Publish derived tables (10/19)

.gitattributes

@@ -137,3 +137,10 @@ data/Kv2.1/extra/conformation_analysis/tables/l403a_s6_relaxation_candidate_rank
 data/Kv2.1/rmsd/Kv21_all_models_vs_8SD3_8SDA_RMSD_PREDEBUG_INVALID.csv filter=lfs diff=lfs merge=lfs -text
 data/Kv2.1/rmsd/Kv21_all_models_vs_8SD3_8SDA_RMSD_v2.csv filter=lfs diff=lfs merge=lfs -text
 data/Kv2.1/rmsd/Kv21_all_models_vs_8SD3_8SDA_RMSD_v5.csv filter=lfs diff=lfs merge=lfs -text
+data/Kv2.1/rmsd/Kv21_hydrophobic_nexus_contacts_v1_long.csv filter=lfs diff=lfs merge=lfs -text
+data/Kv2.1/rmsd/analysis/comparison/paired_reference_preference_by_region.csv filter=lfs diff=lfs merge=lfs -text
+data/Kv2.1/rmsd/analysis/comparison_v5/hydrophobic_nexus_pocket_ca_long_v5.csv filter=lfs diff=lfs merge=lfs -text
+data/Kv2.1/rmsd/analysis/comparison_v5/hydrophobic_nexus_pocket_ca_paired_v5.csv filter=lfs diff=lfs merge=lfs -text
+data/Kv2.1/rmsd/analysis/comparison_v5/hydrophobic_nexus_target_accuracy_all_atom_long_v5.csv filter=lfs diff=lfs merge=lfs -text
+data/Kv2.1/rmsd/analysis/comparison_v5/l403a_hydrophobic_nexus_direct_rmsd_WT_and_mutant_references_v5.csv filter=lfs diff=lfs merge=lfs -text
+data/Kv2.1/rmsd/analysis/comparison_v5/paired_reference_preference_by_region_v5.csv filter=lfs diff=lfs merge=lfs -text

data/Kv2.1/rmsd/Kv21_hydrophobic_nexus_contacts_v1_long.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:74a6e7fe261e513fd15533b406784c47befabdf0d213a3cb4a75f0f4fe19ca9b
+size 299226719

data/Kv2.1/rmsd/Kv21_validation_panel_v2_summary.csv

@@ -0,0 +1,13 @@
+validation_case,dataset,protocol,model_number,seed,recycle_label,reference_id,model_spatial_order,selected_mapping,selected_core_postfit_rmsd_A,all24_best_mapping,all24_best_core_rmsd_A,all24_improvement_over_d4_A,diagnostic_vsd_core_best_mapping,diagnostic_vsd_core_best_rmsd_A,diagnostic_pore_core_best_mapping,diagnostic_pore_core_best_rmsd_A,diagnostic_s6_bundle_best_mapping,diagnostic_s6_bundle_best_rmsd_A,analysis_status,analysis_error
+wt_masked_model4_seed104_high,wt_masked,masked,4,104,final,8SD3,A;B;C;D,A->D;B->B;C->A;D->C,1.0100560454694183,A->D;B->B;C->A;D->C,1.0100560454694183,0.0,A->D;B->B;C->A;D->C,1.1647420318760517,A->D;B->B;C->A;D->C,0.7051980303831105,A->B;B->A;C->C;D->D,0.751705819996092,ok,
+wt_masked_model4_seed104_high,wt_masked,masked,4,104,final,8SDA,A;B;C;D,A->D;B->C;C->B;D->A,1.2542698354005248,A->D;B->C;C->B;D->A,1.2542698354005248,0.0,A->D;B->C;C->B;D->A,1.2106190118802758,A->C;B->B;C->A;D->D,1.2257204232067014,A->D;B->C;C->B;D->A,1.779913511109681,ok,
+wt_vanilla_model4_seed104_low,wt_vanilla,vanilla,4,104,final,8SD3,A;B;C;D,A->B;B->D;C->C;D->A,0.8083323727457753,A->B;B->D;C->C;D->A,0.8083323727457753,0.0,A->B;B->D;C->C;D->A,0.9360153359827951,A->B;B->D;C->C;D->A,0.5989719717419142,A->B;B->D;C->C;D->A,0.7463147394703795,ok,
+wt_vanilla_model4_seed104_low,wt_vanilla,vanilla,4,104,final,8SDA,A;B;C;D,A->C;B->D;C->A;D->B,1.1558918805728866,A->C;B->D;C->A;D->B,1.1558918805728866,0.0,A->B;B->C;C->D;D->A,1.0918874581768583,A->A;B->B;C->C;D->D,1.1928837675612918,A->A;B->B;C->C;D->D,1.7598750134618426,ok,
+wt_masked_model1_seed076_high,wt_masked,masked,1,76,final,8SD3,A;B;C;D,A->D;B->B;C->A;D->C,1.4411911373720536,A->D;B->B;C->A;D->C,1.4411911373720536,0.0,A->D;B->B;C->A;D->C,1.2124191104873268,A->D;B->B;C->A;D->C,1.7603928670116191,A->D;B->B;C->A;D->C,0.6617911816490981,ok,
+wt_masked_model1_seed076_high,wt_masked,masked,1,76,final,8SDA,A;B;C;D,A->C;B->B;C->A;D->D,1.7166245967068108,A->C;B->B;C->A;D->D,1.7166245967068108,0.0,A->A;B->D;C->C;D->B,1.2943017743917207,A->B;B->A;C->D;D->C,2.115150144119778,A->B;B->A;C->D;D->C,1.8738268284557023,ok,
+wt_vanilla_model1_seed076_high,wt_vanilla,vanilla,1,76,final,8SD3,A;B;C;D,A->C;B->D;C->B;D->A,0.9382787527298959,A->C;B->D;C->B;D->A,0.9382787527298959,0.0,A->C;B->D;C->B;D->A,1.1179422451549497,A->B;B->A;C->C;D->D,0.6965671109271998,A->C;B->D;C->B;D->A,0.6091074632299642,ok,
+wt_vanilla_model1_seed076_high,wt_vanilla,vanilla,1,76,final,8SDA,A;B;C;D,A->D;B->C;C->B;D->A,1.1807956804360455,A->D;B->C;C->B;D->A,1.1807956804360455,0.0,A->D;B->C;C->B;D->A,1.016269027479008,A->A;B->D;C->C;D->B,1.3248073635174442,A->A;B->D;C->C;D->B,1.8453503724081612,ok,
+wt_masked_model3_seed076_low,wt_masked,masked,3,76,final,8SD3,A;B;C;D,A->C;B->A;C->B;D->D,1.388248787923416,A->C;B->A;C->B;D->D,1.388248787923416,0.0,A->B;B->D;C->C;D->A,1.1692618087478335,A->C;B->A;C->B;D->D,1.5509338032567381,A->B;B->D;C->C;D->A,0.7070407918503848,ok,
+wt_masked_model3_seed076_low,wt_masked,masked,3,76,final,8SDA,A;B;C;D,A->B;B->C;C->D;D->A,1.7739239051714022,A->B;B->C;C->D;D->A,1.7739239051714022,0.0,A->B;B->C;C->D;D->A,1.514861422041821,A->C;B->D;C->A;D->B,1.9437580573691944,A->C;B->D;C->A;D->B,1.8568255676822507,ok,
+wt_vanilla_model3_seed076_low,wt_vanilla,vanilla,3,76,final,8SD3,A;B;C;D,A->A;B->B;C->D;D->C,0.8378894792342905,A->A;B->B;C->D;D->C,0.8378894792342905,0.0,A->A;B->B;C->D;D->C,0.9375993173749547,A->B;B->D;C->C;D->A,0.5890132465405721,A->D;B->C;C->A;D->B,0.7608119207833811,ok,
+wt_vanilla_model3_seed076_low,wt_vanilla,vanilla,3,76,final,8SDA,A;B;C;D,A->B;B->C;C->D;D->A,1.2026549734217988,A->B;B->C;C->D;D->A,1.2026549734217988,0.0,A->B;B->C;C->D;D->A,1.1420184248674092,A->C;B->D;C->A;D->B,1.1740914237216769,A->C;B->D;C->A;D->B,1.7234101805521536,ok,

data/Kv2.1/rmsd/analysis/comparison/model_counts_allOK3_mappingQC.csv

@@ -0,0 +1,7 @@
+Sequence,Protocol,models
+F412L,Masked,3578
+F412L,Vanilla,4407
+L403A,Masked,3693
+L403A,Vanilla,4371
+WT,Masked,3658
+WT,Vanilla,4562

data/Kv2.1/rmsd/analysis/comparison/paired_reference_preference_by_region.csv

@@ -0,0 +1,3 @@
+version https://git-lfs.github.com/spec/v1
+oid sha256:694d2c05e821382ccf06177938dda5ee367c88c626b347ef6e5b0852a2c34e90
+size 33923107

data/Kv2.1/rmsd/analysis/comparison/reference_preference_summary.csv

@@ -0,0 +1,37 @@
+Region,Sequence,Protocol,n,median_delta_A,p05_delta_A,p95_delta_A,fraction_closer_to_8SDA
+Distal S6,F412L,Masked,3578,0.4574660726314115,-0.38508281609326317,0.924810764802951,0.31581889323644496
+Distal S6,F412L,Vanilla,4407,0.742107504436551,0.17492543614648498,0.9689136669911114,0.019287497163603357
+Distal S6,L403A,Masked,3693,1.2749985590720714,-0.31828975116278696,1.4932714871372237,0.11020850257243434
+Distal S6,L403A,Vanilla,4371,1.3639624914694979,1.0750362361205372,1.5184618074314342,0.01692976435598261
+Distal S6,WT,Masked,3658,1.0901404188799226,-0.33339153661009446,1.4114446543056094,0.17386550027337344
+Distal S6,WT,Vanilla,4562,1.2547884438008605,0.8592981098334908,1.3922325040285566,0.006795265234546251
+F412 region,F412L,Masked,3578,0.1752275540641407,-0.7162089456403286,0.9501038846663379,0.4167132476243712
+F412 region,F412L,Vanilla,4407,0.37614073741201026,-0.3197981395114076,0.7987481503443884,0.2157930565010211
+F412 region,L403A,Masked,3693,1.1160017910461737,-0.656645248084953,1.3968916960611828,0.12997562956945571
+F412 region,L403A,Vanilla,4371,1.218253363259595,0.8653918852959059,1.47952086099774,0.020132692747654998
+F412 region,WT,Masked,3658,0.95498500713,-0.6607999879149444,1.4332613038610458,0.19682886823400766
+F412 region,WT,Vanilla,4562,1.1393202794299149,0.5770168195643895,1.3616072261003127,0.01578255151249452
+Four-chain S6 bundle,F412L,Masked,3578,0.01378840271299997,-0.7058087239366764,0.3241312577197596,0.4821129122414757
+Four-chain S6 bundle,F412L,Vanilla,4407,0.10796196129084157,-0.37140535632158217,0.6151265020517331,0.3392330383480826
+Four-chain S6 bundle,L403A,Masked,3693,1.0046698705377648,-0.6010317004786749,1.2700650456126044,0.13512049823991334
+Four-chain S6 bundle,L403A,Vanilla,4371,1.1300765497944139,0.7693719996661255,1.3496038006918325,0.02127659574468085
+Four-chain S6 bundle,WT,Masked,3658,0.8158711600731166,-0.6298994047340727,1.16887445588643,0.20585019136139968
+Four-chain S6 bundle,WT,Vanilla,4562,1.0006036281268067,0.5069752982107345,1.2636477438104545,0.016220955721174924
+Hydrophobic coupling nexus,F412L,Masked,3578,0.3826362819097197,-0.31863462334713166,0.7958191686644926,0.3144214645053102
+Hydrophobic coupling nexus,F412L,Vanilla,4407,0.5275805171821772,0.07418668124787998,0.7638276603512288,0.029725436805082824
+Hydrophobic coupling nexus,L403A,Masked,3693,1.00506386625381,-0.23877422625483566,1.1632402920189273,0.10912537232602221
+Hydrophobic coupling nexus,L403A,Vanilla,4371,1.0300864589731937,0.7812790994934387,1.167753880342567,0.01692976435598261
+Hydrophobic coupling nexus,WT,Masked,3658,0.9130689328848505,-0.26111676845294474,1.1424602100471588,0.17140513942044833
+Hydrophobic coupling nexus,WT,Vanilla,4562,0.9782918236284222,0.6293197172747407,1.097885370378314,0.008768084173608066
+L403 region,F412L,Masked,3578,0.47120784887141565,-0.11895236378179971,1.0337418505200096,0.20374510899944104
+L403 region,F412L,Vanilla,4407,0.8989289830395523,0.45237986941972586,1.1352230688523424,0.0006807351940095302
+L403 region,L403A,Masked,3693,1.4405002949830745,-0.05222815535450369,1.6407016253924975,0.07636068237205523
+L403 region,L403A,Vanilla,4371,1.5067134505165822,1.2320068439023575,1.6305627226215367,0.0
+L403 region,WT,Masked,3658,1.235398556042369,-0.06703233191935289,1.5009315004252266,0.10005467468562056
+L403 region,WT,Vanilla,4562,1.3744601773236813,1.032165086428107,1.4984342650550861,0.00043840420868040335
+Whole matched tetramer,F412L,Masked,3578,-0.2153428292698114,-0.5930056003284156,0.04459474307583218,0.8510340972610397
+Whole matched tetramer,F412L,Vanilla,4407,-0.2966974258636894,-0.48864128738616247,0.0413363520418074,0.9017472203312912
+Whole matched tetramer,L403A,Masked,3693,0.1412421462925979,-0.4951954410984329,0.35219784500311646,0.29542377470890874
+Whole matched tetramer,L403A,Vanilla,4371,0.18148747576289148,-0.11692551854780142,0.3652352717222299,0.11782200869366277
+Whole matched tetramer,WT,Masked,3658,0.09650732611797308,-0.5106154839749079,0.34378768952281424,0.36741388737014763
+Whole matched tetramer,WT,Vanilla,4562,0.12733572488860234,-0.15705628420301712,0.3492916189013027,0.22994300745287155

data/Kv2.1/rmsd/analysis/comparison_v5/excluded_mapping_warning_rows.csv

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data/Kv2.1/rmsd/analysis/comparison_v5/hydrophobic_nexus_target_accuracy_protocol_effect_v5.csv

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data/Kv2.1/rmsd/analysis/comparison_v5/kv21_l403a_full_system_ca_rmsd_A_reference_preference_v5_summary.csv

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data/Kv2.1/rmsd/analysis/comparison_v5/l403a_best_pocket_D_paper_nexus_contact_matches_to_8SDA_v5.csv

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+Distal S6,WT,Masked,3658,0.9561098122581176,-0.3627719916974064,1.26186208981412,0.17523236741388737
+Distal S6,WT,Vanilla,4562,1.2286083147238984,0.8189714516718307,1.379522409723169,0.0070144673388864535
+F412 region,F412L,Masked,3578,0.21516907948594077,-0.7270076401779793,1.0001519436140809,0.4044158747903857
+F412 region,F412L,Vanilla,4407,0.38586393173288225,-0.3319752432772326,0.7922546186861077,0.21783526208304968
+F412 region,L403A,Masked,3693,1.0626185251881899,-0.666170203404557,1.2969596556781138,0.13078797725426483
+F412 region,L403A,Vanilla,4371,1.2074710276474145,0.8154214806504289,1.450327198569585,0.02059025394646534
+F412 region,WT,Masked,3658,0.9134362782157602,-0.6699760498590316,1.3156111995247213,0.19655549480590487
+F412 region,WT,Vanilla,4562,1.1285264465421219,0.5262618235886476,1.3417211217749365,0.016220955721174924
+Four-chain S6 bundle,F412L,Masked,3578,0.02799388797167801,-0.7298074176322342,0.3451205830409353,0.4742873113471213
+Four-chain S6 bundle,F412L,Vanilla,4407,0.09679770287083045,-0.38959667908037604,0.6054563928878502,0.3505786249149081
+Four-chain S6 bundle,L403A,Masked,3693,0.9173270031291278,-0.6293808218136971,1.1876432894247213,0.1370159761711346
+Four-chain S6 bundle,L403A,Vanilla,4371,1.0945796815276454,0.6923695160246963,1.328479964644494,0.02127659574468085
+Four-chain S6 bundle,WT,Masked,3658,0.7225484664229025,-0.6558791246308658,1.0641186184669482,0.2074904319300164
+Four-chain S6 bundle,WT,Vanilla,4562,0.9655649015117571,0.4399776725315484,1.2407350726086308,0.01797457255589654
+Full system,F412L,Masked,3578,-0.217872045831769,-0.6116090998565097,0.07683953320279757,0.8099496925656792
+Full system,F412L,Vanilla,4407,-0.3134380327429467,-0.5101789139584448,0.03617260232964672,0.908781484002723
+Full system,L403A,Masked,3693,0.12936717916244778,-0.5131749588183527,0.3439025657674215,0.3067966422962361
+Full system,L403A,Vanilla,4371,0.15975463692797454,-0.14724524053766008,0.3610437714862036,0.1477922672157401
+Full system,WT,Masked,3658,0.08792253119500515,-0.5293996058651416,0.3391121910051499,0.37643521049753964
+Full system,WT,Vanilla,4562,0.1041943855071924,-0.18528287406158647,0.3458222283732661,0.2687417799210872
+General TM region,F412L,Masked,3578,0.027445238235810576,-0.32370663492701374,0.3061905834163829,0.4631078814980436
+General TM region,F412L,Vanilla,4407,0.03321571477444629,-0.16487742673890718,0.22166623384736447,0.405264352167007
+General TM region,L403A,Masked,3693,0.241075282544972,-0.2546036475360424,0.38119954994682026,0.14676414838884375
+General TM region,L403A,Vanilla,4371,0.265782891559447,0.10048007106324319,0.40276129318459675,0.027682452528025623
+General TM region,WT,Masked,3658,0.20999419893772198,-0.26957506277018406,0.3864760925924553,0.2263531984691088
+General TM region,WT,Vanilla,4562,0.250776377492835,0.05624974876711764,0.38658290026799197,0.03178430512932924
+L403 region,F412L,Masked,3578,0.31424399751086396,-0.16674808645714134,0.8608089719903805,0.2325321408608161
+L403 region,F412L,Vanilla,4407,0.8982227039903588,0.4544046776128027,1.1474426590177966,0.0009076469253460404
+L403 region,L403A,Masked,3693,1.3241242409584197,-0.08317563982023186,1.5515193769411875,0.08258868128892499
+L403 region,L403A,Vanilla,4371,1.478293656375715,1.187719420284949,1.6169746636882905,0.0011439029970258523
+L403 region,WT,Masked,3658,1.0624872939522172,-0.11077103627826358,1.3734180976276151,0.11700382722799343
+L403 region,WT,Vanilla,4562,1.3427139032743018,0.9978735502738295,1.4897250344555415,0.000657606313020605

data/Kv2.1/rmsd/analysis/f412l/coverage_missing_summary.csv

@@ -0,0 +1,12 @@
+measurement,missing_fraction,available_fraction,label
+whole_matched_tetramer__ca__core_aligned_rmsd_A,0.0,1.0,"Whole matched tetramer (Cα, core-aligned)"
+s6_bundle_working__ca__core_aligned_rmsd_A,0.0,1.0,"Four-chain S6 bundle (Cα, core-aligned)"
+s6_bundle_working__ca__local_aligned_rmsd_A,0.0,1.0,"Four-chain S6 bundle (Cα, locally aligned)"
+distal_s6_working__ca__core_aligned_rmsd_A,0.0,1.0,"Distal S6 (Cα, core-aligned)"
+distal_s6_working__ca__local_aligned_rmsd_A,0.0,1.0,"Distal S6 (Cα, locally aligned)"
+l403_region__ca__core_aligned_rmsd_A,0.0,1.0,"L403 region (Cα, core-aligned)"
+l403_region__ca__local_aligned_rmsd_A,0.0,1.0,"L403 region (Cα, locally aligned)"
+f412_region__ca__core_aligned_rmsd_A,0.0,1.0,"F412 region (Cα, core-aligned)"
+f412_region__ca__local_aligned_rmsd_A,0.0,1.0,"F412 region (Cα, locally aligned)"
+hydrophobic_nexus__ca__core_aligned_rmsd_A,0.0,1.0,"Hydrophobic coupling nexus (Cα, core-aligned)"
+hydrophobic_nexus__ca__local_aligned_rmsd_A,0.0,1.0,"Hydrophobic coupling nexus (Cα, locally aligned)"

data/Kv2.1/rmsd/analysis/f412l/effect_sizes.csv

@@ -0,0 +1,23 @@
+sequence_condition,reference_id,comparison_protocol,measurement,n_vanilla,n_masked,vanilla_median,masked_median,masked_minus_vanilla_median,bootstrap_ci_low,bootstrap_ci_high,cliffs_delta_masked_vs_vanilla,recycle_dependence_note
+f412l,8SD3,Masked,whole_matched_tetramer__ca__core_aligned_rmsd_A,4407,3578,1.6313015598437652,2.250405605132218,0.6191040452884526,0.5993551853883438,0.6372700843750766,0.8344800049415768,Recycle snapshots pooled; effect size is descriptive.
+f412l,8SD3,Masked,s6_bundle_working__ca__core_aligned_rmsd_A,4407,3578,1.5994227998859996,2.1115585711181746,0.512135771232175,0.49122332698910937,0.5295696077438911,0.6082285880116278,Recycle snapshots pooled; effect size is descriptive.
+f412l,8SD3,Masked,s6_bundle_working__ca__local_aligned_rmsd_A,4407,3578,1.3484051742836691,1.9507501488775678,0.6023449745938987,0.5843710884076916,0.6232304569928304,0.7563042839387462,Recycle snapshots pooled; effect size is descriptive.
+f412l,8SD3,Masked,distal_s6_working__ca__core_aligned_rmsd_A,4407,3578,1.1297607980611468,1.5355613084835253,0.4058005104223785,0.38813322664580774,0.4306225517619227,0.6361954271895556,Recycle snapshots pooled; effect size is descriptive.
+f412l,8SD3,Masked,distal_s6_working__ca__local_aligned_rmsd_A,4407,3578,0.9455235665298376,1.1805924721329992,0.23506890560316163,0.22051118526974903,0.2524028760157286,0.62750619187448,Recycle snapshots pooled; effect size is descriptive.
+f412l,8SD3,Masked,l403_region__ca__core_aligned_rmsd_A,4407,3578,1.0719588938365936,1.6405723719197134,0.5686134780831198,0.5435019567565263,0.5868603318871384,0.7460393502232272,Recycle snapshots pooled; effect size is descriptive.
+f412l,8SD3,Masked,l403_region__ca__local_aligned_rmsd_A,4407,3578,0.9194976261398276,1.1186625333653188,0.1991649072254913,0.18471170277377957,0.2133354669650052,0.5684313905300564,Recycle snapshots pooled; effect size is descriptive.
+f412l,8SD3,Masked,f412_region__ca__core_aligned_rmsd_A,4407,3578,1.3968736151518282,1.5937759884656244,0.19690237331379623,0.17790847096535936,0.21528177739669999,0.3133767699971195,Recycle snapshots pooled; effect size is descriptive.
+f412l,8SD3,Masked,f412_region__ca__local_aligned_rmsd_A,4407,3578,1.084554302087717,1.4849006135192602,0.4003463114315431,0.3791132106742746,0.4180660789026079,0.5988063605806251,Recycle snapshots pooled; effect size is descriptive.
+f412l,8SD3,Masked,hydrophobic_nexus__ca__core_aligned_rmsd_A,4407,3578,0.951443193925545,1.2889901993123778,0.3375470053868328,0.32654168008991646,0.3469163854723626,0.6642118597084292,Recycle snapshots pooled; effect size is descriptive.
+f412l,8SD3,Masked,hydrophobic_nexus__ca__local_aligned_rmsd_A,4407,3578,0.9014821942724736,1.0476584157607736,0.1461762214883,0.12829368047512468,0.16729059473844649,0.4611219282093899,Recycle snapshots pooled; effect size is descriptive.
+f412l,8SDA,Masked,whole_matched_tetramer__ca__core_aligned_rmsd_A,4407,3578,1.3473317513930694,1.8948574497289439,0.5475256983358745,0.5322477953922992,0.5615414248168863,0.8435725825180556,Recycle snapshots pooled; effect size is descriptive.
+f412l,8SDA,Masked,s6_bundle_working__ca__core_aligned_rmsd_A,4407,3578,1.7296207113743467,2.1484029598651375,0.4187822484907908,0.4010583983270606,0.43177434688137006,0.5113388007772075,Recycle snapshots pooled; effect size is descriptive.
+f412l,8SDA,Masked,s6_bundle_working__ca__local_aligned_rmsd_A,4407,3578,1.5943752163427598,1.871231492166775,0.2768562758240152,0.26900715749362886,0.28570904874856407,0.5250762830564668,Recycle snapshots pooled; effect size is descriptive.
+f412l,8SDA,Masked,distal_s6_working__ca__core_aligned_rmsd_A,4407,3578,1.863729164132277,2.114487641575134,0.25075847744285684,0.23956163149580847,0.2606897451870353,0.42923670774796374,Recycle snapshots pooled; effect size is descriptive.
+f412l,8SDA,Masked,distal_s6_working__ca__local_aligned_rmsd_A,4407,3578,1.683222027146497,1.79522271977415,0.11200069262765289,0.10585402956446052,0.12692078020296726,0.4717639488881642,Recycle snapshots pooled; effect size is descriptive.
+f412l,8SDA,Masked,l403_region__ca__core_aligned_rmsd_A,4407,3578,1.9916721672484377,2.195711847899057,0.20403968065061928,0.183962009152875,0.2226450638004558,0.36246225483798256,Recycle snapshots pooled; effect size is descriptive.
+f412l,8SDA,Masked,l403_region__ca__local_aligned_rmsd_A,4407,3578,1.7607825003441118,1.867613357972969,0.10683085762885725,0.10059776910631682,0.11214773155453538,0.4310404594144459,Recycle snapshots pooled; effect size is descriptive.
+f412l,8SDA,Masked,f412_region__ca__core_aligned_rmsd_A,4407,3578,1.7893258115258692,1.9471672530478816,0.1578414415220124,0.14768776575642856,0.16844065224827703,0.41755348058369957,Recycle snapshots pooled; effect size is descriptive.
+f412l,8SDA,Masked,f412_region__ca__local_aligned_rmsd_A,4407,3578,1.45693260300128,1.5148345009923205,0.05790189799104062,0.04670213285627401,0.0797130095833662,0.24332027798145717,Recycle snapshots pooled; effect size is descriptive.
+f412l,8SDA,Masked,hydrophobic_nexus__ca__core_aligned_rmsd_A,4407,3578,1.482012398247345,1.8020006276366551,0.31998822938931015,0.300612193621181,0.33310914257603497,0.6211721963241821,Recycle snapshots pooled; effect size is descriptive.
+f412l,8SDA,Masked,hydrophobic_nexus__ca__local_aligned_rmsd_A,4407,3578,1.4098876511084042,1.5390136158782226,0.1291259647698184,0.10822929950235197,0.14233948331624094,0.4002414726406476,Recycle snapshots pooled; effect size is descriptive.

data/Kv2.1/rmsd/analysis/f412l/experimental_baseline_status.csv

@@ -0,0 +1,2 @@
+status
+Separate experimental reference-to-reference baseline unavailable.

data/Kv2.1/rmsd/analysis/f412l/model_counts.csv

@@ -0,0 +1,5 @@
+Protocol,reference_id,rows,unique_models
+Masked,8SD3,3578,3578
+Masked,8SDA,3578,3578
+Vanilla,8SD3,4407,4407
+Vanilla,8SDA,4407,4407

data/Kv2.1/rmsd/analysis/f412l/reference_preference_summary_8SD3_vs_8SDA.csv

@@ -0,0 +1,3 @@
+protocol,reference_a,reference_b,measurement,n_paired_models,median_delta_b_minus_a_A,fraction_closer_to_a,fraction_closer_to_b,fraction_tied
+Masked,8SD3,8SDA,whole_matched_tetramer__ca__core_aligned_rmsd_A,3578,-0.2153428292698114,0.14896590273896032,0.8510340972610397,0.0
+Vanilla,8SD3,8SDA,whole_matched_tetramer__ca__core_aligned_rmsd_A,4407,-0.2966974258636894,0.09825277966870888,0.9017472203312912,0.0

data/Kv2.1/rmsd/analysis/f412l/summary_statistics.csv

@@ -0,0 +1,45 @@
+sequence_condition,protocol,reference_id,measurement,n_unique_models,n_measured,median,q25,q75,iqr,p05,p95,missing_fraction,median_aligned_atoms,median_coverage
+f412l,masked,8SD3,whole_matched_tetramer__ca__core_aligned_rmsd_A,3578,3578,2.250405605132218,1.9235281377806919,2.4848718175823827,0.5613436798016909,1.6529227122007843,2.742372259222464,0.0,948.0,1.0
+f412l,masked,8SD3,s6_bundle_working__ca__core_aligned_rmsd_A,3578,3578,2.1115585711181746,1.7351553501070531,2.8352858193648096,1.1001304692577565,1.4866867491988442,3.6123974758443897,0.0,136.0,1.0
+f412l,masked,8SD3,s6_bundle_working__ca__local_aligned_rmsd_A,3578,3578,1.9507501488775678,1.6148456987362407,2.3910320706045285,0.7761863718682878,1.339844591025755,2.8078365327033774,0.0,136.0,1.0
+f412l,masked,8SD3,distal_s6_working__ca__core_aligned_rmsd_A,3578,3578,1.5355613084835253,1.2718994657001907,2.618171679219735,1.3462722135195442,1.087465340034218,3.5320659183149186,0.0,68.0,1.0
+f412l,masked,8SD3,distal_s6_working__ca__local_aligned_rmsd_A,3578,3578,1.1805924721329992,1.0619626176122337,1.9055145504156097,0.843551932803376,0.9413702111336882,2.2442357956819325,0.0,68.0,1.0
+f412l,masked,8SD3,l403_region__ca__core_aligned_rmsd_A,3578,3578,1.6405723719197134,1.2856673253012603,2.3453407276761546,1.0596734023748944,1.0966534377409167,3.1658416964007903,0.0,48.0,1.0
+f412l,masked,8SD3,l403_region__ca__local_aligned_rmsd_A,3578,3578,1.1186625333653188,0.9870324631782494,1.5876069665150712,0.6005745033368217,0.8603381823646127,1.940379480371753,0.0,48.0,1.0
+f412l,masked,8SD3,f412_region__ca__core_aligned_rmsd_A,3578,3578,1.5937759884656244,1.326614564974105,3.2235010064332164,1.8968864414591113,1.1329258833960585,4.27793973049226,0.0,44.0,1.0
+f412l,masked,8SD3,f412_region__ca__local_aligned_rmsd_A,3578,3578,1.4849006135192602,1.1984646083276354,2.3464695364412362,1.1480049281136009,1.0290671011973977,2.885136925005994,0.0,44.0,1.0
+f412l,masked,8SD3,hydrophobic_nexus__ca__core_aligned_rmsd_A,3578,3578,1.2889901993123778,1.0854637495146884,2.0951291258390476,1.0096653763243593,0.9370813336612558,2.7627345158165055,0.0,80.0,1.0
+f412l,masked,8SD3,hydrophobic_nexus__ca__local_aligned_rmsd_A,3578,3578,1.0476584157607736,0.914685065326822,1.9962888591856234,1.0816037938588012,0.8288753492361751,2.5765464984348254,0.0,80.0,1.0
+f412l,masked,8SDA,whole_matched_tetramer__ca__core_aligned_rmsd_A,3578,3578,1.8948574497289439,1.5950862001329993,2.415587344255643,0.8205011441226437,1.3529633068101763,2.656072852789,0.0,939.0,1.0
+f412l,masked,8SDA,s6_bundle_working__ca__core_aligned_rmsd_A,3578,3578,2.1484029598651375,1.7392754913276858,2.493643714702711,0.7543682233750251,1.6173220743405086,2.9580417320325205,0.0,136.0,1.0
+f412l,masked,8SDA,s6_bundle_working__ca__local_aligned_rmsd_A,3578,3578,1.871231492166775,1.598580023556958,2.1815876780560863,0.5830076544991283,1.5151876373773085,2.4329451306948187,0.0,136.0,1.0
+f412l,masked,8SDA,distal_s6_working__ca__core_aligned_rmsd_A,3578,3578,2.114487641575134,1.8345783807120455,2.4470317312279444,0.6124533505158989,1.7288277743557692,3.1837953436042707,0.0,68.0,1.0
+f412l,masked,8SDA,distal_s6_working__ca__local_aligned_rmsd_A,3578,3578,1.79522271977415,1.6656064029761817,1.9939520390572811,0.32834563608109946,1.594775114857425,2.150505830713804,0.0,68.0,1.0
+f412l,masked,8SDA,l403_region__ca__core_aligned_rmsd_A,3578,3578,2.195711847899057,1.933779460607009,2.4798477469482987,0.5460682863412898,1.8311008901856567,3.0990352819046296,0.0,48.0,1.0
+f412l,masked,8SDA,l403_region__ca__local_aligned_rmsd_A,3578,3578,1.867613357972969,1.7426491747607644,2.0182313374586798,0.27558216269791536,1.6727844174578141,2.234258921334529,0.0,48.0,1.0
+f412l,masked,8SDA,f412_region__ca__core_aligned_rmsd_A,3578,3578,1.9471672530478816,1.7875414945144752,2.6305451947727674,0.8430037002582922,1.6690875223018455,3.5933637699088345,0.0,44.0,1.0
+f412l,masked,8SDA,f412_region__ca__local_aligned_rmsd_A,3578,3578,1.5148345009923205,1.4019164002244229,2.0355264241172373,0.6336100238928144,1.3455955162238522,2.285142490108291,0.0,44.0,1.0
+f412l,masked,8SDA,hydrophobic_nexus__ca__core_aligned_rmsd_A,3578,3578,1.8020006276366551,1.555639745510131,2.108842699525476,0.5532029540153449,1.4091809662720618,2.467114527591148,0.0,80.0,1.0
+f412l,masked,8SDA,hydrophobic_nexus__ca__local_aligned_rmsd_A,3578,3578,1.5390136158782226,1.3878951011569223,1.8746394662848016,0.48674436512787933,1.3034912265657446,2.362299349534079,0.0,80.0,1.0
+f412l,vanilla,8SD3,whole_matched_tetramer__ca__core_aligned_rmsd_A,4407,4407,1.6313015598437652,1.4819679268852313,1.770242245681906,0.28827431879667476,1.323738155646614,2.021919078284572,0.0,948.0,1.0
+f412l,vanilla,8SD3,s6_bundle_working__ca__core_aligned_rmsd_A,4407,4407,1.5994227998859996,1.355445044559233,1.9171226501685348,0.5616776056093018,1.1381721896834345,2.1811014601125325,0.0,136.0,1.0
+f412l,vanilla,8SD3,s6_bundle_working__ca__local_aligned_rmsd_A,4407,4407,1.3484051742836691,1.1820309813847336,1.564784467766762,0.38275348638202833,0.9806695616737514,1.8440292417410253,0.0,136.0,1.0
+f412l,vanilla,8SD3,distal_s6_working__ca__core_aligned_rmsd_A,4407,4407,1.1297607980611468,1.0028354115262892,1.3127337088797657,0.3098982973534765,0.8949608203398965,1.7645486630444585,0.0,68.0,1.0
+f412l,vanilla,8SD3,distal_s6_working__ca__local_aligned_rmsd_A,4407,4407,0.9455235665298376,0.8687679596399063,1.1052281159174537,0.23646015627754746,0.7896674805497141,1.3953279375947363,0.0,68.0,1.0
+f412l,vanilla,8SD3,l403_region__ca__core_aligned_rmsd_A,4407,4407,1.0719588938365936,0.9925803962678745,1.2336378050769923,0.24105740880911775,0.8921375570094998,1.60416753119258,0.0,48.0,1.0
+f412l,vanilla,8SD3,l403_region__ca__local_aligned_rmsd_A,4407,4407,0.9194976261398276,0.8324513978083257,1.058817185416529,0.22636578760820325,0.7333904307904783,1.2383151259936447,0.0,48.0,1.0
+f412l,vanilla,8SD3,f412_region__ca__core_aligned_rmsd_A,4407,4407,1.3968736151518282,1.225731830650639,1.7735491802781365,0.5478173496274974,1.0867301035224795,2.254515172960514,0.0,44.0,1.0
+f412l,vanilla,8SD3,f412_region__ca__local_aligned_rmsd_A,4407,4407,1.084554302087717,0.971204729107704,1.3089720610577333,0.3377673319500294,0.8229941453662452,1.6928701708175597,0.0,44.0,1.0
+f412l,vanilla,8SD3,hydrophobic_nexus__ca__core_aligned_rmsd_A,4407,4407,0.951443193925545,0.8597548016823748,1.101842771449141,0.24208796976676616,0.776866241850319,1.4348051718543477,0.0,80.0,1.0
+f412l,vanilla,8SD3,hydrophobic_nexus__ca__local_aligned_rmsd_A,4407,4407,0.9014821942724736,0.8263720173392779,1.0341562169176561,0.20778419957837824,0.7655502804914606,1.3560755680694951,0.0,80.0,1.0
+f412l,vanilla,8SDA,whole_matched_tetramer__ca__core_aligned_rmsd_A,4407,4407,1.3473317513930694,1.2954993039246205,1.410827905576053,0.11532860165143255,1.2088226368108699,1.6841207532056248,0.0,939.0,1.0
+f412l,vanilla,8SDA,s6_bundle_working__ca__core_aligned_rmsd_A,4407,4407,1.7296207113743467,1.6988683379681615,1.7754913634733511,0.07662302550518962,1.6423494272735355,1.9752127472618537,0.0,136.0,1.0
+f412l,vanilla,8SDA,s6_bundle_working__ca__local_aligned_rmsd_A,4407,4407,1.5943752163427598,1.5585004419461241,1.6431237446711386,0.0846233027250145,1.5222244612752074,1.7544172040133919,0.0,136.0,1.0
+f412l,vanilla,8SDA,distal_s6_working__ca__core_aligned_rmsd_A,4407,4407,1.863729164132277,1.826225290245505,1.9106700647036905,0.08444477445818555,1.7866424323964467,2.006739184097406,0.0,68.0,1.0
+f412l,vanilla,8SDA,distal_s6_working__ca__local_aligned_rmsd_A,4407,4407,1.683222027146497,1.6430219302780031,1.7175266449846451,0.074504714706642,1.6060887770419987,1.7603306286331872,0.0,68.0,1.0
+f412l,vanilla,8SDA,l403_region__ca__core_aligned_rmsd_A,4407,4407,1.9916721672484377,1.9474171821399664,2.0422310981540246,0.0948139160140582,1.8795915753143424,2.1346376467125596,0.0,48.0,1.0
+f412l,vanilla,8SDA,l403_region__ca__local_aligned_rmsd_A,4407,4407,1.7607825003441118,1.7201774152817342,1.8023553947799424,0.08217797949820826,1.683995493154911,1.860437535163312,0.0,48.0,1.0
+f412l,vanilla,8SDA,f412_region__ca__core_aligned_rmsd_A,4407,4407,1.7893258115258692,1.746261318753985,1.8612725048368022,0.11501118608281713,1.710627710849891,2.1112600811584827,0.0,44.0,1.0
+f412l,vanilla,8SDA,f412_region__ca__local_aligned_rmsd_A,4407,4407,1.45693260300128,1.4172343569899262,1.4888654674686144,0.0716311104786882,1.380260618587314,1.6672178045884405,0.0,44.0,1.0
+f412l,vanilla,8SDA,hydrophobic_nexus__ca__core_aligned_rmsd_A,4407,4407,1.482012398247345,1.457217882210772,1.5170865004355218,0.05986861822474987,1.420279718772805,1.6596854783933925,0.0,80.0,1.0
+f412l,vanilla,8SDA,hydrophobic_nexus__ca__local_aligned_rmsd_A,4407,4407,1.4098876511084042,1.3880551035324502,1.4388800513668334,0.05082494783438318,1.3466825019729218,1.517372519191142,0.0,80.0,1.0

data/Kv2.1/rmsd/analysis/kv21_distance_alignment_qc_summary.csv

@@ -0,0 +1,7 @@
+source,output,stable_core_failure_cutoff_A,input_rows,retained_rows,rejected_rows,input_trajectories,retained_trajectories,rejected_trajectories,direct_failed_rows,rows_missing_successful_rmsd_analysis,maximum_retained_stable_core_rmsd_A
+kv21/dataDistances/26-02-11_Kv2.1_f412l_maskedAF2_distances_all_ok_rmsd_3A_structural_interface_qc.csv,kv21/dataDistances/26-02-11_Kv2.1_f412l_maskedAF2_distances_all_ok_rmsd_3A_structural_interface_alignment_qc.csv,4.0,3841,3578,263,448,412,36,0,263,3.3612126407320866
+kv21/dataDistances/26-02-11_Kv2.1_f412l_vanillaAF2_distances_all_ok_rmsd_3A_structural_interface_qc.csv,kv21/dataDistances/26-02-11_Kv2.1_f412l_vanillaAF2_distances_all_ok_rmsd_3A_structural_interface_alignment_qc.csv,4.0,4521,4407,114,487,473,14,114,0,2.017243414272506
+kv21/dataDistances/26-02-11_Kv2.1_l403a_maskedAF2_distances_all_ok_rmsd_3A_structural_interface_qc.csv,kv21/dataDistances/26-02-11_Kv2.1_l403a_maskedAF2_distances_all_ok_rmsd_3A_structural_interface_alignment_qc.csv,4.0,3910,3693,217,459,426,33,0,217,2.799893916383873
+kv21/dataDistances/26-02-11_Kv2.1_l403a_vanillaAF2_distances_all_ok_rmsd_3A_structural_interface_qc.csv,kv21/dataDistances/26-02-11_Kv2.1_l403a_vanillaAF2_distances_all_ok_rmsd_3A_structural_interface_alignment_qc.csv,4.0,4403,4371,32,484,479,5,26,6,2.1694535216461475
+kv21/dataDistances/26-02-11_Kv2.1_wt_maskedAF2_distances_all_ok_rmsd_3A_structural_interface_qc.csv,kv21/dataDistances/26-02-11_Kv2.1_wt_maskedAF2_distances_all_ok_rmsd_3A_structural_interface_alignment_qc.csv,4.0,3925,3658,267,458,419,39,0,267,3.2557392995288876
+kv21/dataDistances/26-02-11_Kv2.1_wt_vanillaAF2_distances_all_ok_rmsd_3A_structural_interface_qc.csv,kv21/dataDistances/26-02-11_Kv2.1_wt_vanillaAF2_distances_all_ok_rmsd_3A_structural_interface_alignment_qc.csv,4.0,4591,4562,29,490,487,3,29,0,2.009081760947842

data/Kv2.1/rmsd/analysis/l403a/coverage_missing_summary.csv

@@ -0,0 +1,12 @@
+measurement,missing_fraction,available_fraction,label
+whole_matched_tetramer__ca__core_aligned_rmsd_A,0.0,1.0,"Whole matched tetramer (Cα, core-aligned)"
+s6_bundle_working__ca__core_aligned_rmsd_A,0.0,1.0,"Four-chain S6 bundle (Cα, core-aligned)"
+s6_bundle_working__ca__local_aligned_rmsd_A,0.0,1.0,"Four-chain S6 bundle (Cα, locally aligned)"
+distal_s6_working__ca__core_aligned_rmsd_A,0.0,1.0,"Distal S6 (Cα, core-aligned)"
+distal_s6_working__ca__local_aligned_rmsd_A,0.0,1.0,"Distal S6 (Cα, locally aligned)"
+l403_region__ca__core_aligned_rmsd_A,0.0,1.0,"L403 region (Cα, core-aligned)"
+l403_region__ca__local_aligned_rmsd_A,0.0,1.0,"L403 region (Cα, locally aligned)"
+f412_region__ca__core_aligned_rmsd_A,0.0,1.0,"F412 region (Cα, core-aligned)"
+f412_region__ca__local_aligned_rmsd_A,0.0,1.0,"F412 region (Cα, locally aligned)"
+hydrophobic_nexus__ca__core_aligned_rmsd_A,0.0,1.0,"Hydrophobic coupling nexus (Cα, core-aligned)"
+hydrophobic_nexus__ca__local_aligned_rmsd_A,0.0,1.0,"Hydrophobic coupling nexus (Cα, locally aligned)"

data/Kv2.1/rmsd/analysis/l403a/effect_sizes.csv

@@ -0,0 +1,23 @@
+sequence_condition,reference_id,comparison_protocol,measurement,n_vanilla,n_masked,vanilla_median,masked_median,masked_minus_vanilla_median,bootstrap_ci_low,bootstrap_ci_high,cliffs_delta_masked_vs_vanilla,recycle_dependence_note
+l403a,8SD3,Masked,whole_matched_tetramer__ca__core_aligned_rmsd_A,4371,3693,1.2364970927714445,1.6394067783354411,0.40290968556399664,0.3908167439298896,0.41531975604397203,0.8372785751645866,Recycle snapshots pooled; effect size is descriptive.
+l403a,8SD3,Masked,s6_bundle_working__ca__core_aligned_rmsd_A,4371,3693,0.8078887360071187,0.965744878371884,0.1578561423647653,0.14932228368615852,0.16622814267115466,0.5821694360394059,Recycle snapshots pooled; effect size is descriptive.
+l403a,8SD3,Masked,s6_bundle_working__ca__local_aligned_rmsd_A,4371,3693,0.6849467716677897,0.768538685485945,0.08359191381815523,0.07556016648635261,0.09118221344896817,0.46617922088590324,Recycle snapshots pooled; effect size is descriptive.
+l403a,8SD3,Masked,distal_s6_working__ca__core_aligned_rmsd_A,4371,3693,0.6739184492997761,0.7920607969019319,0.1181423476021558,0.10975637451209448,0.1267524107083373,0.5765136673951343,Recycle snapshots pooled; effect size is descriptive.
+l403a,8SD3,Masked,distal_s6_working__ca__local_aligned_rmsd_A,4371,3693,0.5299912243905476,0.5354652083905705,0.005473984000022969,-0.0014294229342143138,0.012687064057302699,0.02942324181675704,Recycle snapshots pooled; effect size is descriptive.
+l403a,8SD3,Masked,l403_region__ca__core_aligned_rmsd_A,4371,3693,0.6800695488108383,0.7486589411404164,0.06858939232957817,0.06036568465940716,0.07715927705633065,0.338657794464575,Recycle snapshots pooled; effect size is descriptive.
+l403a,8SD3,Masked,l403_region__ca__local_aligned_rmsd_A,4371,3693,0.5133455030689131,0.5090904444578521,-0.004255058611061013,-0.008030097682463419,0.0003056045736625999,-0.05371524391834204,Recycle snapshots pooled; effect size is descriptive.
+l403a,8SD3,Masked,f412_region__ca__core_aligned_rmsd_A,4371,3693,0.715819947477432,0.916814196979426,0.20099424950199396,0.19068628930035436,0.2090414584524634,0.745400955501275,Recycle snapshots pooled; effect size is descriptive.
+l403a,8SD3,Masked,f412_region__ca__local_aligned_rmsd_A,4371,3693,0.5958758551091454,0.6443882442096168,0.0485123891004714,0.03936171327666205,0.05735843590259041,0.13237190965762013,Recycle snapshots pooled; effect size is descriptive.
+l403a,8SD3,Masked,hydrophobic_nexus__ca__core_aligned_rmsd_A,4371,3693,0.5697338375091939,0.7174168958679695,0.1476830583587756,0.14252821867166787,0.15498309544628738,0.7640186040195629,Recycle snapshots pooled; effect size is descriptive.
+l403a,8SD3,Masked,hydrophobic_nexus__ca__local_aligned_rmsd_A,4371,3693,0.5276827880553708,0.536697616770551,0.009014828715180112,0.0022498523430962564,0.014575542933516344,0.0329659028938174,Recycle snapshots pooled; effect size is descriptive.
+l403a,8SDA,Masked,whole_matched_tetramer__ca__core_aligned_rmsd_A,4371,3693,1.4255289481349098,1.778990406440777,0.3534614583058673,0.3422665209447853,0.366558984230731,0.7206409846350255,Recycle snapshots pooled; effect size is descriptive.
+l403a,8SDA,Masked,s6_bundle_working__ca__core_aligned_rmsd_A,4371,3693,1.9390678210093455,2.01043323759335,0.0713654165840043,0.06546461185376615,0.07770436665422098,0.2768511017430628,Recycle snapshots pooled; effect size is descriptive.
+l403a,8SDA,Masked,s6_bundle_working__ca__local_aligned_rmsd_A,4371,3693,1.8577993252250624,1.8748297301499832,0.017030404924920806,0.010691832116246436,0.0222606797416256,0.08655545067454962,Recycle snapshots pooled; effect size is descriptive.
+l403a,8SDA,Masked,distal_s6_working__ca__core_aligned_rmsd_A,4371,3693,2.0453613462504188,2.1022077749145205,0.05684642866410172,0.046951502779206324,0.06428056708363582,0.38548527413063827,Recycle snapshots pooled; effect size is descriptive.
+l403a,8SDA,Masked,distal_s6_working__ca__local_aligned_rmsd_A,4371,3693,1.9386262986234588,1.9778625492390356,0.039236250615576784,0.034399860085027364,0.045059315347642695,0.3234471369684606,Recycle snapshots pooled; effect size is descriptive.
+l403a,8SDA,Masked,l403_region__ca__core_aligned_rmsd_A,4371,3693,2.186557601463253,2.2173867124843643,0.03082911102111119,0.021948882844457153,0.03834226093743554,0.22415561342905566,Recycle snapshots pooled; effect size is descriptive.
+l403a,8SDA,Masked,l403_region__ca__local_aligned_rmsd_A,4371,3693,2.0221344268743056,2.0711155497653015,0.04898112289099599,0.04372943665510657,0.054198994737911524,0.3647742180805067,Recycle snapshots pooled; effect size is descriptive.
+l403a,8SDA,Masked,f412_region__ca__core_aligned_rmsd_A,4371,3693,1.934724596118087,2.0706880167371757,0.13596342061908873,0.12805256875233717,0.14107277762178372,0.5213268060549483,Recycle snapshots pooled; effect size is descriptive.
+l403a,8SDA,Masked,f412_region__ca__local_aligned_rmsd_A,4371,3693,1.619012842927679,1.6154946467304951,-0.003518196197183965,-0.007381308140057441,0.0007176762979772186,-0.0001945843115980228,Recycle snapshots pooled; effect size is descriptive.
+l403a,8SDA,Masked,hydrophobic_nexus__ca__core_aligned_rmsd_A,4371,3693,1.6074854382754071,1.7556445890995664,0.1481591508241593,0.14172616240491304,0.1535382820050258,0.7008438119865794,Recycle snapshots pooled; effect size is descriptive.
+l403a,8SDA,Masked,hydrophobic_nexus__ca__local_aligned_rmsd_A,4371,3693,1.532071942333687,1.5910806665531254,0.05900872421943837,0.052566486751903195,0.06654235268804776,0.509479279124907,Recycle snapshots pooled; effect size is descriptive.

data/Kv2.1/rmsd/analysis/l403a/experimental_baseline_status.csv

@@ -0,0 +1,2 @@
+status
+Separate experimental reference-to-reference baseline unavailable.

data/Kv2.1/rmsd/analysis/l403a/model_counts.csv

@@ -0,0 +1,5 @@
+Protocol,reference_id,rows,unique_models
+Masked,8SD3,3693,3693
+Masked,8SDA,3693,3693
+Vanilla,8SD3,4371,4371
+Vanilla,8SDA,4371,4371

data/Kv2.1/rmsd/analysis/l403a/reference_preference_summary_8SD3_vs_8SDA.csv

@@ -0,0 +1,3 @@
+protocol,reference_a,reference_b,measurement,n_paired_models,median_delta_b_minus_a_A,fraction_closer_to_a,fraction_closer_to_b,fraction_tied
+Masked,8SD3,8SDA,whole_matched_tetramer__ca__core_aligned_rmsd_A,3693,0.1412421462925979,0.7045762252910912,0.29542377470890874,0.0
+Vanilla,8SD3,8SDA,whole_matched_tetramer__ca__core_aligned_rmsd_A,4371,0.18148747576289148,0.8821779913063372,0.11782200869366277,0.0