{
  "model": "nt",
  "timestamp": "20260714_082334",
  "phase": 6,
  "metric": "perturbation_specificity",
  "preregistration": "PREREGISTRATION_PHASE6_V2.md",
  "offset": 0,
  "seed": 42,
  "tokenizer_caveated": true,
  "results": {
    "per_rna": {
      "5S_rRNA_ecoli": {
        "skipped": true,
        "reason": "< 15 WC pairs (4 found)",
        "n_wc_pairs_total": 4
      },
      "6S_RNA": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "7SK_RNA": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "Bacterial_SRP": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "CRISPR_leader": {
        "skipped": true,
        "reason": "< 15 WC pairs (6 found)",
        "n_wc_pairs_total": 6
      },
      "Corona_5UTR": {
        "best_ps": 0.0,
        "best_layer": 0,
        "per_layer_ps": [
          0.0,
          -7.092952728271484e-06,
          -9.130438168843587e-05,
          -8.483727773030599e-05,
          -8.744001388549805e-05,
          -9.059906005859375e-06,
          -0.00017711520195007324,
          -0.00036781032880147296,
          -0.00016609827677408853,
          -0.00024159749348958334,
          -0.0001392066478729248,
          -0.0002593696117401123,
          -0.00020543734232584635
        ],
        "n_eligible_pairs": 40,
        "n_stems": 16,
        "n_wc_pairs_total": 83,
        "positive_control": {
          "pass": true,
          "p_value": 0.0008384331026261888,
          "mean_stem_delta": 0.029139841881891095,
          "mean_loop_delta": 0.009640845709613391
        },
        "h3_precision": {
          "fraction": 0.0,
          "n": 2,
          "partner_max_count": 0,
          "p_value": 1.0
        },
        "ps_gc_pairs": -1.9868214925130207e-08,
        "ps_au_pairs": 1.9868214925130207e-08,
        "quarantined": false,
        "null_95th_primary": 0.0,
        "null_95th_conservative": 6.1492125193278e-06,
        "null_available": true,
        "exceeds_null_primary": false,
        "exceeds_null_conservative": false
      },
      "Corona_s2m": {
        "skipped": true,
        "reason": "< 15 WC pairs (12 found)",
        "n_wc_pairs_total": 12
      },
      "CrPV_IRES": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "FMN_riboswitch": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "HDV_ribozyme": {
        "skipped": true,
        "reason": "< 15 WC pairs (6 found)",
        "n_wc_pairs_total": 6
      },
      "Hepatitis_C_IRES_III": {
        "best_ps": -5.960464477539063e-08,
        "best_layer": 0,
        "per_layer_ps": [
          -5.960464477539063e-08,
          -2.3990869522094727e-06,
          -5.9410929679870605e-05,
          -0.00010675191879272461,
          -0.0001475512981414795,
          -0.00013718008995056152,
          -0.00023184716701507568,
          -0.00013363361358642578,
          -0.00015813112258911133,
          -0.00022655725479125977,
          -8.021295070648193e-05,
          -0.00022400915622711182,
          -0.0002170354127883911
        ],
        "n_eligible_pairs": 42,
        "n_stems": 19,
        "n_wc_pairs_total": 93,
        "positive_control": {
          "pass": false,
          "p_value": 0.06878623759520149,
          "mean_stem_delta": 0.011011710201484568,
          "mean_loop_delta": 0.019874025687594516
        },
        "h3_precision": {
          "fraction": 0.0,
          "n": 2,
          "partner_max_count": 0,
          "p_value": 1.0
        },
        "ps_gc_pairs": -5.960464477539063e-08,
        "ps_au_pairs": null,
        "quarantined": false,
        "null_95th_primary": -5.960464477539063e-08,
        "null_95th_conservative": 0.00030757486820220947,
        "null_available": true,
        "exceeds_null_primary": false,
        "exceeds_null_conservative": false
      },
      "Histone_3prime": {
        "skipped": true,
        "reason": "< 15 WC pairs (6 found)",
        "n_wc_pairs_total": 6
      },
      "IRES_HCV_domainII": {
        "skipped": true,
        "reason": "< 15 WC pairs (12 found)",
        "n_wc_pairs_total": 12
      },
      "IRE_stem_loop": {
        "skipped": true,
        "reason": "< 15 WC pairs (14 found)",
        "n_wc_pairs_total": 14
      },
      "RNaseP_specificity": {
        "skipped": true,
        "reason": "sequence/dot_bracket length mismatch (94 vs 91)"
      },
      "SAH_riboswitch": {
        "skipped": true,
        "reason": "< 15 WC pairs (13 found)",
        "n_wc_pairs_total": 13
      },
      "SAM_riboswitch": {
        "skipped": true,
        "reason": "< 15 WC pairs (13 found)",
        "n_wc_pairs_total": 13
      },
      "SECIS_element": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "SRP_RNA_helix8": {
        "skipped": true,
        "reason": "< 15 WC pairs (4 found)",
        "n_wc_pairs_total": 4
      },
      "THF_riboswitch": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "TPP_riboswitch": {
        "skipped": true,
        "reason": "< 15 WC pairs (8 found)",
        "n_wc_pairs_total": 8
      },
      "T_box_leader": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "U1_snRNA": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "U2_snRNA_stem": {
        "skipped": true,
        "reason": "< 15 WC pairs (0 found)",
        "n_wc_pairs_total": 0
      },
      "U4_snRNA": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "U5_snRNA": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "U6_snRNA": {
        "skipped": true,
        "reason": "< 15 WC pairs (5 found)",
        "n_wc_pairs_total": 5
      },
      "Vault_RNA": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "Y_RNA": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "ZMP_riboswitch": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "c_di_GMP_riboswitch": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "cobalamin_riboswitch": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "fluoride_riboswitch": {
        "skipped": true,
        "reason": "< 15 WC pairs (8 found)",
        "n_wc_pairs_total": 8
      },
      "glmS_ribozyme": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "glycine_riboswitch": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "group_II_intron_D5": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "group_I_intron_P4P6": {
        "best_ps": 0.005082607269287109,
        "best_layer": 11,
        "per_layer_ps": [
          0.0,
          -9.5367431640625e-07,
          9.5367431640625e-07,
          -7.328391075134277e-05,
          -2.3484230041503906e-05,
          0.0004087686538696289,
          0.0003483593463897705,
          -0.003305494785308838,
          -0.0011810362339019775,
          -0.0008854866027832031,
          0.0031967759132385254,
          0.005082607269287109,
          0.0018053054809570312
        ],
        "n_eligible_pairs": 19,
        "n_stems": 9,
        "n_wc_pairs_total": 43,
        "positive_control": {
          "pass": false,
          "p_value": 0.18650627342216625,
          "mean_stem_delta": 0.015124805738453878,
          "mean_loop_delta": 0.011757048598506993
        },
        "h3_precision": {
          "fraction": 0.0,
          "n": 0,
          "p_value": 1.0
        },
        "ps_gc_pairs": 0.02339911460876465,
        "ps_au_pairs": -0.01323390007019043,
        "quarantined": false,
        "null_95th_primary": 0.0,
        "null_95th_conservative": NaN,
        "null_available": true,
        "exceeds_null_primary": true,
        "exceeds_null_conservative": false
      },
      "hammerhead_ribozyme": {
        "skipped": true,
        "reason": "< 15 WC pairs (0 found)",
        "n_wc_pairs_total": 0
      },
      "hatchet_ribozyme": {
        "best_ps": 0.00045117735862731934,
        "best_layer": 9,
        "per_layer_ps": [
          -8.940696716308594e-08,
          -4.827976226806641e-06,
          -0.00017818808555603027,
          3.9458274841308594e-05,
          2.372264862060547e-05,
          -1.831352710723877e-05,
          -0.00011371076107025146,
          -0.0008329600095748901,
          -0.0004128366708755493,
          0.00045117735862731934,
          -8.347630500793457e-05,
          -0.0005019307136535645,
          -6.0617923736572266e-05
        ],
        "n_eligible_pairs": 14,
        "n_stems": 3,
        "n_wc_pairs_total": 24,
        "positive_control": {
          "pass": false,
          "p_value": 0.2800108721413352,
          "mean_stem_delta": 0.019124814629367607,
          "mean_loop_delta": 0.014719964056224612
        },
        "h3_precision": {
          "fraction": 0.0,
          "n": 2,
          "partner_max_count": 0,
          "p_value": 1.0
        },
        "ps_gc_pairs": -0.001150369644165039,
        "ps_au_pairs": 0.0009850263595581055,
        "quarantined": false,
        "null_95th_primary": 0.0014428943395614624,
        "null_95th_conservative": 0.0032531172037124634,
        "null_available": true,
        "exceeds_null_primary": false,
        "exceeds_null_conservative": false
      },
      "lysine_riboswitch": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "manganese_riboswitch": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "mir_122_precursor": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "mir_155_precursor": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "mir_21_precursor": {
        "skipped": true,
        "reason": "< 15 WC pairs (0 found)",
        "n_wc_pairs_total": 0
      },
      "mir_let7_precursor": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "pistol_ribozyme": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "preQ1_riboswitch": {
        "skipped": true,
        "reason": "< 15 WC pairs (5 found)",
        "n_wc_pairs_total": 5
      },
      "purine_riboswitch": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "tRNA_Ala_human": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "tRNA_Phe_yeast": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "tmRNA": {
        "skipped": true,
        "reason": "no valid PS values"
      },
      "twister_ribozyme": {
        "skipped": true,
        "reason": "no valid PS values"
      }
    },
    "mean_best_ps": 0.0,
    "median_best_ps": 0.0,
    "families_exceeding_null_primary": 0,
    "families_exceeding_null_conservative": 0,
    "families_no_null": [],
    "families_total": 1,
    "families_quarantined": [],
    "families_skipped": [
      "5S_rRNA_ecoli",
      "6S_RNA",
      "7SK_RNA",
      "Bacterial_SRP",
      "CRISPR_leader",
      "Corona_s2m",
      "CrPV_IRES",
      "FMN_riboswitch",
      "HDV_ribozyme",
      "Histone_3prime",
      "IRES_HCV_domainII",
      "IRE_stem_loop",
      "RNaseP_specificity",
      "SAH_riboswitch",
      "SAM_riboswitch",
      "SECIS_element",
      "SRP_RNA_helix8",
      "THF_riboswitch",
      "TPP_riboswitch",
      "T_box_leader",
      "U1_snRNA",
      "U2_snRNA_stem",
      "U4_snRNA",
      "U5_snRNA",
      "U6_snRNA",
      "Vault_RNA",
      "Y_RNA",
      "ZMP_riboswitch",
      "c_di_GMP_riboswitch",
      "cobalamin_riboswitch",
      "fluoride_riboswitch",
      "glmS_ribozyme",
      "glycine_riboswitch",
      "group_II_intron_D5",
      "hammerhead_ribozyme",
      "lysine_riboswitch",
      "manganese_riboswitch",
      "mir_122_precursor",
      "mir_155_precursor",
      "mir_21_precursor",
      "mir_let7_precursor",
      "pistol_ribozyme",
      "preQ1_riboswitch",
      "purine_riboswitch",
      "tRNA_Ala_human",
      "tRNA_Phe_yeast",
      "tmRNA",
      "twister_ribozyme"
    ],
    "families_failed_gate": [
      "Hepatitis_C_IRES_III",
      "group_I_intron_P4P6",
      "hatchet_ribozyme"
    ]
  }
}