[INFO] Console - predicting pockets for proteins from dataset [tbc1d1.pdb]
[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_tbc1d1
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Dataset - processing dataset [tbc1d1.pdb] using 0 threads
[INFO] Dataset - 
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processing [tbc1d1.pdb] (1/1)
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[INFO] Console - processing [tbc1d1.pdb] (1/1)
[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/tbc1d1.pdb]
[INFO] PdbUtils - loading file [../proteins/tbc1d1.pdb]
[INFO] Struct - groups in chain A: 1168
[INFO] Struct - groups in chain A: 1168
[INFO] Struct - 1168 groups in chain A
[INFO] Protein - structure atoms: 9349
[INFO] Protein - protein   atoms: 9182
[INFO] Protein - ignoring ligands
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Protein - SAS points: 30597
[INFO] Protein - exposed protein atoms: 7350 of 9182
[INFO] InstancePredictor - Creating WekaInstancePredictor
[INFO] SLinkClusterer - clustering [106] elements
[INFO] SLinkClusterer - clusters: [id:5( 3 ), id:6( 1 ), id:7( 2 ), id:27( 11 ), id:28( 1 ), id:30( 2 ), id:37( 3 ), id:38( 13 ), id:41( 3 ), id:42( 2 ), id:47( 4 ), id:48( 4 ), id:57( 1 ), id:58( 1 ), id:59( 1 ), id:61( 1 ), id:63( 1 ), id:65( 4 ), id:69( 17 ), id:87( 1 ), id:101( 1 ), id:103( 5 ), id:104( 24 )]
[INFO] SLinkClusterer - clusters together: 106 / 106
[INFO] PocketPredictor - PREDICTING POCKETS.... ====================================
[INFO] PocketPredictor - SAS POINTS: 30597
[INFO] PocketPredictor - LIGANDABLE POINTS: 106
[INFO] PocketPredictor - CLUSTERS: 23
[INFO] PocketPredictor - FILTERED CLUSTERS: 11
[INFO] PocketPredictor - pocket 1 -  surf_atoms:  55   points:  24   score:    7.6
[INFO] PocketPredictor - pocket 2 -  surf_atoms:  31   points:  17   score:    5.3
[INFO] PocketPredictor - pocket 3 -  surf_atoms:  24   points:  11   score:    4.6
[INFO] PocketPredictor - pocket 4 -  surf_atoms:  22   points:  13   score:    4.6
[INFO] PocketPredictor - pocket 5 -  surf_atoms:  24   points:   5   score:    2.1
[INFO] PocketPredictor - pocket 6 -  surf_atoms:  17   points:   4   score:    2.0
[INFO] PocketPredictor - pocket 7 -  surf_atoms:  20   points:   4   score:    1.7
[INFO] PocketPredictor - pocket 8 -  surf_atoms:  14   points:   3   score:    1.6
[INFO] PocketPredictor - pocket 9 -  surf_atoms:  15   points:   4   score:    1.4
[INFO] PocketPredictor - pocket10 -  surf_atoms:  19   points:   3   score:    1.1
[INFO] PocketPredictor - pocket11 -  surf_atoms:  19   points:   3   score:    1.0
[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/tbc1d1.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_tbc1d1/visualizations/data/tbc1d1.pdb]
[INFO] Console - predicting pockets finished in 0 hours 0 minutes 15.786 seconds
[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_tbc1d1]
[INFO] Console - 
[INFO] Console - Finished successfully in 0 hours 0 minutes 17.240 seconds.