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5u9b_validation.xml
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5u9b_validation.xml
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<?xml version="1.0" ?>
<wwPDB-validation-information xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:noNamespaceSchemaLocation="http://wwpdb.org/validation/schema/wwpdb_validation_v002.xsd">
<Entry PDB-R="NotAvailable" PDB-Rfree="NotAvailable" PDB-deposition-date="2016-12-15" PDB-resolution="NotAvailable" PDB-resolution-low="NotAvailable" PDB-revision-date="2017-08-30" PDB-revision-number="2" RNAsuiteness="0.16" RestypesNotcheckedForBondAngleGeometry="ZN" XMLcreationDate="Feb 17, 2018 -- 06:42 am GMT" absolute-percentile-RNAsuiteness="10.4" absolute-percentile-clashscore="99.9" absolute-percentile-percent-rama-outliers="56.5" absolute-percentile-percent-rota-outliers="52.6" angles_rmsz="1.56" attemptedValidationSteps="mogul,molprobity,validation-pack,coreclust,chemicalshifts,percentiles,writexml,writepdf" bonds_rmsz="0.95" chemical_shift_completeness="56.04" chemical_shift_completeness_full_length="57.52" clashscore="0.00" clashscore-full-length="0.08" cyrange_error="success" cyrange_number_of_domains="1" cyrange_version="Kirchner and G\"{u}ntert (2011)" medoid_model="13" nmr_models_consistency_flag="True" nmrclust_error="success" nmrclust_number_of_clusters="3" nmrclust_number_of_models="20" nmrclust_number_of_outliers="1" nmrclust_representative_model="13" nmrclust_version="Kelley et al. (1996)" num-H-reduce="17860" numPDBids-absolute-percentile-RNAsuiteness="3744" numPDBids-absolute-percentile-clashscore="136279" numPDBids-absolute-percentile-percent-rama-outliers="132675" numPDBids-absolute-percentile-percent-rota-outliers="132484" numPDBids-relative-percentile-RNAsuiteness="647" numPDBids-relative-percentile-clashscore="12091" numPDBids-relative-percentile-percent-rama-outliers="10835" numPDBids-relative-percentile-percent-rota-outliers="10811" num_angles_rmsz="30580" num_bonds_rmsz="21720" panav_version="Wang et al. (2010)" pdbid="5U9B" percent-rama-outliers="0.14" percent-rama-outliers-full-length="0.33" percent-rota-outliers="2.62" percent-rota-outliers-full-length="3.29" percentilebins="all,nmr" protein-DNA-RNA-entities="1,2" rci_version="v_1n_11_5_13_A (Berjanski et al., 2005)" relative-percentile-RNAsuiteness="24.0" relative-percentile-clashscore="100.0" relative-percentile-percent-rama-outliers="86.2" relative-percentile-percent-rota-outliers="91.6" shiftchecker_version="trunk30686">
<chemical_shift_list block_name="chemical_shifts_zf12RNA_str.txt" file_id="1" file_name="5u9b_cs.str" list_id="1" number_of_errors_while_mapping="0" number_of_mapped_shifts="939" number_of_parsed_shifts="939" number_of_unparsed_shifts="0" number_of_warnings_while_mapping="0" total_number_of_shifts="939" type="full">
<chemical_shift_outlier atom="HG" chain="A" method="shiftchecker" prediction="1.510" rescode="LEU" resnum="14" value="-0.937" zscore="-7.415"/>
<chemical_shift_outlier atom="CB" chain="A" method="shiftchecker" prediction="31.840" rescode="PRO" resnum="30" value="62.563" zscore="25.818"/>
<chemical_shift_outlier atom="CB" chain="A" method="shiftchecker" prediction="31.840" rescode="PRO" resnum="39" value="62.597" zscore="25.846"/>
<chemical_shift_outlier atom="CB" chain="A" method="shiftchecker" prediction="31.840" rescode="PRO" resnum="7" value="62.264" zscore="25.566"/>
<chemical_shift_outlier atom="CB" chain="A" method="shiftchecker" prediction="31.840" rescode="PRO" resnum="73" value="62.563" zscore="25.818"/>
<random_coil_index chain="A" rescode="ASP" resnum="10" value="0.065"/>
<random_coil_index chain="A" rescode="THR" resnum="11" value="0.049"/>
<random_coil_index chain="A" rescode="LYS" resnum="12" value="0.028"/>
<random_coil_index chain="A" rescode="TRP" resnum="13" value="0.025"/>
<random_coil_index chain="A" rescode="LEU" resnum="14" value="0.023"/>
<random_coil_index chain="A" rescode="THR" resnum="15" value="0.030"/>
<random_coil_index chain="A" rescode="LEU" resnum="16" value="0.037"/>
<random_coil_index chain="A" rescode="GLU" resnum="17" value="0.047"/>
<random_coil_index chain="A" rescode="VAL" resnum="18" value="0.043"/>
<random_coil_index chain="A" rescode="CYS" resnum="19" value="0.033"/>
<random_coil_index chain="A" rescode="ALA" resnum="2" value="0.290"/>
<random_coil_index chain="A" rescode="ARG" resnum="20" value="0.020"/>
<random_coil_index chain="A" rescode="GLU" resnum="21" value="0.015"/>
<random_coil_index chain="A" rescode="PHE" resnum="22" value="0.016"/>
<random_coil_index chain="A" rescode="GLN" resnum="23" value="0.024"/>
<random_coil_index chain="A" rescode="ARG" resnum="24" value="0.045"/>
<random_coil_index chain="A" rescode="GLY" resnum="25" value="0.052"/>
<random_coil_index chain="A" rescode="THR" resnum="26" value="0.055"/>
<random_coil_index chain="A" rescode="CYS" resnum="27" value="0.048"/>
<random_coil_index chain="A" rescode="SER" resnum="28" value="0.044"/>
<random_coil_index chain="A" rescode="ARG" resnum="29" value="0.032"/>
<random_coil_index chain="A" rescode="VAL" resnum="3" value="0.262"/>
<random_coil_index chain="A" rescode="PRO" resnum="30" value="0.017"/>
<random_coil_index chain="A" rescode="ASP" resnum="31" value="0.012"/>
<random_coil_index chain="A" rescode="THR" resnum="32" value="0.014"/>
<random_coil_index chain="A" rescode="GLU" resnum="33" value="0.018"/>
<random_coil_index chain="A" rescode="CYS" resnum="34" value="0.024"/>
<random_coil_index chain="A" rescode="LYS" resnum="35" value="0.027"/>
<random_coil_index chain="A" rescode="PHE" resnum="36" value="0.027"/>
<random_coil_index chain="A" rescode="ALA" resnum="37" value="0.022"/>
<random_coil_index chain="A" rescode="HIS" resnum="38" value="0.017"/>
<random_coil_index chain="A" rescode="PRO" resnum="39" value="0.017"/>
<random_coil_index chain="A" rescode="SER" resnum="4" value="0.218"/>
<random_coil_index chain="A" rescode="SER" resnum="40" value="0.029"/>
<random_coil_index chain="A" rescode="LYS" resnum="41" value="0.035"/>
<random_coil_index chain="A" rescode="SER" resnum="42" value="0.049"/>
<random_coil_index chain="A" rescode="CYS" resnum="43" value="0.050"/>
<random_coil_index chain="A" rescode="GLN" resnum="44" value="0.057"/>
<random_coil_index chain="A" rescode="VAL" resnum="45" value="0.048"/>
<random_coil_index chain="A" rescode="GLU" resnum="46" value="0.042"/>
<random_coil_index chain="A" rescode="ASN" resnum="47" value="0.031"/>
<random_coil_index chain="A" rescode="GLY" resnum="48" value="0.025"/>
<random_coil_index chain="A" rescode="ARG" resnum="49" value="0.019"/>
<random_coil_index chain="A" rescode="VAL" resnum="5" value="0.135"/>
<random_coil_index chain="A" rescode="VAL" resnum="50" value="0.020"/>
<random_coil_index chain="A" rescode="ILE" resnum="51" value="0.038"/>
<random_coil_index chain="A" rescode="ALA" resnum="52" value="0.037"/>
<random_coil_index chain="A" rescode="CYS" resnum="53" value="0.033"/>
<random_coil_index chain="A" rescode="PHE" resnum="54" value="0.012"/>
<random_coil_index chain="A" rescode="ASP" resnum="55" value="0.011"/>
<random_coil_index chain="A" rescode="SER" resnum="56" value="0.012"/>
<random_coil_index chain="A" rescode="LEU" resnum="57" value="0.017"/>
<random_coil_index chain="A" rescode="LYS" resnum="58" value="0.023"/>
<random_coil_index chain="A" rescode="GLY" resnum="59" value="0.034"/>
<random_coil_index chain="A" rescode="THR" resnum="6" value="0.076"/>
<random_coil_index chain="A" rescode="ARG" resnum="60" value="0.038"/>
<random_coil_index chain="A" rescode="CYS" resnum="61" value="0.045"/>
<random_coil_index chain="A" rescode="SER" resnum="62" value="0.042"/>
<random_coil_index chain="A" rescode="ARG" resnum="63" value="0.047"/>
<random_coil_index chain="A" rescode="GLU" resnum="64" value="0.043"/>
<random_coil_index chain="A" rescode="ASN" resnum="65" value="0.050"/>
<random_coil_index chain="A" rescode="CYS" resnum="66" value="0.041"/>
<random_coil_index chain="A" rescode="LYS" resnum="67" value="0.038"/>
<random_coil_index chain="A" rescode="TYR" resnum="68" value="0.024"/>
<random_coil_index chain="A" rescode="LEU" resnum="69" value="0.025"/>
<random_coil_index chain="A" rescode="PRO" resnum="7" value="0.030"/>
<random_coil_index chain="A" rescode="HIS" resnum="70" value="0.022"/>
<random_coil_index chain="A" rescode="PRO" resnum="71" value="0.020"/>
<random_coil_index chain="A" rescode="PRO" resnum="72" value="0.015"/>
<random_coil_index chain="A" rescode="PRO" resnum="73" value="0.012"/>
<random_coil_index chain="A" rescode="HIS" resnum="74" value="0.014"/>
<random_coil_index chain="A" rescode="LEU" resnum="75" value="0.016"/>
<random_coil_index chain="A" rescode="LYS" resnum="76" value="0.016"/>
<random_coil_index chain="A" rescode="THR" resnum="77" value="0.015"/>
<random_coil_index chain="A" rescode="GLN" resnum="78" value="0.017"/>
<random_coil_index chain="A" rescode="LEU" resnum="79" value="0.019"/>
<random_coil_index chain="A" rescode="ILE" resnum="8" value="0.045"/>
<random_coil_index chain="A" rescode="GLU" resnum="80" value="0.020"/>
<random_coil_index chain="A" rescode="ILE" resnum="81" value="0.019"/>
<random_coil_index chain="A" rescode="ASN" resnum="82" value="0.019"/>
<random_coil_index chain="A" rescode="GLY" resnum="83" value="0.021"/>
<random_coil_index chain="A" rescode="ARG" resnum="84" value="0.026"/>
<random_coil_index chain="A" rescode="ASN" resnum="85" value="0.033"/>
<random_coil_index chain="A" rescode="ASN" resnum="86" value="0.045"/>
<random_coil_index chain="A" rescode="LEU" resnum="87" value="0.061"/>
<random_coil_index chain="A" rescode="ILE" resnum="88" value="0.057"/>
<random_coil_index chain="A" rescode="GLN" resnum="89" value="0.049"/>
<random_coil_index chain="A" rescode="ARG" resnum="9" value="0.063"/>
<random_coil_index chain="A" rescode="GLN" resnum="90" value="0.030"/>
<random_coil_index chain="A" rescode="LYS" resnum="91" value="0.035"/>
<random_coil_index chain="A" rescode="ASN" resnum="92" value="0.036"/>
<referencing_offset atom="CB" number_of_measurements="84" precision="0.17" uncertainty="0.50" value="0.23"/>
<referencing_offset atom="C" number_of_measurements="0" precision="0.00" uncertainty="0.50" value="0.00"/>
<referencing_offset atom="CA" number_of_measurements="90" precision="0.13" uncertainty="0.50" value="0.09"/>
<referencing_offset atom="N" number_of_measurements="78" precision="0.63" uncertainty="0.50" value="-0.94"/>
<assignment_completeness_well_defined element="H" number_of_assigned_shifts="207" number_of_shifts="286" number_of_unassigned_shifts="79" type="sidechain"/>
<assignment_completeness_well_defined element="H" number_of_assigned_shifts="132" number_of_shifts="137" number_of_unassigned_shifts="5" type="backbone"/>
<assignment_completeness_well_defined element="H" number_of_assigned_shifts="361" number_of_shifts="615" number_of_unassigned_shifts="254" type="overall"/>
<assignment_completeness_well_defined element="H" number_of_assigned_shifts="22" number_of_shifts="37" number_of_unassigned_shifts="15" type="aromatic"/>
<assignment_completeness_well_defined element="H" number_of_assigned_shifts="0" number_of_shifts="90" number_of_unassigned_shifts="90" type="sugar"/>
<assignment_completeness_well_defined element="H" number_of_assigned_shifts="0" number_of_shifts="65" number_of_unassigned_shifts="65" type="base"/>
<assignment_completeness_well_defined element="C" number_of_assigned_shifts="138" number_of_shifts="166" number_of_unassigned_shifts="28" type="sidechain"/>
<assignment_completeness_well_defined element="C" number_of_assigned_shifts="70" number_of_shifts="142" number_of_unassigned_shifts="72" type="backbone"/>
<assignment_completeness_well_defined element="C" number_of_assigned_shifts="227" number_of_shifts="438" number_of_unassigned_shifts="211" type="overall"/>
<assignment_completeness_well_defined element="C" number_of_assigned_shifts="19" number_of_shifts="27" number_of_unassigned_shifts="8" type="aromatic"/>
<assignment_completeness_well_defined element="C" number_of_assigned_shifts="0" number_of_shifts="75" number_of_unassigned_shifts="75" type="sugar"/>
<assignment_completeness_well_defined element="C" number_of_assigned_shifts="0" number_of_shifts="28" number_of_unassigned_shifts="28" type="base"/>
<assignment_completeness_well_defined element="Total" number_of_assigned_shifts="349" number_of_shifts="478" number_of_unassigned_shifts="129" type="sidechain"/>
<assignment_completeness_well_defined element="Total" number_of_assigned_shifts="263" number_of_shifts="345" number_of_unassigned_shifts="82" type="backbone"/>
<assignment_completeness_well_defined element="Total" number_of_assigned_shifts="654" number_of_shifts="1167" number_of_unassigned_shifts="513" type="overall"/>
<assignment_completeness_well_defined element="Total" number_of_assigned_shifts="42" number_of_shifts="69" number_of_unassigned_shifts="27" type="aromatic"/>
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