[INFO] Console - predicting pockets for proteins from dataset [mfge8.pdb]
[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_mfge8
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Dataset - processing dataset [mfge8.pdb] using 0 threads
[INFO] Dataset - 
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processing [mfge8.pdb] (1/1)
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[INFO] Console - processing [mfge8.pdb] (1/1)
[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/mfge8.pdb]
[INFO] PdbUtils - loading file [mfge8.pdb]
[INFO] Struct - groups in chain A: 387
[INFO] Struct - groups in chain A: 387
[INFO] Struct - 387 groups in chain A
[INFO] Protein - structure atoms: 3038
[INFO] Protein - protein   atoms: 2977
[INFO] Protein - ignoring ligands
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Protein - SAS points: 6766
[INFO] Protein - exposed protein atoms: 1959 of 2977
[INFO] InstancePredictor - Creating WekaInstancePredictor
[INFO] SLinkClusterer - clustering [13] elements
[INFO] SLinkClusterer - clusters: [id:2( 4 ), id:5( 2 ), id:7( 3 ), id:8( 1 ), id:10( 1 ), id:11( 1 ), id:12( 1 )]
[INFO] SLinkClusterer - clusters together: 13 / 13
[INFO] PocketPredictor - PREDICTING POCKETS.... ====================================
[INFO] PocketPredictor - SAS POINTS: 6766
[INFO] PocketPredictor - LIGANDABLE POINTS: 13
[INFO] PocketPredictor - CLUSTERS: 7
[INFO] PocketPredictor - FILTERED CLUSTERS: 2
[INFO] PocketPredictor - pocket 1 -  surf_atoms:  14   points:   3   score:    2.0
[INFO] PocketPredictor - pocket 2 -  surf_atoms:  17   points:   4   score:    1.2
[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/mfge8.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_mfge8/visualizations/data/mfge8.pdb]
[INFO] Console - predicting pockets finished in 0 hours 0 minutes 16.656 seconds
[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_mfge8]
[INFO] Console - 
[INFO] Console - Finished successfully in 0 hours 0 minutes 17.991 seconds.