[modeller_usage] Mismatch between residues of alignment and pdb

I downloaded the pdb_95.pir files, updated on May 14th 2020, from here. I used the tutorial to model one chain of a protein. I downloaded the pdb structure from RCSB-PDB. No changes done from my side in either files. Firstly, I was receiving an error " No atoms were read from the specified input PDB file, since the starting residue number and/or chain id in MODEL_SEGMENT (or the alignment file header) was not found; requested starting position: residue number " 1", chain " "; atom file name: 1r42A.pdb".

I manually changed the chain id from blank to A and another error popped up stating that initial residue isn't matching, so I changed the initial residue from 1 to 19 and the error got resolved. Now, another error is there and isn't getting resolved anyhow. " After running model_single.py, I am getting the following error -

_modeller.ModellerError: read_te_290E> Number of residues in the alignment and pdb files are different: 596 655 For alignment entry: 1 1r42A

". Ideally the pdb_95.pir file should have the same info as pdbs, yet this is popping up. Attaching the alignment section of the stated structure and the PDB is 1r42. Kindly can anyone help me in debugging what the exact issue is. I've been on it since days now. The alignment file has 596 residues while the pdb is supposed to have the same number because it has not been tampered with. Where it is going wrong? How can this be resolved?

The alignment section of stated structure -

>P1;1r42A

structure:1r42A: 19:A: 596: :::-1.00:-1.00
------------------STIEEQAKTFLDKFNHEAEDLFYQSSLASWNYNTNITEENVQNMNNAGDKWSAFLKE
QSTLAQMYPLQEIQNLTVKLQLQALQQNGSSVLSEDKSKRLNTILNTMSTIYSTGKVCNPDNPQECLLLEPGLNE
IMANSLDYNERLWAWESWRSEVGKQLRPLYEEYVVLKNEMARANHYEDYGDYWRGDYEVNGVDGYDYSRGQLIED
VEHTFEEIKPLYEHLHAYVRAKLMNAYPSYISPIGCLPAHLLGDMWGRFWTNLYSLTVPFGQKPNIDVTDAMVDQ
AWDAQRIFKEAEKFFVSVGLPNMTQGFWENSMLTDPGNVQKAVCHPTAWDLGKGDFRILMCTKVTMDDFLTAHHE
MGHIQYDMAYAAQPFLLRNGANEGFHEAVGEIMSLSAATPKHLKSIGLLSPDFQEDNETEINFLLKQALTIVGTL
PFTYMLEKWRWMVFKGEIPKDQWMKKWWEMKREIVGVVEPVPHDETYCDPASLFHVSNDYSFIRYYTRTLYQFQF
QEALCQAAKHEGPLHKCDISNSTEAGQKLFNMLRLGKSEPWTLALENVVGAKNMNVRPLLNYFEPLFTWLKDQNK
NSFVGWSTDWSPYA-------------------------------------------------------------
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Kindly help.

Thanks and Warm Regards

Sunidhi

Center for Computational Biology

Indraprastha Institute of Information Technology (IIIT)

New Delhi 110020 India