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[modeller_usage] Protein not accepted

I had to do an automodelling of a protein based
on a template.

I first ran the seqcheck and use the sequences that I got for the
alignment (using tcoffee).

I prepared the alignment file as follow:

>P1;1GNS
sequence:1GNS:   4 :A: 275 :A:undefined:undefined:-1.00:-1.00
GPYGVSQIKAP-ALHSQGYTGSNVKVAVIDSGID------SSHPALKVAGGASFVPSETN
PFQDNNSHGTHVAGTVLA-------VAPSASLYAVKVLGADGS--GQYSWIINGIEWAIA
NNMDVINMSLGGPSGSAALKAA---VDKAVASGVVVVAAAGNEGTSGSSSTVGYPGKYPS
VIAVGAV-----------DSSNQRASFSSVGP------ELDVMAPGVSIWSTL-------
-----PGNKYGAKSGT-MASPHVAGAAALI------------------------------
-------------LSKHPNWTNTQVRSSLE------------------------------
-----------------NTTTKLGDSFYYG--------------------KGLINVEAAA
---------------Q*
>P1;1WMD
structureX:1WMD:   1 :A: 434 :A:undefined:undefined:-1.00:-1.00
NDVARGIVKADVAQSSYGLYGQGQIVAVADTGLDTGRNDSSMHEAFRGKITALYALGRTN
NANDTNGHGTHVAGSVLGNGSTNKGMAPQANLVFQSIMDSGGGLGGLPSNLQTLFSQAYS
AGARIHTNSWGAAVNGAYTTDSRNVDDYVRKNDMTILFAAGNEGPNGG--TISAPGTAKN
AITVGATENLRPSFGSYADNINHVAQFSSRGPTKDGRIKPDVMAPGTFILSARSSLAPDS
SFWANHDSKYAYMGGTSMATPIVAGNVAQLREHFVKNRGITPKPSLLKAALIAGAADIGL
GYPNGNQGWGRVTLDKSLNVAYVNESSSLSTSQKATYSFTATAGKPLKISLVWSDAPAST
TASVTLVNDLDLVITAPNGTQYVGNDFTSPYNDNWDGRNNVENVFINAPQSGTYTIEVQA
YNVPVGPQTFSLAIVN*

this is my script for the automodelling:

# Homology modelling by the automodel class

from modeller.automodel import *           # Load the automodel class

log.verbose()    # request verbose output
env = environ()  # create a new MODELLER environment to build this model in

# directories for input atom files
env.io.atom_files_directory = './:../home/Bis/gbastian/Documents/Data/ExcerciseModeling/SUBTILISIN BPN/Structure files/' 
a = automodel(env,
             alnfile = 'alignedsequences.ali',   # alignment filename
             knowns = '1WMD',             # codes of the templates
             sequence = '1GNS')           # code of the target

a.starting_model= 1               # index of the first model
a.ending_model = 10                # index of the last model
# (determines how many models to calculate) 
a.make()                          # do the actual homology modelling


and this is what I got after running it:

openf5__224_> Open       11  OLD  SEQUENTIAL  $(LIB)/restyp.lib
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/resdih.lib 
rdrdih__263_> Number of dihedral angle types         :        9
             Maximal number of dihedral angle optima:        3
Dihedral angle names : Alph Phi Psi Omeg chi1 chi2 chi3 chi4 chi5 openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/radii.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/radii14.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/af_mnchdef.lib 
rdwilmo_274_> Mainchain residue conformation classes:  APBLE
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/mnch.lib 
rdclass_257_> Number of classes:        5
openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/mnch1.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/mnch2.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/mnch3.lib openf5__224_> Open 11 OLD SEQUENTIAL ${MODINSTALL8v2}/modlib/xs4.mat 
rdrrwgh_268_> Number of residue types:       21
runcmd______> alignment.append(align_codes=['1WMD', '1GNS'], atom_files=[], file='alignedsequences.ali', (def)remove_gaps=True, (def)alignment_format='PIR', add_sequence=True, (def)rewind_file=False, (def)close_file=True) 
openf___224_> Open           alignedsequences.ali
Dynamically allocated memory at amaxalignment [B,kB,MB]: 2270569 2217.353 2.165 
Dynamically allocated memory at   amaxalignment [B,kB,MB]:      
2293501    2239.747     2.187

Dynamically allocated memory at   amaxalignment [B,kB,MB]:      
2316901    2262.599     2.210

Dynamically allocated memory at   amaxalignment [B,kB,MB]:      
2363701    2308.302     2.254

Dynamically allocated memory at   amaxalignment [B,kB,MB]:      
2457301    2399.708     2.343

Dynamically allocated memory at   amaxalignment [B,kB,MB]:      
2644501    2582.521     2.522

Read the alignment from file       : alignedsequences.ali
Total number of alignment positions:   436

 #  Code        #_Res #_Segm PDB_code    Name
-------------------------------------------------------------------------------
 1       1WMD     434      1        1WMD undefined
 2       1GNS     262      1        1GNS undefined
runcmd______> alignment.check()

check_a_343_> >> BEGINNING OF COMMAND
pdbnam__217W> Filename for PDB code not found:  1WMD

             Directories:  
./:../home/Bis/gbastian/Documents/Data/ExcerciseModeling/SUBTILISIN 
BPN/Structure files/

             Extensions :   :.atm:.pdb:.ent:.crd
rdabrk__288W> Protein not accepted:        1  1WMD
check_a_337E> Structure not read in (please consult the log file
             for more details):        1  1WMD

What's wrong with my PDB??

I checked the name reference and they are all right.

Thanks a lot

Giacomo