Dear Modeller users,

I am trying to search for the best template for my target molecule, and therefore I created a file in PIR format with my sequences and then 
I ran build_profile.py. I got the following error in my log file:


                         MODELLER 9.10, 2011/09/28, r8346

     PROTEIN STRUCTURE MODELLING BY SATISFACTION OF SPATIAL RESTRAINTS


                     Copyright(c) 1989-2011 Andrej Sali
                            All Rights Reserved

                             Written by A. Sali
                               with help from
           B. Webb, M.S. Madhusudhan, M-Y. Shen, M.A. Marti-Renom,
                N. Eswar, F. Alber, M. Topf, B. Oliva, A. Fiser,
                    R. Sanchez, B. Yerkovich, A. Badretdinov,
                      F. Melo, J.P. Overington, E. Feyfant
                 University of California, San Francisco, USA
                    Rockefeller University, New York, USA
                      Harvard University, Cambridge, USA
                   Imperial Cancer Research Fund, London, UK
              Birkbeck College, University of London, London, UK


Kind, OS, HostName, Kernel, Processor: 4, Linux pan 3.0.0-12-generic x86_64
Date and time of compilation         : 2011/09/28 17:58:44
MODELLER executable type             : x86_64-intel8
Job starting time (YY/MM/DD HH:MM:SS): 2012/02/29 16:37:57

openf___224_> Open           $(LIB)/restyp.lib
openf___224_> Open           ${MODINSTALL9v10}/modlib/resgrp.lib
rdresgr_266_> Number of residue groups:        2
openf___224_> Open           ${MODINSTALL9v10}/modlib/sstruc.lib

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:      3234076    3158.277     3.084

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:      3234604    3158.793     3.085
openf___224_> Open           ${MODINSTALL9v10}/modlib/resdih.lib

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:      3283204    3206.254     3.131
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
openf___224_> Open           ${MODINSTALL9v10}/modlib/radii.lib

Dynamically allocated memory at   amaxlibraries [B,KiB,MiB]:      3292444    3215.277     3.140
openf___224_> Open           ${MODINSTALL9v10}/modlib/radii14.lib
openf___224_> Open           ${MODINSTALL9v10}/modlib/af_mnchdef.lib
rdwilmo_274_> Mainchain residue conformation classes:  APBLE
openf___224_> Open           ${MODINSTALL9v10}/modlib/mnch.lib
rdclass_257_> Number of classes:        5
openf___224_> Open           ${MODINSTALL9v10}/modlib/mnch1.lib
openf___224_> Open           ${MODINSTALL9v10}/modlib/mnch2.lib
openf___224_> Open           ${MODINSTALL9v10}/modlib/mnch3.lib
openf___224_> Open           ${MODINSTALL9v10}/modlib/xs4.mat
rdrrwgh_268_> Number of residue types:       21
openf___224_> Open           pdb.pir

Dynamically allocated memory at amaxsequence_db [B,KiB,MiB]:      3293057    3215.876     3.141

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:      3294891    3217.667     3.142

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:      3296341    3219.083     3.144

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:      3299241    3221.915     3.146

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:      3305041    3227.579     3.152

Dynamically allocated memory at amaxsequence_db [B,KiB,MiB]:      3310040    3232.461     3.157

SEQ_DATABASE_FILE         : pdb.pir
SEQ_DATABASE_FORMAT       : PIR
CHAINS_LIST               : ALL
CLEAN_SEQUENCES           :            T
MINMAX_DB_SEQ_LEN         :           30        4000
Number of sequences       :            4
Number of residues        :         1060
Length of longest sequence:          271


SEQ_DATABASE_FILE         : pdb_3.bin
SEQ_DATABASE_FORMAT       : BINARY
SEARCH_CHAINS_LIST        : ALL
Number of sequences       :            4
Number of residues        :         1060
Length of longest sequence:          271


SEQ_DATABASE_FILE         : pdb_3.bin
SEQ_DATABASE_FORMAT       : BINARY
CHAINS_LIST               : ALL
CLEAN_SEQUENCES           :            T
MINMAX_DB_SEQ_LEN         :            0      999999
Number of sequences       :            4
Number of residues        :         1060
Length of longest sequence:          271

openf___224_> Open           chst11.ali

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:      3300046    3222.701     3.147

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:      3301496    3224.117     3.149

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:      3304396    3226.949     3.151

Dynamically allocated memory at   amaxalignment [B,KiB,MiB]:      3310196    3232.613     3.157

Dynamically allocated memory at    amaxsequence [B,KiB,MiB]:      3311600    3233.984     3.158

Read the alignment from file       : chst11.ali
Total number of alignment positions:   352

  #  Code        #_Res #_Segm PDB_code    Name
-------------------------------------------------------------------------------
  1     chst11     352      1      chst11

Dynamically allocated memory at     amaxprofile [B,KiB,MiB]:      3313325    3235.669     3.160
openf___224_> Open           ${LIB}/blosum62.sim.mat
rdrrwgh_268_> Number of residue types:       21
profile_iteration_> processing sequence:       1    352      1     0.0100000     0.0100000     0.0100000     1
regress_657E> Not enough bins in histogram - cannot calculate statistics, nbins:        1

My build_profile.py file is the following:

from modeller import *

log.verbose()
env = environ()

#-- Prepare the input files

#-- Read in the sequence database
sdb = sequence_db(env)
sdb.read(seq_database_file='pdb.pir', seq_database_format='PIR',
         chains_list='ALL', minmax_db_seq_len=(30, 4000), clean_sequences=True)

#-- Write the sequence database in binary form
sdb.write(seq_database_file='pdb_3.bin', seq_database_format='BINARY',
          chains_list='ALL')

#-- Now, read in the binary database
sdb.read(seq_database_file='pdb_3.bin', seq_database_format='BINARY',
         chains_list='ALL')

#-- Read in the target sequence/alignment
aln = alignment(env)
aln.append(file='chst11.ali', alignment_format='PIR', align_codes='ALL')

#-- Convert the input sequence/alignment into
#   profile format
prf = aln.to_profile()

#-- Scan sequence database to pick up homologous sequences
prf.build(sdb, matrix_offset=-450, rr_file='${LIB}/blosum62.sim.mat',
          gap_penalties_1d=(-500, -50), n_prof_iterations=10,
          check_profile=True, max_aln_evalue=0.01)

#-- Write out the profile in text format
prf.write(file='build_profile.prf', profile_format='TEXT')

#-- Convert the profile back to alignment format
aln = prf.to_alignment()

#-- Write out the alignment file
aln.write(file='build_profile.ali', alignment_format='PIR')

If anyone could help me with this I would be grateful.

Many thanks in advance,

Susana