Jungfraujoch/tools/battery/timing.json

{
  "about": "Timing benchmarks (README: 'The timing benchmark'), chosen with battery.py timing --benchmark NAME: each set started from a model rugnux has to place by molecular replacement, timed per step and checked for a right answer. 'standard' needs only open data (the open arm's 9zlo, 9s02, 9gjx and 4nwv); 'inhouse' is the earlier set of two in-house standard proteins and 4nwv. 'start' is the model given to --model: an AlphaFold DB prediction committed in models/ (with its predicted aligned error beside it), or a deposited entry (committed in models/pdb/) moved by a fixed rigid-body transform (strict NCS expanded first, then x' = R (x - c) + c + t, R a rotation by 'deg' about the unit 'axis', c the centroid of the expanded asymmetric unit, t 'shift' in A). The reference model the placement is checked against is the one the battery itself uses for the set (its manifest row's 'model', else the PDB entry of the set id; committed in models/pdb/ for every set here but cytc_x10sa, whose reference_model.cif sits beside its data). 'expect': 'mr_sgno' the space group the placed model is in (the model decides the hand), 'rfree_max' the highest R_FREE accepted, 'cc_min' the lowest correlation of the placed model's intensities with the reference model's (shell-normalised, 10-4 A, best over the lattice's reindexing operators).",
  "benchmarks": {
   "standard": [
    {"set": "9zlo", "arm": "open", "start": {"alphafold": "models/AF-P17090-F1-model_v6.cif", "why": "AlphaFold DB AF-P17090-F1 v6: urease accessory protein UreE, Proteus mirabilis (UniProt P17090), the deposited entity of 9ZLO; two copies to place (P 21 21 21, 2.0 A, EIGER 16M)"}, "expect": {"mr_sgno": 19, "rfree_max": 0.5, "cc_min": 0.3}},
    {"set": "9s02", "arm": "open", "start": {"alphafold": "models/AF-P32322-F1-model_v6.cif", "why": "AlphaFold DB AF-P32322-F1 v6: pyrroline-5-carboxylate reductase 1, Homo sapiens (UniProt P32322; 9S02 deposits isoform 3); five copies to place (P 21 21 2, 1.65 A, EIGER2 16M)"}, "expect": {"mr_sgno": 18, "rfree_max": 0.5, "cc_min": 0.3}},
    {"set": "9gjx", "arm": "open", "start": {"alphafold": "models/AF-Q65MG6-F1-model_v6.cif", "why": "AlphaFold DB AF-Q65MG6-F1 v6: NADH-dependent nitro/flavin oxidoreductase, Bacillus licheniformis (UniProt Q65MG6), the deposited entity of 9GJX; six copies to place (P 1 21 1, 2.4 A, EIGER 16M)"}, "expect": {"mr_sgno": 4, "rfree_max": 0.5, "cc_min": 0.3}},
    {"set": "4nwv", "arm": "open", "start": {"moved": {"pdb": "4nwv", "axis": [0.36, 0.48, 0.8], "deg": 30.0, "shift": [12.0, -18.0, 25.0]}, "why": "the deposited model of 4NWV (I222, a virus capsid: 3 chains and 14 strict NCS operators, 45 chains once expanded), turned 30 deg and shifted 33 A: far outside what the rigid body corrects, so it is rejected and molecular replacement places the whole asymmetric unit"}, "expect": {"mr_sgno": 23, "rfree_max": 0.35, "cc_min": 0.3}}
   ],
   "inhouse": [
    {"set": "myob_x10sa", "arm": "inhouse", "start": {"alphafold": "models/AF-P68082-F1-model_v6.cif", "why": "AlphaFold DB AF-P68082-F1 v6: myoglobin, Equus caballus (UniProt P68082), the species of the battery's reference model 4DC8 (horse heart). No heme"}, "expect": {"mr_sgno": 4, "rfree_max": 0.5, "cc_min": 0.3}},
    {"set": "cytc_x10sa", "arm": "inhouse", "start": {"alphafold": "models/AF-P62894-F1-model_v6.cif", "why": "AlphaFold DB AF-P62894-F1 v6: cytochrome c, Bos taurus (UniProt P62894), the protein of the battery's reference model (bovine heart, placed with 6FF5). No heme; three copies to place, related by a pseudo-translation"}, "expect": {"mr_sgno": 154, "rfree_max": 0.5, "cc_min": 0.3}},
    {"set": "4nwv", "arm": "open", "start": {"moved": {"pdb": "4nwv", "axis": [0.36, 0.48, 0.8], "deg": 30.0, "shift": [12.0, -18.0, 25.0]}, "why": "the deposited model of 4NWV (I222, a virus capsid: 3 chains and 14 strict NCS operators, 45 chains once expanded), turned 30 deg and shifted 33 A: far outside what the rigid body corrects, so it is rejected and molecular replacement places the whole asymmetric unit"}, "expect": {"mr_sgno": 23, "rfree_max": 0.35, "cc_min": 0.3}}
   ]
  }
}