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Update the repository for consistency with the other benchmark #1

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Update the repository for consistency with the other benchmark #1

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978c8ac
DNA updated bound structures
rversin Apr 7, 2026
1f95d01
DNA updated reference structures
rversin Apr 7, 2026
8357f24
DNA updated unbound structures
rversin Apr 7, 2026
aad95b1
correct AIR
rversin Apr 7, 2026
88b4203
reference file name changed
rversin Apr 7, 2026
ec5f3d4
AIR files renamed
rversin Apr 7, 2026
a243a9e
rename unbound pdb
rversin Apr 7, 2026
223d1dd
record for unbound structures
rversin Apr 7, 2026
f8e8e26
rename bound pdb
rversin Apr 7, 2026
3be66ff
rename DNA pdb
rversin Apr 7, 2026
9e59c5f
Updated READMED
rversin Apr 7, 2026
03a71e3
version history added
rversin Apr 7, 2026
a3e611e
typo
rversin Apr 8, 2026
a4b76bc
Update tbl_unbound_pdbs.txt
rversin Apr 8, 2026
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860 changes: 860 additions & 0 deletions 1A74/1A74_b_ambig.tbl
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855 changes: 0 additions & 855 deletions 1A74/1A74_bound-DNA.pdb
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855 changes: 855 additions & 0 deletions 1A74/1A74_d_b.pdb
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903 changes: 903 additions & 0 deletions 1A74/1A74_d_u.pdb
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0 1A74/1A74_bound-protA.pdb → 1A74/1A74_p1_b.pdb
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0 1A74/1EVX_unbound-protA.pdb → 1A74/1A74_p1_u.pdb
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1,708 changes: 854 additions & 854 deletions 1A74/1A74_complex.pdb → 1A74/1A74_target.pdb
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860 changes: 860 additions & 0 deletions 1A74/1A74_u_ambig.tbl
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903 changes: 0 additions & 903 deletions 1A74/DNA_unbound.pdb
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299 changes: 299 additions & 0 deletions 1AZP/1AZP_b_ambig.tbl
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Original file line number Diff line number Diff line change
@@ -0,0 +1,299 @@
!
! HADDOCK unambiquous restraints for molecule A
!
!
assign ( resid 7 and segid A)
(
( resid 14 and segid B)
or
( resid 15 and segid B)
) 2.0 2.0 0.0
!
assign ( resid 8 and segid A)
(
( resid 14 and segid B)
or
( resid 13 and segid B)
or
( resid 12 and segid B and (name H61 or name H62 or name N1 or name N3 or name N7 or name C2 or name C4 or name C5 or name C6 or name C8))
) 2.0 2.0 0.0
!
assign ( resid 9 and segid A)
(
( resid 13 and segid B)
or
( resid 14 and segid B)
or
( resid 12 and segid B and (name C1' or name O4' or name C4' or name C3' or name C2' or name O3' or name C5' or name O5' or name P or name O1P or name O2P or name H5' or name H5'' or name H4' or name H3' or name H2' or name H2'' or name H1'))
) 2.0 2.0 0.0
!
assign ( resid 10 and segid A)
(
( resid 14 and segid B)
) 2.0 2.0 0.0
!
assign ( resid 39 and segid A)
(
( resid 7 and segid B)
) 2.0 2.0 0.0
!
assign ( resid 44 and segid A)
(
( resid 14 and segid B)
or
( resid 15 and segid B)
) 2.0 2.0 0.0
!
assign ( resid 46 and segid A)
(
( resid 15 and segid B and (name C1' or name O4' or name C4' or name C3' or name C2' or name O3' or name C5' or name O5' or name P or name O1P or name O2P or name H5' or name H5'' or name H4' or name H3' or name H2' or name H2'' or name H1'))
or
( resid 16 and segid B)
) 2.0 2.0 0.0
!
assign ( resid 47 and segid A)
(
( resid 15 and segid B and (name C1' or name O4' or name C4' or name C3' or name C2' or name O3' or name C5' or name O5' or name P or name O1P or name O2P or name H5' or name H5'' or name H4' or name H3' or name H2' or name H2'' or name H1'))
) 2.0 2.0 0.0
!
assign ( resid 48 and segid A)
(
( resid 16 and segid B)
) 2.0 2.0 0.0
!
assign ( resid 40 and segid A)
(
( resid 6 and segid B)
or
( resid 7 and segid B)
or
( resid 5 and segid B and (name C1' or name O4' or name C4' or name C3' or name C2' or name O3' or name C5' or name O5' or name P or name O1P or name O2P or name H5' or name H5'' or name H4' or name H3' or name H2' or name H2'' or name H1'))
) 2.0 2.0 0.0
!
assign ( resid 42 and segid A)
(
( resid 5 and segid B)
or
( resid 6 and segid B)
or
( resid 11 and segid B and (name H1 or name H21 or name H22 or name N3 or name N7 or name O6 or name C2 or name C4 or name C5 or name C6 or name C8))
or
( resid 12 and segid B and (name H61 or name H62 or name N1 or name N3 or name N7 or name C2 or name C4 or name C5 or name C6 or name C8))
or
( resid 13 and segid B and (name H3 or name O2 or name O4 or name C2 or name C4 or name C5 or name C6 or name C7))
or
( resid 7 and segid B)
) 2.0 2.0 0.0
!
assign ( resid 21 and segid A)
(
( resid 6 and segid B and (name C1' or name O4' or name C4' or name C3' or name C2' or name O3' or name C5' or name O5' or name P or name O1P or name O2P or name H5' or name H5'' or name H4' or name H3' or name H2' or name H2'' or name H1'))
) 2.0 2.0 0.0
!
assign ( resid 22 and segid A)
(
( resid 5 and segid B)
or
( resid 4 and segid B and (name C1' or name O4' or name C4' or name C3' or name C2' or name O3' or name C5' or name O5' or name P or name O1P or name O2P or name H5' or name H5'' or name H4' or name H3' or name H2' or name H2'' or name H1'))
) 2.0 2.0 0.0
!
assign ( resid 24 and segid A)
(
( resid 3 and segid B)
or
( resid 4 and segid B)
or
( resid 5 and segid B and (name C1' or name O4' or name C4' or name C3' or name C2' or name O3' or name C5' or name O5' or name P or name O1P or name O2P or name H5' or name H5'' or name H4' or name H3' or name H2' or name H2'' or name H1'))
) 2.0 2.0 0.0
!
assign ( resid 25 and segid A)
(
( resid 3 and segid B and (name C1' or name O4' or name C4' or name C3' or name C2' or name O3' or name C5' or name O5' or name P or name O1P or name O2P or name H5' or name H5'' or name H4' or name H3' or name H2' or name H2'' or name H1'))
) 2.0 2.0 0.0
!
assign ( resid 26 and segid A)
(
( resid 2 and segid B)
or
( resid 3 and segid B)
or
( resid 15 and segid B and (name H1 or name H21 or name H22 or name N3 or name N7 or name O6 or name C2 or name C4 or name C5 or name C6 or name C8))
) 2.0 2.0 0.0
!
assign ( resid 27 and segid A)
(
( resid 2 and segid B and (name H41 or name H42 or name N3 or name O2 or name C2 or name C4 or name C5 or name C6))
or
( resid 15 and segid B and (name H1 or name H21 or name H22 or name N3 or name N7 or name O6 or name C2 or name C4 or name C5 or name C6 or name C8))
) 2.0 2.0 0.0
!
assign ( resid 28 and segid A)
(
( resid 15 and segid B and (name H1 or name H21 or name H22 or name N3 or name N7 or name O6 or name C2 or name C4 or name C5 or name C6 or name C8))
or
( resid 16 and segid B)
) 2.0 2.0 0.0
!
assign ( resid 29 and segid A)
(
( resid 15 and segid B)
or
( resid 14 and segid B)
or
( resid 3 and segid B and (name H1 or name H21 or name H22 or name N3 or name N7 or name O6 or name C2 or name C4 or name C5 or name C6 or name C8))
) 2.0 2.0 0.0
!
!
! HADDOCK unambiquous restraints for molecule B
!
!
assign ( resid 2 and segid B)
(
( resid 26 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 2 and segid B and (name H41 or name H42 or name N3 or name O2 or name C2 or name C4 or name C5 or name C6))
(
( resid 27 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 3 and segid B)
(
( resid 24 and segid A)
or
( resid 26 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 3 and segid B and (name H1 or name H21 or name H22 or name N3 or name N7 or name O6 or name C2 or name C4 or name C5 or name C6 or name C8))
(
( resid 29 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 3 and segid B and (name C1' or name O4' or name C4' or name C3' or name C2' or name O3' or name C5' or name O5' or name P or name O1P or name O2P or name H5' or name H5'' or name H4' or name H3' or name H2' or name H2'' or name H1'))
(
( resid 25 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 4 and segid B)
(
( resid 24 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 4 and segid B and (name C1' or name O4' or name C4' or name C3' or name C2' or name O3' or name C5' or name O5' or name P or name O1P or name O2P or name H5' or name H5'' or name H4' or name H3' or name H2' or name H2'' or name H1'))
(
( resid 22 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 5 and segid B)
(
( resid 22 and segid A)
or
( resid 42 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 5 and segid B and (name C1' or name O4' or name C4' or name C3' or name C2' or name O3' or name C5' or name O5' or name P or name O1P or name O2P or name H5' or name H5'' or name H4' or name H3' or name H2' or name H2'' or name H1'))
(
( resid 24 and segid A)
or
( resid 40 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 6 and segid B)
(
( resid 40 and segid A)
or
( resid 42 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 6 and segid B and (name C1' or name O4' or name C4' or name C3' or name C2' or name O3' or name C5' or name O5' or name P or name O1P or name O2P or name H5' or name H5'' or name H4' or name H3' or name H2' or name H2'' or name H1'))
(
( resid 21 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 7 and segid B)
(
( resid 39 and segid A)
or
( resid 40 and segid A)
or
( resid 42 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 11 and segid B and (name H1 or name H21 or name H22 or name N3 or name N7 or name O6 or name C2 or name C4 or name C5 or name C6 or name C8))
(
( resid 42 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 12 and segid B and (name H61 or name H62 or name N1 or name N3 or name N7 or name C2 or name C4 or name C5 or name C6 or name C8))
(
( resid 8 and segid A)
or
( resid 42 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 12 and segid B and (name C1' or name O4' or name C4' or name C3' or name C2' or name O3' or name C5' or name O5' or name P or name O1P or name O2P or name H5' or name H5'' or name H4' or name H3' or name H2' or name H2'' or name H1'))
(
( resid 9 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 13 and segid B)
(
( resid 8 and segid A)
or
( resid 9 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 13 and segid B and (name H3 or name O2 or name O4 or name C2 or name C4 or name C5 or name C6 or name C7))
(
( resid 42 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 14 and segid B)
(
( resid 7 and segid A)
or
( resid 8 and segid A)
or
( resid 9 and segid A)
or
( resid 10 and segid A)
or
( resid 29 and segid A)
or
( resid 44 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 15 and segid B)
(
( resid 7 and segid A)
or
( resid 29 and segid A)
or
( resid 44 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 15 and segid B and (name H1 or name H21 or name H22 or name N3 or name N7 or name O6 or name C2 or name C4 or name C5 or name C6 or name C8))
(
( resid 26 and segid A)
or
( resid 27 and segid A)
or
( resid 28 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 15 and segid B and (name C1' or name O4' or name C4' or name C3' or name C2' or name O3' or name C5' or name O5' or name P or name O1P or name O2P or name H5' or name H5'' or name H4' or name H3' or name H2' or name H2'' or name H1'))
(
( resid 46 and segid A)
or
( resid 47 and segid A)
) 2.0 2.0 0.0
!
assign ( resid 16 and segid B)
(
( resid 28 and segid A)
or
( resid 46 and segid A)
or
( resid 48 and segid A)
) 2.0 2.0 0.0
!
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