (0.13), residues: 2666 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.004 TRP U 129 HIS 0.016 0.004 HIS I 66 PHE 0.042 0.004 PHE R 118 TYR 0.036 0.004 TYR H 62 ARG 0.022 0.003 ARG L 166 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1754 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1744 time to evaluate : 3.896 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL A 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE B 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR C 214 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP H 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR I 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS J 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR K 92 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN L 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN M 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR M 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN N 75 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE O 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL O 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE P 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR Q 214 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET T 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE U 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU U 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR W 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS X 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR Y 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Z 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN a 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR a 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 75 " (corrupted residue). Skipping it. REVERT: A 10 ASP cc_start: 0.7149 (p0) cc_final: 0.6924 (p0) REVERT: A 73 THR cc_start: 0.7408 (t) cc_final: 0.7093 (m) REVERT: A 128 ILE cc_start: 0.8045 (mt) cc_final: 0.7796 (mt) REVERT: B 41 LYS cc_start: 0.7393 (pttt) cc_final: 0.6002 (mptt) REVERT: C 133 SER cc_start: 0.8635 (m) cc_final: 0.8334 (t) REVERT: C 134 PHE cc_start: 0.8535 (p90) cc_final: 0.8275 (p90) REVERT: E 106 ASN cc_start: 0.5825 (m-40) cc_final: 0.5587 (m-40) REVERT: G 71 HIS cc_start: 0.7349 (p-80) cc_final: 0.7128 (p90) REVERT: H 227 LEU cc_start: 0.8103 (tp) cc_final: 0.7825 (tp) REVERT: I 26 VAL cc_start: 0.8999 (m) cc_final: 0.8758 (t) REVERT: J 27 LEU cc_start: 0.7588 (mt) cc_final: 0.7358 (mt) REVERT: K 173 LEU cc_start: 0.7411 (tp) cc_final: 0.7063 (mp) REVERT: M 150 TYR cc_start: 0.7461 (m-80) cc_final: 0.7234 (m-80) REVERT: O 10 ASP cc_start: 0.7135 (p0) cc_final: 0.6632 (p0) REVERT: O 73 THR cc_start: 0.7464 (t) cc_final: 0.7145 (m) REVERT: O 128 ILE cc_start: 0.8067 (mt) cc_final: 0.7860 (mt) REVERT: P 41 LYS cc_start: 0.7352 (pttt) cc_final: 0.6036 (mptt) REVERT: Q 133 SER cc_start: 0.8718 (m) cc_final: 0.8497 (t) REVERT: S 164 ASN cc_start: 0.6924 (t0) cc_final: 0.6694 (t0) REVERT: T 223 ILE cc_start: 0.6922 (mm) cc_final: 0.6454 (mt) REVERT: U 71 HIS cc_start: 0.7309 (p-80) cc_final: 0.7065 (p90) REVERT: V 227 LEU cc_start: 0.8050 (tp) cc_final: 0.7744 (tp) REVERT: W 26 VAL cc_start: 0.8992 (m) cc_final: 0.8781 (t) REVERT: X 27 LEU cc_start: 0.7497 (mt) cc_final: 0.7251 (mt) REVERT: X 170 ASP cc_start: 0.6010 (m-30) cc_final: 0.5754 (m-30) REVERT: Z 76 VAL cc_start: 0.8916 (t) cc_final: 0.8695 (p) REVERT: a 150 TYR cc_start: 0.7425 (m-80) cc_final: 0.7218 (m-80) REVERT: a 191 THR cc_start: 0.6703 (p) cc_final: 0.6474 (p) REVERT: b 57 GLU cc_start: 0.7326 (tt0) cc_final: 0.7020 (tt0) REVERT: b 60 ASP cc_start: 0.7874 (m-30) cc_final: 0.7518 (m-30) outliers start: 10 outliers final: 10 residues processed: 1748 average time/residue: 0.4672 time to fit residues: 1368.0252 Evaluate side-chains 1251 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1241 time to evaluate : 4.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain b residue 75 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 469 optimal weight: 4.9990 chunk 421 optimal weight: 10.0000 chunk 233 optimal weight: 7.9990 chunk 143 optimal weight: 10.0000 chunk 284 optimal weight: 6.9990 chunk 225 optimal weight: 3.9990 chunk 435 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 264 optimal weight: 5.9990 chunk 324 optimal weight: 4.9990 chunk 504 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 74 ASN B 71 HIS B 123 GLN ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 115 GLN ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 164 ASN E 97 ASN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 123 HIS G 130 HIS ** G 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 HIS ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 66 HIS I 109 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 ASN ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 GLN ** L 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 148 ASN ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 86 GLN M 107 HIS ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 186 GLN M 231 ASN N 104 ASN N 170 ASN O 24 GLN O 74 ASN P 71 HIS P 123 GLN ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 115 GLN ** R 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 164 ASN S 97 ASN S 164 ASN ** U 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 123 HIS U 130 HIS ** U 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 219 HIS ** V 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 245 ASN W 66 HIS ** W 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 145 ASN Y 42 ASN ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 29 GLN ** Z 40 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 148 ASN ** Z 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 86 GLN a 107 HIS ** a 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 186 GLN a 231 ASN b 62 GLN b 104 ASN b 170 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6913 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 39914 Z= 0.333 Angle : 0.752 11.062 54552 Z= 0.403 Chirality : 0.047 0.282 6834 Planarity : 0.004 0.050 6918 Dihedral : 7.265 80.531 6056 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 19.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.39 % Favored : 96.54 % Rotamer: Outliers : 5.64 % Allowed : 14.34 % Favored : 80.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.11), residues: 5576 helix: -0.42 (0.11), residues: 1884 sheet: -1.94 (0.14), residues: 1090 loop : -0.60 (0.12), residues: 2602 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP Q 179 HIS 0.013 0.002 HIS W 66 PHE 0.025 0.002 PHE R 118 TYR 0.033 0.002 TYR V 8 ARG 0.012 0.001 ARG K 170 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1589 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 196 poor density : 1393 time to evaluate : 5.175 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL A 234 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE B 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR C 214 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET F 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP H 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR I 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS J 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR K 92 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN L 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN M 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR M 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN N 75 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE O 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL O 234 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE P 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR Q 214 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET T 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU U 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR W 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS X 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR Y 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Z 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN a 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR a 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 75 " (corrupted residue). Skipping it. REVERT: A 128 ILE cc_start: 0.8224 (mt) cc_final: 0.7891 (mt) REVERT: B 41 LYS cc_start: 0.7465 (pttt) cc_final: 0.6125 (mptt) REVERT: C 133 SER cc_start: 0.8723 (m) cc_final: 0.7925 (t) REVERT: C 146 GLN cc_start: 0.5535 (mt0) cc_final: 0.5271 (mt0) REVERT: C 160 PHE cc_start: 0.5980 (m-80) cc_final: 0.5773 (m-80) REVERT: D 35 ILE cc_start: 0.7571 (mm) cc_final: 0.7267 (mm) REVERT: D 36 LYS cc_start: 0.5965 (ttpp) cc_final: 0.5497 (tttm) REVERT: D 83 LEU cc_start: 0.7517 (tp) cc_final: 0.7294 (tp) REVERT: D 90 GLU cc_start: 0.7158 (mt-10) cc_final: 0.6948 (mt-10) REVERT: D 116 GLN cc_start: 0.7234 (tm-30) cc_final: 0.6982 (tm-30) REVERT: E 98 HIS cc_start: 0.6576 (OUTLIER) cc_final: 0.6359 (t-90) REVERT: F 116 TYR cc_start: 0.7423 (m-80) cc_final: 0.7146 (m-80) REVERT: J 170 ASP cc_start: 0.5961 (m-30) cc_final: 0.5603 (m-30) REVERT: K 124 MET cc_start: 0.7029 (OUTLIER) cc_final: 0.6819 (ttp) REVERT: K 173 LEU cc_start: 0.7582 (tp) cc_final: 0.7102 (mp) REVERT: O 128 ILE cc_start: 0.8320 (mt) cc_final: 0.8101 (mt) REVERT: P 41 LYS cc_start: 0.7386 (pttt) cc_final: 0.6147 (mptt) REVERT: Q 133 SER cc_start: 0.8756 (m) cc_final: 0.8004 (t) REVERT: Q 146 GLN cc_start: 0.5487 (mt0) cc_final: 0.5215 (mt0) REVERT: R 90 GLU cc_start: 0.7156 (mt-10) cc_final: 0.6947 (mt-10) REVERT: T 116 TYR cc_start: 0.7447 (m-80) cc_final: 0.7192 (m-80) REVERT: X 170 ASP cc_start: 0.5992 (m-30) cc_final: 0.5671 (m-30) REVERT: Z 76 VAL cc_start: 0.8842 (t) cc_final: 0.8616 (p) outliers start: 196 outliers final: 143 residues processed: 1478 average time/residue: 0.4496 time to fit residues: 1133.9111 Evaluate side-chains 1399 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 1254 time to evaluate : 4.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain B residue 19 LEU Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 161 THR Chi-restraints excluded: chain B residue 163 VAL Chi-restraints excluded: chain C residue 120 SER Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 98 HIS Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 165 THR Chi-restraints excluded: chain F residue 36 VAL Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 113 ILE Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 193 LEU Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 114 HIS Chi-restraints excluded: chain I residue 120 CYS Chi-restraints excluded: chain I residue 160 CYS Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain K residue 124 MET Chi-restraints excluded: chain K residue 128 ASN Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 194 THR Chi-restraints excluded: chain L residue 1 THR Chi-restraints excluded: chain L residue 13 ILE Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 44 THR Chi-restraints excluded: chain L residue 58 TYR Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 15 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 73 ILE Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain N residue 87 THR Chi-restraints excluded: chain N residue 158 ASP Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 183 SER Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain P residue 19 LEU Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 161 THR Chi-restraints excluded: chain P residue 163 VAL Chi-restraints excluded: chain Q residue 120 SER Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain T residue 36 VAL Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 79 SER Chi-restraints excluded: chain T residue 169 THR Chi-restraints excluded: chain T residue 209 THR Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain V residue 210 ILE Chi-restraints excluded: chain V residue 214 VAL Chi-restraints excluded: chain V residue 244 VAL Chi-restraints excluded: chain W residue 3 ILE Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 41 ILE Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 51 ASP Chi-restraints excluded: chain W residue 56 THR Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 114 HIS Chi-restraints excluded: chain W residue 120 CYS Chi-restraints excluded: chain W residue 160 CYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain Y residue 128 ASN Chi-restraints excluded: chain Y residue 155 GLU Chi-restraints excluded: chain Z residue 13 ILE Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 58 TYR Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain a residue 100 ILE Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain b residue 7 VAL Chi-restraints excluded: chain b residue 15 ILE Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 73 ILE Chi-restraints excluded: chain b residue 75 ASN Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 219 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 280 optimal weight: 0.9980 chunk 156 optimal weight: 9.9990 chunk 420 optimal weight: 10.0000 chunk 343 optimal weight: 20.0000 chunk 139 optimal weight: 1.9990 chunk 505 optimal weight: 0.8980 chunk 546 optimal weight: 6.9990 chunk 450 optimal weight: 0.9990 chunk 501 optimal weight: 7.9990 chunk 172 optimal weight: 0.9990 chunk 405 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 123 GLN C 105 GLN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN D 115 GLN ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN ** G 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 ASN ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 ASN L 178 HIS L 180 HIS L 182 ASN M 179 ASN M 231 ASN P 123 GLN Q 105 GLN R 115 GLN ** R 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 89 ASN ** U 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 114 HIS ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 178 HIS Z 180 HIS Z 182 ASN a 179 ASN a 231 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6801 moved from start: 0.3444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 39914 Z= 0.182 Angle : 0.611 11.262 54552 Z= 0.324 Chirality : 0.043 0.210 6834 Planarity : 0.004 0.047 6918 Dihedral : 6.186 83.181 6050 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 15.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 4.86 % Allowed : 18.45 % Favored : 76.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.11), residues: 5576 helix: 0.54 (0.11), residues: 1914 sheet: -1.58 (0.14), residues: 1118 loop : -0.59 (0.13), residues: 2544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP C 179 HIS 0.011 0.001 HIS Y 40 PHE 0.027 0.002 PHE H 207 TYR 0.027 0.002 TYR Z 136 ARG 0.007 0.001 ARG K 170 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1621 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 1452 time to evaluate : 4.637 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL A 234 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE B 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR C 214 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU D 53 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP H 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR I 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS J 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR K 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE K 182 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN L 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN M 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR M 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN N 75 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE O 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL O 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE P 74 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR Q 214 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LEU R 53 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET T 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU U 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR W 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS X 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR Y 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE Y 182 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Z 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN a 179 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR a 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 75 " (corrupted residue). Skipping it. REVERT: C 105 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6407 (tt0) REVERT: C 133 SER cc_start: 0.8597 (m) cc_final: 0.8025 (t) REVERT: D 36 LYS cc_start: 0.5636 (ttpp) cc_final: 0.5275 (tttt) REVERT: D 145 TYR cc_start: 0.6761 (m-10) cc_final: 0.6289 (m-80) REVERT: D 210 THR cc_start: 0.6242 (m) cc_final: 0.5815 (t) REVERT: F 116 TYR cc_start: 0.7156 (m-80) cc_final: 0.6955 (m-80) REVERT: J 170 ASP cc_start: 0.5949 (m-30) cc_final: 0.5489 (m-30) REVERT: K 146 TYR cc_start: 0.5629 (m-80) cc_final: 0.5337 (m-80) REVERT: K 173 LEU cc_start: 0.7731 (tp) cc_final: 0.7119 (mp) REVERT: L 17 ASP cc_start: 0.6973 (p0) cc_final: 0.6725 (p0) REVERT: M 39 THR cc_start: 0.7442 (m) cc_final: 0.7181 (m) REVERT: P 41 LYS cc_start: 0.7242 (pttt) cc_final: 0.6257 (mptt) REVERT: Q 133 SER cc_start: 0.8689 (m) cc_final: 0.8051 (t) REVERT: R 116 GLN cc_start: 0.7107 (tm-30) cc_final: 0.6872 (tm-30) REVERT: R 145 TYR cc_start: 0.6704 (m-10) cc_final: 0.6287 (m-80) REVERT: T 116 TYR cc_start: 0.7232 (m-80) cc_final: 0.7017 (m-80) REVERT: X 170 ASP cc_start: 0.5886 (m-30) cc_final: 0.5447 (m-30) REVERT: Y 146 TYR cc_start: 0.5580 (m-80) cc_final: 0.5285 (m-80) REVERT: Z 17 ASP cc_start: 0.7032 (p0) cc_final: 0.6543 (p0) REVERT: Z 76 VAL cc_start: 0.8541 (t) cc_final: 0.8256 (p) outliers start: 169 outliers final: 101 residues processed: 1535 average time/residue: 0.4455 time to fit residues: 1162.6225 Evaluate side-chains 1385 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 102 poor density : 1283 time to evaluate : 4.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain C residue 105 GLN Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 149 HIS Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 53 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 120 CYS Chi-restraints excluded: chain I residue 160 CYS Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 128 ASN Chi-restraints excluded: chain K residue 185 ASP Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 125 LEU Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain Q residue 105 GLN Chi-restraints excluded: chain Q residue 149 HIS Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 53 LEU Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 169 THR Chi-restraints excluded: chain T residue 209 THR Chi-restraints excluded: chain T residue 232 LEU Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 122 ILE Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain V residue 210 ILE Chi-restraints excluded: chain V residue 214 VAL Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 160 CYS Chi-restraints excluded: chain X residue 15 MET Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 58 LEU Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 97 LEU Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain Y residue 102 CYS Chi-restraints excluded: chain Y residue 185 ASP Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 99 ILE Chi-restraints excluded: chain Z residue 125 LEU Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain b residue 7 VAL Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 219 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 499 optimal weight: 10.0000 chunk 380 optimal weight: 5.9990 chunk 262 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 241 optimal weight: 20.0000 chunk 339 optimal weight: 3.9990 chunk 507 optimal weight: 1.9990 chunk 537 optimal weight: 20.0000 chunk 265 optimal weight: 10.0000 chunk 481 optimal weight: 0.7980 chunk 144 optimal weight: 20.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN D 85 ASN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 117 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 ASN ** G 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 ASN ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 11 ASN ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 ASN M 179 ASN N 89 GLN O 74 ASN ** P 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 119 GLN R 85 ASN ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 144 ASN ** U 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 66 HIS W 109 GLN Y 11 ASN ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 179 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.3775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 39914 Z= 0.196 Angle : 0.606 9.032 54552 Z= 0.319 Chirality : 0.043 0.189 6834 Planarity : 0.003 0.043 6918 Dihedral : 5.991 84.033 6044 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.99 % Allowed : 20.61 % Favored : 73.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.11), residues: 5576 helix: 0.91 (0.12), residues: 1922 sheet: -1.29 (0.14), residues: 1124 loop : -0.59 (0.13), residues: 2530 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Y 117 HIS 0.010 0.001 HIS K 40 PHE 0.022 0.002 PHE b 223 TYR 0.029 0.002 TYR X 98 ARG 0.007 0.000 ARG M 56 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1539 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 208 poor density : 1331 time to evaluate : 4.562 Fit side-chains TARDY: cannot create tardy model for: "ILE A 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL A 234 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE B 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS B 162 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR C 214 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET F 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP H 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR I 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS J 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR K 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE K 182 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLN L 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN M 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR M 234 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE O 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL O 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE P 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS P 162 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR Q 214 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "MET T 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU U 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR W 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS X 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR Y 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE Y 182 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Z 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN a 179 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR a 234 " (corrupted residue). Skipping it. REVERT: C 133 SER cc_start: 0.8736 (m) cc_final: 0.8099 (t) REVERT: D 36 LYS cc_start: 0.5569 (ttpp) cc_final: 0.5254 (tttt) REVERT: D 210 THR cc_start: 0.6153 (m) cc_final: 0.5749 (t) REVERT: F 116 TYR cc_start: 0.7161 (m-80) cc_final: 0.6955 (m-80) REVERT: F 172 GLU cc_start: 0.6925 (mm-30) cc_final: 0.6268 (mm-30) REVERT: H 84 ASP cc_start: 0.7237 (t0) cc_final: 0.7022 (t0) REVERT: J 98 TYR cc_start: 0.6248 (t80) cc_final: 0.5960 (t80) REVERT: J 170 ASP cc_start: 0.5861 (m-30) cc_final: 0.5419 (m-30) REVERT: K 173 LEU cc_start: 0.7717 (tp) cc_final: 0.7161 (mp) REVERT: P 41 LYS cc_start: 0.7338 (pttt) cc_final: 0.6352 (mptt) REVERT: Q 105 GLN cc_start: 0.6540 (tt0) cc_final: 0.6316 (tt0) REVERT: Q 133 SER cc_start: 0.8741 (m) cc_final: 0.8100 (t) REVERT: R 210 THR cc_start: 0.6224 (m) cc_final: 0.5847 (t) REVERT: S 234 THR cc_start: 0.5850 (m) cc_final: 0.5601 (p) REVERT: T 116 TYR cc_start: 0.7204 (m-80) cc_final: 0.6958 (m-80) REVERT: X 149 PHE cc_start: 0.7639 (p90) cc_final: 0.7367 (p90) REVERT: X 170 ASP cc_start: 0.5839 (m-30) cc_final: 0.5403 (m-30) REVERT: Y 146 TYR cc_start: 0.5530 (m-80) cc_final: 0.5311 (m-80) REVERT: Y 178 TYR cc_start: 0.7277 (m-80) cc_final: 0.7013 (m-80) REVERT: Z 17 ASP cc_start: 0.7499 (p0) cc_final: 0.6628 (p0) REVERT: Z 76 VAL cc_start: 0.8544 (t) cc_final: 0.8213 (p) outliers start: 208 outliers final: 160 residues processed: 1427 average time/residue: 0.4603 time to fit residues: 1124.9160 Evaluate side-chains 1406 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 160 poor density : 1246 time to evaluate : 4.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 149 HIS Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 61 HIS Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 168 ASN Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 80 VAL Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 120 CYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 160 CYS Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 128 ASN Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 185 ASP Chi-restraints excluded: chain L residue 1 THR Chi-restraints excluded: chain L residue 14 VAL Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 158 ASP Chi-restraints excluded: chain N residue 198 THR Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 149 HIS Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 63 ILE Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 169 THR Chi-restraints excluded: chain T residue 185 GLU Chi-restraints excluded: chain T residue 209 THR Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 122 ILE Chi-restraints excluded: chain V residue 3 ILE Chi-restraints excluded: chain V residue 18 SER Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 61 HIS Chi-restraints excluded: chain V residue 62 TYR Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain V residue 210 ILE Chi-restraints excluded: chain V residue 214 VAL Chi-restraints excluded: chain W residue 3 ILE Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 51 ASP Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 104 ASP Chi-restraints excluded: chain W residue 120 CYS Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 160 CYS Chi-restraints excluded: chain X residue 15 MET Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 58 LEU Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 97 LEU Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 128 ASN Chi-restraints excluded: chain Y residue 155 GLU Chi-restraints excluded: chain Y residue 185 ASP Chi-restraints excluded: chain Z residue 1 THR Chi-restraints excluded: chain Z residue 14 VAL Chi-restraints excluded: chain Z residue 51 ASP Chi-restraints excluded: chain Z residue 99 ILE Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 100 ILE Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain b residue 7 VAL Chi-restraints excluded: chain b residue 23 ILE Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 219 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 447 optimal weight: 0.3980 chunk 305 optimal weight: 8.9990 chunk 7 optimal weight: 20.0000 chunk 400 optimal weight: 0.0470 chunk 221 optimal weight: 4.9990 chunk 458 optimal weight: 7.9990 chunk 371 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 274 optimal weight: 5.9990 chunk 482 optimal weight: 9.9990 chunk 135 optimal weight: 0.9990 overall best weight: 2.4884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 ASN C 146 GLN ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 ASN ** G 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 HIS ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 GLN M 179 ASN N 170 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 146 GLN ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 144 ASN ** U 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 219 HIS V 232 ASN W 109 GLN ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 29 GLN a 179 ASN b 170 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 moved from start: 0.3955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 39914 Z= 0.218 Angle : 0.610 12.787 54552 Z= 0.319 Chirality : 0.043 0.192 6834 Planarity : 0.003 0.041 6918 Dihedral : 5.900 81.910 6044 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer: Outliers : 7.17 % Allowed : 20.47 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.34 (0.11), residues: 5576 helix: 1.00 (0.12), residues: 1962 sheet: -1.14 (0.14), residues: 1116 loop : -0.66 (0.13), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP Y 117 HIS 0.012 0.001 HIS W 66 PHE 0.026 0.002 PHE H 207 TYR 0.027 0.002 TYR Z 136 ARG 0.007 0.001 ARG K 170 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1537 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 249 poor density : 1288 time to evaluate : 4.644 Fit side-chains TARDY: cannot create tardy model for: "ILE A 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL A 234 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE B 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS B 162 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR C 214 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE E 241 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET F 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP H 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR I 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS J 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR K 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE K 182 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN M 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR M 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN N 75 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE O 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL O 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE P 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS P 162 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR Q 214 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE S 241 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET T 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU U 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR W 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS X 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR Y 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE Y 182 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Z 89 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN a 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR a 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 75 " (corrupted residue). Skipping it. REVERT: C 102 ASN cc_start: 0.7477 (OUTLIER) cc_final: 0.7211 (t0) REVERT: C 133 SER cc_start: 0.8706 (m) cc_final: 0.8111 (t) REVERT: D 36 LYS cc_start: 0.5660 (ttpp) cc_final: 0.5323 (tttt) REVERT: D 210 THR cc_start: 0.6178 (m) cc_final: 0.5736 (t) REVERT: F 172 GLU cc_start: 0.7025 (mm-30) cc_final: 0.6405 (mm-30) REVERT: J 98 TYR cc_start: 0.6374 (t80) cc_final: 0.5947 (t80) REVERT: J 149 PHE cc_start: 0.7638 (p90) cc_final: 0.7376 (p90) REVERT: J 170 ASP cc_start: 0.5947 (m-30) cc_final: 0.5447 (m-30) REVERT: K 173 LEU cc_start: 0.7733 (tp) cc_final: 0.7164 (mp) REVERT: L 17 ASP cc_start: 0.6632 (p0) cc_final: 0.6209 (p0) REVERT: P 41 LYS cc_start: 0.7320 (pttt) cc_final: 0.6319 (mptt) REVERT: Q 133 SER cc_start: 0.8719 (m) cc_final: 0.8150 (t) REVERT: R 210 THR cc_start: 0.6158 (m) cc_final: 0.5733 (t) REVERT: X 98 TYR cc_start: 0.6007 (t80) cc_final: 0.5715 (t80) REVERT: X 149 PHE cc_start: 0.7611 (p90) cc_final: 0.7388 (p90) REVERT: X 170 ASP cc_start: 0.5924 (m-30) cc_final: 0.5397 (m-30) REVERT: Z 76 VAL cc_start: 0.8591 (t) cc_final: 0.8339 (p) outliers start: 249 outliers final: 200 residues processed: 1400 average time/residue: 0.4679 time to fit residues: 1123.9243 Evaluate side-chains 1439 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 201 poor density : 1238 time to evaluate : 3.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain C residue 102 ASN Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 149 HIS Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 87 THR Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 221 GLN Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 61 HIS Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 120 CYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 160 CYS Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 128 ASN Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 185 ASP Chi-restraints excluded: chain L residue 1 THR Chi-restraints excluded: chain L residue 29 GLN Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 50 THR Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 72 ASN Chi-restraints excluded: chain N residue 89 GLN Chi-restraints excluded: chain N residue 158 ASP Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 130 VAL Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 149 HIS Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 89 ILE Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain S residue 241 ILE Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 169 THR Chi-restraints excluded: chain T residue 185 GLU Chi-restraints excluded: chain T residue 209 THR Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 122 ILE Chi-restraints excluded: chain U residue 238 THR Chi-restraints excluded: chain V residue 3 ILE Chi-restraints excluded: chain V residue 18 SER Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 61 HIS Chi-restraints excluded: chain V residue 62 TYR Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain V residue 210 ILE Chi-restraints excluded: chain V residue 214 VAL Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 3 ILE Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 51 ASP Chi-restraints excluded: chain W residue 55 THR Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 104 ASP Chi-restraints excluded: chain W residue 120 CYS Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 160 CYS Chi-restraints excluded: chain X residue 15 MET Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 58 LEU Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 97 LEU Chi-restraints excluded: chain X residue 144 CYS Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 102 CYS Chi-restraints excluded: chain Y residue 128 ASN Chi-restraints excluded: chain Y residue 155 GLU Chi-restraints excluded: chain Y residue 185 ASP Chi-restraints excluded: chain Z residue 1 THR Chi-restraints excluded: chain Z residue 29 GLN Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 81 THR Chi-restraints excluded: chain Z residue 86 ILE Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 100 ILE Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain b residue 7 VAL Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 23 ILE Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 72 ASN Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 198 THR Chi-restraints excluded: chain b residue 219 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 180 optimal weight: 6.9990 chunk 483 optimal weight: 10.0000 chunk 106 optimal weight: 0.4980 chunk 315 optimal weight: 10.0000 chunk 132 optimal weight: 0.6980 chunk 537 optimal weight: 4.9990 chunk 446 optimal weight: 6.9990 chunk 249 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 282 optimal weight: 20.0000 overall best weight: 2.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 100 ASN C 146 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 ASN ** G 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 232 ASN I 109 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 GLN L 182 ASN M 179 ASN N 112 ASN O 74 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 100 ASN Q 146 GLN ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 218 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 89 ASN U 144 ASN ** U 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 109 GLN ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 29 GLN Z 182 ASN ** a 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 170 ASN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6843 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 39914 Z= 0.214 Angle : 0.603 13.104 54552 Z= 0.315 Chirality : 0.043 0.183 6834 Planarity : 0.004 0.048 6918 Dihedral : 5.859 81.898 6044 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 7.23 % Allowed : 21.91 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.11), residues: 5576 helix: 1.09 (0.12), residues: 1988 sheet: -1.09 (0.14), residues: 1126 loop : -0.69 (0.13), residues: 2462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 179 HIS 0.009 0.001 HIS Y 40 PHE 0.022 0.002 PHE H 207 TYR 0.028 0.002 TYR Z 136 ARG 0.008 0.001 ARG K 170 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1552 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 251 poor density : 1301 time to evaluate : 4.583 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL A 234 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE B 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS B 162 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR C 214 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE E 241 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET F 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP H 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR I 90 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS J 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR K 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE K 182 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASN M 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR M 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN N 75 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE O 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL O 234 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE P 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS P 162 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR Q 214 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE S 241 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET T 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE U 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU U 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR W 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS X 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR Y 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE Y 182 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Z 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASN a 179 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR a 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 75 " (corrupted residue). Skipping it. REVERT: D 36 LYS cc_start: 0.5721 (ttpp) cc_final: 0.5365 (tttt) REVERT: D 210 THR cc_start: 0.5973 (m) cc_final: 0.5562 (t) REVERT: F 172 GLU cc_start: 0.7024 (mm-30) cc_final: 0.6453 (mm-30) REVERT: F 209 THR cc_start: 0.5253 (OUTLIER) cc_final: 0.4765 (m) REVERT: H 173 ILE cc_start: 0.8008 (pp) cc_final: 0.7608 (pt) REVERT: H 242 THR cc_start: 0.3799 (OUTLIER) cc_final: 0.3289 (m) REVERT: J 98 TYR cc_start: 0.6283 (t80) cc_final: 0.5800 (t80) REVERT: J 149 PHE cc_start: 0.7606 (p90) cc_final: 0.7358 (p90) REVERT: J 170 ASP cc_start: 0.5907 (m-30) cc_final: 0.5425 (m-30) REVERT: K 124 MET cc_start: 0.7193 (ttp) cc_final: 0.6945 (ttp) REVERT: K 173 LEU cc_start: 0.7720 (tp) cc_final: 0.7158 (mp) REVERT: Q 133 SER cc_start: 0.8721 (m) cc_final: 0.8128 (t) REVERT: R 210 THR cc_start: 0.6123 (m) cc_final: 0.5711 (t) REVERT: T 172 GLU cc_start: 0.6322 (mm-30) cc_final: 0.6036 (mm-30) REVERT: X 98 TYR cc_start: 0.6267 (t80) cc_final: 0.5846 (t80) REVERT: X 149 PHE cc_start: 0.7531 (p90) cc_final: 0.7310 (p90) REVERT: X 170 ASP cc_start: 0.5873 (m-30) cc_final: 0.5402 (m-30) outliers start: 251 outliers final: 210 residues processed: 1422 average time/residue: 0.4402 time to fit residues: 1066.5186 Evaluate side-chains 1464 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 212 poor density : 1252 time to evaluate : 3.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 149 HIS Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 221 GLN Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 61 HIS Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 120 CYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 160 CYS Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 128 ASN Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 185 ASP Chi-restraints excluded: chain K residue 192 TYR Chi-restraints excluded: chain L residue 1 THR Chi-restraints excluded: chain L residue 58 TYR Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 72 ASN Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 72 ILE Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 149 HIS Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 89 ILE Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain S residue 241 ILE Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 79 SER Chi-restraints excluded: chain T residue 169 THR Chi-restraints excluded: chain T residue 185 GLU Chi-restraints excluded: chain T residue 209 THR Chi-restraints excluded: chain T residue 221 GLN Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 122 ILE Chi-restraints excluded: chain U residue 238 THR Chi-restraints excluded: chain V residue 3 ILE Chi-restraints excluded: chain V residue 18 SER Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 61 HIS Chi-restraints excluded: chain V residue 62 TYR Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain V residue 193 LEU Chi-restraints excluded: chain V residue 210 ILE Chi-restraints excluded: chain V residue 214 VAL Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 3 ILE Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 51 ASP Chi-restraints excluded: chain W residue 55 THR Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 104 ASP Chi-restraints excluded: chain W residue 120 CYS Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 160 CYS Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 58 LEU Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 97 LEU Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 102 CYS Chi-restraints excluded: chain Y residue 128 ASN Chi-restraints excluded: chain Y residue 155 GLU Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Y residue 185 ASP Chi-restraints excluded: chain Z residue 1 THR Chi-restraints excluded: chain Z residue 29 GLN Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 86 ILE Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 98 LYS Chi-restraints excluded: chain a residue 100 ILE Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain b residue 7 VAL Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 23 ILE Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 72 ASN Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 198 THR Chi-restraints excluded: chain b residue 219 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 518 optimal weight: 7.9990 chunk 60 optimal weight: 0.9990 chunk 306 optimal weight: 8.9990 chunk 392 optimal weight: 10.0000 chunk 304 optimal weight: 10.0000 chunk 452 optimal weight: 20.0000 chunk 300 optimal weight: 6.9990 chunk 535 optimal weight: 0.9980 chunk 335 optimal weight: 4.9990 chunk 326 optimal weight: 9.9990 chunk 247 optimal weight: 0.0770 overall best weight: 2.8144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 146 GLN D 85 ASN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 ASN ** G 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 179 ASN N 104 ASN N 112 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 164 ASN ** U 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 99 ASN U 144 ASN ** U 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 35 HIS W 109 GLN ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 72 ASN Z 29 GLN a 179 ASN b 112 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6861 moved from start: 0.4195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 39914 Z= 0.232 Angle : 0.615 14.575 54552 Z= 0.320 Chirality : 0.043 0.189 6834 Planarity : 0.003 0.040 6918 Dihedral : 5.855 81.568 6044 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 7.66 % Allowed : 22.48 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.27 (0.11), residues: 5576 helix: 1.12 (0.12), residues: 1980 sheet: -1.01 (0.15), residues: 1120 loop : -0.77 (0.13), residues: 2476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP W 42 HIS 0.009 0.001 HIS Y 40 PHE 0.023 0.002 PHE H 207 TYR 0.025 0.002 TYR Z 136 ARG 0.008 0.001 ARG K 170 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1547 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 266 poor density : 1281 time to evaluate : 4.616 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL A 234 " (corrupted residue). Skipping it. revert: symmetry clash revert: symmetry clash TARDY: cannot create tardy model for: "ILE B 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS B 162 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR C 214 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE E 241 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET F 237 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP H 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR I 90 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS J 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR K 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE K 182 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASN M 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR M 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN N 75 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE O 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL O 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE P 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS P 162 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR Q 214 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE S 241 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 237 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE U 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU U 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR W 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS X 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR Y 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Z 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASN a 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR a 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 75 " (corrupted residue). Skipping it. REVERT: D 36 LYS cc_start: 0.5744 (ttpp) cc_final: 0.5387 (tttt) REVERT: F 209 THR cc_start: 0.5240 (OUTLIER) cc_final: 0.4751 (m) REVERT: J 98 TYR cc_start: 0.6264 (t80) cc_final: 0.5784 (t80) REVERT: J 149 PHE cc_start: 0.7609 (p90) cc_final: 0.7372 (p90) REVERT: J 170 ASP cc_start: 0.6026 (m-30) cc_final: 0.5499 (m-30) REVERT: K 124 MET cc_start: 0.7243 (ttp) cc_final: 0.7019 (ttp) REVERT: K 173 LEU cc_start: 0.7779 (tp) cc_final: 0.7191 (mp) REVERT: L 17 ASP cc_start: 0.7190 (p0) cc_final: 0.6097 (p0) REVERT: O 130 VAL cc_start: 0.7928 (t) cc_final: 0.7665 (t) REVERT: P 41 LYS cc_start: 0.7435 (pttt) cc_final: 0.6265 (mptt) REVERT: R 210 THR cc_start: 0.5937 (m) cc_final: 0.5551 (t) REVERT: T 116 TYR cc_start: 0.7197 (m-80) cc_final: 0.6844 (m-80) REVERT: T 172 GLU cc_start: 0.6412 (mm-30) cc_final: 0.6110 (mm-30) REVERT: X 98 TYR cc_start: 0.6288 (t80) cc_final: 0.5757 (t80) REVERT: X 149 PHE cc_start: 0.7510 (p90) cc_final: 0.7299 (p90) REVERT: X 170 ASP cc_start: 0.5919 (m-30) cc_final: 0.5421 (m-30) REVERT: Y 60 PHE cc_start: 0.7582 (t80) cc_final: 0.7258 (t80) REVERT: Y 64 ASN cc_start: 0.7569 (m110) cc_final: 0.7210 (m110) outliers start: 266 outliers final: 231 residues processed: 1406 average time/residue: 0.4351 time to fit residues: 1042.8418 Evaluate side-chains 1479 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 232 poor density : 1247 time to evaluate : 4.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 149 HIS Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 141 VAL Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain F residue 221 GLN Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 61 HIS Chi-restraints excluded: chain H residue 62 TYR Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 120 CYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 160 CYS Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 128 ASN Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 185 ASP Chi-restraints excluded: chain K residue 192 TYR Chi-restraints excluded: chain L residue 1 THR Chi-restraints excluded: chain L residue 58 TYR Chi-restraints excluded: chain L residue 64 LYS Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 110 ASN Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain M residue 41 ILE Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 98 LYS Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 199 ILE Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain N residue 7 VAL Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 72 ASN Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain N residue 158 ASP Chi-restraints excluded: chain N residue 198 THR Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 72 ILE Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 113 TYR Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 149 HIS Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 89 ILE Chi-restraints excluded: chain S residue 103 TYR Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain S residue 241 ILE Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 79 SER Chi-restraints excluded: chain T residue 169 THR Chi-restraints excluded: chain T residue 209 THR Chi-restraints excluded: chain T residue 221 GLN Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 122 ILE Chi-restraints excluded: chain U residue 141 SER Chi-restraints excluded: chain U residue 238 THR Chi-restraints excluded: chain V residue 3 ILE Chi-restraints excluded: chain V residue 18 SER Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 61 HIS Chi-restraints excluded: chain V residue 62 TYR Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain V residue 210 ILE Chi-restraints excluded: chain V residue 214 VAL Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 3 ILE Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 51 ASP Chi-restraints excluded: chain W residue 55 THR Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 104 ASP Chi-restraints excluded: chain W residue 120 CYS Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 160 CYS Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 58 LEU Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 144 CYS Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 102 CYS Chi-restraints excluded: chain Y residue 128 ASN Chi-restraints excluded: chain Y residue 155 GLU Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Y residue 185 ASP Chi-restraints excluded: chain Z residue 1 THR Chi-restraints excluded: chain Z residue 29 GLN Chi-restraints excluded: chain Z residue 44 THR Chi-restraints excluded: chain Z residue 86 ILE Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain a residue 41 ILE Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 98 LYS Chi-restraints excluded: chain a residue 100 ILE Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain b residue 7 VAL Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 23 ILE Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 72 ASN Chi-restraints excluded: chain b residue 75 ASN Chi-restraints excluded: chain b residue 158 ASP Chi-restraints excluded: chain b residue 198 THR Chi-restraints excluded: chain b residue 219 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 331 optimal weight: 5.9990 chunk 214 optimal weight: 0.6980 chunk 320 optimal weight: 9.9990 chunk 161 optimal weight: 2.9990 chunk 105 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 chunk 340 optimal weight: 0.0170 chunk 365 optimal weight: 3.9990 chunk 264 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 421 optimal weight: 8.9990 overall best weight: 2.1424 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 221 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 ASN ** G 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 GLN M 179 ASN N 104 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 164 ASN ** U 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 144 ASN ** U 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 29 GLN ** a 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 104 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6841 moved from start: 0.4355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 39914 Z= 0.206 Angle : 0.608 15.167 54552 Z= 0.315 Chirality : 0.043 0.186 6834 Planarity : 0.003 0.040 6918 Dihedral : 5.773 81.823 6044 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 15.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 7.20 % Allowed : 23.43 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.22 (0.11), residues: 5576 helix: 1.19 (0.12), residues: 1984 sheet: -0.97 (0.15), residues: 1138 loop : -0.77 (0.13), residues: 2454 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP I 42 HIS 0.009 0.001 HIS Y 40 PHE 0.021 0.002 PHE H 207 TYR 0.020 0.002 TYR M 150 ARG 0.009 0.001 ARG K 170 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1546 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 250 poor density : 1296 time to evaluate : 4.149 Fit side-chains revert: symmetry clash TARDY: cannot create tardy model for: "ILE A 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL A 234 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE B 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS B 162 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR C 214 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE E 241 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET F 237 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP H 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR I 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS J 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR K 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE K 182 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASN M 179 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR M 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN N 75 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE O 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL O 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE P 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS P 162 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR Q 214 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE S 241 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 237 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU U 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR W 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS X 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR Y 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Z 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASN a 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR a 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 75 " (corrupted residue). Skipping it. REVERT: B 41 LYS cc_start: 0.7397 (pttt) cc_final: 0.6222 (mptt) REVERT: D 36 LYS cc_start: 0.5601 (ttpp) cc_final: 0.5261 (tttt) REVERT: F 169 THR cc_start: 0.7059 (OUTLIER) cc_final: 0.6819 (m) REVERT: F 209 THR cc_start: 0.5139 (OUTLIER) cc_final: 0.4825 (m) REVERT: H 173 ILE cc_start: 0.8125 (pp) cc_final: 0.7641 (pt) REVERT: H 242 THR cc_start: 0.3885 (OUTLIER) cc_final: 0.3290 (m) REVERT: J 98 TYR cc_start: 0.6275 (t80) cc_final: 0.5694 (t80) REVERT: J 149 PHE cc_start: 0.7579 (p90) cc_final: 0.7261 (p90) REVERT: J 170 ASP cc_start: 0.5999 (m-30) cc_final: 0.5474 (m-30) REVERT: K 124 MET cc_start: 0.7236 (ttp) cc_final: 0.6966 (tmm) REVERT: K 170 ARG cc_start: 0.6267 (mtm180) cc_final: 0.5968 (mtm-85) REVERT: K 173 LEU cc_start: 0.7702 (tp) cc_final: 0.7162 (mp) REVERT: L 105 ASP cc_start: 0.4869 (p0) cc_final: 0.4539 (p0) REVERT: O 130 VAL cc_start: 0.7804 (t) cc_final: 0.7548 (t) REVERT: P 41 LYS cc_start: 0.7437 (pttt) cc_final: 0.6276 (mptt) REVERT: P 123 GLN cc_start: 0.7675 (OUTLIER) cc_final: 0.6542 (tt0) REVERT: Q 135 LEU cc_start: 0.6973 (mm) cc_final: 0.6717 (mp) REVERT: T 116 TYR cc_start: 0.7067 (m-80) cc_final: 0.6822 (m-80) REVERT: T 169 THR cc_start: 0.7112 (m) cc_final: 0.6910 (m) REVERT: T 172 GLU cc_start: 0.6473 (mm-30) cc_final: 0.6218 (mm-30) REVERT: T 209 THR cc_start: 0.5194 (OUTLIER) cc_final: 0.4852 (m) REVERT: X 98 TYR cc_start: 0.6197 (t80) cc_final: 0.5760 (t80) REVERT: X 149 PHE cc_start: 0.7427 (p90) cc_final: 0.7191 (p90) REVERT: X 170 ASP cc_start: 0.6018 (m-30) cc_final: 0.5520 (m-30) REVERT: Y 60 PHE cc_start: 0.7593 (t80) cc_final: 0.7253 (t80) REVERT: Y 64 ASN cc_start: 0.7550 (m110) cc_final: 0.7151 (m110) REVERT: Y 170 ARG cc_start: 0.6344 (mtm180) cc_final: 0.6053 (mtm-85) outliers start: 250 outliers final: 211 residues processed: 1423 average time/residue: 0.4516 time to fit residues: 1101.2135 Evaluate side-chains 1457 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 216 poor density : 1241 time to evaluate : 4.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 149 HIS Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 23 LEU Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 61 HIS Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 168 ASN Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 14 LEU Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 43 CYS Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 120 CYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 160 CYS Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain K residue 46 LEU Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 119 ASP Chi-restraints excluded: chain K residue 128 ASN Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 185 ASP Chi-restraints excluded: chain K residue 192 TYR Chi-restraints excluded: chain L residue 1 THR Chi-restraints excluded: chain L residue 58 TYR Chi-restraints excluded: chain L residue 81 THR Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain M residue 51 LEU Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 199 ILE Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 72 ASN Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain N residue 198 THR Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 72 ILE Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 113 TYR Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 183 SER Chi-restraints excluded: chain O residue 185 LEU Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 123 GLN Chi-restraints excluded: chain Q residue 32 SER Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 149 HIS Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 103 TYR Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain S residue 241 ILE Chi-restraints excluded: chain T residue 42 ASP Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 46 VAL Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 79 SER Chi-restraints excluded: chain T residue 209 THR Chi-restraints excluded: chain T residue 221 GLN Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 122 ILE Chi-restraints excluded: chain U residue 141 SER Chi-restraints excluded: chain V residue 3 ILE Chi-restraints excluded: chain V residue 18 SER Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 61 HIS Chi-restraints excluded: chain V residue 62 TYR Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain V residue 168 ASN Chi-restraints excluded: chain V residue 210 ILE Chi-restraints excluded: chain V residue 214 VAL Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 3 ILE Chi-restraints excluded: chain W residue 14 LEU Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 51 ASP Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 104 ASP Chi-restraints excluded: chain W residue 120 CYS Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 160 CYS Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 97 LEU Chi-restraints excluded: chain X residue 144 CYS Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 102 CYS Chi-restraints excluded: chain Y residue 128 ASN Chi-restraints excluded: chain Y residue 155 GLU Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Y residue 185 ASP Chi-restraints excluded: chain Y residue 192 TYR Chi-restraints excluded: chain Z residue 1 THR Chi-restraints excluded: chain Z residue 29 GLN Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 101 LEU Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 98 LYS Chi-restraints excluded: chain a residue 100 ILE Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain b residue 7 VAL Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 23 ILE Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 72 ASN Chi-restraints excluded: chain b residue 75 ASN Chi-restraints excluded: chain b residue 198 THR Chi-restraints excluded: chain b residue 219 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 487 optimal weight: 2.9990 chunk 513 optimal weight: 1.9990 chunk 468 optimal weight: 5.9990 chunk 499 optimal weight: 20.0000 chunk 300 optimal weight: 9.9990 chunk 217 optimal weight: 7.9990 chunk 392 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 451 optimal weight: 6.9990 chunk 472 optimal weight: 8.9990 chunk 497 optimal weight: 9.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN E 227 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 104 ASN N 112 ASN N 170 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 227 GLN ** U 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 108 ASN U 144 ASN ** U 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 29 GLN ** a 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 104 ASN b 112 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6927 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 39914 Z= 0.327 Angle : 0.692 15.491 54552 Z= 0.359 Chirality : 0.045 0.202 6834 Planarity : 0.004 0.043 6918 Dihedral : 6.088 81.354 6044 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 18.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 7.25 % Allowed : 23.89 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.42 (0.11), residues: 5576 helix: 1.02 (0.12), residues: 1956 sheet: -1.05 (0.14), residues: 1168 loop : -0.86 (0.13), residues: 2452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 117 HIS 0.009 0.002 HIS Y 40 PHE 0.027 0.002 PHE N 223 TYR 0.042 0.002 TYR P 24 ARG 0.007 0.001 ARG K 170 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1490 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 252 poor density : 1238 time to evaluate : 4.411 Fit side-chains TARDY: cannot create tardy model for: "ILE A 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL A 234 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE B 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS B 162 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR C 214 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE E 241 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET F 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU G 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP H 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR I 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS J 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR K 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASN M 179 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR M 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN N 75 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE O 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL O 234 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE P 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS P 162 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR Q 214 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE S 241 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 237 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE U 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU U 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR W 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS X 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR Y 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Z 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASN a 179 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR a 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 75 " (corrupted residue). Skipping it. REVERT: B 41 LYS cc_start: 0.7504 (pttt) cc_final: 0.6600 (mmtm) REVERT: D 36 LYS cc_start: 0.5725 (ttpp) cc_final: 0.5341 (tttt) REVERT: F 169 THR cc_start: 0.7008 (OUTLIER) cc_final: 0.6760 (m) REVERT: J 98 TYR cc_start: 0.6453 (t80) cc_final: 0.5838 (t80) REVERT: J 170 ASP cc_start: 0.5910 (m-30) cc_final: 0.5371 (m-30) REVERT: K 170 ARG cc_start: 0.6423 (mtm180) cc_final: 0.5849 (mtm-85) REVERT: K 173 LEU cc_start: 0.7803 (tp) cc_final: 0.7224 (mp) REVERT: K 178 TYR cc_start: 0.7690 (m-80) cc_final: 0.7406 (m-80) REVERT: N 112 ASN cc_start: 0.7386 (t0) cc_final: 0.7071 (t0) REVERT: P 123 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.6711 (tt0) REVERT: R 210 THR cc_start: 0.6006 (m) cc_final: 0.5589 (t) REVERT: T 116 TYR cc_start: 0.7227 (m-80) cc_final: 0.6916 (m-80) REVERT: T 169 THR cc_start: 0.7109 (m) cc_final: 0.6887 (m) REVERT: X 98 TYR cc_start: 0.6216 (t80) cc_final: 0.5686 (t80) REVERT: X 149 PHE cc_start: 0.7492 (p90) cc_final: 0.7209 (p90) REVERT: X 170 ASP cc_start: 0.5969 (m-30) cc_final: 0.5439 (m-30) outliers start: 252 outliers final: 224 residues processed: 1366 average time/residue: 0.4371 time to fit residues: 1017.4673 Evaluate side-chains 1444 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 226 poor density : 1218 time to evaluate : 4.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 149 HIS Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 169 THR Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 51 ILE Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 61 HIS Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 168 ASN Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 120 CYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 160 CYS Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 128 ASN Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 185 ASP Chi-restraints excluded: chain K residue 192 TYR Chi-restraints excluded: chain L residue 1 THR Chi-restraints excluded: chain L residue 58 TYR Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 72 ASN Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain N residue 198 THR Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 50 ILE Chi-restraints excluded: chain O residue 72 ILE Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 113 TYR Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 183 SER Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 123 GLN Chi-restraints excluded: chain Q residue 32 SER Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 149 HIS Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 89 ILE Chi-restraints excluded: chain S residue 103 TYR Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain S residue 241 ILE Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 79 SER Chi-restraints excluded: chain T residue 209 THR Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 122 ILE Chi-restraints excluded: chain U residue 141 SER Chi-restraints excluded: chain U residue 238 THR Chi-restraints excluded: chain V residue 3 ILE Chi-restraints excluded: chain V residue 18 SER Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 61 HIS Chi-restraints excluded: chain V residue 62 TYR Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain V residue 168 ASN Chi-restraints excluded: chain V residue 210 ILE Chi-restraints excluded: chain V residue 214 VAL Chi-restraints excluded: chain V residue 244 VAL Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 3 ILE Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 41 ILE Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 51 ASP Chi-restraints excluded: chain W residue 56 THR Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 104 ASP Chi-restraints excluded: chain W residue 120 CYS Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 160 CYS Chi-restraints excluded: chain X residue 12 VAL Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 144 CYS Chi-restraints excluded: chain X residue 151 VAL Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 102 CYS Chi-restraints excluded: chain Y residue 128 ASN Chi-restraints excluded: chain Y residue 155 GLU Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Y residue 185 ASP Chi-restraints excluded: chain Y residue 192 TYR Chi-restraints excluded: chain Z residue 1 THR Chi-restraints excluded: chain Z residue 29 GLN Chi-restraints excluded: chain Z residue 86 ILE Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 101 LEU Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 98 LYS Chi-restraints excluded: chain a residue 100 ILE Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain b residue 7 VAL Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 15 ILE Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 23 ILE Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 72 ASN Chi-restraints excluded: chain b residue 75 ASN Chi-restraints excluded: chain b residue 198 THR Chi-restraints excluded: chain b residue 219 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 327 optimal weight: 6.9990 chunk 528 optimal weight: 7.9990 chunk 322 optimal weight: 0.7980 chunk 250 optimal weight: 6.9990 chunk 367 optimal weight: 20.0000 chunk 553 optimal weight: 4.9990 chunk 509 optimal weight: 6.9990 chunk 441 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 chunk 340 optimal weight: 6.9990 chunk 270 optimal weight: 10.0000 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 144 ASN ** G 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 221 GLN ** U 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 29 GLN ** a 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 104 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.4324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 39914 Z= 0.323 Angle : 0.698 15.491 54552 Z= 0.363 Chirality : 0.045 0.207 6834 Planarity : 0.004 0.047 6918 Dihedral : 6.193 81.316 6044 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 19.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 6.97 % Allowed : 24.99 % Favored : 68.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.11), residues: 5576 helix: 0.90 (0.12), residues: 1954 sheet: -1.22 (0.14), residues: 1166 loop : -0.95 (0.13), residues: 2456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP W 42 HIS 0.011 0.002 HIS Y 40 PHE 0.028 0.002 PHE N 223 TYR 0.041 0.002 TYR B 24 ARG 0.010 0.001 ARG Y 170 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11152 Ramachandran restraints generated. 5576 Oldfield, 0 Emsley, 5576 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1473 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 242 poor density : 1231 time to evaluate : 4.876 Fit side-chains TARDY: cannot create tardy model for: "ILE A 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL A 234 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE B 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS B 162 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR C 214 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE E 241 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "MET F 237 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "GLU G 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP H 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR I 90 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "LYS J 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR K 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN L 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASN M 179 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "THR M 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN N 75 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE O 149 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "VAL O 234 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE P 74 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "CYS P 162 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR Q 214 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE S 241 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "MET T 237 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ILE U 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLU U 178 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "TYR W 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "LYS X 212 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR Y 92 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "GLN Z 89 " (corrupted residue). Skipping it. revert: symmetry clash TARDY: cannot create tardy model for: "ASN a 179 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "THR a 234 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASN b 75 " (corrupted residue). Skipping it. REVERT: D 36 LYS cc_start: 0.5833 (ttpp) cc_final: 0.5354 (tttt) REVERT: D 210 THR cc_start: 0.6113 (m) cc_final: 0.5727 (t) REVERT: F 116 TYR cc_start: 0.7234 (m-80) cc_final: 0.6977 (m-80) REVERT: F 169 THR cc_start: 0.7029 (m) cc_final: 0.6758 (m) REVERT: J 98 TYR cc_start: 0.6491 (t80) cc_final: 0.5865 (t80) REVERT: J 170 ASP cc_start: 0.5922 (m-30) cc_final: 0.5399 (m-30) REVERT: K 173 LEU cc_start: 0.7849 (tp) cc_final: 0.7186 (mp) REVERT: K 178 TYR cc_start: 0.7779 (m-80) cc_final: 0.7463 (m-80) REVERT: M 40 VAL cc_start: 0.8709 (OUTLIER) cc_final: 0.8493 (p) REVERT: N 49 LYS cc_start: 0.7662 (mtpt) cc_final: 0.7311 (mttm) REVERT: O 43 LYS cc_start: 0.5219 (tppt) cc_final: 0.4830 (ttmt) REVERT: P 123 GLN cc_start: 0.7874 (OUTLIER) cc_final: 0.6721 (tt0) REVERT: R 210 THR cc_start: 0.6025 (m) cc_final: 0.5611 (t) REVERT: S 76 CYS cc_start: 0.8301 (p) cc_final: 0.7786 (p) REVERT: T 116 TYR cc_start: 0.7201 (m-80) cc_final: 0.6923 (m-80) REVERT: T 169 THR cc_start: 0.7059 (OUTLIER) cc_final: 0.6842 (m) REVERT: X 98 TYR cc_start: 0.6300 (t80) cc_final: 0.5749 (t80) REVERT: X 170 ASP cc_start: 0.6000 (m-30) cc_final: 0.5487 (m-30) REVERT: b 49 LYS cc_start: 0.7683 (mtpt) cc_final: 0.7324 (mttm) outliers start: 242 outliers final: 230 residues processed: 1346 average time/residue: 0.4493 time to fit residues: 1032.9061 Evaluate side-chains 1435 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 233 poor density : 1202 time to evaluate : 3.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 50 ILE Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 113 TYR Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 121 CYS Chi-restraints excluded: chain A residue 183 SER Chi-restraints excluded: chain A residue 231 VAL Chi-restraints excluded: chain A residue 244 ILE Chi-restraints excluded: chain A residue 250 ASP Chi-restraints excluded: chain B residue 11 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 33 SER Chi-restraints excluded: chain B residue 45 ILE Chi-restraints excluded: chain B residue 48 THR Chi-restraints excluded: chain C residue 111 VAL Chi-restraints excluded: chain C residue 136 ILE Chi-restraints excluded: chain C residue 149 HIS Chi-restraints excluded: chain C residue 153 SER Chi-restraints excluded: chain C residue 155 ASN Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain D residue 9 VAL Chi-restraints excluded: chain D residue 71 LEU Chi-restraints excluded: chain D residue 167 ILE Chi-restraints excluded: chain D residue 204 VAL Chi-restraints excluded: chain E residue 31 ILE Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 89 ILE Chi-restraints excluded: chain E residue 103 TYR Chi-restraints excluded: chain E residue 236 ASP Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain F residue 30 LYS Chi-restraints excluded: chain F residue 42 ASP Chi-restraints excluded: chain F residue 44 VAL Chi-restraints excluded: chain F residue 63 ILE Chi-restraints excluded: chain F residue 75 SER Chi-restraints excluded: chain F residue 79 SER Chi-restraints excluded: chain F residue 185 GLU Chi-restraints excluded: chain F residue 209 THR Chi-restraints excluded: chain G residue 30 SER Chi-restraints excluded: chain G residue 47 ILE Chi-restraints excluded: chain G residue 122 ILE Chi-restraints excluded: chain G residue 141 SER Chi-restraints excluded: chain G residue 238 THR Chi-restraints excluded: chain H residue 3 ILE Chi-restraints excluded: chain H residue 41 LEU Chi-restraints excluded: chain H residue 46 SER Chi-restraints excluded: chain H residue 56 ILE Chi-restraints excluded: chain H residue 61 HIS Chi-restraints excluded: chain H residue 89 ASP Chi-restraints excluded: chain H residue 151 LEU Chi-restraints excluded: chain H residue 168 ASN Chi-restraints excluded: chain H residue 210 ILE Chi-restraints excluded: chain H residue 214 VAL Chi-restraints excluded: chain H residue 242 THR Chi-restraints excluded: chain H residue 244 VAL Chi-restraints excluded: chain I residue 2 THR Chi-restraints excluded: chain I residue 3 ILE Chi-restraints excluded: chain I residue 7 VAL Chi-restraints excluded: chain I residue 26 VAL Chi-restraints excluded: chain I residue 32 SER Chi-restraints excluded: chain I residue 41 ILE Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 55 THR Chi-restraints excluded: chain I residue 56 THR Chi-restraints excluded: chain I residue 81 SER Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain I residue 103 VAL Chi-restraints excluded: chain I residue 104 ASP Chi-restraints excluded: chain I residue 120 CYS Chi-restraints excluded: chain I residue 137 VAL Chi-restraints excluded: chain I residue 160 CYS Chi-restraints excluded: chain I residue 174 ASP Chi-restraints excluded: chain J residue 15 MET Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 56 SER Chi-restraints excluded: chain J residue 69 LEU Chi-restraints excluded: chain J residue 94 SER Chi-restraints excluded: chain J residue 97 LEU Chi-restraints excluded: chain J residue 144 CYS Chi-restraints excluded: chain J residue 151 VAL Chi-restraints excluded: chain J residue 155 THR Chi-restraints excluded: chain J residue 203 LEU Chi-restraints excluded: chain K residue 53 ASP Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 67 LEU Chi-restraints excluded: chain K residue 102 CYS Chi-restraints excluded: chain K residue 128 ASN Chi-restraints excluded: chain K residue 155 GLU Chi-restraints excluded: chain K residue 185 ASP Chi-restraints excluded: chain K residue 192 TYR Chi-restraints excluded: chain L residue 1 THR Chi-restraints excluded: chain L residue 58 TYR Chi-restraints excluded: chain L residue 87 LEU Chi-restraints excluded: chain L residue 101 LEU Chi-restraints excluded: chain L residue 150 ASP Chi-restraints excluded: chain M residue 40 VAL Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 100 ILE Chi-restraints excluded: chain M residue 137 ILE Chi-restraints excluded: chain M residue 234 THR Chi-restraints excluded: chain N residue 13 ILE Chi-restraints excluded: chain N residue 21 ILE Chi-restraints excluded: chain N residue 23 ILE Chi-restraints excluded: chain N residue 46 ILE Chi-restraints excluded: chain N residue 58 LEU Chi-restraints excluded: chain N residue 67 LEU Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 72 ASN Chi-restraints excluded: chain N residue 75 ASN Chi-restraints excluded: chain N residue 186 LEU Chi-restraints excluded: chain N residue 198 THR Chi-restraints excluded: chain N residue 219 THR Chi-restraints excluded: chain O residue 14 THR Chi-restraints excluded: chain O residue 72 ILE Chi-restraints excluded: chain O residue 108 LEU Chi-restraints excluded: chain O residue 113 TYR Chi-restraints excluded: chain O residue 115 VAL Chi-restraints excluded: chain O residue 121 CYS Chi-restraints excluded: chain O residue 183 SER Chi-restraints excluded: chain O residue 231 VAL Chi-restraints excluded: chain O residue 244 ILE Chi-restraints excluded: chain O residue 250 ASP Chi-restraints excluded: chain P residue 11 THR Chi-restraints excluded: chain P residue 20 VAL Chi-restraints excluded: chain P residue 33 SER Chi-restraints excluded: chain P residue 45 ILE Chi-restraints excluded: chain P residue 48 THR Chi-restraints excluded: chain P residue 123 GLN Chi-restraints excluded: chain Q residue 32 SER Chi-restraints excluded: chain Q residue 136 ILE Chi-restraints excluded: chain Q residue 149 HIS Chi-restraints excluded: chain Q residue 153 SER Chi-restraints excluded: chain Q residue 235 LEU Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 26 VAL Chi-restraints excluded: chain R residue 71 LEU Chi-restraints excluded: chain R residue 167 ILE Chi-restraints excluded: chain R residue 175 ASN Chi-restraints excluded: chain R residue 204 VAL Chi-restraints excluded: chain S residue 31 ILE Chi-restraints excluded: chain S residue 46 VAL Chi-restraints excluded: chain S residue 57 THR Chi-restraints excluded: chain S residue 87 THR Chi-restraints excluded: chain S residue 89 ILE Chi-restraints excluded: chain S residue 141 VAL Chi-restraints excluded: chain S residue 198 ILE Chi-restraints excluded: chain S residue 241 ILE Chi-restraints excluded: chain T residue 8 THR Chi-restraints excluded: chain T residue 44 VAL Chi-restraints excluded: chain T residue 63 ILE Chi-restraints excluded: chain T residue 79 SER Chi-restraints excluded: chain T residue 169 THR Chi-restraints excluded: chain T residue 185 GLU Chi-restraints excluded: chain T residue 209 THR Chi-restraints excluded: chain U residue 30 SER Chi-restraints excluded: chain U residue 38 LEU Chi-restraints excluded: chain U residue 47 ILE Chi-restraints excluded: chain U residue 51 ILE Chi-restraints excluded: chain U residue 113 ILE Chi-restraints excluded: chain U residue 122 ILE Chi-restraints excluded: chain U residue 141 SER Chi-restraints excluded: chain U residue 238 THR Chi-restraints excluded: chain V residue 3 ILE Chi-restraints excluded: chain V residue 13 MET Chi-restraints excluded: chain V residue 18 SER Chi-restraints excluded: chain V residue 41 LEU Chi-restraints excluded: chain V residue 46 SER Chi-restraints excluded: chain V residue 61 HIS Chi-restraints excluded: chain V residue 62 TYR Chi-restraints excluded: chain V residue 89 ASP Chi-restraints excluded: chain V residue 151 LEU Chi-restraints excluded: chain V residue 168 ASN Chi-restraints excluded: chain V residue 210 ILE Chi-restraints excluded: chain V residue 214 VAL Chi-restraints excluded: chain V residue 244 VAL Chi-restraints excluded: chain W residue 2 THR Chi-restraints excluded: chain W residue 3 ILE Chi-restraints excluded: chain W residue 26 VAL Chi-restraints excluded: chain W residue 32 SER Chi-restraints excluded: chain W residue 41 ILE Chi-restraints excluded: chain W residue 43 CYS Chi-restraints excluded: chain W residue 51 ASP Chi-restraints excluded: chain W residue 55 THR Chi-restraints excluded: chain W residue 56 THR Chi-restraints excluded: chain W residue 80 VAL Chi-restraints excluded: chain W residue 95 VAL Chi-restraints excluded: chain W residue 103 VAL Chi-restraints excluded: chain W residue 104 ASP Chi-restraints excluded: chain W residue 120 CYS Chi-restraints excluded: chain W residue 137 VAL Chi-restraints excluded: chain W residue 160 CYS Chi-restraints excluded: chain X residue 39 THR Chi-restraints excluded: chain X residue 56 SER Chi-restraints excluded: chain X residue 69 LEU Chi-restraints excluded: chain X residue 94 SER Chi-restraints excluded: chain X residue 144 CYS Chi-restraints excluded: chain X residue 155 THR Chi-restraints excluded: chain Y residue 61 ILE Chi-restraints excluded: chain Y residue 67 LEU Chi-restraints excluded: chain Y residue 102 CYS Chi-restraints excluded: chain Y residue 111 ASP Chi-restraints excluded: chain Y residue 128 ASN Chi-restraints excluded: chain Y residue 155 GLU Chi-restraints excluded: chain Y residue 173 LEU Chi-restraints excluded: chain Y residue 185 ASP Chi-restraints excluded: chain Y residue 192 TYR Chi-restraints excluded: chain Z residue 1 THR Chi-restraints excluded: chain Z residue 29 GLN Chi-restraints excluded: chain Z residue 86 ILE Chi-restraints excluded: chain Z residue 87 LEU Chi-restraints excluded: chain Z residue 101 LEU Chi-restraints excluded: chain Z residue 150 ASP Chi-restraints excluded: chain a residue 51 LEU Chi-restraints excluded: chain a residue 60 SER Chi-restraints excluded: chain a residue 100 ILE Chi-restraints excluded: chain a residue 137 ILE Chi-restraints excluded: chain a residue 191 THR Chi-restraints excluded: chain a residue 234 THR Chi-restraints excluded: chain b residue 7 VAL Chi-restraints excluded: chain b residue 13 ILE Chi-restraints excluded: chain b residue 15 ILE Chi-restraints excluded: chain b residue 21 ILE Chi-restraints excluded: chain b residue 23 ILE Chi-restraints excluded: chain b residue 46 ILE Chi-restraints excluded: chain b residue 58 LEU Chi-restraints excluded: chain b residue 67 LEU Chi-restraints excluded: chain b residue 69 THR Chi-restraints excluded: chain b residue 72 ASN Chi-restraints excluded: chain b residue 75 ASN Chi-restraints excluded: chain b residue 186 LEU Chi-restraints excluded: chain b residue 198 THR Chi-restraints excluded: chain b residue 219 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 350 optimal weight: 0.9990 chunk 469 optimal weight: 4.9990 chunk 135 optimal weight: 5.9990 chunk 406 optimal weight: 2.9990 chunk 65 optimal weight: 0.9980 chunk 122 optimal weight: 0.0030 chunk 441 optimal weight: 0.9990 chunk 184 optimal weight: 0.0170 chunk 453 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 overall best weight: 0.6032 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 GLN E 227 GLN ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 114 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 72 ASN ** K 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 23 GLN ** S 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 227 GLN T 221 GLN ** U 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 73 ASN U 144 ASN U 217 ASN U 231 ASN ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 29 GLN ** a 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3947 r_free = 0.3947 target = 0.158266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3826 r_free = 0.3826 target = 0.149219 restraints weight = 79838.450| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.151398 restraints weight = 46089.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.152958 restraints weight = 29804.530| |-----------------------------------------------------------------------------| r_work (final): 0.3880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.4752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 39914 Z= 0.171 Angle : 0.613 16.109 54552 Z= 0.317 Chirality : 0.042 0.237 6834 Planarity : 0.003 0.051 6918 Dihedral : 5.695 83.409 6044 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 4.58 % Allowed : 27.89 % Favored : 67.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.11), residues: 5576 helix: 1.22 (0.12), residues: 1966 sheet: -0.89 (0.15), residues: 1148 loop : -0.87 (0.12), residues: 2462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP C 179 HIS 0.011 0.001 HIS Y 40 PHE 0.023 0.002 PHE H 153 TYR 0.040 0.001 TYR B 24 ARG 0.006 0.001 ARG Y 170 =============================================================================== Job complete usr+sys time: 14628.84 seconds wall clock time: 259 minutes 50.12 seconds (15590.12 seconds total)