[INFO] Console - predicting pockets for proteins from dataset [rnf186.pdb]
[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_rnf186
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Dataset - processing dataset [rnf186.pdb] using 0 threads
[INFO] Dataset - 
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processing [rnf186.pdb] (1/1)
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[INFO] Console - processing [rnf186.pdb] (1/1)
[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/rnf186.pdb]
[INFO] PdbUtils - loading file [../proteins/rnf186.pdb]
[INFO] Struct - groups in chain A: 227
[INFO] Struct - groups in chain A: 227
[INFO] Struct - 227 groups in chain A
[INFO] Protein - structure atoms: 1682
[INFO] Protein - protein   atoms: 1657
[INFO] Protein - ignoring ligands
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Protein - SAS points: 7132
[INFO] Protein - exposed protein atoms: 1479 of 1657
[INFO] InstancePredictor - Creating WekaInstancePredictor
[INFO] PocketPredictor - PREDICTING POCKETS.... ====================================
[INFO] PocketPredictor - SAS POINTS: 7132
[INFO] PocketPredictor - LIGANDABLE POINTS: 1
[INFO] PocketPredictor - CLUSTERS: 1
[INFO] PocketPredictor - FILTERED CLUSTERS: 0
[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/rnf186.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_rnf186/visualizations/data/rnf186.pdb]
[INFO] Console - predicting pockets finished in 0 hours 0 minutes 10.453 seconds
[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_rnf186]
[INFO] Console - 
[INFO] Console - Finished successfully in 0 hours 0 minutes 11.914 seconds.