Issues

• P2: REFMAC publication is not bound to the admitted directory across concurrent replacement

  CultureBotAI/protstruct_review#1050 · Filter by author realmarcin opened on Nov 7, 2026

• P1: REFMAC final-pair correction references an undefined collision collection

  CultureBotAI/protstruct_review#1049 · Filter by author realmarcin opened on Nov 7, 2026

• Evaluation design for agentic PHENIX: human vs agentic, default-pipeline baselines, R-free primary + multi-metric endpoints, and density/geometry-grounded active-site criteria beyond sequence regexes

  CultureBotAI/protstruct_review#1048 · Filter by author realmarcin opened on Nov 7, 2026

• Stratify PHENIX parameter selection by structure resolution category (ultra-high, high, medium, low) and repeat slide-deck refinement assessment

  CultureBotAI/protstruct_review#1047 · Filter by author realmarcin opened on Nov 7, 2026

• P2: REFMAC cell audit invents a fixed header-rounding tolerance

  CultureBotAI/protstruct_review#1046 · Filter by author realmarcin opened on Nov 6, 2026
  2

• P2: REFMAC JSON writer deletes a pre-existing temporary artifact

  CultureBotAI/protstruct_review#1045 · Filter by author realmarcin opened on Nov 6, 2026

• P2: REFMAC audit exceptions escape without an operation failure record

  CultureBotAI/protstruct_review#1044 · Filter by author realmarcin opened on Nov 6, 2026
  14

• P1: REFMAC PDB audit rejects unchanged models through incompatible helper calls

  CultureBotAI/protstruct_review#1043 · Filter by author realmarcin opened on Nov 6, 2026

• P2: REFMAC XML reconciliation double-rounds printed values

  CultureBotAI/protstruct_review#1042 · Filter by author realmarcin opened on Nov 6, 2026
  1

• P1: REFMAC collector reverses work and free sets despite FREE 1

  CultureBotAI/protstruct_review#1041 · Filter by author realmarcin opened on Nov 6, 2026

• P1: REFMAC collector reads a ledger schema that staging never emits

  CultureBotAI/protstruct_review#1040 · Filter by author realmarcin opened on Nov 6, 2026
  1

• P2: REFMAC generic numeric parsing accepts underscore-corrupted tokens

  CultureBotAI/protstruct_review#1039 · Filter by author realmarcin opened on Nov 6, 2026

• P1: REFMAC transport tests use nonlocal without an enclosing function

  CultureBotAI/protstruct_review#1038 · Filter by author realmarcin opened on Nov 6, 2026
  1

• P3: REFMAC parser labels numerically equal R tokens as conflicting

  CultureBotAI/protstruct_review#1037 · Filter by author realmarcin opened on Nov 6, 2026
  1

• P2: REFMAC parser accepts impossible free-reflection percentages

  CultureBotAI/protstruct_review#1036 · Filter by author realmarcin opened on Nov 6, 2026
  1

• P2: REFMAC FOM count totals can contradict their components

  CultureBotAI/protstruct_review#1035 · Filter by author realmarcin opened on Nov 6, 2026

• P2: REFMAC FOM tables accept contradictory cycle identities

  CultureBotAI/protstruct_review#1034 · Filter by author realmarcin opened on Nov 6, 2026

• P2: REFMAC parser accepts then discards malformed recognized diagnostics

  CultureBotAI/protstruct_review#1033 · Filter by author realmarcin opened on Nov 6, 2026

• P2: REFMAC parser ignores contradictory native cycle markers

  CultureBotAI/protstruct_review#1032 · Filter by author realmarcin opened on Nov 6, 2026
  2

• P2: malformed extra REFMAC final R rows bypass label validation

  CultureBotAI/protstruct_review#1031 · Filter by author realmarcin opened on Nov 6, 2026

• P2: REFMAC parser invents a numeric sentinel cutoff at 99

  CultureBotAI/protstruct_review#1030 · Filter by author realmarcin opened on Nov 6, 2026
  1

• P1: REFMAC parser skips numeric validation of intermediate R tables

  CultureBotAI/protstruct_review#1029 · Filter by author realmarcin opened on Nov 6, 2026

• P3: new REFMAC test executable breaks with spaced Python paths

  CultureBotAI/protstruct_review#1028 · Filter by author realmarcin opened on Nov 6, 2026

• P2: run_refmac can silently replace an explicitly supplied environment

  CultureBotAI/protstruct_review#1027 · Filter by author realmarcin opened on Nov 6, 2026

• P1: REFMAC parser regression suite fails three fixture checks

  CultureBotAI/protstruct_review#1026 · Filter by author realmarcin opened on Nov 6, 2026
  2