Table 2. Results of four representative macromolecular structures successfully determined using the IPCAS pipeline with the identified heavy-atom sites solved by the modified phase-retrieval algorithm as input.
| PDB entry | Type | n sites† | Programs‡ | FOM | Rwork/Rfree | Completeness | Accuracy | R.m.s.d.§ (Å) | Run time | |
|---|---|---|---|---|---|---|---|---|---|---|
| Phase retrieval for each trial (s) | IPCAS for each cycle (min) | |||||||||
| 4qk0 | Protein | 56/63 Se | O + D + P/B | 0.387 | 0.213/0.251 | 2405/2484 (96.82%) | 2390/2484 (96.22%) | 0.26 | 28 | 117 |
| 3s2s | Protein | 4/4 Zn + 4/4 As | O + D + P/B | 0.351 | 0.216/0.236 | 721/726 (99.31%) | 716/726 (98.62%) | 0.23 | 71 | 48 |
| 3fys | Protein | 9/10 S | O + D + P/B | 0.376 | 0.202/0.256 | 275/282 (97.52%) | 276/282 (97.87%) | 0.23 | 9 | 35 |
| 5ndi | RNA | 4/4 Br | O + D + B/P | 0.401 | 0.279/0.311 | 63/76 (78.95%) | 71/76 (93.42) | 0.24 | 15 | 44 |
†
Number of sites found in the asymmetric unit (a.u.) compared with the published values.
‡
Programs used in the cycle of model extension iterations in IPCAS (alternate mode). Program codes: O = OASIS, D = DM, B = Buccaneer, P = Phenix.AutoBuild (quick mode).
§
Root mean square deviations of the Cα positions after structural alignment against the final PDB structures.