[modeller_usage] Alignment file.

I'm doing something wrong, I'm a novice though, so I know what what.
I'm using a fairly simple TOP script to generate a model a nitroreductase.
I've used blast on NCBI to find a simialr protein to the one I have the pdb
model for. The blast results look like this :

Query: 1   MDIISVALKRHSTKAFDASKKLTPEQAEQIKTLLQYSPSSTNSQPWHFIVASTEEGKARV 60
           MDIISVALKRHSTKAFDASKKLT E+AE+IKTLLQYSPSSTNSQPWHFIVASTEEGKARV
Sbjct: 1   MDIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARV 60

Query: 61  AKSAAGNYVFNERKMLDASHVVVFCAKTAMDDVWLKLVVDQEDADGRFATPEAKAANDKG 120
           AKSAAG YVFNERKMLDASHVVVFCAKTAMDD WL+ VVDQE+ADGRF TPEAKAAN KG
Sbjct: 61  AKSAAGTYVFNERKMLDASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKG 120

Query: 121 RKFFADMHRKDLHDDAEWMAKQVYLNVGNFXXXXXXXXXXXXPIEGFDAAILDAEFGLKE 180
           R +FADMHR DL DD +WMAKQVYLNVGNF            PIEGFDAAILD EFGLKE
Sbjct: 121 RTYFADMHRVDLKDDDQWMAKQVYLNVGNFLLGVGAMGLDAVPIEGFDAAILDEEFGLKE 180

Query: 181 KGYTSLVVVPVGHHSVEDFNATLPKSRLPQNITLTE 216
           KG+TSLVVVPVGHHSVEDFNATLPKSRLP +  +TE
Sbjct: 181 KGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTE 216


How do I then transform this into a successful alignment file?
My attempt looks something like this:
>P1;1OO5
structureX:1OO5:   2 :A: 217 :D:undefined:undefined:-1.00:-1.00
mdiisvalkrhstkafdaskkltpeqaeqiktllqyspsstnsqpwhfivasteegkarvaksaagnyvfnerkml
dashvvvfcaktamddvwlklvvdqedadgrfatpeakaandkgrkffadmhrkdlhddaewmakqvylnvgnfll
gvaalgldavpiegfdaaildaefglkekgytslvvvpvghhsvedfnatlpksrlpq nitltev*

>P1;1NEC
sequence:1NEC:   2 :A: 216 :D:undefined:undefined:-1.00:-1.00
DIISVALKRHSTKAFDASKKLTAEEAEKIKTLLQYSPSSTNSQPWHFIVASTEEGKARVAKSAAGTYVFNERKML
DASHVVVFCAKTAMDDAWLERVVDQEEADGRFNTPEAKAANHKGRTYFADMHRVDLKDDDQWMAKQVYLNVGNFL
LGVGAMGLDAVPIEGFDAAILDEEFGLKEKGFTSLVVVPVGHHSVEDFNATLPKSRLPLSTIVTE*

I've basically taken the Query sequence (1OO5) which I have the pdb file for and
placed it in the sequence section, then taken the result sequence which has
been matched to it (1NEC) and placed it in the second position of the alignment
file with the sequence label.
However, when I run it, in my mod.log file, I'm getting the error:

Dynamically allocated memory at         amaxseq [B,kB,MB]:      2205269
2153.583     2.103
openf5__224_> Open       11  OLD  SEQUENTIAL  1OO5.ali

Dynamically allocated memory at         amaxbnd [B,kB,MB]:      5377489
5251.454     5.128
openf5__224_> Open       11  OLD  SEQUENTIAL  1OO5.ali
read_al_375E> Unknown residue type,position,sequence:  m        1        1
recover____E> ERROR_STATUS >= STOP_ON_ERROR:        1       1



As far as I can gatherThis means that it doesn't like the residue at position
one. I don't however know what it doesn't like about the residue at that
position. Am I creating the alignment file in the wrong manner? Is there
something else wrong?

In case it of any use, the top file looks like:
INCLUDE                             # Include the predefined TOP routines
SET OUTPUT_CONTROL = 1 1 1 1 1      # uncomment to produce a large log file
SET ALNFILE  = '1ICV.ali'           # alignment filename
SET KNOWNS   = '1ICV'               # codes of the templates
SET SEQUENCE = '1NEC'               # code of the target
# SET HYDROGEN_IO = on
SET HETATM_IO = on
SET ATOM_FILES_DIRECTORY = '../pdb' # directories for input atom files
SET STARTING_MODEL= 1               # index of the first model
SET ENDING_MODEL  = 10              # index of the last model
                                    # (determines how many models to calculate)
SET PDB_EXT = '.modlr.pdb'
SET MD_LEVEL = 'refine_5'
SET LIBRARY_SCHEDULE = 1
CALL ROUTINE = 'model


Thanks.
Ben.