Blame for processed_data/edge_cases.csv

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