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  1. test_both/metadata/8qz6_B__A_sample_4.json +1138 -0
  2. test_both/metadata/8sfx_D__B_sample_4.json +1230 -0
  3. test_both/metadata/8sgi_H_L_A_sample_3.json +4277 -0
  4. test_both/metadata/8t04_C_D_A_sample_0.json +842 -0
  5. test_both/metadata/8ty1_C_B_A_sample_4.json +0 -0
  6. test_both/metadata/8v4f_B_D_A_sample_0.json +780 -0
  7. test_both/metadata/8vuh_H_L_A_sample_1.json +2465 -0
  8. test_both/metadata/8wej_H_L_B_sample_1.json +2371 -0
  9. test_both/metadata/8xk6_H_L_A_sample_3.json +2239 -0
  10. train_before_20210930/logs/stage2_20260121_233054.log +14 -0
  11. train_before_20210930/proteinix_cif/1XGU_B_A_C.cif +0 -0
  12. train_before_20210930/proteinix_cif/2Q8B_H_L_A.cif +0 -0
  13. train_before_20210930/proteinix_cif/2R9H_E_F_B.cif +0 -0
  14. train_before_20210930/proteinix_cif/2VDQ_H_L_A.cif +0 -0
  15. train_before_20210930/proteinix_cif/3BE1_H_L_A.cif +0 -0
  16. train_before_20210930/proteinix_cif/3DET_C_D_A.cif +0 -0
  17. train_before_20210930/proteinix_cif/3G9A_B__A.cif +0 -0
  18. train_before_20210930/proteinix_cif/3HPL_A_B_C.cif +0 -0
  19. train_before_20210930/proteinix_cif/3K80_A__C.cif +0 -0
  20. train_before_20210930/proteinix_cif/3KLH_D_C_B.cif +0 -0
  21. train_before_20210930/proteinix_cif/3KR3_H_L_D.cif +0 -0
  22. train_before_20210930/proteinix_cif/3OGC_A_B_C.cif +0 -0
  23. train_before_20210930/proteinix_cif/3OGO_G__B.cif +0 -0
  24. train_before_20210930/proteinix_cif/3SO3_C_B_A.cif +0 -0
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  26. train_before_20210930/proteinix_cif/3ULV_F_E_A.cif +0 -0
  27. train_before_20210930/proteinix_cif/3V4V_H_L_AB.cif +0 -0
  28. train_before_20210930/proteinix_cif/3WFB_H_L_BC.cif +0 -0
  29. train_before_20210930/proteinix_cif/3WSQ_H_L_A.cif +0 -0
  30. train_before_20210930/proteinix_cif/4C58_B__A.cif +0 -0
  31. train_before_20210930/proteinix_cif/4D9Q_E_D_B.cif +0 -0
  32. train_before_20210930/proteinix_cif/4HKZ_B_A_EH.cif +0 -0
  33. train_before_20210930/proteinix_cif/4I18_H_L_C.cif +0 -0
  34. train_before_20210930/proteinix_cif/4J4P_H_L_A.cif +0 -0
  35. train_before_20210930/proteinix_cif/4KRL_B__A.cif +0 -0
  36. train_before_20210930/proteinix_cif/4LVH_K_L_J.cif +0 -0
  37. train_before_20210930/proteinix_cif/4M5Z_H_L_A.cif +0 -0
  38. train_before_20210930/proteinix_cif/4OD2_B_A_S.cif +0 -0
  39. train_before_20210930/proteinix_cif/4OKV_A_B_F.cif +0 -0
  40. train_before_20210930/proteinix_cif/4OT1_H_L_A.cif +0 -0
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  42. train_before_20210930/proteinix_cif/4XVS_H_L_G.cif +0 -0
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  49. train_before_20210930/proteinix_cif/5LXG_H_L_A.cif +0 -0
  50. train_before_20210930/proteinix_cif/5MHR_P_O_E.cif +0 -0
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train_before_20210930/logs/stage2_20260121_233054.log ADDED
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1
+ 2026-01-21 23:30:54,911 - INFO - root - Stage 2 Pipeline: input=v4/train_before_20210930/proteinix_cif, output=v4/train_before_20210930
2
+ 2026-01-21 23:30:54,911 - INFO - root - Antibody mode enabled
3
+ 2026-01-21 23:30:54,911 - INFO - root - Using local mkdssp binary for DSSP computation (default)
4
+ 2026-01-21 23:30:54,911 - INFO - root - Checking dependencies...
5
+ 2026-01-21 23:30:54,912 - INFO - root - All dependencies available.
6
+ 2026-01-21 23:30:54,948 - INFO - root - Found 3401 structure files
7
+ 2026-01-21 23:30:54,949 - INFO - root - Processing 3401 pending structures
8
+ 2026-01-21 23:31:16,694 - INFO - root - Progress: 500/3401 (492 success, 6 failed) @ 23.0/s
9
+ 2026-01-21 23:31:34,816 - INFO - root - Progress: 1000/3401 (990 success, 6 failed) @ 25.1/s
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+ 2026-01-21 23:31:51,544 - INFO - root - Progress: 1500/3401 (1482 success, 7 failed) @ 26.5/s
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+ 2026-01-21 23:32:10,094 - INFO - root - Progress: 2000/3401 (1978 success, 7 failed) @ 26.6/s
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+ 2026-01-21 23:32:26,156 - INFO - root - Progress: 2500/3401 (2469 success, 7 failed) @ 27.4/s
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+ 2026-01-21 23:32:42,209 - INFO - root - Progress: 3000/3401 (2952 success, 7 failed) @ 28.0/s
14
+ 2026-01-21 23:33:05,983 - INFO - root - Stage 2 complete: {'total': 3401, 'processed': 3401, 'success': 3350, 'failed': 7, 'skipped': 44, 'qc_passed': 340, 'qc_failed': 3010, 'elapsed_seconds': 131.032630443573, 'rate': 25.95536690736422}
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