data_URB001 # _entry.id URB001 # _audit.revision_id 1 _audit.creation_date 2001-10-03 _audit.update_record ; This preliminary mmCIF data file was originally created by the Nucleic Acid Database Project and is being released as part of the RCSB PDB data uniformity project. This data file is provided for test purposes. This file is not the author approved archival version of this entry which can be obtained in PDB format from ftp://ftp.rcsb.org or one of the PDB ftp mirror sites. ; # loop_ _audit_conform.dict_name _audit_conform.dict_version _audit_conform.dict_location cif_mm.dic 2.0.03 http://pdb.rutgers.edu/mmcif/dictionaries/ascii/cif_mm.dic cif_pdbx.dic 0.8.07 http://pdb.rutgers.edu/mmcif/dictionaries/ascii/pdbx_exchange.dic # _database.entry_id URB001 _database.code_CSD BIXXIP10 # loop_ _database_2.database_id _database_2.database_code NDB URB001 RCSB URB001 # loop_ _database_PDB_rev.num _database_PDB_rev.date _database_PDB_rev.date_original _database_PDB_rev.status _database_PDB_rev.replaces _database_PDB_rev.mod_type 1 1988-08-18 1988-08-18 ? ? 0 2 2001-09-21 ? ? ? 5 # loop_ _audit_author.name 'Parthasarathy, R.' 'Malik, M.' 'Fridey, S.M.' # loop_ _citation.id _citation.title _citation.journal_abbrev _citation.journal_volume _citation.page_first _citation.page_last _citation.year _citation.journal_id_ASTM _citation.country _citation.journal_id_ISSN _citation.journal_id_CSD _citation.book_publisher primary ;X-Ray Structure of a Dinucleoside Monophosphate A2'P5'C that Contains a 2'-5' Link Found in (2'-5')oligo(A)s Induced By Interferons: Single-Stranded Helical Conformation of 2'-5'-Linked Oligonucleotides ; Proc.Nat.Acad.Sci.USA 79 7292 7296 1982 PNASA6 US 0027-8424 0040 ? 1 ;Reciprocal Conformational Relationships of 2',5' and 3',5' Polynucleotides: Single Stranded Helices of 2',5' Polynucleotides ; 'Conformation in Biology' ? 267 274 1982 ? ? 0-940030-05-5 0961 'Adenine Press, New York' # loop_ _citation_author.citation_id _citation_author.name primary 'Parthasarathy, R.' primary 'Malik, M.' primary 'Fridey, S.M.' 1 'Parthasarathy, R.' 1 'Rajeswaran, M.' 1 'Kieber-Emmons, T.' 1 'Rein, R.' # _cell.entry_id URB001 _cell.length_a 8.631 _cell.length_b 18.099 _cell.length_c 16.101 _cell.angle_alpha 90.00 _cell.angle_beta 90.00 _cell.angle_gamma 90.00 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id URB001 _symmetry.space_group_name_H-M 'P 21 21 21' _symmetry.pdbx_full_space_group_name_H-M ? _symmetry.cell_setting ? _symmetry.Int_Tables_number ? # loop_ _entity.id _entity.type _entity.src_method _entity.pdbx_description _entity.formula_weight _entity.pdbx_number_of_molecules _entity.details 1 polymer man ;RNA (5'-R(*AP*)-2'-5'-R(*C)-3') ; 589.435 1 ? 2 water nat water 18.015 2 ? # _entity_poly.entity_id 1 _entity_poly.type polyribonucleotide _entity_poly.nstd_linkage no _entity_poly.nstd_monomer no # loop_ _entity_poly_seq.entity_id _entity_poly_seq.num _entity_poly_seq.mon_id 1 1 A 1 2 C # loop_ _chem_comp.id _chem_comp.type _chem_comp.mon_nstd_flag _chem_comp.name _chem_comp.pdbx_synonyms _chem_comp.formula _chem_comp.formula_weight A 'RNA linking' y 'ADENOSINE-5'-MONOPHOSPHATE' ? 'C10 H14 N5 O7 P1' 347.224 C 'RNA linking' y 'CYTIDINE-5'-MONOPHOSPHATE' ? 'C9 H14 N3 O8 P1' 323.199 HOH non-polymer . WATER ? 'H2 O1' 18.015 # _exptl.entry_id URB001 _exptl.method 'X-RAY DIFFRACTION' _exptl.crystals_number ? # _exptl_crystal.id 1 _exptl_crystal.density_meas 1.6200 _exptl_crystal.density_Matthews ? _exptl_crystal.density_percent_sol ? _exptl_crystal.description ? # _exptl_crystal_grow.crystal_id ? _exptl_crystal_grow.method ? _exptl_crystal_grow.temp ? _exptl_crystal_grow.temp_details 'ROOM TEMPERATURE' _exptl_crystal_grow.pH ? _exptl_crystal_grow.pdbx_details ? _exptl_crystal_grow.pdbx_pH_range ? # _exptl_crystal_grow_comp.crystal_id 1 _exptl_crystal_grow_comp.id 1 _exptl_crystal_grow_comp.sol_id 1 _exptl_crystal_grow_comp.name 'WATER (ACIDIC)' _exptl_crystal_grow_comp.volume 1 _exptl_crystal_grow_comp.conc 2 _exptl_crystal_grow_comp.details 3 # _diffrn.id 1 _diffrn.ambient_temp ? _diffrn.ambient_temp_details 'ROOM TEMPERATURE' _diffrn.crystal_id 1 # _diffrn_detector.diffrn_id 1 _diffrn_detector.detector DIFFRACTOMETER _diffrn_detector.type 'ENRAF-NONIUS CAD4' _diffrn_detector.pdbx_collection_date ? _diffrn_detector.details ? # _diffrn_radiation.diffrn_id 1 _diffrn_radiation.wavelength_id 1 _diffrn_radiation.pdbx_monochromatic_or_laue_m_l M _diffrn_radiation.monochromator ? _diffrn_radiation.pdbx_diffrn_protocol 'SINGLE WAVELENGTH' # _diffrn_radiation_wavelength.id 1 _diffrn_radiation_wavelength.wavelength 1.5400 # _diffrn_source.diffrn_id 1 _diffrn_source.source ? _diffrn_source.type ? _diffrn_source.pdbx_synchrotron_site ? _diffrn_source.pdbx_synchrotron_beamline ? # _reflns.entry_id URB001 _reflns.observed_criterion_sigma_I ? _reflns.observed_criterion_sigma_F 3.000 _reflns.d_resolution_low ? _reflns.d_resolution_high 0.800 _reflns.number_obs 4062 _reflns.number_all 5998 _reflns.percent_possible_obs ? _reflns.pdbx_Rmerge_I_obs ? _reflns.pdbx_Rsym_value ? _reflns.pdbx_netI_over_av_sigmaI ? _reflns.B_iso_Wilson_estimate ? _reflns.pdbx_redundancy ? _reflns.R_free_details ? # _computing.entry_id URB001 _computing.data_collection ? _computing.data_reduction ? _computing.structure_solution ? _computing.structure_refinement ? _computing.pdbx_structure_refinement_method 'FULL MATRIX LEAST SQUARES' # _refine.entry_id URB001 _refine.ls_number_reflns_obs 4062 _refine.ls_number_reflns_all ? _refine.pdbx_ls_sigma_I ? _refine.pdbx_ls_sigma_F 1.500 _refine.pdbx_data_cutoff_high_absF ? _refine.pdbx_data_cutoff_low_absF ? _refine.pdbx_data_cutoff_high_rms_absF ? _refine.ls_d_res_low ? _refine.ls_d_res_high 0.800 _refine.ls_percent_reflns_obs ? _refine.ls_R_factor_obs 0.0310000 _refine.ls_R_factor_all ? _refine.ls_R_factor_R_work ? _refine.ls_R_factor_R_free ? _refine.ls_R_factor_R_free_error ? _refine.ls_R_factor_R_free_error_details ? _refine.ls_percent_reflns_R_free ? _refine.ls_number_reflns_R_free ? _refine.ls_number_parameters ? _refine.ls_number_restraints ? _refine.occupancy_min ? _refine.occupancy_max ? _refine.B_iso_mean ? _refine.aniso_B[1][1] ? _refine.aniso_B[2][2] ? _refine.aniso_B[3][3] ? _refine.aniso_B[1][2] ? _refine.aniso_B[1][3] ? _refine.aniso_B[2][3] ? _refine.solvent_model_details ? _refine.solvent_model_param_ksol ? _refine.solvent_model_param_bsol ? _refine.pdbx_ls_cross_valid_method ? _refine.details ? _refine.pdbx_starting_model ? _refine.pdbx_method_to_determine_struct ? _refine.pdbx_isotropic_thermal_model ? _refine.pdbx_stereochemistry_target_values ? _refine.pdbx_stereochem_target_val_spec_case ? _refine.pdbx_R_Free_selection_details ? _refine.pdbx_overall_ESU_R_Free ? _refine.ls_redundancy_reflns_obs ? _refine.correlation_coeff_Fo_to_Fc ? _refine.correlation_coeff_Fo_to_Fc_free ? _refine.overall_SU_R_Cruickshank_DPI ? _refine.overall_SU_R_free ? _refine.overall_SU_ML ? _refine.overall_SU_B ? # _refine_hist.cycle_id LAST _refine_hist.pdbx_number_atoms_protein 0 _refine_hist.pdbx_number_atoms_nucleic_acid 54 _refine_hist.pdbx_number_atoms_ligand 0 _refine_hist.number_atoms_solvent 2 _refine_hist.number_atoms_total 56 _refine_hist.d_res_high 0.800 _refine_hist.d_res_low . # loop_ _refine_ls_restr.type _refine_ls_restr.dev_ideal _refine_ls_restr.dev_ideal_target _refine_ls_restr.weight _refine_ls_restr.number o_bond_d ? ? ? ? o_bond_d_na ? ? ? ? o_bond_d_prot ? ? ? ? o_angle_d ? ? ? ? o_angle_d_na ? ? ? ? o_angle_d_prot ? ? ? ? o_angle_deg ? ? ? ? o_angle_deg_na ? ? ? ? o_angle_deg_prot ? ? ? ? o_dihedral_angle_d ? ? ? ? o_dihedral_angle_d_na ? ? ? ? o_dihedral_angle_d_prot ? ? ? ? o_improper_angle_d ? ? ? ? o_improper_angle_d_na ? ? ? ? o_improper_angle_d_prot ? ? ? ? o_mcbond_it ? ? ? ? o_mcangle_it ? ? ? ? o_scbond_it ? ? ? ? o_scangle_it ? ? ? ? # _struct.entry_id URB001 _struct.title ;X-RAY STRUCTURE OF A DINUCLEOSIDE MONOPHOSPHATE A2'P5'C THAT CONTAINS A 2'-5' LINK FOUND IN (2'-5')OLIGO(A)S INDUCED BY INTERFERONS: SINGLE-STRANDED HELICAL CONFORMATION OF 2'-5'-LINKED OLIGONUCLEOTIDES ; _struct.pdbx_model_details ? # _struct_keywords.entry_id URB001 _struct_keywords.pdbx_keywords RNA _struct_keywords.text 'U-RNA, SINGLE STRAND, OPEN' # loop_ _struct_asym.id _struct_asym.pdbx_modified _struct_asym.entity_id _struct_asym.details A N 1 ? B N 2 ? # _struct_biol.id 1 _struct_biol.pdbx_parent_biol_id ? _struct_biol.details ? # loop_ _struct_biol_gen.biol_id _struct_biol_gen.asym_id _struct_biol_gen.symmetry _struct_biol_gen.details _struct_biol_gen.pdbx_full_symmetry_operation 1 A 1_555 ? x,y,z 1 B 1_555 ? x,y,z # _database_PDB_matrix.entry_id URB001 _database_PDB_matrix.origx[1][1] 1.000000 _database_PDB_matrix.origx[1][2] 0.000000 _database_PDB_matrix.origx[1][3] 0.000000 _database_PDB_matrix.origx[2][1] 0.000000 _database_PDB_matrix.origx[2][2] 1.000000 _database_PDB_matrix.origx[2][3] 0.000000 _database_PDB_matrix.origx[3][1] 0.000000 _database_PDB_matrix.origx[3][2] 0.000000 _database_PDB_matrix.origx[3][3] 1.000000 _database_PDB_matrix.origx_vector[1] 0.00000 _database_PDB_matrix.origx_vector[2] 0.00000 _database_PDB_matrix.origx_vector[3] 0.00000 # _atom_sites.entry_id URB001 _atom_sites.Cartn_transform_axes ? _atom_sites.fract_transf_matrix[1][1] 0.115861 _atom_sites.fract_transf_matrix[1][2] 0.000000 _atom_sites.fract_transf_matrix[1][3] 0.000000 _atom_sites.fract_transf_matrix[2][1] 0.000000 _atom_sites.fract_transf_matrix[2][2] 0.055252 _atom_sites.fract_transf_matrix[2][3] 0.000000 _atom_sites.fract_transf_matrix[3][1] 0.000000 _atom_sites.fract_transf_matrix[3][2] 0.000000 _atom_sites.fract_transf_matrix[3][3] 0.062108 _atom_sites.fract_transf_vector[1] 0.00000 _atom_sites.fract_transf_vector[2] 0.00000 _atom_sites.fract_transf_vector[3] 0.00000 # _atom_sites_alt.id . _atom_sites_alt.details ? # loop_ _atom_type.symbol O C N H P # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_alt_id _atom_site.label_comp_id _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.label_seq_id _atom_site.pdbx_PDB_ins_code _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.Cartn_x_esd _atom_site.Cartn_y_esd _atom_site.Cartn_z_esd _atom_site.occupancy_esd _atom_site.B_iso_or_equiv_esd _atom_site.auth_seq_id _atom_site.auth_comp_id _atom_site.auth_asym_id _atom_site.auth_atom_id _atom_site.pdbx_PDB_model_num ATOM 1 O O5* . A A 1 1 ? 5.400 2.201 1.747 1.00 10.00 ? ? ? ? ? 1 A A O5* 1 ATOM 2 C C5* . A A 1 1 ? 4.884 2.997 0.686 1.00 10.00 ? ? ? ? ? 1 A A C5* 1 ATOM 3 C C4* . A A 1 1 ? 4.234 4.273 1.153 1.00 10.00 ? ? ? ? ? 1 A A C4* 1 ATOM 4 O O4* . A A 1 1 ? 3.051 3.965 1.944 1.00 10.00 ? ? ? ? ? 1 A A O4* 1 ATOM 5 C C3* . A A 1 1 ? 5.091 5.176 2.043 1.00 10.00 ? ? ? ? ? 1 A A C3* 1 ATOM 6 O O3* . A A 1 1 ? 4.675 6.504 1.775 1.00 10.00 ? ? ? ? ? 1 A A O3* 1 ATOM 7 C C2* . A A 1 1 ? 4.661 4.735 3.442 1.00 10.00 ? ? ? ? ? 1 A A C2* 1 ATOM 8 O O2* . A A 1 1 ? 4.851 5.679 4.477 1.00 10.00 ? ? ? ? ? 1 A A O2* 1 ATOM 9 C C1* . A A 1 1 ? 3.169 4.527 3.236 1.00 10.00 ? ? ? ? ? 1 A A C1* 1 ATOM 10 N N9 . A A 1 1 ? 2.566 3.636 4.206 1.00 10.00 ? ? ? ? ? 1 A A N9 1 ATOM 11 C C8 . A A 1 1 ? 1.728 4.027 5.236 1.00 10.00 ? ? ? ? ? 1 A A C8 1 ATOM 12 N N7 . A A 1 1 ? 1.453 3.079 6.075 1.00 10.00 ? ? ? ? ? 1 A A N7 1 ATOM 13 C C5 . A A 1 1 ? 2.139 1.989 5.582 1.00 10.00 ? ? ? ? ? 1 A A C5 1 ATOM 14 C C6 . A A 1 1 ? 2.273 0.684 6.062 1.00 10.00 ? ? ? ? ? 1 A A C6 1 ATOM 15 N N6 . A A 1 1 ? 1.746 0.315 7.250 1.00 10.00 ? ? ? ? ? 1 A A N6 1 ATOM 16 N N1 . A A 1 1 ? 2.935 -0.212 5.310 1.00 10.00 ? ? ? ? ? 1 A A N1 1 ATOM 17 C C2 . A A 1 1 ? 3.540 0.230 4.185 1.00 10.00 ? ? ? ? ? 1 A A C2 1 ATOM 18 N N3 . A A 1 1 ? 3.572 1.461 3.679 1.00 10.00 ? ? ? ? ? 1 A A N3 1 ATOM 19 C C4 . A A 1 1 ? 2.822 2.306 4.418 1.00 10.00 ? ? ? ? ? 1 A A C4 1 ATOM 20 H 2H19 . A A 1 1 ? 1.528 0.995 7.873 1.00 10.00 ? ? ? ? ? 1 A A 2H19 1 ATOM 21 H '1H 6' . A A 1 1 ? 4.281 2.534 0.129 1.00 10.00 ? ? ? ? ? 1 A A '1H 6' 1 ATOM 22 H 1H19 . A A 1 1 ? 1.830 -0.471 7.455 1.00 10.00 ? ? ? ? ? 1 A A 1H19 1 ATOM 23 H 'H 7' . A A 1 1 ? 3.996 4.778 0.354 1.00 10.00 ? ? ? ? ? 1 A A 'H 7' 1 ATOM 24 H 'H 9' . A A 1 1 ? 6.102 5.050 1.900 1.00 10.00 ? ? ? ? ? 1 A A 'H 9' 1 ATOM 25 H '2H 6' . A A 1 1 ? 5.610 3.312 0.032 1.00 10.00 ? ? ? ? ? 1 A A '2H 6' 1 ATOM 26 H 1H1 . A A 1 1 ? 5.058 4.018 3.655 1.00 10.00 ? ? ? ? ? 1 A A 1H1 1 ATOM 27 H 0H1 . A A 1 1 ? 5.066 7.276 2.206 1.00 10.00 ? ? ? ? ? 1 A A 0H1 1 ATOM 28 H 'H 5' . A A 1 1 ? 4.902 2.045 2.238 1.00 10.00 ? ? ? ? ? 1 A A 'H 5' 1 ATOM 29 H 1H2 . A A 1 1 ? 3.962 -0.380 3.671 1.00 10.00 ? ? ? ? ? 1 A A 1H2 1 ATOM 30 H 3H1 . A A 1 1 ? 2.710 5.321 3.301 1.00 10.00 ? ? ? ? ? 1 A A 3H1 1 ATOM 31 H 5H1 . A A 1 1 ? 1.415 4.887 5.217 1.00 10.00 ? ? ? ? ? 1 A A 5H1 1 ATOM 32 P P . C A 1 2 ? 6.177 5.680 5.395 1.00 10.00 ? ? ? ? ? 2 C A P 1 ATOM 33 O O1P . C A 1 2 ? 5.910 6.736 6.407 1.00 10.00 ? ? ? ? ? 2 C A O1P 1 ATOM 34 O O2P . C A 1 2 ? 7.383 5.790 4.536 1.00 10.00 ? ? ? ? ? 2 C A O2P 1 ATOM 35 O O5* . C A 1 2 ? 6.224 4.220 6.032 1.00 10.00 ? ? ? ? ? 2 C A O5* 1 ATOM 36 C C5* . C A 1 2 ? 5.321 3.873 7.101 1.00 10.00 ? ? ? ? ? 2 C A C5* 1 ATOM 37 C C4* . C A 1 2 ? 5.583 2.458 7.548 1.00 10.00 ? ? ? ? ? 2 C A C4* 1 ATOM 38 O O4* . C A 1 2 ? 5.305 1.545 6.455 1.00 10.00 ? ? ? ? ? 2 C A O4* 1 ATOM 39 C C3* . C A 1 2 ? 6.984 2.078 7.989 1.00 10.00 ? ? ? ? ? 2 C A C3* 1 ATOM 40 O O3* . C A 1 2 ? 7.235 2.562 9.292 1.00 10.00 ? ? ? ? ? 2 C A O3* 1 ATOM 41 C C2* . C A 1 2 ? 6.905 0.550 7.867 1.00 10.00 ? ? ? ? ? 2 C A C2* 1 ATOM 42 O O2* . C A 1 2 ? 6.169 0.008 8.936 1.00 10.00 ? ? ? ? ? 2 C A O2* 1 ATOM 43 C C1* . C A 1 2 ? 6.113 0.391 6.579 1.00 10.00 ? ? ? ? ? 2 C A C1* 1 ATOM 44 N N1 . C A 1 2 ? 7.000 0.300 5.379 1.00 10.00 ? ? ? ? ? 2 C A N1 1 ATOM 45 C C2 . C A 1 2 ? 7.586 -0.925 5.157 1.00 10.00 ? ? ? ? ? 2 C A C2 1 ATOM 46 O O2 . C A 1 2 ? 7.372 -1.897 5.865 1.00 10.00 ? ? ? ? ? 2 C A O2 1 ATOM 47 N N3 . C A 1 2 ? 8.438 -0.994 4.074 1.00 10.00 ? ? ? ? ? 2 C A N3 1 ATOM 48 C C4 . C A 1 2 ? 8.723 0.036 3.246 1.00 10.00 ? ? ? ? ? 2 C A C4 1 ATOM 49 N N4 . C A 1 2 ? 9.571 -0.130 2.277 1.00 10.00 ? ? ? ? ? 2 C A N4 1 ATOM 50 C C5 . C A 1 2 ? 8.069 1.274 3.507 1.00 10.00 ? ? ? ? ? 2 C A C5 1 ATOM 51 C C6 . C A 1 2 ? 7.256 1.361 4.563 1.00 10.00 ? ? ? ? ? 2 C A C6 1 ATOM 52 H 2H18 . C A 1 2 ? 10.081 -0.887 2.077 1.00 10.00 ? ? ? ? ? 2 C A 2H18 1 ATOM 53 H 9H1 . C A 1 2 ? 8.191 1.973 2.963 1.00 10.00 ? ? ? ? ? 2 C A 9H1 1 ATOM 54 H 1H18 . C A 1 2 ? 9.805 0.579 1.610 1.00 10.00 ? ? ? ? ? 2 C A 1H18 1 HETATM 55 O O . HOH B 2 . ? 4.385 -4.504 10.362 1.00 10.00 ? ? ? ? ? 3 HOH ? O 1 HETATM 56 O O . HOH B 2 . ? 2.841 -2.033 8.711 1.00 10.00 ? ? ? ? ? 4 HOH ? O 1 # _atom_site_anisotrop.id ? _atom_site_anisotrop.type_symbol ? _atom_site_anisotrop.pdbx_label_atom_id ? _atom_site_anisotrop.pdbx_label_alt_id ? _atom_site_anisotrop.pdbx_label_comp_id ? _atom_site_anisotrop.pdbx_label_asym_id ? _atom_site_anisotrop.pdbx_label_seq_id ? _atom_site_anisotrop.U[1][1] ? _atom_site_anisotrop.U[1][2] ? _atom_site_anisotrop.U[1][3] ? _atom_site_anisotrop.U[2][2] ? _atom_site_anisotrop.U[2][3] ? _atom_site_anisotrop.U[3][3] ? _atom_site_anisotrop.U[1][1]_esd ? _atom_site_anisotrop.U[1][2]_esd ? _atom_site_anisotrop.U[1][3]_esd ? _atom_site_anisotrop.U[2][2]_esd ? _atom_site_anisotrop.U[2][3]_esd ? _atom_site_anisotrop.U[3][3]_esd ? _atom_site_anisotrop.pdbx_auth_seq_id ? _atom_site_anisotrop.pdbx_auth_comp_id ? _atom_site_anisotrop.pdbx_auth_asym_id ? # loop_ _pdbx_poly_seq_scheme.asym_id _pdbx_poly_seq_scheme.entity_id _pdbx_poly_seq_scheme.seq_id _pdbx_poly_seq_scheme.mon_id _pdbx_poly_seq_scheme.ndb_seq_num _pdbx_poly_seq_scheme.pdb_seq_num _pdbx_poly_seq_scheme.auth_seq_num _pdbx_poly_seq_scheme.pdb_mon_id _pdbx_poly_seq_scheme.auth_mon_id _pdbx_poly_seq_scheme.pdb_strand_id A 1 1 A 1 1 1 A A A A 1 2 C 2 2 2 C C A # _refine_B_iso.class 'ALL ATOMS' _refine_B_iso.details TR _refine_B_iso.treatment anisotropic # _refine_occupancy.class 'ALL ATOMS' _refine_occupancy.treatment fix #