Thank you Pavel, I was able to figure this issue out. It seems like some other conversion programs may also use "x", which seems to be more of a catch all status for unreliable reflections. An important distinction seems to be that the "<" status is associated with an _refln.observed_criterion, which presumably could be adjusted. Another list member shared with me offline a link to the most recent mmcif dictionary definitions. I'll pay it forward here for anyone that may come across this topic in the future. https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/ Item Index mmcif_pdbx.dichttps://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v50.dic/Items/ PDBx/mmCIF Data Dictionary Item Index mmcif_pdbx.dic mmcif.wwpdb.org Best Regards, Dale ============================= Dale Kreitler AMX Beamline Scientist National Synchrotron Light Source II Building 745, Rm. 5L143 Upton, NY 11973 631-344-7318 ________________________________ From: Pavel Afonine Sent: Thursday, May 16, 2024 8:29 PM To: Kreitler, Dale ; [email protected] Subject: Re: [phenixbb] "<" symbol in reflection mmcif status column Hi Dale, AFAIK, status "<" means excluded reflection and I see the corresponding _refln.pdbx_r_free_flag is 19 which looks like you used it as a free-R flag to mark test reflections. This is what I can guess from what I see. If this isn't enough hints to solve this and you want us to have a closer look, please send us input/output files from refinement that produces this tile and we will have a closer look. Pavel On 5/9/24 12:22, Kreitler, Dale wrote: Looking at some output reflection cif files from phenix.refine I'm wondering what does "<" mean in the status column and why would F_calc_with_sovlent structure factors also be missing for these reflections? In some cases I can see it coincides with unobserved reflections, but this doesn't seem consistent. Any insight or links to documentation that describe these values would be much appreciated. Thank you, Dale loop_ _refln.index_h _refln.index_k _refln.index_l _refln.F_meas_au _refln.F_meas_sigma_au _refln.pdbx_FWT _refln.pdbx_PHWT _refln.pdbx_DELFWT _refln.pdbx_DELPHWT _refln.pdbx_r_free_flag _refln.status _refln.pdbx_F_calc_with_solvent _refln.pdbx_phase_calc_with_solvent ... 30 0 48 65.2227 18.9183 72.4766 0 5.77152 -2.25565e-14 3 o 77.6435 1.95165e-15 30 0 49 206.068 7.45891 200.645 120 ? ? 19 < ? ? 30 0 50 33.324 17.5773 1.10423 -120 0.328059 -120 10 o 0.916822 -120 30 0 51 23.7705 14.8724 10.7438 180 2.40893 1.88332e-14 6 o 16.3173 180 ... 32 7 2 ? ? 11.4163 118.276 ? ? 5 < ? ? 32 7 3 ? ? 52.373 -121.74 ? ? 10 < ? ? 32 7 4 ? ? 33.1269 -26.1149 ? ? 3 < ? ? 32 7 5 ? ? 106.054 -86.2146 ? ? 19 < ? ? ============================= Dale Kreitler AMX Beamline Scientist National Synchrotron Light Source II Building 745, Rm. 5L143 Upton, NY 11973 631-344-7318 _______________________________________________ phenixbb mailing list [email protected]mailto:[email protected] http://phenix-online.org/mailman/listinfo/phenixbbhttps://urldefense.com/v3/__http://phenix-online.org/mailman/listinfo/phenix... Unsubscribe: [email protected]mailto:[email protected]