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<p>Dear developers and users,</p>
<p><br>
</p>
<p>My phenix.real_space_refine run crashes with the error mentioned below when I have used following command to run it on a complete ribosome (containing coordinates for small subunit and large subunit in a single pdb file):</p>
<p><span>phenix.real_space_refine model.pdb map.mrc resolution=4.5 reference_coordinate_restraints.enabled=true reference_coordinate_restraints.selection="chain A and resseq 2:700" reference_coordinate_restraints.sigma=0.05 secondary_structure.enabled=True
res.eff > out.out</span><br>
</p>
<p><span><br>
</span></p>
<p><span>From the out.out file I can see that, it ran for 5 macro_cycles and started group b-factor refinement which reads (last few lines):</span></p>
<p><span><br>
</span></p>
<p><span></p>
<div>|-----------------------------------------------------------------------------|</div>
<div>|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|</div>
<div>| r_work = 0.3809 r_free = 0.3809 target = 0.153923 restraints weight = None |</div>
<div>|-----------------------------------------------------------------------------|</div>
<div>|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|</div>
<div>| r_work = 0.3687 r_free = 0.3687 target = 0.144348 restraints weight = 1067.479|</div>
<div>|-----------------------------------------------------------------------------|</div>
<div>|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|</div>
<div>| r_work = 0.3724 r_free = 0.3724 target = 0.147257 restraints weight = 482.176|</div>
<div>|-----------------------------------------------------------------------------|</div>
<div>|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|</div>
<div>| r_work = 0.3747 r_free = 0.3747 target = 0.149066 restraints weight = 262.900|</div>
<div>|-----------------------------------------------------------------------------|</div>
<br>
</span>
<p></p>
<p><span>The run crashes at this point....</span></p>
<p><span><br>
</span></p>
<p>However, phenix.real_space_refine runs fine when I am refining a protein chain or a complex (for eg: just the large or the small subunit of a ribosome). Does it have to do with my pdb file being so big after merging of both subunits where I have also crossed
99999 atoms and atom serial numbers start from A0000? A related question: What is the latest consensus of using chain IDs and atom serial numbers to use in phenix.real_space_refine for handling large files like ribosome pdbs ? I have found some information
on: <a href="http://cci.lbl.gov/hybrid_36/" class="OWAAutoLink" id="LPlnk576142" previewremoved="true">http://cci.lbl.gov/hybrid_36/</a></p>
<br>
<p><br>
</p>
<p>The error in terminal reads:</p>
<p><br>
</p>
<p></p>
<div>Traceback (most recent call last):</div>
<div> File "/usr/local/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 782, in <module></div>
<div> o = run(sys.argv[1:])</div>
<div> File "/usr/local/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 518, in __init__</div>
<div> self.caller(func = self.run_macro_cycles, prefix="Macro-cycles")</div>
<div> File "/usr/local/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 547, in caller</div>
<div> status = func(prefix=prefix, **kwargs)</div>
<div> File "/usr/local/phenix-1.11.1-2575/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 540, in run_macro_cycles</div>
<div> log = self.log)</div>
<div> File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 66, in __init__</div>
<div> self.caller(self.refine_adp, "ADP refinement")</div>
<div> File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 71, in caller</div>
<div> status = func(prefix=prefix)</div>
<div> File "/usr/local/phenix-1.11.1-2575/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 317, in refine_adp</div>
<div> adp_refinery.refine()</div>
<div> File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/refinement/real_space/adp.py", line 78, in refine</div>
<div> b_isos_refined = self.refine_box_with_selected(selection=sel)</div>
<div> File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/refinement/real_space/adp.py", line 56, in refine_box_with_selected</div>
<div> fmodel.update_all_scales(update_f_part1=False, apply_back_trace=True)</div>
<div> File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 1452, in update_all_scales</div>
<div> self.apply_scale_k1_to_f_obs()</div>
<div> File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 1500, in apply_scale_k1_to_f_obs</div>
<div> r_start = self.r_work()</div>
<div> File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 2004, in r_work</div>
<div> selection = selection)</div>
<div> File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 1972, in _r_factor</div>
<div> f_model = self.f_model_scaled_with_k1_w().data()</div>
<div> File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 1730, in f_model_scaled_with_k1_w</div>
<div> data = self.scale_k1_w()*self.f_model_work().data())</div>
<div> File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 2048, in scale_k1_w</div>
<div> selection=selection)</div>
<div> File "/usr/local/phenix-1.11.1-2575/modules/cctbx_project/mmtbx/f_model/f_model.py", line 182, in _scale_helper</div>
<div> raise RuntimeError("Zero denominator in scale calculation.")</div>
<div>RuntimeError: Zero denominator in scale calculation.</div>
<div><br>
</div>
<br>
<p></p>
<p>Best regards,</p>
<p>Tofayel</p>
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