the final RMSD is very high

[Admire7494]

I tried to use rfd3,mpnn and rf3 to make a demo.
First, i used rfd3 to redesign the sequence of A179-230 with cotig parameter.
The output use the ligandmpnn to redesign the sequence in A179-230 and resultec in "DTARFD3, id=1, T=0.1, seed=111, overall_confidence=0.5297, ligand_confidence=0.5339, seq_rec=0.3500
"
It seems very low.
Finally, i used the json file as below:
{
"name": "dimer_PLP_MN_complex",
"components": [
{
"seq": "RGIALPPAAQPGDPLARVDTPSLVLDLPAFEANLRAMQAWADRHEVALRPHAKAHKCPEIALRQLALGARGICCQKVSEALPFVAAGIRDIHISNEVVGPAKLALLGQLARAAKISVCVDNAENLAQLSAAMTRAGAEIDVLVEVDVGQGRCGVSDDATVLALAQQARALPGLRCVGVDDSARAVPGLRTVGGGTGSVEFDAASGVYTELQAGSYAFMDSDYGANEWNGPLKFQNSLFVLSTVMSTPAPGRVILDAGLKSTTAECGPPAVYGEPGLTYAAINDEHGVVRVEPGAQAPALGAVLRLVPSHVDPTFNLHDGLVVVKDGVVQDVWEIAARGFSR",
"chain_id": "A"
},
{
"seq": "GIALPPAAQPGDPLARVDTPSLVLDLPAFEANLRAMQAWADRHEVALRPHAKAHKCPEIALRQLALGARGICCQKVSEALPFVAAGIRDIHISNEVVGPAKLALLGQLARAAKISVCVDNAENLAQLSAAMTRAGAEIDVLVEVDVGQGRCGVSDDATVLALAQQARALPGLNFAGLQAYHGSVQHYRTREERAAVCRQAARIAASYAQLLRESGIACDTITGGGTGSVEFDAASGVYTELQAGSYAFMDSDYGANEWNGPLKFQNSLFVLSTVMSTPAPGRVILDAGLKSTTAECGPPAVYGEPGLTYAAINDEHGVVRVEPGAQAPALGAVLRLVPSHVDPTFNLHDGLVVVKDGVVQDVWEIAARGFSR",
"chain_id": "B"
},
{
"ccd_code": "PLP",
"chain_id": "C"
},
{
"ccd_code": "PLP",
"chain_id": "D"
},
{
"ccd_code": "PLP",
"chain_id": "E"
},
{
"ccd_code": "PLP",
"chain_id": "F"
},
{
"ccd_code": "MN",
"chain_id": "G"
},
{
"ccd_code": "MN",
"chain_id": "H"
}
]
}

and the predicted structure is not very good, with the score as below:
{
"chain_ptm": [0.69,0.7,0.6,0.59,0.59,0.59,0.61,0.6],
"chain_pair_pae_min": [
[null,19.69,19.33,17.34,11.66,12.59,12.78,12.45],
[null,null,9.1,13.19,17.95,17.28,12.25,12.64],
[null,null,null,16.05,18.24,18.66,12.66,12.56],
[null,null,null,null,18.34,18.23,12.99,12.78],
[null,null,null,null,null,17.27,13.14,12.83],
[null,null,null,null,null,null,12.9,13.01],
[null,null,null,null,null,null,null,12.37],
[null,null,null,null,null,null,null,null]
],
"chain_pair_pde_min": [
[null,8.49,8.51,7.87,6.38,6.62,10.98,11.1],
[null,null,4.71,6.55,8.14,7.91,10.9,10.63],
[null,null,null,5.13,6.75,6.59,12.44,11.08],
[null,null,null,null,6.47,6.81,12.86,11.92],
[null,null,null,null,null,6.26,12.31,12.46],
[null,null,null,null,null,null,12.1,13.35],
[null,null,null,null,null,null,null,15.57],
[null,null,null,null,null,null,null,null]
],
"chain_pair_pae": [
[null,25.8,24.87,24.08,21.4,22.09,17.17,16.93],
[null,null,19.46,21.65,24.33,24.17,16.66,16.95],
[null,null,null,19.78,23.19,23.25,16.05,16.0],
[null,null,null,null,22.68,23.24,16.3,16.23],
[null,null,null,null,null,21.27,16.37,16.12],
[null,null,null,null,null,null,16.17,16.25],
[null,null,null,null,null,null,null,12.54],
[null,null,null,null,null,null,null,null]
],
"chain_pair_pde": [
[null,11.62,10.45,10.2,9.13,9.6,12.67,12.77],
[null,null,7.79,9.17,10.24,10.25,12.57,12.34],
[null,null,null,7.16,8.25,8.35,13.45,12.05],
[null,null,null,null,8.16,8.46,13.75,12.65],
[null,null,null,null,null,8.35,13.2,13.41],
[null,null,null,null,null,null,12.75,14.16],
[null,null,null,null,null,null,null,15.57],
[null,null,null,null,null,null,null,null]
],
"overall_plddt": 0.6909,
"overall_pde": 9.3398,
"overall_pae": 21.6883,
"ptm": 0.4506063461303711,
"iptm": 0.3327164351940155,
"has_clash": false,
"ranking_score": 0.3563
}

The RMSD between model_0.cif (predicted by rf3) RFD3 output is 20.434.
Is there any problem in my workflow? The demo used structure (PDB 4v15)

[r-krishna]

If I understand correctly, you only remodeled 50 residues? I think that for cases that are more "native looking", rf3 requires a MSA for accurate prediction. For designs that are totally from scratch, it has an emergent property that it can predict it from single sequence. Maybe try predicting the structure with an MSA?