Software | Name | Version | Classification |
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PHENIX | 1.20.1_4487refinementXDS | | data reductionXSCALE | | data scalingPHASER | | phasing | | | | |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.79→40.31 Å / SU ML: 0.1439 / Cross valid method: FREE R-VALUE / σ(F): 1.35 / Phase error: 16.998 Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
| Rfactor | Num. reflection | % reflection | Selection details |
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Rfree | 0.1678 | 2000 | 1.93 % | Random |
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Rwork | 0.138 | 101411 | - | - |
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obs | 0.1385 | 103411 | 99.91 % | - |
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL |
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Displacement parameters | Biso mean: 31.93 Å2 |
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Refinement step | Cycle: LAST / Resolution: 1.79→40.31 Å
| Protein | Nucleic acid | Ligand | Solvent | Total |
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Num. atoms | 7769 | 0 | 293 | 846 | 8908 |
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Refine LS restraints | Refine-ID | Type | Dev ideal | Number |
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X-RAY DIFFRACTION | f_bond_d0.0136 | 8234 | X-RAY DIFFRACTION | f_angle_d1.321 | 11211 | X-RAY DIFFRACTION | f_chiral_restr0.0721 | 1308 | X-RAY DIFFRACTION | f_plane_restr0.012 | 1424 | X-RAY DIFFRACTION | f_dihedral_angle_d14.0646 | 2913 | | | | | |
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LS refinement shell | Resolution (Å) | Rfactor Rfree | Num. reflection Rfree | Rfactor Rwork | Num. reflection Rwork | Refine-ID | % reflection obs (%) |
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1.79-1.83 | 0.2338 | 142 | 0.2092 | 7183 | X-RAY DIFFRACTION | 99.88 | 1.83-1.88 | 0.2312 | 141 | 0.1913 | 7199 | X-RAY DIFFRACTION | 99.88 | 1.88-1.94 | 0.2136 | 142 | 0.1754 | 7185 | X-RAY DIFFRACTION | 99.93 | 1.94-2 | 0.1954 | 142 | 0.1569 | 7225 | X-RAY DIFFRACTION | 99.93 | 2-2.07 | 0.1586 | 143 | 0.1411 | 7203 | X-RAY DIFFRACTION | 99.99 | 2.07-2.16 | 0.1836 | 143 | 0.1341 | 7235 | X-RAY DIFFRACTION | 99.97 | 2.16-2.26 | 0.1339 | 143 | 0.1318 | 7242 | X-RAY DIFFRACTION | 99.93 | 2.26-2.37 | 0.1786 | 142 | 0.131 | 7225 | X-RAY DIFFRACTION | 99.96 | 2.37-2.52 | 0.1691 | 143 | 0.1337 | 7232 | X-RAY DIFFRACTION | 99.89 | 2.52-2.72 | 0.1673 | 142 | 0.138 | 7232 | X-RAY DIFFRACTION | 99.89 | 2.72-2.99 | 0.1623 | 144 | 0.1401 | 7289 | X-RAY DIFFRACTION | 99.93 | 2.99-3.42 | 0.1512 | 142 | 0.1402 | 7245 | X-RAY DIFFRACTION | 99.92 | 3.42-4.31 | 0.162 | 145 | 0.1209 | 7304 | X-RAY DIFFRACTION | 99.95 | 4.31-40.31 | 0.1651 | 146 | 0.1346 | 7412 | X-RAY DIFFRACTION | 99.72 |
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION ID | L11 (°2) | L12 (°2) | L13 (°2) | L22 (°2) | L23 (°2) | L33 (°2) | S11 (Å °) | S12 (Å °) | S13 (Å °) | S21 (Å °) | S22 (Å °) | S23 (Å °) | S31 (Å °) | S32 (Å °) | S33 (Å °) | T11 (Å2) | T12 (Å2) | T13 (Å2) | T22 (Å2) | T23 (Å2) | T33 (Å2) | Origin x (Å) | Origin y (Å) | Origin z (Å) |
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1 | 2.58995209793 | 0.650385790595 | 1.17630396985 | 1.26974475977 | -0.27030114481 | 2.65329682743 | 0.101560532985 | 0.190659794163 | 0.358347182202 | -0.311473889436 | -0.135165445909 | -0.305487591405 | -0.0955328436866 | 0.133334306462 | 0.0272263546858 | 0.2843914963 | 0.0450838101812 | 0.112088529746 | 0.300812508721 | 0.0151400258194 | 0.421233361873 | 25.0116680767 | -9.05707716231 | 13.8488301519 | 2 | 2.41178886386 | -1.6251128017 | -0.0157654256135 | 5.36534966081 | -2.20004998305 | 4.26455909006 | 0.341371553413 | 0.528795489719 | -0.178304869072 | -1.03470538374 | -0.488818411779 | -0.303120731702 | 0.495212735042 | 0.369624363088 | -0.0659898888155 | 0.431318099089 | 0.127387959021 | 0.124010125915 | 0.393762052454 | 0.00315801709042 | 0.471273064996 | 30.1667421248 | -17.588481386 | 6.80807232674 | 3 | 2.05954833886 | -0.864983707372 | -0.0734158194756 | 4.17473034758 | -1.37426748358 | 3.52696866117 | 0.0589281382158 | -0.160155758525 | 0.209888962331 | -0.0562745867901 | -0.0586149517592 | -0.729375343415 | 0.0755594350408 | 0.554806356675 | 0.0445551780445 | 0.256171018799 | 0.0521503480076 | 0.0597547756525 | 0.37804347502 | -0.028197686103 | 0.545074321636 | 34.0348112717 | -16.6816407504 | 20.7108391353 | 4 | 0.921761671793 | 0.40551476827 | -0.232248114882 | 2.5198934223 | -0.00765706110965 | 1.1649693526 | -0.0435786520269 | -0.0645126492418 | 0.0587151315163 | -0.210520590659 | -0.00113391407666 | -0.318792734736 | 0.101970099061 | 0.137140353955 | -0.0287829398573 | 0.264294090867 | 0.0868560840022 | 0.0086084452315 | 0.222441680915 | -0.0239355880881 | 0.288918600682 | 18.5451553535 | -24.8893309118 | 21.0428265144 | 5 | 1.56179875902 | 0.528056118288 | 0.191404766165 | 3.74729669318 | 0.395089744626 | 1.41731296505 | 0.0330620652914 | 0.0255316216388 | -0.0586169698744 | 0.0313791426082 | 0.0847184473133 | -0.678071592515 | 0.138194831261 | 0.335104371451 | -0.0724526152348 | 0.246647996456 | 0.0587745979568 | -0.00334998747941 | 0.339270864752 | -0.0333157688659 | 0.333867402924 | 23.6112839 | -20.872149623 | 28.7184395115 | 6 | 0.762154448601 | 0.219282126099 | 0.02756251392 | 1.95721366541 | -0.0898140238269 | 1.07617179751 | 0.0488785400689 | -0.0441181133834 | 0.0848245164774 | -0.0360803646301 | -0.0323957748942 | -0.206481464565 | 0.0888356885653 | 0.0321830534636 | -0.0159107156506 | 0.220636530609 | 0.0392956365987 | 0.00707307025025 | 0.213068889031 | -0.0295201031902 | 0.230262556167 | 13.1507033423 | -16.8496077111 | 24.8382609976 | 7 | 8.98551641203 | 7.51590548351 | 6.71631899545 | 7.80556981369 | 5.85811958865 | 5.03155649643 | 0.0871350747617 | 0.345776952826 | -0.412055011662 | -0.961419577456 | 0.269452773215 | -0.645404350679 | 0.594681670573 | 0.461241952986 | -0.412141517752 | 0.62210878447 | 0.0708352195737 | 0.0311552276314 | 0.281030408035 | -0.0251643308831 | 0.287067770424 | 10.2489115036 | -32.3976010876 | 6.24262742145 | 8 | 0.590909000717 | 0.493304092124 | 0.94297519233 | 0.711671050155 | 1.72508747448 | 4.38710220137 | 0.250104914172 | 0.285681581981 | -0.0778248657541 | -1.15149257876 | -0.0619825874177 | 0.209167829951 | -0.116284525839 | -0.214993541103 | -0.0906327289372 | 0.723257671332 | 0.0496475186496 | -0.0383927110341 | 0.281331863117 | -0.0198786336867 | 0.215575787732 | 2.91737791133 | -28.8209643036 | 3.93808989928 | 9 | 1.3446365109 | 0.349528929585 | 0.309266578589 | 1.3515402548 | -0.00726408473876 | 1.59316171102 | 0.0453200479533 | 0.0372788139044 | 0.13992598264 | -0.143839306561 | 0.02458130966 | -0.171980483112 | 0.0253192610479 | 0.0680069790188 | -0.0671427045584 | 0.265408863066 | 0.0422090983365 | 0.0272113866223 | 0.191727218423 | -0.0208090647628 | 0.230376350023 | 8.8323912849 | -10.6347128681 | 16.8868798602 | 10 | 2.85134413354 | 0.881543760006 | 0.389002579288 | 4.11994805404 | -0.29477499042 | 4.72497348189 | -0.0594603328114 | 0.0985605649973 | 0.267614983643 | -0.29774191639 | 0.218335669997 | -0.157699692544 | -0.0191021977227 | 0.123178621527 | -0.233413203731 | 0.327028812364 | 0.00819930317973 | 0.0489966929342 | 0.142186689063 | -0.00359599329859 | 0.306468578701 | 2.04232504947 | 9.02831963142 | 11.6329085125 | 11 | 2.18156155019 | 1.08302305215 | -0.33387605851 | 3.26538797009 | -0.478830765599 | 3.17870979937 | 0.112850547403 | -0.0964260743293 | 0.352929813289 | 0.0970300877188 | 0.0697279484678 | -0.316569681592 | -0.211796872843 | 0.138094507738 | -0.167787250547 | 0.329586560332 | 0.000759017128269 | 0.0636368581149 | 0.182496232734 | -0.0210059165531 | 0.379758066461 | 2.81573013168 | 11.4733913836 | 15.9954357327 | 12 | 3.80367473963 | 0.652607968418 | -1.50543884805 | 3.11904898798 | 0.161013458146 | 2.15729674667 | 0.127097849676 | 0.0073411377653 | 0.553798908237 | -0.0538391018504 | 0.156234715507 | 0.130505796315 | -0.453038656234 | -0.126203125876 | -0.27237731384 | 0.388179190706 | 0.0755893760627 | 0.0669569410313 | 0.217748170662 | 0.0555731021688 | 0.441186672688 | -7.17002019227 | 15.9023382631 | 14.5471256355 | 13 | 0.724253252683 | 0.122306248301 | -0.361085293513 | 1.244566985 | -0.209641842706 | 1.66393164228 | 0.0302967341682 | -0.0190281278452 | 0.163731721111 | 0.0276538529947 | 0.113129660255 | 0.0851478468182 | -0.155183910752 | -0.121364926056 | -0.147582088553 | 0.24041765882 | 0.0417036431055 | 0.0100526342003 | 0.187049784114 | 0.00145672744395 | 0.24310523175 | -7.99966416754 | -0.456840379064 | 22.6297847243 | 14 | 5.53365552624 | 2.73399199847 | 0.376911856689 | 4.72485471441 | 3.26350369443 | 2.85262974224 | -0.0639706772484 | -0.881896732645 | 0.878755614394 | 0.658907119356 | 0.255863385077 | 0.190332652103 | -0.863924028238 | -0.00748325037771 | -0.224417673114 | 0.778665202006 | 0.0949039518604 | -0.0161288201745 | 0.418158823388 | -0.180251708911 | 0.44886183973 | -1.78762890585 | 11.0897526915 | 42.4208539039 | 15 | 1.29011138747 | -0.921532593061 | -0.885935517733 | 3.25254370442 | 1.99279607171 | 1.35081235476 | -0.33796225169 | -0.953190995273 | 0.517123958005 | 0.738332238038 | 0.284133121691 | 0.0264096612607 | -0.849912913212 | 0.218471495341 | -0.319667205054 | 0.822510952635 | 0.0719710702159 | -0.120605607707 | 0.520476818781 | -0.282553585224 | 0.431611771301 | 5.35703266485 | 7.30319019165 | 45.2970968869 | 16 | 1.22441663873 | 0.252432170218 | 0.386706562595 | 1.80680294739 | -0.785435506397 | 2.409707695 | 0.00711711715322 | -0.0651026330712 | 0.175321087523 | 0.0516965478873 | 0.0342777567187 | -0.17604864811 | -0.161106233462 | 0.14934321016 | -0.0396612106589 | 0.217196835418 | 0.0290224368576 | 0.0173579623862 | 0.178538206102 | -0.0538428022052 | 0.253636284972 | 6.68799037924 | -2.11786712965 | 23.8855920386 | 17 | 4.2115732736 | -0.228613421258 | 0.635899582637 | 2.64429902028 | 2.11854161945 | 3.5848241665 | 0.0375088475186 | -0.181316256175 | -0.312783826903 | 0.119776346676 | 0.000866279191029 | 0.2954138847 | 0.298737498508 | -0.192250070635 | -0.0629246824687 | 0.255316796376 | -0.0190539693257 | 0.0489500861044 | 0.327006182976 | 0.0841251725994 | 0.325756351455 | -26.733381529 | -24.5009673534 | 41.7185176371 | 18 | 3.05984780027 | -0.156138569604 | -0.0118338326644 | 5.58018750161 | -0.911580822054 | 3.1197164816 | 0.1162348406 | -0.0225553163626 | -0.0642405857095 | -0.0862478032663 | 0.0398029764143 | 0.597918677389 | 0.0278502668877 | -0.666228342068 | -0.177391779329 | 0.198849066227 | 0.0307444290119 | 0.0438471412622 | 0.485007321238 | 0.0952567709607 | 0.40734197225 | -34.5942396367 | -17.012973738 | 39.1719374104 | 19 | 0.79183051899 | 0.145000801997 | 0.0814377411099 | 1.16495719264 | -0.428067800747 | 2.10441630374 | -0.0039372274488 | -0.0421468122016 | 0.0641019062971 | 0.0616964716716 | 0.144286628156 | 0.204044288795 | -0.0363361791424 | -0.231985394267 | -0.137240358124 | 0.208669500646 | 0.0344398321267 | 0.0205194837574 | 0.252288890525 | 0.0292111203675 | 0.255233835825 | -17.9545681649 | -12.2488885207 | 32.9732346522 | 20 | 1.59052700016 | -2.90225676111 | -2.0112520941 | 5.56565428787 | 4.09713255506 | 3.21396640432 | 0.027347096042 | 0.768357774175 | -0.000379521536922 | -0.616428277657 | 0.061372444719 | 1.00634164437 | 0.0642889931245 | -1.13848805087 | 0.0114517955192 | 0.545254412879 | -0.155176684847 | -0.224999271685 | 0.629505904912 | 0.102698735283 | 0.442012611442 | -24.436510065 | -23.9256446305 | 13.1896223567 | 21 | 8.38923533459 | 2.25221296733 | 6.35517712677 | 0.890358015527 | 2.05122550685 | 5.24303906076 | 0.539613735553 | 0.523582073691 | -1.02960421078 | -0.389175864392 | -0.216984805018 | 0.324153790231 | 1.8138332062 | -0.361621724175 | -0.372826444672 | 0.863234526591 | -0.146589389902 | -0.184930287158 | 0.574998779815 | -0.0380704805037 | 0.400407331045 | -19.4498805751 | -30.6657229163 | 11.2367847381 | 22 | 1.5389463581 | 0.142008978725 | -0.331192121307 | 1.83120729678 | 0.169937689582 | 1.02388873084 | -0.00223092470959 | 0.0225565375864 | -0.062571781953 | -0.0608741611105 | 0.0569433720683 | 0.177080847855 | 0.16169283895 | -0.184724899499 | -0.0691826322659 | 0.259675762597 | 0.00765101582352 | -0.0362455432873 | 0.211237737276 | 0.0254370846834 | 0.202757709526 | -12.0674971041 | -25.7842769477 | 32.8923999345 | 23 | 4.81921079786 | -1.24188190301 | 2.01953386105 | 3.53828952204 | 0.832603399175 | 5.61037374795 | 0.0498272873044 | -0.186561098684 | -0.411874725274 | 0.0881441573887 | 0.084576552294 | 0.182344692349 | 0.33758864962 | -0.369237147305 | -0.152102806136 | 0.371056574633 | 0.00322643414687 | -0.0408388990842 | 0.179103189019 | 0.0854578568259 | 0.151044275894 | -4.33897292207 | -41.9859924117 | 45.5082105594 | 24 | 5.32115186279 | 0.119213066814 | 1.55177595711 | 1.46246153204 | -0.234771285839 | 3.59879290538 | 0.0579794926485 | -0.327628181114 | 0.0361476579974 | 0.159046295272 | 0.0115525415171 | 0.177489381745 | 0.0577499912547 | -0.0809669007552 | -0.0569926918691 | 0.358354770214 | 0.0396762169545 | -0.0173582947665 | 0.223929152349 | 0.0306334772255 | 0.156837181614 | -1.106048522 | -38.7785428755 | 49.385409137 | 25 | 5.99348761031 | 1.7533835921 | -3.09953343592 | 2.14723382237 | -1.46780717007 | 4.39570660655 | 0.0562870316416 | -1.08120415193 | 0.0559921395513 | 0.563633580359 | -0.124871318068 | -0.239137025719 | -0.00861808342955 | 0.616651763961 | -0.140226630106 | 0.509005814434 | 0.0717625514144 | -0.109312698949 | 0.368480953089 | 0.00682771968855 | 0.271457770078 | 6.62387177825 | -41.5239952425 | 56.0380225889 | 26 | 4.32759738027 | 1.47528027799 | -2.00342716187 | 1.70006117156 | -1.08557672415 | 2.97881478649 | -0.051422750651 | -0.00664720507599 | -0.240124119695 | -0.208297984761 | 0.0631704456898 | -0.156457375762 | 0.58747653055 | 0.236531688741 | 0.063336871967 | 0.453342773856 | 0.105723562316 | -0.0583283677351 | 0.256704003146 | 0.0203823348131 | 0.238849984712 | 8.812795344 | -46.9976472151 | 42.9256790648 | 27 | 0.942916436136 | 0.40765771666 | 0.0805980889225 | 1.45987627719 | -0.210266141423 | 0.907206826175 | 0.035898001748 | -0.0167795892439 | 0.092749656091 | 0.112916856309 | -0.0164323588698 | -0.120725722845 | 0.142026328231 | 0.157263390903 | -0.013286095013 | 0.282489141826 | 0.064365183728 | -0.0449448311509 | 0.259772110873 | -0.0218282382878 | 0.219266261522 | 12.2902250851 | -30.1265121373 | 41.2008138867 | 28 | 2.08665856571 | 1.14555449516 | 0.120495548214 | 2.21887624309 | 0.177643884535 | 1.30127883555 | 0.0745670304157 | -0.0798748006635 | -0.23241082688 | 0.0631612163488 | -0.0289202480538 | -0.304068953312 | 0.381192334814 | 0.167395224886 | -0.0481825468359 | 0.34958577043 | 0.0730636162086 | -0.0403145371792 | 0.218989894515 | -0.00336756707417 | 0.213829604458 | 11.5373968905 | -36.6507694558 | 34.0744168553 | 29 | 0.680202544647 | 0.141107228916 | -0.117955373863 | 1.36986901458 | -0.213321512934 | 0.875663435872 | 0.00789415218162 | -0.0737184725857 | 0.0154481233461 | 0.00675806792111 | 0.0346018048324 | 0.000625948778608 | 0.0894555959606 | 0.047129314035 | -0.0370325385061 | 0.286407184306 | 0.0376685217572 | -0.0330578631298 | 0.210522751309 | -0.0150362539257 | 0.179076994036 | 3.90000492617 | -27.5066401615 | 35.8275904304 | 30 | 6.93196646318 | 5.71189318493 | 4.59307307709 | 7.57658025522 | 3.98727114771 | 3.74531135109 | 0.252994482776 | -0.157861064978 | -0.335602738228 | 0.591740416729 | 0.0513864519181 | -0.514853900258 | 0.239590335342 | 0.364192179964 | -0.429635652872 | 0.435584460164 | 0.0182331014183 | -0.0686393024052 | 0.349652253049 | -0.0630785866005 | 0.234807056652 | 15.0462790584 | -18.518255984 | 55.1236410777 | 31 | 4.7565921357 | 1.8195814992 | 4.65822651434 | 2.34416555335 | 2.20862434095 | 5.3171669754 | 0.0468222350148 | -0.340847733623 | 0.294527097581 | 0.500981890698 | -0.223708938031 | 0.114636417366 | -0.188006697953 | -0.362085576316 | 0.243663278045 | 0.402797863 | -0.0202853572032 | -0.0273201264537 | 0.289401315783 | -0.0739406288805 | 0.229170394936 | 9.36000231859 | -11.8266747665 | 55.8933749827 | 32 | 1.25477141059 | 1.48730602974 | 0.499279944415 | 4.57751716516 | 0.890076677769 | 1.90488053402 | 0.0446768108267 | -0.149099402922 | 0.02467969868 | 0.21638253266 | 0.0226717045766 | 0.125178969954 | 0.0235974345327 | -0.0821643379158 | -0.0611085969548 | 0.219648850764 | 0.0528067710386 | -0.0130549506157 | 0.21342576253 | -0.0126908065857 | 0.157254391491 | -4.54865596629 | -24.5933031626 | 42.2325884802 |
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Refinement TLS group | Refine-ID: X-RAY DIFFRACTION ID | Refine TLS-ID | Selection details | Auth asym-ID | Label asym-ID | Auth seq-ID | Label seq-ID |
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1 | 1 | chain 'A' and (resid 5 through 41 )AA5 - 41 | 1 - 37 | 2 | 2 | chain 'A' and (resid 42 through 58 )AA42 - 58 | 38 - 54 | 3 | 3 | chain 'A' and (resid 59 through 85 )AA59 - 85 | 55 - 81 | 4 | 4 | chain 'A' and (resid 86 through 108 )AA86 - 108 | 82 - 104 | 5 | 5 | chain 'A' and (resid 109 through 137 )AA109 - 137 | 105 - 133 | 6 | 6 | chain 'A' and (resid 138 through 195 )AA138 - 195 | 134 - 191 | 7 | 7 | chain 'A' and (resid 196 through 209 )AA196 - 209 | 192 - 205 | 8 | 8 | chain 'A' and (resid 210 through 225 )AA210 - 225 | 206 - 221 | 9 | 9 | chain 'A' and (resid 226 through 266 )AA226 - 266 | 222 - 262 | 10 | 10 | chain 'B' and (resid 5 through 20 )BE5 - 20 | 1 - 16 | 11 | 11 | chain 'B' and (resid 21 through 41 )BE21 - 41 | 17 - 37 | 12 | 12 | chain ' | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
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