Workunit: P000002

Title:P2

Model Details: Batch.1

model pic
Target:
modelled residue
154 to 319
range:
based on template 3nmeA (2.40 A)
Sequence Identity
23.81
[%]:
Evalue: 5.9E-41

Alignment

TARGET 154 AMH YSRILPNIWL GSCPRQVEHV TIKLKHELGV TAVMNFQTEW

3nmeA 90 yrhel--gxn ynfirpdliv gsclqtpedv d-kl-rkigv ktifclqqdp

TARGET s ssss ssss sss hh ssssss hh

3nmeA s ssss ssss sss hhh h hh h ssssss h

TARGET 197 DIVQNSSGCN RYPEPMTPDT MIKLY-KEEG LAYIWMPTPD MSTEGRVQML

3nmeA 136 dleyf--gvd i-------ss iqayakkysd iqhirceird fdafdlrxrl

TARGET hhh hh hhh h hhh sssss hhhhhhhh

3nmeA hhhhh hh hhhhhh sssss hhhhhhhh

TARGET 246 PQAVCLLHAL LEK-GHTVYV HCNAGVGRST AAVCGWLQYV LGWSRRKVQY

3nmeA 177 pavvgtlyka vkrnggvtyv hstagxgrap avaltyxfwv qgyklxeahk

TARGET hhhhhhhhhh h sss ss hh hhhhhhhhhh hhhhhh

3nmeA hhhhhhhhhh hhhh sss ss hhh hhhhhhhhhh hhhhhh

TARGET 295 FLVAKRPAVY IDEEALARAE EDFYQ ---- ---------- ----------

3nmeA 227 llxskrs-cf pkldairnat idiltglkrk tvtltlkdkg fsrveisgld

TARGET hhhhh hhhhhhhh hhhh

3nmeA hhhhh hhhhhhhh hhhh s ssssssss sssssss

1
TARGET ---------- ---------- ---------- ---------- ----------
3nmeA 276 igwgqriplt lgkgtgfwil krelpegqfe ykyiidgewt hneaepfigp

TARGET
3nmeA ssss ss sssss ssss ssss ssssss sss sss

TARGET ---------- ---------- ---------- ---------- ----------

3nmeA 326 nkdghtnnya kvvddptsvd gttrerlsse dpelleeers kliqfletcs

TARGET
3nmeA ssss ss hhhhh hhhhh hhhhhhhhh

TARGET ----
3nmeA 376 eaev

TARGET
3nmeA

Anolea

Modelling log

3.70 (SP3)
Loading Template: 3nmeA.pdb
Loading Raw Sequence
Renumber target sequence starting from (154)
Loading Alignment: ./NXXX.align.submit.fasta
Removing HET groups from template structure
Refining Raw Sequence Alignment
ProModII: doing simple assignment of backbone
ProModII: adding blocking groups

2
Adding Missing Sidechains
AddPolar H
BuildDeletetedLoopsModel
Trying Ligating with anchor residues TYR 221 and GLU 224
Number of Ligations found: 3
all loops are bad; continuing CSP with larger segment
Trying Ligating with anchor residues TYR 221 and GLY 225
Number of Ligations found: 64
all loops are bad; continuing CSP with larger segment
Trying Ligating with anchor residues TYR 221 and LEU 226
Number of Ligations found: 500
all loops are bad; continuing CSP with larger segment
Trying Ligating with anchor residues LEU 220 and LEU 226
Number of Ligations found: 500
ACCEPTING loop 162: clash= 0 FF= 671.2 PP= -2.00
Trying Ligating with anchor residues LYS 258 and THR 261
Trying Ligating with anchor residues GLU 257 and THR 261
Trying Ligating with anchor residues GLU 257 and VAL 262
Number of Ligations found: 57
ACCEPTING loop 56: clash= 0 FF= 99.2 PP= -4.00
Building CSP loop with anchor residues THR 177 and LEU 180
connectivity problem --> including residue LEU 28
Building CSP loop with anchor residues THR 177 and LYS 181
Building CSP loop with anchor residues THR 177 and HIS 182
Number of Ligations found: 19
all loops are bad; continuing CSP with larger segment
Building CSP loop with anchor residues THR 177 and GLU 183
Number of Ligations found: 131
ACCEPTING loop 14: clash= 0 FF= 399.8 PP= -3.00
Building CSP loop with anchor residues ASN 201 and GLY 204
Building CSP loop with anchor residues GLN 200 and GLY 204
Building CSP loop with anchor residues GLN 200 and CYS 205
Number of Ligations found: 181
ACCEPTING loop 132: clash= 0 FF= -357.6 PP= -3.00
Building CSP loop with anchor residues ARG 207 and ASP 215
Number of Ligations found: 500
all loops are bad; continuing CSP with larger segment
Building CSP loop with anchor residues ASN 206 and ASP 215
Number of Ligations found: 500
all loops are bad; continuing CSP with larger segment
Building CSP loop with anchor residues CYS 205 and ASP 215
Number of Ligations found: 500
all loops are bad; continuing CSP with larger segment
+++ Warning: CSP Loop Insertion Failed, will use SparePart later
Building CSP loop with anchor residues PRO 301 and TYR 304
Number of Ligations found: 8
ACCEPTING loop 1: clash= 0 FF= 646.6 PP= 0.00
Finding Spare-Part loop with anchor residues SER 203 and PRO 214
ACCEPTING loop 132 from 2NACA Clash= 4 FF= -39.0 PP=-30.54
BadPhi= 1 BadGX= 0 BadXP= 1 weakXP= 1 Score= 7.75 rms= 0.00
Optimizing Sidechains
Adding Hydrogens
Optimizing loops and OXT (nb = 33)
Final Total Energy: -1892.989 KJ/mol
Dumping Sequence Alignment

Model Details: Batch.2

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model pic
Target:
modelled residue
10 to 103
range:
based on template 1d3cA (1.78 A)
Sequence Identity
23.404
[%]:
Evalue: 1.2E-09

Alignment

1d3cA 1 apdtsvsnkq nfstdviyqi ftdrfsdgnp annptgaafd gtctnlrlyc

1d3cA sssss hhh

1d3cA 51 ggdwqgiink indgyltgmg vtaiwisqpv eniysiinys gvnntayhgy

1d3cA hhhhhhh h hhhhh sssss ss sss sss sss

1d3cA 101 wardfkktnp aygtiadfqn liaaahakni kviidfapnh tspassdqps

1d3cA sss sss hhhhhh hhhhhh ssssss ss ssss

1d3cA 151 faengrlydn gtllggytnd tqnlfhhngg tdfsttengi yknlydladl

1d3cA sss sss sss hhhhh sssss

1d3cA 201 nhnnstvdvy lkdaikmwld lgidgirmna vkhmpfgwqk sfmaavnnyk

1d3cA s hhhhhh hhhhhhhhhh sssss hhhhh hhhhhhh

1d3cA 251 pvftfgqwfl gvnevspenh kfanesgmsl ldfrfaqkvr qvfrdntdnm

1d3cA sssss hhhh hhhh ss s hhhhhhhh hhh h

1d3cA 301 yglkamlegs aadyaqvddq vtfidnhdme rfhasnanrr kleqalaftl

4
1d3cA hhhhhhhhhh hhh s ss h hhhhhhhhhh

1d3cA 351 tsrgvpaiyy gteqymsggt dpdnrarips fststtayqv iqklaplrkc

1d3cA h ssssss hhhhh hhhhhhhhh

1d3cA 401 npaiaygstq erwinndvli yerkfgsnva vvavnrnlna pasisglvts

1d3cA hhh sss sssss ssss sssss ssss ssssss sss sss

1d3cA 451 lpqgsyndvl ggllngntls vgsggaasnf tlaaggtavw qytaatatpt

1d3cA sss ss ss ssss s ss sssss ssss ss

1d3cA 501 ighvgpmmak pgvtitidgr gfgsskgtvy fgttavsgad itswedtqik

1d3cA sssss sss ssssssss s sss ss sss s sssss ssss

TARGET 10 SPAVA
1d3cA 551 vkipavaggn ynikvanaag tasnvydnfe vlsgdqvsvr fvv--nnatt

TARGET
1d3cA sss ss sssssss sss ss ss ssssss sss ss

TARGET 15 GAGPELLVVG SRPELGRWEP SGAVRLRPAG TAAGAGALAL QEPGLWLGEV

1d3cA 599 algqnvyltg svselgnwdp akaigpmynq vvyqy----- --p-nwyydv

TARGET ssssss ss ssss ss s sss

1d3cA ssssss ss ssss s ssssss

TARGET 65 ELAAEEAAQD GAEPGRVDTF WYKFLKREPG GELSWEGNG ----------

1d3cA 641 svpagkt--- ---------i efkflkkq-g stvtweggsn htftapssgt

TARGET sss ss sssss ssssssss sssss

1d3cA sssssss s ssssssss sssss ssssss

TARGET ---------
1d3cA 678 atinvnwqp

TARGET
1d3cA sssssss

5
Anolea

Modelling log

3.70 (SP3)
Loading Template: 1d3cA.pdb
Loading Raw Sequence
Renumber target sequence starting from (10)
Loading Alignment: ./NXXX.align.submit.fasta
Removing HET groups from template structure
Refining Raw Sequence Alignment
ProModII: doing simple assignment of backbone
ProModII: adding blocking groups
Adding Missing Sidechains
AddPolar H
BuildDeletetedLoopsModel
Building CSP loop with anchor residues ALA 49 and PRO 57
connectivity problem --> including residue PRO 49
Building CSP loop with anchor residues ALA 49 and GLY 58
Building CSP loop with anchor residues ALA 49 and LEU 59
Number of Ligations found: 500
ACCEPTING loop 362: clash= 0 FF= 322.0 PP= -1.00
Building CSP loop with anchor residues PRO 93 and GLU 96
Building CSP loop with anchor residues GLU 92 and GLU 96
Number of Ligations found: 110
ACCEPTING loop 58: clash= 0 FF= 39.2 PP= -2.00
Finding Spare-Part loop with anchor residues ALA 71 and PHE 84
Sorry, no loop could be found in the database
Finding Spare-Part loop with anchor residues GLU 70 and PHE 84
ACCEPTING loop 1 from 2FB4L Clash= 4 FF= 227.0 PP=-10.76
BadPhi= 2 BadGX= 0 BadXP= 1 weakXP= 1 Score= 8.75 rms= 0.00
Optimizing Sidechains
Adding Hydrogens
Optimizing loops and OXT (nb = 27)
Final Total Energy: 347.161 KJ/mol
Dumping Sequence Alignment

Model Details: Batch.3

6
model pic
Target:
modelled residue
124 to 307
range:
based on template 1oheA (2.20 A)
Sequence Identity
12.273
[%]:
Evalue: 4.6E-19

Alignment

1oheA 42 rdpqddvyld itdrlcfail ysrpksasnv hyfsidnele yenfyadfgp

1oheA ssss s sssssss ss sss

1oheA 92 lnlamvyryc ckinkklksi tmlrkkivhf tgsdqrkqan aaflvgcymv

1oheA hhhhhhhh hhhhhhhh sssss s hhhhhh hhhhhhhhhh

TARGET 124 LPIGHWIEAT GHTNEMKHTT DFY-------

1oheA 142 iylgrtpeea yrilifge-- tsyipfrdaa ygscnfyitl ldcfhavkka

TARGET
1oheA h hhhh hhhhh h hhhhhhhhhh

TARGET 147 ------F--- -----NIAGH Q--AMHYSRI LP-NIWLGSC PR--------

1oheA 190 mqygflnfns fnldeyehye kaengdlnwi ipdrfiafcg phsrarlesg

TARGET hhh sssss ssssss

1oheA hhh hhhhhhh sssss s sssssss sss

TARGET 172 ----QVEHVT IKLKHELGVT AVMNFQTEWD IVQNSSGCNR YPEPMTPDTM

1oheA 240 yhqhspety- iqyfknhnvt tiirlnkrm- ---------- y--------d

TARGET hhhh s sssss s ssss sssss

1oheA sss hhhhhh s sssss

TARGET 218 IKLYKEEGLA YIWMPTPDMS TEGRVQMLPQ AVCLLHALLE KGHTVYVHCN

1oheA 270 akrftdagfd hhdlffadgs tptd-a---i vkefldicen aegaiavhsk

TARGET hhhh s ssss hhhhhhhhhh sssss

1oheA hhhhh s ssss h h h hhhhhhhhhh sssss

TARGET 268 AGVGRSTAAV CGWLQYVLGW SRRKVQYFLV AKRPAVYIDE ---------

1oheA 316 aglgrtgtli acyimkhyrm taaetiawvr icrpgsvigp qqqflvmkqt

7
TARGET hhhhhh hhhhhhh hhhhhhhhh hh
1oheA hhhhhhh hhhhhhh hhhhhhhhh hh hhhhhh h

TARGET ---------- ----

1oheA 366 nlwlegdyfr qklk

TARGET
1oheA hhhhhhhhhh hh

Anolea

Modelling log

3.70 (SP3)
Loading Template: 1oheA.pdb
Loading Raw Sequence
Renumber target sequence starting from (124)
Loading Alignment: ./NXXX.align.submit.fasta
Removing HET groups from template structure
Refining Raw Sequence Alignment
ProModII: doing simple assignment of backbone
ProModII: adding blocking groups
Adding Missing Sidechains
AddPolar H
BuildDeletetedLoopsModel
Trying Ligating with anchor residues PHE 145 and ASN 148
Trying Ligating with anchor residues ASP 144 and ASN 148
Trying Ligating with anchor residues THR 143 and ASN 148
Trying Ligating with anchor residues THR 142 and ASN 148
Trying Ligating with anchor residues HIS 141 and ASN 148
Trying Ligating with anchor residues LYS 140 and ASN 148
Trying Ligating with anchor residues MET 139 and ASN 148
Trying Ligating with anchor residues GLU 138 and ASN 148

8
+++ Warning: Ligation Failed, SparePart will be inserted later
+++ It is usually the sign that the region is misaligned.
Trying Ligating with anchor residues HIS 152 and MET 155
Number of Ligations found: 18
ACCEPTING loop 6: clash= 0 FF= -295.2 PP= -2.00
Trying Ligating with anchor residues LEU 161 and ILE 164
Number of Ligations found: 3
ACCEPTING loop 2: clash= 0 FF= 1040.4 PP= -2.00
Trying Ligating with anchor residues PRO 170 and VAL 173
Trying Ligating with anchor residues PRO 170 and GLU 174
Number of Ligations found: 2
all loops are bad; continuing CSP with larger segment
Trying Ligating with anchor residues PRO 170 and HIS 175
Number of Ligations found: 13
ACCEPTING loop 0: clash= 0 FF= -435.3 PP= -2.00
Building CSP loop with anchor residues VAL 176 and LYS 179
Building CSP loop with anchor residues HIS 175 and LYS 179
Number of Ligations found: 27
ACCEPTING loop 10: clash= 0 FF= 696.3 PP= 1.00
Building CSP loop with anchor residues TYR 208 and MET 217
Number of Ligations found: 500
all loops are bad; continuing CSP with larger segment
Building CSP loop with anchor residues ARG 207 and MET 217
+++ Warning: CSP Loop Insertion Failed, will use SparePart later
Building CSP loop with anchor residues ARG 241 and MET 244
Building CSP loop with anchor residues ARG 241 and LEU 245
Building CSP loop with anchor residues ARG 241 and PRO 246
Building CSP loop with anchor residues ARG 241 and GLN 247
Number of Ligations found: 23
ACCEPTING loop 20: clash= 0 FF= -80.1 PP= -3.00
Finding Spare-Part loop with anchor residues THR 136 and PHE 147
connectivity problem --> including residue PHE 25
Finding Spare-Part loop with anchor residues THR 136 and ASN 148
all loops are bad; continuing scan with larger segment
Finding Spare-Part loop with anchor residues HIS 135 and ASN 148
all loops are bad; continuing scan with larger segment
Finding Spare-Part loop with anchor residues GLY 134 and ASN 148
Sorry, no loop could be found in the database
Finding Spare-Part loop with anchor residues THR 133 and ASN 148
all loops are bad; continuing scan with larger segment
Finding Spare-Part loop with anchor residues ALA 132 and ASN 148
ACCEPTING loop 6 from 2PRK_ Clash= 4 FF= 603.4 PP= 6.27
BadPhi= 2 BadGX= 0 BadXP= 0 weakXP= 0 Score= 8.00 rms= 0.00
Finding Spare-Part loop with anchor residues TRP 196 and THR 216
ACCEPTING loop 14 from 2KAUC Clash= 7 FF= 76.7 PP= 9.27
BadPhi= 2 BadGX= 0 BadXP= 2 weakXP= 2 Score=14.00 rms= 0.00
Optimizing Sidechains
Adding Hydrogens
Optimizing loops and OXT (nb = 41)
Final Total Energy: 5375.517 KJ/mol
Dumping Sequence Alignment

Template Selection Log:

- Start SMR-Pipeline in automated mode on BC2-cluster at Sat Jan 22 08:21:57 2011

- Start BLAST for highly similar template structure identification

- No suitable templates found!

9
 - Run HHSearch to detect remotely related template structures
- Send 3 target-template alignments for modeling

- @@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@@
- ****************************************
- building model based on 3nmeA (154-319) was successfull
- ***********************
- building model based on 1d3cA (10-103) was successfull
- ********************************************
- building model based on 1oheA (124-307) was successfull
- Workspace Pipeline parameter

Cut-off parameters to model the target based on a BLAST target-template alignment

Evalue : 0.0001
Minimum Template size (aa) for ranking : 25
Minimum Sequence identity : 60

Cut-off parameters to model the target based on a HHSearch target-template alignment

Evalue : 0.0001
Probability : 50
MAC : 0.3

Parameters for model selection

Minimal number of uncovered target
residues after BLAST to run HHSEARCH : 50
Minimal number of uncovered target
residues to model an additional template : 25

- Finish SMR-Pipeline in automated mode on BC2-cluster at Sat Jan 22 08:41:00 2011

If you publish results using SWISS-MODEL, please cite the following papers:

• Arnold K., Bordoli L., Kopp J., and Schwede T. (2006). The SWISS-MODEL Workspace: A
web-based environment for protein structure homology modelling.
Bioinformatics, 22,195-201.
• Schwede T, Kopp J, Guex N, and Peitsch MC (2003) SWISS-MODEL: an automated protein
homology-modeling server.
Nucleic Acids Research 31: 3381-3385.
• Guex, N. and Peitsch, M. C. (1997) SWISS-MODEL and the Swiss-PdbViewer: An
environment for comparative protein modelling.
Electrophoresis 18: 2714-2723.

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