Starting phenix.real_space_refine (version: 1.21rc1) on Tue May 16 06:41:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fmg_3231/05_2023/5fmg_3231_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fmg_3231/05_2023/5fmg_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_3231/05_2023/5fmg_3231.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fmg_3231/05_2023/5fmg_3231.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fmg_3231/05_2023/5fmg_3231_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5fmg_3231/05_2023/5fmg_3231_updated.pdb" } resolution = 3.6 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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: 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4953/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: 20.26, per 1000 atoms: 0.52 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: 16.36 Conformation dependent library (CDL) restraints added in 6.6 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: 3.27 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: 14.26 Time building geometry restraints manager: 17.57 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: 22918 19.99 - 39.98: 382 39.98 - 59.97: 60 59.97 - 79.97: 18 79.97 - 99.96: 8 Dihedral angle restraints: 23386 sinusoidal: 6802 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 23383 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: 0.940 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: 0.030 Extract box with map and model: 7.550 Check model and map are aligned: 0.580 Set scattering table: 0.330 Process input model: 100.100 Find NCS groups from input model: 4.690 Set up NCS constraints: 0.370 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 117.340 ------------------------------------------------------------------------------- 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 : 9.275 99.956 12670 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 % 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 *********************** 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 : 4.745 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. outliers start: 10 outliers final: 10 residues processed: 1748 average time/residue: 0.4631 time to fit residues: 1356.9406 Evaluate side-chains 1245 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 1235 time to evaluate : 4.542 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP H 89 " (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 U 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 89 " (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. outliers start: 10 outliers final: 8 residues processed: 10 average time/residue: 0.3354 time to fit residues: 12.4591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 10.0000 chunk 435 optimal weight: 1.9990 chunk 168 optimal weight: 5.9990 chunk 264 optimal weight: 5.9990 chunk 324 optimal weight: 8.9990 chunk 504 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- 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 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 71 HIS 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** H 245 ASN 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 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 ** U 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 71 HIS 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: 47 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6935 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.058 39914 Z= 0.371 Angle : 0.768 10.980 54552 Z= 0.411 Chirality : 0.047 0.230 6834 Planarity : 0.005 0.050 6918 Dihedral : 6.845 78.333 5996 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 19.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.77 % Favored : 96.16 % Rotamer Outliers : 6.28 % 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: -1.34 (0.11), residues: 5576 helix: -0.38 (0.11), residues: 1868 sheet: -1.93 (0.14), residues: 1080 loop : -0.62 (0.12), residues: 2628 *********************** 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 1598 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 218 poor density : 1380 time to evaluate : 4.705 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: "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. 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: "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: "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. outliers start: 218 outliers final: 162 residues processed: 1472 average time/residue: 0.4756 time to fit residues: 1198.4012 Evaluate side-chains 1403 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 162 poor density : 1241 time to evaluate : 4.520 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP H 89 " (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 U 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 89 " (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. outliers start: 162 outliers final: 8 residues processed: 162 average time/residue: 0.3683 time to fit residues: 120.1899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 280 optimal weight: 6.9990 chunk 156 optimal weight: 9.9990 chunk 420 optimal weight: 9.9990 chunk 343 optimal weight: 20.0000 chunk 139 optimal weight: 1.9990 chunk 505 optimal weight: 7.9990 chunk 546 optimal weight: 6.9990 chunk 450 optimal weight: 6.9990 chunk 501 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 405 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN 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 85 ASN D 115 GLN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** 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** ** H 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 GLN I 109 GLN I 114 HIS ** K 64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 40 ASN ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 179 ASN M 231 ASN O 74 ASN P 123 GLN Q 105 GLN ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 ASN R 115 GLN ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 159 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 164 ASN ** 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 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 ** 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 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 179 ASN a 231 ASN b 170 ASN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6978 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.079 39914 Z= 0.394 Angle : 0.753 11.693 54552 Z= 0.401 Chirality : 0.047 0.201 6834 Planarity : 0.004 0.047 6918 Dihedral : 6.575 81.084 5996 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 20.24 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.90 % Favored : 95.07 % Rotamer Outliers : 4.35 % 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: -1.25 (0.11), residues: 5576 helix: 0.03 (0.11), residues: 1890 sheet: -1.78 (0.14), residues: 1102 loop : -0.90 (0.12), residues: 2584 *********************** 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 1453 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 1302 time to evaluate : 4.649 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. 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. 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. 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: "TYR Q 214 " (corrupted residue). Skipping it. 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: "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. outliers start: 151 outliers final: 100 residues processed: 1386 average time/residue: 0.4690 time to fit residues: 1109.6478 Evaluate side-chains 1309 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1209 time to evaluate : 4.482 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE E 241 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP H 89 " (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 S 241 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE U 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 89 " (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. outliers start: 100 outliers final: 10 residues processed: 100 average time/residue: 0.3678 time to fit residues: 76.2146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 499 optimal weight: 7.9990 chunk 380 optimal weight: 10.0000 chunk 262 optimal weight: 0.0870 chunk 55 optimal weight: 0.9990 chunk 241 optimal weight: 20.0000 chunk 339 optimal weight: 10.0000 chunk 507 optimal weight: 0.8980 chunk 537 optimal weight: 7.9990 chunk 265 optimal weight: 5.9990 chunk 481 optimal weight: 4.9990 chunk 144 optimal weight: 20.0000 overall best weight: 2.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN B 123 GLN C 100 ASN C 105 GLN ** C 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 85 ASN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 ASN ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN K 64 ASN ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 179 ASN N 104 ASN O 74 ASN ** Q 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 85 ASN ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 117 GLN ** 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** ** V 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 219 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 109 GLN ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 179 ASN b 104 ASN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6900 moved from start: 0.3541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 39914 Z= 0.233 Angle : 0.640 10.694 54552 Z= 0.339 Chirality : 0.044 0.230 6834 Planarity : 0.004 0.045 6918 Dihedral : 6.124 81.959 5996 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.41 % Favored : 96.59 % Rotamer Outliers : 3.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.11), residues: 5576 helix: 0.58 (0.12), residues: 1908 sheet: -1.62 (0.14), residues: 1144 loop : -0.82 (0.13), residues: 2524 *********************** 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 1466 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 129 poor density : 1337 time to evaluate : 4.212 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: "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. 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. 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: "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: "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. outliers start: 129 outliers final: 90 residues processed: 1388 average time/residue: 0.4530 time to fit residues: 1068.1400 Evaluate side-chains 1323 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 1233 time to evaluate : 4.118 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE E 241 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP H 89 " (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 S 241 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE U 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 89 " (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. outliers start: 90 outliers final: 10 residues processed: 90 average time/residue: 0.3309 time to fit residues: 61.7825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 447 optimal weight: 7.9990 chunk 305 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 400 optimal weight: 10.0000 chunk 221 optimal weight: 10.0000 chunk 458 optimal weight: 9.9990 chunk 371 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 274 optimal weight: 20.0000 chunk 482 optimal weight: 10.0000 chunk 135 optimal weight: 20.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 119 GLN C 146 GLN ** D 21 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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** ** H 168 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 219 HIS I 35 HIS I 109 GLN ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 19 HIS N 104 ASN Q 100 ASN Q 105 GLN Q 119 GLN Q 146 GLN ** R 21 HIS ** 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 89 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** V 219 HIS W 35 HIS W 109 GLN ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 40 ASN ** Z 158 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 19 HIS b 104 ASN b 167 HIS b 170 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7059 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.088 39914 Z= 0.551 Angle : 0.865 14.084 54552 Z= 0.455 Chirality : 0.051 0.250 6834 Planarity : 0.005 0.050 6918 Dihedral : 6.853 80.046 5996 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.04 % Allowed : 5.85 % Favored : 94.12 % Rotamer Outliers : 5.96 % 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: -1.40 (0.11), residues: 5576 helix: 0.09 (0.11), residues: 1886 sheet: -1.59 (0.15), residues: 1052 loop : -1.32 (0.12), residues: 2638 *********************** 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 1411 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 207 poor density : 1204 time to evaluate : 4.468 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. 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. 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. 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: "TYR Q 214 " (corrupted residue). Skipping it. 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. 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. outliers start: 207 outliers final: 147 residues processed: 1303 average time/residue: 0.4610 time to fit residues: 1022.1191 Evaluate side-chains 1300 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 147 poor density : 1153 time to evaluate : 4.352 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE E 241 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP H 89 " (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 S 241 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE U 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 89 " (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. outliers start: 147 outliers final: 10 residues processed: 147 average time/residue: 0.3555 time to fit residues: 105.2920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 180 optimal weight: 4.9990 chunk 483 optimal weight: 0.9990 chunk 106 optimal weight: 5.9990 chunk 315 optimal weight: 7.9990 chunk 132 optimal weight: 0.6980 chunk 537 optimal weight: 6.9990 chunk 446 optimal weight: 8.9990 chunk 249 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 chunk 177 optimal weight: 2.9990 chunk 282 optimal weight: 20.0000 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 ASN C 105 GLN D 69 ASN ** 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** H 168 ASN H 219 HIS ** H 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 180 HIS ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 74 ASN ** Q 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 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 U 231 ASN V 219 HIS ** V 232 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 180 HIS ** a 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 104 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6909 moved from start: 0.4004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 39914 Z= 0.220 Angle : 0.650 13.365 54552 Z= 0.340 Chirality : 0.044 0.265 6834 Planarity : 0.004 0.052 6918 Dihedral : 6.121 81.266 5996 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 17.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 2.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.11), residues: 5576 helix: 0.63 (0.12), residues: 1948 sheet: -1.48 (0.15), residues: 1096 loop : -1.12 (0.12), residues: 2532 *********************** 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 1399 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 99 poor density : 1300 time to evaluate : 4.438 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 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. 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. 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. 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. 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. outliers start: 99 outliers final: 70 residues processed: 1343 average time/residue: 0.4716 time to fit residues: 1073.6283 Evaluate side-chains 1296 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 1226 time to evaluate : 4.781 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE E 241 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP H 89 " (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 S 241 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE U 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 89 " (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. outliers start: 70 outliers final: 10 residues processed: 70 average time/residue: 0.3794 time to fit residues: 56.3314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 518 optimal weight: 9.9990 chunk 60 optimal weight: 30.0000 chunk 306 optimal weight: 9.9990 chunk 392 optimal weight: 10.0000 chunk 304 optimal weight: 3.9990 chunk 452 optimal weight: 5.9990 chunk 300 optimal weight: 5.9990 chunk 535 optimal weight: 0.9990 chunk 335 optimal weight: 0.9990 chunk 326 optimal weight: 10.0000 chunk 247 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 170 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN ** C 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN ** D 146 GLN ** 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 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 231 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 ASN H 219 HIS ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 GLN ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 GLN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 119 GLN ** Q 149 HIS ** 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** V 219 HIS W 109 GLN ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 29 GLN ** a 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 62 GLN b 104 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6916 moved from start: 0.4151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 39914 Z= 0.251 Angle : 0.657 14.018 54552 Z= 0.341 Chirality : 0.044 0.236 6834 Planarity : 0.004 0.064 6918 Dihedral : 5.976 80.441 5996 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer Outliers : 2.88 % 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: -0.77 (0.11), residues: 5576 helix: 0.78 (0.12), residues: 1954 sheet: -1.39 (0.14), residues: 1150 loop : -1.04 (0.13), residues: 2472 *********************** 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 1340 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 1240 time to evaluate : 5.077 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: "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. 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. 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. 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. outliers start: 100 outliers final: 75 residues processed: 1282 average time/residue: 0.4810 time to fit residues: 1054.6529 Evaluate side-chains 1286 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 1211 time to evaluate : 4.359 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE E 241 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP H 89 " (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 S 241 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE U 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 89 " (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. outliers start: 75 outliers final: 10 residues processed: 75 average time/residue: 0.3812 time to fit residues: 60.1600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 331 optimal weight: 10.0000 chunk 214 optimal weight: 5.9990 chunk 320 optimal weight: 9.9990 chunk 161 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 103 optimal weight: 5.9990 chunk 340 optimal weight: 0.9980 chunk 365 optimal weight: 2.9990 chunk 264 optimal weight: 1.9990 chunk 49 optimal weight: 4.9990 chunk 421 optimal weight: 9.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN ** C 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** G 34 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** H 219 HIS ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 106 HIS ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 112 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 119 GLN ** Q 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 164 ASN ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 219 HIS W 109 GLN ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6921 moved from start: 0.4262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 39914 Z= 0.268 Angle : 0.666 14.983 54552 Z= 0.346 Chirality : 0.045 0.250 6834 Planarity : 0.004 0.075 6918 Dihedral : 5.946 80.205 5996 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 17.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.38 % Favored : 95.62 % Rotamer Outliers : 1.81 % 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: -0.69 (0.11), residues: 5576 helix: 0.88 (0.12), residues: 1948 sheet: -1.29 (0.14), residues: 1172 loop : -1.06 (0.13), residues: 2456 *********************** 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 1290 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 1227 time to evaluate : 4.669 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: "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. 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. 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. 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. revert: symmetry clash 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. revert: symmetry clash 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. outliers start: 63 outliers final: 50 residues processed: 1250 average time/residue: 0.4737 time to fit residues: 1005.6271 Evaluate side-chains 1243 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1193 time to evaluate : 4.498 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE E 241 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP H 89 " (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 S 241 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE U 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 89 " (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. outliers start: 50 outliers final: 10 residues processed: 50 average time/residue: 0.3624 time to fit residues: 40.0960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 487 optimal weight: 10.0000 chunk 513 optimal weight: 3.9990 chunk 468 optimal weight: 10.0000 chunk 499 optimal weight: 7.9990 chunk 300 optimal weight: 6.9990 chunk 217 optimal weight: 4.9990 chunk 392 optimal weight: 9.9990 chunk 153 optimal weight: 0.9980 chunk 451 optimal weight: 3.9990 chunk 472 optimal weight: 0.6980 chunk 497 optimal weight: 10.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 221 GLN ** G 34 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** H 219 HIS ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 109 GLN ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 29 GLN ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 119 GLN ** Q 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 97 ASN ** T 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 219 HIS ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 114 GLN ** a 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6906 moved from start: 0.4377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.047 39914 Z= 0.246 Angle : 0.655 14.619 54552 Z= 0.339 Chirality : 0.044 0.238 6834 Planarity : 0.004 0.054 6918 Dihedral : 5.826 80.226 5996 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer Outliers : 1.58 % 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: -0.62 (0.11), residues: 5576 helix: 0.96 (0.12), residues: 1950 sheet: -1.25 (0.14), residues: 1190 loop : -1.02 (0.13), residues: 2436 *********************** 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 1275 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 1220 time to evaluate : 4.508 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. 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. 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. 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: "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. revert: symmetry clash 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. revert: symmetry clash 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. outliers start: 55 outliers final: 37 residues processed: 1245 average time/residue: 0.3553 time to fit residues: 751.2519 Evaluate side-chains 1234 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 1197 time to evaluate : 2.937 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE E 241 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP H 89 " (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 S 241 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE U 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 89 " (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. outliers start: 37 outliers final: 10 residues processed: 37 average time/residue: 0.2464 time to fit residues: 21.0284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 327 optimal weight: 2.9990 chunk 528 optimal weight: 7.9990 chunk 322 optimal weight: 6.9990 chunk 250 optimal weight: 10.0000 chunk 367 optimal weight: 0.0010 chunk 553 optimal weight: 10.0000 chunk 509 optimal weight: 9.9990 chunk 441 optimal weight: 0.9980 chunk 45 optimal weight: 0.0040 chunk 340 optimal weight: 0.0470 chunk 270 optimal weight: 4.9990 overall best weight: 0.8098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 GLN A 133 GLN ** B 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 119 GLN ** C 149 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 69 ASN ** D 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 23 GLN E 227 GLN ** F 117 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 217 ASN G 231 ASN H 219 HIS ** I 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 85 GLN ** K 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 123 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 112 ASN ** P 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 149 HIS R 146 GLN S 164 ASN S 227 GLN ** T 117 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 231 ASN V 219 HIS ** Y 69 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 106 HIS ** a 179 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6803 moved from start: 0.4729 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= 0.169 Angle : 0.619 15.684 54552 Z= 0.319 Chirality : 0.043 0.262 6834 Planarity : 0.003 0.048 6918 Dihedral : 5.442 81.192 5996 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 1.01 % 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: -0.39 (0.11), residues: 5576 helix: 1.19 (0.12), residues: 1952 sheet: -1.03 (0.14), residues: 1174 loop : -0.99 (0.12), residues: 2450 ********************** 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 1368 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 1333 time to evaluate : 4.339 Fit side-chains 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: "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. TARDY: cannot create tardy model for: "TYR I 90 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "TYR I 142 " (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. 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. 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. 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. 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. revert: symmetry clash 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. outliers start: 35 outliers final: 23 residues processed: 1351 average time/residue: 0.4003 time to fit residues: 920.4955 Evaluate side-chains 1249 residues out of total 4988 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1226 time to evaluate : 3.390 Switching outliers to nearest non-outliers TARDY: cannot create tardy model for: "ILE E 241 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE G 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP H 89 " (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 S 241 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ILE U 51 " (corrupted residue). Skipping it. TARDY: cannot create tardy model for: "ASP V 89 " (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. outliers start: 23 outliers final: 10 residues processed: 23 average time/residue: 0.3324 time to fit residues: 18.4415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 556 random chunks: chunk 350 optimal weight: 9.9990 chunk 469 optimal weight: 7.9990 chunk 135 optimal weight: 3.9990 chunk 406 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 chunk 122 optimal weight: 6.9990 chunk 441 optimal weight: 2.9990 chunk 184 optimal weight: 8.9990 chunk 453 optimal weight: 9.9990 chunk 55 optimal weight: 9.9990 chunk 81 optimal weight: 6.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: