The mean isotropic displacement parameter (B value) for the coordinate set.
The minimum isotropic displacement parameter (B value) found in the coordinate set.
The [1][1] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure.
The [1][2] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure.
The [1][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure.
The [2][2] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure.
The [2][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure.
The [3][3] element of the matrix that defines the overall anisotropic displacement model if one was refined for this structure.
The correlation coefficient between the observed and calculated structure factors for reflections included in the refinement.
The correlation coefficient is scale-independent and gives
an idea of the quality of the refined model.
sum~i~(Fo~i~ Fc~i~ - <Fo><Fc>)
Rcorr = ------------------------------------------------------------
SQRT{sumi(Foi)^2^-i(Fci)^2^-
Fo = observed structure factors
Fc = calculated structure factors
<> denotes average value
summation is over reflections included in the refinement
The correlation coefficient between the observed and calculated structure factors for reflections not included in the refinement (free reflections).
The correlation coefficient is scale-independent and gives
an idea of the quality of the refined model.
sum~i~(Fo~i~ Fc~i~ - <Fo><Fc>)
Rcorr = ------------------------------------------------------------
SQRT{sumi(Foi)^2^-i(Fci)^2^-
Fo = observed structure factors
Fc = calculated structure factors
<> denotes average value
summation is over reflections not included
in the refinement (free reflections)
Description of special aspects of the refinement process.
Examples: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details.
sum|F~obs~ - F~calc~|
R = ---------------------
sum|Fobs|
Fobs = the observed structure-factor amplitudes
Fcalc = the calculated structure-factor amplitudes
sum is taken over the specified reflections
The estimated error in _refine.ls_R_factor_R_free. The method used to estimate the error is described in the item _refine.ls_R_factor_R_free_error_details.
Special aspects of the method used to estimated the error in _refine.ls_R_factor_R_free.
Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details.
_refine.ls_R_factor_obs should not be confused with _refine.ls_R_factor_R_work; the former reports the results of a refinement in which all observed reflections were used, the latter a refinement in which a subset of the observed reflections were excluded from refinement for the calculation of a 'free' R factor. However, it would be meaningful to quote both values if a 'free' R factor were calculated for most of the refinement, but all of the observed reflections were used in the final rounds of refinement; such a protocol should be explained in _refine.details.
sum|F~obs~ - F~calc~|
R = ---------------------
sum|Fobs|
Fobs = the observed structure-factor amplitudes
Fcalc = the calculated structure-factor amplitudes
sum is taken over the specified reflections
Residual factor R for all reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low.
sum|F~obs~ - F~calc~|
R = ---------------------
sum|Fobs|
Fobs = the observed structure-factor amplitudes
Fcalc = the calculated structure-factor amplitudes
sum is taken over the specified reflections
Residual factor R for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion.
_refine.ls_R_factor_obs should not be confused with _refine.ls_R_factor_R_work; the former reports the results of a refinement in which all observed reflections were used, the latter a refinement in which a subset of the observed reflections were excluded from refinement for the calculation of a 'free' R factor. However, it would be meaningful to quote both values if a 'free' R factor were calculated for most of the refinement, but all of the observed reflections were used in the final rounds of refinement; such a protocol should be explained in _refine.details.
sum|F~obs~ - F~calc~|
R = ---------------------
sum|Fobs|
Fobs = the observed structure-factor amplitudes
Fcalc = the calculated structure-factor amplitudes
sum is taken over the specified reflections
The smallest value for the interplanar spacings for the reflection data used in the refinement in angstroms. This is called the highest resolution.
The largest value for the interplanar spacings for the reflection data used in the refinement in angstroms. This is called the lowest resolution.
Type of matrix used to accumulate the least-squares derivatives.
Allowable values: atomblock, diagonal, full, fullcycle, sparse, userblock
The number of parameters refined in the least-squares process. If possible, this number should include some contribution from the restrained parameters. The restrained parameters are distinct from the constrained parameters (where one or more parameters are linearly dependent on the refined value of another). Least-squares restraints often depend on geometry or energy considerations and this makes their direct contribution to this number, and to the goodness-of-fit calculation, difficult to assess.
The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details.
The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details.
The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low.
The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion.
The number of restrained parameters. These are parameters which are not directly dependent on another refined parameter. Restrained parameters often involve geometry or energy dependencies. See also _atom_site.constraints and _atom_site.refinement_flags. A general description of refinement constraints may appear in _refine.details.
The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits.
The number of reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits.
The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low to the number of crystallographically unique reflections that satisfy the same limits.
The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion to the number of crystallographically unique reflections that satisfy the same limits.
Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e. were excluded from the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details.
( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
wR = ( ---------------------------- )
( sum|w Yobs^2^| )
Yobs = the observed amplitude specified by
_refine.ls_structure_factor_coef
Ycalc = the calculated amplitude specified by
_refine.ls_structure_factor_coef
w = the least-squares weight
sum is taken over the specified reflections
Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine.ls_d_res_high and _refine.ls_d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e. were included in the refinement) when the refinement included the calculation of a 'free' R factor. Details of how reflections were assigned to the working and test sets are given in _reflns.R_free_details.
( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^
wR = ( ---------------------------- )
( sum|w Yobs^2^| )
Yobs = the observed amplitude specified by
_refine.ls_structure_factor_coef
Ycalc = the calculated amplitude specified by
_refine.ls_structure_factor_coef
w = the least-squares weight
sum is taken over the specified reflections
The maximum value for occupancy found in the coordinate set.
The minimum value for occupancy found in the coordinate set.
Average figure of merit of phases of reflections not included in the refinement.
This value is derived from the likelihood function.
FOM = I1(X)/I0(X)
I0, I1 = zero- and first-order modified Bessel functions
of the first kind
X = sigmaA |Eo| |Ec|/SIGMA
Eo, Ec = normalized observed and calculated structure
factors
sigmaA = <cos 2 pi s deltax> SQRT(SigmaP/SigmaN)
estimated using maximum likelihood
SigmaP = sum{atoms in model} f^2^
SigmaN = sum{atoms in crystal} f^2^
f = form factor of atoms
deltax = expected error
SIGMA = (sigma{E;exp})^2^ + epsilon [1-(sigmaA)^2^]
sigma{E;exp} = uncertainties of normalized observed
structure factors
epsilon = multiplicity of the diffracting plane
Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255.
Average figure of merit of phases of reflections included in the refinement.
This value is derived from the likelihood function.
FOM = I1(X)/I0(X)
I0, I1 = zero- and first-order modified Bessel functions
of the first kind
X = sigmaA |Eo| |Ec|/SIGMA
Eo, Ec = normalized observed and calculated structure
factors
sigmaA = <cos 2 pi s deltax> SQRT(SigmaP/SigmaN)
estimated using maximum likelihood
SigmaP = sum{atoms in model} f^2^
SigmaN = sum{atoms in crystal} f^2^
f = form factor of atoms
deltax = expected error
SIGMA = (sigma{E;exp})^2^ + epsilon [1-(sigmaA)^2^]
sigma{E;exp} = uncertainties of normalized observed
structure factors
epsilon = multiplicity of the diffracting plane
Ref: Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255.
The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on a maximum-likelihood residual.
The overall standard uncertainty (sigma~B~)^2^ gives an idea
of the uncertainty in the B values of averagely defined
atoms (atoms with B values equal to the average B value).
N~a~
(sigmaB)^2^ = 8 ----------------------------------------------
sumi {1/Sigma - (Eo)^2^ (1-m^2^)s^4^}
N~a~ = number of atoms
E~o~ = normalized structure factors
m = figure of merit of phases of reflections
included in the summation
s = reciprocal-space vector
SUM_AS = (sigma~A~)^2^/Sigma^2^
Sigma = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^]
sigma~{E;exp}~ = experimental uncertainties of normalized
structure factors
sigma~A~ = <cos 2 pi s delta~x~> SQRT(Sigma~P~/Sigma~N~)
estimated using maximum likelihood
Sigma~P~ = sum~{atoms in model}~ f^2^
Sigma~N~ = sum~{atoms in crystal}~ f^2^
f = atom form factor
delta~x~ = expected error
epsilon = multiplicity of diffracting plane
summation is over all reflections included in refinement
Ref: (sigma~A~ estimation) "Refinement of macromolecular
structures by the maximum-likelihood method",
Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).
Acta Cryst. D53, 240-255.
(SU B estimation) Murshudov, G. N. & Dodson,
E. J. (1997). Simplified error estimation a la
Cruickshank in macromolecular crystallography.
CCP4 Newsletter on Protein Crystallography, No. 33,
January 1997, pp. 31-39.
http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html
The overall standard uncertainty (estimated standard deviation) of the positional parameters based on a maximum likelihood residual.
The overall standard uncertainty (sigma~X~)^2^ gives an
idea of the uncertainty in the position of averagely
defined atoms (atoms with B values equal to average B value)
3 N~a~
(sigmaX)^2^ = ---------------------------------------------------------
8 pi^2^ sumi {1/Sigma - (Eo)^2^ (1-m^2^)s^2^}
N~a~ = number of atoms
E~o~ = normalized structure factors
m = figure of merit of phases of reflections
included in the summation
s = reciprocal-space vector
SUM_AS = (sigma~A~)^2^/Sigma^2^
Sigma = (sigma~{E;exp}~)^2^ + epsilon [1-(sigma~A~)^2^]
sigma~{E;exp}~ = experimental uncertainties of normalized
structure factors
sigma~A~ = <cos 2 pi s delta~x~> SQRT(Sigma~P~/Sigma~N~)
estimated using maximum likelihood
Sigma~P~ = sum~{atoms in model}~ f^2^
Sigma~N~ = sum~{atoms in crystal}~ f^2^
f = atom form factor
delta~x~ = expected error
epsilon = multiplicity of diffracting plane
summation is over all reflections included in refinement
Ref: (sigma_A estimation) "Refinement of macromolecular
structures by the maximum-likelihood method",
Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997).
Acta Cryst. D53, 240-255.
(SU ML estimation) Murshudov, G. N. & Dodson,
E. J. (1997). Simplified error estimation a la
Cruickshank in macromolecular crystallography.
CCP4 Newsletter on Protein Crystallography, No. 33,
January 1997, pp. 31-39.
http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html
The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the crystallographic R value, expressed in a formalism known as the dispersion precision indicator (DPI).
The overall standard uncertainty (sigmaB) gives an idea
of the uncertainty in the B values of averagely defined
atoms (atoms with B values equal to the average B value).
N~a~
(sigmaB)^2^ = 0.65 ---------- (Rvalue)^2^ (Dmin)^2^ C^-2/3^
(No-Np)
Na = number of atoms included in refinement
No = number of observations
Np = number of parameters refined
Rvalue = conventional crystallographic R value
Dmin = maximum resolution
C = completeness of data
Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601.
Murshudov, G. N. & Dodson,
E. J. (1997). Simplified error estimation a la
Cruickshank in macromolecular crystallography.
CCP4 Newsletter on Protein Crystallography, No. 33,
January 1997, pp. 31-39.
http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html
The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the free R value.
The overall standard uncertainty (sigmaB) gives an idea
of the uncertainty in the B values of averagely defined
atoms (atoms with B values equal to the average B value).
N~a~
(sigmaB)^2^ = 0.65 ---------- (Rfree)^2^ (Dmin)^2^ C^-2/3^
(No-Np)
Na = number of atoms included in refinement
No = number of observations
Np = number of parameters refined
Rfree = conventional free crystallographic R value calculated
using reflections not included in refinement
Dmin = maximum resolution
C = completeness of data
Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601.
Murshudov, G. N. & Dodson,
E. J. (1997). Simplified error estimation a la
Cruickshank in macromolecular crystallography.
CCP4 Newsletter on Protein Crystallography, No. 33,
January 1997, pp. 31-39.
http://www.ccp4.ac.uk/newsletters/newsletter33/murshudov.html
Details of the manner in which the cross validation reflections were selected.
Examples: Random selection
A flag for TLS refinements identifying the type of atomic displacement parameters stored in _atom_site.B_iso_or_equiv.
Allowable values: LIKELY RESIDUAL, UNVERIFIED
Average Fourier Shell Correlation (avgFSC) between model and observed structure factors for reflections not included in refinement.
The average FSC is a measure of the agreement between observed and calculated structure factors.
sum(N~i~ FSC~free-i~)
avgFSCfree = ---------------------
sum(Ni)
Ni = the number of free reflections in the resolution shell i
FSCfree-i = FSC for free reflections in the i-th resolution shell calculated as:
(sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~)))
FSCfree-i = -------------------------------------------
(sum(|Fo|^2^) (sum(|Fc|^2^)))^1/2^
|Fo| = amplitude of observed structure factor
|Fc| = amplitude of calculated structure factor
phio = phase of observed structure factor
phic = phase of calculated structure factor
fom = figure of merit of the experimental phases.
Summation of FSCfree-i is carried over all free reflections in the resolution shell.
Summation of avgFSCfree is carried over all resolution shells.
Ref: Rosenthal P.B., Henderson R. "Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. Journal of Molecular Biology. 2003;333(4):721-745, equation (A6).
Overall average Fourier Shell Correlation (avgFSC) between model and observed structure factors for all reflections.
The average FSC is a measure of the agreement between observed and calculated structure factors.
sum(N~i~ FSC~i~)
avgFSC = ----------------
sum(Ni)
Ni = the number of all reflections in the resolution shell i
FSCi = FSC for all reflections in the i-th resolution shell calculated as:
(sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~)))
FSCi = -------------------------------------------
(sum(|Fo|^2^) (sum(|Fc|^2^)))^1/2^
|Fo| = amplitude of observed structure factor
|Fc| = amplitude of calculated structure factor
phio = phase of observed structure factor
phic = phase of calculated structure factor
fom = figure of merit of the experimental phases.
Summation of FSCi is carried over all reflections in the resolution shell.
Summation of avgFSC is carried over all resolution shells.
Ref: Rosenthal P.B., Henderson R. "Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. Journal of Molecular Biology. 2003;333(4):721-745, equation (A6).
Average Fourier Shell Correlation (avgFSC) between model and observed structure factors for reflections included in refinement.
The average FSC is a measure of the agreement between observed and calculated structure factors.
sum(N~i~ FSC~work-i~)
avgFSCwork = ---------------------
sum(Ni)
Ni = the number of working reflections in the resolution shell i
FSCwork-i = FSC for working reflections in the i-th resolution shell calculated as:
(sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~)))
FSCwork-i = -------------------------------------------
(sum(|Fo|^2^) (sum(|Fc|^2^)))^1/2^
|Fo| = amplitude of observed structure factor
|Fc| = amplitude of calculated structure factor
phio = phase of observed structure factor
phic = phase of calculated structure factor
fom = figure of merit of the experimental phases.
Summation of FSCwork-i is carried over all working reflections in the resolution shell.
Summation of avgFSCwork is carried over all resolution shells.
Ref: Rosenthal P.B., Henderson R. "Optimal determination of particle orientation, absolute hand, and contrast loss in single-particle electron cryomicroscopy. Journal of Molecular Biology. 2003;333(4):721-745, equation (A6).
Value of F at "high end" of data cutoff.
Value of RMS |F| used as high data cutoff.
Examples: null
Value of F at "low end" of data cutoff.
Examples: null
An identifier for the diffraction data set used in this refinement.
Multiple diffraction data sets specified as a comma separated list.
Whether the structure was refined with indvidual isotropic, anisotropic or overall temperature factor.
Examples: Isotropic, Overall
Whether the cross validataion method was used through out or only at the end.
Examples: FREE R-VALUE
Data cutoff (SIGMA(F))
Data cutoff (SIGMA(F^2))
Data cutoff (SIGMA(I))
Method(s) used to determine the structure.
Examples: AB INITIO PHASING, DM, ISAS, ISIR, ISIRAS, MAD, MIR, MIRAS, MR, SIR, SIRAS
Overall estimated standard uncertainties of positional parameters based on R value.
Overall estimated standard uncertainties of positional parameters based on R free value.
The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the crystallographic R value, expressed in a formalism known as the dispersion precision indicator (DPI).
Ref: Blow, D (2002) Acta Cryst. D58, 792-797
The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the crystallographic R-free value, expressed in a formalism known as the dispersion precision indicator (DPI).
Ref: Blow, D (2002) Acta Cryst. D58, 792-797
The overall standard uncertainty (estimated standard deviation) of the displacement parameters based on the crystallographic R-free value, expressed in a formalism known as the dispersion precision indicator (DPI).
Ref: Cruickshank, D. W. J. (1999). Acta Cryst. D55, 583-601.
The overall phase error for all reflections after refinement using the current refinement target.
Examples: null
This data item uniquely identifies a refinement within an entry. _refine.pdbx_refine_id can be used to distinguish the results of joint refinements.
For bulk solvent mask calculation, the amount that the ionic radii of atoms, which can be ions, are increased used.
For bulk solvent mask calculation, amount mask is shrunk after taking away atoms with new radii and a constant value assigned to this new region.
For bulk solvent mask calculation, the value by which the vdw radii of non-ion atoms (like carbon) are increased and used.
Starting model for refinement. Starting model for molecular replacement should refer to a previous structure or experiment.
Examples: 1XYZ, 2XYZ, BDL001
Special case of stereochemistry target values used in SHELXL refinement.
Stereochemistry target values used in refinement.
Special aspects of the solvent model used during refinement.
The value of the BSOL solvent-model parameter describing the average isotropic displacement parameter of disordered solvent atoms.
This is one of the two parameters (the other is _refine.solvent_model_param_ksol) in Tronrud's method of modelling the contribution of bulk solvent to the scattering. The standard scale factor is modified according to the expression
k0 exp(-B0 * s^2^)[1-KSOL * exp(-BSOL * s^2^)]
where k0 and B0 are the scale factors for the protein.
Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268.
The value of the KSOL solvent-model parameter describing the ratio of the electron density in the bulk solvent to the electron density in the molecular solute.
This is one of the two parameters (the other is _refine.solvent_model_param_bsol) in Tronrud's method of modelling the contribution of bulk solvent to the scattering. The standard scale factor is modified according to the expression
k0 exp(-B0 * s^2^)[1-KSOL * exp(-BSOL * s^2^)]
where k0 and B0 are the scale factors for the protein.
Ref: Tronrud, D. E. (1997). Methods Enzymol. 277, 243-268.
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The maximum isotropic displacement parameter (B value) found in the coordinate set.