Unexpected sampling results

Description

After installation, I ran batch sampling using the following command:

rfd3 design out_dir=RF3_PD \
 inputs=./PD_L1.json \
 skip_existing=False \
 dump_trajectories=False \
 align_trajectory_structures=True \
 ckpt_path=./checkpoints/rfd3_latest.ckpt \
 cleanup_virtual_atoms=True \
 diffusion_batch_size=4 \
 n_batches=25 \
 output_full_json=False

The PD_L1.json configuration file uses the example content from the doc:

{
    "pdl1": {
        "dialect": 2,
        "infer_ori_strategy": "hotspots",
        "input": "./RFD3/models/rfd3/docs/input_pdbs/5o45_cropped.pdb",
        "contig": "50-120,/0,A17-131",
        "select_hotspots": {
            "A56": "CG,OH",
            "A115": "CG,SD",
            "A123": "CD2,OH"
        }
    }
}

Issue

When using AF3 to screen the 100 generated binders, almost none of them pass the interaction quality filter (min PAE interaction < 1.5). Is there anything incorrect in my sampling configuration?

Start with the rfd3 design sampling entry point and compare the documented PD_L1.json example with the command-line configuration shown here. Reproduce the sampling run using 5o45_cropped.pdb and the listed checkpoint, then determine whether the configuration explains the AF3 interaction-quality results; done means identifying a confirmed configuration issue or documenting that the setup is valid.