java.lang.Object
- org.rcsb.cif.model.BaseCategory
- - org.rcsb.cif.model.generated.RefineLsShell

All Implemented Interfaces:

Category
```
@Generated("org.rcsb.cif.generator.SchemaGenerator")
public class RefineLsShell
extends BaseCategory
```
Data items in the REFINE_LS_SHELL category record details about the results of the least-squares refinement broken down into shells of resolution.

Field Summary
- Fields inherited from class org.rcsb.cif.model.BaseCategory
  isText, textFields

Constructor Summary

Constructors
Constructor	Description
`RefineLsShell(String name)`
`RefineLsShell(String name, int rowCount, Object[] encodedColumns)`
`RefineLsShell(String name, Map<String,Column> columns)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`FloatColumn`	`getDResHigh()`	The lowest value for the interplanar spacings for the reflection data in this shell.
`FloatColumn`	`getDResLow()`	The highest value for the interplanar spacings for the reflection data in this shell.
`IntColumn`	`getNumberReflnsAll()`	The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low.
`IntColumn`	`getNumberReflnsObs()`	The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion.
`IntColumn`	`getNumberReflnsRFree()`	The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e.
`IntColumn`	`getNumberReflnsRWork()`	The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e.
`FloatColumn`	`getPdbxFscFree()`	Fourier Shell Correlation (FSC) between model and observed structure factors for reflections not included in refinement.
`FloatColumn`	`getPdbxFscWork()`	Fourier Shell Correlation (FSC) between model and observed structure factors for reflections included in refinement.
`FloatColumn`	`getPdbxPhaseError()`	The average phase error for all reflections in the resolution shell.
`StrColumn`	`getPdbxRefineId()`	This data item uniquely identifies a refinement within an entry.
`IntColumn`	`getPdbxTotalNumberOfBinsUsed()`	Total number of bins used.
`FloatColumn`	`getPercentReflnsObs()`	The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits.
`FloatColumn`	`getPercentReflnsRFree()`	The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e.
`FloatColumn`	`getRedundancyReflnsAll()`	The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low to the number of crystallographically unique reflections that satisfy the same limits.
`FloatColumn`	`getRedundancyReflnsObs()`	The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion to the number of crystallographically unique reflections that satisfy the same limits.
`FloatColumn`	`getRFactorAll()`	Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low.
`FloatColumn`	`getRFactorObs()`	Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion.
`FloatColumn`	`getRFactorRFree()`	Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e.
`FloatColumn`	`getRFactorRFreeError()`	The estimated error in _refine_ls_shell.R_factor_R_free.
`FloatColumn`	`getRFactorRWork()`	Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e.
`FloatColumn`	`getWRFactorAll()`	Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low.
`FloatColumn`	`getWRFactorObs()`	Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion.
`FloatColumn`	`getWRFactorRFree()`	Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the test reflections (i.e.
`FloatColumn`	`getWRFactorRWork()`	Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation limit established by _reflns.observed_criterion, and that were used as the working reflections (i.e.

Methods inherited from class org.rcsb.cif.model.BaseCategory
getBinaryColumn, getCategoryName, getColumn, getColumnNames, getRowCount, isDefined

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface org.rcsb.cif.model.Category
columnNames, columns, get

- Constructor Detail
  - RefineLsShell
```
public RefineLsShell(String name,
                     Map<String,Column> columns)
```
  - RefineLsShell
```
public RefineLsShell(String name,
                     int rowCount,
                     Object[] encodedColumns)
```
  - RefineLsShell
```
public RefineLsShell(String name)
```
- Method Detail
  - getPdbxRefineId
```
public StrColumn getPdbxRefineId()
```
    This data item uniquely identifies a refinement within an entry. _refine_ls_shell.pdbx_refine_id can be used to distinguish the results of joint refinements.
    
    Returns:
    
    StrColumn
  - getDResHigh
```
public FloatColumn getDResHigh()
```
    The lowest value for the interplanar spacings for the reflection data in this shell. This is called the highest resolution.
    
    Returns:
    
    FloatColumn
  - getDResLow
```
public FloatColumn getDResLow()
```
    The highest value for the interplanar spacings for the reflection data in this shell. This is called the lowest resolution.
    
    Returns:
    
    FloatColumn
  - getNumberReflnsAll
```
public IntColumn getNumberReflnsAll()
```
    The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low.
    
    Returns:
    
    IntColumn
  - getNumberReflnsObs
```
public IntColumn getNumberReflnsObs()
```
    The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion.
    
    Returns:
    
    IntColumn
  - getNumberReflnsRFree
```
public IntColumn getNumberReflnsRFree()
```
    The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.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.
    
    Returns:
    
    IntColumn
  - getNumberReflnsRWork
```
public IntColumn getNumberReflnsRWork()
```
    The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.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.
    
    Returns:
    
    IntColumn
  - getPercentReflnsObs
```
public FloatColumn getPercentReflnsObs()
```
    The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion, expressed as a percentage of the number of geometrically observable reflections that satisfy the resolution limits.
    
    Returns:
    
    FloatColumn
  - getPercentReflnsRFree
```
public FloatColumn getPercentReflnsRFree()
```
    The number of reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.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 reflection limits.
    
    Returns:
    
    FloatColumn
  - getRFactorAll
```
public FloatColumn getRFactorAll()
```
    Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections
    
    Returns:
    
    FloatColumn
  - getRFactorObs
```
public FloatColumn getRFactorObs()
```
    Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion. sum|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections
    
    Returns:
    
    FloatColumn
  - getRFactorRFree
```
public FloatColumn getRFactorRFree()
```
    Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.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|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections
    
    Returns:
    
    FloatColumn
  - getRFactorRFreeError
```
public FloatColumn getRFactorRFreeError()
```
    The estimated error in _refine_ls_shell.R_factor_R_free. The method used to estimate the error is described in the item _refine.ls_R_factor_R_free_error_details.
    
    Returns:
    
    FloatColumn
  - getRFactorRWork
```
public FloatColumn getRFactorRWork()
```
    Residual factor R for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.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|F~obs~ - F~calc~| R = --------------------- sum|F~obs~| F~obs~ = the observed structure-factor amplitudes F~calc~ = the calculated structure-factor amplitudes sum is taken over the specified reflections
    
    Returns:
    
    FloatColumn
  - getRedundancyReflnsAll
```
public FloatColumn getRedundancyReflnsAll()
```
    The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low to the number of crystallographically unique reflections that satisfy the same limits.
    
    Returns:
    
    FloatColumn
  - getRedundancyReflnsObs
```
public FloatColumn getRedundancyReflnsObs()
```
    The ratio of the total number of observations of the reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion to the number of crystallographically unique reflections that satisfy the same limits.
    
    Returns:
    
    FloatColumn
  - getWRFactorAll
```
public FloatColumn getWRFactorAll()
```
    Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections
    
    Returns:
    
    FloatColumn
  - getWRFactorObs
```
public FloatColumn getWRFactorObs()
```
    Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.d_res_low and the observation criterion established by _reflns.observed_criterion. ( sum|w |Y~obs~ - Y~calc~|^2^| )^1/2^ wR = ( ---------------------------- ) ( sum|w Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections
    
    Returns:
    
    FloatColumn
  - getWRFactorRFree
```
public FloatColumn getWRFactorRFree()
```
    Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.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 Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections
    
    Returns:
    
    FloatColumn
  - getWRFactorRWork
```
public FloatColumn getWRFactorRWork()
```
    Weighted residual factor wR for reflections that satisfy the resolution limits established by _refine_ls_shell.d_res_high and _refine_ls_shell.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 Y~obs~^2^| ) Y~obs~ = the observed amplitude specified by _refine.ls_structure_factor_coef Y~calc~ = the calculated amplitude specified by _refine.ls_structure_factor_coef w = the least-squares weight sum is taken over the specified reflections
    
    Returns:
    
    FloatColumn
  - getPdbxTotalNumberOfBinsUsed
```
public IntColumn getPdbxTotalNumberOfBinsUsed()
```
    Total number of bins used.
    
    Returns:
    
    IntColumn
  - getPdbxPhaseError
```
public FloatColumn getPdbxPhaseError()
```
    The average phase error for all reflections in the resolution shell.
    
    Returns:
    
    FloatColumn
  - getPdbxFscWork
```
public FloatColumn getPdbxFscWork()
```
    Fourier Shell Correlation (FSC) between model and observed structure factors for reflections included in refinement. FSC is a measure of the agreement between observed and calculated structure factors as complex numbers. (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~))) FSC~work~ = -------------------------------------- (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^ |F~o~| = amplitude of observed structure factor |F~c~| = amplitude of calculated structure factor phi~o~ = phase of observed structure factor phi~c~ = phase of calculated structure factor fom = figure of merit of the experimental phases. Summation is carried over all working reflections in the resolution shell. 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).
    
    Returns:
    
    FloatColumn
  - getPdbxFscFree
```
public FloatColumn getPdbxFscFree()
```
    Fourier Shell Correlation (FSC) between model and observed structure factors for reflections not included in refinement. FSC is a measure of the agreement between observed and calculated structure factors as complex numbers. (sum(|F~o~| |F~c~| fom cos(phi~c~-phi~o~))) FSC~free~ = -------------------------------------- (sum(|F~o~|^2^) (sum(|F~c~|^2^)))^1/2^ |F~o~| = amplitude of observed structure factor |F~c~| = amplitude of calculated structure factor phi~o~ = phase of observed structure factor phi~c~ = phase of calculated structure factor fom = figure of merit of the experimental phases. Summation is carried over all free reflections in the resolution shell. 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).
    
    Returns:
    
    FloatColumn

Class RefineLsShell

Field Summary

Fields inherited from class org.rcsb.cif.model.BaseCategory

Constructor Summary

Method Summary

Methods inherited from class org.rcsb.cif.model.BaseCategory

Methods inherited from class java.lang.Object

Methods inherited from interface org.rcsb.cif.model.Category

Constructor Detail

RefineLsShell

RefineLsShell

RefineLsShell

Method Detail

getPdbxRefineId

getDResHigh

getDResLow

getNumberReflnsAll

getNumberReflnsObs

getNumberReflnsRFree

getNumberReflnsRWork

getPercentReflnsObs

getPercentReflnsRFree

getRFactorAll

getRFactorObs

getRFactorRFree

getRFactorRFreeError

getRFactorRWork

getRedundancyReflnsAll

getRedundancyReflnsObs

getWRFactorAll

getWRFactorObs

getWRFactorRFree

getWRFactorRWork

getPdbxTotalNumberOfBinsUsed

getPdbxPhaseError

getPdbxFscWork

getPdbxFscFree