Rename universal_v2 -> main_benchmark (scripts, bench/ dir, env vars SF_MAIN_BENCH_*, README)

README_main_benchmark.md

@@ -0,0 +1,50 @@
+# Main_benchmark benchmark — scoring scripts + reference structures
+
+Two-state / multi-conformer benchmark of 60 cases across four patterns
+(FS fold-switch, AL allosteric, ID disorder-to-order, OL oligomer), 6 MSA-subsampling
+methods each. This package ships the **scoring code** and the **per-case reference
+structures + region definitions** so predictions can be scored and the benchmark
+tables regenerated on CPU. The AlphaFold2 prediction PDBs (~16 GB) are **not**
+distributed here — bring your own, or score the reference set.
+
+## Contents
+
+- `eval/main_benchmark_evaluate.py` — per-prediction scorer. For each state (a, b):
+  Cα RMSD on the common core, optional TM-score, and `hit_primary` (§9.1 binding
+  3-condition: RMSD ≤ 3 Å on common core AND mean pLDDT ≥ 70 AND switch-region
+  pLDDT ≥ 70). Pure CPU: `numpy`, `biopython`, `pyyaml`. TMalign optional (extra
+  columns only).
+- `eval/aggregate_main_benchmark.py` — aggregate per-(case, method) `evals.tsv` into
+  `main_table.csv` (per case×method hit counts/rates) and `pattern_summary.csv`
+  (per pattern×method means).
+- `bench/main_benchmark/structures/<case_id>/{state_a,state_b}.pdb` — 60 cases, 120 references.
+- `bench/main_benchmark/annotations/<case_id>/state_region_FINAL.tsv` — common-core and
+  switch-region residue indices (evaluator input only; oracle annotation, not a feature).
+- `bench/main_benchmark/cases.yaml` — case metadata.
+
+## Usage
+
+```bash
+pip install numpy biopython pyyaml   # TMalign optional
+
+# Score one case×method directory of prediction PDBs:
+python eval/main_benchmark_evaluate.py \
+    --case SFB_FS_A1AT_1QLPA_1OPHA \
+    --root /path/to/predictions/<case>/<method>/refine_per_state \
+    --out evals.tsv
+
+# Aggregate a full results tree (SF_MAIN_BENCH_RESULTS/<case>/<method>/refine_per_state/evals.tsv):
+SF_MAIN_BENCH_RESULTS=/path/to/results python eval/aggregate_main_benchmark.py
+```
+
+`SF_MAIN_BENCH_DATA` defaults to the bundled `bench/main_benchmark` (structures + annotations +
+cases.yaml); override to point elsewhere. `SF_MAIN_BENCH_RESULTS` supplies the predictions tree.
+
+## Verification
+
+The scorer is deterministic. Re-scoring the internal prediction set reproduces the
+published hit flags exactly (2594/2594 predictions across a 12-case stratified sample;
+`main_table` → `pattern_summary` aggregation reproduces 24/24 rows; `main_table` hit
+counts reproduce from `evals.tsv` 360/360). Headline: mosaic-SF beats AF-Cluster by
+~5–18 pp across patterns but is statistically indistinguishable from depth-matched
+random subsampling.

bench/main_benchmark/annotations/SFB_AL_AKE_4AKEA_1AKEA/state_region_BLIND_proxy.tsv

@@ -0,0 +1,218 @@
+# CASE-BLIND proxy. To be filled in wave 2 by FrustrAI-Seq (query-only) and MSA column variance.
+# fi_top25: 1 if residue is in top-25% per-residue FI (placeholder = 0 here)
+# msa_var_top25: 1 if residue is in top-25% MSA column variance (placeholder = 0 here)
+residue_index_query	fi_top25	msa_var_top25
+1	0	0
+2	0	0
+3	1	0
+4	1	0
+5	1	0
+6	1	0
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bench/main_benchmark/annotations/SFB_AL_AKE_4AKEA_1AKEA/state_region_FINAL.tsv

@@ -0,0 +1,218 @@
+# ORACLE annotation. DO NOT use as feature input. Evaluator only.
+# common_core: residues with CA in both states AND |displacement| < 3.0 A (after iterative Kabsch w/ outlier trimming)
+# switch_region_3A: residues with CA in both states AND |displacement| >= 3.0 A
+residue_index_query	resnum_state_A	displacement_A	common_core	switch_region_3A
+1	1	0.914	1	0
+2	2	0.533	1	0
+3	3	0.679	1	0
+4	4	0.954	1	0
+5	5	1.086	1	0
+6	6	1.620	1	0
+7	7	2.000	1	0
+8	8	1.441	1	0
+9	9	1.393	1	0
+10	10	2.196	1	0
+11	11	2.215	1	0
+12	12	2.447	1	0
+13	13	1.673	1	0
+14	14	1.385	1	0
+15	15	1.377	1	0
+16	16	0.900	1	0
+17	17	1.439	1	0
+18	18	1.507	1	0
+19	19	0.938	1	0
+20	20	0.299	1	0
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bench/main_benchmark/annotations/SFB_AL_CALM_1CFDA_1CLLA/state_region_BLIND_proxy.tsv

@@ -0,0 +1,152 @@
+# CASE-BLIND proxy. To be filled in wave 2 by FrustrAI-Seq (query-only) and MSA column variance.
+# fi_top25: 1 if residue is in top-25% per-residue FI (placeholder = 0 here)
+# msa_var_top25: 1 if residue is in top-25% MSA column variance (placeholder = 0 here)
+residue_index_query	fi_top25	msa_var_top25
+1	0	0
+2	0	0
+3	0	0
+4	1	0
+5	1	0
+6	0	0
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bench/main_benchmark/annotations/SFB_AL_CALM_1CFDA_1CLLA/state_region_FINAL.tsv

@@ -0,0 +1,148 @@
+# ORACLE annotation. DO NOT use as feature input. Evaluator only.
+# common_core: residues with CA in both states AND |displacement| < 3.0 A (after iterative Kabsch w/ outlier trimming)
+# switch_region_3A: residues with CA in both states AND |displacement| >= 3.0 A
+residue_index_query	resnum_state_A	displacement_A	common_core	switch_region_3A
+4	4	18.021	0	1
+5	5	15.868	0	1
+6	6	14.746	0	1
+7	7	14.074	0	1
+8	8	13.376	0	1
+9	9	10.822	0	1
+10	10	9.607	0	1
+11	11	9.133	0	1
+12	12	7.952	0	1
+13	13	5.988	0	1
+14	14	4.639	0	1
+15	15	5.151	0	1
+16	16	3.210	0	1
+17	17	0.914	1	0
+18	18	2.036	1	0
+19	19	3.951	0	1
+20	20	3.050	0	1
+21	21	5.587	0	1
+22	22	6.338	0	1
+23	23	5.307	0	1
+24	24	6.156	0	1
+25	25	4.733	0	1
+26	26	3.150	0	1
+27	27	2.402	1	0
+28	28	2.910	1	0
+29	29	3.074	0	1
+30	30	2.373	1	0
+31	31	0.732	1	0
+32	32	1.607	1	0
+33	33	1.157	1	0
+34	34	1.604	1	0
+35	35	2.627	1	0
+36	36	3.147	0	1
+37	37	3.188	0	1
+38	38	4.018	0	1
+39	39	4.267	0	1
+40	40	4.178	0	1
+41	41	3.540	0	1
+42	42	2.874	1	0
+43	43	1.991	1	0
+44	44	1.765	1	0
+45	45	1.905	1	0
+46	46	1.450	1	0
+47	47	1.013	1	0
+48	48	1.290	1	0
+49	49	2.833	1	0
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+147	147	15.158	0	1

bench/main_benchmark/annotations/SFB_AL_CDK6_1BI7A_2EUFB/state_region_BLIND_proxy.tsv

@@ -0,0 +1,273 @@
+# CASE-BLIND proxy. To be filled in wave 2 by FrustrAI-Seq (query-only) and MSA column variance.
+# fi_top25: 1 if residue is in top-25% per-residue FI (placeholder = 0 here)
+# msa_var_top25: 1 if residue is in top-25% MSA column variance (placeholder = 0 here)
+residue_index_query	fi_top25	msa_var_top25
+1	0	0
+2	0	0
+3	0	0
+4	0	0
+5	0	0
+6	1	1
+7	1	0
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bench/main_benchmark/annotations/SFB_AL_CDK6_1BI7A_2EUFB/state_region_FINAL.tsv

@@ -0,0 +1,259 @@
+# ORACLE annotation. DO NOT use as feature input. Evaluator only.
+# common_core: residues with CA in both states AND |displacement| < 3.0 A (after iterative Kabsch w/ outlier trimming)
+# switch_region_3A: residues with CA in both states AND |displacement| >= 3.0 A
+residue_index_query	resnum_state_A	displacement_A	common_core	switch_region_3A
+1	10	5.864	0	1
+2	11	7.562	0	1
+3	12	4.549	0	1
+4	13	5.417	0	1
+5	14	5.852	0	1
+6	15	6.503	0	1
+7	16	6.362	0	1
+8	17	7.579	0	1
+9	18	7.080	0	1
+10	19	6.532	0	1
+11	20	6.705	0	1
+12	21	7.045	0	1
+13	22	6.394	0	1
+14	23	6.339	0	1
+15	24	7.718	0	1
+16	25	7.948	0	1
+17	26	6.980	0	1
+18	27	5.480	0	1
+19	28	5.337	0	1
+20	29	5.062	0	1
+21	30	4.939	0	1
+22	31	4.087	0	1
+23	32	3.805	0	1
+24	33	4.038	0	1
+25	34	3.647	0	1
+26	35	2.552	1	0
+27	36	4.319	0	1
+28	37	5.074	0	1
+29	38	3.862	0	1
+30	39	3.675	0	1
+31	40	3.024	0	1
+32	41	3.471	0	1
+33	42	4.477	0	1
+34	43	5.147	0	1
+35	44	6.863	0	1
+36	45	7.798	0	1
+37	46	10.989	0	1
+38	47	11.721	0	1
+39	48	15.397	0	1
+40	72	2.563	1	0
+41	73	1.039	1	0
+42	74	0.538	1	0
+43	75	0.395	1	0
+44	76	0.549	1	0
+45	77	0.596	1	0
+46	78	1.512	1	0
+47	79	2.254	1	0
+48	80	1.947	1	0
+49	81	3.141	0	1
+50	82	4.557	0	1
+51	83	4.867	0	1
+52	84	6.254	0	1
+53	85	5.726	0	1
+54	86	6.911	0	1
+55	87	13.793	0	1
+56	88	14.238	0	1
+57	89	19.937	0	1
+58	90	20.072	0	1
+59	91	14.476	0	1
+60	92	11.405	0	1
+61	93	9.129	0	1
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+82	114	1.996	1	0
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+86	118	0.564	1	0
+87	119	0.463	1	0
+88	120	0.460	1	0
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+92	124	0.092	1	0
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+94	126	0.542	1	0
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+100	132	0.689	1	0
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+120	152	0.389	1	0
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+197	229	0.930	1	0
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+266	298	0.342	1	0
+267	299	0.281	1	0
+268	300	0.643	1	0
+269	301	1.438	1	0

bench/main_benchmark/annotations/SFB_AL_CHEY_3CHYA_1FQWA/state_region_BLIND_proxy.tsv

@@ -0,0 +1,132 @@
+# CASE-BLIND proxy. To be filled in wave 2 by FrustrAI-Seq (query-only) and MSA column variance.
+# fi_top25: 1 if residue is in top-25% per-residue FI (placeholder = 0 here)
+# msa_var_top25: 1 if residue is in top-25% MSA column variance (placeholder = 0 here)
+residue_index_query	fi_top25	msa_var_top25
+1	0	0
+2	0	0
+3	0	0
+4	0	0
+5	1	0
+6	0	0
+7	1	0
+8	1	0
+9	1	0
+10	1	0
+11	0	0
+12	0	0
+13	0	0
+14	0	1
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+25	0	0
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+69	0	0
+70	0	1
+71	1	0
+72	0	0
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+128	0	0

bench/main_benchmark/annotations/SFB_AL_CHEY_3CHYA_1FQWA/state_region_FINAL.tsv

@@ -0,0 +1,132 @@
+# ORACLE annotation. DO NOT use as feature input. Evaluator only.
+# common_core: residues with CA in both states AND |displacement| < 3.0 A (after iterative Kabsch w/ outlier trimming)
+# switch_region_3A: residues with CA in both states AND |displacement| >= 3.0 A
+residue_index_query	resnum_state_A	displacement_A	common_core	switch_region_3A
+1	2	1.261	1	0
+2	3	0.423	1	0
+3	4	0.873	1	0
+4	5	0.914	1	0
+5	6	0.480	1	0
+6	7	0.267	1	0
+7	8	0.271	1	0
+8	9	0.144	1	0
+9	10	0.225	1	0
+10	11	0.294	1	0
+11	12	0.443	1	0
+12	13	0.549	1	0
+13	14	0.400	1	0
+14	15	0.949	1	0
+15	16	1.278	1	0
+16	17	0.957	1	0
+17	18	0.694	1	0
+18	19	0.660	1	0
+19	20	0.756	1	0
+20	21	0.638	1	0
+21	22	0.281	1	0
+22	23	0.390	1	0
+23	24	0.650	1	0
+24	25	0.505	1	0
+25	26	0.600	1	0
+26	27	0.779	1	0
+27	28	0.947	1	0
+28	29	0.797	1	0
+29	30	0.889	1	0
+30	31	0.753	1	0
+31	32	0.597	1	0
+32	33	0.457	1	0
+33	34	0.130	1	0
+34	35	0.198	1	0
+35	36	0.218	1	0
+36	37	0.310	1	0
+37	38	0.407	1	0
+38	39	0.302	1	0
+39	40	0.445	1	0
+40	41	0.291	1	0
+41	42	0.274	1	0
+42	43	0.335	1	0
+43	44	0.548	1	0
+44	45	0.479	1	0
+45	46	0.168	1	0
+46	47	0.142	1	0
+47	48	0.444	1	0
+48	49	0.741	1	0
+49	50	0.323	1	0
+50	51	0.167	1	0
+51	52	0.601	1	0
+52	53	0.390	1	0
+53	54	0.280	1	0
+54	55	0.354	1	0
+55	56	0.421	1	0
+56	57	0.183	1	0
+57	58	0.935	1	0
+58	59	0.746	1	0
+59	60	0.593	1	0
+60	61	0.689	1	0
+61	62	1.112	1	0
+62	63	0.356	1	0
+63	64	0.338	1	0
+64	65	0.435	1	0
+65	66	0.293	1	0
+66	67	0.190	1	0
+67	68	0.168	1	0
+68	69	0.352	1	0
+69	70	0.422	1	0
+70	71	0.411	1	0
+71	72	0.301	1	0
+72	73	0.367	1	0
+73	74	0.680	1	0
+74	75	0.702	1	0
+75	76	0.749	1	0
+76	77	0.766	1	0
+77	78	0.808	1	0
+78	79	0.668	1	0
+79	80	0.530	1	0
+80	81	0.476	1	0
+81	82	0.335	1	0
+82	83	0.283	1	0
+83	84	0.353	1	0
+84	85	0.469	1	0
+85	86	1.122	1	0
+86	87	1.322	1	0
+87	88	0.937	1	0
+88	89	3.591	0	1
+89	90	1.283	1	0
+90	91	1.028	1	0
+91	92	0.601	1	0
+92	93	0.573	1	0
+93	94	0.472	1	0
+94	95	0.771	1	0
+95	96	0.821	1	0
+96	97	0.501	1	0
+97	98	0.394	1	0
+98	99	0.801	1	0
+99	100	0.757	1	0
+100	101	0.656	1	0
+101	102	0.702	1	0
+102	103	0.406	1	0
+103	104	0.102	1	0
+104	105	0.366	1	0
+105	106	0.378	1	0
+106	107	0.235	1	0
+107	108	0.889	1	0
+108	109	1.417	1	0
+109	110	1.738	1	0
+110	111	1.618	1	0
+111	112	2.260	1	0
+112	113	1.965	1	0
+113	114	1.365	1	0
+114	115	1.020	1	0
+115	116	0.845	1	0
+116	117	0.748	1	0
+117	118	0.193	1	0
+118	119	0.338	1	0
+119	120	0.589	1	0
+120	121	0.759	1	0
+121	122	0.617	1	0
+122	123	0.628	1	0
+123	124	0.918	1	0
+124	125	1.143	1	0
+125	126	1.479	1	0
+126	127	1.565	1	0
+127	128	1.935	1	0
+128	129	1.546	1	0

bench/main_benchmark/annotations/SFB_AL_DHFR_1RX1A_1RX4A/state_region_BLIND_proxy.tsv

@@ -0,0 +1,163 @@
+# CASE-BLIND proxy. To be filled in wave 2 by FrustrAI-Seq (query-only) and MSA column variance.
+# fi_top25: 1 if residue is in top-25% per-residue FI (placeholder = 0 here)
+# msa_var_top25: 1 if residue is in top-25% MSA column variance (placeholder = 0 here)
+residue_index_query	fi_top25	msa_var_top25
+1	0	0
+2	1	0
+3	0	0
+4	1	0
+5	1	0
+6	0	0
+7	0	0
+8	1	1
+9	0	0
+10	1	1
+11	0	0
+12	0	0
+13	1	0
+14	1	0
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+152	1	1
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+154	0	1
+155	1	1
+156	1	0
+157	0	0
+158	0	0
+159	0	0

bench/main_benchmark/annotations/SFB_AL_DHFR_1RX1A_1RX4A/state_region_FINAL.tsv

@@ -0,0 +1,163 @@
+# ORACLE annotation. DO NOT use as feature input. Evaluator only.
+# common_core: residues with CA in both states AND |displacement| < 3.0 A (after iterative Kabsch w/ outlier trimming)
+# switch_region_3A: residues with CA in both states AND |displacement| >= 3.0 A
+residue_index_query	resnum_state_A	displacement_A	common_core	switch_region_3A
+1	1	0.328	1	0
+2	2	0.301	1	0
+3	3	0.273	1	0
+4	4	0.126	1	0
+5	5	0.077	1	0
+6	6	0.189	1	0
+7	7	0.245	1	0
+8	8	0.044	1	0
+9	9	0.297	1	0
+10	10	0.217	1	0
+11	11	0.369	1	0
+12	12	0.628	1	0
+13	13	0.649	1	0
+14	14	0.305	1	0
+15	15	1.398	1	0
+16	16	5.989	0	1
+17	17	9.629	0	1
+18	18	7.281	0	1
+19	19	2.819	1	0
+20	20	2.783	1	0
+21	21	2.787	1	0
+22	22	1.539	1	0
+23	23	0.979	1	0
+24	24	0.979	1	0
+25	25	0.841	1	0
+26	26	0.771	1	0
+27	27	0.336	1	0
+28	28	0.429	1	0
+29	29	0.491	1	0
+30	30	0.392	1	0
+31	31	0.133	1	0
+32	32	0.221	1	0
+33	33	0.267	1	0
+34	34	0.150	1	0
+35	35	0.306	1	0
+36	36	0.375	1	0
+37	37	0.225	1	0
+38	38	0.184	1	0
+39	39	0.211	1	0
+40	40	0.123	1	0
+41	41	0.079	1	0
+42	42	0.162	1	0
+43	43	0.097	1	0
+44	44	0.166	1	0
+45	45	0.333	1	0
+46	46	0.064	1	0
+47	47	0.131	1	0
+48	48	0.145	1	0
+49	49	0.576	1	0
+50	50	0.229	1	0
+51	51	0.172	1	0
+52	52	0.154	1	0
+53	53	0.202	1	0
+54	54	0.077	1	0
+55	55	0.144	1	0
+56	56	0.139	1	0
+57	57	0.348	1	0
+58	58	0.297	1	0
+59	59	0.100	1	0
+60	60	0.303	1	0
+61	61	0.240	1	0
+62	62	0.313	1	0
+63	63	0.256	1	0
+64	64	0.413	1	0
+65	65	0.279	1	0
+66	66	0.187	1	0
+67	67	0.503	1	0
+68	68	0.346	1	0
+69	69	0.235	1	0
+70	70	0.307	1	0
+71	71	0.294	1	0
+72	72	0.136	1	0
+73	73	0.159	1	0
+74	74	0.239	1	0
+75	75	0.267	1	0
+76	76	0.484	1	0
+77	77	0.261	1	0
+78	78	0.155	1	0
+79	79	0.234	1	0
+80	80	0.241	1	0
+81	81	0.258	1	0
+82	82	0.202	1	0
+83	83	0.292	1	0
+84	84	0.370	1	0
+85	85	0.211	1	0
+86	86	0.154	1	0
+87	87	0.198	1	0
+88	88	0.433	1	0
+89	89	0.257	1	0
+90	90	0.084	1	0
+91	91	0.173	1	0
+92	92	0.206	1	0
+93	93	0.091	1	0
+94	94	0.182	1	0
+95	95	0.677	1	0
+96	96	0.452	1	0
+97	97	0.525	1	0
+98	98	0.647	1	0
+99	99	0.227	1	0
+100	100	0.161	1	0
+101	101	0.240	1	0
+102	102	0.284	1	0
+103	103	0.198	1	0
+104	104	0.292	1	0
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+108	108	0.435	1	0
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+114	114	0.269	1	0
+115	115	0.490	1	0
+116	116	0.319	1	0
+117	117	0.746	1	0
+118	118	0.971	1	0
+119	119	0.814	1	0
+120	120	0.972	1	0
+121	121	0.891	1	0
+122	122	0.716	1	0
+123	123	0.629	1	0
+124	124	0.422	1	0
+125	125	0.372	1	0
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+128	128	0.206	1	0
+129	129	0.577	1	0
+130	130	0.610	1	0
+131	131	0.543	1	0
+132	132	0.511	1	0
+133	133	0.179	1	0
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+141	141	0.355	1	0
+142	142	0.327	1	0
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+144	144	0.369	1	0
+145	145	0.701	1	0
+146	146	0.640	1	0
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+148	148	1.140	1	0
+149	149	0.576	1	0
+150	150	0.433	1	0
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+158	158	0.183	1	0
+159	159	0.389	1	0

bench/main_benchmark/annotations/SFB_AL_EGFR_2GS2A_1XKKA/state_region_BLIND_proxy.tsv

@@ -0,0 +1,309 @@
+# CASE-BLIND proxy. To be filled in wave 2 by FrustrAI-Seq (query-only) and MSA column variance.
+# fi_top25: 1 if residue is in top-25% per-residue FI (placeholder = 0 here)
+# msa_var_top25: 1 if residue is in top-25% MSA column variance (placeholder = 0 here)
+residue_index_query	fi_top25	msa_var_top25
+1	0	0
+2	0	0
+3	0	0
+4	0	0
+5	0	0
+6	0	0
+7	0	0
+8	0	0
+9	1	0
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bench/main_benchmark/annotations/SFB_AL_EGFR_2GS2A_1XKKA/state_region_FINAL.tsv

@@ -0,0 +1,256 @@
+# ORACLE annotation. DO NOT use as feature input. Evaluator only.
+# common_core: residues with CA in both states AND |displacement| < 3.0 A (after iterative Kabsch w/ outlier trimming)
+# switch_region_3A: residues with CA in both states AND |displacement| >= 3.0 A
+residue_index_query	resnum_state_A	displacement_A	common_core	switch_region_3A
+31	702	7.782	0	1
+32	703	6.193	0	1
+33	704	6.169	0	1
+34	705	5.797	0	1
+35	706	5.727	0	1
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+298	987	44.802	0	1

bench/main_benchmark/annotations/SFB_AL_GLNBP_1GGGA_1WDNA/state_region_BLIND_proxy.tsv

@@ -0,0 +1,224 @@
+# CASE-BLIND proxy. To be filled in wave 2 by FrustrAI-Seq (query-only) and MSA column variance.
+# fi_top25: 1 if residue is in top-25% per-residue FI (placeholder = 0 here)
+# msa_var_top25: 1 if residue is in top-25% MSA column variance (placeholder = 0 here)
+residue_index_query	fi_top25	msa_var_top25
+1	0	0
+2	0	0
+3	1	0
+4	0	0
+5	0	0
+6	0	0
+7	0	1
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+9	0	0
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bench/main_benchmark/annotations/SFB_AL_GLNBP_1GGGA_1WDNA/state_region_FINAL.tsv

@@ -0,0 +1,224 @@
+# ORACLE annotation. DO NOT use as feature input. Evaluator only.
+# common_core: residues with CA in both states AND |displacement| < 3.0 A (after iterative Kabsch w/ outlier trimming)
+# switch_region_3A: residues with CA in both states AND |displacement| >= 3.0 A
+residue_index_query	resnum_state_A	displacement_A	common_core	switch_region_3A
+1	5	0.709	1	0
+2	6	0.743	1	0
+3	7	0.620	1	0
+4	8	0.808	1	0
+5	9	0.617	1	0
+6	10	1.208	1	0
+7	11	0.879	1	0
+8	12	0.865	1	0
+9	13	1.002	1	0
+10	14	1.211	1	0
+11	15	1.129	1	0
+12	16	0.913	1	0
+13	17	0.752	1	0
+14	18	0.870	1	0
+15	19	0.951	1	0
+16	20	1.471	1	0
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+18	22	1.238	1	0
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+21	25	0.367	1	0
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+23	27	0.744	1	0
+24	28	0.709	1	0
+25	29	0.660	1	0
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+27	31	0.773	1	0
+28	32	0.398	1	0
+29	33	0.212	1	0
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+32	36	0.305	1	0
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+84	88	0.572	1	0
+85	89	1.338	1	0
+86	90	4.272	0	1
+87	91	6.168	0	1
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+90	94	13.611	0	1
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+95	99	21.277	0	1
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+152	156	6.948	0	1
+153	157	4.073	0	1
+154	158	2.508	1	0
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+185	189	0.419	1	0
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+188	192	0.954	1	0
+189	193	0.912	1	0
+190	194	0.972	1	0
+191	195	1.609	1	0
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+194	198	1.287	1	0
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+197	201	0.324	1	0
+198	202	0.405	1	0
+199	203	0.477	1	0
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+202	206	0.724	1	0
+203	207	0.820	1	0
+204	208	0.971	1	0
+205	209	1.028	1	0
+206	210	1.346	1	0
+207	211	1.226	1	0
+208	212	1.175	1	0
+209	213	1.087	1	0
+210	214	1.464	1	0
+211	215	1.551	1	0
+212	216	1.199	1	0
+213	217	1.276	1	0
+214	218	1.743	1	0
+215	219	1.644	1	0
+216	220	1.482	1	0
+217	221	1.756	1	0
+218	222	1.835	1	0
+219	223	3.222	0	1
+220	224	3.348	0	1

bench/main_benchmark/annotations/SFB_AL_LIVBP_2LIVA_1Z15A/state_region_BLIND_proxy.tsv

@@ -0,0 +1,348 @@
+# CASE-BLIND proxy. To be filled in wave 2 by FrustrAI-Seq (query-only) and MSA column variance.
+# fi_top25: 1 if residue is in top-25% per-residue FI (placeholder = 0 here)
+# msa_var_top25: 1 if residue is in top-25% MSA column variance (placeholder = 0 here)
+residue_index_query	fi_top25	msa_var_top25
+1	0	0
+2	0	0
+3	1	0
+4	0	0
+5	1	0
+6	0	0
+7	1	1
+8	1	1
+9	0	0
+10	0	0
+11	0	0
+12	0	0
+13	0	0
+14	0	1
+15	1	1
+16	0	0
+17	0	1
+18	0	1
+19	0	0
+20	0	1
+21	0	1
+22	0	1
+23	1	1
+24	0	0
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+339	0	0
+340	0	0
+341	0	0
+342	0	0
+343	0	0
+344	0	0

bench/main_benchmark/annotations/SFB_AL_LIVBP_2LIVA_1Z15A/state_region_FINAL.tsv

@@ -0,0 +1,348 @@
+# ORACLE annotation. DO NOT use as feature input. Evaluator only.
+# common_core: residues with CA in both states AND |displacement| < 3.0 A (after iterative Kabsch w/ outlier trimming)
+# switch_region_3A: residues with CA in both states AND |displacement| >= 3.0 A
+residue_index_query	resnum_state_A	displacement_A	common_core	switch_region_3A
+1	1	3.065	0	1
+2	2	1.099	1	0
+3	3	1.414	1	0
+4	4	1.371	1	0
+5	5	1.091	1	0
+6	6	1.171	1	0
+7	7	1.052	1	0
+8	8	1.244	1	0
+9	9	1.190	1	0
+10	10	1.368	1	0
+11	11	2.231	1	0
+12	12	1.785	1	0
+13	13	2.675	1	0
+14	14	2.879	1	0
+15	15	1.936	1	0
+16	16	1.727	1	0
+17	17	2.025	1	0
+18	18	1.508	1	0
+19	19	0.979	1	0
+20	20	1.449	1	0
+21	21	1.281	1	0
+22	22	0.958	1	0
+23	23	0.878	1	0
+24	24	1.122	1	0
+25	25	0.898	1	0
+26	26	0.686	1	0
+27	27	0.886	1	0
+28	28	0.776	1	0
+29	29	0.279	1	0
+30	30	0.367	1	0
+31	31	0.374	1	0
+32	32	0.240	1	0
+33	33	0.263	1	0
+34	34	0.321	1	0
+35	35	0.549	1	0
+36	36	0.526	1	0
+37	37	0.543	1	0
+38	38	0.844	1	0
+39	39	1.016	1	0
+40	40	1.337	1	0
+41	41	1.447	1	0
+42	42	1.170	1	0
+43	43	1.020	1	0
+44	44	0.965	1	0
+45	45	1.205	1	0
+46	46	1.199	1	0
+47	47	1.031	1	0
+48	48	1.048	1	0
+49	49	1.301	1	0
+50	50	1.349	1	0
+51	51	1.882	1	0
+52	52	1.579	1	0
+53	53	1.370	1	0
+54	54	1.664	1	0
+55	55	1.465	1	0
+56	56	1.514	1	0
+57	57	1.837	1	0
+58	58	1.433	1	0
+59	59	1.212	1	0
+60	60	1.730	1	0
+61	61	1.445	1	0
+62	62	1.020	1	0
+63	63	1.483	1	0
+64	64	1.612	1	0
+65	65	1.375	1	0
+66	66	1.348	1	0
+67	67	1.571	1	0
+68	68	1.704	1	0
+69	69	1.579	1	0
+70	70	1.613	1	0
+71	71	1.293	1	0
+72	72	0.800	1	0
+73	73	0.624	1	0
+74	74	0.346	1	0
+75	75	1.125	1	0
+76	76	1.068	1	0
+77	77	1.122	1	0
+78	78	1.360	1	0
+79	79	1.247	1	0
+80	80	1.159	1	0
+81	81	1.161	1	0
+82	82	0.733	1	0
+83	83	0.890	1	0
+84	84	0.884	1	0
+85	85	0.542	1	0
+86	86	0.794	1	0
+87	87	0.373	1	0
+88	88	0.940	1	0
+89	89	0.681	1	0
+90	90	0.400	1	0
+91	91	0.760	1	0
+92	92	0.559	1	0
+93	93	0.682	1	0
+94	94	0.649	1	0
+95	95	0.445	1	0
+96	96	0.387	1	0
+97	97	0.179	1	0
+98	98	0.741	1	0
+99	99	0.804	1	0
+100	100	1.185	1	0
+101	101	1.230	1	0
+102	102	1.502	1	0
+103	103	1.327	1	0
+104	104	1.282	1	0
+105	105	1.286	1	0
+106	106	0.848	1	0
+107	107	0.831	1	0
+108	108	0.958	1	0
+109	109	0.742	1	0
+110	110	0.815	1	0
+111	111	0.508	1	0
+112	112	0.459	1	0
+113	113	0.364	1	0
+114	114	0.187	1	0
+115	115	0.508	1	0
+116	116	0.481	1	0
+117	117	0.484	1	0
+118	118	1.031	1	0
+119	119	1.189	1	0
+120	120	1.161	1	0
+121	121	1.223	1	0
+122	122	1.269	1	0
+123	123	0.935	1	0
+124	124	0.921	1	0
+125	125	0.849	1	0
+126	126	0.792	1	0
+127	127	0.515	1	0
+128	128	0.330	1	0
+129	129	0.443	1	0
+130	130	0.618	1	0
+131	131	0.416	1	0
+132	132	0.478	1	0
+133	133	0.589	1	0
+134	134	0.823	1	0
+135	135	0.337	1	0
+136	136	0.644	1	0
+137	137	0.890	1	0
+138	138	1.010	1	0
+139	139	1.290	1	0
+140	140	1.033	1	0
+141	141	0.697	1	0
+142	142	0.761	1	0
+143	143	0.422	1	0
+144	144	0.488	1	0
+145	145	0.586	1	0
+146	146	0.989	1	0
+147	147	0.964	1	0
+148	148	0.871	1	0
+149	149	1.066	1	0
+150	150	1.372	1	0
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+156	156	0.265	1	0
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+160	160	0.923	1	0
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+163	163	1.123	1	0
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+167	167	1.052	1	0
+168	168	1.131	1	0
+169	169	0.749	1	0
+170	170	1.036	1	0
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+172	172	0.618	1	0
+173	173	0.726	1	0
+174	174	0.595	1	0
+175	175	1.374	1	0
+176	176	1.170	1	0
+177	177	1.519	1	0
+178	178	1.683	1	0
+179	179	1.673	1	0
+180	180	2.050	1	0
+181	181	2.118	1	0
+182	182	1.898	1	0
+183	183	2.105	1	0
+184	184	2.119	1	0
+185	185	1.601	1	0
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+187	187	1.878	1	0
+188	188	1.576	1	0
+189	189	1.628	1	0
+190	190	2.133	1	0
+191	191	1.625	1	0
+192	192	1.242	1	0
+193	193	2.019	1	0
+194	194	1.420	1	0
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+197	197	0.830	1	0
+198	198	0.293	1	0
+199	199	0.719	1	0
+200	200	0.716	1	0
+201	201	1.120	1	0
+202	202	1.382	1	0
+203	203	1.526	1	0
+204	204	1.707	1	0
+205	205	1.506	1	0
+206	206	1.575	1	0
+207	207	1.793	1	0
+208	208	2.088	1	0
+209	209	1.544	1	0
+210	210	1.530	1	0
+211	211	2.251	1	0
+212	212	2.337	1	0
+213	213	1.939	1	0
+214	214	1.957	1	0
+215	215	2.500	1	0
+216	216	2.417	1	0
+217	217	2.399	1	0
+218	218	2.101	1	0
+219	219	1.893	1	0
+220	220	1.403	1	0
+221	221	0.995	1	0
+222	222	0.769	1	0
+223	223	0.550	1	0
+224	224	0.584	1	0
+225	225	0.904	1	0
+226	226	0.976	1	0
+227	227	1.742	1	0
+228	228	1.710	1	0
+229	229	1.673	1	0
+230	230	2.296	1	0
+231	231	2.917	1	0
+232	232	3.027	0	1
+233	233	2.554	1	0
+234	234	2.713	1	0
+235	235	3.654	0	1
+236	236	2.718	1	0
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+239	239	2.160	1	0
+240	240	1.975	1	0
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+242	242	1.264	1	0
+243	243	0.882	1	0
+244	244	0.763	1	0
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+273	273	1.475	1	0
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+275	275	1.024	1	0
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+289	289	0.978	1	0
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+291	291	0.868	1	0
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+295	295	1.099	1	0
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+301	301	0.622	1	0
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+303	303	1.219	1	0
+304	304	0.874	1	0
+305	305	0.938	1	0
+306	306	0.920	1	0
+307	307	1.270	1	0
+308	308	1.014	1	0
+309	309	0.651	1	0
+310	310	0.925	1	0
+311	311	0.636	1	0
+312	312	0.704	1	0
+313	313	0.724	1	0
+314	314	0.788	1	0
+315	315	1.081	1	0
+316	316	1.065	1	0
+317	317	0.820	1	0
+318	318	0.797	1	0
+319	319	1.028	1	0
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+321	321	0.665	1	0
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+323	323	0.911	1	0
+324	324	0.833	1	0
+325	325	1.395	1	0
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+327	327	0.917	1	0
+328	328	0.790	1	0
+329	329	0.913	1	0
+330	330	0.912	1	0
+331	331	0.423	1	0
+332	332	0.624	1	0
+333	333	0.714	1	0
+334	334	1.068	1	0
+335	335	1.387	1	0
+336	336	1.520	1	0
+337	337	2.089	1	0
+338	338	1.998	1	0
+339	339	1.418	1	0
+340	340	0.653	1	0
+341	341	0.723	1	0
+342	342	0.723	1	0
+343	343	0.535	1	0
+344	344	0.946	1	0

bench/main_benchmark/annotations/SFB_AL_MBP_1OMPA_1ANFA/state_region_BLIND_proxy.tsv

@@ -0,0 +1,374 @@
+# CASE-BLIND proxy. To be filled in wave 2 by FrustrAI-Seq (query-only) and MSA column variance.
+# fi_top25: 1 if residue is in top-25% per-residue FI (placeholder = 0 here)
+# msa_var_top25: 1 if residue is in top-25% MSA column variance (placeholder = 0 here)
+residue_index_query	fi_top25	msa_var_top25
+1	0	0
+2	1	0
+3	1	0
+4	1	0
+5	0	0
+6	0	0
+7	1	0
+8	1	0
+9	1	0
+10	0	0
+11	1	1
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+19	0	0
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+370	0	0

bench/main_benchmark/annotations/SFB_AL_MBP_1OMPA_1ANFA/state_region_FINAL.tsv

@@ -0,0 +1,374 @@
+# ORACLE annotation. DO NOT use as feature input. Evaluator only.
+# common_core: residues with CA in both states AND |displacement| < 3.0 A (after iterative Kabsch w/ outlier trimming)
+# switch_region_3A: residues with CA in both states AND |displacement| >= 3.0 A
+residue_index_query	resnum_state_A	displacement_A	common_core	switch_region_3A
+1	1	12.199	0	1
+2	2	13.947	0	1
+3	3	14.859	0	1
+4	4	17.253	0	1
+5	5	16.667	0	1
+6	6	15.431	0	1
+7	7	13.325	0	1
+8	8	12.734	0	1
+9	9	10.782	0	1
+10	10	9.919	0	1
+11	11	8.593	0	1
+12	12	8.748	0	1
+13	13	10.479	0	1
+14	14	8.993	0	1
+15	15	7.732	0	1
+16	16	8.530	0	1
+17	17	10.068	0	1
+18	18	11.180	0	1
+19	19	9.803	0	1
+20	20	9.970	0	1
+21	21	12.059	0	1
+22	22	12.220	0	1
+23	23	11.702	0	1
+24	24	12.847	0	1
+25	25	14.343	0	1
+26	26	14.109	0	1
+27	27	14.143	0	1
+28	28	15.673	0	1
+29	29	17.591	0	1
+30	30	17.393	0	1
+31	31	17.064	0	1
+32	32	17.802	0	1
+33	33	16.326	0	1
+34	34	15.775	0	1
+35	35	14.066	0	1
+36	36	13.937	0	1
+37	37	12.191	0	1
+38	38	12.189	0	1
+39	39	11.210	0	1
+40	40	12.079	0	1
+41	41	12.111	0	1
+42	42	10.479	0	1
+43	43	9.750	0	1
+44	44	7.925	0	1
+45	45	8.961	0	1
+46	46	10.412	0	1
+47	47	8.949	0	1
+48	48	7.869	0	1
+49	49	10.229	0	1
+50	50	11.439	0	1
+51	51	9.926	0	1
+52	52	9.403	0	1
+53	53	11.621	0	1
+54	54	11.540	0	1
+55	55	11.813	0	1
+56	56	11.559	0	1
+57	57	11.265	0	1
+58	58	11.057	0	1
+59	59	9.188	0	1
+60	60	7.731	0	1
+61	61	6.416	0	1
+62	62	5.141	0	1
+63	63	3.286	0	1
+64	64	2.070	1	0
+65	65	2.313	1	0
+66	66	3.410	0	1
+67	67	2.894	1	0
+68	68	1.325	1	0
+69	69	2.819	1	0
+70	70	4.357	0	1
+71	71	3.863	0	1
+72	72	2.845	1	0
+73	73	5.255	0	1
+74	74	6.259	0	1
+75	75	6.904	0	1
+76	76	6.745	0	1
+77	77	7.797	0	1
+78	78	7.390	0	1
+79	79	8.417	0	1
+80	80	9.541	0	1
+81	81	9.420	0	1
+82	82	10.755	0	1
+83	83	10.693	0	1
+84	84	11.368	0	1
+85	85	9.917	0	1
+86	86	8.787	0	1
+87	87	9.413	0	1
+88	88	8.125	0	1
+89	89	6.315	0	1
+90	90	5.783	0	1
+91	91	6.578	0	1
+92	92	4.884	0	1
+93	93	3.793	0	1
+94	94	5.177	0	1
+95	95	4.552	0	1
+96	96	1.954	1	0
+97	97	2.858	1	0
+98	98	3.711	0	1
+99	99	2.659	1	0
+100	100	4.171	0	1
+101	101	5.392	0	1
+102	102	5.606	0	1
+103	103	5.747	0	1
+104	104	5.235	0	1
+105	105	5.278	0	1
+106	106	5.720	0	1
+107	107	4.026	0	1
+108	108	3.848	0	1
+109	109	1.764	1	0
+110	110	0.371	1	0
+111	111	0.506	1	0
+112	112	1.029	1	0
+113	113	0.802	1	0
+114	114	0.701	1	0
+115	115	0.525	1	0
+116	116	0.521	1	0
+117	117	0.450	1	0
+118	118	0.237	1	0
+119	119	0.390	1	0
+120	120	0.346	1	0
+121	121	0.445	1	0
+122	122	0.203	1	0
+123	123	1.088	1	0
+124	124	0.757	1	0
+125	125	0.589	1	0
+126	126	0.683	1	0
+127	127	0.778	1	0
+128	128	0.687	1	0
+129	129	0.402	1	0
+130	130	0.580	1	0
+131	131	0.655	1	0
+132	132	0.372	1	0
+133	133	0.426	1	0
+134	134	0.626	1	0
+135	135	0.594	1	0
+136	136	0.628	1	0
+137	137	0.678	1	0
+138	138	1.041	1	0
+139	139	0.847	1	0
+140	140	1.025	1	0
+141	141	1.650	1	0
+142	142	0.912	1	0
+143	143	0.949	1	0
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+175	175	2.038	1	0
+176	176	1.379	1	0
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+179	179	0.675	1	0
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+200	200	0.374	1	0
+201	201	0.575	1	0
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+205	205	0.747	1	0
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+213	213	0.668	1	0
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+215	215	0.385	1	0
+216	216	0.390	1	0
+217	217	0.194	1	0
+218	218	0.511	1	0
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bench/main_benchmark/annotations/SFB_AL_MEK1_3EQIA_3MBLA/state_region_BLIND_proxy.tsv

@@ -0,0 +1,319 @@
+# CASE-BLIND proxy. To be filled in wave 2 by FrustrAI-Seq (query-only) and MSA column variance.
+# fi_top25: 1 if residue is in top-25% per-residue FI (placeholder = 0 here)
+# msa_var_top25: 1 if residue is in top-25% MSA column variance (placeholder = 0 here)
+residue_index_query	fi_top25	msa_var_top25
+1	0	0
+2	0	0
+3	0	0
+4	1	0
+5	1	0
+6	1	0
+7	0	0
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bench/main_benchmark/annotations/SFB_AL_MEK1_3EQIA_3MBLA/state_region_FINAL.tsv

@@ -0,0 +1,294 @@
+# ORACLE annotation. DO NOT use as feature input. Evaluator only.
+# common_core: residues with CA in both states AND |displacement| < 3.0 A (after iterative Kabsch w/ outlier trimming)
+# switch_region_3A: residues with CA in both states AND |displacement| >= 3.0 A
+residue_index_query	resnum_state_A	displacement_A	common_core	switch_region_3A
+23	61	0.747	1	0
+24	62	0.809	1	0
+25	63	0.729	1	0
+26	64	0.618	1	0
+27	65	0.274	1	0
+28	66	0.446	1	0
+29	67	0.447	1	0
+30	68	0.354	1	0
+31	69	0.543	1	0
+32	70	0.639	1	0
+33	71	0.678	1	0
+34	72	0.575	1	0
+35	73	0.504	1	0
+36	74	0.438	1	0
+37	75	0.824	1	0
+38	76	0.396	1	0
+39	77	0.608	1	0
+40	78	1.555	1	0
+41	79	2.199	1	0
+42	80	0.571	1	0
+43	81	0.269	1	0
+44	82	0.192	1	0
+45	83	0.461	1	0
+46	84	0.527	1	0
+47	85	0.418	1	0
+48	86	0.444	1	0
+49	87	0.169	1	0
+50	88	0.183	1	0
+51	89	0.206	1	0
+52	90	0.344	1	0
+53	91	0.330	1	0
+54	92	0.627	1	0
+55	93	0.601	1	0
+56	94	0.365	1	0
+57	95	0.235	1	0
+58	96	0.103	1	0
+59	97	0.228	1	0
+60	98	0.639	1	0
+61	99	0.846	1	0
+62	100	1.285	1	0
+63	101	1.728	1	0
+64	102	2.805	1	0
+65	103	2.248	1	0
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+67	105	1.595	1	0
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+314	381	1.416	1	0

bench/main_benchmark/annotations/SFB_AL_PHOB_1B00A_1ZESA/state_region_BLIND_proxy.tsv

@@ -0,0 +1,126 @@
+# CASE-BLIND proxy. To be filled in wave 2 by FrustrAI-Seq (query-only) and MSA column variance.
+# fi_top25: 1 if residue is in top-25% per-residue FI (placeholder = 0 here)
+# msa_var_top25: 1 if residue is in top-25% MSA column variance (placeholder = 0 here)
+residue_index_query	fi_top25	msa_var_top25
+1	0	0
+2	0	0
+3	0	0
+4	1	0
+5	1	0
+6	1	0
+7	1	0
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bench/main_benchmark/annotations/SFB_AL_PHOB_1B00A_1ZESA/state_region_FINAL.tsv

@@ -0,0 +1,125 @@
+# ORACLE annotation. DO NOT use as feature input. Evaluator only.
+# common_core: residues with CA in both states AND |displacement| < 3.0 A (after iterative Kabsch w/ outlier trimming)
+# switch_region_3A: residues with CA in both states AND |displacement| >= 3.0 A
+residue_index_query	resnum_state_A	displacement_A	common_core	switch_region_3A
+2	3	0.815	1	0
+3	4	0.514	1	0
+4	5	0.296	1	0
+5	6	0.414	1	0
+6	7	0.402	1	0
+7	8	0.396	1	0
+8	9	0.516	1	0
+9	10	0.659	1	0
+10	11	0.627	1	0
+11	12	1.270	1	0
+12	13	1.323	1	0
+13	14	0.622	1	0
+14	15	0.466	1	0
+15	16	0.972	1	0
+16	17	1.016	1	0
+17	18	0.445	1	0
+18	19	0.376	1	0
+19	20	0.455	1	0
+20	21	0.357	1	0
+21	22	0.402	1	0
+22	23	0.364	1	0
+23	24	0.745	1	0
+24	25	0.924	1	0
+25	26	1.087	1	0
+26	27	0.364	1	0
+27	28	0.170	1	0
+28	29	0.425	1	0
+29	30	0.399	1	0
+30	31	0.414	1	0
+31	32	0.407	1	0
+32	33	0.293	1	0
+33	34	0.111	1	0
+34	35	0.192	1	0
+35	36	0.141	1	0
+36	37	0.307	1	0
+37	38	0.458	1	0
+38	39	0.519	1	0
+39	40	0.726	1	0
+40	41	0.851	1	0
+41	42	1.438	1	0
+42	43	1.197	1	0
+43	44	0.766	1	0
+44	45	0.104	1	0
+45	46	0.581	1	0
+46	47	0.758	1	0
+47	48	0.664	1	0
+48	49	0.371	1	0
+49	50	0.450	1	0
+50	51	0.637	1	0
+51	52	0.706	1	0
+52	53	0.353	1	0
+53	54	0.666	1	0
+54	55	0.690	1	0
+55	56	1.452	1	0
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+57	58	0.825	1	0
+58	59	0.705	1	0
+59	60	2.619	1	0
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+61	62	1.847	1	0
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+63	64	1.031	1	0
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+67	68	1.126	1	0
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+83	84	1.601	1	0
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+87	88	7.027	0	1
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+89	90	5.215	0	1
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+91	92	5.297	0	1
+92	93	4.562	0	1
+93	94	6.960	0	1
+94	95	7.094	0	1
+95	96	3.865	0	1
+96	97	2.395	1	0
+97	98	1.606	1	0
+98	99	0.992	1	0
+99	100	0.963	1	0
+100	101	0.482	1	0
+101	102	0.832	1	0
+102	103	1.249	1	0
+103	104	1.456	1	0
+104	105	1.216	1	0
+105	106	1.952	1	0
+106	107	2.260	1	0
+107	108	1.151	1	0
+108	109	0.812	1	0
+109	110	0.368	1	0
+110	111	0.832	1	0
+111	112	0.967	1	0
+112	113	0.669	1	0
+113	114	0.329	1	0
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+115	116	0.374	1	0
+116	117	0.423	1	0
+117	118	0.346	1	0
+118	119	0.663	1	0
+119	120	1.050	1	0
+120	121	1.044	1	0
+121	122	1.388	1	0
+122	123	3.697	0	1

bench/main_benchmark/annotations/SFB_AL_PKA_1ATPE_2CPKE/state_region_BLIND_proxy.tsv

@@ -0,0 +1,338 @@
+# CASE-BLIND proxy. To be filled in wave 2 by FrustrAI-Seq (query-only) and MSA column variance.
+# fi_top25: 1 if residue is in top-25% per-residue FI (placeholder = 0 here)
+# msa_var_top25: 1 if residue is in top-25% MSA column variance (placeholder = 0 here)
+residue_index_query	fi_top25	msa_var_top25
+1	0	0
+2	0	0
+3	0	0
+4	0	0
+5	1	0
+6	0	0
+7	1	0
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bench/main_benchmark/annotations/SFB_AL_PKA_1ATPE_2CPKE/state_region_FINAL.tsv

@@ -0,0 +1,337 @@
+# ORACLE annotation. DO NOT use as feature input. Evaluator only.
+# common_core: residues with CA in both states AND |displacement| < 3.0 A (after iterative Kabsch w/ outlier trimming)
+# switch_region_3A: residues with CA in both states AND |displacement| >= 3.0 A
+residue_index_query	resnum_state_A	displacement_A	common_core	switch_region_3A
+1	15	0.790	1	0
+2	16	0.588	1	0
+3	17	0.596	1	0
+4	18	0.564	1	0
+5	19	0.162	1	0
+6	20	0.453	1	0
+7	21	0.186	1	0
+8	22	0.323	1	0
+9	23	0.252	1	0
+10	24	0.229	1	0
+11	25	0.347	1	0
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+13	27	0.289	1	0
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bench/main_benchmark/annotations/SFB_AL_RAS_4Q21A_5P21A/state_region_BLIND_proxy.tsv

@@ -0,0 +1,173 @@
+# CASE-BLIND proxy. To be filled in wave 2 by FrustrAI-Seq (query-only) and MSA column variance.
+# fi_top25: 1 if residue is in top-25% per-residue FI (placeholder = 0 here)
+# msa_var_top25: 1 if residue is in top-25% MSA column variance (placeholder = 0 here)
+residue_index_query	fi_top25	msa_var_top25
+1	0	0
+2	0	0
+3	0	0
+4	0	0
+5	0	0
+6	1	0
+7	1	0
+8	1	0
+9	1	0
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+11	0	0
+12	0	0
+13	0	0
+14	1	0
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+169	0	0

bench/main_benchmark/annotations/SFB_AL_RAS_4Q21A_5P21A/state_region_FINAL.tsv

@@ -0,0 +1,170 @@
+# ORACLE annotation. DO NOT use as feature input. Evaluator only.
+# common_core: residues with CA in both states AND |displacement| < 3.0 A (after iterative Kabsch w/ outlier trimming)
+# switch_region_3A: residues with CA in both states AND |displacement| >= 3.0 A
+residue_index_query	resnum_state_A	displacement_A	common_core	switch_region_3A
+1	1	2.630	1	0
+2	2	1.381	1	0
+3	3	0.446	1	0
+4	4	0.197	1	0
+5	5	0.163	1	0
+6	6	0.308	1	0
+7	7	0.371	1	0
+8	8	0.158	1	0
+9	9	0.243	1	0
+10	10	0.276	1	0
+11	11	0.388	1	0
+12	12	0.688	1	0
+13	13	0.445	1	0
+14	14	0.372	1	0
+15	15	0.584	1	0
+16	16	0.271	1	0
+17	17	0.420	1	0
+18	18	0.125	1	0
+19	19	0.251	1	0
+20	20	0.401	1	0
+21	21	0.340	1	0
+22	22	0.447	1	0
+23	23	0.433	1	0
+24	24	0.575	1	0
+25	25	0.453	1	0
+26	26	0.663	1	0
+27	27	0.376	1	0
+28	28	0.459	1	0
+29	29	0.700	1	0
+30	30	1.638	1	0
+31	31	1.499	1	0
+32	32	5.077	0	1
+33	33	1.663	1	0
+34	34	0.765	1	0
+35	35	2.970	1	0
+36	36	3.270	0	1
+37	37	1.347	1	0
+38	38	0.332	1	0
+39	39	0.649	1	0
+40	40	0.499	1	0
+41	41	1.146	1	0
+42	42	1.763	1	0
+43	43	1.740	1	0
+44	44	1.531	1	0
+45	45	1.291	1	0
+46	46	1.230	1	0
+47	47	1.201	1	0
+48	48	1.188	1	0
+49	49	0.852	1	0
+50	50	1.091	1	0
+51	51	1.612	1	0
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+54	54	0.341	1	0
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+57	57	0.365	1	0
+58	58	0.285	1	0
+59	59	0.755	1	0
+60	60	5.048	0	1
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+62	62	2.620	1	0
+63	63	2.776	1	0
+64	64	3.707	0	1
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+86	86	0.453	1	0
+87	87	0.265	1	0
+88	88	0.329	1	0
+89	89	0.377	1	0
+90	90	0.349	1	0
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+93	93	0.518	1	0
+94	94	0.561	1	0
+95	95	0.474	1	0
+96	96	0.493	1	0
+97	97	0.330	1	0
+98	98	0.595	1	0
+99	99	0.853	1	0
+100	100	0.704	1	0
+101	101	0.793	1	0
+102	102	1.053	1	0
+103	103	0.802	1	0
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+163	163	0.310	1	0
+164	164	0.461	1	0
+165	165	0.568	1	0
+166	166	0.564	1	0

bench/main_benchmark/annotations/SFB_AL_RBP_1URPA_2DRIA/state_region_BLIND_proxy.tsv

@@ -0,0 +1,275 @@
+# CASE-BLIND proxy. To be filled in wave 2 by FrustrAI-Seq (query-only) and MSA column variance.
+# fi_top25: 1 if residue is in top-25% per-residue FI (placeholder = 0 here)
+# msa_var_top25: 1 if residue is in top-25% MSA column variance (placeholder = 0 here)
+residue_index_query	fi_top25	msa_var_top25
+1	0	0
+2	0	0
+3	0	0
+4	1	0
+5	0	0
+6	1	0
+7	1	0
+8	1	1
+9	0	1
+10	0	0
+11	0	0
+12	0	1
+13	0	0
+14	0	0
+15	0	0
+16	0	0
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+18	0	1
+19	1	0
+20	0	1
+21	0	1
+22	0	0
+23	0	0
+24	0	0
+25	0	1
+26	0	0
+27	0	0
+28	0	0
+29	0	0
+30	1	1
+31	0	0
+32	0	0
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+34	1	0
+35	1	1
+36	1	0
+37	1	1
+38	0	0
+39	0	0
+40	0	0
+41	0	1
+42	0	0
+43	0	1
+44	0	0
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+118	0	0
+119	0	1
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+121	0	0
+122	0	0
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+124	0	0
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bench/main_benchmark/annotations/SFB_AL_RBP_1URPA_2DRIA/state_region_FINAL.tsv

@@ -0,0 +1,275 @@
+# ORACLE annotation. DO NOT use as feature input. Evaluator only.
+# common_core: residues with CA in both states AND |displacement| < 3.0 A (after iterative Kabsch w/ outlier trimming)
+# switch_region_3A: residues with CA in both states AND |displacement| >= 3.0 A
+residue_index_query	resnum_state_A	displacement_A	common_core	switch_region_3A
+1	1	16.083	0	1
+2	2	13.866	0	1
+3	3	12.853	0	1
+4	4	10.535	0	1
+5	5	9.936	0	1
+6	6	8.507	0	1
+7	7	8.606	0	1
+8	8	8.377	0	1
+9	9	8.810	0	1
+10	10	10.118	0	1
+11	11	10.586	0	1
+12	12	11.145	0	1
+13	13	8.932	0	1
+14	14	7.682	0	1
+15	15	5.494	0	1
+16	16	6.499	0	1
+17	17	8.136	0	1
+18	18	6.566	0	1
+19	19	5.528	0	1
+20	20	7.878	0	1
+21	21	8.634	0	1
+22	22	7.399	0	1
+23	23	7.889	0	1
+24	24	10.282	0	1
+25	25	10.661	0	1
+26	26	10.178	0	1
+27	27	11.314	0	1
+28	28	13.256	0	1
+29	29	13.217	0	1
+30	30	13.179	0	1
+31	31	14.823	0	1
+32	32	13.157	0	1
+33	33	13.581	0	1
+34	34	11.892	0	1
+35	35	12.354	0	1
+36	36	11.466	0	1
+37	37	11.688	0	1
+38	38	11.786	0	1
+39	39	11.461	0	1
+40	40	12.713	0	1
+41	41	11.719	0	1
+42	42	12.492	0	1
+43	43	11.301	0	1
+44	44	13.002	0	1
+45	45	13.167	0	1
+46	46	10.601	0	1
+47	47	10.455	0	1
+48	48	12.531	0	1
+49	49	11.699	0	1
+50	50	9.654	0	1
+51	51	11.130	0	1
+52	52	12.785	0	1
+53	53	11.311	0	1
+54	54	10.072	0	1
+55	55	11.479	0	1
+56	56	13.108	0	1
+57	57	11.737	0	1
+58	58	10.865	0	1
+59	59	10.060	0	1
+60	60	7.968	0	1
+61	61	6.928	0	1
+62	62	5.957	0	1
+63	63	5.646	0	1
+64	64	5.593	0	1
+65	65	6.496	0	1
+66	66	8.443	0	1
+67	67	8.160	0	1
+68	68	6.532	0	1
+69	69	8.237	0	1
+70	70	9.370	0	1
+71	71	7.336	0	1
+72	72	6.336	0	1
+73	73	7.673	0	1
+74	74	7.465	0	1
+75	75	5.094	0	1
+76	76	5.275	0	1
+77	77	7.221	0	1
+78	78	6.303	0	1
+79	79	4.078	0	1
+80	80	5.493	0	1
+81	81	7.337	0	1
+82	82	6.175	0	1
+83	83	6.716	0	1
+84	84	5.261	0	1
+85	85	3.990	0	1
+86	86	3.230	0	1
+87	87	2.387	1	0
+88	88	2.394	1	0
+89	89	2.138	1	0
+90	90	3.612	0	1
+91	91	3.309	0	1
+92	92	4.099	0	1
+93	93	5.674	0	1
+94	94	5.018	0	1
+95	95	3.126	0	1
+96	96	0.828	1	0
+97	97	0.865	1	0
+98	98	2.759	1	0
+99	99	2.653	1	0
+100	100	1.132	1	0
+101	101	1.409	1	0
+102	102	0.779	1	0
+103	103	1.301	1	0
+104	104	1.273	1	0
+105	105	1.401	1	0
+106	106	1.317	1	0
+107	107	1.199	1	0
+108	108	1.139	1	0
+109	109	1.016	1	0
+110	110	0.979	1	0
+111	111	1.014	1	0
+112	112	0.698	1	0
+113	113	0.526	1	0
+114	114	0.705	1	0
+115	115	0.529	1	0
+116	116	0.269	1	0
+117	117	0.608	1	0
+118	118	0.639	1	0
+119	119	0.368	1	0
+120	120	0.646	1	0
+121	121	0.864	1	0
+122	122	1.205	1	0
+123	123	1.302	1	0
+124	124	0.979	1	0
+125	125	0.985	1	0
+126	126	0.516	1	0
+127	127	0.486	1	0
+128	128	0.406	1	0
+129	129	0.685	1	0
+130	130	0.905	1	0
+131	131	1.344	1	0
+132	132	1.792	1	0
+133	133	1.788	1	0
+134	134	1.501	1	0
+135	135	1.937	1	0
+136	136	2.035	1	0
+137	137	1.856	1	0
+138	138	1.400	1	0
+139	139	1.113	1	0
+140	140	1.375	1	0
+141	141	1.255	1	0
+142	142	1.024	1	0
+143	143	1.049	1	0
+144	144	1.241	1	0
+145	145	0.825	1	0
+146	146	0.834	1	0
+147	147	1.283	1	0
+148	148	1.005	1	0
+149	149	0.860	1	0
+150	150	1.386	1	0
+151	151	1.437	1	0
+152	152	1.320	1	0
+153	153	1.374	1	0
+154	154	0.978	1	0
+155	155	0.934	1	0
+156	156	0.509	1	0
+157	157	0.688	1	0
+158	158	0.456	1	0
+159	159	0.355	1	0
+160	160	0.768	1	0
+161	161	1.191	1	0
+162	162	1.345	1	0
+163	163	1.569	1	0
+164	164	1.547	1	0
+165	165	1.763	1	0
+166	166	1.762	1	0
+167	167	1.850	1	0
+168	168	1.713	1	0
+169	169	1.281	1	0
+170	170	1.478	1	0
+171	171	1.690	1	0
+172	172	1.333	1	0
+173	173	1.130	1	0
+174	174	1.552	1	0
+175	175	1.537	1	0
+176	176	1.240	1	0
+177	177	1.380	1	0
+178	178	1.824	1	0
+179	179	1.062	1	0
+180	180	1.256	1	0
+181	181	1.624	1	0
+182	182	1.576	1	0
+183	183	1.104	1	0
+184	184	0.958	1	0
+185	185	0.405	1	0
+186	186	0.364	1	0
+187	187	0.310	1	0
+188	188	0.556	1	0
+189	189	0.836	1	0
+190	190	1.078	1	0
+191	191	1.056	1	0
+192	192	1.397	1	0
+193	193	1.100	1	0
+194	194	0.822	1	0
+195	195	1.103	1	0
+196	196	1.127	1	0
+197	197	0.916	1	0
+198	198	0.962	1	0
+199	199	1.361	1	0
+200	200	1.331	1	0
+201	201	1.377	1	0
+202	202	2.021	1	0
+203	203	2.266	1	0
+204	204	2.128	1	0
+205	205	2.169	1	0
+206	206	1.669	1	0
+207	207	1.139	1	0
+208	208	1.222	1	0
+209	209	1.028	1	0
+210	210	0.274	1	0
+211	211	0.271	1	0
+212	212	0.294	1	0
+213	213	0.655	1	0
+214	214	0.837	1	0
+215	215	1.193	1	0
+216	216	0.895	1	0
+217	217	1.100	1	0
+218	218	1.154	1	0
+219	219	1.001	1	0
+220	220	0.905	1	0
+221	221	0.687	1	0
+222	222	0.629	1	0
+223	223	0.429	1	0
+224	224	0.384	1	0
+225	225	0.251	1	0
+226	226	0.312	1	0
+227	227	0.393	1	0
+228	228	0.413	1	0
+229	229	0.427	1	0
+230	230	0.253	1	0
+231	231	0.551	1	0
+232	232	0.708	1	0
+233	233	1.059	1	0
+234	234	0.877	1	0
+235	235	0.425	1	0
+236	236	1.679	1	0
+237	237	2.997	1	0
+238	238	4.720	0	1
+239	239	4.424	0	1
+240	240	3.147	0	1
+241	241	5.168	0	1
+242	242	6.560	0	1
+243	243	5.746	0	1
+244	244	5.237	0	1
+245	245	7.330	0	1
+246	246	8.074	0	1
+247	247	6.758	0	1
+248	248	7.287	0	1
+249	249	9.493	0	1
+250	250	9.378	0	1
+251	251	7.905	0	1
+252	252	9.701	0	1
+253	253	11.313	0	1
+254	254	10.116	0	1
+255	255	9.949	0	1
+256	256	8.521	0	1
+257	257	6.909	0	1
+258	258	6.287	0	1
+259	259	4.524	0	1
+260	260	3.525	0	1
+261	261	3.804	0	1
+262	262	3.624	0	1
+263	263	2.437	1	0
+264	264	2.095	1	0
+265	265	0.615	1	0
+266	266	0.785	1	0
+267	267	0.746	1	0
+268	268	0.815	1	0
+269	269	0.482	1	0
+270	270	0.339	1	0
+271	271	1.193	1	0

bench/main_benchmark/annotations/SFB_AL_SRC_2SRCA_1Y57A/state_region_BLIND_proxy.tsv

@@ -0,0 +1,453 @@
+# CASE-BLIND proxy. To be filled in wave 2 by FrustrAI-Seq (query-only) and MSA column variance.
+# fi_top25: 1 if residue is in top-25% per-residue FI (placeholder = 0 here)
+# msa_var_top25: 1 if residue is in top-25% MSA column variance (placeholder = 0 here)
+residue_index_query	fi_top25	msa_var_top25
+1	0	0
+2	0	0
+3	1	0
+4	1	0
+5	0	0
+6	1	0
+7	0	0
+8	0	0
+9	0	0
+10	1	0
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+12	1	0
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+30	0	0
+31	0	0
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+33	0	0
+34	0	0
+35	0	0
+36	0	0
+37	1	1
+38	0	0
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+40	0	0
+41	0	0
+42	0	1
+43	0	0
+44	0	0
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bench/main_benchmark/annotations/SFB_AL_SRC_2SRCA_1Y57A/state_region_FINAL.tsv

@@ -0,0 +1,453 @@
+# ORACLE annotation. DO NOT use as feature input. Evaluator only.
+# common_core: residues with CA in both states AND |displacement| < 3.0 A (after iterative Kabsch w/ outlier trimming)
+# switch_region_3A: residues with CA in both states AND |displacement| >= 3.0 A
+residue_index_query	resnum_state_A	displacement_A	common_core	switch_region_3A
+1	84	12.255	0	1
+2	85	9.624	0	1
+3	86	5.961	0	1
+4	87	4.731	0	1
+5	88	5.407	0	1
+6	89	5.716	0	1
+7	90	9.024	0	1
+8	91	11.588	0	1
+9	92	10.753	0	1
+10	93	13.341	0	1
+11	94	12.643	0	1
+12	95	12.312	0	1
+13	96	11.729	0	1
+14	97	13.602	0	1
+15	98	11.481	0	1
+16	99	9.941	0	1
+17	100	11.133	0	1
+18	101	12.470	0	1
+19	102	11.641	0	1
+20	103	12.291	0	1
+21	104	9.895	0	1
+22	105	8.686	0	1
+23	106	10.160	0	1
+24	107	9.483	0	1
+25	108	9.534	0	1
+26	109	11.222	0	1
+27	110	9.524	0	1
+28	111	10.583	0	1
+29	112	9.685	0	1
+30	113	8.305	0	1
+31	114	9.688	0	1
+32	115	6.835	0	1
+33	116	6.905	0	1
+34	117	3.489	0	1
+35	118	1.933	1	0
+36	119	5.305	0	1
+37	120	8.622	0	1
+38	121	9.665	0	1
+39	122	12.921	0	1
+40	123	13.247	0	1
+41	124	15.286	0	1
+42	125	16.958	0	1
+43	126	18.284	0	1
+44	127	18.455	0	1
+45	128	16.573	0	1
+46	129	14.040	0	1
+47	130	11.079	0	1
+48	131	7.167	0	1
+49	132	4.876	0	1
+50	133	2.366	1	0
+51	134	1.111	1	0
+52	135	4.068	0	1
+53	136	3.966	0	1
+54	137	1.244	1	0
+55	138	1.459	1	0
+56	139	4.817	0	1
+57	140	5.319	0	1
+58	141	5.732	0	1
+59	142	5.268	0	1
+60	143	5.214	0	1
+61	144	4.376	0	1
+62	145	0.782	1	0
+63	146	1.451	1	0
+64	147	5.517	0	1
+65	148	6.545	0	1
+66	149	6.828	0	1
+67	150	10.476	0	1
+68	151	11.680	0	1
+69	152	15.705	0	1
+70	153	17.422	0	1
+71	154	20.712	0	1
+72	155	21.119	0	1
+73	156	23.674	0	1
+74	157	21.639	0	1
+75	158	18.483	0	1
+76	159	20.911	0	1
+77	160	22.946	0	1
+78	161	19.748	0	1
+79	162	18.394	0	1
+80	163	21.919	0	1
+81	164	22.414	0	1
+82	165	25.057	0	1
+83	166	23.022	0	1
+84	167	19.342	0	1
+85	168	18.497	0	1
+86	169	17.225	0	1
+87	170	13.460	0	1
+88	171	13.602	0	1
+89	172	11.347	0	1
+90	173	10.379	0	1
+91	174	9.753	0	1
+92	175	12.531	0	1
+93	176	15.017	0	1
+94	177	18.101	0	1
+95	178	21.395	0	1
+96	179	23.692	0	1
+97	180	22.335	0	1
+98	181	21.893	0	1
+99	182	18.491	0	1
+100	183	17.029	0	1
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+102	185	13.719	0	1
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+104	187	13.970	0	1
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+106	189	16.954	0	1
+107	190	18.524	0	1
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+109	192	23.599	0	1
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+112	195	26.559	0	1
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+118	201	16.649	0	1
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+120	203	15.757	0	1
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+123	206	16.329	0	1
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+136	219	11.167	0	1
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+201	284	25.635	0	1
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+449	533	78.669	0	1

bench/main_benchmark/annotations/SFB_FS_A1AT_1QLPA_1OPHA/state_region_BLIND_proxy.tsv

@@ -0,0 +1,376 @@
+# CASE-BLIND proxy. To be filled in wave 2 by FrustrAI-Seq (query-only) and MSA column variance.
+# fi_top25: 1 if residue is in top-25% per-residue FI (placeholder = 0 here)
+# msa_var_top25: 1 if residue is in top-25% MSA column variance (placeholder = 0 here)
+residue_index_query	fi_top25	msa_var_top25
+1	0	0
+2	0	0
+3	0	0
+4	1	0
+5	0	0
+6	0	1
+7	0	0
+8	1	0
+9	0	0
+10	0	0
+11	1	0
+12	0	0
+13	1	0
+14	0	0
+15	1	0
+16	0	0
+17	0	0
+18	0	1
+19	1	0
+20	0	0
+21	0	1
+22	0	1
+23	0	1
+24	0	1
+25	0	1
+26	0	0
+27	0	0
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+29	0	0
+30	0	0
+31	0	0
+32	0	0
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+49	0	1
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+55	1	1
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bench/main_benchmark/annotations/SFB_FS_A1AT_1QLPA_1OPHA/state_region_FINAL.tsv

@@ -0,0 +1,376 @@
+# ORACLE annotation. DO NOT use as feature input. Evaluator only.
+# common_core: residues with CA in both states AND |displacement| < 3.0 A (after iterative Kabsch w/ outlier trimming)
+# switch_region_3A: residues with CA in both states AND |displacement| >= 3.0 A
+residue_index_query	resnum_state_A	displacement_A	common_core	switch_region_3A
+1	23	3.195	0	1
+2	24	2.956	1	0
+3	25	2.139	1	0
+4	26	1.209	1	0
+5	27	0.662	1	0
+6	28	0.498	1	0
+7	29	0.455	1	0
+8	30	0.366	1	0
+9	31	0.076	1	0
+10	32	0.086	1	0
+11	33	0.071	1	0
+12	34	0.036	1	0
+13	35	0.066	1	0
+14	36	0.281	1	0
+15	37	0.281	1	0
+16	38	0.170	1	0
+17	39	0.034	1	0
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+19	41	0.626	1	0
+20	42	0.582	1	0
+21	43	1.063	1	0
+22	44	1.595	1	0
+23	45	1.622	1	0
+24	46	1.712	1	0
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bench/main_benchmark/annotations/SFB_FS_CLIC1_1K0MA_1K0NA/state_region_BLIND_proxy.tsv

@@ -0,0 +1,239 @@
+# CASE-BLIND proxy. To be filled in wave 2 by FrustrAI-Seq (query-only) and MSA column variance.
+# fi_top25: 1 if residue is in top-25% per-residue FI (placeholder = 0 here)
+# msa_var_top25: 1 if residue is in top-25% MSA column variance (placeholder = 0 here)
+residue_index_query	fi_top25	msa_var_top25
+1	0	0
+2	0	0
+3	1	0
+4	0	0
+5	1	0
+6	1	0
+7	1	0
+8	0	0
+9	0	0
+10	0	0
+11	0	1
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bench/main_benchmark/annotations/SFB_FS_CLIC1_1K0MA_1K0NA/state_region_FINAL.tsv

@@ -0,0 +1,229 @@
+# ORACLE annotation. DO NOT use as feature input. Evaluator only.
+# common_core: residues with CA in both states AND |displacement| < 3.0 A (after iterative Kabsch w/ outlier trimming)
+# switch_region_3A: residues with CA in both states AND |displacement| >= 3.0 A
+residue_index_query	resnum_state_A	displacement_A	common_core	switch_region_3A
+1	6	0.579	1	0
+2	7	0.135	1	0
+3	8	0.088	1	0
+4	9	0.166	1	0
+5	10	0.153	1	0
+6	11	0.191	1	0
+7	12	0.257	1	0
+8	13	0.688	1	0
+9	14	0.319	1	0
+10	15	0.552	1	0
+11	16	0.719	1	0
+12	17	0.349	1	0
+13	18	0.365	1	0
+14	19	0.249	1	0
+15	20	0.380	1	0
+16	21	0.702	1	0
+17	22	0.635	1	0
+18	23	0.407	1	0
+19	24	0.344	1	0
+20	25	0.209	1	0
+21	26	0.164	1	0
+22	27	0.431	1	0
+23	28	0.207	1	0
+24	29	0.197	1	0
+25	30	0.211	1	0
+26	31	0.248	1	0
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+28	33	0.266	1	0
+29	34	0.197	1	0
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+234	239	1.479	1	0
+235	240	1.026	1	0

bench/main_benchmark/annotations/SFB_FS_DLC8_2PG1A_1F3CA/state_region_BLIND_proxy.tsv

@@ -0,0 +1,89 @@
+# CASE-BLIND proxy. To be filled in wave 2 by FrustrAI-Seq (query-only) and MSA column variance.
+# fi_top25: 1 if residue is in top-25% per-residue FI (placeholder = 0 here)
+# msa_var_top25: 1 if residue is in top-25% MSA column variance (placeholder = 0 here)
+residue_index_query	fi_top25	msa_var_top25
+1	0	0
+2	0	0
+3	0	0
+4	1	0
+5	0	0
+6	0	1
+7	0	1
+8	0	0
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+83	0	0
+84	0	0
+85	0	0

bench/main_benchmark/annotations/SFB_FS_DLC8_2PG1A_1F3CA/state_region_FINAL.tsv

@@ -0,0 +1,89 @@
+# ORACLE annotation. DO NOT use as feature input. Evaluator only.
+# common_core: residues with CA in both states AND |displacement| < 3.0 A (after iterative Kabsch w/ outlier trimming)
+# switch_region_3A: residues with CA in both states AND |displacement| >= 3.0 A
+residue_index_query	resnum_state_A	displacement_A	common_core	switch_region_3A
+1	5	3.342	0	1
+2	6	2.044	1	0
+3	7	1.345	1	0
+4	8	1.402	1	0
+5	9	1.004	1	0
+6	10	0.687	1	0
+7	11	0.696	1	0
+8	12	0.993	1	0
+9	13	1.171	1	0
+10	14	1.008	1	0
+11	15	1.145	1	0
+12	16	1.140	1	0
+13	17	0.702	1	0
+14	18	1.163	1	0
+15	19	1.427	1	0
+16	20	0.948	1	0
+17	21	0.556	1	0
+18	22	1.404	1	0
+19	23	1.334	1	0
+20	24	0.972	1	0
+21	25	1.400	1	0
+22	26	1.525	1	0
+23	27	1.445	1	0
+24	28	1.115	1	0
+25	29	0.870	1	0
+26	30	0.907	1	0
+27	31	0.592	1	0
+28	32	0.556	1	0
+29	33	1.783	1	0
+30	34	1.330	1	0
+31	35	1.113	1	0
+32	36	1.109	1	0
+33	37	0.846	1	0
+34	38	0.571	1	0
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+41	45	1.281	1	0
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+43	47	0.754	1	0
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+78	82	0.989	1	0
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+82	86	0.444	1	0
+83	87	0.368	1	0
+84	88	1.430	1	0
+85	89	4.650	0	1

bench/main_benchmark/annotations/SFB_FS_GA98GB98_2LHCA_2LHDA/state_region_BLIND_proxy.tsv

@@ -0,0 +1,60 @@
+# CASE-BLIND proxy. To be filled in wave 2 by FrustrAI-Seq (query-only) and MSA column variance.
+# fi_top25: 1 if residue is in top-25% per-residue FI (placeholder = 0 here)
+# msa_var_top25: 1 if residue is in top-25% MSA column variance (placeholder = 0 here)
+residue_index_query	fi_top25	msa_var_top25
+1	0	0
+2	0	0
+3	0	0
+4	0	0
+5	1	0
+6	1	1
+7	1	1
+8	0	1
+9	1	0
+10	0	1
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+50	0	0
+51	0	0
+52	0	0
+53	0	0
+54	1	0
+55	0	0
+56	0	0

bench/main_benchmark/annotations/SFB_FS_GA98GB98_2LHCA_2LHDA/state_region_FINAL.tsv

@@ -0,0 +1,60 @@
+# ORACLE annotation. DO NOT use as feature input. Evaluator only.
+# common_core: residues with CA in both states AND |displacement| < 3.0 A (after iterative Kabsch w/ outlier trimming)
+# switch_region_3A: residues with CA in both states AND |displacement| >= 3.0 A
+residue_index_query	resnum_state_A	displacement_A	common_core	switch_region_3A
+1	1	27.140	0	1
+2	2	26.366	0	1
+3	3	27.781	0	1
+4	4	23.384	0	1
+5	5	18.083	0	1
+6	6	11.747	0	1
+7	7	8.312	0	1
+8	8	3.004	0	1
+9	9	5.396	0	1
+10	10	8.973	0	1
+11	11	10.805	0	1
+12	12	9.914	0	1
+13	13	8.754	0	1
+14	14	7.010	0	1
+15	15	3.639	0	1
+16	16	4.154	0	1
+17	17	6.026	0	1
+18	18	5.073	0	1
+19	19	3.752	0	1
+20	20	4.325	0	1
+21	21	7.612	0	1
+22	22	8.878	0	1
+23	23	9.122	0	1
+24	24	9.195	0	1
+25	25	4.748	0	1
+26	26	3.334	0	1
+27	27	2.157	1	0
+28	28	1.400	1	0
+29	29	0.548	1	0
+30	30	0.962	1	0
+31	31	0.798	1	0
+32	32	0.326	1	0
+33	33	1.536	1	0
+34	34	1.664	1	0
+35	35	0.178	1	0
+36	36	1.615	1	0
+37	37	3.043	0	1
+38	38	4.974	0	1
+39	39	9.911	0	1
+40	40	16.559	0	1
+41	41	17.834	0	1
+42	42	17.133	0	1
+43	43	17.746	0	1
+44	44	20.958	0	1
+45	45	18.703	0	1
+46	46	17.644	0	1
+47	47	22.240	0	1
+48	48	23.662	0	1
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+50	50	15.508	0	1
+51	51	18.597	0	1
+52	52	19.043	0	1
+53	53	25.026	0	1
+54	54	28.949	0	1
+55	55	32.092	0	1
+56	56	36.460	0	1

bench/main_benchmark/annotations/SFB_FS_IscU_1WFZA_2KQKA/state_region_BLIND_proxy.tsv

@@ -0,0 +1,134 @@
+# CASE-BLIND proxy. To be filled in wave 2 by FrustrAI-Seq (query-only) and MSA column variance.
+# fi_top25: 1 if residue is in top-25% per-residue FI (placeholder = 0 here)
+# msa_var_top25: 1 if residue is in top-25% MSA column variance (placeholder = 0 here)
+residue_index_query	fi_top25	msa_var_top25
+1	0	0
+2	0	0
+3	0	0
+4	0	0
+5	0	0
+6	0	0
+7	0	0
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+130	0	0

bench/main_benchmark/annotations/SFB_FS_IscU_1WFZA_2KQKA/state_region_FINAL.tsv

@@ -0,0 +1,132 @@
+# ORACLE annotation. DO NOT use as feature input. Evaluator only.
+# common_core: residues with CA in both states AND |displacement| < 3.0 A (after iterative Kabsch w/ outlier trimming)
+# switch_region_3A: residues with CA in both states AND |displacement| >= 3.0 A
+residue_index_query	resnum_state_A	displacement_A	common_core	switch_region_3A
+1	1	20.590	0	1
+2	2	16.056	0	1
+3	3	16.976	0	1
+4	4	12.797	0	1
+5	5	13.087	0	1
+6	6	11.118	0	1
+7	7	15.864	0	1
+8	8	18.333	0	1
+9	9	11.837	0	1
+10	10	12.370	0	1
+11	11	9.400	0	1
+12	12	11.849	0	1
+13	13	12.802	0	1
+14	14	9.594	0	1
+15	15	12.879	0	1
+16	16	8.354	0	1
+17	17	10.150	0	1
+18	18	11.742	0	1
+19	19	11.435	0	1
+20	20	9.822	0	1
+21	21	11.761	0	1
+22	22	8.836	0	1
+23	23	8.636	0	1
+24	24	13.777	0	1
+25	25	17.491	0	1
+26	26	18.847	0	1
+27	27	18.931	0	1
+28	28	18.661	0	1
+29	29	18.896	0	1
+30	30	18.964	0	1
+31	31	18.335	0	1
+32	32	17.854	0	1
+33	33	13.940	0	1
+34	34	8.167	0	1
+35	35	5.824	0	1
+36	36	5.745	0	1
+37	37	5.065	0	1
+38	38	7.458	0	1
+39	39	7.318	0	1
+40	40	7.080	0	1
+41	41	7.322	0	1
+42	42	7.598	0	1
+43	43	7.026	0	1
+44	44	7.127	0	1
+45	45	6.957	0	1
+46	46	5.585	0	1
+47	47	4.485	0	1
+48	48	10.503	0	1
+49	49	16.912	0	1
+50	50	18.520	0	1
+51	51	18.820	0	1
+52	52	18.162	0	1
+53	53	17.898	0	1
+54	54	21.175	0	1
+55	55	21.464	0	1
+56	56	20.739	0	1
+57	57	21.665	0	1
+58	58	21.135	0	1
+59	59	20.723	0	1
+60	60	16.243	0	1
+61	61	16.294	0	1
+62	62	10.325	0	1
+63	63	6.939	0	1
+64	64	6.661	0	1
+65	65	8.201	0	1
+66	66	6.551	0	1
+67	67	1.189	1	0
+68	68	2.056	1	0
+69	69	1.284	1	0
+70	70	1.786	1	0
+71	71	2.466	1	0
+72	72	1.586	1	0
+73	73	2.612	1	0
+74	74	3.736	0	1
+75	75	2.746	1	0
+76	76	2.520	1	0
+77	77	1.254	1	0
+78	78	6.164	0	1
+79	79	7.942	0	1
+80	80	6.632	0	1
+81	81	11.259	0	1
+82	82	10.264	0	1
+83	83	11.487	0	1
+84	84	11.747	0	1
+85	85	12.745	0	1
+86	86	15.863	0	1
+87	87	16.924	0	1
+88	88	13.842	0	1
+89	89	12.664	0	1
+90	90	11.553	0	1
+91	91	11.849	0	1
+92	92	12.372	0	1
+93	93	12.347	0	1
+94	94	11.376	0	1
+95	95	12.101	0	1
+96	96	16.742	0	1
+97	97	15.747	0	1
+98	98	14.450	0	1
+99	99	9.229	0	1
+100	100	5.555	0	1
+101	101	5.871	0	1
+102	102	4.518	0	1
+103	103	4.726	0	1
+104	104	2.670	1	0
+105	105	1.877	1	0
+106	106	2.367	1	0
+107	107	2.146	1	0
+108	108	1.520	1	0
+109	109	1.160	1	0
+110	110	1.444	1	0
+111	111	1.874	1	0
+112	112	1.852	1	0
+113	113	1.515	1	0
+114	114	1.747	1	0
+115	115	1.329	1	0
+116	116	1.078	1	0
+117	117	0.952	1	0
+118	118	1.275	1	0
+119	119	1.182	1	0
+120	120	1.776	1	0
+121	121	2.294	1	0
+122	122	2.448	1	0
+123	123	2.675	1	0
+124	124	3.190	0	1
+125	125	8.006	0	1
+126	126	8.426	0	1
+127	127	11.194	0	1
+128	128	16.080	0	1

bench/main_benchmark/annotations/SFB_FS_KAIA_1R8JA_1R8QA/state_region_BLIND_proxy.tsv

@@ -0,0 +1,276 @@
+# CASE-BLIND proxy. To be filled in wave 2 by FrustrAI-Seq (query-only) and MSA column variance.
+# fi_top25: 1 if residue is in top-25% per-residue FI (placeholder = 0 here)
+# msa_var_top25: 1 if residue is in top-25% MSA column variance (placeholder = 0 here)
+residue_index_query	fi_top25	msa_var_top25
+1	0	0
+2	0	0
+3	0	0
+4	0	0
+5	1	0
+6	0	0
+7	1	0
+8	1	0
+9	1	1
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bench/main_benchmark/annotations/SFB_FS_KAIA_1R8JA_1R8QA/state_region_FINAL.tsv

@@ -0,0 +1,173 @@
+# ORACLE annotation. DO NOT use as feature input. Evaluator only.
+# common_core: residues with CA in both states AND |displacement| < 3.0 A (after iterative Kabsch w/ outlier trimming)
+# switch_region_3A: residues with CA in both states AND |displacement| >= 3.0 A
+residue_index_query	resnum_state_A	displacement_A	common_core	switch_region_3A
+2	2	7.829	0	1
+3	3	5.017	0	1
+4	4	5.683	0	1
+5	5	6.573	0	1
+6	6	9.830	0	1
+7	7	17.117	0	1
+8	8	19.502	0	1
+9	9	22.768	0	1
+10	10	28.477	0	1
+11	11	33.733	0	1
+12	12	35.478	0	1
+13	13	40.056	0	1
+14	14	38.099	0	1
+15	15	40.131	0	1
+16	16	35.481	0	1
+17	17	28.688	0	1
+18	18	29.601	0	1
+19	19	27.636	0	1
+20	20	21.962	0	1
+21	21	20.780	0	1
+22	22	21.902	0	1
+23	23	21.357	0	1
+24	24	19.348	0	1
+25	25	23.573	0	1
+26	26	23.197	0	1
+27	27	22.862	0	1
+28	28	19.874	0	1
+29	29	13.330	0	1
+30	30	11.640	0	1
+31	31	7.308	0	1
+32	32	10.844	0	1
+33	33	12.714	0	1
+34	34	12.136	0	1
+35	35	16.478	0	1
+36	36	22.247	0	1
+37	37	22.108	0	1
+38	38	23.197	0	1
+39	39	23.323	0	1
+40	40	20.737	0	1
+41	41	24.378	0	1
+42	42	23.164	0	1
+43	43	19.643	0	1
+44	44	22.604	0	1
+45	45	22.915	0	1
+46	46	22.332	0	1
+47	47	20.894	0	1
+48	48	22.190	0	1
+49	49	25.264	0	1
+50	50	20.656	0	1
+51	51	16.018	0	1
+52	52	16.107	0	1
+53	53	12.989	0	1
+54	54	8.418	0	1
+55	55	11.826	0	1
+56	56	16.470	0	1
+57	57	23.038	0	1
+58	58	28.967	0	1
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+119	125	1.864	1	0
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+123	129	15.470	0	1
+124	130	18.541	0	1
+125	131	17.639	0	1
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+127	133	14.951	0	1
+128	134	13.577	0	1
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+131	137	15.748	0	1
+132	138	14.454	0	1
+133	139	13.100	0	1
+134	140	11.373	0	1
+135	141	4.755	0	1
+136	146	11.237	0	1
+137	147	5.857	0	1
+138	148	1.049	1	0
+139	149	4.570	0	1
+140	150	8.546	0	1
+141	151	4.872	0	1
+142	152	4.603	0	1
+143	153	3.970	0	1
+144	154	1.101	1	0
+145	155	7.771	0	1
+146	156	8.147	0	1
+147	157	8.308	0	1
+148	158	12.226	0	1
+149	159	15.840	0	1
+150	160	11.627	0	1
+151	161	15.706	0	1
+152	162	16.182	0	1
+153	163	10.147	0	1
+154	164	6.145	0	1
+155	165	5.393	0	1
+156	166	10.424	0	1
+157	167	11.273	0	1
+158	168	12.810	0	1
+159	169	19.611	0	1
+160	170	23.040	0	1
+161	171	24.828	0	1
+162	172	25.013	0	1
+163	173	30.807	0	1
+164	174	33.954	0	1
+165	175	31.442	0	1
+166	176	35.598	0	1
+167	177	41.189	0	1
+168	178	40.436	0	1
+169	179	42.522	0	1
+170	180	42.926	0	1

bench/main_benchmark/annotations/SFB_FS_KAIB_2QKEB_5JYTA/state_region_BLIND_proxy.tsv

@@ -0,0 +1,95 @@
+# CASE-BLIND proxy. To be filled in wave 2 by FrustrAI-Seq (query-only) and MSA column variance.
+# fi_top25: 1 if residue is in top-25% per-residue FI (placeholder = 0 here)
+# msa_var_top25: 1 if residue is in top-25% MSA column variance (placeholder = 0 here)
+residue_index_query	fi_top25	msa_var_top25
+1	0	0
+2	0	0
+3	0	0
+4	0	0
+5	1	1
+6	1	0
+7	0	0
+8	1	0
+9	0	0
+10	1	0
+11	0	0
+12	0	0
+13	0	1
+14	0	0
+15	0	0
+16	0	1
+17	0	0
+18	0	1
+19	0	0
+20	0	0
+21	1	0
+22	0	1
+23	0	0
+24	1	0
+25	0	0
+26	0	1
+27	1	0
+28	1	0
+29	0	0
+30	0	1
+31	0	1
+32	0	0
+33	0	1
+34	0	0
+35	1	1
+36	0	0
+37	0	1
+38	1	0
+39	0	0
+40	1	0
+41	1	0
+42	0	0
+43	1	0
+44	0	1
+45	0	0
+46	0	1
+47	0	0
+48	0	1
+49	0	0
+50	0	0
+51	0	1
+52	0	1
+53	0	0
+54	0	0
+55	1	0
+56	0	0
+57	0	0
+58	0	0
+59	0	0
+60	0	0
+61	1	0
+62	0	0
+63	0	0
+64	1	1
+65	0	1
+66	0	0
+67	0	1
+68	0	0
+69	0	1
+70	0	0
+71	0	0
+72	1	0
+73	1	0
+74	0	0
+75	0	0
+76	1	0
+77	0	0
+78	0	0
+79	0	1
+80	0	1
+81	0	0
+82	1	0
+83	0	0
+84	1	1
+85	0	0
+86	1	0
+87	0	0
+88	1	0
+89	0	0
+90	0	0
+91	0	0

bench/main_benchmark/annotations/SFB_FS_KAIB_2QKEB_5JYTA/state_region_FINAL.tsv

@@ -0,0 +1,95 @@
+# ORACLE annotation. DO NOT use as feature input. Evaluator only.
+# common_core: residues with CA in both states AND |displacement| < 3.0 A (after iterative Kabsch w/ outlier trimming)
+# switch_region_3A: residues with CA in both states AND |displacement| >= 3.0 A
+residue_index_query	resnum_state_A	displacement_A	common_core	switch_region_3A
+1	5	12.125	0	1
+2	6	9.521	0	1
+3	7	3.739	0	1
+4	8	1.530	1	0
+5	9	1.645	1	0
+6	10	0.584	1	0
+7	11	0.555	1	0
+8	12	1.187	1	0
+9	13	1.398	1	0
+10	14	2.132	1	0
+11	15	2.753	1	0
+12	16	2.998	1	0
+13	17	2.274	1	0
+14	18	0.816	1	0
+15	19	3.560	0	1
+16	20	5.123	0	1
+17	21	2.949	1	0
+18	22	1.272	1	0
+19	23	3.668	0	1
+20	24	3.505	0	1
+21	25	0.965	1	0
+22	26	1.874	1	0
+23	27	2.710	1	0
+24	28	1.781	1	0
+25	29	0.517	1	0
+26	30	1.420	1	0
+27	31	0.751	1	0
+28	32	0.988	1	0
+29	33	1.829	1	0
+30	34	1.167	1	0
+31	35	1.598	1	0
+32	36	1.284	1	0
+33	37	1.293	1	0
+34	38	0.844	1	0
+35	39	0.857	1	0
+36	40	0.501	1	0
+37	41	2.135	1	0
+38	42	1.902	1	0
+39	43	1.705	1	0
+40	44	1.428	1	0
+41	45	0.905	1	0
+42	46	1.157	1	0
+43	47	0.819	1	0
+44	48	0.566	1	0
+45	49	0.366	1	0
+46	50	0.849	1	0
+47	51	1.254	1	0
+48	52	1.568	1	0
+49	53	1.987	1	0
+50	54	8.987	0	1
+51	55	11.072	0	1
+52	56	9.048	0	1
+53	57	5.888	0	1
+54	58	7.490	0	1
+55	59	5.800	0	1
+56	60	10.182	0	1
+57	61	8.896	0	1
+58	62	9.500	0	1
+59	63	11.944	0	1
+60	64	10.902	0	1
+61	65	7.676	0	1
+62	66	6.395	0	1
+63	67	10.101	0	1
+64	68	11.668	0	1
+65	69	11.721	0	1
+66	70	14.909	0	1
+67	71	19.780	0	1
+68	72	21.350	0	1
+69	73	15.888	0	1
+70	74	11.297	0	1
+71	75	13.188	0	1
+72	76	9.945	0	1
+73	77	6.095	0	1
+74	78	2.550	1	0
+75	79	2.276	1	0
+76	80	4.383	0	1
+77	81	8.729	0	1
+78	82	10.931	0	1
+79	83	13.443	0	1
+80	84	16.147	0	1
+81	85	16.058	0	1
+82	86	15.439	0	1
+83	87	16.900	0	1
+84	88	20.238	0	1
+85	89	14.517	0	1
+86	90	12.833	0	1
+87	91	15.759	0	1
+88	92	13.442	0	1
+89	93	12.411	0	1
+90	94	12.829	0	1
+91	95	19.180	0	1

bench/main_benchmark/annotations/SFB_FS_MAD2_1DUJA_1GO4A/state_region_BLIND_proxy.tsv

@@ -0,0 +1,191 @@
+# CASE-BLIND proxy. To be filled in wave 2 by FrustrAI-Seq (query-only) and MSA column variance.
+# fi_top25: 1 if residue is in top-25% per-residue FI (placeholder = 0 here)
+# msa_var_top25: 1 if residue is in top-25% MSA column variance (placeholder = 0 here)
+residue_index_query	fi_top25	msa_var_top25
+1	0	0
+2	0	0
+3	1	0
+4	0	0
+5	1	0
+6	0	0
+7	0	0
+8	0	0
+9	0	0
+10	0	1
+11	1	0
+12	1	0
+13	0	1
+14	0	0
+15	1	0
+16	1	0
+17	0	1
+18	1	0
+19	0	0
+20	1	0
+21	0	0
+22	0	0
+23	1	0
+24	0	0
+25	0	0
+26	0	0
+27	0	0
+28	0	0
+29	1	0
+30	0	0
+31	0	0
+32	0	0
+33	0	0
+34	0	0
+35	0	0
+36	0	1
+37	0	1
+38	1	0
+39	0	0
+40	0	0
+41	0	0
+42	0	0
+43	1	0
+44	0	0
+45	1	0
+46	1	0
+47	1	0
+48	0	0
+49	0	1
+50	0	0
+51	0	0
+52	0	1
+53	1	0
+54	1	0
+55	0	1
+56	0	0
+57	1	0
+58	0	1
+59	0	1
+60	1	0
+61	1	0
+62	0	1
+63	0	0
+64	1	0
+65	0	1
+66	0	1
+67	0	0
+68	1	0
+69	0	1
+70	0	1
+71	1	0
+72	0	1
+73	1	0
+74	0	1
+75	0	0
+76	1	0
+77	1	0
+78	1	0
+79	1	0
+80	1	0
+81	0	1
+82	0	0
+83	0	0
+84	0	0
+85	0	0
+86	0	1
+87	0	0
+88	0	0
+89	0	0
+90	0	0
+91	0	0
+92	0	0
+93	0	0
+94	1	0
+95	0	0
+96	1	0
+97	0	0
+98	1	1
+99	0	1
+100	0	1
+101	0	1
+102	0	1
+103	1	1
+104	0	1
+105	0	1
+106	0	1
+107	0	1
+108	0	1
+109	0	1
+110	0	1
+111	0	0
+112	0	0
+113	0	1
+114	0	0
+115	0	0
+116	1	0
+117	0	0
+118	0	1
+119	0	0
+120	1	0
+121	0	0
+122	0	0
+123	1	0
+124	1	0
+125	0	0
+126	0	0
+127	1	0
+128	0	0
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+130	0	0
+131	1	0
+132	0	0
+133	0	0
+134	1	0
+135	0	0
+136	0	0
+137	0	0
+138	0	0
+139	1	1
+140	0	1
+141	0	0
+142	0	0
+143	1	0
+144	0	0
+145	1	0
+146	1	0
+147	1	0
+148	0	0
+149	0	0
+150	0	0
+151	0	1
+152	0	0
+153	0	1
+154	0	1
+155	0	0
+156	0	0
+157	0	1
+158	0	0
+159	0	0
+160	0	1
+161	0	0
+162	0	0
+163	0	0
+164	0	0
+165	0	1
+166	0	1
+167	0	0
+168	0	1
+169	0	0
+170	0	0
+171	0	0
+172	0	1
+173	1	0
+174	0	0
+175	0	0
+176	0	0
+177	0	0
+178	0	0
+179	0	0
+180	0	0
+181	0	1
+182	1	1
+183	0	0
+184	0	0
+185	0	0
+186	0	0
+187	0	0

bench/main_benchmark/annotations/SFB_FS_MAD2_1DUJA_1GO4A/state_region_FINAL.tsv

@@ -0,0 +1,191 @@
+# ORACLE annotation. DO NOT use as feature input. Evaluator only.
+# common_core: residues with CA in both states AND |displacement| < 3.0 A (after iterative Kabsch w/ outlier trimming)
+# switch_region_3A: residues with CA in both states AND |displacement| >= 3.0 A
+residue_index_query	resnum_state_A	displacement_A	common_core	switch_region_3A
+1	11	28.918	0	1
+2	12	27.105	0	1
+3	13	22.253	0	1
+4	14	20.069	0	1
+5	15	15.615	0	1
+6	16	10.207	0	1
+7	17	10.520	0	1
+8	18	10.005	0	1
+9	19	7.020	0	1
+10	20	5.380	0	1
+11	21	8.158	0	1
+12	22	8.317	0	1
+13	23	6.096	0	1
+14	24	5.761	0	1
+15	25	8.413	0	1
+16	26	8.051	0	1
+17	27	5.760	0	1
+18	28	6.089	0	1
+19	29	7.759	0	1
+20	30	7.634	0	1
+21	31	6.446	0	1
+22	32	6.120	0	1
+23	33	7.160	0	1
+24	34	7.687	0	1
+25	35	7.282	0	1
+26	36	5.998	0	1
+27	37	4.163	0	1
+28	38	4.113	0	1
+29	39	7.715	0	1
+30	40	9.019	0	1
+31	41	8.164	0	1
+32	42	1.738	1	0
+33	43	3.023	0	1
+34	44	3.644	0	1
+35	45	4.889	0	1
+36	46	3.021	0	1
+37	47	3.261	0	1
+38	48	1.964	1	0
+39	49	3.079	0	1
+40	50	4.317	0	1
+41	51	8.371	0	1
+42	52	11.403	0	1
+43	53	9.720	0	1
+44	54	9.918	0	1
+45	55	9.135	0	1
+46	56	9.194	0	1
+47	57	9.433	0	1
+48	58	7.849	0	1
+49	59	7.449	0	1
+50	60	5.856	0	1
+51	61	5.607	0	1
+52	62	3.589	0	1
+53	63	4.282	0	1
+54	64	4.487	0	1
+55	65	4.988	0	1
+56	66	4.360	0	1
+57	67	4.164	0	1
+58	68	5.002	0	1
+59	69	5.179	0	1
+60	70	3.681	0	1
+61	71	4.722	0	1
+62	72	5.490	0	1
+63	73	3.632	0	1
+64	74	4.046	0	1
+65	75	6.433	0	1
+66	76	4.474	0	1
+67	77	4.298	0	1
+68	78	1.988	1	0
+69	79	3.238	0	1
+70	80	8.031	0	1
+71	81	10.643	0	1
+72	82	7.804	0	1
+73	83	7.874	0	1
+74	84	8.542	0	1
+75	85	8.475	0	1
+76	86	8.368	0	1
+77	87	7.398	0	1
+78	88	7.530	0	1
+79	89	7.310	0	1
+80	90	7.698	0	1
+81	91	6.011	0	1
+82	92	5.948	0	1
+83	93	4.730	0	1
+84	94	7.545	0	1
+85	95	7.359	0	1
+86	96	7.460	0	1
+87	97	7.115	0	1
+88	98	7.082	0	1
+89	99	7.218	0	1
+90	100	6.905	0	1
+91	101	6.384	0	1
+92	102	6.700	0	1
+93	103	6.663	0	1
+94	104	6.896	0	1
+95	105	6.556	0	1
+96	106	6.930	0	1
+97	107	7.766	0	1
+98	108	8.999	0	1
+99	109	10.376	0	1
+100	110	8.803	0	1
+101	111	8.780	0	1
+102	112	7.459	0	1
+103	113	3.351	0	1
+104	114	3.604	0	1
+105	115	3.800	0	1
+106	116	1.888	1	0
+107	117	8.098	0	1
+108	118	9.998	0	1
+109	119	7.004	0	1
+110	120	2.129	1	0
+111	121	2.389	1	0
+112	122	4.676	0	1
+113	123	3.443	0	1
+114	124	6.865	0	1
+115	125	9.319	0	1
+116	126	5.266	0	1
+117	127	2.907	1	0
+118	128	7.202	0	1
+119	129	7.426	0	1
+120	130	3.922	0	1
+121	131	3.134	0	1
+122	132	5.863	0	1
+123	133	5.989	0	1
+124	134	4.343	0	1
+125	135	3.144	0	1
+126	136	5.499	0	1
+127	137	6.318	0	1
+128	138	4.676	0	1
+129	139	1.595	1	0
+130	140	5.087	0	1
+131	141	7.953	0	1
+132	142	7.688	0	1
+133	143	5.417	0	1
+134	144	2.461	1	0
+135	145	5.970	0	1
+136	146	7.390	0	1
+137	147	5.956	0	1
+138	148	4.252	0	1
+139	149	3.988	0	1
+140	150	4.803	0	1
+141	151	5.502	0	1
+142	152	5.058	0	1
+143	153	5.087	0	1
+144	154	3.926	0	1
+145	155	4.366	0	1
+146	156	3.970	0	1
+147	157	4.287	0	1
+148	158	6.306	0	1
+149	159	7.765	0	1
+150	160	10.219	0	1
+151	161	9.811	0	1
+152	162	12.641	0	1
+153	163	11.043	0	1
+154	164	11.121	0	1
+155	165	11.282	0	1
+156	166	12.424	0	1
+157	167	8.450	0	1
+158	168	11.665	0	1
+159	169	11.275	0	1
+160	170	12.660	0	1
+161	171	14.335	0	1
+162	172	13.067	0	1
+163	173	15.940	0	1
+164	174	20.081	0	1
+165	175	20.773	0	1
+166	176	25.190	0	1
+167	177	27.087	0	1
+168	178	26.533	0	1
+169	179	29.404	0	1
+170	180	31.987	0	1
+171	181	32.996	0	1
+172	182	32.811	0	1
+173	183	29.899	0	1
+174	184	31.138	0	1
+175	185	28.975	0	1
+176	186	32.019	0	1
+177	187	31.273	0	1
+178	188	28.902	0	1
+179	189	28.790	0	1
+180	190	22.687	0	1
+181	191	18.958	0	1
+182	192	17.280	0	1
+183	193	16.248	0	1
+184	194	17.317	0	1
+185	195	17.951	0	1
+186	196	20.958	0	1
+187	197	22.330	0	1

bench/main_benchmark/annotations/SFB_FS_MPT53_1LU4A_3EMXA/state_region_BLIND_proxy.tsv

@@ -0,0 +1,136 @@
+# CASE-BLIND proxy. To be filled in wave 2 by FrustrAI-Seq + MSA col variance.
+residue_index_query	fi_top25	msa_var_top25
+1	0	0
+2	0	0
+3	0	0
+4	1	0
+5	1	0
+6	0	0
+7	1	0
+8	0	0
+9	0	0
+10	0	1
+11	0	0
+12	1	0
+13	0	0
+14	0	0
+15	0	1
+16	0	1
+17	1	0
+18	0	0
+19	0	0
+20	0	0
+21	0	0
+22	1	0
+23	0	0
+24	0	0
+25	0	0
+26	0	0
+27	0	0
+28	1	0
+29	1	0
+30	0	0
+31	1	0
+32	0	0
+33	0	0
+34	0	0
+35	0	0
+36	1	0
+37	0	0
+38	1	0
+39	1	0
+40	0	0
+41	0	0
+42	0	0
+43	0	0
+44	0	0
+45	0	1
+46	1	0
+47	0	1
+48	0	1
+49	1	0
+50	0	0
+51	0	1
+52	0	1
+53	0	0
+54	0	1
+55	0	0
+56	1	0
+57	0	1
+58	1	0
+59	1	0
+60	0	0
+61	1	0
+62	0	0
+63	0	1
+64	0	1
+65	0	0
+66	0	0
+67	1	1
+68	0	1
+69	0	1
+70	0	0
+71	0	1
+72	0	1
+73	1	0
+74	1	0
+75	0	1
+76	0	1
+77	0	1
+78	0	0
+79	1	0
+80	0	1
+81	1	0
+82	0	0
+83	0	1
+84	1	0
+85	0	1
+86	0	0
+87	0	1
+88	0	0
+89	0	0
+90	1	1
+91	1	0
+92	0	1
+93	0	1
+94	0	1
+95	0	0
+96	0	0
+97	1	0
+98	0	1
+99	0	0
+100	0	0
+101	0	0
+102	0	0
+103	1	0
+104	1	0
+105	1	0
+106	0	0
+107	0	0
+108	0	0
+109	1	0
+110	0	0
+111	0	1
+112	0	0
+113	0	1
+114	0	1
+115	1	0
+116	0	1
+117	0	0
+118	0	0
+119	0	1
+120	0	0
+121	0	0
+122	0	0
+123	0	0
+124	0	0
+125	0	0
+126	0	0
+127	1	0
+128	0	0
+129	0	0
+130	0	0
+131	1	0
+132	0	0
+133	0	0
+134	0	0

bench/main_benchmark/annotations/SFB_FS_MPT53_1LU4A_3EMXA/state_region_FINAL.tsv

@@ -0,0 +1,131 @@
+# ORACLE annotation. DO NOT use as feature input. Evaluator only.
+# NOTE: This case uses POSITIONAL (index-based) CA pairing because
+#       1LU4 uses residue numbering 1001..1134 while 3EMX uses 224..347.
+#       residue_index_query reflects the 1-based query position; resnum_state_A
+#       gives the original 1LU4 residue number.
+# common_core: |displacement| < 3.0 A; switch_region_3A: |displacement| >= 3.0 A
+residue_index_query	resnum_state_A	displacement_A	common_core	switch_region_3A
+1	1001	27.589	0	1
+2	1002	27.947	0	1
+3	1003	32.482	0	1
+4	1004	29.458	0	1
+5	1005	23.283	0	1
+6	1006	25.094	0	1
+7	1007	22.146	0	1
+8	1008	17.679	0	1
+9	1009	10.852	0	1
+10	1010	5.837	0	1
+11	1011	4.731	0	1
+12	1012	8.578	0	1
+13	1013	12.730	0	1
+14	1014	15.733	0	1
+15	1015	12.824	0	1
+16	1016	9.220	0	1
+17	1017	6.969	0	1
+18	1018	8.754	0	1
+19	1019	13.659	0	1
+20	1020	17.701	0	1
+21	1021	21.515	0	1
+22	1022	23.997	0	1
+23	1023	26.473	0	1
+24	1024	26.356	0	1
+25	1025	25.515	0	1
+26	1026	27.450	0	1
+27	1027	23.489	0	1
+28	1028	18.082	0	1
+29	1029	14.686	0	1
+30	1030	17.200	0	1
+31	1031	13.233	0	1
+32	1032	13.764	0	1
+33	1033	12.103	0	1
+34	1034	13.086	0	1
+35	1035	11.413	0	1
+36	1036	8.705	0	1
+37	1037	8.118	0	1
+38	1038	8.667	0	1
+39	1039	7.573	0	1
+40	1040	8.258	0	1
+41	1041	10.097	0	1
+42	1042	7.994	0	1
+43	1043	6.337	0	1
+44	1044	3.460	0	1
+45	1045	5.450	0	1
+46	1046	5.440	0	1
+47	1047	4.597	0	1
+48	1048	6.185	0	1
+49	1049	6.261	0	1
+50	1050	1.607	1	0
+51	1051	8.245	0	1
+52	1052	11.802	0	1
+53	1053	9.106	0	1
+54	1054	7.912	0	1
+55	1055	11.240	0	1
+56	1056	8.453	0	1
+57	1057	4.331	0	1
+58	1058	8.254	0	1
+59	1059	9.291	0	1
+60	1060	12.239	0	1
+61	1061	9.340	0	1
+62	1062	9.282	0	1
+63	1063	8.913	0	1
+64	1064	9.306	0	1
+65	1065	8.786	0	1
+66	1066	7.525	0	1
+67	1067	7.591	0	1
+68	1068	6.778	0	1
+69	1069	5.420	0	1
+70	1070	9.546	0	1
+71	1071	7.218	0	1
+72	1072	5.582	0	1
+73	1073	12.079	0	1
+74	1074	16.286	0	1
+75	1075	18.068	0	1
+76	1076	16.326	0	1
+77	1077	16.890	0	1
+78	1078	22.157	0	1
+79	1079	20.451	0	1
+80	1080	20.225	0	1
+81	1081	22.340	0	1
+82	1082	22.708	0	1
+83	1083	16.869	0	1
+84	1084	16.264	0	1
+85	1085	17.712	0	1
+86	1086	16.102	0	1
+87	1087	15.401	0	1
+88	1088	18.262	0	1
+89	1089	16.130	0	1
+90	1090	23.062	0	1
+91	1091	21.945	0	1
+92	1092	17.472	0	1
+93	1093	19.571	0	1
+94	1094	18.044	0	1
+95	1095	11.599	0	1
+96	1096	9.474	0	1
+97	1097	3.469	0	1
+98	1098	3.612	0	1
+99	1099	9.377	0	1
+100	1100	15.189	0	1
+101	1101	15.462	0	1
+102	1102	13.803	0	1
+103	1103	14.130	0	1
+104	1104	14.229	0	1
+105	1105	15.531	0	1
+106	1106	17.820	0	1
+107	1107	19.318	0	1
+108	1108	25.021	0	1
+109	1109	26.732	0	1
+110	1110	23.166	0	1
+111	1111	18.616	0	1
+112	1112	13.279	0	1
+113	1113	9.082	0	1
+114	1114	7.552	0	1
+115	1115	4.763	0	1
+116	1116	7.130	0	1
+117	1117	12.441	0	1
+118	1118	14.774	0	1
+119	1119	13.970	0	1
+120	1120	16.896	0	1
+121	1121	18.942	0	1
+122	1122	16.869	0	1
+123	1123	21.177	0	1
+124	1124	24.333	0	1

bench/main_benchmark/annotations/SFB_FS_NTRC2_1NY3A_3DZEA/state_region_BLIND_proxy.tsv

@@ -0,0 +1,281 @@
+# CASE-BLIND proxy. To be filled in wave 2 by FrustrAI-Seq (query-only) and MSA column variance.
+# fi_top25: 1 if residue is in top-25% per-residue FI (placeholder = 0 here)
+# msa_var_top25: 1 if residue is in top-25% MSA column variance (placeholder = 0 here)
+residue_index_query	fi_top25	msa_var_top25
+1	0	0
+2	0	0
+3	1	0
+4	0	0
+5	0	0
+6	0	0
+7	1	0
+8	0	0
+9	1	0
+10	0	0
+11	0	0
+12	0	0
+13	0	0
+14	1	0
+15	1	0
+16	0	0
+17	0	0
+18	0	0
+19	0	0
+20	1	1
+21	0	1
+22	0	1
+23	0	1
+24	1	1
+25	1	0
+26	0	0
+27	0	1
+28	0	0
+29	0	1
+30	0	0
+31	0	0
+32	0	1
+33	1	0
+34	1	1
+35	0	0
+36	1	0
+37	0	1
+38	0	1
+39	0	0
+40	1	1
+41	0	0
+42	0	0
+43	0	1
+44	0	1
+45	1	0
+46	0	0
+47	1	0
+48	0	0
+49	0	0
+50	1	0
+51	0	1
+52	0	0
+53	1	1
+54	0	1
+55	0	1
+56	0	1
+57	0	1
+58	0	0
+59	0	0
+60	1	0
+61	0	1
+62	1	0
+63	0	0
+64	0	1
+65	0	0
+66	0	1
+67	0	0
+68	0	1
+69	1	0
+70	0	0
+71	0	0
+72	1	0
+73	1	0
+74	0	0
+75	1	0
+76	1	1
+77	0	0
+78	1	0
+79	0	0
+80	0	0
+81	0	0
+82	0	0
+83	0	0
+84	0	0
+85	0	0
+86	0	1
+87	0	1
+88	1	1
+89	1	0
+90	1	0
+91	1	0
+92	1	0
+93	1	0
+94	0	0
+95	1	0
+96	1	0
+97	0	1
+98	0	0
+99	0	0
+100	0	0
+101	1	0
+102	0	0
+103	0	0
+104	0	0
+105	1	0
+106	0	1
+107	0	1
+108	0	0
+109	0	0
+110	0	1
+111	0	0
+112	0	0
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+114	0	1
+115	1	0
+116	1	0
+117	0	1
+118	0	0
+119	1	0
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+122	0	0
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+149	0	0
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+154	1	0
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+163	0	1
+164	0	0
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