Hi Julia,

In addition to Dorothee's response to your another e-mail, I would indeed recommend check the model geometry, in particular, bad atomic clashes (where 2 atoms are very close to each other). You can find them in the .geo file which should be created by this point or in log, under "Nonbonded interactions:". The worst clashes will be the first in the list.

Best regards,

Oleg Sobolev.

On Mon, Oct 24, 2016 at 3:19 AM, Flis, Julia <[email protected]> wrote:

Hello,

my question is about the Phenix real space refinement. I am using the Phenix version phenix-1.11-2563.

My command looks as follows:
phenix.real_space_refine secondary_structure.enable=true Model.pdb VOL.map elbow.Model_pdb.001.cif Model.pdb_ss.eff resolution=3.8 weight=1

My problem is that the refinement suddenly stops during the first refinement cycle:

Model_real_space_refined.log says:

********************** REFINEMENT MACRO_CYCLE 1 OF 5 *************************
-------------------------------------------------------------------------------
Update NCS operators
********************
-------------------------------------------------------------------------------
Update rotamer restraints
*************************
-------------------------------------------------------------------------------
Global refinement
*****************
END

In the shell I get this :

[...]
distance: 184426 - 184921:   3.388
distance: 184428 - 184920:   3.342
distance: 184448 - 184898:   3.373
distance: 184449 - 184897:   3.187
distance: 184491 - 184860:   3.066
distance: 184531 - 184770:   3.203
distance: 184554 - 184746:   3.137

then it stops and the only files generated are Model_real_space_refined.log and Model_initial.geo.

Could you give me an advise? I have no clue what the problem could be.

Thank you,

Julia