[INFO] Console - predicting pockets for proteins from dataset [adcy5.pdb]
[INFO] PredictPocketsRoutine - outdir: /oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_adcy5
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Dataset - processing dataset [adcy5.pdb] using 0 threads
[INFO] Dataset - 
------------------------------------------------------------------------------------------------------------------------
processing [adcy5.pdb] (1/1)
------------------------------------------------------------------------------------------------------------------------

[INFO] Console - processing [adcy5.pdb] (1/1)
[INFO] Protein - loading protein [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/proteins/adcy5.pdb]
[INFO] PdbUtils - loading file [proteins/adcy5.pdb]
[INFO] Struct - groups in chain A: 1261
[INFO] Struct - groups in chain A: 1261
[INFO] Struct - 1261 groups in chain A
[INFO] Protein - structure atoms: 9748
[INFO] Protein - protein   atoms: 9553
[INFO] Protein - ignoring ligands
[INFO] FeatureSetup - enabledFeatures: [chem, volsite, protrusion, bfactor, atom_table]
[INFO] Protein - SAS points: 24834
[INFO] Protein - exposed protein atoms: 7060 of 9553
[INFO] InstancePredictor - Creating WekaInstancePredictor
[INFO] SLinkClusterer - clustering [262] elements
[INFO] SLinkClusterer - clusters: [id:1( 2 ), id:2( 1 ), id:23( 1 ), id:24( 1 ), id:41( 41 ), id:50( 2 ), id:56( 8 ), id:63( 31 ), id:75( 1 ), id:121( 16 ), id:129( 15 ), id:130( 1 ), id:133( 9 ), id:151( 4 ), id:158( 17 ), id:171( 1 ), id:173( 2 ), id:174( 2 ), id:177( 3 ), id:178( 1 ), id:180( 1 ), id:182( 3 ), id:189( 1 ), id:191( 3 ), id:219( 31 ), id:221( 1 ), id:225( 6 ), id:226( 1 ), id:227( 1 ), id:230( 1 ), id:235( 29 ), id:236( 1 ), id:249( 20 ), id:255( 3 ), id:261( 1 )]
[INFO] SLinkClusterer - clusters together: 262 / 262
[INFO] PocketPredictor - PREDICTING POCKETS.... ====================================
[INFO] PocketPredictor - SAS POINTS: 24834
[INFO] PocketPredictor - LIGANDABLE POINTS: 262
[INFO] PocketPredictor - CLUSTERS: 35
[INFO] PocketPredictor - FILTERED CLUSTERS: 16
[INFO] PocketPredictor - pocket 1 -  surf_atoms:  51   points:  41   score:   16.0
[INFO] PocketPredictor - pocket 2 -  surf_atoms:  64   points:  31   score:   10.5
[INFO] PocketPredictor - pocket 3 -  surf_atoms:  37   points:  29   score:   10.4
[INFO] PocketPredictor - pocket 4 -  surf_atoms:  43   points:  31   score:   10.2
[INFO] PocketPredictor - pocket 5 -  surf_atoms:  29   points:  20   score:    7.8
[INFO] PocketPredictor - pocket 6 -  surf_atoms:  44   points:  17   score:    6.9
[INFO] PocketPredictor - pocket 7 -  surf_atoms:  16   points:  15   score:    6.7
[INFO] PocketPredictor - pocket 8 -  surf_atoms:  33   points:  16   score:    5.2
[INFO] PocketPredictor - pocket 9 -  surf_atoms:  23   points:   9   score:    3.2
[INFO] PocketPredictor - pocket10 -  surf_atoms:  22   points:   8   score:    2.6
[INFO] PocketPredictor - pocket11 -  surf_atoms:  21   points:   6   score:    1.8
[INFO] PocketPredictor - pocket12 -  surf_atoms:  15   points:   3   score:    1.5
[INFO] PocketPredictor - pocket13 -  surf_atoms:  17   points:   3   score:    1.2
[INFO] PocketPredictor - pocket14 -  surf_atoms:  11   points:   4   score:    1.1
[INFO] PocketPredictor - pocket15 -  surf_atoms:  13   points:   3   score:    1.0
[INFO] PocketPredictor - pocket16 -  surf_atoms:   9   points:   3   score:    1.0
[INFO] OldPymolRenderer - copying [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/proteins/adcy5.pdb] to [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_adcy5/visualizations/data/adcy5.pdb]
[INFO] Console - predicting pockets finished in 0 hours 0 minutes 15.612 seconds
[INFO] Console - results saved to directory [/oak/stanford/groups/mrivas/projects/multiomics/tlmenest/LLMChemCreator/p2rank_2.4.1/test_output/predict_adcy5]
[INFO] Console - 
[INFO] Console - Finished successfully in 0 hours 0 minutes 16.447 seconds.