PMID- 21460454
OWN - NLM
STAT- MEDLINE
DA  - 20110404
DCOM- 20110627
LR  - 20131018
IS  - 1399-0047 (Electronic)
IS  - 0907-4449 (Linking)
VI  - 67
IP  - Pt 4
DP  - 2011 Apr
TI  - REFMAC5 for the refinement of macromolecular crystal structures.
PG  - 355-67
LID - 10.1107/S0907444911001314 [doi]
AB  - This paper describes various components of the macromolecular crystallographic
      refinement program REFMAC5, which is distributed as part of the CCP4 suite.
      REFMAC5 utilizes different likelihood functions depending on the diffraction data
      employed (amplitudes or intensities), the presence of twinning and the
      availability of SAD/SIRAS experimental diffraction data. To ensure chemical and
      structural integrity of the refined model, REFMAC5 offers several classes of
      restraints and choices of model parameterization. Reliable models at resolutions 
      at least as low as 4 A can be achieved thanks to low-resolution refinement tools 
      such as secondary-structure restraints, restraints to known homologous
      structures, automatic global and local NCS restraints, `jelly-body' restraints
      and the use of novel long-range restraints on atomic displacement parameters
      (ADPs) based on the Kullback-Leibler divergence. REFMAC5 additionally offers TLS 
      parameterization and, when high-resolution data are available, fast refinement of
      anisotropic ADPs. Refinement in the presence of twinning is performed in a fully 
      automated fashion. REFMAC5 is a flexible and highly optimized refinement package 
      that is ideally suited for refinement across the entire resolution spectrum
      encountered in macromolecular crystallography.
FAU - Murshudov, Garib N
AU  - Murshudov GN
AD  - Structural Biology Laboratory, Department of Chemistry, University of York,
      Heslington, York, England. garib@ysbl.york.ac.uk
FAU - Skubak, Pavol
AU  - Skubak P
FAU - Lebedev, Andrey A
AU  - Lebedev AA
FAU - Pannu, Navraj S
AU  - Pannu NS
FAU - Steiner, Roberto A
AU  - Steiner RA
FAU - Nicholls, Robert A
AU  - Nicholls RA
FAU - Winn, Martyn D
AU  - Winn MD
FAU - Long, Fei
AU  - Long F
FAU - Vagin, Alexei A
AU  - Vagin AA
LA  - eng
GR  - 064405/Z/01/A/Wellcome Trust/United Kingdom
GR  - BB/F0202281/Biotechnology and Biological Sciences Research Council/United Kingdom
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20110318
PL  - England
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
SB  - IM
MH  - Anisotropy
MH  - Crystallography, X-Ray/*methods
MH  - Likelihood Functions
MH  - *Software
PMC - PMC3069751
OID - NLM: PMC3069751
EDAT- 2011/04/05 06:00
MHDA- 2011/06/28 06:00
CRDT- 2011/04/05 06:00
PHST- 2010/07/14 [received]
PHST- 2011/01/10 [accepted]
PHST- 2011/03/18 [epublish]
AID - S0907444911001314 [pii]
AID - 10.1107/S0907444911001314 [doi]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 2011 Apr;67(Pt 4):355-67. doi:
      10.1107/S0907444911001314. Epub 2011 Mar 18.
URL - http://www.ncbi.nlm.nih.gov/pubmed/21460454

PMID- 15572771
OWN - NLM
STAT- MEDLINE
DA  - 20041201
DCOM- 20050222
LR  - 20081121
IS  - 0907-4449 (Print)
IS  - 0907-4449 (Linking)
VI  - 60
IP  - Pt 12 Pt 1
DP  - 2004 Dec
TI  - REFMAC5 dictionary: organization of prior chemical knowledge and guidelines for
      its use.
PG  - 2184-95
AB  - One of the most important aspects of macromolecular structure refinement is the
      use of prior chemical knowledge. Bond lengths, bond angles and other chemical
      properties are used in restrained refinement as subsidiary conditions. This
      contribution describes the organization and some aspects of the use of the
      flexible and human/machine-readable dictionary of prior chemical knowledge used
      by the maximum-likelihood macromolecular-refinement program REFMAC5. The
      dictionary stores information about monomers which represent the constitutive
      building blocks of biological macromolecules (amino acids, nucleic acids and
      saccharides) and about numerous organic/inorganic compounds commonly found in
      macromolecular crystallography. It also describes the modifications the building 
      blocks undergo as a result of chemical reactions and the links required for
      polymer formation. More than 2000 monomer entries, 100 modification entries and
      200 link entries are currently available. Algorithms and tools for updating and
      adding new entries to the dictionary have also been developed and are presented
      here. In many cases, the REFMAC5 dictionary allows entirely automatic generation 
      of restraints within REFMAC5 refinement runs.
FAU - Vagin, Alexei A
AU  - Vagin AA
AD  - Structural Biology Laboratory, Department of Chemistry, University of York, York 
      YO10 5YW, England.
FAU - Steiner, Roberto A
AU  - Steiner RA
FAU - Lebedev, Andrey A
AU  - Lebedev AA
FAU - Potterton, Liz
AU  - Potterton L
FAU - McNicholas, Stuart
AU  - McNicholas S
FAU - Long, Fei
AU  - Long F
FAU - Murshudov, Garib N
AU  - Murshudov GN
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20041126
PL  - Denmark
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
RN  - 0 (Peptide Library)
RN  - 0 (Proteins)
SB  - IM
MH  - Chemical Phenomena
MH  - Chemistry
MH  - *Computational Biology
MH  - Crystallography, X-Ray
MH  - Dictionaries as Topic
MH  - Internet
MH  - Models, Molecular
MH  - Peptide Library
MH  - Protein Conformation
MH  - Proteins/*chemistry
MH  - *Software
EDAT- 2004/12/02 09:00
MHDA- 2005/02/23 09:00
CRDT- 2004/12/02 09:00
PHST- 2004/04/19 [received]
PHST- 2004/09/22 [accepted]
PHST- 2004/11/26 [epublish]
AID - S0907444904023510 [pii]
AID - 10.1107/S0907444904023510 [doi]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 2004 Dec;60(Pt 12 Pt 1):2184-95. Epub 2004
      Nov 26.

PMID- 15299926
OWN - NLM
STAT- PubMed-not-MEDLINE
DA  - 20040809
DCOM- 20050217
LR  - 20070724
IS  - 0907-4449 (Print)
IS  - 0907-4449 (Linking)
VI  - 53
IP  - Pt 3
DP  - 1997 May 1
TI  - Refinement of macromolecular structures by the maximum-likelihood method.
PG  - 240-55
AB  - This paper reviews the mathematical basis of maximum likelihood. The likelihood
      function for macromolecular structures is extended to include prior phase
      information and experimental standard uncertainties. The assumption that
      different parts of a structure might have different errors is considered. A
      method for estimating sigma(A) using 'free' reflections is described and its
      effects analysed. The derived equations have been implemented in the program
      REFMAC. This has been tested on several proteins at different stages of
      refinement (bacterial alpha-amylase, cytochrome c', cross-linked insulin and
      oligopeptide binding protein). The results derived using the maximum-likelihood
      residual are consistently better than those obtained from least-squares
      refinement.
FAU - Murshudov, G N
AU  - Murshudov GN
AD  - Chemistry Department, University of York, Heslington, England.
FAU - Vagin, A A
AU  - Vagin AA
FAU - Dodson, E J
AU  - Dodson EJ
LA  - eng
PT  - Journal Article
PL  - Denmark
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
EDAT- 1997/05/01 00:00
MHDA- 1997/05/01 00:01
CRDT- 1997/05/01 00:00
AID - 10.1107/S0907444996012255 [doi]
AID - S0907444996012255 [pii]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 1997 May 1;53(Pt 3):240-55.


PMID- 22505260
OWN - NLM
STAT- MEDLINE
DA  - 20120416
DCOM- 20120619
LR  - 20140220
IS  - 1399-0047 (Electronic)
IS  - 0907-4449 (Linking)
VI  - 68
IP  - Pt 4
DP  - 2012 Apr
TI  - Low-resolution refinement tools in REFMAC5.
PG  - 404-17
LID - 10.1107/S090744491105606X [doi]
AB  - Two aspects of low-resolution macromolecular crystal structure analysis are
      considered: (i) the use of reference structures and structural units for
      provision of structural prior information and (ii) map sharpening in the presence
      of noise and the effects of Fourier series termination. The generation of
      interatomic distance restraints by ProSMART and their subsequent application in
      REFMAC5 is described. It is shown that the use of such external structural
      information can enhance the reliability of derived atomic models and stabilize
      refinement. The problem of map sharpening is considered as an inverse deblurring 
      problem and is solved using Tikhonov regularizers. It is demonstrated that this
      type of map sharpening can automatically produce a map with more structural
      features whilst maintaining connectivity. Tests show that both of these
      directions are promising, although more work needs to be performed in order to
      further exploit structural information and to address the problem of reliable
      electron-density calculation.
FAU - Nicholls, Robert A
AU  - Nicholls RA
AD  - Structural Studies Division, MRC Laboratory of Molecular Biology, Cambridge CB2
      0QH, England.
FAU - Long, Fei
AU  - Long F
FAU - Murshudov, Garib N
AU  - Murshudov GN
LA  - eng
GR  - MC_UP_A025_1012/Medical Research Council/United Kingdom
GR  - MC_US_A025_0104/Medical Research Council/United Kingdom
GR  - Biotechnology and Biological Sciences Research Council/United Kingdom
GR  - Wellcome Trust/United Kingdom
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 20120316
PL  - United States
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
RN  - 0 (Proteins)
SB  - IM
MH  - Crystallography, X-Ray/*methods
MH  - Models, Molecular
MH  - Protein Structure, Secondary
MH  - Protein Structure, Tertiary
MH  - Proteins/analysis/chemistry
PMC - PMC3322599
OID - NLM: PMC3322599
EDAT- 2012/04/17 06:00
MHDA- 2012/06/20 06:00
CRDT- 2012/04/17 06:00
PHST- 2011/11/02 [received]
PHST- 2011/12/28 [accepted]
PHST- 2012/03/16 [epublish]
AID - S090744491105606X [pii]
AID - 10.1107/S090744491105606X [doi]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 2012 Apr;68(Pt 4):404-17. doi:
      10.1107/S090744491105606X. Epub 2012 Mar 16.

PMID- 10089417
OWN - NLM
STAT- MEDLINE
DA  - 19990503
DCOM- 19990503
LR  - 20070724
IS  - 0907-4449 (Print)
IS  - 0907-4449 (Linking)
VI  - 55
IP  - Pt 1
DP  - 1999 Jan
TI  - Efficient anisotropic refinement of macromolecular structures using FFT.
PG  - 247-55
AB  - This paper gives the equations for the use of fast Fourier transformations in
      individual atomic anisotropic refinement. Restraints on bonded atoms, on the
      sphericity of each atom and between non-crystallographic symmetry related atoms
      are described. These have been implemented in the program REFMAC and its
      performance with several examples is analysed. All the tests show that
      anisotropic refinement not only reduces the R value and Rfree but also improves
      the fit to geometric targets, indicating that this parameterization is valuable
      for improving models derived from experimental data. The computer time taken is
      comparable to that for isotropic refinements.
FAU - Murshudov, G N
AU  - Murshudov GN
AD  - Chemistry Department, University of York, Heslington, York YO1 5DD, England and
      CLRC, Daresbury Laboratory, Daresbury, Warrington WA4 4AD,
      England.garib@yorvic.york.ac.uk
FAU - Vagin, A A
AU  - Vagin AA
FAU - Lebedev, A
AU  - Lebedev A
FAU - Wilson, K S
AU  - Wilson KS
FAU - Dodson, E J
AU  - Dodson EJ
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
DEP - 19990101
PL  - DENMARK
TA  - Acta Crystallogr D Biol Crystallogr
JT  - Acta crystallographica. Section D, Biological crystallography
JID - 9305878
RN  - 0 (Macromolecular Substances)
RN  - EC 1.11.1.6 (Catalase)
RN  - EC 3.1.- (Ribonucleases)
SB  - IM
MH  - Catalase/chemistry
MH  - *Crystallography, X-Ray
MH  - *Fluorescence Polarization
MH  - *Fourier Analysis
MH  - Macromolecular Substances
MH  - Models, Molecular
MH  - Protein Conformation
MH  - Ribonucleases/chemistry
MH  - Software
EDAT- 1999/03/25 03:01
MHDA- 2000/06/23 11:00
CRDT- 1999/03/25 03:01
PHST- 1998/10/02 [received]
PHST- 1998/10/25 [accepted]
PHST- 1999/01/01 [epublish]
AID - 10.1107/S090744499801405X [doi]
AID - S090744499801405X [pii]
PST - ppublish
SO  - Acta Crystallogr D Biol Crystallogr. 1999 Jan;55(Pt 1):247-55. Epub 1999 Jan 1.

PMID- 14696379
OWN - NLM
STAT- MEDLINE
DA  - 20031230
DCOM- 20040204
LR  - 20091119
IS  - 0076-6879 (Print)
IS  - 0076-6879 (Linking)
VI  - 374
DP  - 2003
TI  - Macromolecular TLS refinement in REFMAC at moderate resolutions.
PG  - 300-21
FAU - Winn, Martyn D
AU  - Winn MD
AD  - Daresbury Laboratory, Daresbury, Warrington, WA4 4AD, United Kingdom.
FAU - Murshudov, Garib N
AU  - Murshudov GN
FAU - Papiz, Miroslav Z
AU  - Papiz MZ
LA  - eng
PT  - Journal Article
PT  - Research Support, Non-U.S. Gov't
PL  - United States
TA  - Methods Enzymol
JT  - Methods in enzymology
JID - 0212271
RN  - 0 (Proteins)
SB  - IM
MH  - Chemistry Techniques, Analytical/*methods
MH  - Crystallography, X-Ray/methods
MH  - *Data Interpretation, Statistical
MH  - Likelihood Functions
MH  - Models, Molecular
MH  - Protein Structure, Tertiary
MH  - Proteins/*chemistry
MH  - *Software
EDAT- 2003/12/31 05:00
MHDA- 2004/02/05 05:00
CRDT- 2003/12/31 05:00
AID - 10.1016/S0076-6879(03)74014-2 [doi]
AID - S0076687903740142 [pii]
PST - ppublish
SO  - Methods Enzymol. 2003;374:300-21.