[INFO] Console - predicting pockets for proteins from dataset [cfhr5.pdb]
[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_cfhr5
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Dataset - processing dataset [cfhr5.pdb] using 0 threads
[INFO] Dataset - 
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processing [cfhr5.pdb] (1/1)
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[INFO] Console - processing [cfhr5.pdb] (1/1)
[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/cfhr5.pdb]
[INFO] PdbUtils - loading file [../proteins/cfhr5.pdb]
[INFO] Struct - groups in chain A: 569
[INFO] Struct - groups in chain A: 569
[INFO] Struct - 569 groups in chain A
[INFO] Protein - structure atoms: 4513
[INFO] Protein - protein   atoms: 4433
[INFO] Protein - ignoring ligands
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Protein - SAS points: 11807
[INFO] Protein - exposed protein atoms: 3475 of 4433
[INFO] InstancePredictor - Creating WekaInstancePredictor
[INFO] SLinkClusterer - clustering [62] elements
[INFO] SLinkClusterer - clusters: [id:1( 31 ), id:28( 5 ), id:32( 4 ), id:45( 10 ), id:46( 2 ), id:48( 4 ), id:49( 5 ), id:61( 1 )]
[INFO] SLinkClusterer - clusters together: 62 / 62
[INFO] PocketPredictor - PREDICTING POCKETS.... ====================================
[INFO] PocketPredictor - SAS POINTS: 11807
[INFO] PocketPredictor - LIGANDABLE POINTS: 62
[INFO] PocketPredictor - CLUSTERS: 8
[INFO] PocketPredictor - FILTERED CLUSTERS: 6
[INFO] PocketPredictor - pocket 1 -  surf_atoms:  54   points:  31   score:   10.1
[INFO] PocketPredictor - pocket 2 -  surf_atoms:  26   points:  10   score:    3.1
[INFO] PocketPredictor - pocket 3 -  surf_atoms:  22   points:   4   score:    1.7
[INFO] PocketPredictor - pocket 4 -  surf_atoms:  28   points:   5   score:    1.7
[INFO] PocketPredictor - pocket 5 -  surf_atoms:  16   points:   5   score:    1.4
[INFO] PocketPredictor - pocket 6 -  surf_atoms:  18   points:   4   score:    1.3
[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/proteins/cfhr5.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_cfhr5/visualizations/data/cfhr5.pdb]
[INFO] Console - predicting pockets finished in 0 hours 0 minutes 11.148 seconds
[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_cfhr5]
[INFO] Console - 
[INFO] Console - Finished successfully in 0 hours 0 minutes 12.587 seconds.