| Stages | Sub-stages | Parameters | Comments |
|---|---|---|---|
| Solve structure for dense fragment |
Semi definite programming |
$\gamma = 1$ | $\gamma >0$ is a well known low rank approximator |
| $w_{ij} = 2$ | Weights with upper bounds | ||
| $w_{ij}^\prime = 2$ | Weights with lower bouonds | ||
| Default parameters used by SDPT3 solver | |||
| Refinement | Refinement after solving structure for fragments |
$w_\mathcal{E} = 2$ | Weight with equality bounds |
| $w_\mathcal{U} = 1$ | Weight with upper bounds | ||
| $w_\mathcal{L} = 1$ | Weight with lower bounds | ||
| $w$ | Weight with regularizer |
||
| Refinement after registration of structure for fragments | Same as "Refinement after solving structure for fragment" | ||
| Gap-filling | Modeller for gap filling | Default parameters used by loop modelling for modeller | |
| Anchored localization | $w_{\mathcal{E}} = 2$ | Weight with equality bounds | |
| $w_{\mathcal{U}} = 1$ | Weight with upper bounds | ||
| $w_{\mathcal{L}} = 1$ | Weight with lower bounds | ||
| $w$ | Weight with regularizer | ||
| Bad Gap correction |
Good/Bad Gap | If a gap has at least $1$ outlier it is declared as "bad" gap | |
| Steps for gap correction (for bad gaps) | As explained in literature | ||
| Post-process | Gromacs MD | MD files attached | Same as that followed by other optimization based papers (SPROS, PRASD, and Riemann). We additionally add experimental distance restraints files during energy minimization. |
| Parameter | Short Description |
|---|---|
| aug_bounds | Augment upper bounds with triangle in equality if sum is less than aug_bounds |
| $\eta_{lo}$ | Lower bound of density of fragments in divide stage |
| $\eta_{hi}$ | Higher bounds of desity of fragments in divide stage |
| include_neighbour | Expand residue groups to include any other residue if it shares at least include_neighbour number of upper bounds with the group in total |
| multi_expand_k2 | Expand atom groups to include any other atom if it shares greater than multi_expand_k2 number of upper bounds with the group in total |
| multi_expand_size_cutoff | Termination condition-1 (over group size) for atom group expansion |
| multi_expand_grp_min | Termination condition-2 (over group size increments) for atom group expansion |
| grp_expand | Expand atom groups to include atoms having marginal upper bounds with the group |