[phenixbb] Error in PDB Validation letter

[Pavel Afonine]

Hi Raja,

first of all I would have a look in .geo file that phenix.refine 
generates. Just run phenix.refine like this with your model:

phenix.refine model.pdb data.mtz --dry-run

and then inspect the .geo file for atoms you list below. Do the ideal 
values in phenix.refine are in close agreement with those in PDB?  If 
not, you should tell us. If the ideal values in PDB and in .geo are 
close then you probably need to do one more round of refinement to 
achieve with more weight put on restraints.

Pavel.


On 4/30/10 12:37 PM, Raja Dey wrote:
> Hi,
>     I am getting two errors in pdb validation report as follows:
> I think I need to use B-DNA constraint in the refinement. This is a 2.4 A data. How can I do that in PHENIX in cammand line promt.
>
> Another thing is, I have a small molecule in the complex, which I called as BML. I think that's might be the problem. This is known as BML210. What I should call this compound? Should I also give a chain ID for this compound? See the errors given below.
>
>     *** Covalent Angle Values:
>
>     The overall RMS deviation for covalent angles relative to the standard 
>     dictionary is    1.4 degrees.
>
>     The following table contains a list of the covalent bond angles
>     greater than 6 times standard deviation.
>
>
>  Deviation  Residue  Chain  Sequence  AT1  -  AT2  -  AT3    Bond    Dictionary  Standard
>              Name     ID     Number                          Angle      Value    Deviation
> -------------------------------------------------------------------------------------------
>     -4.8     DA       E        1      C1'  -  C2'  -  C3'     97.6     102.4        0.8
>     -5.8     DA       E        2      C1'  -  C2'  -  C3'     96.6     102.4        0.8
>      3.3     DA       E        2      N9   -  C1'  -  O4'    111.6     108.3        0.3
>     -5.0     DC       E        5      N1   -  C1'  -  O4'    103.0     108.0        0.7
>     -5.1     DT       E        6      C1'  -  C2'  -  C3'     97.3     102.4        0.8
>     -6.7     DT       E        8      C1'  -  O4'  -  C4'    103.4     110.1        1.0
>      2.3     DT       E        8      N1   -  C1'  -  O4'    110.6     108.3        0.3
>     -4.5     DT       E       11      N1   -  C1'  -  O4'    103.5     108.0        0.7
>     -6.1     DA       F        2      C1'  -  C2'  -  C3'     96.3     102.4        0.8
>      3.0     DA       F        2      N9   -  C1'  -  O4'    111.3     108.3        0.3
>     -5.3     DC       F        5      N1   -  C1'  -  O4'    102.7     108.0        0.7
>     -4.9     DT       F        6      C1'  -  C2'  -  C3'     97.5     102.4        0.8
>     -4.5     DA       F       10      N9   -  C1'  -  O4'    103.5     108.0        0.7
>     -7.8     DA       F       11      N9   -  C1'  -  O4'    100.2     108.0        0.7
>
>
>
> ==> The following residues have extra atoms:                         
>     
>      RES MOD#C SEQ          ATOMS
>     
>      BML(      100)          N1  C10  C11  C12  C13  C14  C15  C16  C17  C18 
>                             C19   O2   N2  C20   N3   C7   C8   C9 
>
>
>
>
> ERROR: dissociated residue(s):
> 	BML  100
>
>
> Raja 
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