Hi,

Recently I deposited a structure to PDB. However, I was told

>> The R value of SF check are different from your reported value.
>> 
>>     R work in SF check = 0.2859
>>     your reported R work = 0.1474
>> Also there are no R free flags in your sending files, but you reported R 
>> free value in your all deposition.

well, SF check is not the best tool to check things - it's not just my only vision, see lots of conversations on this topic on bb.

Just run

phenix.model_vs_data model.pdb data.hkl

and if output statistics matches the one you deposited to PDB, then you are 100% good. If it doesn't match then there is something to worry about.

So, I rerun my deposited file with phenix.refine, and it gave a R-work=0.1475, R-free=0.1742.

Sounds good.

However, when I tried to run the same file with refmac5, error came with "Free R label has not been set". I guess phenix.refine gives Rree-R label that other program could not recognize.

No surprises. Jumping between programs is tricky. You have to account for a lot of things to match things that different programs expect differently.

Could anyone please help me to solve this problem?

Step-by-step:

1) Run
phenix.model_vs_data model.pdb data.hkl

2) if output statistics matches the one you deposited to PDB, then you are 100% good. Come back to PDB and say this.

3) If it doesn't match then there is something that you need to fix. If you can't fix or have no idea what's wrong, you can send me the data and model and I will have a look.

Pavel.