2026-07-26 19:15:15 [NCLEdetector.run_nativeNCLE] INFO: args: Namespace(pdb_file='/scratch/ims86/NCLEdetector_Datastore/user_input/reference_structures/1zmr_model_clean.pdb', outdir='/scratch/ims86/NCLEdetector_Datastore/outputs/workflow1', ID='1ZMR', chain='A', organism='Ecoli', gene='P00558', CG=False, Calpha=False, g_threshold=0.6, density=1.0, cut_off=None, model='EXP', ent_detection_method=2, log_level='INFO', logdir=None)
2026-07-26 19:15:15 [NCLEdetector.run_nativeNCLE] INFO: ================================================================================
Processing chain A
================================================================================
2026-07-26 19:15:15 [NCLEdetector.GaussianEntanglement] INFO: Creating directory: /scratch/ims86/NCLEdetector_Datastore/outputs/workflow1/NCLE/unmapped_missing_residues
2026-07-26 19:15:15 [NCLEdetector.GaussianEntanglement] INFO: 
####################################################################################################
COMPUTING ENTANGLEMENTS FOR 1zmr_model_clean with ID 1ZMR
2026-07-26 19:15:15 [NCLEdetector.GaussianEntanglement] INFO: Checking for disulfide bonds
2026-07-26 19:15:15 [NCLEdetector.GaussianEntanglement] INFO: All-atom model and contacts: Selecting all heavy atoms (no hydrogens) for entanglement calculations
2026-07-26 19:17:20 [NCLEdetector.GaussianEntanglement] INFO: SAVED: /scratch/ims86/NCLEdetector_Datastore/outputs/workflow1/NCLE/1ZMR_NCLE.csv
2026-07-26 19:17:20 [NCLEdetector.run_nativeNCLE] INFO: Native entanglements saved to /scratch/ims86/NCLEdetector_Datastore/outputs/workflow1/NCLE/1ZMR_NCLE.csv
2026-07-26 19:17:20 [NCLEdetector.GaussianEntanglement] INFO: Creating directory: /scratch/ims86/NCLEdetector_Datastore/outputs/workflow1/HQ_NCLE
2026-07-26 19:17:20 [NCLEdetector.GaussianEntanglement] INFO: GE FILE: /scratch/ims86/NCLEdetector_Datastore/outputs/workflow1/NCLE/1ZMR_NCLE.csv
2026-07-26 19:17:20 [NCLEdetector.GaussianEntanglement] INFO: 
##################################################
Removing slipknots...
2026-07-26 19:17:20 [NCLEdetector.GaussianEntanglement] INFO: SAVED: /scratch/ims86/NCLEdetector_Datastore/outputs/workflow1/HQ_NCLE/1ZMR.csv
2026-07-26 19:17:20 [NCLEdetector.run_nativeNCLE] INFO: High-quality native entanglements saved to /scratch/ims86/NCLEdetector_Datastore/outputs/workflow1/HQ_NCLE/1ZMR.csv
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: Clustering Ecoli Native Entanglements with dist_cutoff: 57
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: Loading /scratch/ims86/NCLEdetector_Datastore/outputs/workflow1/HQ_NCLE/1ZMR.csv
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: # Step 1
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: 
====================================================================================================
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: STEP 1 SUMMARY: Data Loading and Grouping by Unique Crossing Sets
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: ====================================================================================================
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: Total raw entanglements loaded: 57
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: Number of protein IDs: 1
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:   - 1ZMR: 57 raw entanglements
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: Unique crossing patterns identified: 15
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: Disulfide bonds found: 0
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: 
# Step 2a
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: ====================================================================================================
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: STEP 2A SUMMARY: Minimal Loop Identification for Unique Crossing Sets
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: ====================================================================================================
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: 1ZMR: 57 raw entanglements grouped into 15 representative loops
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:   Representative 1: Loop (15, 99), Crossings=['+107'], Represents 1 raw entanglement(s)
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:   Representative 2: Loop (55, 99), Crossings=['+108'], Represents 7 raw entanglement(s)
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:   Representative 3: Loop (43, 166), Crossings=['+18'], Represents 3 raw entanglement(s)
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:   Representative 4: Loop (43, 139), Crossings=['+17'], Represents 3 raw entanglement(s)
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:   Representative 5: Loop (141, 365), Crossings=['-377'], Represents 1 raw entanglement(s)
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:   Representative 6: Loop (151, 377), Crossings=['-144'], Represents 1 raw entanglement(s)
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:   Representative 7: Loop (197, 307), Crossings=['+188'], Represents 7 raw entanglement(s)
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:   Representative 8: Loop (197, 342), Crossings=['+189'], Represents 3 raw entanglement(s)
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:   Representative 9: Loop (204, 305), Crossings=['+187'], Represents 1 raw entanglement(s)
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:   Representative 10: Loop (222, 274), Crossings=['-283'], Represents 1 raw entanglement(s)
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:   Representative 11: Loop (228, 274), Crossings=['+221'], Represents 9 raw entanglement(s)
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:   Representative 12: Loop (227, 275), Crossings=['+220'], Represents 8 raw entanglement(s)
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:   Representative 13: Loop (230, 277), Crossings=['+221', '-283'], Represents 1 raw entanglement(s)
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:   Representative 14: Loop (269, 317), Crossings=['-258'], Represents 4 raw entanglement(s)
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:   Representative 15: Loop (271, 287), Crossings=['-257'], Represents 7 raw entanglement(s)
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: ====================================================================================================
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: STEP 2B: Merging of Entanglements Based on Crossing Proximity
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: ====================================================================================================
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: 
  Processing 1ZMR: Analyzing 12 representative entanglements for merging...
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:   Before merge: 12 representatives
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:   After merge: 3 merges completed
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:   Reformatting entanglement data...
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:   Result: 12 representative entanglements after merging (tracking 57 total raw)
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: ====================================================================================================
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: STEP 3: Removing Duplicate Entanglements (Same Crossings, Different Loop Sizes)
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: ====================================================================================================
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:   1ZMR: Checking 12 entanglements for duplicates...
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: 
STEP 3 RESULTS:
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:   1ZMR: 7 representative entanglements remaining (tracking 57 raw)
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: ====================================================================================================
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: STEP 4 PREP: Grouping Entanglements by Number and Chirality of Crossings
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: ====================================================================================================
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: 
Grouping Summary:
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:   1ZMR_1_['+']: 3 entanglements
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:   1ZMR_1_['-']: 3 entanglements
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:   1ZMR_2_['+', '-']: 1 entanglements
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: ====================================================================================================
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: STEP 4: Primary Structure Clustering Within Each Group
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: ====================================================================================================
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: 
  Group: 1ZMR_1_['-']
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:     Total entanglements: 3
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:     Pairwise comparisons: 3
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:     Primary structure clusters formed: 3
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:     Single-entanglement clusters: 3
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: 
  Group: 1ZMR_2_['+', '-']
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:     Total entanglements: 1
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:     Pairwise comparisons: 0
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:     Primary structure clusters formed: 1
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:     Single-entanglement clusters: 1
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: 
  Group: 1ZMR_1_['+']
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:     Total entanglements: 3
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:     Pairwise comparisons: 3
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:     Primary structure clusters formed: 3
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO:     Single-entanglement clusters: 3
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: 
====================================================================================================
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: STEP 4 FINAL RESULTS: Primary Structure Clustering Summary
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: ====================================================================================================
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: 1ZMR: 57 raw → 57 raw in 7 final clusters
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: ====================================================================================================
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: STEP 5: Writing Output File
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: ====================================================================================================
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: Creating directory: /scratch/ims86/NCLEdetector_Datastore/outputs/workflow1/clustered_HQ_NCLE
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: SAVED: /scratch/ims86/NCLEdetector_Datastore/outputs/workflow1/clustered_HQ_NCLE/1ZMR.csv
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: 
====================================================================================================
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: CLUSTERING COMPLETE: Final Summary
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: ====================================================================================================
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: Total raw entanglements processed: 57
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: Total final representative entanglements: 7
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: Clustering by organism: Ecoli
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: Spatial distance cutoff: 57
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: Output file: /scratch/ims86/NCLEdetector_Datastore/outputs/workflow1/clustered_HQ_NCLE/1ZMR.csv
2026-07-26 19:17:20 [NCLEdetector.ClusterNativeEntanglements] INFO: ====================================================================================================

2026-07-26 19:17:20 [NCLEdetector.run_nativeNCLE] INFO: Clustered native entanglements saved to /scratch/ims86/NCLEdetector_Datastore/outputs/workflow1/clustered_HQ_NCLE/1ZMR.csv
2026-07-26 19:17:21 [NCLEdetector.FeatureGen] INFO: Unique entanglement features saved to /scratch/ims86/NCLEdetector_Datastore/outputs/workflow1/clustered_HQ_NCLE_features/P00558_1ZMR_A_uent_features.csv
2026-07-26 19:17:21 [NCLEdetector.run_nativeNCLE] INFO: Entanglement features saved to /scratch/ims86/NCLEdetector_Datastore/outputs/workflow1/clustered_HQ_NCLE_features/P00558_1ZMR_A_uent_features.csv
2026-07-26 19:17:21 [NCLEdetector.run_nativeNCLE] INFO: NORMAL TERMINATION - 126.1 seconds