[INFO] Console - predicting pockets for proteins from dataset [il33.pdb]
[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_il33
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Dataset - processing dataset [il33.pdb] using 0 threads
[INFO] Dataset - 
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processing [il33.pdb] (1/1)
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[INFO] Console - processing [il33.pdb] (1/1)
[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/proteins/il33.pdb]
[INFO] PdbUtils - loading file [proteins/il33.pdb]
[INFO] Struct - groups in chain A: 270
[INFO] Struct - groups in chain A: 270
[INFO] Struct - 270 groups in chain A
[INFO] Protein - structure atoms: 2155
[INFO] Protein - protein   atoms: 2129
[INFO] Protein - ignoring ligands
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Protein - SAS points: 7352
[INFO] Protein - exposed protein atoms: 1743 of 2129
[INFO] InstancePredictor - Creating WekaInstancePredictor
[INFO] SLinkClusterer - clustering [20] elements
[INFO] SLinkClusterer - clusters: [id:1( 2 ), id:2( 1 ), id:5( 1 ), id:11( 1 ), id:12( 1 ), id:16( 8 ), id:17( 4 ), id:18( 1 ), id:19( 1 )]
[INFO] SLinkClusterer - clusters together: 20 / 20
[INFO] PocketPredictor - PREDICTING POCKETS.... ====================================
[INFO] PocketPredictor - SAS POINTS: 7352
[INFO] PocketPredictor - LIGANDABLE POINTS: 20
[INFO] PocketPredictor - CLUSTERS: 9
[INFO] PocketPredictor - FILTERED CLUSTERS: 2
[INFO] PocketPredictor - pocket 1 -  surf_atoms:  16   points:   8   score:    2.1
[INFO] PocketPredictor - pocket 2 -  surf_atoms:  10   points:   4   score:    1.5
[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/proteins/il33.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_il33/visualizations/data/il33.pdb]
[INFO] Console - predicting pockets finished in 0 hours 0 minutes 10.379 seconds
[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_il33]
[INFO] Console - 
[INFO] Console - Finished successfully in 0 hours 0 minutes 11.873 seconds.