{
  "summary": {
    "generated_at": "2026-05-17T20:46:12.835Z",
    "source_manifest": "pilot/data/test_set_v1_phase1a.json",
    "source_results": "pilot/data/simplefold3b_phase1a_summary.json",
    "target_count": 8,
    "acceptable_for_operational_viability": 8,
    "biological_interpretation_blocked": 2,
    "by_biological_context_class": {
      "paired_membrane_lipoprotein_control": 2,
      "clean_lipid_transfer_domain": 1,
      "complex_derived_coverage_probe": 1,
      "membrane_complex_stress_case": 1,
      "long_membrane_transport_stress_case": 1,
      "long_enzyme_context": 1,
      "long_enzyme_ligand_context": 1
    },
    "by_review_recommendation": {
      "acceptable_for_operational_viability": 6,
      "acceptable_for_operational_viability_with_coverage_caveat": 1,
      "acceptable_for_operational_viability_with_context_caveat": 1
    },
    "conclusion": "The 8-target Phase 1A set is appropriate for an operational viability benchmark, but biological interpretation must remain caveated. It is intentionally mixed across clean X-ray targets, membrane/transport stress cases, long enzyme contexts, and complex-derived coverage probes."
  },
  "rows": [
    {
      "target_label": "13CZ:A",
      "title": "Crystal structure of DcrB from Salmonella enterica at pH 5.0",
      "entity_description": "Inner membrane lipoprotein DcrB",
      "source_organism": "Salmonella enterica subsp. enterica serovar Typhimurium",
      "length": 161,
      "length_bin": "mid",
      "experimental_method": "X-RAY DIFFRACTION",
      "resolution_angstrom": 2.136,
      "context_flags": "membrane_or_transport_hint",
      "phase1a_role": "mid_bin_repeat_control",
      "biological_context_class": "paired_membrane_lipoprotein_control",
      "review_recommendation": "acceptable_for_operational_viability",
      "interpretation_scope": "operational_viability; pre_freeze_evidence; membrane_stress_case",
      "caveat": "Paired DcrB pH structures are useful controls but should not overweight one protein family in broader claims.",
      "reason_for_inclusion": "Repeat-control anchor for same-target SimpleFold-3B CLI variability.",
      "lddt": 0.8613,
      "tm_score": 0.9224,
      "aligned_residues": 150,
      "peak_memory_gb": 31.99,
      "wall_clock_seconds": 378.916,
      "rcsb_entry_url": "https://www.rcsb.org/structure/13CZ",
      "rcsb_data_api_entry": "https://data.rcsb.org/rest/v1/core/entry/13CZ",
      "rcsb_data_api_instance": "https://data.rcsb.org/rest/v1/core/polymer_entity_instance/13CZ/A"
    },
    {
      "target_label": "13EE:A",
      "title": "Crystal structure of DcrB from Salmonella enterica at pH 4.0",
      "entity_description": "Inner membrane lipoprotein DcrB",
      "source_organism": "Salmonella enterica subsp. enterica serovar Typhimurium",
      "length": 161,
      "length_bin": "mid",
      "experimental_method": "X-RAY DIFFRACTION",
      "resolution_angstrom": 1.729,
      "context_flags": "membrane_or_transport_hint",
      "phase1a_role": "mid_bin_benchmark_slice",
      "biological_context_class": "paired_membrane_lipoprotein_control",
      "review_recommendation": "acceptable_for_operational_viability",
      "interpretation_scope": "operational_viability; pre_freeze_evidence; membrane_stress_case",
      "caveat": "Paired DcrB pH structures are useful controls but should not overweight one protein family in broader claims.",
      "reason_for_inclusion": "Mid-bin DcrB benchmark slice paired with 13CZ under a different pH condition.",
      "lddt": 0.8581707816329163,
      "tm_score": 0.92119,
      "aligned_residues": 148,
      "peak_memory_gb": 38.54290771484375,
      "wall_clock_seconds": 401.635,
      "rcsb_entry_url": "https://www.rcsb.org/structure/13EE",
      "rcsb_data_api_entry": "https://data.rcsb.org/rest/v1/core/entry/13EE",
      "rcsb_data_api_instance": "https://data.rcsb.org/rest/v1/core/polymer_entity_instance/13EE/A"
    },
    {
      "target_label": "13FT:A",
      "title": "START domain of Caenorhabditis elegans StAR-related lipid transfer protein 3 (STARD3)",
      "entity_description": "START domain-containing protein",
      "source_organism": "Caenorhabditis elegans",
      "length": 228,
      "length_bin": "mid",
      "experimental_method": "X-RAY DIFFRACTION",
      "resolution_angstrom": 2.01,
      "context_flags": "none",
      "phase1a_role": "mid_bin_benchmark_slice",
      "biological_context_class": "clean_lipid_transfer_domain",
      "review_recommendation": "acceptable_for_operational_viability",
      "interpretation_scope": "operational_viability; pre_freeze_evidence",
      "caveat": "No major biological caveat beyond single-run computational-benchmark scope.",
      "reason_for_inclusion": "Clean X-ray mid-bin lipid-transfer domain with no context flags.",
      "lddt": 0.8915167765363028,
      "tm_score": 0.95878,
      "aligned_residues": 212,
      "peak_memory_gb": 31.252212524414062,
      "wall_clock_seconds": 390.276,
      "rcsb_entry_url": "https://www.rcsb.org/structure/13FT",
      "rcsb_data_api_entry": "https://data.rcsb.org/rest/v1/core/entry/13FT",
      "rcsb_data_api_instance": "https://data.rcsb.org/rest/v1/core/polymer_entity_instance/13FT/A"
    },
    {
      "target_label": "11BC:C",
      "title": "Human Nap1 in complex with HIV-1 Rev",
      "entity_description": "Protein Rev",
      "source_organism": "Human immunodeficiency virus 1",
      "length": 116,
      "length_bin": "hard",
      "experimental_method": "ELECTRON MICROSCOPY",
      "resolution_angstrom": 3.3,
      "context_flags": "multi_protein_entry; complex_or_fragment_context",
      "phase1a_role": "hard_bin_alignment_coverage_probe",
      "biological_context_class": "complex_derived_coverage_probe",
      "review_recommendation": "acceptable_for_operational_viability_with_coverage_caveat",
      "interpretation_scope": "operational_viability; pre_freeze_evidence; not_biological_generalization; coverage_limited_lddt",
      "caveat": "Only 63 aligned reference residues were scored, so lDDT supports operational/scoring QA but not a full-chain biological-quality claim.",
      "reason_for_inclusion": "Hard-bin alignment-coverage probe exposing complex-derived scoring caveats.",
      "lddt": 0.749159535549332,
      "tm_score": 0.65686,
      "aligned_residues": 63,
      "peak_memory_gb": 41.40596008300781,
      "wall_clock_seconds": 337.455,
      "rcsb_entry_url": "https://www.rcsb.org/structure/11BC",
      "rcsb_data_api_entry": "https://data.rcsb.org/rest/v1/core/entry/11BC",
      "rcsb_data_api_instance": "https://data.rcsb.org/rest/v1/core/polymer_entity_instance/11BC/C"
    },
    {
      "target_label": "12OY:A",
      "title": "Single particle cryo-EM structure of human MTCH2",
      "entity_description": "Mitochondrial carrier homolog 2,Mitochondrial brown fat uncoupling protein 1",
      "source_organism": "Homo sapiens",
      "length": 304,
      "length_bin": "hard",
      "experimental_method": "ELECTRON MICROSCOPY",
      "resolution_angstrom": 3.6,
      "context_flags": "multi_protein_entry; complex_or_fragment_context; membrane_or_transport_hint",
      "phase1a_role": "hard_bin_membrane_context",
      "biological_context_class": "membrane_complex_stress_case",
      "review_recommendation": "acceptable_for_operational_viability_with_context_caveat",
      "interpretation_scope": "operational_viability; prospective_evidence; membrane_stress_case; not_biological_generalization",
      "caveat": "Membrane/complex cryo-EM context and 3.6 A resolution make this a stress case; use for viability, not biological generality.",
      "reason_for_inclusion": "Hard membrane/complex stress case included prospectively after freeze.",
      "lddt": 0.8134924777204056,
      "tm_score": 0.87235,
      "aligned_residues": 285,
      "peak_memory_gb": 33.23228454589844,
      "wall_clock_seconds": 308.066,
      "rcsb_entry_url": "https://www.rcsb.org/structure/12OY",
      "rcsb_data_api_entry": "https://data.rcsb.org/rest/v1/core/entry/12OY",
      "rcsb_data_api_instance": "https://data.rcsb.org/rest/v1/core/polymer_entity_instance/12OY/A"
    },
    {
      "target_label": "9H8N:A",
      "title": "Structure of BmrA T123C-S428C reduced form (apo state)",
      "entity_description": "Multidrug resistance ABC transporter ATP-binding/permease protein BmrA",
      "source_organism": "Bacillus subtilis",
      "length": 604,
      "length_bin": "long",
      "experimental_method": "ELECTRON MICROSCOPY",
      "resolution_angstrom": 3.21,
      "context_flags": "membrane_or_transport_hint",
      "phase1a_role": "long_bin_membrane_transport",
      "biological_context_class": "long_membrane_transport_stress_case",
      "review_recommendation": "acceptable_for_operational_viability",
      "interpretation_scope": "operational_viability; prospective_evidence; membrane_stress_case",
      "caveat": "Long membrane transporter cryo-EM target; strong for memory/runtime stress, cautious for general quality interpretation.",
      "reason_for_inclusion": "Long membrane transport stress target for runtime and memory viability.",
      "lddt": 0.8420449864602215,
      "tm_score": 0.84912,
      "aligned_residues": 568,
      "peak_memory_gb": 34.64080810546875,
      "wall_clock_seconds": 739.974,
      "rcsb_entry_url": "https://www.rcsb.org/structure/9H8N",
      "rcsb_data_api_entry": "https://data.rcsb.org/rest/v1/core/entry/9H8N",
      "rcsb_data_api_instance": "https://data.rcsb.org/rest/v1/core/polymer_entity_instance/9H8N/A"
    },
    {
      "target_label": "9K9X:A",
      "title": "Crystal structure of bicyclogermacrene synthase",
      "entity_description": "Bicyclogermacrene synthase",
      "source_organism": "Phyla dulcis",
      "length": 565,
      "length_bin": "long",
      "experimental_method": "X-RAY DIFFRACTION",
      "resolution_angstrom": 2.03,
      "context_flags": "multi_protein_entry",
      "phase1a_role": "long_bin_enzyme_context",
      "biological_context_class": "long_enzyme_context",
      "review_recommendation": "acceptable_for_operational_viability",
      "interpretation_scope": "operational_viability; prospective_evidence",
      "caveat": "No major biological caveat beyond single-run computational-benchmark scope.",
      "reason_for_inclusion": "Long enzyme context with high-quality X-ray reference.",
      "lddt": 0.8815117469339959,
      "tm_score": 0.94668,
      "aligned_residues": 522,
      "peak_memory_gb": 34.02386474609375,
      "wall_clock_seconds": 713.29,
      "rcsb_entry_url": "https://www.rcsb.org/structure/9K9X",
      "rcsb_data_api_entry": "https://data.rcsb.org/rest/v1/core/entry/9K9X",
      "rcsb_data_api_instance": "https://data.rcsb.org/rest/v1/core/polymer_entity_instance/9K9X/A"
    },
    {
      "target_label": "9K9Y:A",
      "title": "Crystal structure of bicyclogermacrene synthase with FsPP",
      "entity_description": "Bicyclogermacrene synthase",
      "source_organism": "Phyla dulcis",
      "length": 565,
      "length_bin": "long",
      "experimental_method": "X-RAY DIFFRACTION",
      "resolution_angstrom": 2.89,
      "context_flags": "none",
      "phase1a_role": "long_bin_enzyme_ligand_context",
      "biological_context_class": "long_enzyme_ligand_context",
      "review_recommendation": "acceptable_for_operational_viability",
      "interpretation_scope": "operational_viability; prospective_evidence; ligand_context_not_affinity_claim",
      "caveat": "Ligand-bound title is useful context, but this benchmark does not evaluate ligand placement or affinity.",
      "reason_for_inclusion": "Long enzyme ligand-context target paired conceptually with 9K9X, without making ligand claims.",
      "lddt": 0.9156731082367677,
      "tm_score": 0.98263,
      "aligned_residues": 487,
      "peak_memory_gb": 34.12742614746094,
      "wall_clock_seconds": 753.399,
      "rcsb_entry_url": "https://www.rcsb.org/structure/9K9Y",
      "rcsb_data_api_entry": "https://data.rcsb.org/rest/v1/core/entry/9K9Y",
      "rcsb_data_api_instance": "https://data.rcsb.org/rest/v1/core/polymer_entity_instance/9K9Y/A"
    }
  ]
}