TM-score/TM-align between two proteins of identical sequence

Hello,
I am not sure how to calculate the TM-score between two proteins of identical sequences. The TM-score server seems to insert gaps into one of the sequence so does misalign the proteins and produces
RMSD of the common residues= 20.260

The TM-align does a more drastic re-alignment of the sequences and produces
Aligned length= 301, RMSD= 3.09

Idependent verification of the RMSD with Swiss-pdb viewer gives 18.42 Angstrom over all residues, which I believe is the correct number. I have no means of veryfying the TM-score, but I assume something is not working correctly here. In particular the TM-score server should not attemp alignment of the sequences.
I would be grateful for any help.

Best wishes
Andreas

Output:
*****************************************************************************
* TM-SCORE *
* A scoring function to assess the similarity of protein structures *
* Based on statistics: *
* 0.0 < TM-score < 0.17, random structural similarity *
* 0.5 < TM-score < 1.00, in about the same fold *
* Reference: Yang Zhang and Jeffrey Skolnick, Proteins 2004 57: 702-710 *
* For comments, please email to: zhng@umich.edu *
*****************************************************************************

Structure1: A950606 Length= 460
Structure2: B950606 Length= 460 (by which all scores are normalized)
Number of residues in common= 452
RMSD of the common residues= 20.260

TM-score = 0.3555 (d0= 7.67)
MaxSub-score= 0.1396 (d0= 3.50)
GDT-TS-score= 0.1913 %(d<1)=0.1000 %(d<2)=0.1261 %(d<4)=0.2087 %(d<8)=0.3304
GDT-HA-score= 0.1207 %(d<0.5)=0.0478 %(d<1)=0.1000 %(d<2)=0.1261 %(d<4)=0.2087

-------- rotation matrix to rotate Chain-1 to Chain-2 ------
i t(i) u(i,1) u(i,2) u(i,3)
1 98.8172023274 -0.9876216551 0.1511161222 0.0420402664
2 160.2322018699 -0.1567096555 -0.9621389444 -0.2230038915
3 -12.6233875120 0.0067490942 -0.2268315881 0.9739106121

Superposition in the TM-score: Length(d<5.0)=107 RMSD= 2.77
(":" denotes the residue pairs of distance < 5.0 Angstrom)
AYDSNRASCIPSVWNNYNLTGEGILVGFLDTGIDYTHNAFKDAEGNTRIEYIYDLENGVVYDKNKINEALKSEDPFSIVPEIDLSGHGTHVAGIACAGGNINFDNYGVAYKSSIA-VKITGENSLRAALSTQL-RGLKFL-DKSNEINKPLVVNISLSTNDGSHNGSSLLEKYIQTFTQLQKAVIVVAAGNEGNSAHHVGGK-KKEEDLDLNIGDGEKGIILDFFKPVLVDVSVEVISPTGISTGPIELSESYKERFVGREKIVVYSTGPKPFDIQGQTTISILPLGDTITSGGWRIIVRKLNNYEGYFDIWLP---GLNERTRFLQPSVYNTLGIPATVEGVISVGSYNFLNNNLSAFSGRGVVRPEWLIKPDLVAPGENILSTVEEQGFDTKSGTS-AAPQVSGICALLFEWGIIRNNDPFLYGERIKYYLIKGAKRTIFGEAYPNPDLGYGFVCLDRTELLINRR
:::::::::::::::::::::::: :::::::::::::: :: : ::::::::::::::::: ::: :::::::::::: : ::::::::::: :: :: :::: : : ::::::::: : ::
AYDSNRASCIPSVWNNYNLTGEGILVGFLDTGIDYTHNAFKDAEGNTRIEYIYDLENGVVYDKNKINEALKSEDPFSIVPEIDLSGHGTHVAGIACAGGNINFDNYGVAYKSSIAVKITGENSLRAALSTQLRGLKFLDKSNEINKPLVVNISLSTNDGSHNGSSLLEKYIQTFTQLQKAVIVVAAGNEGNSAHHVGGKKKEEDLDLNIGDGEKGIILDFFKPVLVDVSVEVISPTGISTGPIELSESYKERFVGREKIVVYSTGPKPFDIQGQTTISILPLGDTITSGGWRIIVRKLNNYEGYFDIWLPGLNERTRFLQPSVYNTLGIPATVEGVISVGSYNFLNNNLSAFSGRGVVRPEWLIKPDLVAPGENILSTVEEQGFDTKSGTSAAPQVSGICALLFEWGIIRNNDPFLYGERIKYYLIKGAKRTIFGEAYPNPDLGYGFVCLDRTELLINRR--------
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**************************************************************************
* TM-align (Version 20170708) *
* An algorithm for protein structure alignment and comparison *
* Based on statistics: *
* 0.0 < TM-score < 0.30, random structural similarity *
* 0.5 < TM-score < 1.00, in about the same fold *
* Reference: Y Zhang and J Skolnick, Nucl Acids Res 33, 2302-9 (2005) *
* Please email your comments and suggestions to: zhng@umich.edu *
**************************************************************************

Name of Chain_1: A408601
Name of Chain_2: B408601
Length of Chain_1: 460 residues
Length of Chain_2: 460 residues

Aligned length= 301, RMSD= 3.09, Seq_ID=n_identical/n_aligned= 0.930
TM-score= 0.59414 (if normalized by length of Chain_1)
TM-score= 0.59414 (if normalized by length of Chain_2)
(You should use TM-score normalized by length of the reference protein)

(":" denotes aligned residue pairs of d < 5.0 A, "." denotes other aligned residues)
AYDSNRASCIPSVWNNYN------------------LTGEGILVGFLDTGIDYTHNAFKDAEGNTRIEYIYDLENGVVYD-KN-KINEALKSEDPFS-------IVPEIDLSGHGTHVAGIACAGGNINFDNYGVAYKSSIAVKITGENSLRAALSTQLRGLKFLDKSNEINKPLVVNISLSTNDGSHNGSSLLEKYIQTFTQLQKAVIVVAAGNEGN-----------------------------------------------------------------------------------------------------------------------------------SAHHVGGK-KKEEDLDLNIGDGEKGIILDFFKPVLVDVSVEVISPTGISTGPIELSESYKERFVGREKIVVYSTGPKPFDIQGQTTISILPLGDTITSGGWRIIVRKLNNYEGYFDIWLPGLNERTRFLQPSVYNTLGIPATVEGVISVGSYNFLNNNLSAFSGRGVVRPEWLIKPDLVAPGENILSTVEEQGFDTKSGTSAAPQVSGICALLFEWGIIRNNDPFLYGERIKYYLIKGAKRTIFGEAYPNPDLGYGFVCLDRTELLINRR
..:::::::::::::::::::::::....::::::::::::.. . .::... ....:::::::::::::::::.:::.:::::::::::::::::..::.::::::::::::::::::::::::::::::::.::::::::::::::::.:::::::::::::::. :::::::: ::::::::::::: : : :::::::::::...::::::::::::::::::::::::::::::::::::::::::::::....::::::::::::::::::::::::::::::::::::::::::::::::..
------------------AYDSNRASCIPSVWNNYNLTGEGILVGFLDTGIDYTHNAFKDAEGNTRIEYIYDLENGVVY-DK-NKINEAL-------KSEDPFSIVPEIDLSGHGTHVAGIACAGGNINFDNYGVAYKSSIAVKITGENSLRAALSTQLRGLKFLDKSNEINKPLVVNISLSTNDGSHNGSSLLEKYIQTFTQLQKAVIVVAAGNEGNSAHHVGGKKKEEDLDLNIGDGEKGIILDFFKPVLVDVSVEVISPTGISTGPIELSESYKERFVGREKIVVYSTGPKPFDIQGQTTISILPLGDTITSGGWRIIVRKLNNYEGYFDIWLPGLNERTRFLQPSVYNTLGIPATVEGVISVGSYNF-L----------------------------------------------------------------------------------------------------------------------------------N-NNLSAFSGRGVVRPEWLIKPDLVAPGENILSTVEEQGFDTKSGTSAAPQVSGICALLFEWGIIRNNDPFLYGERIKYYLIKGAKRTIFGEAYPNPDLGYGFVCLDRTELLINRR