[INFO] Console - predicting pockets for proteins from dataset [inhbe.pdb]
[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_inhbe
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Dataset - processing dataset [inhbe.pdb] using 0 threads
[INFO] Dataset - 
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processing [inhbe.pdb] (1/1)
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[INFO] Console - processing [inhbe.pdb] (1/1)
[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/inhbe.pdb]
[INFO] PdbUtils - loading file [../proteins/inhbe.pdb]
[INFO] Struct - groups in chain A: 350
[INFO] Struct - groups in chain A: 350
[INFO] Struct - 350 groups in chain A
[INFO] Protein - structure atoms: 2713
[INFO] Protein - protein   atoms: 2637
[INFO] Protein - ignoring ligands
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Protein - SAS points: 7397
[INFO] Protein - exposed protein atoms: 2076 of 2637
[INFO] InstancePredictor - Creating WekaInstancePredictor
[INFO] SLinkClusterer - clustering [49] elements
[INFO] SLinkClusterer - clusters: [id:0( 1 ), id:11( 1 ), id:12( 1 ), id:15( 1 ), id:18( 4 ), id:19( 2 ), id:22( 9 ), id:30( 18 ), id:31( 2 ), id:40( 2 ), id:46( 3 ), id:48( 5 )]
[INFO] SLinkClusterer - clusters together: 49 / 49
[INFO] PocketPredictor - PREDICTING POCKETS.... ====================================
[INFO] PocketPredictor - SAS POINTS: 7397
[INFO] PocketPredictor - LIGANDABLE POINTS: 49
[INFO] PocketPredictor - CLUSTERS: 12
[INFO] PocketPredictor - FILTERED CLUSTERS: 5
[INFO] PocketPredictor - pocket 1 -  surf_atoms:  43   points:  18   score:    5.7
[INFO] PocketPredictor - pocket 2 -  surf_atoms:  23   points:   9   score:    2.8
[INFO] PocketPredictor - pocket 3 -  surf_atoms:  18   points:   5   score:    2.5
[INFO] PocketPredictor - pocket 4 -  surf_atoms:  13   points:   4   score:    1.4
[INFO] PocketPredictor - pocket 5 -  surf_atoms:   8   points:   3   score:    1.0
[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/inhbe.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_inhbe/visualizations/data/inhbe.pdb]
[INFO] Console - predicting pockets finished in 0 hours 0 minutes 10.715 seconds
[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_inhbe]
[INFO] Console - 
[INFO] Console - Finished successfully in 0 hours 0 minutes 12.221 seconds.