Refinement with REFMAC Garib N Murshudov York Structural Laboratory Chemistry Department University of York 1

Refinement with REFMAC

Garib N Murshudov

York Structural Laboratory

Chemistry Department

University of York

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Contents

1) Refinement program – Refmac

2) Simple refinement: Selection of weights

3) Automatic twin refinement – Rfactor warnings

4) Low resolution refinement tools

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What can REFMAC do?• Simple maximum likelihood restrained refinement

• Twin refinement

• Phased refinement (with Hendrickson-Lattmann coefficients)

• SAD/SIRAS refinement

• Structure idealisation

• Library for more than 10000 ligands (from the next version)

• Covalent links between ligands and ligand-protein

• Rigid body refinement

• Low res: NCS local, restraints to external structures, jelly body

• TLS refinement

• Map sharpening

• Occupancy refinement

• etc 5

Simple refinement

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Simple refinement

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“Optimisation” of weights

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“Optimisation” of weightsAfter refinement final statistics are:

Initial Final

R factor 0.2783 0.1831

R free 0.2668 0.2030

Rms BondLength 0.0284 0.0327

Rms BondAngle 4.5704 2.3083

Rms ChirVolume 0.1696 0.1645

RMSD of bond lengths is too large.

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• If rmsd of bond lengths is too large (>0.022) or too tight (<0.01) then you may want to change weights. It can be done using weight matrix on the interface.

• Look at the log file. Refmac prints out current weights it is using.

Weight matrix 4.4438701

Actual weight 10.000000 is applied to the X-ray term

If rmsd is large then you can use half of currently used weight matrix (around 2.2).

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Change weight matrix


With new weights RMSD is reasonable.

Initial Final

R factor 0.2783 0.1876

R free 0.2668 0.2052




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Twin refinement

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merohedral and pseudo-merohedral twinning

Crystal symmetry: P3 P2 P2Constrain: - β = 90º -Lattice symmetry *: P622 P222 P2(rotations only)Possible twinning: merohedral pseudo-merohedral -

Domain 1

Domain 2

Twinning operator

-

Crystal lattice is invariant with respect to twinning operator.

The crystal is NOT invariant with respect to twinning operator.14

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Twin refinement (it works with older version also

Twin refinementTwin refinement in REFMAC is carried out in several stages

1) Stage 1: Identify potential twin operators. It is done by analysis of lattice and crystal symmetry.

In this case space group is P31 and there are four potential twin operators

Potential twin domain 1 with operator: H, K, L, metric score 0.000

Potential twin domain 2 with operator: -K, -H, -L, metric score 0.000

Potential twin domain 3 with operator: -H, -K, L, metric score 0.000

Potential twin domain 4 with operator: K, H, -L, metric score 0.000

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Twin refinement: Group/subgroup

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Twin refinement2) Stage 2: Filter using agreement between “twin” related

reflections (using Rmerge)

Filtering out small twin domains, step 1

Twin ops with Rm > 0.44 will be removed

SymOp= -K,-H,-L:R_m=0.248:twin is probable

SymOp= -H,-K, L:R_m=0.237:twin is probable

SymOp= K, H,-L:R_m=0.027:twin or higher symm

At this stage REFMAC may suggest that space group could be higher

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Twin refinement: Effect of twin on Rmerge

R merges without experimental error

No twinning 50%

Along non twinned axes with another axis than twin 37.5%

Twin

Non twin

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Twin refinement3) Stage 3: Estimate twin fractions and remove small twin domains

Filtering out small twin domains, step 2

Twin domains with fraction < 7.00000003E-02 are removed

Twin operators with estimated twin fractions

Twin op: H, K, L: Fr = 0.391; Eq ops: K, -H-K, L; -H-K, H, L

Twin op: -K, -H, -L:Fr = 0.112; Eq ops: -H, H+K, -L; H+K, -K, -L

Twin op: -H, -K, L:Fr = 0.108; Eq ops: -K, H+K, L; H+K, -H, L

Twin op: K, H, -L:Fr = 0.390; Eq ops: H, -H-K, -L; -H-K, K, -L

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Twin refinement3) Stage 4: Perform twin refinement with all survived twin

operators (in this example all four operators survive):

Twin fractions = 0.3773 0.1246 0.1206 0.3775

Rfactors look very good:

Initial Final

R factor 0.1912 0.1566

R free 0.1796 0.2047




Rfactors from non-twinned refinement

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Initial Final R factor 0.3103 0.2779 R free 0.3184 0.3496 Rms BondLength 0.0088 0.0129 Rms BondAngle 1.4825 1.5648 Rms ChirVolume 0.1077 0.1034

Twin refinement: Rfactors – be careful

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Cyan – perfect twin and twin modelledBlack – no twin and not modelledRed – perfect twin and not modelledBlue – no twin and perfect twin modelled

Rfactor drop can be as large as 15% without atomic model improvement

Twin refinement: Alternative indexing

If crystal can be twinned then there may be more than one indexing of hkl. Different indexing are related with the symmetry operator of lattice but not the crystal.

Best way of dealing with indexing “problem” is to use the program pointless by Phil Evans. You can either give a reference mtz file or a reference structure. Then all subsequent data will be indexed in consistent manner.

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Low resolution refinement

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Low resolution refinement tools

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1. Jelly body (implicit normal modes) refinement2. NCS: local and global restraints3. NCS constraints4. Restraints to reference structures5. Regularised map sharpening6. Long range B value restraints based on Kullback-Liebler distances

Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA “REFMAC5 for the Refinement of Macromolecular Crystal Structures” Acta Cryst: , D67, 355-367

Restraints to external structures are generated by the program ProSmart:1) Aligns structure in the presence of conformational changes. Sequence is not used2) Gernates restraints for aligned atoms3) Identifies secondary structures (at the moment helix and strand, but the approach is general and can be extended to any motif).4) Generates restraints for secondary structures

Note 1: ProSmart has been written by Rob Nocholls and available from him (now). It will be distributed by ccp4 (hopefully from the next release)

Note 2: Robust estimator functions are used for restraints. I.e. if differences between target and model is very large then their contributions are downweighted

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External (reference structure restraints)

Restraints to current distances

The term is added to the target function:

Summation is over all pairs in the same chain and within given distance (default 4.2A). dcurrent is recalculated at every cycle. This function does not contribute to gradients. It only contributes to the second derivative matrix.

It is equivalent to adding springs between atom pairs. During refinement inter-atomic distances are not changed very much. If all pairs would be used and weights would be very large then it would be equivalent to rigid body refinement.

It could be called “implicit normal modes”, “soft” body or “jelly” body refinement.

€

w(| d | − | dcurrent |)2

pairs

∑

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The program will be available from ccp4. Currently if you want to try it you should ask Rob Nicholls at [email protected]

Once you have downloaded you can run using this command

prosmart –p1 refined_structure.pdb –p2 reference_structure.pdb

It will generate many useful info including restraints to the reference structure.

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External (reference structure restraints)

Auto NCS: local and global1. Align all chains with all chains using Needleman-Wunsh method2. If alignment score is higher than predefined (e.g.80%) value then consider them as similar3.Find local RMS and if average local RMS is less than predefined value then consider them aligned4. Find correspondence between atoms5. If global restraints (i.e. restraints based on RMS between atoms of aligned chains) then identify domains6.For local NCS make the list of corresponding interatomic distances (remove bond and angle related atom pairs)7.Design weights

The list of interatomic distance pairs is calculated at every cycle

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Add external keywords file in refmac interface

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Browse files


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Select keywords file


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Keywords file

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# Jelly bodyRidge dist sigma 0.01ridge dist dmax 4.2

# ncs ncsr local

# to control restraints to reference structures. # Restraints are generated by prosmart external dmax 4.2external weight scale 4external cut 10

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Instructions you may want to play with

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Low resolution refinement: Some results

Initial Simple Jelly NCS local Jelly/NCS Reference structure

R 0.3605 0.2218 0.2533 0.2232 0.2535 0.2557

Rfree 0.3563 0.3116 2961 0.3124 0.2955 0.2907

If you want to use current version then you may need to run several time to get parameters right. In this case maximum radius for reference structure restraint was 4.0, maximum radius for NCS local was 4.2, if deviation between reference distance and current distance was more than 10 sigma then it was excluded, sigmas for reference structures were 0.07.

At lower resolution (5-7Å) radius may need to be 5.5 and sigma 0.02

Conclusions

• Auto weight works fine for large class of cases, however you may need to change weights

• Twin is automatic but Rfactors are poor indicators

• Use of available information may improve low resolution refinement

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AcknowledgmentYork Leiden

Alexei Vagin Pavol Skubak

Andrey Lebedev Raj Pannu

Rob Nocholls

Fei Long

CCP4, YSBL people

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REFMAC is available from CCP4 or from York’s ftp site:

www.ysbl.york.ac.uk/refmac/latest_refmac.html

Balbes and other programs:

www.ysbl.york.ac.uk/refmac/YSBLPrograms/index.jsp

This and other presentations can be found on:

www.ysbl.york.ac.uk/refmac/Presentations/

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Documents

Refinement with REFMAC Garib N Murshudov York Structural Laboratory Chemistry Department University of York 1