YASARA Homology Modeling Report for T0454

1. The homology modeling target T0454

The three-dimensional structure of the following target sequence has been predicted by YASARA's homology modeling experiment:

>T0454

MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQ
FACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPA
IASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDE
ELIRQYVAIFTRGIMADGGAAPA

The target sequence contains 203 residues in 1 molecule.

2. The homology modeling parameters

Not surprisingly, homology modeling involves a speed/accuracy trade-off. For this target, the requested speed was Slow, which implied the following parameters (some may have been set manually with the respective keywords):

3. The homology modeling templates

Since the target sequence was the only available information, possible templates had to be identified by running PSI-BLAST to search the PDB for known structures with a similar sequence (i.e. hits with an E-value below the homology modeling cutoff 1.0).

The following 50 hits were found:

TemplateTotal scoreBLAST E-valueBLAST scoreIDResolutionHeader
138.00 0.00138.02OFL-B2.90 AChain B, Structural Genomics, The Crystal Structure Of A Tetr-Family Transcriptional Regulator From Streptomyces Coelicolor A3(2)
235.56 5e-0956.02JJ7-B2.10 AChain B, Crystal Structure Of The Hlyiir Mutant Protein With Residues 170-185 Substituted By Alanine (183 residues with quality score 0.635)
332.90 3e-0647.02FBQ-A1.80 AChain A, The Crystal Structure Of Transcriptional Regulator Pa3006 (213 residues with quality score 0.700)
432.90 3e-0647.0BFBQ-AUnknown or NMRThis template is a re-refined version of the previous template, based on the structure factors deposited at the PDB. Trying both templates raises the chances for a good model. Visit the PDB-redo database [Joosten et al., www.cmbi.ru.nl/pdb_redo] for more details.To distinguish this template from the original, the first '2' has been replaced with 'B'.
532.02 1e-0441.02EH3-A1.55 AChain A, Crystal Structure Of Aq_1058, A Transcriptional Regulator (TerrACRR FAMILY) FROM AQUIFEX AEOLICUS VF5 (171 residues with quality score 0.781)
630.96 0.000440.03BHQ-A1.54 AChain A, Crystal Structure Of Tetr-Family Transcriptional Regulator (Np_105615.1) From Mesorhizobium Loti At 1.54 A Resolution (202 residues with quality score 0.774)
730.83 1e-0854.02FX0-A2.40 AChain A, Crystal Structure Of Hlyiir, A Hemolysin Ii Transcriptional Regulator (179 residues with quality score 0.571)
830.53 3e-0853.01PB6-B2.50 AChain B, Crystal Structure Of Hypothetical Transcriptional Regulator Ycdc (198 residues with quality score 0.576)
930.32 8e-0542.02IBD-A1.50 AChain A, Crystal Structure Of Probable Transcriptional Regulatory Protein Rha5900 (192 residues with quality score 0.722)
1029.60 0.00337.02IEK-A1.83 AChain A, New Crystal Form Of Transcriptional Regulator Tm1030 From Thermotoga Maritima (199 residues with quality score 0.800)
1029.25 0.000739.02QIB-A-Chain A, Crystal Structure Of Tetr-Family Transcriptional Regulator From Streptomyces Coelicolor (222 residues with quality score 0.750). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1028.53 0.00237.02NP5-B-Chain B, Crystal Structure Of A Transcriptional Regulator (Rha1_ro04179) From Rhodococcus Sp. Rha1. (187 residues with quality score 0.771) . NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1028.40 0.00536.02HYT-A-Chain A, Crystal Structure Of Tetr-Family Transcriptional Regulator (Yp_049917.1) From Erwinia Cartovora Atroseptica Scri1043 At 1.64 A Resolution (193 residues with quality score 0.789). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1028.28 0.000440.02GEN-A-Chain A, Structural Genomics, The Crystal Structure Of A Probable Transcriptional Regulator From Pseudomonas Aeruginosa Pao1 (188 residues with quality score 0.707). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1027.97 0.00238.02ZCM-B-Chain B, Crystal Structure Of Icar, A Repressor Of The Tetr Family (180 residues with quality score 0.736). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1027.92 0.000340.02IAI-A-Chain A, Crystal Structure Of Sco3833, A Member Of The Tetr Transcriptional Regulator Family From Streptomyces Coelicolor A3 (201 residues with quality score 0.698). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1027.90 0.00337.02ID6-A-Chain A, Crystal Structure Of Transcriptional Regulator (Tm1030) At 1.75a Resolution (202 residues with quality score 0.754). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1027.05 0.00337.01Z77-A-Chain A, Crystal Structure Of Transcriptional Regulator Protein From Thermotoga Maritima. (200 residues with quality score 0.731). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1026.71 0.00337.02ZCN-D-Chain D, Crystal Structure Of Icar, A Repressor Of The Tetr Family (184 residues with quality score 0.722) . NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1025.67 0.00436.02G3B-B-Chain B, Crystal Structure Of Putative Tetr-Family Transcriptional Regulator From Rhodococcus Sp (188 residues with quality score 0.713). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1025.46 0.00138.01T33-A-Chain A, Structural Genomics, The Crystal Structure Of A Putative Transcriptional Repressor (TetrACRR FAMILY) FROM Salmonella Typhimurim Lt2 (220 residues with quality score 0.670). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1025.01 0.00337.01ZKG-B-Chain B, Crystal Structure Of Transcriptional Regulator, Tetr Family (Tm1030) From Thermotoga Maritima At 2.30 A Resolution (199 residues with quality score 0.676). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1024.98 0.03733.02RAS-A-Chain A, Crystal Structure Of Predicted Transcriptional Regulator Of TetrACRR FAMILY (YP_495839.1) FROM NOVOSPHINGOBIUM Aromaticivorans Dsm 12444 At 1.80 A Resolution (200 residues with quality score 0.757). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1024.97 0.00138.02DG8-A-Chain A, Crystal Structure Of The Putative Trasncriptional Regulator Sco7518 From Streptomyces Coelicolor A3(2) (175 residues with quality score 0.657) . NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1024.58 0.01634.02QTQ-A-Chain A, Crystal Structure Of Predicted Dna-Binding Transcriptional Regulator (Yp_496351.1) From Novosphingobium Aromaticivorans Dsm 12444 At 1.85 A Resolution (204 residues with quality score 0.723) . NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1023.90 0.01634.02RHA-A-Chain A, Crystal Structure Of Predicted Dna-Binding Transcriptional Regulator (Yp_496351.1) From Novosphingobium Aromaticivorans Dsm 12444 At 2.10 A Resolution (203 residues with quality score 0.703). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1023.87 0.00636.01JT6-A-Chain A, Crystal Structure Of The Multidrug Binding Protein Qacr Bound To Dequalinium (186 residues with quality score 0.663) . NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1023.72 0.00337.02D6Y-B-Chain B, Crystal Structure Of Transcriptional Factor Sco4008 From Streptomyces Coelicolor A3(2) (188 residues with quality score 0.641). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1023.43 0.04833.02I10-B-Chain B, Putative Tetr Transcriptional Regulator From Rhodococcus Sp. Rha1 (182 residues with quality score 0.710). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1023.22 0.01734.01UI5-A-Chain A, Crystal Structure Of Gamma-Butyrolactone Receptor (Arpa Like Protein) (199 residues with quality score 0.683). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1022.92 0.01834.01UI6-A-Chain A, Crystal Structure Of Gamma-Butyrolactone Receptor (Arpa- Like Protein) (192 residues with quality score 0.674). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1022.42 0.00437.02HKU-A-Chain A, Structural Genomics, The Crystal Structure Of A Putative Transcriptional Regulator From Rhodococcus Sp. Rha1 (191 residues with quality score 0.606). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1022.38 0.1331.02REK-B-Chain B, Crystal Structure Of Tetr-Family Transcriptional Regulator (175 residues with quality score 0.722). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1022.10 0.02334.01SGM-B-Chain B, Crystal Structure Of Hypothetical Protein Yxaf (184 residues with quality score 0.650). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1022.07 0.00536.01JUS-A-Chain A, Crystal Structure Of The Multidrug Binding Transcriptional Repressor Qacr Bound To Rhodamine 6g (186 residues with quality score 0.613) . NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1021.42 0.00436.02NP3-B-Chain B, Crystal Structure Of Tetr-Family Regulator (Sco0857) From Streptomyces Coelicolor A3 (180 residues with quality score 0.595). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1021.15 0.3430.02FD5-A-Chain A, The Crystal Structure Of A Transcriptional Regulator From Pseudomonas Aeruginosa Pao1 (180 residues with quality score 0.705). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1020.99 0.00636.01RKW-A-Chain A, Crystal Structure Of The Multidrug Binding Transcriptional Repressor Qacr Bound To Pentamadine (186 residues with quality score 0.583) . NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1020.70 0.06332.02RAE-A-Chain A, Crystal Structure Of A TetrACRR FAMILY TRANSCRIPTIONAL Regulator From Rhodococcus Sp. Rha1 (193 residues with quality score 0.647). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1020.59 0.00636.01JTX-A-Chain A, Crystal Structure Of The Multidrug Binding Transcriptional Regulator Qacr Bound To Crystal Violet (186 residues with quality score 0.572). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1020.05 0.00636.01QVT-A-Chain A, Crystal Structure Of The Multidrug Binding Transcriptional Repressor Qacr Bound To The Drug Proflavine (186 residues with quality score 0.557) . NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1019.97 0.1132.02QWT-A-Chain A, Crystal Structure Of The Tetr Transcription Regulatory Protein From Mycobacterium Vanbaalenii (167 residues with quality score 0.624). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1019.73 1e-0648.02QOP-A-Chain A, Crystal Structure Of The Transcriptional Regulator Acrr From Escherichia Coli (207 residues with quality score 0.411) . NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1019.56 0.2730.03CJD-B-Chain B, Crystal Structure Of Putative Tetr Transcriptional Regulator (Yp_510936.1) From Jannaschia Sp. Ccs1 At 1.79 A Resolution (182 residues with quality score 0.652). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1019.06 0.00237.02PZ9-A-Chain A, Crystal Structure Of Putative Transcriptional Regulator Sco4942 From Streptomyces Coelicolor (179 residues with quality score 0.515). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1018.50 0.00636.01QVU-A-Chain A, Crystal Structure Of The Multidrug Binding Transcriptional Repressor Qacr Bound To Two Drugs: Ethidium And Proflavine (186 residues with quality score 0.514). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1018.47 0.00138.03C07-A-Chain A, Crystal Structure Of A Tetr Family Transcriptional Regulator From Streptomyces Coelicolor A3(2) (221 residues with quality score 0.486). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1017.37 0.0234.02QCO-A-Chain A, Crystal Structure Of The Transcriptional Regulator Cmer From Campylobacter Jejuni (202 residues with quality score 0.511). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1016.47 0.5329.02PBX-B-Chain B, Vibrio Cholerae Hapr (197 residues with quality score 0.568). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1016.08 1e-0648.03BCG-B-Chain B, Conformational Changes Of The Acrr Regulator Reveal A Mechanism Of Induction (207 residues with quality score 0.335). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).
1014.66 0.09932.03CDL-A-Chain A, Crystal Structure Of A Tetr Family Transcriptional Regulator From Pseudomonas Syringae Pv. Tomato Str. Dc3000 (187 residues with quality score 0.458). NOTE: This template was deliberately discarded: 10 templates with a higher score have already been found, and that is the requested maximum (use the 'Templates' keyword to change it).

The 'Total score' in the second column is simply the product of the BLAST alignment score and the WHAT_CHECK [Hooft et al.,Nature 381:272] quality score in the PDBFinderII database. This makes sure that good template structures are used even if the alignment score is low. If no quality score has been determined yet in the PDBFinderII, a perfect score of 1.000 is assumed.

4. The secondary structure prediction

To aid alignment correction and loop modeling, a secondary structure prediction for the target sequence had to be obtained. This was achieved by running BLAST to retrieve homologous sequences, creating a multiple sequence alignment and feeding it to the 'Discrimination of Secondary structure Class (DSC)' prediction algorithm [King&Sternberg, Protein Sci. 5:2298-2310].

The resulting prediction is listed below, the lines 'PreHel', 'PreStr' and 'PreCoi' indicate the estimated prediction accuracy for the three secondary structure classes helix, strand and coil.

Sequence: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
SecStr : CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
PreHel : 11232555679998999999766432349999975323111111221124569999999999999999997653214797574445667854311557553232211111125766525699999999999997678979977555677999998555643468665565754212457999999999987621222211111
PreStr : 00111012110001000000000014560100000123778888410000010000000000000000001111000001323333221110100111335432100000011122210000001001000000001010011000000000001012136321000001121000000000000000011110121000000
PreCoi : 99767543321111111111344664201011135664221111479986531111111111111111112346896312213332222146699442222446799999974222375411110000111113431121122555433111111543331321445544235898653111111111112379767899999

5. The initial homology models

For each of the templates listed above, models were built. Either a single model if the alignment was certain, or a number of alternative models if the alignment was ambiguous.

5.1. Homology model 1/42, based on template 2OFL-B, alignment variant 01

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: : R: ||E:A :LF ||G| :::R |AQ AG:S|: Y|F:GKE L : :: A D A |:: L| |: H: Q::| : P F: : A :::I | | L: G|V Y:::: : : : |: :L : V:| ||
Template:.KSEQTRALILETAMRLFQERGYDRTTMRAIAQEAGVSVGNAYYYFAGKEHLIQGFYDRIAAEHRAAV.......DLEARLAGVLKVWLdYHEFAVQFFKNAA.....PLSPFSPESEHARVEAIGIHRAVLA..............ELMWLSQMGLVLYWIFDRTEGRERSYRLAERGARLTARGVVLARFRVLRPLVREVH
SecStr: .HHHHHHHHHHHHHHHHHHHHHTTTTHHHHHHCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH.......HHHHHCHHHHHHHHHHHHHHHHHHHHHH.....CCTTTTCCHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCTTTTTTTTHHHH

The following 5 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1AESIEAGMTRGLFRRDLHAVNSAL
2FGQLDDIRGQAGDPLAV
3RWTIQRHRNNPQLL
4LRFYTSELTNPTPCFAAIVSP
5NoneMTRADC

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2ofl-b01_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-2.334Poor
Packing 1D-3.011Bad
Packing 3D-2.752Poor
Overall-2.792Poor

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2ofl-b01_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.599Good
Packing 1D-1.571Satisfactory
Packing 3D-0.660Good
Overall-1.007Satisfactory

Since the overall quality Z-score improved to -1.007 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 1 residue contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2ofl-b01.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.2. Homology model 2/42, based on template 2OFL-B, alignment variant 02

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: : R: ||E:A :LF ||G| :::R |AQ AG:S|: Y|F:GKE L : :: A D A |:: L| |: |: | :: ::P F: : A :::I | | L: G|V Y:::: : : : |: :L : V:| ||
Template:.KSEQTRALILETAMRLFQERGYDRTTMRAIAQEAGVSVGNAYYYFAGKEHLIQGFYDRIAAEHRAAV.......DLEARLAGVLKVWLDIATPYHEFAVQFFKNAADP...FSPESEHARVEAIGIHRAVLA..............ELMWLSQMGLVLYWIFDRTEGRERSYRLAERGARLTARGVVLARFRVLRPLVREVH
SecStr: .HHHHHHHHHHHHHHHHHHHHHTTTTHHHHHHCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH.......HHHHHCHHHHHHHHHHCCCHHHHHHHHHHHHHTT...TTCCHHHHHHHHHHHHHHHHH..............HHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCTTTTTTTTHHHH

The following 4 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1AESIEAGMTRGLFRRDLHAVNSAL
2FGQLDDIRGQAGDPLAV
3SELTNPTPCFAAIVS
4NoneMTRADC

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2ofl-b02_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-2.874Poor
Packing 1D-3.193Bad
Packing 3D-3.040Bad
Overall-3.076Bad

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2ofl-b02_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-1.648Satisfactory
Packing 1D-1.352Satisfactory
Packing 3D-1.312Satisfactory
Overall-1.376Satisfactory

Since the overall quality Z-score improved to -1.376 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: The non-satisfactory model quality can have many reasons like limited structural similarity between template and target, alignment errors, bad template quality or large floppy loops. This model must be treated with extreme caution.

NOTE: 1 residue contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2ofl-b02.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.3. Homology model 3/42, based on template 2OFL-B, alignment variant 03

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: : R: ||E:A :LF ||G| :::R |AQ AG:S|: Y|F:GKE L : :: A D A |:: L| |: |: | :: ::P F: : A :::I | | RD| L: G|V Y:::: : : : |: :L : V:| :
Template:.KSEQTRALILETAMRLFQERGYDRTTMRAIAQEAGVSVGNAYYYFAGKEHLIQGFYDRIAAEHRAAV.......DLEARLAGVLKVWLDIATPYHEFAVQFFKNAADP...FSPESEHARVEAIGIHRAVLA.........RDILPELMWLSQMGLVLYWIFDRTEGRERSYRLAERGARLTARGVVLA..........REV
SecStr: .HHHHHHHHHHHHHHHHHHHHHTTTTHHHHHHCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH.......HHHHHCHHHHHHHHHHCCCHHHHHHHHHHHHHTT...TTCCHHHHHHHHHHHHHHHHH.........CCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHH..........HHH

The following 5 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1AESIEAGMTRGLFRRDLHAV
2FGQLDDIRGQAGDPLAV
3YVAIFTRGIMADGGAAPA
4SELTNPTPCFAAIVS
5NoneMTRADC

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2ofl-b03_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-3.062Bad
Packing 1D-2.897Poor
Packing 3D-2.871Poor
Overall-2.909Poor

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2ofl-b03_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-1.371Satisfactory
Packing 1D-1.273Satisfactory
Packing 3D-1.073Satisfactory
Overall-1.194Satisfactory

Since the overall quality Z-score improved to -1.194 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 1 residue contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2ofl-b03.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.4. Homology model 4/42, based on template 2OFL-B, alignment variant 04

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: : R: ||E:A :LF ||G| :::R |AQ AG:S|: Y|F:GKE L : :: A D A |:: L| |: H: Q::| : P F: : A :::I | | RD| L: G|V Y:::: : : : |: :L : V:| :
Template:.KSEQTRALILETAMRLFQERGYDRTTMRAIAQEAGVSVGNAYYYFAGKEHLIQGFYDRIAAEHRAAV.......DLEARLAGVLKVWLdYHEFAVQFFKNAA.....PLSPFSPESEHARVEAIGIHRAVLA.........RDILPELMWLSQMGLVLYWIFDRTEGRERSYRLAERGARLTARGVVLA........REVHE
SecStr: .HHHHHHHHHHHHHHHHHHHHHTTTTHHHHHHCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH.......HHHHHCHHHHHHHHHHHHHHHHHHHHHH.....CCTTTTCCHHHHHHHHHHHHHHHHH.........CCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHH........HHHHH

The following 6 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1AESIEAGMTRGLFRRDLHAV
2FGQLDDIRGQAGDPLAV
3YVAIFTRGIMADGGAAPA
4RWTIQRHRNNPQLL
5LRFYTSELTNPTPCFAAIVSP
6NoneMTRADC

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2ofl-b04_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-2.484Poor
Packing 1D-3.098Bad
Packing 3D-2.732Poor
Overall-2.839Poor

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2ofl-b04_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.463Good
Packing 1D-1.431Satisfactory
Packing 3D-0.619Good
Overall-0.913Good

Since the overall quality Z-score improved to -0.913 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 1 residue contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2ofl-b04.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.5. Homology model 5/42, based on template 2OFL-B, alignment variant 05

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: : R: ||E:A :LF ||G| :::R |AQ AG:S|: Y|F:GKE L : :: A D A |:: L| |: |: | :: ::P F: : A :::I | | :: T RD| L: G|V Y:::: : : : |: :L : V:| :
Template:.KSEQTRALILETAMRLFQERGYDRTTMRAIAQEAGVSVGNAYYYFAGKEHLIQGFYDRIAAEHRAAV.......DLEARLAGVLKVWLDIATPYHEFAVQFFKNAADP...FSPESEHARVEAIGIHRAVLAGAKT.....RDILPELMWLSQMGLVLYWIFDRTEGRERSYRLAERGARLTARGVVLA........REVHE
SecStr: .HHHHHHHHHHHHHHHHHHHHHTTTTHHHHHHCCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHH.......HHHHHCHHHHHHHHHHCCCHHHHHHHHHHHHHTT...TTCCHHHHHHHHHHHHHHHHHCCCC.....CCHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHH........HHHHH

The following 5 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1IEAGMTRGLFRRDLHAV
2FGQLDDIRGQAGDPLAV
3YVAIFTRGIMADGGAAPA
4SELTNPTPCFAAIVS
5NoneMTRADC

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2ofl-b05_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-3.271Bad
Packing 1D-2.734Poor
Packing 3D-2.999Poor
Overall-2.935Poor

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2ofl-b05_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-1.257Satisfactory
Packing 1D-1.148Satisfactory
Packing 3D-1.025Satisfactory
Overall-1.107Satisfactory

Since the overall quality Z-score improved to -1.107 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 1 residue contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2ofl-b05.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.6. Homology model 6/42, based on template 2JJ7-B, alignment variant 01

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: :R : ::||::A : F:||G| G:SI:E|A: A ::|:M SY|F:GKE:LY V::: : : |: : :P| :| YL : |:NP|| : :E| : |:P : : :: L E || G :G:F: : : :: F :: |L| : |: :T
Template:ASREQTMENILKAAKKKFGERGYEGTSIQEIAKEAKVNVAMASYYFNGKENLYYEVFKKYGLANELPNFLEKNQFNPINALREYLTVFTTHIKENPEIGTLAYEEIIK....RLEKIKPYFIGSFEQLKEILQEGEKQGVFHFFSINHTIHWITSIVLFPKF...............DSADLVSRIISALTD...........
SecStr: CHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCHHHHHHHHHCHHHHHHHHHHHHHCCCCCCCHHHHHHCCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHH....HHHHHHCCHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHTTTT...............HHHHHHHHHHHHHHH...........

The following 3 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1MVNYFFLSTLATEGLTSHSPDQDEEL
2SELTNPTPCFAAIV
3AIFTRGIMADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2jj7-b01_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.148Satisfactory
Packing 1D-1.719Satisfactory
Packing 3D-1.254Satisfactory
Overall-1.420Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2jj7-b01_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.390Good
Packing 1D-0.635Good
Packing 3D-0.878Good
Overall-0.712Good

Since the overall quality Z-score improved to -0.712 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 11 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2jj7-b01.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.7. Homology model 7/42, based on template 2JJ7-B, alignment variant 02

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: :R : ::||::A : F:||G| G:SI:E|A: A ::|:M SY|F:GKE:LY V::: : : |: : :P| :| YL : |:NP|| : :E| : : : I : : :: L E || G :G:F: : : :: F :: |L| : |: :T
Template:ASREQTMENILKAAKKKFGERGYEGTSIQEIAKEAKVNVAMASYYFNGKENLYYEVFKKYGLANELPNFLEKNQFNPINALREYLTVFTTHIKENPEIGTLAYEEIIKESARLEKIK...FIGSFEQLKEILQEGEKQGVFHFFSINHTIHWITSIVLFPKF...............DSADLVSRIISALTD...........
SecStr: CHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCHHHHHHHHHCHHHHHHHHHHHHHCCCCCCCHHHHHHCCHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHCCCHHHHHH...HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHTTTT...............HHHHHHHHHHHHHHH...........

The following 3 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1MVNYFFLSTLATEGLTSHSPDQDEEL
2FAAIVSPAIASVI
3AIFTRGIMADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2jj7-b02_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.448Satisfactory
Packing 1D-1.436Satisfactory
Packing 3D-1.291Satisfactory
Overall-1.370Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2jj7-b02_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.902Good
Packing 1D-0.415Good
Packing 3D-0.843Good
Overall-0.685Good

Since the overall quality Z-score improved to -0.685 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 11 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2jj7-b02.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.8. Homology model 8/42, based on template 2FBQ-A, alignment variant 01

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: :::| :R|||:A |LFA|KGF :S|R |:: AG::|: |:YHFG:K::L AV::: :: F | : :| : :: :: :|R: ::: : :: : ::V:R |: : |: : | G : | : : A : E|::: V :F: G: A|:G
Template:.AQSETVERILDAAEQLFAEKGFAETSLRLITSKAGVNLAAVNYHFGSKKALIQAVFSRFLGPFCASLEKEL......DLLHLLVSQAMA..NDLSIFMRLLGLAFSQSQGHLRKYLEEVYGKVFRRYMLLVNEAA......PPIELFWRVHFMLGAAAFsIKALRAMAETDFGVNTSTEQVMHLMVPFFAAGMRAESG....
SecStr: .HHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHHHHHHHHH..HHHHHHHHHHHHHHHHCHHHHHHHHHHHCHHHHHHHHHHHHHHH......HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCC....

The following 6 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1IEAGMTRGLFRRDLHA
2DDIRGQAGDPLAVMTA
3RWTIQRHRNNPQL
4MVNYFFLSTLAT
5NoneMTRADC
6MADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2fbq-a01_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.144Satisfactory
Packing 1D-1.781Satisfactory
Packing 3D-0.827Good
Overall-1.246Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2fbq-a01_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.571Good
Packing 1D-0.988Good
Packing 3D-0.632Good
Overall-0.762Good

Since the overall quality Z-score improved to -0.762 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 5 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2fbq-a01.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.9. Homology model 9/42, based on template 2FBQ-A, alignment variant 02

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: :::| :R|||:A |LFA|KGF :S|R |:: AG::|: |:YHFG:K::L AV::: :: F | : :| : :: :: :|R: ::: : :: : ::V:R |: : |: : | G : | : : A ::|:: : E|::: V :F: G: A|:G
Template:.AQSETVERILDAAEQLFAEKGFAETSLRLITSKAGVNLAAVNYHFGSKKALIQAVFSRFLGPFCASLEKEL......DLLHLLVSQAMA..NDLSIFMRLLGLAFSQSQGHLRKYLEEVYGKVFRRYMLLVNEAA......PPIELFWRVHFMLGAAAFSMSGIKALRAMAE....STEQVMHLMVPFFAAGMRAESG....
SecStr: .HHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHHHHHHHHH..HHHHHHHHHHHHHHHHCHHHHHHHHHHHCHHHHHHHHHHHHHHH......HHHHHHHHHHHHHHHHHHHHHCHHHHHHHHH....HHHHHHHHHHHHHHHHHHCCCC....

The following 6 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1IEAGMTRGLFRRDLHA
2DDIRGQAGDPLAVMTA
3RWTIQRHRNNPQL
4EGLTSHSPDQDEEL
5NoneMTRADC
6MADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2fbq-a02_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.364Satisfactory
Packing 1D-1.586Satisfactory
Packing 3D-0.795Good
Overall-1.186Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2fbq-a02_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.579Good
Packing 1D-0.884Good
Packing 3D-0.538Good
Overall-0.679Good

Since the overall quality Z-score improved to -0.679 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 5 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2fbq-a02.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.10. Homology model 10/42, based on template 2FBQ-A, alignment variant 03

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: :::| :R|||:A |LFA|KGF :S|R |:: AG::|: |:YHFG:K::L AV::: :: F | : :| : :: :: :|R: ::: : :: : ::V:R |: : L |L | A: : |::L : : T: : E|::: V :F: G: A|:G
Template:.AQSETVERILDAAEQLFAEKGFAETSLRLITSKAGVNLAAVNYHFGSKKALIQAVFSRFLGPFCASLEKEL......DLLHLLVSQAMA..NDLSIFMRLLGLAFSQSQGHLRKYLEEVYGKVFRRYMLLVNEAA...LPPIELFWRVHFMLGAAAFSMSGIKALRAMAETDF...STEQVMHLMVPFFAAGMRAESG....
SecStr: .HHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHHHHHHHHH..HHHHHHHHHHHHHHHHCHHHHHHHHHHHCHHHHHHHHHHHHHHH...CHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHCCCC....

The following 6 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1IEAGMTRGLFRRDL
2DDIRGQAGDPLAVMTA
3RWTIQRHRNNPQL
4GLTSHSPDQDEEL
5NoneMTRADC
6MADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2fbq-a03_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.300Satisfactory
Packing 1D-1.435Satisfactory
Packing 3D-0.667Good
Overall-1.059Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2fbq-a03_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.700Good
Packing 1D-0.671Good
Packing 3D-0.461Good
Overall-0.578Good

Since the overall quality Z-score improved to -0.578 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 5 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2fbq-a03.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.11. Homology model 11/42, based on template 2FBQ-A, alignment variant 04

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: :::| :R|||:A |LFA|KGF :S|R |:: AG::|: |:YHFG:K::L AV::: :: F | : :| : :: :: :|R: ::: : :: : ::V:R |: : L |L | A: : : : A : E|::: V :F: G: A|:G
Template:.AQSETVERILDAAEQLFAEKGFAETSLRLITSKAGVNLAAVNYHFGSKKALIQAVFSRFLGPFCASLEKEL......DLLHLLVSQAMA..NDLSIFMRLLGLAFSQSQGHLRKYLEEVYGKVFRRYMLLVNEAA...LPPIELFWRVHFMLGAAAFSMsIKALRAMAETDFGVNTSTEQVMHLMVPFFAAGMRAESG....
SecStr: .HHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHHHHHHHHH..HHHHHHHHHHHHHHHHCHHHHHHHHHHHCHHHHHHHHHHHHHHH...CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCC....

The following 6 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1IEAGMTRGLFRRDL
2DDIRGQAGDPLAVMTA
3RWTIQRHRNNPQL
4MVNYFFLSTLAT
5NoneMTRADC
6MADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2fbq-a04_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.084Satisfactory
Packing 1D-1.826Satisfactory
Packing 3D-0.711Good
Overall-1.201Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2fbq-a04_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.428Good
Packing 1D-1.031Satisfactory
Packing 3D-0.539Good
Overall-0.715Good

Since the overall quality Z-score improved to -0.715 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 5 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2fbq-a04.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.12. Homology model 12/42, based on template 2FBQ-A, alignment variant 05

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: :::| :R|||:A |LFA|KGF :S|R |:: AG::|: |:YHFG:K::L AV::: :: F | : :| : :: :: :|R: ::: : :: : ::V:R |: : L |: V: L: A:: : : A : E|::: V :F: G: A|:G
Template:.AQSETVERILDAAEQLFAEKGFAETSLRLITSKAGVNLAAVNYHFGSKKALIQAVFSRFLGPFCASLEKEL......DLLHLLVSQAMA..NDLSIFMRLLGLAFSQSQGHLRKYLEEVYGKVFRRYMLLVNEAA...LPPIeFWRVHFMLGAAAFSMSGIKALRAMAETDFGVNTSTEQVMHLMVPFFAAGMRAESG....
SecStr: .HHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHHHHHHHHH..HHHHHHHHHHHHHHHHCHHHHHHHHHHHCHHHHHHHHHHHHHHH...CHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCC....

The following 6 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1IEAGMTRGLFRRDL
2DDIRGQAGDPLAVMTA
3RWTIQRHRNNPQL
4GLFRRDLHAVN
5NoneMTRADC
6MADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2fbq-a05_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.351Satisfactory
Packing 1D-1.770Satisfactory
Packing 3D-0.754Good
Overall-1.238Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2fbq-a05_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.506Good
Packing 1D-1.118Satisfactory
Packing 3D-0.631Good
Overall-0.803Good

Since the overall quality Z-score improved to -0.803 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 5 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2fbq-a05.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.13. Homology model 13/42, based on template BFBQ-A, alignment variant 01

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: :::| :R|||:A |LFA|KGF :S|R |:: AG::|: |:YHFG:K::L AV::: :: F | : :| : :: :: :|R: ::: : :: : ::V:R |: : |: : | G : | : : A : E|::: V :F: G: A|:G
Template:.AQSETVERILDAAEQLFAEKGFAETSLRLITSKAGVNLAAVNYHFGSKKALIQAVFSRFLGPFCASLEKEL......DLLHLLVSQAMA..NDLSIFMRLLGLAFSQSQGHLRKYLEEVYGKVFRRYMLLVNEAA......PPIELFWRVHFMLGAAAFsIKALRAMAETDFGVNTSTEQVMHLMVPFFAAGMRAESG....
SecStr: .HHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHHHHHHHHH..HHHHHHHHHHHHHHHHCHHHHHHHHHHHCHHHHHHHHHHHHHHH......HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCC....

The following 6 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1IEAGMTRGLFRRDLHA
2DDIRGQAGDPLAVMTA
3RWTIQRHRNNPQL
4MVNYFFLSTLAT
5NoneMTRADC
6MADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_bfbq-a01_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.337Satisfactory
Packing 1D-1.673Satisfactory
Packing 3D-0.853Good
Overall-1.243Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_bfbq-a01_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.654Good
Packing 1D-0.792Good
Packing 3D-0.551Good
Overall-0.660Good

Since the overall quality Z-score improved to -0.660 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 5 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_bfbq-a01.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.14. Homology model 14/42, based on template BFBQ-A, alignment variant 02

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: :::| :R|||:A |LFA|KGF :S|R |:: AG::|: |:YHFG:K::L AV::: :: F | : :| : :: :: :|R: ::: : :: : ::V:R |: : |: : | G : | : : A ::|:: : E|::: V :F: G: A|:G
Template:.AQSETVERILDAAEQLFAEKGFAETSLRLITSKAGVNLAAVNYHFGSKKALIQAVFSRFLGPFCASLEKEL......DLLHLLVSQAMA..NDLSIFMRLLGLAFSQSQGHLRKYLEEVYGKVFRRYMLLVNEAA......PPIELFWRVHFMLGAAAFSMSGIKALRAMAE....STEQVMHLMVPFFAAGMRAESG....
SecStr: .HHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHHHHHHHHH..HHHHHHHHHHHHHHHHCHHHHHHHHHHHCHHHHHHHHHHHHHHH......HHHHHHHHHHHHHHHHHHHHHCHHHHHHHHH....HHHHHHHHHHHHHHHHHHCCCC....

The following 6 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1IEAGMTRGLFRRDLHA
2DDIRGQAGDPLAVMTA
3RWTIQRHRNNPQL
4EGLTSHSPDQDEEL
5NoneMTRADC
6MADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_bfbq-a02_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.226Satisfactory
Packing 1D-1.387Satisfactory
Packing 3D-0.664Good
Overall-1.028Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_bfbq-a02_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.657Good
Packing 1D-0.585Good
Packing 3D-0.449Good
Overall-0.532Good

Since the overall quality Z-score improved to -0.532 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 5 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_bfbq-a02.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.15. Homology model 15/42, based on template BFBQ-A, alignment variant 03

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: :::| :R|||:A |LFA|KGF :S|R |:: AG::|: |:YHFG:K::L AV::: :: F | : :| : :: :: :|R: ::: : :: : ::V:R |: : L |L | A: : |::L : : T: : E|::: V :F: G: A|:G
Template:.AQSETVERILDAAEQLFAEKGFAETSLRLITSKAGVNLAAVNYHFGSKKALIQAVFSRFLGPFCASLEKEL......DLLHLLVSQAMA..NDLSIFMRLLGLAFSQSQGHLRKYLEEVYGKVFRRYMLLVNEAA...LPPIELFWRVHFMLGAAAFSMSGIKALRAMAETDF...STEQVMHLMVPFFAAGMRAESG....
SecStr: .HHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHHHHHHHHH..HHHHHHHHHHHHHHHHCHHHHHHHHHHHCHHHHHHHHHHHHHHH...CHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHH...HHHHHHHHHHHHHHHHHHCCCC....

The following 6 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1IEAGMTRGLFRRDL
2DDIRGQAGDPLAVMTA
3RWTIQRHRNNPQL
4GLTSHSPDQDEEL
5NoneMTRADC
6MADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_bfbq-a03_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.373Satisfactory
Packing 1D-1.417Satisfactory
Packing 3D-0.583Good
Overall-1.024Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_bfbq-a03_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.469Good
Packing 1D-0.500Good
Packing 3D-0.148Good
Overall-0.332Good

Since the overall quality Z-score improved to -0.332 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 5 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_bfbq-a03.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.16. Homology model 16/42, based on template BFBQ-A, alignment variant 04

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: :::| :R|||:A |LFA|KGF :S|R |:: AG::|: |:YHFG:K::L AV::: :: F | : :| : :: :: :|R: ::: : :: : ::V:R |: : L |L | A: : : : A : E|::: V :F: G: A|:G
Template:.AQSETVERILDAAEQLFAEKGFAETSLRLITSKAGVNLAAVNYHFGSKKALIQAVFSRFLGPFCASLEKEL......DLLHLLVSQAMA..NDLSIFMRLLGLAFSQSQGHLRKYLEEVYGKVFRRYMLLVNEAA...LPPIELFWRVHFMLGAAAFSMsIKALRAMAETDFGVNTSTEQVMHLMVPFFAAGMRAESG....
SecStr: .HHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHHHHHHHHH..HHHHHHHHHHHHHHHHCHHHHHHHHHHHCHHHHHHHHHHHHHHH...CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCC....

The following 6 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1IEAGMTRGLFRRDL
2DDIRGQAGDPLAVMTA
3RWTIQRHRNNPQL
4MVNYFFLSTLAT
5NoneMTRADC
6MADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_bfbq-a04_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.247Satisfactory
Packing 1D-1.504Satisfactory
Packing 3D-0.655Good
Overall-1.072Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_bfbq-a04_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.524Good
Packing 1D-0.814Good
Packing 3D-0.503Good
Overall-0.627Good

Since the overall quality Z-score improved to -0.627 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 5 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_bfbq-a04.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.17. Homology model 17/42, based on template BFBQ-A, alignment variant 05

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: :::| :R|||:A |LFA|KGF :S|R |:: AG::|: |:YHFG:K::L AV::: :: F | : :| : :: :: :|R: ::: : :: : ::V:R |: : L |: V: L: A:: : : A : E|::: V :F: G: A|:G
Template:.AQSETVERILDAAEQLFAEKGFAETSLRLITSKAGVNLAAVNYHFGSKKALIQAVFSRFLGPFCASLEKEL......DLLHLLVSQAMA..NDLSIFMRLLGLAFSQSQGHLRKYLEEVYGKVFRRYMLLVNEAA...LPPIeFWRVHFMLGAAAFSMSGIKALRAMAETDFGVNTSTEQVMHLMVPFFAAGMRAESG....
SecStr: .HHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHCCHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH......HHHHHHHHHHHH..HHHHHHHHHHHHHHHHCHHHHHHHHHHHCHHHHHHHHHHHHHHH...CHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCC....

The following 6 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1IEAGMTRGLFRRDL
2DDIRGQAGDPLAVMTA
3RWTIQRHRNNPQL
4GLFRRDLHAVN
5NoneMTRADC
6MADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_bfbq-a05_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.077Satisfactory
Packing 1D-1.729Satisfactory
Packing 3D-0.612Good
Overall-1.116Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_bfbq-a05_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.421Good
Packing 1D-1.023Satisfactory
Packing 3D-0.558Good
Overall-0.720Good

Since the overall quality Z-score improved to -0.720 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 5 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_bfbq-a05.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.18. Homology model 18/42, based on template 2EH3-A, alignment variant 01

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: |:R||EV: ELF |KG| G:S|:E|:: A: S : : |HF :KE L : |||: :: :|| P :| |L: : ::: :| |L F I I :: R : : |E | S | L: | : :: :| E : P E:L : IF
Template:....GTKERILEVSKELFFEKGYQGTSVEEIVKRANLSKGAFYFHFKSKEELITEIIERTHkIISLFEEN.....TPEELLEMFLEVLYR.....KKVVYIFLFDLL.....FRNIYFEKIEDAKRRFEKFLE...........KAEILSEIILGFLRQLILHYVIKEE....ELPFLKEKLREGLKLIF.............
SecStr: ....HHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH.....HHHHHHHHHHHHHHH.....HHHHHHHHHHHH.....HHHHHHHHHHHHHHHHHHHHH...........HHHHHHHHHHHHHHHHHHHHHHCCC....HHHHHHHHHHHHHHHHH.............

The following 8 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1AESIEAGMTRGLFRRDLHAVN
2STLATEGLTSHSPDQ
3QLDDIRGQAGDPLAV
4YVAIFTRGIMADGGAAPANone
5RWTIQRHRNNPQLLR
6LQEQFACFGQL
7TSELTNPTPCFAAIV
8NoneMTRADCRSR

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2eh3-a01_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.240Satisfactory
Packing 1D-1.221Satisfactory
Packing 3D-0.513Good
Overall-0.895Good

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2eh3-a01_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.729Good
Packing 1D-0.581Good
Packing 3D-0.464Good
Overall-0.548Good

Since the overall quality Z-score improved to -0.548 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 17 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2eh3-a01.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.19. Homology model 19/42, based on template 2EH3-A, alignment variant 02

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: |:R||EV: ELF |KG| G:S|:E|:: A: S : : |HF :KE L : |||: :: :|| P :| |L: :| L: : SE F I I :: R : : |E | S | L: | : :: :| E : P E:L : IF
Template:....GTKERILEVSKELFFEKGYQGTSVEEIVKRANLSKGAFYFHFKSKEELITEIIERTHkIISLFEEN.....TPEELLEMFLEVLYrKKVVYIFLFDLLCSE.......FRNIYFEKIEDAKRRFEKFLE...........KAEILSEIILGFLRQLILHYVIKEE....ELPFLKEKLREGLKLIF.............
SecStr: ....HHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH.....HHHHHHHHHHHHHHHHHHHHHHHHHHHCCC.......HHHHHHHHHHHHHHHHHHHHH...........HHHHHHHHHHHHHHHHHHHHHHCCC....HHHHHHHHHHHHHHHHH.............

The following 8 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1AESIEAGMTRGLFRRDLHAVN
2STLATEGLTSHSPDQ
3QLDDIRGQAGDPLAV
4YVAIFTRGIMADGGAAPANone
5LQEQFACFGQL
6RWTIQRHRNNPQ
7LRFYTSELTNPTPCFAAIV
8NoneMTRADCRSR

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2eh3-a02_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.062Satisfactory
Packing 1D-1.836Satisfactory
Packing 3D-0.806Good
Overall-1.246Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2eh3-a02_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.727Good
Packing 1D-0.968Good
Packing 3D-0.800Good
Overall-0.855Good

Since the overall quality Z-score improved to -0.855 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 17 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2eh3-a02.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.20. Homology model 20/42, based on template 2EH3-A, alignment variant 03

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: |:R||EV: ELF |KG| G:S|:E|:: A: S : : |HF :KE L : |||: :: :|| P :| |L: : : : F : L F I I :: R : : |E | S | L: | : :: :| E : P E:L : IF
Template:....GTKERILEVSKELFFEKGYQGTSVEEIVKRANLSKGAFYFHFKSKEELITEIIERTHkIISLFEEN.....TPEELLEMFLEVLYR....KKVVYIFLFDLL......FRNIYFEKIEDAKRRFEKFLE...........KAEILSEIILGFLRQLILHYVIKEE....ELPFLKEKLREGLKLIF.............
SecStr: ....HHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH.....HHHHHHHHHHHHHHH....HHHHHHHHHHHH......HHHHHHHHHHHHHHHHHHHHH...........HHHHHHHHHHHHHHHHHHHHHHCCC....HHHHHHHHHHHHHHHHH.............

The following 8 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1AESIEAGMTRGLFRRDLHAVN
2STLATEGLTSHSPDQ
3QLDDIRGQAGDPLAV
4YVAIFTRGIMADGGAAPANone
5RWTIQRHRNNPQLL
6LQEQFACFGQL
7YTSELTNPTPCFAAIV
8NoneMTRADCRSR

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2eh3-a03_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.021Satisfactory
Packing 1D-1.684Satisfactory
Packing 3D-0.585Good
Overall-1.077Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2eh3-a03_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.865Good
Packing 1D-0.869Good
Packing 3D-0.675Good
Overall-0.778Good

Since the overall quality Z-score improved to -0.778 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 17 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2eh3-a03.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.21. Homology model 21/42, based on template 2EH3-A, alignment variant 04

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: |:R||EV: ELF |KG| G:S|:E|:: A: S : : |HF :KE L : |||: :: :|| P :| |L: : ::: :| |L F I I :: R : : |E | S | | G::: ::L : E : P E:L : IF
Template:....GTKERILEVSKELFFEKGYQGTSVEEIVKRANLSKGAFYFHFKSKEELITEIIERTHkIISLFEEN.....TPEELLEMFLEVLYR.....KKVVYIFLFDLL.....FRNIYFEKIEDAKRRFEKFLE...........KAEILSEI.ILGFLRQLILHYVIKE....ELPFLKEKLREGLKLIF.............
SecStr: ....HHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH.....HHHHHHHHHHHHHHH.....HHHHHHHHHHHH.....HHHHHHHHHHHHHHHHHHHHH...........HHHHHHHH.HHHHHHHHHHHHHHCC....HHHHHHHHHHHHHHHHH.............

The following 9 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1AESIEAGMTRGLFRRDLHAVN
2TLATEGLTSHSPDQ
3QLDDIRGQAGDPLAV
4YVAIFTRGIMADGGAAPANone
5AVNSALALAGMV
6RWTIQRHRNNPQLLR
7LQEQFACFGQL
8TSELTNPTPCFAAIV
9NoneMTRADCRSR

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2eh3-a04_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.367Satisfactory
Packing 1D-1.540Satisfactory
Packing 3D-0.781Good
Overall-1.162Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2eh3-a04_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.966Good
Packing 1D-0.743Good
Packing 3D-0.721Good
Overall-0.765Good

Since the overall quality Z-score improved to -0.765 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 17 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2eh3-a04.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.22. Homology model 22/42, based on template 2EH3-A, alignment variant 05

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: |:R||EV: ELF |KG| G:S|:E|:: A: S : : |HF :KE L : |||: : :L | : P :| |L: : ::: :| |L F I I :: R : : |E | S | L: | : :: :| E : P E:L : IF
Template:....GTKERILEVSKELFFEKGYQGTSVEEIVKRANLSKGAFYFHFKSKEELITEIIERTHKKIISLFEEN....TPEELLEMFLEVLYR.....KKVVYIFLFDLL.....FRNIYFEKIEDAKRRFEKFLE...........KAEILSEIILGFLRQLILHYVIKEE....ELPFLKEKLREGLKLIF.............
SecStr: ....HHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHH....HHHHHHHHHHHHHHH.....HHHHHHHHHHHH.....HHHHHHHHHHHHHHHHHHHHH...........HHHHHHHHHHHHHHHHHHHHHHCCC....HHHHHHHHHHHHHHHHH.............

The following 7 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1AESIEAGMTRGLFRRDLHAVN
2STLATEGLTSHSPDQ
3LDDIRGQAGDPLAV
4YVAIFTRGIMADGGAAPANone
5RWTIQRHRNNPQLLR
6TSELTNPTPCFAAIV
7NoneMTRADCRSR

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2eh3-a05_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.033Satisfactory
Packing 1D-1.124Satisfactory
Packing 3D-0.383Good
Overall-0.767Good

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2eh3-a05_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.591Good
Packing 1D-0.707Good
Packing 3D-0.512Good
Overall-0.600Good

Since the overall quality Z-score improved to -0.600 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 17 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2eh3-a05.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.23. Homology model 23/42, based on template 3BHQ-A, alignment variant 01

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: A :|:|:AT F :KG| G:S::E|A AGAS : | HF KE L|: V: : : ::| | : A :| :: :L R: :: : A : :: :| A: :| :RGL :A L GM: |: |: G : :S | E: V F
Template:TRSARKDREIIQAATAAFISKGYDGTSMEEIATKAGASKQTVYKHFTDKETLFGEVVLSTASQVNDIIESVTTLL..GLQQLARRLIAVLMDEELLKLRRLIIANADRMPQLGRAWYEKGFERMLASTASCFQKLTNRGL.....DPYLAASHLFGMLLWIPMNEAMFTGSNRRSKAELERHADASVEAFLAVY.........
SecStr: HHHHHHHHHHHHHHHHHHHHHTTTTCHHHHHHHHHHCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHCHHHHHHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHHHHCC.....HHHHHHHHHHHHHCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH.........

The following 3 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1AGMTRGLFRRDLHAVNS
2RGQAGDPLAVMTA
3FTRGIMADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_3bhq-a01_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.735Satisfactory
Packing 1D-1.171Satisfactory
Packing 3D-0.505Good
Overall-0.943Good

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_3bhq-a01_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-1.257Satisfactory
Packing 1D-0.075Good
Packing 3D-0.342Good
Overall-0.370Good

Since the overall quality Z-score improved to -0.370 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 9 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_3bhq-a01.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.24. Homology model 24/42, based on template 3BHQ-A, alignment variant 02

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: T A :|:|:AT F :KG| G:S::E|A AGAS : | HF KE L|: V: : : ::| | : A :| :: :L R: :: : A : :: :| A: :| :RGL :A L GM: |: |: G : :S | E: V F
Template:EtSARKDREIIQAATAAFISKGYDGTSMEEIATKAGASKQTVYKHFTDKETLFGEVVLSTASQVNDIIESVTTLL..GLQQLARRLIAVLMDEELLKLRRLIIANADRMPQLGRAWYEKGFERMLASTASCFQKLTNRGL.....DPYLAASHLFGMLLWIPMNEAMFTGSNRRSKAELERHADASVEAFLAVY.........
SecStr: CHHHHHHHHHHHHHHHHHHHHTTTTCHHHHHHHHHHCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHH..HHHHHHHHHHHHHHCHHHHHHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHHHHCC.....HHHHHHHHHHHHHCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH.........

The following 4 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1AGMTRGLFRRDLHAVNS
2MTRADCRS
3RGQAGDPLAVMTA
4FTRGIMADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_3bhq-a02_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.899Satisfactory
Packing 1D-1.305Satisfactory
Packing 3D-0.692Good
Overall-1.106Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_3bhq-a02_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-1.253Satisfactory
Packing 1D-0.289Good
Packing 3D-0.469Good
Overall-0.512Good

Since the overall quality Z-score improved to -0.512 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 9 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_3bhq-a02.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.25. Homology model 25/42, based on template 3BHQ-A, alignment variant 03

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: A :|:|:AT F :KG| G:S::E|A AGAS : | HF KE L|: V: : : ::| | ::: A :| :: :L R: :: : A : :: :| A: :| :RGL :A L GM: |: |: G : :S | E: V F
Template:TRSARKDREIIQAATAAFISKGYDGTSMEEIATKAGASKQTVYKHFTDKETLFGEVVLSTASQVNDIIESVT...MEGGlQLARRLIAVLMDEELLKLRRLIIANADRMPQLGRAWYEKGFERMLASTASCFQKLTNRGL.....DPYLAASHLFGMLLWIPMNEAMFTGSNRRSKAELERHADASVEAFLAVY.........
SecStr: HHHHHHHHHHHHHHHHHHHHHTTTTCHHHHHHHHHHCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHH...HHHHHHHHHHHHHHHHCHHHHHHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHHHHCC.....HHHHHHHHHHHHHCHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHH.........

The following 4 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1AGMTRGLFRRDLHAVNS
2DDIRGQAGDPLAV
3GDPLAVMTAYL
4FTRGIMADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_3bhq-a03_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.554Satisfactory
Packing 1D-1.428Satisfactory
Packing 3D-0.483Good
Overall-1.007Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_3bhq-a03_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-1.046Satisfactory
Packing 1D-0.368Good
Packing 3D-0.180Good
Overall-0.379Good

Since the overall quality Z-score improved to -0.379 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 9 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_3bhq-a03.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.26. Homology model 26/42, based on template 2FX0-A, alignment variant 01

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: :R : ::||::A : F:||G| G:SI:E|A: A ::|:M SY|F:GKE:LY V::: : : |: : :P| :| YL : |:NP|| : :E| |:P : : :: L E || G :G:F: : : :: : : D L| : |: :T
Template:.SREQTMENILKAAKKKFGERGYEGTSIQEIAKEAKVNVAMASYYFNGKENLYYEVFKKYGLANELPNFLEKNQFNPINALREYLTVFTTHIKENPEIGTLAYEEII.....RLEKIKPYFIGSFEQLKEILQEGEKQGVFHFFSINHTIHWITSIVL.............PKFKKFID..LVSRIISALTD...........
SecStr: .HHHHHHHHHHHHHHHHHHHHTTTTCHHHHHHHHHHCHHHHHHHHHCHHHHHHHHHHHHHCTTTTCCHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH.....HHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHH.............HHHHHHHH..HHHHHHHHHHH...........

The following 5 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1LAGMVNYFFLSTLATEGLTSHSP
2SPDQDEELIRQY
3TSELTNPTPCFAAIV
4NoneMTRADC
5AIFTRGIMADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2fx0-a01_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.925Satisfactory
Packing 1D-2.155Poor
Packing 3D-1.927Satisfactory
Overall-2.016Poor

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2fx0-a01_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.904Good
Packing 1D-0.889Good
Packing 3D-1.091Satisfactory
Overall-0.985Good

Since the overall quality Z-score improved to -0.985 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 12 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2fx0-a01.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.27. Homology model 27/42, based on template 2FX0-A, alignment variant 02

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: :R : ::||::A : F:||G| G:SI:E|A: A ::|:M SY|F:GKE:LY V::: : : |: : :P| :| YL : |:NP|| : :E| |:P : : :: L E || G :G:F: : : :: F : | L| : |: :T
Template:.SREQTMENILKAAKKKFGERGYEGTSIQEIAKEAKVNVAMASYYFNGKENLYYEVFKKYGLANELPNFLEKNQFNPINALREYLTVFTTHIKENPEIGTLAYEEII.....RLEKIKPYFIGSFEQLKEILQEGEKQGVFHFFSINHTIHWITSIVLFPKFKKFID..............LVSRIISALTD...........
SecStr: .HHHHHHHHHHHHHHHHHHHHTTTTCHHHHHHHHHHCHHHHHHHHHCHHHHHHHHHHHHHCTTTTCCHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH.....HHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCHHHHHHHH..............HHHHHHHHHHH...........

The following 4 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1LSTLATEGLTSHSPDQDEELIRQY
2TSELTNPTPCFAAIV
3NoneMTRADC
4AIFTRGIMADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2fx0-a02_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.153Satisfactory
Packing 1D-2.114Poor
Packing 3D-1.427Satisfactory
Overall-1.655Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2fx0-a02_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.593Good
Packing 1D-0.816Good
Packing 3D-0.731Good
Overall-0.744Good

Since the overall quality Z-score improved to -0.744 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 12 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2fx0-a02.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.28. Homology model 28/42, based on template 2FX0-A, alignment variant 03

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: :R : ::||::A : F:||G| G:SI:E|A: A ::|:M SY|F:GKE:LY V::: : : |: : :P| :| YL : |:NP|| : :E| |:P : : :: L E || G :G:F: : : :: : | L| : |: :T
Template:.SREQTMENILKAAKKKFGERGYEGTSIQEIAKEAKVNVAMASYYFNGKENLYYEVFKKYGLANELPNFLEKNQFNPINALREYLTVFTTHIKENPEIGTLAYEEII.....RLEKIKPYFIGSFEQLKEILQEGEKQGVFHFFSINHTIHWITSIVL......PKFKKFID.........LVSRIISALTD...........
SecStr: .HHHHHHHHHHHHHHHHHHHHTTTTCHHHHHHHHHHCHHHHHHHHHCHHHHHHHHHHHHHCTTTTCCHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH.....HHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHH......HHHHHHHH.........HHHHHHHHHHH...........

The following 5 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1LAGMVNYFFLSTLATE
2TEGLTSHSPDQDEELIRQY
3TSELTNPTPCFAAIV
4NoneMTRADC
5AIFTRGIMADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2fx0-a03_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.858Satisfactory
Packing 1D-2.187Poor
Packing 3D-1.909Satisfactory
Overall-2.010Poor

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2fx0-a03_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.765Good
Packing 1D-0.921Good
Packing 3D-0.961Good
Overall-0.917Good

Since the overall quality Z-score improved to -0.917 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 12 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2fx0-a03.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.29. Homology model 29/42, based on template 2FX0-A, alignment variant 04

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: :R : ::||::A : F:||G| G:SI:E|A: A ::|:M SY|F:GKE:LY V::: : : |: : :P| :| YL : |:NP|| : :E| |:P : : :: L E || G :G:F: : : :: : D L| : |: :T
Template:.SREQTMENILKAAKKKFGERGYEGTSIQEIAKEAKVNVAMASYYFNGKENLYYEVFKKYGLANELPNFLEKNQFNPINALREYLTVFTTHIKENPEIGTLAYEEII.....RLEKIKPYFIGSFEQLKEILQEGEKQGVFHFFSINHTIHWITSIVL...........PKFKKFID....LVSRIISALTD...........
SecStr: .HHHHHHHHHHHHHHHHHHHHTTTTCHHHHHHHHHHCHHHHHHHHHCHHHHHHHHHHHHHCTTTTCCHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH.....HHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHH...........HHHHHHHH....HHHHHHHHHHH...........

The following 5 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1LAGMVNYFFLSTLATEGLTSH
2SHSPDQDEELIRQY
3TSELTNPTPCFAAIV
4NoneMTRADC
5AIFTRGIMADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2fx0-a04_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-2.223Poor
Packing 1D-1.708Satisfactory
Packing 3D-1.994Satisfactory
Overall-1.916Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2fx0-a04_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-1.234Satisfactory
Packing 1D-0.519Good
Packing 3D-1.280Satisfactory
Overall-0.976Good

Since the overall quality Z-score improved to -0.976 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 12 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2fx0-a04.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.30. Homology model 30/42, based on template 2FX0-A, alignment variant 05

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: :R : ::||::A : F:||G| G:SI:E|A: A ::|:M SY|F:GKE:LY V::: : : |: : :P| :| YL : |:NP|| : :E| |:P : : :: L E || G :G:F: : |:::V | :: : L| : |: :T
Template:.SREQTMENILKAAKKKFGERGYEGTSIQEIAKEAKVNVAMASYYFNGKENLYYEVFKKYGLANELPNFLEKNQFNPINALREYLTVFTTHIKENPEIGTLAYEEII.....RLEKIKPYFIGSFEQLKEILQEGEKQGVFHFFSINHTIHW.ITSIVLFPKFKKFID.............LVSRIISALTD...........
SecStr: .HHHHHHHHHHHHHHHHHHHHTTTTCHHHHHHHHHHCHHHHHHHHHCHHHHHHHHHHHHHCTTTTCCHHHHHCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH.....HHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHH.HHHHHHCHHHHHHHH.............HHHHHHHHHHH...........

The following 5 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1STLATEGLTSHSPDQDEELIRQY
2VNSALALAGMVN
3TSELTNPTPCFAAIV
4NoneMTRADC
5AIFTRGIMADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2fx0-a05_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.689Satisfactory
Packing 1D-1.933Satisfactory
Packing 3D-1.587Satisfactory
Overall-1.737Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2fx0-a05_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.901Good
Packing 1D-0.495Good
Packing 3D-0.915Good
Overall-0.749Good

Since the overall quality Z-score improved to -0.749 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 12 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2fx0-a05.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.31. Homology model 31/42, based on template 1PB6-B, alignment variant 01

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: : : |: ||::A | F:Q GF|G: |:||A| AG:S : | Y|F :KE:LY AVL:| : : | PLA:: Y|R || R: PQ R:| E| :P : :: | ::I : I : : G H | A : F :: A: G T :: :| |:: I: :GI
Template:.AVSAKKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQILDIWLAPLKAFREDFAPLAAIKEYIRLKLEVSRDYPQASRLFCMEMLAGAPLLMDELTGDLKALIDEKSALIAGWVKSG....PQHLIFMIWASTQHYADFAPQVEAVTGATLRDEVFFNQTVENVQRIIIEGI.........
SecStr: .HHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCCCCCHHHHHHCHHHHHHHHHHHHHHHHHHHC....HHHHHHHHHHHHHHHHHCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHC.........

The following 3 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1AGMTRGLFRRDLHAV
2NoneMTRADC
3FTRGIMADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_1pb6-b01_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.921Satisfactory
Packing 1D-2.029Poor
Packing 3D-1.598Satisfactory
Overall-1.813Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_1pb6-b01_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-1.029Satisfactory
Packing 1D-0.571Good
Packing 3D-0.507Good
Overall-0.608Good

Since the overall quality Z-score improved to -0.608 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 10 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_1pb6-b01.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.32. Homology model 32/42, based on template 1PB6-B, alignment variant 02

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: :::|: ||::A | F:Q GF|G: |:||A| AG:S : | Y|F :KE:LY AVL:| : : | PLA:: Y|R || R: PQ R:| E| :P : :: | ::I : I : : G H | A : F :: A: G T :: :| |:: I: :GI
Template:..AVSaKKAILSAALDTFSQFGFHGTRLEQIAELAGVSKTNLLYYFPSKEALYIAVLRQILDIWLAPLKAFREDFAPLAAIKEYIRLKLEVSRDYPQASRLFCMEMLAGAPLLMDELTGDLKALIDEKSALIAGWVKSG....PQHLIFMIWASTQHYADFAPQVEAVTGATLRDEVFFNQTVENVQRIIIEGI.........
SecStr: ..HHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHCHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHCCCCCHHHHHHCHHHHHHHHHHHHHHHHHHHC....HHHHHHHHHHHHHHHHHCHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHC.........

The following 4 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1AGMTRGLFRRDLHAV
2MTRADCRSRLM
3NoneMTRADCR
4FTRGIMADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_1pb6-b02_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-2.025Poor
Packing 1D-2.020Poor
Packing 3D-1.679Satisfactory
Overall-1.862Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_1pb6-b02_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-1.102Satisfactory
Packing 1D-0.635Good
Packing 3D-0.728Good
Overall-0.746Good

Since the overall quality Z-score improved to -0.746 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 11 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_1pb6-b02.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.33. Homology model 33/42, based on template 2IBD-A, alignment variant 01

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: |: R::L|||A: LFA||G: :::|R||A:AAG : | |HF :KE:| |L: : : : D A:| A : : | :: | : : F : :S :: :L |EAG: G FR D| : : L : | : |QY::I G A:P
Template:.GKSGRRTELLDIAATLFAERGLRATTVRDIADAAGILSGSLYHHFDSKESMVDEILRGFLDDLFGKYREIVAS.DSRATLEALVTTSYEAIdHSAVAIYQDEVKHLVANERF.TYLSELNTEFRELWMGVLEAGVKDGSFRSDIDVELAFRFLRDTA...................TVDTVAKQYLSIVLDG......ASP.
SecStr: .HHHHHHHHHHHHHHHHHHHHHTTTTHHHHHHHHHCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHCTTTTCCTTTT.HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH...................HHHHHHHHHHHHHHHC......CCC.

The following 7 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1LAGMVNYFFLSTLATEGLTSHSPDQDEEL
2YTSELTNPTPCFAAIVSP
3TIQRHRNNPQL
4IRGQAGDPLAVMT
5IFTRGIMADGGAAPA
6NoneMTRADC
7GGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2ibd-a01_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-0.968Good
Packing 1D-1.896Satisfactory
Packing 3D-0.861Good
Overall-1.281Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2ibd-a01_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.598Good
Packing 1D-1.072Satisfactory
Packing 3D-0.655Good
Overall-0.809Good

Since the overall quality Z-score improved to -0.809 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 2 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2ibd-a01.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.34. Homology model 34/42, based on template 2IBD-A, alignment variant 02

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: |: R::L|||A: LFA||G: :::|R||A:AAG : | |HF :KE:| |L: : : : D A:| A : : | :: | : : :S :: :L |EAG: G FR D| : : L : | : |QY::I G
Template:.GKSGRRTELLDIAATLFAERGLRATTVRDIADAAGILSGSLYHHFDSKESMVDEILRGFLDDLFGKYREIVAS.DSRATLEALVTTSYEA.HSAVAIYQD.............TYLSELNTEFRELWMGVLEAGVKDGSFRSDIDVELAFRFLRDTA...................TVDTVAKQYLSIVLDG..........
SecStr: .HHHHHHHHHHHHHHHHHHHHHTTTTHHHHHHHHHCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHH.HHHHHHHHH.............HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH...................HHHHHHHHHHHHHHHC..........

The following 6 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1LAGMVNYFFLSTLATEGLTSHSPDQDEEL
2QLLRFYTSELTNPTPCFAAIVSP
3IRGQAGDPLAVMT
4WTIQRHRNNPQ
5NoneMTRADC
6IFTRGIMADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2ibd-a02_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-0.586Good
Packing 1D-2.068Poor
Packing 3D-0.633Good
Overall-1.186Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2ibd-a02_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.193Good
Packing 1D-1.311Satisfactory
Packing 3D-0.386Good
Overall-0.719Good

Since the overall quality Z-score improved to -0.719 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 11 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2ibd-a02.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.35. Homology model 35/42, based on template 2IBD-A, alignment variant 03

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: |: R::L|||A: LFA||G: :::|R||A:AAG : | |HF :KE:| |L: : : : D A:| A : : | : : : :Y : :S :: :L |EAG: G FR D| : : L : | : |QY::I G A:P
Template:.GKSGRRTELLDIAATLFAERGLRATTVRDIADAAGILSGSLYHHFDSKESMVDEILRGFLDDLFGKYREIVAS.DSRATLEALVTTSYEAIDASHSAVAIY............TYLSELNTEFRELWMGVLEAGVKDGSFRSDIDVELAFRFLRDTA...................TVDTVAKQYLSIVLDG......ASP.
SecStr: .HHHHHHHHHHHHHHHHHHHHHTTTTHHHHHHHHHCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHCHHHHHHH............HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH...................HHHHHHHHHHHHHHHC......CCC.

The following 6 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1LAGMVNYFFLSTLATEGLTSHSPDQDEEL
2LLRFYTSELTNPTPCFAAIVSP
3IRGQAGDPLAVMT
4IFTRGIMADGGAAPA
5NoneMTRADC
6GGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2ibd-a03_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-0.784Good
Packing 1D-1.905Satisfactory
Packing 3D-0.784Good
Overall-1.222Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2ibd-a03_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.546Good
Packing 1D-0.908Good
Packing 3D-0.497Good
Overall-0.665Good

Since the overall quality Z-score improved to -0.665 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 2 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2ibd-a03.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.36. Homology model 36/42, based on template 2IBD-A, alignment variant 04

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: |: R::L|||A: LFA||G: :::|R||A:AAG : | |HF :KE:| |L: : : : D A:| A : : | :: | : : : F : :S :: :L |EAG: G FR D| : : L : | : |QY::I G A:P
Template:.GKSGRRTELLDIAATLFAERGLRATTVRDIADAAGILSGSLYHHFDSKESMVDEILRGFLDDLFGKYREIVAS.DSRATLEALVTTSYEA.HSAVAIYQ.DEVKHLVANERF.TYLSELNTEFRELWMGVLEAGVKDGSFRSDIDVELAFRFLRDTA...................TVDTVAKQYLSIVLDG......ASP.
SecStr: .HHHHHHHHHHHHHHHHHHHHHTTTTHHHHHHHHHCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHH.HHHHHHHH.HCTTTTCCTTTT.HHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH...................HHHHHHHHHHHHHHHC......CCC.

The following 8 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1LAGMVNYFFLSTLATEGLTSHSPDQDEEL
2YTSELTNPTPCFAAIVSP
3IRGQAGDPLAVMT
4WTIQRHRNNPQ
5PQLLRFYTSELT
6IFTRGIMADGGAAPA
7NoneMTRADC
8GGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2ibd-a04_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-0.816Good
Packing 1D-2.159Poor
Packing 3D-0.641Good
Overall-1.259Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2ibd-a04_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.434Good
Packing 1D-1.333Satisfactory
Packing 3D-0.554Good
Overall-0.840Good

Since the overall quality Z-score improved to -0.840 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 2 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2ibd-a04.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.37. Homology model 37/42, based on template 2IBD-A, alignment variant 05

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: |: R::L|||A: LFA||G: :::|R||A:AAG : | |HF :KE:| |L: : : : D A:| A : : | :: | : : F: | : :: :L |EAG: G FR D| : : L : | : |QY::I G A:P
Template:.GKSGRRTELLDIAATLFAERGLRATTVRDIADAAGILSGSLYHHFDSKESMVDEILRGFLDDLFGKYREIVAS.DSRATLEALVTTSYEAIdHSAVAIYQDEVKHLVANERFTYLSE.LNTEFRELWMGVLEAGVKDGSFRSDIDVELAFRFLRDTA...................TVDTVAKQYLSIVLDG......ASP.
SecStr: .HHHHHHHHHHHHHHHHHHHHHTTTTHHHHHHHHHCCHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH.HHHHHHHHHHHHHHHHHHHHHHHHHHHCTTTTCCTTTTHHHHH.HHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHH...................HHHHHHHHHHHHHHHC......CCC.

The following 7 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1LAGMVNYFFLSTLATEGLTSHSPDQDEEL
2AAIVSPAIASVI
3TIQRHRNNPQL
4IRGQAGDPLAVMT
5IFTRGIMADGGAAPA
6NoneMTRADC
7GGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2ibd-a05_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.061Satisfactory
Packing 1D-1.451Satisfactory
Packing 3D-0.868Good
Overall-1.123Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2ibd-a05_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.798Good
Packing 1D-0.519Good
Packing 3D-0.683Good
Overall-0.636Good

Since the overall quality Z-score improved to -0.636 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 2 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2ibd-a05.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.38. Homology model 38/42, based on template 2IEK-A, alignment variant 01

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: : R: ||::A:E:F::KG| :: E|A| AG:: :|I ||F :KE LY : :: : : | : : |: RW :| : P| F : :: : | | : R:: | |: | : :D: : L : : F L T : :D : | | V |: R |
Template:....SKRDAILKAAVEVFGKKGYDRATTDEIAEKAGVAKGLIFHYFKNKEELYYQAYMSVTEKLQKEFENFLMKNRNRDIFDFMERWIEKKLEY.PEEADFLITLVSVDEG.LRKRILLDLEKSQRVFFDFVREKLKDLDLAEDVTEEIALKFLMWFFSGFEEVYLRTYQGKPELLKRDMNTLVEEVKVMLRILKKGMT....
SecStr: ....HHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHCCCHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH.HHHHHHHHTTTTCHHH.HHHHHHHHHHHHCHHHHHHHHHHHCCCCCTTTTHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH....

The following 4 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1QRHRNNPQLLRFY
2TNPTPCFAAIVS
3NoneMTRADCRSR
4MADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2iek-a01_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.121Satisfactory
Packing 1D-2.008Poor
Packing 3D-0.505Good
Overall-1.181Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2iek-a01_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.484Good
Packing 1D-0.873Good
Packing 3D-0.134Good
Overall-0.473Good

Since the overall quality Z-score improved to -0.473 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 8 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2iek-a01.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.39. Homology model 39/42, based on template 2IEK-A, alignment variant 02

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: : R: ||::A:E:F::KG| :: E|A| AG:: :|I ||F :KE LY : :: : : | : : |: RW :| : P| F : | | : R:: | |: | : :D: : L : : F L T : :D : | | V |: R |
Template:....SKRDAILKAAVEVFGKKGYDRATTDEIAEKAGVAKGLIFHYFKNKEELYYQAYMSVTEKLQKEFENFLMKNRNRDIFDFMERWIEKKLEY.PEEADFLI......DEGLRKRILLDLEKSQRVFFDFVREKLKDLDLAEDVTEEIALKFLMWFFSGFEEVYLRTYQGKPELLKRDMNTLVEEVKVMLRILKKGMT....
SecStr: ....HHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHCCCHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH.HHHHHHHH......HHHHHHHHHHHHHHHCHHHHHHHHHHHCCCCCTTTTHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH....

The following 4 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1QRHRNNPQLLRFY
2LRFYTSELTNPTPCFA
3NoneMTRADCRSR
4MADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2iek-a02_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.021Satisfactory
Packing 1D-2.048Poor
Packing 3D-0.457Good
Overall-1.160Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2iek-a02_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.259Good
Packing 1D-1.044Satisfactory
Packing 3D-0.128Good
Overall-0.504Good

Since the overall quality Z-score improved to -0.504 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 8 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2iek-a02.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.40. Homology model 40/42, based on template 2IEK-A, alignment variant 03

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: : R: ||::A:E:F::KG| :: E|A| AG:: :|I ||F :KE LY : :: : : | : : |: RW :| : P| F : :: : | | : R:: | |: | : :D: : L : : F L T : :D : | | V |: R I| G :
Template:....SKRDAILKAAVEVFGKKGYDRATTDEIAEKAGVAKGLIFHYFKNKEELYYQAYMSVTEKLQKEFENFLMKNRNRDIFDFMERWIEKKLEY.PEEADFLITLVSVDEG.LRKRILLDLEKSQRVFFDFVREKLKDLDLAEDVTEEIALKFLMWFFSGFEEVYLRTYQGKPELLKRDMNTLVEEVKVMLR.ILKKGMT...
SecStr: ....HHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHCCCHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH.HHHHHHHHTTTTCHHH.HHHHHHHHHHHHCHHHHHHHHHHHCCCCCTTTTHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH.HHHHHHH...

The following 5 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1QRHRNNPQLLRFY
2TNPTPCFAAIVS
3VAIFTRGIMADG
4ADGGAAPANone
5NoneMTRADCRSR

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2iek-a03_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.153Satisfactory
Packing 1D-2.133Poor
Packing 3D-0.553Good
Overall-1.257Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2iek-a03_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.576Good
Packing 1D-1.125Satisfactory
Packing 3D-0.266Good
Overall-0.646Good

Since the overall quality Z-score improved to -0.646 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 7 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2iek-a03.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.41. Homology model 41/42, based on template 2IEK-A, alignment variant 04

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: : R: ||::A:E:F::KG| :: E|A| AG:: :|I ||F :KE LY : :: : : | : : |: RW :| : P| F : | | : R:: | |: | : :D: : L : : F L T : :D : | | V |: R I| G :
Template:....SKRDAILKAAVEVFGKKGYDRATTDEIAEKAGVAKGLIFHYFKNKEELYYQAYMSVTEKLQKEFENFLMKNRNRDIFDFMERWIEKKLEY.PEEADFLI......DEGLRKRILLDLEKSQRVFFDFVREKLKDLDLAEDVTEEIALKFLMWFFSGFEEVYLRTYQGKPELLKRDMNTLVEEVKVMLR.ILKKGMT...
SecStr: ....HHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHCCCHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH.HHHHHHHH......HHHHHHHHHHHHHHHCHHHHHHHHHHHCCCCCTTTTHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH.HHHHHHH...

The following 5 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1QRHRNNPQLLRFY
2VAIFTRGIMADG
3LRFYTSELTNPTPCFA
4ADGGAAPANone
5NoneMTRADCRSR

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2iek-a04_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.044Satisfactory
Packing 1D-2.279Poor
Packing 3D-0.628Good
Overall-1.333Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2iek-a04_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.428Good
Packing 1D-1.163Satisfactory
Packing 3D-0.305Good
Overall-0.658Good

Since the overall quality Z-score improved to -0.658 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 7 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2iek-a04.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

5.42. Homology model 42/42, based on template 2IEK-A, alignment variant 05

This model is a monomer, and based on the following alignment:

SecStr:  CCCCCHHHHHHHHHHHHHHHHHHCCEEEHHHHHHHCCCEEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCHHHHHEECCCCCCCCCCHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHEHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
Target: MTRADCRSRLMEVATELFAQKGFYGVSIRELAQAAGASISMISYHFGGKEGLYAAVLQEQFACFGQLDDIRGQAGDPLAVMTAYLRWTIQRHRNNPQLLRFYTSELTNPTPCFAAIVSPAIASVIRLLAESIEAGMTRGLFRRDLHAVNSALALAGMVNYFFLSTLATEGLTSHSPDQDEELIRQYVAIFTRGIMADGGAAPA
Match: : R: ||::A:E:F::KG| :: E|A| AG:: :|I ||F :KE LY : :: : : | : : |: RW :| : P| F : :: I: S R:: | |: | : :D: : L : : F L T : :D : | | V |: R |
Template:....SKRDAILKAAVEVFGKKGYDRATTDEIAEKAGVAKGLIFHYFKNKEELYYQAYMSVTEKLQKEFENFLMKNRNRDIFDFMERWIEKKLEY.PEEADFLITLVSVDEGLRKRILLDLEKS..RVFFDFVREKLKDLDLAEDVTEEIALKFLMWFFSGFEEVYLRTYQGKPELLKRDMNTLVEEVKVMLRILKKGMT....
SecStr: ....HHHHHHHHHHHHHHHHHCTTTTHHHHHHHHHHCCCHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH.HHHHHHHHTTTTCHHHHHHHHHHHHHHH..HHHHHHHHHHHCCCCCTTTTHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH....

The following 4 loops had to be modeled:

LoopN-terminal anchorLoop sequenceC-terminal anchor
1PAIASVIRLLAE
2QRHRNNPQLLRFY
3NoneMTRADCRSR
4MADGGAAPANone

After the side-chains had been built, optimized and fine-tuned, all newly modeled parts were subjected to a combined steepest descent and simulated annealing minimization (i.e. the backbone atoms of aligned residues were kept fixed to avoid potential damage).

The resulting half-refined model has been saved as t0454_2iek-a05_refined050.yob and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-1.066Satisfactory
Packing 1D-2.071Poor
Packing 3D-0.404Good
Overall-1.151Satisfactory

Then a full unrestrained simulated annealing minimization was run for the entire model. The result has been saved as t0454_2iek-a05_refined100.yob, the corresponding Z-scores are listed below:

Check typeQuality Z-scoreComment
Dihedrals-0.508Good
Packing 1D-0.924Good
Packing 3D-0.113Good
Overall-0.487Good

Since the overall quality Z-score improved to -0.487 during the minimization, this fully refined model has been accepted as the final one for this template and alignment.

NOTE: 8 residues contained in N- and C-terminal floppy tails of the monomeric model have been excluded from the Z-scores in both tables above, since they would have mainly added noise to the result.

The final model for this template and alignment has been saved as t0454_2iek-a05.yob, and is shown below, together with a plot of its average per-residue quality Z-scores:

6. The model ranking

The following table lists the 42 models sorted by their overall quality Z-scores. The models have been superposed and saved together as t0454.sce.

RankZ-scoreStructureStateModel IDFilenameOriginal numberComment
1-0.332monomericBFBQ-A03t0454_bfbq-a03.yob15Good
2-0.370monomeric3BHQ-A01t0454_3bhq-a01.yob23Good
3-0.379monomeric3BHQ-A03t0454_3bhq-a03.yob25Good
4-0.473monomeric2IEK-A01t0454_2iek-a01.yob38Good
5-0.487monomeric2IEK-A05t0454_2iek-a05.yob42Good
6-0.504monomeric2IEK-A02t0454_2iek-a02.yob39Good
7-0.512monomeric3BHQ-A02t0454_3bhq-a02.yob24Good
8-0.532monomericBFBQ-A02t0454_bfbq-a02.yob14Good
9-0.548monomeric2EH3-A01t0454_2eh3-a01.yob18Good
10-0.578monomeric2FBQ-A03t0454_2fbq-a03.yob10Good
11-0.600monomeric2EH3-A05t0454_2eh3-a05.yob22Good
12-0.608monomeric1PB6-B01t0454_1pb6-b01.yob31Good
13-0.627monomericBFBQ-A04t0454_bfbq-a04.yob16Good
14-0.636monomeric2IBD-A05t0454_2ibd-a05.yob37Good
15-0.646monomeric2IEK-A03t0454_2iek-a03.yob40Good
16-0.658monomeric2IEK-A04t0454_2iek-a04.yob41Good
17-0.660monomericBFBQ-A01t0454_bfbq-a01.yob13Good
18-0.665monomeric2IBD-A03t0454_2ibd-a03.yob35Good
19-0.679monomeric2FBQ-A02t0454_2fbq-a02.yob9Good
20-0.685monomeric2JJ7-B02t0454_2jj7-b02.yob7Good
21-0.712monomeric2JJ7-B01t0454_2jj7-b01.yob6Good
22-0.715monomeric2FBQ-A04t0454_2fbq-a04.yob11Good
23-0.719monomeric2IBD-A02t0454_2ibd-a02.yob34Good
24-0.720monomericBFBQ-A05t0454_bfbq-a05.yob17Good
25-0.744monomeric2FX0-A02t0454_2fx0-a02.yob27Good
26-0.746monomeric1PB6-B02t0454_1pb6-b02.yob32Good
27-0.749monomeric2FX0-A05t0454_2fx0-a05.yob30Good
28-0.762monomeric2FBQ-A01t0454_2fbq-a01.yob8Good
29-0.765monomeric2EH3-A04t0454_2eh3-a04.yob21Good
30-0.778monomeric2EH3-A03t0454_2eh3-a03.yob20Good
31-0.803monomeric2FBQ-A05t0454_2fbq-a05.yob12Good
32-0.809monomeric2IBD-A01t0454_2ibd-a01.yob33Good
33-0.840monomeric2IBD-A04t0454_2ibd-a04.yob36Good
34-0.855monomeric2EH3-A02t0454_2eh3-a02.yob19Good
35-0.913monomeric2OFL-B04t0454_2ofl-b04.yob4Good
36-0.917monomeric2FX0-A03t0454_2fx0-a03.yob28Good
37-0.976monomeric2FX0-A04t0454_2fx0-a04.yob29Good
38-0.985monomeric2FX0-A01t0454_2fx0-a01.yob26Good
39-1.007monomeric2OFL-B01t0454_2ofl-b01.yob1Satisfactory
40-1.107monomeric2OFL-B05t0454_2ofl-b05.yob5Satisfactory
41-1.194monomeric2OFL-B03t0454_2ofl-b03.yob3Satisfactory
42-1.376monomeric2OFL-B02t0454_2ofl-b02.yob2Satisfactory

7. The hybrid model

Finally, YASARA tried to combine the best parts of the 42 models to obtain a hybrid model, hoping to increase the accuracy beyond each of the contributors. Starting with the best scoring model t0454_bfbq-a03.yob, the following fragments were successfully copied from other models:

TransferFirst residueLast residueLengthFrom modelEnergy after transfer [kcal/mol]
1ILE A 116SER A 11832IEK-A04-21362
2PRO A 176GLN A 17832EH3-A05-21480

The resulting hybrid model was subjected to a final round of simulated annealing minimization in explicit solvent and obtained the following quality Z-scores:

Check typeQuality Z-scoreComment
Dihedrals-0.656Good
Packing 1D-0.223Good
Packing 3D-0.206Good
Overall-0.278Good

The following figure shows the original best model in blue, with all parts copied from other models colored yellow.

Since this hybrid model scored better than all previous models, it was saved as the final model t0454.yob.