[INFO] Console - predicting pockets for proteins from dataset [ubash3a.pdb]
[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_ubash3a
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Dataset - processing dataset [ubash3a.pdb] using 0 threads
[INFO] Dataset - 
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processing [ubash3a.pdb] (1/1)
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[INFO] Console - processing [ubash3a.pdb] (1/1)
[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/ubash3a.pdb]
[INFO] PdbUtils - loading file [../proteins/ubash3a.pdb]
[INFO] Struct - groups in chain A: 451
[INFO] Struct - groups in chain A: 451
[INFO] Struct - 451 groups in chain A
[INFO] Protein - structure atoms: 3548
[INFO] Protein - protein   atoms: 3471
[INFO] Protein - ignoring ligands
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Protein - SAS points: 9818
[INFO] Protein - exposed protein atoms: 2625 of 3471
[INFO] InstancePredictor - Creating WekaInstancePredictor
[INFO] SLinkClusterer - clustering [86] elements
[INFO] SLinkClusterer - clusters: [id:1( 2 ), id:10( 27 ), id:20( 13 ), id:25( 2 ), id:46( 1 ), id:47( 1 ), id:55( 30 ), id:77( 8 ), id:84( 1 ), id:85( 1 )]
[INFO] SLinkClusterer - clusters together: 86 / 86
[INFO] PocketPredictor - PREDICTING POCKETS.... ====================================
[INFO] PocketPredictor - SAS POINTS: 9818
[INFO] PocketPredictor - LIGANDABLE POINTS: 86
[INFO] PocketPredictor - CLUSTERS: 10
[INFO] PocketPredictor - FILTERED CLUSTERS: 4
[INFO] PocketPredictor - pocket 1 -  surf_atoms:  38   points:  30   score:   10.3
[INFO] PocketPredictor - pocket 2 -  surf_atoms:  50   points:  27   score:   10.1
[INFO] PocketPredictor - pocket 3 -  surf_atoms:  20   points:  13   score:    4.3
[INFO] PocketPredictor - pocket 4 -  surf_atoms:  21   points:   8   score:    1.5
[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/ubash3a.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_ubash3a/visualizations/data/ubash3a.pdb]
[INFO] Console - predicting pockets finished in 0 hours 0 minutes 16.827 seconds
[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_ubash3a]
[INFO] Console - 
[INFO] Console - Finished successfully in 0 hours 0 minutes 19.160 seconds.