[INFO] Console - predicting pockets for proteins from dataset [tnfsf15.pdb]
[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_tnfsf15
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Dataset - processing dataset [tnfsf15.pdb] using 0 threads
[INFO] Dataset - 
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processing [tnfsf15.pdb] (1/1)
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[INFO] Console - processing [tnfsf15.pdb] (1/1)
[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/tnfsf15.pdb]
[INFO] PdbUtils - loading file [../proteins/tnfsf15.pdb]
[INFO] Struct - groups in chain A: 251
[INFO] Struct - groups in chain A: 251
[INFO] Struct - 251 groups in chain A
[INFO] Protein - structure atoms: 1975
[INFO] Protein - protein   atoms: 1942
[INFO] Protein - ignoring ligands
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Protein - SAS points: 6534
[INFO] Protein - exposed protein atoms: 1540 of 1942
[INFO] InstancePredictor - Creating WekaInstancePredictor
[INFO] SLinkClusterer - clustering [6] elements
[INFO] SLinkClusterer - clusters: [id:0( 1 ), id:2( 3 ), id:3( 1 ), id:5( 1 )]
[INFO] SLinkClusterer - clusters together: 6 / 6
[INFO] PocketPredictor - PREDICTING POCKETS.... ====================================
[INFO] PocketPredictor - SAS POINTS: 6534
[INFO] PocketPredictor - LIGANDABLE POINTS: 6
[INFO] PocketPredictor - CLUSTERS: 4
[INFO] PocketPredictor - FILTERED CLUSTERS: 1
[INFO] PocketPredictor - pocket 1 -  surf_atoms:  15   points:   3   score:    1.9
[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/tnfsf15.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_tnfsf15/visualizations/data/tnfsf15.pdb]
[INFO] Console - predicting pockets finished in 0 hours 0 minutes 9.071 seconds
[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_tnfsf15]
[INFO] Console - 
[INFO] Console - Finished successfully in 0 hours 0 minutes 10.361 seconds.