[INFO] Console - predicting pockets for proteins from dataset [gpr75.pdb]
[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_gpr75
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Dataset - processing dataset [gpr75.pdb] using 0 threads
[INFO] Dataset - 
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processing [gpr75.pdb] (1/1)
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[INFO] Console - processing [gpr75.pdb] (1/1)
[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/gpr75.pdb]
[INFO] PdbUtils - loading file [../proteins/gpr75.pdb]
[INFO] Struct - groups in chain A: 540
[INFO] Struct - groups in chain A: 540
[INFO] Struct - 540 groups in chain A
[INFO] Protein - structure atoms: 4169
[INFO] Protein - protein   atoms: 4115
[INFO] Protein - ignoring ligands
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Protein - SAS points: 15433
[INFO] Protein - exposed protein atoms: 3484 of 4115
[INFO] InstancePredictor - Creating WekaInstancePredictor
[INFO] SLinkClusterer - clustering [161] elements
[INFO] SLinkClusterer - clusters: [id:5( 1 ), id:19( 96 ), id:20( 2 ), id:46( 1 ), id:48( 1 ), id:49( 1 ), id:53( 1 ), id:55( 2 ), id:58( 3 ), id:59( 1 ), id:66( 9 ), id:79( 1 ), id:83( 1 ), id:87( 2 ), id:89( 1 ), id:95( 1 ), id:96( 3 ), id:111( 2 ), id:112( 5 ), id:115( 8 ), id:121( 6 ), id:126( 9 ), id:134( 2 ), id:149( 2 )]
[INFO] SLinkClusterer - clusters together: 161 / 161
[INFO] PocketPredictor - PREDICTING POCKETS.... ====================================
[INFO] PocketPredictor - SAS POINTS: 15433
[INFO] PocketPredictor - LIGANDABLE POINTS: 161
[INFO] PocketPredictor - CLUSTERS: 24
[INFO] PocketPredictor - FILTERED CLUSTERS: 8
[INFO] PocketPredictor - pocket 1 -  surf_atoms:  88   points:  96   score:   30.8
[INFO] PocketPredictor - pocket 2 -  surf_atoms:  26   points:   9   score:    3.3
[INFO] PocketPredictor - pocket 3 -  surf_atoms:  14   points:   9   score:    2.4
[INFO] PocketPredictor - pocket 4 -  surf_atoms:  10   points:   8   score:    2.2
[INFO] PocketPredictor - pocket 5 -  surf_atoms:  13   points:   6   score:    1.8
[INFO] PocketPredictor - pocket 6 -  surf_atoms:  14   points:   3   score:    1.2
[INFO] PocketPredictor - pocket 7 -  surf_atoms:  11   points:   5   score:    1.0
[INFO] PocketPredictor - pocket 8 -  surf_atoms:  20   points:   3   score:    0.9
[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/gpr75.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_gpr75/visualizations/data/gpr75.pdb]
[INFO] Console - predicting pockets finished in 0 hours 0 minutes 17.014 seconds
[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_gpr75]
[INFO] Console - 
[INFO] Console - Finished successfully in 0 hours 0 minutes 19.672 seconds.