Servalcat 0.4.142: Crystallographic Refinement Workbench

Input files

Coordinates	rnase-bandicoot.cif 1SAR_BC · 1,474 atoms · 29 residue types (P2₁2₁2₁)
Reflections	rnasa-1.8-all_refmac1.mtz P 21 21 21 · 17,554 reflns · 16.32–1.85 Å · 13 columns
Ligand CIFs	Bundled CCP4 Monomer Library subset + on-demand fetch 0 custom ligand files staged (56 standard monomers bundled)

Amplitude (F)

Sigma (Q)

Free-R Flag (I)

Scattering form factor

Resolution limits (d_min – d_max Å)

Inspect all 13 MTZ header columns & datasets

Label	Type	Dataset	Min	Max	Assign

Refinement settings

General

Refinement cycles

Data-geometry weight Automatic weight adjustment

Starting weight:

Target bond RMSZ range

VDW repulsion weight

Hydrogen atoms

Output coordinates Write hydrogen atoms to output

B-factors and coordinates

Atomic B-factor model

B-factor restraint mode

B-factor restraint weight

Max ADP restraint distance (Å)

Reset initial B-factors (Å²)

Atomic positions Refine XYZ coordinates

Solvent and restraints

Bulk solvent mask Include flat bulk-solvent contribution

Covalent & metal links Detect disulfide, metal & glycosidic links

Local NCS restraints Automatic local NCS restraints

Jelly-body restraints Enable jelly-body restraints

Jelly-body σ (Å) & d_max (Å)

d_max

Positional restraints Unrestrained refinement

Geometry weights

Passed via Servalcat’s REFMAC keyword parser into Geom.calc_kwds. Leave blank for upstream default (1.0); set 0 to disable a term.

Bond distances (dist)

Bond angles (angle)

Torsion angles (torsion)

Planarity (plane)

Chirality (chiral)

Runtime details

Pinned runtime packages

36.0 MiB pinned

Every wheel and WebAssembly binary is verified against its SHA-256 Subresource Integrity pin in servalcat/manifest.json before execution. Unpinned network requests are rejected by the worker.

Artifact	Version	Size	SHA-256 Prefix
servalcat (wasm32 wheel)	0.4.142	526 KiB	fc8b2be8…
gemmi (wasm32 wheel)	0.7.5	1.34 MiB	a931d03c…
pyodide.asm.wasm	314.0.7	9.15 MiB	cc36e3ca…
scipy / numpy / pandas	1.18 / 2.4 / 3.0	20.19 MiB	c551e9af…

Refinement results

Sample results from RNase Sa. Run refinement to see your results.

Sample · 5 cycles

Statistic / Parameter	Initial (Cycle 0)	Final (Cycle 5)	Shift (Δ)

Convergence

R_work (left axis) R_free (left axis) Bond r.m.s.Z (right axis)

Cycle 5 (Final) Rwork: 0.2492 · Rfree: 0.2901 · FOM: 0.7775 · Bond rmsd: 0.0095 Å (rmsZ 0.785)

Outputs will be available after refinement.

Results by cycle

Hover to inspect

Cycle	R_work	R_free	R_free − R_work	FOM	−LL	Weight	Bond r.m.s.d. (Å)	Bond r.m.s.Z	Angle r.m.s.d. (°)

Run log

Ready

The first run downloads approximately 36 MiB.

Ready to run.