[INFO] Console - predicting pockets for proteins from dataset [il4r.pdb]
[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_il4r
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Dataset - processing dataset [il4r.pdb] using 0 threads
[INFO] Dataset - 
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processing [il4r.pdb] (1/1)
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[INFO] Console - processing [il4r.pdb] (1/1)
[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/il4r.pdb]
[INFO] PdbUtils - loading file [../proteins/il4r.pdb]
[INFO] Struct - groups in chain A: 825
[INFO] Struct - groups in chain A: 825
[INFO] Struct - 825 groups in chain A
[INFO] Protein - structure atoms: 6290
[INFO] Protein - protein   atoms: 6198
[INFO] Protein - ignoring ligands
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Protein - SAS points: 29317
[INFO] Protein - exposed protein atoms: 5672 of 6198
[INFO] InstancePredictor - Creating WekaInstancePredictor
[INFO] SLinkClusterer - clustering [8] elements
[INFO] SLinkClusterer - clusters: [id:0( 1 ), id:1( 1 ), id:3( 2 ), id:4( 1 ), id:5( 1 ), id:6( 1 ), id:7( 1 )]
[INFO] SLinkClusterer - clusters together: 8 / 8
[INFO] PocketPredictor - PREDICTING POCKETS.... ====================================
[INFO] PocketPredictor - SAS POINTS: 29317
[INFO] PocketPredictor - LIGANDABLE POINTS: 8
[INFO] PocketPredictor - CLUSTERS: 7
[INFO] PocketPredictor - FILTERED CLUSTERS: 0
[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/il4r.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_il4r/visualizations/data/il4r.pdb]
[INFO] Console - predicting pockets finished in 0 hours 0 minutes 13.629 seconds
[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_il4r]
[INFO] Console - 
[INFO] Console - Finished successfully in 0 hours 0 minutes 15.090 seconds.