[modeller_usage] Problems modelling sections of sequence on different templates

Hi all,

I am trying to model my protein on two templates  except in a small region in
the middle of my sequence which I want to model on a third template only. I
have altered the .ali files so that there are gaps in the correct parts of the
alignments and changed the pdb files to have corresponding gaps. When I run
this it comes up with an error and doesn't make a _fit file:

fit2xyz_296E> Number of equivalent positions < 3:        0
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1

If I don't model this small piece and leave the gaps in the other templates it
works fine so this suggests that there is something wrong with the third
template or how I assigned it but I cannot figure it out. 

Any help would be greatly appreciated as I have a deadline approaching!
Thanks!

Below are the .ali and .top files

>P1;1XFD
structureX:1XFD:127:A:849:A::::
------------------------------------------------------------
---------------------QKKKVTVEDLFSEDFKIHDPEAKWISDTEFIYREQKGTV
RLWNVETNTSTVLIEGKKIESLRAIR--YEISPDREYALFSYNVEPIYQHSYTGYYVLSK
IPHGDPQSLDPPEVSNAKLQYAGWGPKG-QQLIFIFENNIYYCAHVGKQAIRVVSTG---
---KEGVIYNGLSDWLYEEEILKTHIAHWWS------PDG--------------------
-----------------------PSISLHVIGLN--------GPTHDLEMMPPDDPRMRE
YYITMVKWATSTKVAV-TWLNRAQNVSILTLCDATTGVCTKKHEDESEAWLHRQN-----
-------------------EEPVFSKDGRKFFFIRAIPQGGRGKFYHITVS---------
-----SSQPNSSNDNIQSITSGDWDVTK----ILAYDEKGNKIYFLSTEDLPRRRQLYSA
NTVGNFNRQCLSCDLVEN-CTYFSASFSHSMDFFLLKCEGPGVPMVTVHNTTDKKKMFDL
ETNEHVKKAINDR--QMPKVEYRDIEIDDYNLPMQILKPATFTDTTHYPLLLVVDGTPGS
QSVAEKFE--VSWETVMVSSHGAVVVKCDGRGSGFQGTKLLHEVRRRLGLLEEKDQMEAV
RTML-KEQYIDRTRVAVFGKDYGGYLSTYILPAKGENQGQTFTCGSALSPITDFKLYASA
FSERYLGLHGLDN--RAYEMTKVAHRVSALEEQQFLIIHPTADEKIHFQHTAELITQLIR
GKANYSLQIYPDESHYFTSSSLKQHLYRSIINFFVECFRI----------------*

>P1;1H2W
structureX:1H2W:208:A:250:A::::
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
----------------------------------------QKLYYHVLGTDQSEDILCAE
FPDEPKWMGGAELSDDGRYVLLS-------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
------------------------------------------------------------
--------------------------------------------------------*

>P1;1N1M
structureX:1N1M:39:A:764:A::::
------------------------------------------------------------
---------------------SRKTYTLTDYLKNTYRLKLYSLRWISDHEYLYKQENN-I
LVFNAEYGNSSVFLENSTFDEFGHSINDYSISPDGQFILLEYNYVKQWRHSYTASYDIYD
LN---KRQLITEERIPNNTQWVTWSPVG-HKLAYVWNNDIYVKIEPNLPSYRITWTG---
---KEDIIYNGITDWVYEEEVFSAYSALWWS------PNG--------------------
-----------------------PTVKFFVVNTDSLSS---VTNATSIQITAPASMLIGD
HYLCDVTWATQERISL-QWLRRIQNYSVMDICDYDESSGRWNCLVARQHIEMSTTGWVG-
---------------RFRPSEPHFTLDGNSFYKIISNEEGYRHICYFQID----------
------------KKDCTFITKGTWEVIG----IEALTSDYLYYISNEYKGMPGGRNLYKI
QLSDYTKVTCLSCELNPERCQYYSVSFSKEAKYYQLRCSGPGLPLYTLHSSVNDKGLRVL
EDNSALDKMLQNV--QMPSKKLDFIILNETKFWYQMILPPHFDKSKKYPLLLDVYAGPCS
QKADTVFR--LNWATYLASTENIIVASFDGRGSGYQGDKIMHAINRRLGTFEVEDQIEAA
RQFS-KMGFVDNKRIAIWGWSYGGYVTSMVLG----SGSGVFKCGIAVAPVSRWEYYDSV
YTERYMGLPTPEDNLDHYRNSTVMSRAENFKQVEYLLIHGTADDNVHFQQSAQISKALVD
VGVDFQAMWYTDEDHGIASSTAHQHIYTHMSHFIKQCFS-----------------*

>P1;DP8mod
sequence:DP8mod:.:.:.:.::::
MAAAMETEQLGVEIFETADCEENIESQDRPKLEPFYVERYSWSQLKKLLADTRKYHGYMM
AKAPHDFMFVKRNDPDGPHSDRIYYLAMSGENRENTLFYSEIPKTINRAAVLMLSWKPLL
DLFQATLDYGMYSREEELLRERKRIGTVGIASYDYHQGSGTFLFQAGSGIYHVKDGGPQG
FTQQPLRPNLVETSCPNIRMDPKLCPADPDWIAFIHSNDIWISNIVTREERRLTYVHNEL
ANMEEDARSAGVATFVLQEEFDR-YSGYWWCPKAETTPSGGKILRILYEENDESEVEIIH
VTSPMLETRRADSFRYPKTGTANPKVTFKMSEIMIDAEGRIIDVIDKELIQPFEILFEGV
EYIARAGWTPEGKYAWSILLDRSQTRLQIVLISPELFIPVEDDVMERQRLIESVPDSVTP
LIIYEETTDIWINIHDIFHVFPQSHEEEIEFIFASECKTGFRHLYKITSILKESKYKRSS
GGLPAPSDFKCPIKEEIAITSGEWEVLGRHGSNIQVDEVRRLVYFEGTKDSPLEHHLYVV
SYVNPGEVTRLTDRGYSHSCCISQHCDFFISKYSNQKNP-HCVSLYKLSSPEDDPTCKTK
EFWATILDSAGPLPDYTPPEIFSFESTTGFTLYGMLYKPHDLQPGKKYPTVLFIYGGPQV
QLVNNRFKGVKYFRLNTLASLGYVVVVIDNRGSCHRGLKFEGAFKYKMGQIEIDDQVEGL
QYLASRYDFIDLDRVGIHGWSYGGYLSLMALMQ----RSDIFRVAIAGAPVTLWIFYDTG
YTERYMGHPDQNEQGYYLGSVAMQAEKFPSEPNRLLLLHGFLDENVHFAHTSILLSFLVR
AGKPYDLQIYPQERHSIRVPESGEHYELHLLHYLQENLGSRIAALKVI--------*


INCLUDE      # Include the predefined TOP routines

SET ALNFILE = 'C:\Program Files\Modeller7v7\Models\DP8mod.ali'  # Alignment
filename
SET KNOWNS = '1XFD' '1H2W' '1N1M' 		# Code of the template
SET SEQUENCE = 'DP8mod'
SET STARTING_MODEL = 1
SET ENDING_MODEL = 1

SET DEVIATION = 4.0   # Amount of randomization between models

SET LIBRARY_SCHEDULE = 1  # thorough VTF schedule
SET MAX_VAR_ITERATIONS = 300

SET FINAL_MALIGN3D = 1   # MALIGN3D and write superposed
      # templates & models
SET MD_LEVEL = 'refine_1'  # thorough MD annealing

CALL ROUTINE = 'model'