[INFO] Console - predicting pockets for proteins from dataset [apol1.pdb]
[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_apol1
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Dataset - processing dataset [apol1.pdb] using 0 threads
[INFO] Dataset - 
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processing [apol1.pdb] (1/1)
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[INFO] Console - processing [apol1.pdb] (1/1)
[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/proteins/apol1.pdb]
[INFO] PdbUtils - loading file [proteins/apol1.pdb]
[INFO] Struct - groups in chain A: 398
[INFO] Struct - groups in chain A: 398
[INFO] Struct - 398 groups in chain A
[INFO] Protein - structure atoms: 3094
[INFO] Protein - protein   atoms: 3038
[INFO] Protein - ignoring ligands
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Protein - SAS points: 10324
[INFO] Protein - exposed protein atoms: 2605 of 3038
[INFO] InstancePredictor - Creating WekaInstancePredictor
[INFO] SLinkClusterer - clustering [142] elements
[INFO] SLinkClusterer - clusters: [id:49( 114 ), id:50( 4 ), id:53( 2 ), id:58( 2 ), id:59( 5 ), id:88( 10 ), id:126( 2 ), id:128( 2 ), id:134( 1 )]
[INFO] SLinkClusterer - clusters together: 142 / 142
[INFO] PocketPredictor - PREDICTING POCKETS.... ====================================
[INFO] PocketPredictor - SAS POINTS: 10324
[INFO] PocketPredictor - LIGANDABLE POINTS: 142
[INFO] PocketPredictor - CLUSTERS: 9
[INFO] PocketPredictor - FILTERED CLUSTERS: 4
[INFO] PocketPredictor - pocket 1 -  surf_atoms: 123   points: 114   score:   43.1
[INFO] PocketPredictor - pocket 2 -  surf_atoms:  36   points:  10   score:    3.5
[INFO] PocketPredictor - pocket 3 -  surf_atoms:  20   points:   5   score:    1.7
[INFO] PocketPredictor - pocket 4 -  surf_atoms:  11   points:   4   score:    1.3
[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/proteins/apol1.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_apol1/visualizations/data/apol1.pdb]
[INFO] Console - predicting pockets finished in 0 hours 0 minutes 12.901 seconds
[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_apol1]
[INFO] Console - 
[INFO] Console - Finished successfully in 0 hours 0 minutes 13.744 seconds.