Protein sequence

>WP_004100416: 1-412

1-60:

M

I

V

R

P

F

R

G

L

R

P

K

N

M

I

E

K

V

A

K

P

Y

D

V

T

E

A

R

K

E

A

E

R

N

P

Y

T

F

Y

K

V

T

R

P

E

I

N

F

D

R

E

V

D

T

H

61-119:

S

D

E

V

I

L

K

G

K

E

V

L

E

F

Q

K

N

G

I

M

I

L

E

D

K

P

A

I

Y

V

Y

K

E

W

K

G

L

S

Q

I

G

I

Y

A

T

F

S

T

K

E

Y

R

D

G

K

I

K

121-179:

H

E

L

T

R

K

D

K

E

D

E

R

A

R

H

V

K

L

K

A

H

T

G

P

V

F

L

M

Y

R

S

K

P

E

L

D

T

L

I

K

H

T

S

K

I

P

E

Y

D

Y

V

D

E

T

G

I

H

181-239:

T

L

W

V

K

D

E

N

E

I

N

E

I

V

E

A

F

K

S

V

D

A

F

Y

I

A

D

G

H

R

A

R

A

E

F

A

K

E

N

P

N

H

T

G

N

E

Y

N

F

L

241-299:

A

V

L

F

P

H

N

Q

L

N

I

L

D

Y

N

R

V

K

D

L

N

G

L

S

E

F

L

N

K

V

S

E

K

F

D

V

E

R

V

E

K

S

P

Y

K

P

T

K

H

E

F

G

M

Y

L

N

301-359:

K

W

Y

K

L

T

P

K

G

T

F

D

E

N

D

V

S

L

D

V

S

I

L

Q

E

N

L

N

P

I

L

G

I

E

N

P

R

T

D

K

R

I

D

F

V

G

I

K

G

I

E

L

E

361-412:

R

L

V

D

S

G

E

F

K

V

A

F

A

L

Y

P

T

S

I

D

L

K

V

A

D

E

G

K

I

M

P

K

S

T

W

F

E

P

K

L

K

S

G

I

V

H

L

I

Secondary structure prediction (H: Helix E: Strand C: Coil)

1-60:

C

E

C

H

C

H

C

E

C

61-119:

C

H

C

E

C

E

C

E

C

E

C

121-179:

C

H

C

E

C

H

C

E

C

E

181-239:

E

C

H

C

E

C

H

C

E

241-299:

E

C

H

E

C

H

C

E

C

E

C

301-359:

C

E

C

H

C

E

C

H

361-412:

H

C

E

C

H

C

E

C

E

C

H(Helix): 125(30.34%)

E(Strand): 85(20.63%)

C(Coil): 202(49.03%)

Solvent accessibility prediction (e: Exposed b: Buried)

1-60:

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

61-119:

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

121-179:

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

181-239:

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

241-299:

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

301-359:

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

361-412:

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

B

E

e(Exposed): 203(49.27%)

b(Buried): 209(50.73%)

Disorder prediction (N: Normal T: Disorder)

1-60:

N

61-119:

N

121-179:

N

181-239:

N

241-299:

N

301-359:

N

361-412:

N

N(Normal): 412(100%)

T(Disorder): 0(0%)

Predicted contact map and distance map

Predicted distance map

Predicted contact map

Probability to Precision

Long-Range	Average probability	Predicted precision
TopL/5	0.97	96.75
TopL/2	0.94	97.68

Note: The linear model (Average probability vs Predicted precision) was trained on CASP14 dataset

Predicted Top 1 Tertiary structure

Predicted Model 1

Model 1 vs Contact (Top L/5)

./work/multicom-WP_004100416/full_length/casp1_contact/L5_long.png

Model 1 vs Contact (Top L/2)

./work/multicom-WP_004100416/full_length/casp1_contact/L2_long.png

Model 1 vs Contact (Top L)

./work/multicom-WP_004100416/full_length/casp1_contact/L_long.png

Model 1 vs Contact (Top 2L)

./work/multicom-WP_004100416/full_length/casp1_contact/2L_long.png

Predicted Contact Accuracy
( Contact file )

Long-Range	Precision
TopL/5	82.93
TopL/2	72.82
TopL	72.09
Top2L	57.40

( Alignment file )

Alignment	Number
N	6712
Neff	1985

Model comparsion

Model	TM-score
Model 2	0.9130
Model 3	0.8312
Model 4	0.8239
Model 5	0.8163
Average	0.84610

Radius Gyration

RG	RG/(2.0*L^0.4)
24.04	1.08130

Note: Radius Gyration is calculated based on wiki

Similar pdbs

PDB	TM-score
5ujd	0.43793
5x0e	0.43657
5x0j	0.43636
5x0k	0.42838
5x0b	0.42799

Note: This is multi-domain structure, check alignments and domain qualities in individual domains!

Predicted Top 2 Tertiary structure

Predicted Model 2

script 1 started

FileManager.getAtomSetCollectionFromFile(work/multicom-WP_004100416/full_length/WP_004100416.casp2.pdb)

FileManager opening url http://sysbio.rnet.missouri.edu/nihr01duf/work/multicom-WP_004100416/full_length/WP_004100416.casp2.pdb

The Resolver thinks Pdb

loadClass J.adapter.readers.pdb.PdbReader

JSmol exec jsmolApplet_M23d3 start applet null

Jmol JavaScript applet jsmolApplet_M23d3__43853221620889__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jsmolApplet_M23d3__43853221620889__)

nographics false

headless false

vwrOptions:

{ "name":"jsmolApplet_M23d3","applet":true,"documentBase":"http://sysbio.rnet.missouri.edu/nihr01duf/status.php?domain_class=full_length&method=multicom&target_name=WP_004100416","platform":"J.awtjs2d.Platform","fullName":"jsmolApplet_M23d3__43853221620889__","codePath":"http://sysbio.rnet.missouri.edu/nihr01duf/js/j2s/","display":"jsmolApplet_M23d3_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"43853221620889","bgcolor":"#FFFFFF" }

setting document base to "http://sysbio.rnet.missouri.edu/nihr01duf/status.php?domain_class=full_length&method=multicom&target_name=WP_004100416"

Jmol Version: 14.4.0_2015.12.02 2015-12-01 21:40

java.vendor: Java2Script (HTML5)

java.version: 2015-12-01 12:38:36 (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:jsmolApplet_M23d3 (signed)

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor #FFFFFF

backgroundColor = "#FFFFFF"

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 jsmolApplet_M23d3__43853221620889__ ready

Model 2 vs Contact (Top L/5)

./work/multicom-WP_004100416/full_length/casp2_contact/L5_long.png

Model 2 vs Contact (Top L/2)

./work/multicom-WP_004100416/full_length/casp2_contact/L2_long.png

Model 2 vs Contact (Top L)

./work/multicom-WP_004100416/full_length/casp2_contact/L_long.png

Model 2 vs Contact (Top 2L)

./work/multicom-WP_004100416/full_length/casp2_contact/2L_long.png

Predicted Contact Accuracy
( Contact file )

Long-Range	Precision
TopL/5	79.27
TopL/2	71.84
TopL	71.84
Top2L	58.37

( Alignment file )

Alignment	Number
N	6712
Neff	1985

Model comparsion

Model	TM-score
Model 1	0.9130
Model 3	0.8376
Model 4	0.8027
Model 5	0.7985
Average	0.83795

Radius Gyration

RG	RG/(2.0*L^0.4)
24.41	1.09794

Note: Radius Gyration is calculated based on wiki

Similar pdbs

PDB	TM-score
5ujd	0.43484
5x0j	0.43133
5x0e	0.43123
5x0b	0.42520
5x0k	0.42466

Note: This is multi-domain structure, check alignments and domain qualities in individual domains!

Predicted Top 3 Tertiary structure

Predicted Model 3

loadClass core.package

loadClass java.lang.String

loadClass core.package

JSmol exec jsmolApplet_M23d1 start applet null

Jmol JavaScript applet jsmolApplet_M23d1__43853221620889__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jsmolApplet_M23d1__43853221620889__)

nographics false

headless false

vwrOptions:

{ "name":"jsmolApplet_M23d1","applet":true,"documentBase":"http://sysbio.rnet.missouri.edu/nihr01duf/status.php?domain_class=full_length&method=multicom&target_name=WP_004100416","platform":"J.awtjs2d.Platform","fullName":"jsmolApplet_M23d1__43853221620889__","codePath":"http://sysbio.rnet.missouri.edu/nihr01duf/js/j2s/","display":"jsmolApplet_M23d1_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"43853221620889","bgcolor":"#FFFFFF" }

setting document base to "http://sysbio.rnet.missouri.edu/nihr01duf/status.php?domain_class=full_length&method=multicom&target_name=WP_004100416"

Jmol Version: 14.4.0_2015.12.02 2015-12-01 21:40

java.vendor: Java2Script (HTML5)

java.version: 2015-12-01 12:38:36 (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:jsmolApplet_M23d1 (signed)

loadClass JS.ScriptManager

JSmol exec jsmolApplet_M23d2 start applet null

Jmol JavaScript applet jsmolApplet_M23d2__43853221620889__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jsmolApplet_M23d2__43853221620889__)

nographics false

headless false

vwrOptions:

{ "name":"jsmolApplet_M23d2","applet":true,"documentBase":"http://sysbio.rnet.missouri.edu/nihr01duf/status.php?domain_class=full_length&method=multicom&target_name=WP_004100416","platform":"J.awtjs2d.Platform","fullName":"jsmolApplet_M23d2__43853221620889__","codePath":"http://sysbio.rnet.missouri.edu/nihr01duf/js/j2s/","display":"jsmolApplet_M23d2_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"43853221620889","bgcolor":"#FFFFFF" }

setting document base to "http://sysbio.rnet.missouri.edu/nihr01duf/status.php?domain_class=full_length&method=multicom&target_name=WP_004100416"

Jmol Version: 14.4.0_2015.12.02 2015-12-01 21:40

java.vendor: Java2Script (HTML5)

java.version: 2015-12-01 12:38:36 (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:jsmolApplet_M23d2 (signed)

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor #FFFFFF

backgroundColor = "#FFFFFF"

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 jsmolApplet_M23d2__43853221620889__ ready

script 1 started

FileManager.getAtomSetCollectionFromFile(work/multicom-WP_004100416/full_length/WP_004100416.casp3.pdb)

FileManager opening url http://sysbio.rnet.missouri.edu/nihr01duf/work/multicom-WP_004100416/full_length/WP_004100416.casp3.pdb

The Resolver thinks Pdb

Time for openFile(work/multicom-WP_004100416/full_length/WP_004100416.casp3.pdb): 321 ms

reading 4130 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 Babel

4130 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Jmol 14.4.0_2015.12.02 2015-12-01 21:40 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.

NOTE: Backbone amide hydrogen positions are present and will be ignored. Their positions will be approximated, as in standard DSSP analysis.

Use SET dsspCalculateHydrogenAlways FALSE to not use this approximation.

null

loadClass J.thread.SpinThread

Script completed

Jmol script terminated

Time for openFile(work/multicom-WP_004100416/full_length/WP_004100416.casp2.pdb): 1209 ms

reading 4130 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 Babel

4130 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Jmol 14.4.0_2015.12.02 2015-12-01 21:40 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.

NOTE: Backbone amide hydrogen positions are present and will be ignored. Their positions will be approximated, as in standard DSSP analysis.

Use SET dsspCalculateHydrogenAlways FALSE to not use this approximation.

null

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor #FFFFFF

backgroundColor = "#FFFFFF"

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 jsmolApplet_M23d1__43853221620889__ ready

Model 3 vs Contact (Top L/5)

./work/multicom-WP_004100416/full_length/casp3_contact/L5_long.png

Model 3 vs Contact (Top L/2)

./work/multicom-WP_004100416/full_length/casp3_contact/L2_long.png

Model 3 vs Contact (Top L)

./work/multicom-WP_004100416/full_length/casp3_contact/L_long.png

Model 3 vs Contact (Top 2L)

./work/multicom-WP_004100416/full_length/casp3_contact/2L_long.png

Predicted Contact Accuracy
( Contact file )

Long-Range	Precision
TopL/5	81.71
TopL/2	73.30
TopL	71.84
Top2L	57.65

( Alignment file )

Alignment	Number
N	6712
Neff	1985

Model comparsion

Model	TM-score
Model 1	0.8312
Model 2	0.8376
Model 4	0.8121
Model 5	0.8004
Average	0.82032

Radius Gyration

RG	RG/(2.0*L^0.4)
23.84	1.07230

Note: Radius Gyration is calculated based on wiki

Similar pdbs

PDB	TM-score
5ujd	0.43774
5x0j	0.43507
5x0e	0.43387
5x0k	0.42787
5x0b	0.42779

Note: This is multi-domain structure, check alignments and domain qualities in individual domains!

Predicted Top 4 Tertiary structure

Predicted Model 4

script 1 started

FileManager.getAtomSetCollectionFromFile(work/multicom-WP_004100416/full_length/WP_004100416.casp4.pdb)

FileManager opening url http://sysbio.rnet.missouri.edu/nihr01duf/work/multicom-WP_004100416/full_length/WP_004100416.casp4.pdb

The Resolver thinks Pdb

Time for openFile(work/multicom-WP_004100416/full_length/WP_004100416.casp4.pdb): 227 ms

reading 4130 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 Babel

4130 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Jmol 14.4.0_2015.12.02 2015-12-01 21:40 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.

NOTE: Backbone amide hydrogen positions are present and will be ignored. Their positions will be approximated, as in standard DSSP analysis.

Use SET dsspCalculateHydrogenAlways FALSE to not use this approximation.

null

Script completed

Jmol script terminated

JSmol exec jsmolApplet_M23d5 start applet null

Jmol JavaScript applet jsmolApplet_M23d5__43853221620889__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jsmolApplet_M23d5__43853221620889__)

nographics false

headless false

vwrOptions:

{ "name":"jsmolApplet_M23d5","applet":true,"documentBase":"http://sysbio.rnet.missouri.edu/nihr01duf/status.php?domain_class=full_length&method=multicom&target_name=WP_004100416","platform":"J.awtjs2d.Platform","fullName":"jsmolApplet_M23d5__43853221620889__","codePath":"http://sysbio.rnet.missouri.edu/nihr01duf/js/j2s/","display":"jsmolApplet_M23d5_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"43853221620889","bgcolor":"#FFFFFF" }

setting document base to "http://sysbio.rnet.missouri.edu/nihr01duf/status.php?domain_class=full_length&method=multicom&target_name=WP_004100416"

Jmol Version: 14.4.0_2015.12.02 2015-12-01 21:40

java.vendor: Java2Script (HTML5)

java.version: 2015-12-01 12:38:36 (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:jsmolApplet_M23d5 (signed)

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor #FFFFFF

backgroundColor = "#FFFFFF"

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 jsmolApplet_M23d5__43853221620889__ ready

Model 4 vs Contact (Top L/5)

./work/multicom-WP_004100416/full_length/casp4_contact/L5_long.png

Model 4 vs Contact (Top L/2)

./work/multicom-WP_004100416/full_length/casp4_contact/L2_long.png

Model 4 vs Contact (Top L)

./work/multicom-WP_004100416/full_length/casp4_contact/L_long.png

Model 4 vs Contact (Top 2L)

./work/multicom-WP_004100416/full_length/casp4_contact/2L_long.png

Predicted Contact Accuracy
( Contact file )

Long-Range	Precision
TopL/5	87.80
TopL/2	80.10
TopL	74.76
Top2L	60.92

( Alignment file )

Alignment	Number
N	6712
Neff	1985

Model comparsion

Model	TM-score
Model 1	0.8239
Model 2	0.8027
Model 3	0.8121
Model 5	0.9489
Average	0.84690

Radius Gyration

RG	RG/(2.0*L^0.4)
20.89	0.93961

Note: Radius Gyration is calculated based on wiki

Similar pdbs

PDB	TM-score
5x0e	0.44019
5x0j	0.43979
5ujd	0.43855
5x0b	0.42523
5x0k	0.42452

Note: This is multi-domain structure, check alignments and domain qualities in individual domains!

Predicted Top 5 Tertiary structure

Predicted Model 5

spinFPS is set too fast (30) -- can't keep up!

Script completed

Jmol script terminated

JSmol exec jsmolApplet_M23d4 loadClazz null

JSmol exec jsmolApplet_M23d4 start applet null

Jmol JavaScript applet jsmolApplet_M23d4__43853221620889__ initializing

Jmol getValue debug null

Jmol getValue logLevel null

Jmol getValue allowjavascript null

AppletRegistry.checkIn(jsmolApplet_M23d4__43853221620889__)

nographics false

headless false

vwrOptions:

{ "name":"jsmolApplet_M23d4","applet":true,"documentBase":"http://sysbio.rnet.missouri.edu/nihr01duf/status.php?domain_class=full_length&method=multicom&target_name=WP_004100416","platform":"J.awtjs2d.Platform","fullName":"jsmolApplet_M23d4__43853221620889__","codePath":"http://sysbio.rnet.missouri.edu/nihr01duf/js/j2s/","display":"jsmolApplet_M23d4_canvas2d","signedApplet":"true","appletReadyCallback":"Jmol._readyCallback","statusListener":"[J.appletjs.Jmol object]","syncId":"43853221620889","bgcolor":"#FFFFFF" }

setting document base to "http://sysbio.rnet.missouri.edu/nihr01duf/status.php?domain_class=full_length&method=multicom&target_name=WP_004100416"

Jmol Version: 14.4.0_2015.12.02 2015-12-01 21:40

java.vendor: Java2Script (HTML5)

java.version: 2015-12-01 12:38:36 (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:jsmolApplet_M23d4 (signed)

Jmol getValue emulate null

defaults = "Jmol"

Jmol getValue boxbgcolor null

Jmol getValue bgcolor #FFFFFF

backgroundColor = "#FFFFFF"

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 jsmolApplet_M23d4__43853221620889__ ready

script 1 started

FileManager.getAtomSetCollectionFromFile(work/multicom-WP_004100416/full_length/WP_004100416.casp5.pdb)

FileManager opening url http://sysbio.rnet.missouri.edu/nihr01duf/work/multicom-WP_004100416/full_length/WP_004100416.casp5.pdb

The Resolver thinks Pdb

Time for openFile(work/multicom-WP_004100416/full_length/WP_004100416.casp5.pdb): 225 ms

reading 4130 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 Babel

4130 atoms created

ModelSet: autobonding; use autobond=false to not generate bonds automatically

Jmol 14.4.0_2015.12.02 2015-12-01 21:40 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.

NOTE: Backbone amide hydrogen positions are present and will be ignored. Their positions will be approximated, as in standard DSSP analysis.

Use SET dsspCalculateHydrogenAlways FALSE to not use this approximation.

null

Script completed

Jmol script terminated

spinFPS is set too fast (30) -- can't keep up!

Model 5 vs Contact (Top L/5)

./work/multicom-WP_004100416/full_length/casp5_contact/L5_long.png

Model 5 vs Contact (Top L/2)

./work/multicom-WP_004100416/full_length/casp5_contact/L2_long.png

Model 5 vs Contact (Top L)

./work/multicom-WP_004100416/full_length/casp5_contact/L_long.png

Model 5 vs Contact (Top 2L)

./work/multicom-WP_004100416/full_length/casp5_contact/2L_long.png

Predicted Contact Accuracy
( Contact file )

Long-Range	Precision
TopL/5	86.59
TopL/2	78.64
TopL	73.30
Top2L	59.59

( Alignment file )

Alignment	Number
N	6712
Neff	1985

Model comparsion

Model	TM-score
Model 1	0.8163
Model 2	0.7985
Model 3	0.8004
Model 4	0.9489
Average	0.84103

Radius Gyration

RG	RG/(2.0*L^0.4)
21.03	0.94591

Note: Radius Gyration is calculated based on wiki

Similar pdbs

PDB	TM-score
5x0e	0.44337
5x0j	0.44328
5ujd	0.44122
5x0b	0.43296
5x0k	0.43280

Note: This is multi-domain structure, check alignments and domain qualities in individual domains!

Domain Boundary prediction ( View )

Protein sequence

Secondary structure prediction (H: Helix E: Strand C: Coil)

Solvent accessibility prediction (e: Exposed b: Buried)

Disorder prediction (N: Normal T: Disorder)

Predicted contact map and distance map

Probability to Precision

Predicted Top 1 Tertiary structure

Predicted Contact Accuracy
( Contact file )

( Alignment file )

Model comparsion

Radius Gyration

Similar pdbs

Predicted Top 2 Tertiary structure

Predicted Contact Accuracy
( Contact file )

( Alignment file )

Model comparsion

Radius Gyration

Similar pdbs

Predicted Top 3 Tertiary structure

Predicted Contact Accuracy
( Contact file )

( Alignment file )

Model comparsion

Radius Gyration

Similar pdbs

Predicted Top 4 Tertiary structure

Predicted Contact Accuracy
( Contact file )

( Alignment file )

Model comparsion

Radius Gyration

Similar pdbs

Predicted Top 5 Tertiary structure

Predicted Contact Accuracy
( Contact file )

( Alignment file )

Model comparsion

Radius Gyration

Similar pdbs

References

Domain Boundary prediction ( View )

Predicted contact map and distance map

Probability to Precision

Predicted Top 1 Tertiary structure

Predicted Contact Accuracy ( Contact file )

Model comparsion

Radius Gyration

Similar pdbs

Predicted Top 2 Tertiary structure

Predicted Contact Accuracy ( Contact file )

Model comparsion

Radius Gyration

Similar pdbs

Predicted Top 3 Tertiary structure

Predicted Contact Accuracy ( Contact file )

Model comparsion

Radius Gyration

Similar pdbs

Predicted Top 4 Tertiary structure

Predicted Contact Accuracy ( Contact file )

Model comparsion

Radius Gyration

Similar pdbs

Predicted Top 5 Tertiary structure

Predicted Contact Accuracy ( Contact file )

Model comparsion

Radius Gyration

Similar pdbs

References

Predicted Contact Accuracy
( Contact file )

Predicted Contact Accuracy
( Contact file )

Predicted Contact Accuracy
( Contact file )

Predicted Contact Accuracy
( Contact file )

Predicted Contact Accuracy
( Contact file )