Hi Reza,

this may mean several things. Perhaps TLS group selection isn't optimal or incorrect? phenix.find_tls_groups relies on B factors to annotate TLS groups. Were B factors meaningful (refined before running phenix.find_tls_groups)?

You can try weight optimization.

Values of TLS matrices cannot be interpreted directly, they can be positive or negative. This is discussed in great details here:

http://journals.iucr.org/d/issues/2015/08/00/rr5096/rr5096.pdf

You can check if TLS matrices are physically meaningful by running

phenix.tls_analysis model.pdb

If it runs all the way till completion - all is  good. Otherwise, in case of nonsensical TLS it will stop and tell what's wrong.

Perhaps you enabled TLS refinement too early (model isn't good yet)?

Pavel


On 4/30/17 05:30, Reza Khayat wrote:

Hi,


I'm having difficulty with performing TLS refinement on a highly symmetric system. The difference between the R_work and R_free increases with TLS refinement (16.5/21.4 changes to 14.4/22.2). The TLS tensors for some of the group are not sensible (if I understand the literature correctly) -there are some negative numbers for the T and L tensors (see below). The TLS groups were identified with phenix.find_tls_groups. Any suggestions would be appreciated. 


REMARK   3    SELECTION: chain 'A' and (resid   38  through   68 )

REMARK   3    ORIGIN FOR THE GROUP (A):  56.6459 -23.5648 -59.0695

REMARK   3    T TENSOR

REMARK   3      T11:   0.2105 T22:   0.2895

REMARK   3      T33:   0.0962 T12:   0.0829

REMARK   3      T13:   0.0473 T23:   0.0007

REMARK   3    L TENSOR

REMARK   3      L11:   0.0446 L22:   0.0120

REMARK   3      L33:   0.0096 L12:   0.0246

REMARK   3      L13:   0.0209 L23:   0.0106

REMARK   3    S TENSOR

REMARK   3      S11:   0.0228 S12:  -0.0268 S13:  -0.0023

REMARK   3      S21:  -0.0507 S22:   0.0526 S23:  -0.0287

REMARK   3      S31:  -0.0296 S32:  -0.0137 S33:   0.0534​


The data set is complete at 2.3Å resolution and there are no strange crystal phenotypes. 


Best wishes,
Reza


Reza Khayat, PhD
Assistant Professor 
City College of New York
Department of Chemistry
New York, NY 10031


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