{
  "confidence": {
    "boltz2": "pair_chains_iptm[0][1]; native ligand_iptm retained separately because heme is also a ligand entity",
    "chai1": "per_chain_pair_iptm[0,0,1]",
    "esmfold2": "pair_chains_iptm[0,1]",
    "openfold3": "chain_pair_iptm[(A, L)]",
    "primary_field": "directed protein-to-intended-ligand chain-pair iPTM",
    "protenix_v1": "chain_pair_iptm[0][1]"
  },
  "coordinate_alignment": {
    "aligned_coordinate_root": "structures/predicted",
    "anchor_count": 187,
    "anchor_map": "anchor_map.csv",
    "coordinate_action": "One rigid transform applied to every atom; ligand, heme, pocket fitting, trimming and remapping are excluded.",
    "fit": "proper-rotation Kabsch over frozen C-alpha correspondences",
    "invariant": "cyp3a4_1tqn_conserved_scaffold_ca_v1",
    "numbering": {
      "CYP1A2": "generated index 1 maps to UniProt 27",
      "CYP2C9": "generated index 1 maps to UniProt 30",
      "CYP2D6": "generated index 1 maps to UniProt 34",
      "CYP3A4": "generated index 1 maps to UniProt 30"
    },
    "reference": "1TQN chain A"
  },
  "name": "cyp_cofold_postprocess_20260804",
  "scoring": {
    "add_mdl_contacts": false,
    "class": "ost.mol.alg.ligand_scoring_lddtpli.LDDTPLIScorer",
    "metric": "ost_lddt_pli",
    "model_ligand": "intended crystal-ligand chain only; heme excluded",
    "model_receptor": "generated chain A peptide",
    "no_score_policy": "Retain NO_ASSIGNMENT; no proxy or imputation.",
    "radius_A": 6.0,
    "software": "OpenStructure 2.11.1",
    "substructure_match": false,
    "target_ligand": "manifest-selected CCD copy in author chain A, or the exact governed residue for the 10-system pilot",
    "target_receptor": "truth crystal author chain A peptide",
    "thresholds_A": [
      0.5,
      1.0,
      2.0,
      4.0
    ]
  },
  "selector_analysis": {
    "candidate_counts": {
      "boltz2": 20,
      "chai1": 20,
      "esmfold2": 50,
      "openfold3": 20,
      "protenix_v1": 20
    },
    "metrics": [
      "within-system Spearman rho",
      "top-iPTM uplift over ensemble-mean LDDT-PLI",
      "top-iPTM truth percentile",
      "oracle-minus-selected regret"
    ],
    "passed_only_sensitivity": "method_selector_summary_passed_cells.csv",
    "primary_scope": "complete method-system cells only",
    "uncertainty": "5000 system-level bootstrap replicates; seed 20260804"
  }
}