| pdb_id,chain,note,tier,kind,action | |
| 29QJ,D,"53 atom(s) modelled in more than one conformation; kept 31 from altloc A, 22 from altloc B",1,altloc_atoms,repaired | |
| 43SN,B,11 atom(s) modelled in more than one conformation; kept 11 from altloc B,1,altloc_atoms,repaired | |
| 43SN,D,11 atom(s) modelled in more than one conformation; kept 11 from altloc B,1,altloc_atoms,repaired | |
| 43SN,F,11 atom(s) modelled in more than one conformation; kept 11 from altloc B,1,altloc_atoms,repaired | |
| 43SN,H,11 atom(s) modelled in more than one conformation; kept 11 from altloc B,1,altloc_atoms,repaired | |
| 43SN,J,11 atom(s) modelled in more than one conformation; kept 11 from altloc B,1,altloc_atoms,repaired | |
| 8EBK,B,15 atom(s) modelled in more than one conformation; kept 15 from altloc A,1,altloc_atoms,repaired | |
| 8GAK,D,8 atom(s) modelled in more than one conformation; kept 8 from altloc B,1,altloc_atoms,repaired | |
| 8PKU,P,3 atom(s) modelled in more than one conformation; kept 3 from altloc A,1,altloc_atoms,repaired | |
| 8PKV,P,3 atom(s) modelled in more than one conformation; kept 3 from altloc A,1,altloc_atoms,repaired | |
| 8PKW,P,6 atom(s) modelled in more than one conformation; kept 6 from altloc A,1,altloc_atoms,repaired | |
| 8PKX,P,3 atom(s) modelled in more than one conformation; kept 3 from altloc A,1,altloc_atoms,repaired | |
| 8Q1N,b,6 atom(s) modelled in more than one conformation; kept 6 from altloc B,1,altloc_atoms,repaired | |
| 8ZXR,B,"12 atom(s) modelled in more than one conformation; kept 6 from altloc A, 6 from altloc B",1,altloc_atoms,repaired | |
| 9CS2,B,16 atom(s) modelled in more than one conformation; kept 16 from altloc A,1,altloc_atoms,repaired | |
| 9DXU,B,"17 atom(s) modelled in more than one conformation; kept 11 from altloc A, 6 from altloc B",1,altloc_atoms,repaired | |
| 9HGD,B,8 atom(s) modelled in more than one conformation; kept 8 from altloc A,1,altloc_atoms,repaired | |
| 9HGD,D,60 atom(s) modelled in more than one conformation; kept 60 from altloc A,1,altloc_atoms,repaired | |
| 9NZH,B,3 atom(s) modelled in more than one conformation; kept 3 from altloc B,1,altloc_atoms,repaired | |
| 9PHD,G,20 atom(s) modelled in more than one conformation; kept 20 from altloc A,1,altloc_atoms,repaired | |
| 9Q1L,C,17 atom(s) modelled in more than one conformation; kept 17 from altloc A,1,altloc_atoms,repaired | |
| 9R4D,A,9 atom(s) modelled in more than one conformation; kept 9 from altloc A,1,altloc_atoms,repaired | |
| 9RA5,D,8 atom(s) modelled in more than one conformation; kept 8 from altloc A,1,altloc_atoms,repaired | |
| 9SVZ,C,5 atom(s) modelled in more than one conformation; kept 5 from altloc A,1,altloc_atoms,repaired | |
| 8EBK,B,1 bond(s) have one _struct_conn record per alternate conformation; kept the record for the conformer the atoms came from,1,altloc_bond_records,repaired | |
| 8PKU,P,1 bond(s) have one _struct_conn record per alternate conformation; kept the record for the conformer the atoms came from,1,altloc_bond_records,repaired | |
| 8PKV,P,1 bond(s) have one _struct_conn record per alternate conformation; kept the record for the conformer the atoms came from,1,altloc_bond_records,repaired | |
| 8PKW,P,2 bond(s) have one _struct_conn record per alternate conformation; kept the record for the conformer the atoms came from,1,altloc_bond_records,repaired | |
| 8PKX,P,1 bond(s) have one _struct_conn record per alternate conformation; kept the record for the conformer the atoms came from,1,altloc_bond_records,repaired | |
| 9HGD,D,1 bond(s) have one _struct_conn record per alternate conformation; kept the record for the conformer the atoms came from,1,altloc_bond_records,repaired | |
| 9PHD,G,2 bond(s) have one _struct_conn record per alternate conformation; kept the record for the conformer the atoms came from,1,altloc_bond_records,repaired | |
| 8X8N,C,"2 atom(s) were displaced to make room for a linkage, which is what the CCD's leaving-atom convention describes: CYS2[F].SG.HG(hydrogen), CYS7[F].SG.HG(hydrogen)",1,leaving_atoms,repaired | |
| 9NN4,D,"1 atom(s) were displaced to make room for a linkage, which is what the CCD's leaving-atom convention describes: CYS92[C].SG.HG(hydrogen)",1,leaving_atoms,repaired | |
| 9UPK,C,"1 atom(s) were displaced to make room for a linkage, which is what the CCD's leaving-atom convention describes: MVA11[C].N.H(leaving-H)",1,leaving_atoms,repaired | |
| 9UPK,D,"1 atom(s) were displaced to make room for a linkage, which is what the CCD's leaving-atom convention describes: MVA11[D].N.H(leaving-H)",1,leaving_atoms,repaired | |
| 7QPB,H,"a disulf record crosses a symmetry operation (1_555/2_556); skipped, because this characterises the asymmetric unit",1,symmetry_generated_bond,dropped | |
| 7QPB,H,"a disulf record crosses a symmetry operation (1_555/2_556); skipped, because this characterises the asymmetric unit",1,symmetry_generated_bond,dropped | |
| 7QPB,I,"a disulf record crosses a symmetry operation (1_555/2_556); skipped, because this characterises the asymmetric unit",1,symmetry_generated_bond,dropped | |
| 7QPB,I,"a disulf record crosses a symmetry operation (1_555/2_556); skipped, because this characterises the asymmetric unit",1,symmetry_generated_bond,dropped | |
| 8Q1N,a,"a disulf record crosses a symmetry operation (1_555/6_545); skipped, because this characterises the asymmetric unit",1,symmetry_generated_bond,dropped | |
| 8Q1N,b,"a disulf record crosses a symmetry operation (1_555/6_545); skipped, because this characterises the asymmetric unit",1,symmetry_generated_bond,dropped | |
| 9JU1,C,"a disulf record crosses a symmetry operation (1_555/10_665); skipped, because this characterises the asymmetric unit",1,symmetry_generated_bond,dropped | |
| 9QBS,C,"a disulf record crosses a symmetry operation (1_555/7_455); skipped, because this characterises the asymmetric unit",1,symmetry_generated_bond,dropped | |
| 9QBS,D,"a disulf record crosses a symmetry operation (1_555/7_455); skipped, because this characterises the asymmetric unit",1,symmetry_generated_bond,dropped | |
| 9QBT,B,"a disulf record crosses a symmetry operation (1_555/12_555); skipped, because this characterises the asymmetric unit",1,symmetry_generated_bond,dropped | |
| 9QDU,B,"a disulf record crosses a symmetry operation (1_555/7_555); skipped, because this characterises the asymmetric unit",1,symmetry_generated_bond,dropped | |
| 22IZ,B,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 380, C 14] contacts)",2,crystal_packing,repaired | |
| 22IZ,D,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept C of [C 295, A 12] contacts)",2,crystal_packing,repaired | |
| 24HS,K,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept C of [C 527, B 89, D 0] contacts)",2,crystal_packing,repaired | |
| 24HS,L,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept D of [D 461, C 0] contacts)",2,crystal_packing,repaired | |
| 24HS,M,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept E of [E 471, G 79] contacts)",2,crystal_packing,repaired | |
| 24HS,P,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept H of [H 460, F 69] contacts)",2,crystal_packing,repaired | |
| 28KD,C,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B of [B 679, A 9] contacts)",2,crystal_packing,repaired | |
| 7XTG,A,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B of [B 99] contacts; kept Y of [Y 217] contacts; kept Z of [Z 333, I 34] contacts)",2,crystal_packing,repaired | |
| 7XTG,C,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept F of [F 87] contacts; kept D of [D 262] contacts; kept E of [E 318, Z 25] contacts)",2,crystal_packing,repaired | |
| 7XTG,G,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept J of [J 82] contacts; kept H of [H 260] contacts; kept I of [I 317, E 23] contacts)",2,crystal_packing,repaired | |
| 8BWF,a,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A,D of [A 131, D 73, N 1] contacts; more than one copy of a receptor entity is above the keep fraction, so this peptide sits at a real interface between copies rather than in one of them)",2,crystal_packing,repaired | |
| 8BWF,b,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B of [B 166, C 13] contacts)",2,crystal_packing,repaired | |
| 8BWF,c,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept C of [C 189, B 59, E 6] contacts)",2,crystal_packing,repaired | |
| 8BWF,d,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept D of [D 129, A 35, N 2] contacts)",2,crystal_packing,repaired | |
| 8BWF,f,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept F of [F 120, I 16] contacts)",2,crystal_packing,repaired | |
| 8BWF,g,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept G,H of [G 117, H 61, K 20] contacts; more than one copy of a receptor entity is above the keep fraction, so this peptide sits at a real interface between copies rather than in one of them)",2,crystal_packing,repaired | |
| 8BWF,h,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept H of [H 118, G 25] contacts)",2,crystal_packing,repaired | |
| 8BWF,j,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept J of [J 125, E 23] contacts)",2,crystal_packing,repaired | |
| 8BWF,l,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept L of [L 147, K 20] contacts)",2,crystal_packing,repaired | |
| 8BWF,m,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept M,N of [M 142, N 69, A 2] contacts; more than one copy of a receptor entity is above the keep fraction, so this peptide sits at a real interface between copies rather than in one of them)",2,crystal_packing,repaired | |
| 8BWF,n,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept N of [N 125, M 21] contacts)",2,crystal_packing,repaired | |
| 8BWF,o,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept O of [O 146, P 20] contacts)",2,crystal_packing,repaired | |
| 8BWF,p,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept O,P of [P 131, O 85, I 9] contacts; more than one copy of a receptor entity is above the keep fraction, so this peptide sits at a real interface between copies rather than in one of them)",2,crystal_packing,repaired | |
| 8C5G,C,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 274, B 0] contacts)",2,crystal_packing,repaired | |
| 8DNQ,C,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 475, B 1] contacts)",2,crystal_packing,repaired | |
| 8DNQ,D,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B of [B 487, A 1] contacts)",2,crystal_packing,repaired | |
| 8EHZ,C,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 351, B 0] contacts)",2,crystal_packing,repaired | |
| 8EI1,G,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept C of [C 234, B 0] contacts)",2,crystal_packing,repaired | |
| 8EI1,H,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept D of [D 240, A 0] contacts)",2,crystal_packing,repaired | |
| 8FIF,D,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 393, B 0] contacts)",2,crystal_packing,repaired | |
| 8FIF,G,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept C of [C 376, A 0] contacts)",2,crystal_packing,repaired | |
| 8G8N,P,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept L of [L 81, I 0] contacts; kept H of [H 251] contacts)",2,crystal_packing,repaired | |
| 8GAJ,B,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 418, C 0] contacts)",2,crystal_packing,repaired | |
| 8GAJ,D,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept C of [C 462, A 2] contacts)",2,crystal_packing,repaired | |
| 8GAK,B,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 448, C 4] contacts)",2,crystal_packing,repaired | |
| 8GAL,B,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 426, C 0] contacts)",2,crystal_packing,repaired | |
| 8ONI,A,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept C of [C 4, H 0] contacts; kept D of [D 3] contacts)",2,crystal_packing,repaired | |
| 8ONI,B,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept H of [H 307, C 0] contacts; kept L of [L 270] contacts)",2,crystal_packing,repaired | |
| 8ONI,F,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept C of [C 293, H 37] contacts; kept D of [D 276] contacts)",2,crystal_packing,repaired | |
| 8ONI,I,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept H of [H 5, C 0] contacts; kept L of [L 3] contacts)",2,crystal_packing,repaired | |
| 8Q1N,a,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 244, B 0] contacts)",2,crystal_packing,repaired | |
| 8RYK,C,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 560, B 162] contacts)",2,crystal_packing,repaired | |
| 8RYK,D,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B of [B 556, A 0] contacts)",2,crystal_packing,repaired | |
| 8SDP,I,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 414, C 40] contacts)",2,crystal_packing,repaired | |
| 8SDP,X,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B of [B 534, A 125] contacts)",2,crystal_packing,repaired | |
| 8SDP,Y,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept C of [C 350, B 23] contacts)",2,crystal_packing,repaired | |
| 8SE7,G,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept D of [D 438, F 27] contacts)",2,crystal_packing,repaired | |
| 8SE7,H,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept E of [E 468, D 27, A 2] contacts)",2,crystal_packing,repaired | |
| 8SE7,I,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 408, C 12] contacts)",2,crystal_packing,repaired | |
| 8SE7,J,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept F of [F 371, E 13, R 10] contacts)",2,crystal_packing,repaired | |
| 8SE7,N,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept K of [K 498, M 17] contacts)",2,crystal_packing,repaired | |
| 8SE7,O,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept L of [L 420, K 53] contacts)",2,crystal_packing,repaired | |
| 8SE7,U,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept R of [R 431, Q 31] contacts)",2,crystal_packing,repaired | |
| 8SE7,V,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept S of [S 448, R 15, E 8] contacts)",2,crystal_packing,repaired | |
| 8SE7,X,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B of [B 490, A 64, D 15] contacts)",2,crystal_packing,repaired | |
| 8SE7,Y,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept C of [C 464, B 33] contacts)",2,crystal_packing,repaired | |
| 8V30,G,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B,C of [C 170, B 91, A 12] contacts; more than one copy of a receptor entity is above the keep fraction, so this peptide sits at a real interface between copies rather than in one of them)",2,crystal_packing,repaired | |
| 8V30,H,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept C,D of [D 160, C 93, B 14] contacts; more than one copy of a receptor entity is above the keep fraction, so this peptide sits at a real interface between copies rather than in one of them)",2,crystal_packing,repaired | |
| 8V30,I,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept D,E of [E 159, D 100, C 14] contacts; more than one copy of a receptor entity is above the keep fraction, so this peptide sits at a real interface between copies rather than in one of them)",2,crystal_packing,repaired | |
| 8V30,J,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept E of [E 97, D 14] contacts)",2,crystal_packing,repaired | |
| 9B0A,C,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B of [B 308, A 46] contacts)",2,crystal_packing,repaired | |
| 9B0A,D,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 275, B 38] contacts)",2,crystal_packing,repaired | |
| 9BT3,a,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 579, G 85] contacts)",2,crystal_packing,repaired | |
| 9BT3,b,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B of [B 575, F 77] contacts)",2,crystal_packing,repaired | |
| 9BT3,c,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept C of [C 584, E 0] contacts)",2,crystal_packing,repaired | |
| 9BT3,d,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept D of [D 567, H 0] contacts)",2,crystal_packing,repaired | |
| 9BT3,e,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept E of [E 606, C 0] contacts)",2,crystal_packing,repaired | |
| 9BT3,f,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept F of [F 592, B 24] contacts)",2,crystal_packing,repaired | |
| 9BT3,g,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept G of [G 596, A 41] contacts)",2,crystal_packing,repaired | |
| 9BT3,h,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept H of [H 598, D 0] contacts)",2,crystal_packing,repaired | |
| 9CDZ,B,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 380, C 0] contacts)",2,crystal_packing,repaired | |
| 9CDZ,D,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept C of [C 354, A 55] contacts)",2,crystal_packing,repaired | |
| 9DEK,C,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 731, B 0] contacts)",2,crystal_packing,repaired | |
| 9DEN,C,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 623, B 0] contacts)",2,crystal_packing,repaired | |
| 9DEN,D,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B of [B 654, A 0] contacts)",2,crystal_packing,repaired | |
| 9EMZ,G,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept D of [D 346, C 11] contacts)",2,crystal_packing,repaired | |
| 9FBL,L,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 231, B 0] contacts)",2,crystal_packing,repaired | |
| 9FBL,P,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept C of [C 233, A 0] contacts)",2,crystal_packing,repaired | |
| 9GF9,G,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 473, B 0, C 0] contacts)",2,crystal_packing,repaired | |
| 9GF9,H,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B of [B 444, A 0, D 0] contacts)",2,crystal_packing,repaired | |
| 9GF9,I,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A,C of [C 475, A 176, B 0, E 0] contacts; more than one copy of a receptor entity is above the keep fraction, so this peptide sits at a real interface between copies rather than in one of them)",2,crystal_packing,repaired | |
| 9GF9,J,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B,D of [D 502, B 208, A 3, F 0] contacts; more than one copy of a receptor entity is above the keep fraction, so this peptide sits at a real interface between copies rather than in one of them)",2,crystal_packing,repaired | |
| 9GF9,K,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept E of [E 465, C 1, F 0] contacts)",2,crystal_packing,repaired | |
| 9GF9,L,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept F of [F 486, D 1, E 0] contacts)",2,crystal_packing,repaired | |
| 9GFK,F,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept D of [D 388, C 79, B 33] contacts)",2,crystal_packing,repaired | |
| 9GFK,G,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B of [B 408, A 73, D 50, C 0] contacts)",2,crystal_packing,repaired | |
| 9GFK,H,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 415, B 66, C 43] contacts)",2,crystal_packing,repaired | |
| 9GFK,J,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept C of [C 409, D 96, A 40, B 0] contacts)",2,crystal_packing,repaired | |
| 9GLU,C,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 522, B 40] contacts)",2,crystal_packing,repaired | |
| 9GVU,D,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B of [B 490, A 0] contacts)",2,crystal_packing,repaired | |
| 9GVU,F,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 582, B 28] contacts)",2,crystal_packing,repaired | |
| 9GXE,D,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 260, B 12] contacts)",2,crystal_packing,repaired | |
| 9GXE,E,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B of [B 250, C 10] contacts)",2,crystal_packing,repaired | |
| 9GXE,F,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept C of [C 257, A 14] contacts)",2,crystal_packing,repaired | |
| 9GXG,G,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 254, B 10] contacts)",2,crystal_packing,repaired | |
| 9GXG,H,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B of [B 245, C 9] contacts)",2,crystal_packing,repaired | |
| 9GXG,I,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept C of [C 254, A 11] contacts)",2,crystal_packing,repaired | |
| 9HYT,D,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 324, B 26] contacts)",2,crystal_packing,repaired | |
| 9HYT,F,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept C of [C 317, A 25, B 0] contacts)",2,crystal_packing,repaired | |
| 9IFM,L,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 109] contacts; kept B of [B 965, b 143] contacts; kept R of [R 26] contacts; kept D of [D 545] contacts)",2,crystal_packing,repaired | |
| 9IFM,l,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept a of [a 113] contacts; kept b of [b 617, B 86] contacts; kept r of [r 26] contacts; kept d of [d 546] contacts)",2,crystal_packing,repaired | |
| 9IFM,m,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept o of [o 9] contacts; kept a of [a 6] contacts; kept b of [b 162, B 15] contacts; kept d of [d 83] contacts)",2,crystal_packing,repaired | |
| 9L3Q,T,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B of [B 323, A 50] contacts)",2,crystal_packing,repaired | |
| 9L3Q,U,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 311, C 19] contacts)",2,crystal_packing,repaired | |
| 9L3Q,V,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept C of [C 349, B 21] contacts)",2,crystal_packing,repaired | |
| 9LGU,B,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 541, G 164, C 19, E 14] contacts)",2,crystal_packing,repaired | |
| 9LGU,D,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept C of [C 558, E 154, A 18, G 15] contacts)",2,crystal_packing,repaired | |
| 9LGU,F,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept E of [E 533, C 155, I 17, K 0] contacts)",2,crystal_packing,repaired | |
| 9LGU,H,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept G of [G 548, A 170, K 18, I 0] contacts)",2,crystal_packing,repaired | |
| 9LGU,L,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept I of [I 540, E 19, C 13, K 0] contacts)",2,crystal_packing,repaired | |
| 9LGU,M,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept K of [K 553, G 23, A 15, I 0] contacts)",2,crystal_packing,repaired | |
| 9MPD,D,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B of [B 364, A 0] contacts)",2,crystal_packing,repaired | |
| 9MPM,G,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B of [B 160, A 41] contacts)",2,crystal_packing,repaired | |
| 9MXK,B,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A,D of [A 418, D 186, I 0] contacts; more than one copy of a receptor entity is above the keep fraction, so this peptide sits at a real interface between copies rather than in one of them)",2,crystal_packing,repaired | |
| 9MXK,E,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept D,I of [D 417, I 205, A 0] contacts; more than one copy of a receptor entity is above the keep fraction, so this peptide sits at a real interface between copies rather than in one of them)",2,crystal_packing,repaired | |
| 9MXK,J,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A,I of [I 408, A 197, D 0] contacts; more than one copy of a receptor entity is above the keep fraction, so this peptide sits at a real interface between copies rather than in one of them)",2,crystal_packing,repaired | |
| 9N3G,C,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 479, B 0] contacts)",2,crystal_packing,repaired | |
| 9N3G,D,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B of [B 426, A 0] contacts)",2,crystal_packing,repaired | |
| 9NN3,C,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B of [B 240, A 0] contacts)",2,crystal_packing,repaired | |
| 9NN3,D,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 163, B 0] contacts)",2,crystal_packing,repaired | |
| 9NN4,D,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 256, B 0] contacts)",2,crystal_packing,repaired | |
| 9NN4,E,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B of [B 237, A 0] contacts)",2,crystal_packing,repaired | |
| 9NNT,D,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 305, C 11] contacts)",2,crystal_packing,repaired | |
| 9PIB,N,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 81, E 18] contacts; kept B of [B 293] contacts)",2,crystal_packing,repaired | |
| 9PIB,O,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept E of [E 76, A 20] contacts; kept F of [F 270] contacts)",2,crystal_packing,repaired | |
| 9PUZ,F,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B of [B 517, A 23] contacts)",2,crystal_packing,repaired | |
| 9PUZ,G,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept C of [C 468, B 84, A 47] contacts)",2,crystal_packing,repaired | |
| 9PVF,I,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 458, B 112, E 82] contacts)",2,crystal_packing,repaired | |
| 9PVF,K,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept C of [C 464, A 118] contacts)",2,crystal_packing,repaired | |
| 9PVF,M,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept E of [E 470, F 119, A 81] contacts)",2,crystal_packing,repaired | |
| 9Q1L,C,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B of [B 184, E 0] contacts; kept A of [A 228] contacts)",2,crystal_packing,repaired | |
| 9Q1L,F,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept E of [E 199, B 0] contacts; kept D of [D 222] contacts)",2,crystal_packing,repaired | |
| 9SVZ,C,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept B of [B 393, A 0] contacts)",2,crystal_packing,repaired | |
| 9X2X,B,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept A of [A 749, C 4] contacts)",2,crystal_packing,repaired | |
| 9X2X,D,"the annotation's partner list mixes this copy's receptor with chains of a neighbouring copy; resolved from interface size (kept C of [C 753, A 5] contacts)",2,crystal_packing,repaired | |
| 8WTW,B,"The C-terminal NH2 cap is modelled at position 15, no _struct_conn record involves it, and its nearest non-NH2 atom is 3.26 A away (HYP13.O) -- far too distant to infer a bond. So the cap's coordinates are in the file and its connection to the peptide is not, and the assembled molecule is two disconnected fragments. The unbonded fragment is dropped and the fact recorded, and only the encodings that require one connected molecule are skipped; the sequence encodings are unaffected, so the chain stays in the benchmark. Inventing the missing bond would put chemistry in the benchmark that the deposition does not support, and is the one thing not to do here. [decided: keep_arbitrary]",2,detached_fragment,dropped | |
| 7Y99,B,"_entity_poly gives the peptide's sequence as APIRYEWDEFC, 11 residues, so the A is SEQRES position 1, modelled as auth ALA2. Only its C and O are modelled -- at B-factors of 16.2 and 15.1 A^2 and occupancy 1.00, while every other residue of the chain is complete. A B-factor of 16 is well ordered; this is not disorder and ""partially modelled"" is the wrong description. What is there is an acyl group: the macrocycle closes through the linker IQ8, with IQ8.C20 to CYS12.SG at one end and IQ8.C19 to that carbonyl carbon at the other. The position has no amine and no C-alpha, and its carbon's four bonds are all accounted for (O at 1.237 A, PRO3.N at 1.345 A, IQ8.C19 at 1.643 A). The A is a label for a position in the construct whose amine and side chain were consumed by the cyclisation chemistry; it is not a statement that an alanine is present. Writing A into an 11-residue sequence makes the model build a complete alanine with an N, a C-alpha and a C-beta, and then asks that alanine's carbonyl carbon to hold the next residue's nitrogen and the linker -- five bonds. Protenix left that bond at 3.30 A against a deposited 1.643 A; it could not build what it was asked for. Expressing the position as the ligand entity it is describes the deposition instead of overstating it. [decided: exclude]",2,label_overstates_chemistry,excluded | |
| 7YA5,B,"JFF names 32 heavy atoms and 16 are modelled, and C1's CCD neighbours S1 and C2 are among the absent ones. As deposited, JFF101.C1 is already valence-satisfied: CYS1.N at 1.388 A, JFF.C9 at 1.502 A, CYS1.SG at 1.611 A, plus one hydrogen. The config names the complete component, so the model builds the other 16 atoms and the bond no longer fits. Protenix failed both of this chain's bonds (3.40 A and 2.20 A against 1.388 and 1.611). Unlike 9PMW-C there is no sibling copy to say what the intended full component was, so the resolution is to express the position as the truncated entity the deposition actually contains rather than to repair it towards a component nobody has evidence for. [decided: exclude]",2,label_overstates_chemistry,excluded | |
| 9PMW,C,"bond redeclared from ACE@1.C-CYS@18.SG to ACE@1.CH3-CYS@18.SG: the deposition records it from an atom that is already valence-satisfied, and sibling copies of the same peptide record it from the other one",2,label_overstates_chemistry,repaired | |
| 9PMW,C,"The one unambiguous repair anywhere in this work, and it is a one-atom correction. 9PMW and 9PN0 contain six copies of the same acetyl-capped thioether peptide. Five of them -- 9PMW-D, 9PMW-E, 9PN0-C, 9PN0-D, 9PN0-E -- record the thioether from ACE.CH3, the methyl carbon, which is where a thioether belongs: S-CH2-C(=O)-N. 9PMW-C does not model ACE.CH3 at all, so it has no methyl to name and records the bond from the carbonyl carbon ACE.C instead, which is a different linkage on paper: S-C(=O)-N. The consequence is not cosmetic. ACE.C in chain C is already valence-satisfied by the atoms that were modelled -- its own O at 1.406 A, TYR2.N at 1.482 A and CYS18.SG at 1.784 A, which is four bonds -- and the config names the complete ACE component, whose CCD entry gives that carbon a methyl as well. So the model is asked to build a carbon with five bonds. AF3 built it at 1.656 A regardless, which is why this needed a check on the input rather than on the prediction. Given five identical siblings the intended chemistry is not in doubt, and declaring ACE.CH3-CYS.SG lets the model build a complete ACE. This is the only place in the benchmark where a sibling copy settles the question outright. [decided: redeclare_bond]",2,label_overstates_chemistry,repaired | |
| 8WTW,B,"the assembled molecule is 2 disconnected fragments, so no single SMILES describes it; encodings that take one connected molecule have to be skipped for this chain",2,smiles_disconnected,dropped | |
| 9JPB,b,"the assembled molecule is 2 disconnected fragments, so no single SMILES describes it; encodings that take one connected molecule have to be skipped for this chain",2,smiles_disconnected,dropped | |
| 9JPB,d,"the assembled molecule is 2 disconnected fragments, so no single SMILES describes it; encodings that take one connected molecule have to be skipped for this chain",2,smiles_disconnected,dropped | |
| 9JPB,p,"the assembled molecule is 2 disconnected fragments, so no single SMILES describes it; encodings that take one connected molecule have to be skipped for this chain",2,smiles_disconnected,dropped | |
| 9I95,C,"a declared distance SG-C02 could not be applied: CYS16[C].SG cannot hold it (2.12 A); the evidence does not choose: the best two candidates differ by 0.004 A in deviation from the ideal C–S length, below the 0.05 A margin, so the surviving bond is arbitrary",3,bond_not_applied,dropped | |
| 9I97,C,a declared covale SG-C07 could not be applied: CYS0[C].SG cannot hold it (2.14 A); kept the better-evidenced bond on the same atom,3,bond_not_applied,dropped | |
| 9JPB,b,a declared covale O-C20 could not be applied: GLY27[FA].O cannot hold it (1.38 A); kept the better-evidenced bond on the same atom,3,bond_not_applied,dropped | |
| 9JPB,d,a declared covale NE1-OBB could not be applied: BCL101[XC].OBB cannot hold it (1.30 A); kept the better-evidenced bond on the same atom,3,bond_not_applied,dropped | |
| 9JPB,p,a declared covale O-CM7 could not be applied: GLY27[M].O cannot hold it (1.38 A); kept the better-evidenced bond on the same atom,3,bond_not_applied,dropped | |
| 9I95,C,"2 atom(s) were asked to hold more bonds than the element can, with nothing left to displace: CYS16[C].SG: 1 bond(s) too many -- nothing left to displace, A1I1E101[F].C02: 1 bond(s) too many -- nothing left to displace",3,overvalent_atom,repaired | |
| 9I97,C,"2 atom(s) were asked to hold more bonds than the element can, with nothing left to displace: CYS0[C].SG: 1 bond(s) too many -- nothing left to displace, A1I1D101[E].C07: 1 bond(s) too many -- nothing left to displace",3,overvalent_atom,repaired | |
| 9JPB,b,"1 atom(s) were asked to hold more bonds than the element can, with nothing left to displace: GLY27[FA].O: 1 bond(s) too many -- nothing left to displace",3,overvalent_atom,repaired | |
| 9JPB,d,"1 atom(s) were asked to hold more bonds than the element can, with nothing left to displace: BCL101[XC].OBB: 1 bond(s) too many -- nothing left to displace",3,overvalent_atom,repaired | |
| 9JPB,p,"1 atom(s) were asked to hold more bonds than the element can, with nothing left to displace: GLY27[M].O: 1 bond(s) too many -- nothing left to displace",3,overvalent_atom,repaired | |
| 9L6B,C,"Four cysteines in a CxC...CC redox-active motif of a ROS-sensing transcription factor, at 2.30 A by X-ray with B ~ 120 A^2 and no metals or ligands in the entry. Three of the sulfurs are mutually 2.01-2.05 A apart, i.e. inside a sphere of radius 1.18 A -- that is one region of density modelled three times, not three candidate disulfides that happen to overlap. The deposition records all three pairwise combinations as disulf, at full occupancy with no altlocs. Cys150 is 3.3-4.7 A from every other sulfur and cannot be in a disulfide as modelled, so the geometry supports at most one bond among {138, 140, 149} and none involving 150. All three candidate pairings sit inside the S-S band within 0.035 A, so no criterion available to us separates them, and for a redox-sensing motif the oxidation state is the biology rather than a detail. No paper is available for the entry, so there is no external statement of intent to fall back on. Keeping an arbitrary pick would assert a specific pairing the data cannot support, and the macrocycle's ring size depends on which one: 9 residues for 140-149, 11 for 138-149, a strained 2 for 138-140. Keeping none makes the chain acyclic, which puts it outside the benchmark's own definition anyway. [decided: exclude]",4,excluded_by_decision,excluded | |
| 9I95,C,"1 over-subscribed atom(s) whose candidate bonds the evidence does not separate, so the surviving bond is an arbitrary pick: CYS16[C].SG: SG-C03 dev 0.310 A, SG-C02 dev 0.314 A (margin 0.004 A < 0.05 A)",4,unresolvable_bond_choice,dropped | |
| 9I95,C,"Promoted from tier 3. Cys16's sulfur (B = 147.8 A^2) sits 1.500 A from A1I1E.C03 and 2.124 A from A1I1E.C02, and those two carbons are 1.529 A apart -- a normal C-C bond -- so bonding the sulfur to both would close an impossible three-membered ring. Neither bond is declared: _struct_conn has three records and neither of these is among them, so both were inferred from distance. The evidence cannot choose. Against the 1.81 A reference C-S length the two candidates are 0.310 A and 0.314 A away, a margin of 0.004 A, and **neither is inside the C-S band at all**: 1.500 A is as wrong for C-S as 2.124 A is. The sulfur is modelled between the two carbons rather than bonded to either cleanly. SG-C03 is kept because it is the bond a thiol can actually make and it preserves the macrocycle, but the pick is arbitrary and is recorded as such rather than presented as the geometry's answer. The chain stays in the benchmark; what is asserted about it is one bond whose identity is uncertain, not its existence. [decided: keep_arbitrary]",4,unresolvable_bond_choice,dropped | |