[INFO] Console - predicting pockets for proteins from dataset [card6.pdb]
[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_card6
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Dataset - processing dataset [card6.pdb] using 0 threads
[INFO] Dataset - 
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processing [card6.pdb] (1/1)
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[INFO] Console - processing [card6.pdb] (1/1)
[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/card6.pdb]
[INFO] PdbUtils - loading file [../proteins/card6.pdb]
[INFO] Struct - groups in chain A: 1037
[INFO] Struct - groups in chain A: 1037
[INFO] Struct - 1037 groups in chain A
[INFO] Protein - structure atoms: 8178
[INFO] Protein - protein   atoms: 8046
[INFO] Protein - ignoring ligands
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Protein - SAS points: 33308
[INFO] Protein - exposed protein atoms: 6763 of 8046
[INFO] InstancePredictor - Creating WekaInstancePredictor
[INFO] SLinkClusterer - clustering [104] elements
[INFO] SLinkClusterer - clusters: [id:3( 1 ), id:4( 2 ), id:16( 1 ), id:23( 10 ), id:27( 2 ), id:40( 12 ), id:44( 2 ), id:45( 1 ), id:60( 1 ), id:62( 4 ), id:63( 1 ), id:65( 3 ), id:76( 4 ), id:77( 2 ), id:84( 19 ), id:87( 2 ), id:95( 34 ), id:102( 2 ), id:103( 1 )]
[INFO] SLinkClusterer - clusters together: 104 / 104
[INFO] PocketPredictor - PREDICTING POCKETS.... ====================================
[INFO] PocketPredictor - SAS POINTS: 33308
[INFO] PocketPredictor - LIGANDABLE POINTS: 104
[INFO] PocketPredictor - CLUSTERS: 19
[INFO] PocketPredictor - FILTERED CLUSTERS: 7
[INFO] PocketPredictor - pocket 1 -  surf_atoms:  37   points:  34   score:   13.4
[INFO] PocketPredictor - pocket 2 -  surf_atoms:  27   points:  19   score:    5.9
[INFO] PocketPredictor - pocket 3 -  surf_atoms:  25   points:  12   score:    4.9
[INFO] PocketPredictor - pocket 4 -  surf_atoms:  31   points:  10   score:    3.8
[INFO] PocketPredictor - pocket 5 -  surf_atoms:  18   points:   4   score:    1.8
[INFO] PocketPredictor - pocket 6 -  surf_atoms:  14   points:   4   score:    1.7
[INFO] PocketPredictor - pocket 7 -  surf_atoms:   3   points:   3   score:    1.0
[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/card6.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_card6/visualizations/data/card6.pdb]
[INFO] Console - predicting pockets finished in 0 hours 0 minutes 14.310 seconds
[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_card6]
[INFO] Console - 
[INFO] Console - Finished successfully in 0 hours 0 minutes 15.874 seconds.