[phenixbb] completeness issue

yong zhou zy_dut at hotmail.com
Sun Mar 17 00:27:33 PDT 2019

Dear Pavel,

Thanks for your reply.
The output file is attached. Please check.
Look forward to the reply.

Best regards

Yong Zhou
From: Pavel Afonine <pafonine at lbl.gov>
Sent: Tuesday, March 12, 2019 6:47 PM
To: yong zhou; phenixbb at phenix-online.org
Subject: Re: [phenixbb] completeness issue

Can you send the file to me off-list? I'll have a closer look once I have the file.

On 3/11/19 16:10, yong zhou wrote:


Recently I deposited a structure to PDB. However, I was told there is a large difference between reported (77.89%) and calculated (88.36%) values for data completeness.

In order to confirm the information, I used the command phenix.reflection_statistics and the result is as following.

Resolution range: 31.6787 1.91132

Completeness in resolution range: 0.783333

Completeness with d_max=infinity: 0.783193

Anomalous completeness in resolution range: 0.599544

Bijvoet pairs: 15786

Lone Bijvoet mates: 9291

Mean anomalous difference: 0.0671

Space group of the intensities: P 2 2 2

Space group of the metric:      P m m m

  Tolerance used in the determination of the

  lattice symmetry: 3 degrees

Possible twin laws: None

Completeness of 4-8-(GlcNAc)5/output4-8.sca:I(+),SIGI(+),I(-),SIGI(-):

unused:         - 31.6830 [    0/9    ] 0.000

bin  1: 31.6830 -  1.9113 [28083/29673] 0.946

unused:  1.9113 -         [    0/0    ]

There are two completeness values 0.783 and 0.946.

So which is the correct one?

Look forward to the reply.

Yong Zhou

phenixbb mailing list
phenixbb at phenix-online.org<mailto:phenixbb at phenix-online.org>
Unsubscribe: phenixbb-leave at phenix-online.org<mailto:phenixbb-leave at phenix-online.org>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20190317/925ce8b5/attachment-0001.htm>
-------------- next part --------------
An embedded and charset-unspecified text was scrubbed...
Name: ref-stat.txt
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20190317/925ce8b5/attachment-0001.txt>

More information about the phenixbb mailing list