* Cyclic polymers (1sfi, 6dny, 1HVZ)
* B-DNA (1bna)
* Missing carbonyl oxygen (1gfl)
* Mono-saccharides with alt locs (1B5F)
* Microheterogeneity
    * Protein (1EJG, 3NIR)
    * DNA (3VOK)
* PNA: peptide nucleic acid (5eme, 1xj9)
* Peptide derived residues
    * GFP chromophores (5Z6Y)
* Nucleotides that don’t have a parent base set, i.e. detect purine/pyrimidine from geometry (THX in 1AUL, OMC in e.g. 5D3G)
* Bases with modified ring atoms
    * DZ has C1 instead of N1 (e.g. 6I4N)
    * DP has N5 instead of C5 and C7 instead of N7 (e.g. 6I4N)
* Beta & Gamma peptides (e.g. 1GAC, 6PQF)
* Mixed (heterogeneous) all-atom/trace-only RNA model (1JGQ)
* Polymers with residues with missing trace atoms (e.g. 2QFJ)
* Modified RNA bases (1y26, 5L4O)
* Discontinuous chains, i.e. gaps in the sequence (3sn6)
* Lots of sheets (1cbs)
* DNA (2np2, 1d66)
* C-alpha only (2rcj)
* Not cyclic, but termini are backbone-only and within distance but seqIds are not compatible (6SW3)
* Close backbone atoms but not linked (e.g. 4HIV)
* Non-standard residues
    * Protein (1BRR, 5Z6Y)
    * DNA (5D3G)
* Multiple models with different sets of ligands or missing ligands (1J6T, 1VRC, 2ICY, 1O2F)
* Long linear sugar chain (4HG6)
* Anisotropic B-factors/Ellipsoids (1EJG)
* NOS bridges (LYS-CSO in 7B0L, 6ZWJ, 6ZWH)

Assembly symmetries
* 5M30 (Assembly 1, C3 local and pseudo)
* 1RB8 (Assembly 1, I global)