I-TASSER-MR:Molecular replacement using I-TASSER model

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Sequence Information of T2297kq8l(your_protein)

SMQEEDTFRELRIFLRNVTHRLAIDKRFRVFTKPVDPDEVPDYVTVIKQPMDLSSVISKIDLHKYLTVKDYLRDIDLICS
NALEYNPDRDPGDRLIRHRACALRDTAYAIIKEELDEDFEQLCEEIQESR

The Input Parameters

Unit cell (a,b,c):	(79.6160,79.6160,137.5500)
Unit cell (α,β,γ):	(90.0000,90.0000,120.0000)
Space Group:	P 65 2 2
Copy Number:	1
Lowest Resolution:	68.949
Highest Resolution:	1.950
mtz file:	Download

Best Models with the lowest R-free

MR Model		Refined Model
Jmol._Canvas2D (Jmol) "appletdiv"[x] script 1 started antialiasDisplay = true FileManager.getAtomSetCollectionFromFile(model_lr.pdb) FileManager opening url https://zhanglab.comp.nus.edu.sg/I-TASSER-MR/example/model_lr.pdb The Resolver thinks Pdb Setting space group name to P 65 2 2 Time for openFile(model_lr.pdb): 480 ms reading 982 atoms ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. Default Van der Waals type for model set to Jmol 982 atoms created ModelSet: autobonding; use autobond=false to not generate bonds automatically Jmol 14.4.2_2016.02.14 2016-02-14 21:09 DSSP analysis for model 1.1 - null W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637 We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software, and we thank the CMBI for maintaining it to the extent that it was easy to re-engineer for our purposes. At this point in time, we make no guarantee that this code gives precisely the same analysis as the code available via license from CMBI at http://swift.cmbi.ru.nl/gv/dssp All bioshapes have been deleted and must be regenerated. loadScript /I-TASSER-MR/j2s/core/corescriptcmd.z.js Script completed Jmol script terminated loadScript /I-TASSER-MR/j2s/J/g3d/HermiteRenderer.js Script completed Jmol script terminated		Jmol._Canvas2D (Jmol) "appletdiv2"[x] loadScript /I-TASSER-MR/j2s/core/package.js loadScript /I-TASSER-MR/j2s/core/corejmol.z.js JSmol exec appletdiv start applet null Jmol JavaScript applet appletdiv__1216298146943386__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript true AppletRegistry.checkIn(appletdiv__1216298146943386__) vwrOptions: { "name":"appletdiv","allowJavaScript":true,"applet":true,"documentBase":"https://zhanglab.comp.nus.edu.sg/I-TASSER-MR/example/index.html","platform":"J.awtjs2d.Platform","fullName":"appletdiv__1216298146943386__","codePath":"https:/I-TASSER-MR/j2s/","display":"appletdiv_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"1216298146943386","bgcolor":"black" } setting document base to "https://zhanglab.comp.nus.edu.sg/I-TASSER-MR/example/index.html" (C) 2015 Jmol Development Jmol Version: 14.4.2_2016.02.14 2016-02-14 21:09 java.vendor: Java2Script (HTML5) java.version: 2016-02-14 19:46:51 (JSmol/j2s) os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com) Access: ALL memory: 0.0/0.0 processors available: 1 useCommandThread: false appletId:appletdiv (signed) loadScript /I-TASSER-MR/j2s/core/corescript.z.js JSmol exec appletdiv2 start applet null Jmol JavaScript applet appletdiv2__1216298146943386__ initializing Jmol getValue debug null Jmol getValue logLevel null Jmol getValue allowjavascript true AppletRegistry.checkIn(appletdiv2__1216298146943386__) vwrOptions: { "name":"appletdiv2","allowJavaScript":true,"applet":true,"documentBase":"https://zhanglab.comp.nus.edu.sg/I-TASSER-MR/example/index.html","platform":"J.awtjs2d.Platform","fullName":"appletdiv2__1216298146943386__","codePath":"https:/I-TASSER-MR/j2s/","display":"appletdiv2_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"1216298146943386","bgcolor":"black" } setting document base to "https://zhanglab.comp.nus.edu.sg/I-TASSER-MR/example/index.html" (C) 2015 Jmol Development Jmol Version: 14.4.2_2016.02.14 2016-02-14 21:09 java.vendor: Java2Script (HTML5) java.version: 2016-02-14 19:46:51 (JSmol/j2s) os.name: Mozilla/5.0 AppleWebKit/537.36 (KHTML, like Gecko; compatible; ClaudeBot/1.0; +claudebot@anthropic.com) Access: ALL memory: 0.0/0.0 processors available: 1 useCommandThread: false appletId:appletdiv2 (signed) Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor black backgroundColor = "black" Jmol getValue ANIMFRAMECallback null Jmol getValue APPLETREADYCallback Jmol._readyCallback APPLETREADYCallback = "Jmol._readyCallback" callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY Jmol getValue ATOMMOVEDCallback null Jmol getValue CLICKCallback null Jmol getValue DRAGDROPCallback null Jmol getValue ECHOCallback null Jmol getValue ERRORCallback null Jmol getValue EVALCallback null Jmol getValue HOVERCallback null Jmol getValue IMAGECallback null Jmol getValue LOADSTRUCTCallback null Jmol getValue MEASURECallback null Jmol getValue MESSAGECallback null Jmol getValue MINIMIZATIONCallback null Jmol getValue SERVICECallback null Jmol getValue PICKCallback null Jmol getValue RESIZECallback null Jmol getValue SCRIPTCallback null Jmol getValue SYNCCallback null Jmol getValue STRUCTUREMODIFIEDCallback null Jmol getValue doTranslate null language=en_US Jmol getValue popupMenu null Jmol getValue script null Jmol getValue loadInline null Jmol getValue load null Jmol applet appletdiv2__1216298146943386__ ready script 1 started antialiasDisplay = true FileManager.getAtomSetCollectionFromFile(model_lr.pdb) FileManager opening url https://zhanglab.comp.nus.edu.sg/I-TASSER-MR/example/model_lr.pdb The Resolver thinks Pdb loadScript /I-TASSER-MR/j2s/core/corebio.z.js Setting space group name to P 65 2 2 Time for openFile(model_lr.pdb): 1268 ms reading 982 atoms ModelSet: haveSymmetry:false haveUnitcells:false haveFractionalCoord:false 1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them. Default Van der Waals type for model set to Jmol 982 atoms created ModelSet: autobonding; use autobond=false to not generate bonds automatically Jmol 14.4.2_2016.02.14 2016-02-14 21:09 DSSP analysis for model 1.1 - null W. Kabsch and C. Sander, Biopolymers, vol 22, 1983, pp 2577-2637 We thank Wolfgang Kabsch and Chris Sander for writing the DSSP software, and we thank the CMBI for maintaining it to the extent that it was easy to re-engineer for our purposes. At this point in time, we make no guarantee that this code gives precisely the same analysis as the code available via license from CMBI at http://swift.cmbi.ru.nl/gv/dssp All bioshapes have been deleted and must be regenerated. Jmol getValue emulate null defaults = "Jmol" Jmol getValue boxbgcolor null Jmol getValue bgcolor black backgroundColor = "black" Jmol getValue ANIMFRAMECallback null Jmol getValue APPLETREADYCallback Jmol._readyCallback APPLETREADYCallback = "Jmol._readyCallback" callback set for APPLETREADYCallback Jmol._readyCallback APPLETREADY Jmol getValue ATOMMOVEDCallback null Jmol getValue CLICKCallback null Jmol getValue DRAGDROPCallback null Jmol getValue ECHOCallback null Jmol getValue ERRORCallback null Jmol getValue EVALCallback null Jmol getValue HOVERCallback null Jmol getValue IMAGECallback null Jmol getValue LOADSTRUCTCallback null Jmol getValue MEASURECallback null Jmol getValue MESSAGECallback null Jmol getValue MINIMIZATIONCallback null Jmol getValue SERVICECallback null Jmol getValue PICKCallback null Jmol getValue RESIZECallback null Jmol getValue SCRIPTCallback null Jmol getValue SYNCCallback null Jmol getValue STRUCTUREMODIFIEDCallback null Jmol getValue doTranslate null language=en_US Jmol getValue popupMenu null Jmol getValue script null Jmol getValue loadInline null Jmol getValue load null Jmol applet appletdiv__1216298146943386__ ready
MR-T2297kq8l-1-M1 R_free=0.4758		Refine-T2297kq8l-1-M1 R_free=0.3553

I-TASSER-MR Results of Sequence T2297kq8l

I-TASSER
Models

I-TASSER-MR Models

Model1

Search Model	MR Model	Refined Model	Starting Rwork	Final Rwork	Starting Rfree	Final Rfree
Search-T2297kq8l-1-M1	MR-T2297kq8l-1-M1	Refine-T2297kq8l-1-M1	0.4623	0.3330	0.4758	0.3553
Search-T2297kq8l-2-M1	MR-T2297kq8l-2-M1	Refine-T2297kq8l-2-M1	0.4620	0.3326	0.4752	0.3589
Search-T2297kq8l-3-M1	MR-T2297kq8l-3-M1	Refine-T2297kq8l-3-M1	0.4615	0.3327	0.4755	0.3598
Search-T2297kq8l-4-M1	MR-T2297kq8l-4-M1	Refine-T2297kq8l-4-M1	0.4618	0.3378	0.4726	0.3644
Search-T2297kq8l-5-M1	MR-T2297kq8l-5-M1	Refine-T2297kq8l-5-M1	0.4614	0.3315	0.4712	0.3648

I-TASSER Models:the models predicted by I-TASSER;
I-TASSER-MR Models: top 5 search models, MR models and refined models ranked by the final Rfreee of the refined models;
Search Model: top 5 search models edited by progressive model truncation;
MR Model: top 5 models produced by MR-REX from the corresponding top 5 search models;
Starting Rwork: the starting Rwork of the refined models;
Final Rwork: the final Rwork of the refined models;
Starting Rfree: the starting Rfree of the refined models;
Final Rfree: the final Rfree of the refined models.

I-TASSER Search Models for Sequence T2297kq8l
I-TASSER Models	Distribution of the AVS-score	Download
Model1 cscore:0.84		Download

I-TASSER Models: the models predicted by I-TASSER;
Download: the dowload file includes the AVS score file and all the edited search models;

Top 10 templates used by I-TASSER for Sequence T2297kq8l
Rank	Template	Aligned Length	Coverage	Z-score	Program	Alignments
1	3daiA	130	1.000	20.598	MUSTER	Download
2	5epb_A	129	0.992	19.351	HHpred_local	Download
3	5e74a	113	0.869	19.383	SP3	Download
4	3daiA	130	1.000	8.315	PROSPECT2	Download
5	3daiA	130	1.000	41.312	PPA-I	Download
6	5epb_A	130	1.000	17.790	HHpred_global	Download
7	4nr9a	113	0.869	18.539	SPARKS2	Download
8	2dkwA	125	0.962	17.643	MUSTER	Download
9	2dkw_A	124	0.954	17.755	HHpred_local	Download
10	4nr9a	113	0.869	19.352	SP3	Download

Rank of templates: represents the top ten threading templates used by I-TASSER;
Aligned length: the number of aligned residues;
Coverage: it represents the coverage of the threading alignment and is equal to the number of aligned residues divided by the length of query protein;
Z-score: Z-score is the normalized Z-score of the threading alignment;
Download Alignments: Provides the 3D structure of the aligned regions of the threading templates.

Download

All the result files shown in the page can be downloaded as a tarball package.

References:

Y. Wang, J. Virtanen, Z. Xue, Y. Zhang. I-TASSER-MR: automated molecular replacement for proteins without close homologs using iterative fragment assembly and progressive sequence truncation, submitted (2017).
Y. Wang, J. Virtanen, Z. Xue, J. J. G. Tesmer and Y. Zhang. Using iterative fragment assembly and progressive sequence truncation to facilitate phasing and crystal structure determination of distantly related proteins. Acta Cryst. (2016). D72, 616-628

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