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mmCIF extension dictionary


Dear Colleagues,

Please find the following summary of the actions taken in response to 
those issues raised in the technical review of the mmCIF extension 
dictionary.   We are also attaching a copy of the final set of 
definitions, and we request that these be approved for incorporation 
into the mmCIF dictionary version 2.0.

Best regards,

Paula Fitzgerald
Helen Berman 
John Westbrook


---------------------------------------------
Summary of mmCIF extension dictionary issues:
---------------------------------------------

D83.3 mmCIF dictionary extension
--------------------------------

******************************************************************************
David Brown's many comments and technical corrections seems to have been
adequately reponded to by Brian, both in his comments to the list and in
his editting of the draft dictionary.  They will not be dealt with further
in this response.

We will, though, respond to each of Brian's comments, as follows. 
******************************************************************************


------------------------------------------------------------------------------
save__phasing_MIR_der.power_acentric
The meaning of the following phrase is not clear:
"Phasing power is <FH / Lack_of_closure>." 
    - what is FH?
    - what is Lack_of_closure? If a general descriptive phase, the
      underscores may be omitted (cf "Isomorphous difference" in
      save__phasing_MIR_der.R_cullis_acentric). If a single symbolic
      reference, it should be properly defined.
    - do the angle brackets have any meaning (e.g. "expectation value")?
      If not, should they be dropped altogether? Replaced by parentheses?
      Is the placement correct? (i.e. not <FH>/<Lack_of_closure>?)
------------------------------------------------------------------------------
******************************************************************************
The phrase <FH / Lack_of_closure> is a shorthand for the formal expression
    of phasing power that is given in the equation that follows it.  Since
    the shorthand version seems to be causing confusion, and since we
    don't carry it in the other data items concerning phasing power in the
    main mmCIF dictionary, it is perhaps easiest to just delete it here.
    This has been done
******************************************************************************


------------------------------------------------------------------------------
save__phasing_MIR_der.R_cullis_acentric
Same comments as above regarding "Lack_of_closure" and angle brackets.
------------------------------------------------------------------------------
******************************************************************************
Same action - it is gone.
******************************************************************************


------------------------------------------------------------------------------
The meaning of this sentence is not clear:
"NB:  This is tabulated for acentric and anomalous terms,
      extending the former definition."
    - what is the former definition? Presumably it is the equation

                           sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ |
               R~cullis~ = ----------------------------------------
                                   sum|Fph~obs~ - Fp~obs~|

      given in save__phasing_MIR_der_shell.R_cullis, in which case
      reference should be made to the location of this definition.
    - is there a reference to the tabulation for acentric and anomalous
      terms?
    - should the literature reference to the paper of Cullis et al.:
               Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G.
                    & North, A. C. T. (1961). Proc. R. Soc. A265, 15-38.
      appear in any case?
    - i.e. is the quantity still properly named as a "Cullis R factor"?
Here is a suggested alternative definition:
    _item_description.description
;              Residual factor R~cullis~ for acentric reflections in this
               derivative.

               The Cullis R factor is the ratio of the lack of closure and
               isomorphous difference terms. It is defined in terms of an
               analytical formula for centric reflections, but must be
               extracted or interpolated for acentric and anomalous
               reflections from the tabulation of XXXXX XXXXX XXXXX XXXX.

               Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G.
                    & North, A. C. T. (1961). Proc. R. Soc. A265, 15-38.
;
------------------------------------------------------------------------------
******************************************************************************
How about the following - a bit of Brian's expanded definition, and the
    equation and reference pulled from the main mmCIF dictionary:

    _item_description.description
;              Residual factor R~cullis~ for acentric reflections in this
               derivative.

               The Cullis R factor was originally defined only for centric
               reflections.  It is, however, also a useful statistical
               measure for acentric reflections, which is how it is used in
               this data item.

                           sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ |
               R~cullis~ = ----------------------------------------
                                   sum|Fph~obs~ - Fp~obs~|

               Fp~obs~  = the observed structure factor amplitude of the native
               Fph~obs~ = the observed structure factor amplitude of the
                          derivative
               Fh~calc~ = the calculated structure factor amplitude from the
                          heavy atom model

               sum is taken over the specified reflections

               Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G.
                    & North, A. C. T. (1961). Proc. Roy. Soc. A265, 15-38.
******************************************************************************


------------------------------------------------------------------------------
save__phasing_MIR_der.R_cullis_anomalous
The quantity is defined twice:
"Cullis R factor is <Lack_of_closure>/<Isomorphous difference>."
"Cullis  Rfactor is <Lack_of_closure>/<Anomalous difference>"
    - have two definitions been conflated?

I find the nomenclature confusing and not fully explained - what are FPHi(+)
and FPHi(-)? What is FHi"? The various Dano terms? RC(ano) should be
called something else - R~cullis~ or R~cullis~^ano^ perhaps?

Small point - "Sum" in the equation should be "sum" for consistency with
other such expressions.

Is the Cullis et al. literature reference appropriate here too?
------------------------------------------------------------------------------
******************************************************************************
The definition for this data item has been completely revised.  If we have
done a good job, all should be clear now.
******************************************************************************


------------------------------------------------------------------------------
save__phasing_MIR_shell.reflns_anomalous
Doesn't exist - should it? (i.e. there are _centric and _acentric
definitions, but no _anomalous.)
------------------------------------------------------------------------------
******************************************************************************
This data item has been added.
******************************************************************************


------------------------------------------------------------------------------
REFLN_SYS_ABS
Is not this entire category a candidate for the Core dictionary?
------------------------------------------------------------------------------
******************************************************************************
We would have no objection to that.
******************************************************************************


------------------------------------------------------------------------------
save__refln_sys_abs.index_l
Typo: "Miller index h of the reflection." should of course be "Miller index l
of the reflection."
------------------------------------------------------------------------------
******************************************************************************
Yes, and you have already fixed that.
******************************************************************************


------------------------------------------------------------------------------
save__refine.overall_ESU_B
"Overall estimated standard uncertainties" should be "Overall standard
uncertainty". Presumably this is the quantity sigma_B (the equation gives
(sigma_B)^2).
------------------------------------------------------------------------------
******************************************************************************
According to Kim Henrick, the program from which he is harvesting data
outputs (sigma_B)^2, ergo I have modified the definition to refer to
(sigma_b)^2.
******************************************************************************


------------------------------------------------------------------------------
save__refine.overall_ESU_ML
Seems identical to the sigma_B definition apart from the numerical factor
(3/8 versus 8). Is this correct?
------------------------------------------------------------------------------
******************************************************************************
The definition have been modified to refer to (sigma_U)^2.

No, the term ESU_B reflects uncertainty in the thermal parameters, while
ESU_ML reflects uncertainty in the coordinates.  ESU_B has 8 and s^4
while ESU_ML has 3/(8 * pi^2) and s^2.

Also, the definition has been modified to refer to (sigma_U)^2.
****************************************************************************2*


------------------------------------------------------------------------------
save__refine.overall_ESU_R_Cruickshanks_DPI
Better named as "_refine.overall_ESU_R_Cruickshank_DPI" (i.e. without the s
at the end of Cruickshank)?

What does DPI stand for?
------------------------------------------------------------------------------
******************************************************************************
DPI stands for Dipsersion Precision Indicator, a measure of error developed
by Cruikshank.  The definition has been modified to make this clear.
******************************************************************************


------------------------------------------------------------------------------
save__refine.overall_ESU_Rfree
better named as "_refine.overall_ESU_R_free" (i.e. with an _ after the R)?
------------------------------------------------------------------------------
******************************************************************************
Fine, and you have already make that change.
******************************************************************************


------------------------------------------------------------------------------
save__refine.overall_FOM_free_Rset
better named as "_refine.overall_FOM_free_R_set" (i.e. with an _ after the R)?

_item.name is incorrectly given as '_refine.overall_FOM_work_Rset' (and
likewise _item_aliases.alias_name as '_refine.ebi_overall_FOM_work_Rset').
------------------------------------------------------------------------------
******************************************************************************
Yes, and you have already fixed the one and changed the other.
******************************************************************************


------------------------------------------------------------------------------
save__refine.overall_FOM_work_Rset
better named as "_refine.overall_FOM_work_R_set" (i.e. with an _ after the R)?
------------------------------------------------------------------------------
******************************************************************************
Fine, and you have already make that change.
******************************************************************************


------------------------------------------------------------------------------
save__refine_analyze.RG_d_res_high
refers to "__refine_analyze.ls_RG_free" - typo? Also in 
save__refine_analyze.RG_d_res_low.
------------------------------------------------------------------------------
******************************************************************************
Yes, and you have already fixed both.
******************************************************************************


------------------------------------------------------------------------------
save__refine_analyze.RG_work_free_ratio
would be better as "_refine_analyze.RG_free_work_ratio" (to match the
definition as the free/work ratio).
------------------------------------------------------------------------------
******************************************************************************
Yes, and I have also reworded the definition to emphasis the ratio.
******************************************************************************


------------------------------------------------------------------------------
save__refine_funct_minimized.numterms
would be better as "save__refine_funct_minimized.number_terms"
------------------------------------------------------------------------------
******************************************************************************
Fine, and you have already make that change.
******************************************************************************


------------------------------------------------------------------------------
save__refine_ls_restr.type
The new RESTRAIN labels are verbose - not necessarily a problem, though
there may be an implication to a casual user that any old sentence or phrase
could go in here. 
------------------------------------------------------------------------------
******************************************************************************
I take your point, but really these labels are intended to be in the nature
    of enumerations, without actually *being* enumerations, as is discussed in
    the defintion.  It is not inteded that the user would be adding to the
    list.
******************************************************************************


------------------------------------------------------------------------------
save__refine_ls_restr.U_sigma_wghts
Should we go for the extra two letters of .U_sigma_weights for clarity?

"The expected r.m.s. differences in thermal parameter, either Uiso or Uaniso,
are listed for each shell in  _refine_ls_restr.ebi_rmsdev_dictionary."
    - _refine_ls_restr.ebi_rmsdev_dictionary is not defined in this batch of
      data names
    - is it a generally useful data name or does it have application only to
      the RESTRAIN program? 
    - the same question might indeed be asked of the .U_sigma_weights
      data name itself.
    - the .ebi_rmsdev_dictionary refers presumably to a tabulation of
      values that are to be regarded as a set of standards characterising
      the particular structure under investigation. This use of the term
      "dictionary" (also used elsewhere in protein structural science
      for standard tabulations, if I am not mistaken) is unfortunate
      within the nomenclature of CIF and its associated data dictionaries.
      Is there a suitable synonym acceptable to the macromolecular community?

"...in both cases, WU is the value stored in _refine_ls_restr.U_sigma_wghts."
    - _refine_ls_restr.U_sigma_wghts (or _weights) is not defined: is this a
      typo for _refine_ls_restr_type.U_sigma_wghts? Likewise the definition
      begins with a reference to refine_ls_restr.ebi_U_sigma_wghts - should
      this be _refine_ls_restr_type.ebi_U_sigma_wghts (note also the missing
      initial underscore)?
------------------------------------------------------------------------------
******************************************************************************
In consultation with Kim Henrick, this data item has been deleted.
******************************************************************************

--------------------------
mmCIF Extension Dictionary
--------------------------

data_cif_mm.dic-ext-v4

#################
## PHASING_MIR ##
#################
#
############################################################
## proposed additional data items in an existing category ##
############################################################
#
#########################################
## Submitted by Kim Henrick            ##
## Content review by Paula Fitzgerald  ##
## Editorial review by HB, JW and PMDF ##
#########################################


save__phasing_MIR.d_res_high
    _item_description.description
;              The highest resolution in angstroms for the interplanar spacing
               in the reflection data used for the native data set. This is
               the smallest d value.
;
    _item.name                  '_phasing_MIR.d_res_high'
    _item.category_id             phasing_MIR
    _item.mandatory_code          yes
    _item_aliases.alias_name    '_phasing_MIR.ebi_d_res_high'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum            .    0.0
                                  0.0   0.0
    _item_type.code               float
    _item_units.code              angstroms
     save_

save__phasing_MIR.d_res_low
    _item_description.description
;              The lowest resolution in angstroms for the interplanar spacing
               in the reflection data used for the native data set. This is
               the largest d value.
;
    _item.name                  '_phasing_MIR.d_res_low'
    _item.category_id             phasing_MIR
    _item.mandatory_code          yes
    _item_aliases.alias_name    '_phasing_MIR.ebi_d_res_low'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum            .    0.0
                                  0.0   0.0
    _item_type.code               float
    _item_units.code              angstroms
     save_

save__phasing_MIR.fom
    _item_description.description
;              The mean value of the figure of merit m for all reflections
               phased in the native data set.

                   int P~alpha~ exp(i*alpha) dalpha
               m = --------------------------------
                         int P~alpha~ dalpha

               P~a~ = the probability that phase angle a is correct

               int is taken over the range alpha = 0 to 2 pi.
;
    _item.name                  '_phasing_MIR.fom'
    _item.category_id             phasing_MIR
    _item.mandatory_code          no
    _item_aliases.alias_name    '_phasing_MIR.ebi_fom'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum            .    0.0
                                  0.0   0.0
    _item_type.code               float
     save_

save__phasing_MIR.fom_acentric
    _item_description.description
;              The mean value of the figure of merit m for the acentric
               reflections phased in the native data set.

                   int P~alpha~ exp(i*alpha) dalpha
               m = --------------------------------
                         int P~alpha~ dalpha

               P~a~ = the probability that phase angle a is correct

               int is taken over the range alpha = 0 to 2 pi.
;
    _item.name                  '_phasing_MIR.fom_acentric'
    _item.category_id             phasing_MIR
    _item.mandatory_code          no
    _item_aliases.alias_name    '_phasing_MIR.ebi_fom_acentric'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum            .    0.0
                                  0.0   0.0
    _item_type.code               float
     save_

save__phasing_MIR.fom_centric
    _item_description.description
;              The mean value of the figure of merit m for the centric
               reflections phased in the native data set.

                   int P~alpha~ exp(i*alpha) dalpha
               m = --------------------------------
                         int P~alpha~ dalpha

               P~a~ = the probability that phase angle a is correct

               int is taken over the range alpha = 0 to 2 pi.
;
    _item.name                  '_phasing_MIR.fom_centric'
    _item.category_id             phasing_MIR
    _item.mandatory_code          no
    _item_aliases.alias_name    '_phasing_MIR.ebi_fom_centric'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum            .    0.0
                                  0.0   0.0
    _item_type.code               float
     save_

save__phasing_MIR.reflns
    _item_description.description
;              The total number of reflections phased in the native data set.
;
    _item.name                  '_phasing_MIR.reflns'
    _item.category_id             phasing_MIR
    _item.mandatory_code          no
    _item_aliases.alias_name    '_phasing_MIR.ebi_reflns'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum           .   0
                                  0   0
    _item_type.code               int
     save_

save__phasing_MIR.reflns_acentric
    _item_description.description
;              The number of acentric reflections phased in the native data
               set.
;
    _item.name                  '_phasing_MIR.reflns_acentric'
    _item.category_id             phasing_MIR
    _item.mandatory_code          no
    _item_aliases.alias_name    '_phasing_MIR.ebi_reflns_acentric'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum           .   0
                                  0   0
    _item_type.code               int
     save_

save__phasing_MIR.reflns_centric
    _item_description.description
;              The number of centric reflections phased in the native data
               set.
;
    _item.name                  '_phasing_MIR.reflns_centric'
    _item.category_id             phasing_MIR
    _item.mandatory_code          no
    _item_aliases.alias_name    '_phasing_MIR.ebi_reflns_centric'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum           .   0
                                  0   0
    _item_type.code               int
     save_

save__phasing_MIR.reflns_criterion
    _item_description.description
;              Criterion used to limit the reflections used in the phasing
               calculations.
;
    _item.name                  '_phasing_MIR.reflns_criterion'
    _item.category_id             phasing_MIR
    _item_aliases.alias_name    '_phasing_MIR.ebi_reflns_criteria'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
    _item.mandatory_code          no
    _item_type.code               text
    _item_examples.case          '> 4 \s(I)'
     save_

#####################
## PHASING_MIR_DER ##
#####################
#
############################################################
## proposed additional data items in an existing category ##
############################################################
#
#########################################
## Submitted by Kim Henrick            ##
## Content review by Paula Fitzgerald  ##
## Editorial review by HB, JW and PMDF ##
#########################################

save__phasing_MIR_der.power_acentric
    _item_description.description
;              The mean phasing power P for acentric reflections in this
               derivative.

                          sum|Fh~calc~^2^|
               P = (----------------------------)^1/2^
                    sum|Fph~obs~ - Fph~calc~|^2^

               Fph~obs~  = the observed structure factor amplitude of this
                           derivative
               Fph~calc~ = the calculated structure factor amplitude of this
                           derivative
               Fh~calc~  = the calculated structure factor amplitude from the
                           heavy atom model

               sum is taken over the specified reflections
;
    _item.name                  '_phasing_MIR_der.power_acentric'
    _item.category_id             phasing_MIR_der
    _item.mandatory_code          no
    _item_aliases.alias_name    '_phasing_MIR_der.ebi_power_acentric'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum            .    0.0
                                  0.0   0.0
    _item_type.code               float
     save_

save__phasing_MIR_der.power_centric
    _item_description.description
;              The mean phasing power P for centric reflections in this
               derivative.

                          sum|Fh~calc~^2^|
               P = (----------------------------)^1/2^
                    sum|Fph~obs~ - Fph~calc~|^2^

               Fph~obs~  = the observed structure factor amplitude of the
                           derivative
               Fph~calc~ = the calculated structure factor amplitude of the
                           derivative
               Fh~calc~  = the calculated structure factor amplitude from the
                           heavy atom model

               sum is taken over the specified reflections
;
    _item.name                  '_phasing_MIR_der.power_centric'
    _item.category_id             phasing_MIR_der
    _item.mandatory_code          no
    _item_aliases.alias_name    '_phasing_MIR_der.ebi_power_centric'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum            .    0.0
                                  0.0   0.0
    _item_type.code               float
     save_

save__phasing_MIR_der.R_cullis_acentric
    _item_description.description
;              Residual factor R~cullis,acen~ for acentric reflections in this
               derivative.

               The Cullis R factor was originally defined only for centric
               reflections.  It is, however, also a useful statistical
               measure for acentric reflections, which is how it is used in
               this data item.

                           sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ |
          R~cullis,acen~ = ----------------------------------------
                                   sum|Fph~obs~ - Fp~obs~|

               Fp~obs~  = the observed structure factor amplitude of the native
               Fph~obs~ = the observed structure factor amplitude of the
                          derivative
               Fh~calc~ = the calculated structure factor amplitude from the
                          heavy atom model

               sum is taken over the specified reflections

               Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G.
                    & North, A. C. T. (1961). Proc. Roy. Soc. A265, 15-38.
;
    _item.name                  '_phasing_MIR_der.R_cullis_acentric'
    _item.category_id             phasing_MIR_der
    _item.mandatory_code          no
    _item_aliases.alias_name    '_phasing_MIR_der.ebi_Rcullis_acentric'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum            .    0.0
                                  0.0   0.0
    _item_type.code               float
     save_

save__phasing_MIR_der.R_cullis_anomalous
    _item_description.description
;              Residual factor R~cullis,ano~ for anomalous reflections in this
               derivative.

               The Cullis R factor was originally defined only for centric
               reflections.  It is, however, also a useful statistical
               measure for anomalous  reflections, which is how it is used in
               this data item.

               This is tabulated for acentric terms.  Any value <1.0  means
               there is some contribution to the phasing from the anomalous
               data.

                           sum| |Fph+~obs~Fph-~obs~ - Fh+~calc~ - Fh-~calc~| |
            R~cullis,ano~ = ---------------------------------------------------
                                   sum|Fph+~obs~ - Fph-~obs~|

               Fph+~obs~  = the observed positive Friedel structure factor
                            amplitude for the derivative
               Fph-~obs~  = the observed negative Friedel structure factor
                            amplitude for the derivative

               Fh+~calc~  = the calculated postitive Friedel structure factor
                            amplitude from the heavy atom model
               Fh-~calc~  = the calculated negative Friedel structure factor
                            amplitude from the heavy atom model

               sum is taken over the specified reflections

               Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G.
                    & North, A. C. T. (1961). Proc. Roy. Soc. A265, 15-38.

;
    _item.name                  '_phasing_MIR_der.R_cullis_anomalous'
    _item.category_id             phasing_MIR_der
    _item.mandatory_code          no
    _item_aliases.alias_name    '_phasing_MIR_der.ebi_Rcullis_anomalous'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum            .    0.0
                                  0.0   0.0
    _item_type.code               float
     save_

save__phasing_MIR_der.R_cullis_centric
    _item_description.description
;              Residual factor R~cullis~ for centric reflections in this
               derivative.

                           sum| |Fph~obs~ +/- Fp~obs~| - Fh~calc~ |
               R~cullis~ = ----------------------------------------
                                   sum|Fph~obs~ - Fp~obs~|

               Fp~obs~  = the observed structure factor amplitude of the native
               Fph~obs~ = the observed structure factor amplitude of the
                          derivative
               Fh~calc~ = the calculated structure factor amplitude from the
                          heavy atom model

               sum is taken over the specified reflections

               Ref: Cullis, A. F., Muirhead, H., Perutz, M. F., Rossmann, M. G.
                    & North, A. C. T. (1961). Proc. Roy. Soc. A265, 15-38.
;
    _item.name                  '_phasing_MIR_der.R_cullis_centric'
    _item.category_id             phasing_MIR_der
    _item.mandatory_code          no
    _item_aliases.alias_name    '_phasing_MIR_der.ebi_Rcullis_centric'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum            .    0.0
                                  0.0   0.0
    _item_type.code               float
     save_

save__phasing_MIR_der.reflns_acentric
    _item_description.description
;              The number of acentric reflections used in phasing for this
               derivative.
;
    _item.name                  '_phasing_MIR_der.reflns_acentric'
    _item.category_id             phasing_MIR_der
    _item.mandatory_code          no
    _item_aliases.alias_name    '_phasing_MIR_der.ebi_reflns_acentric'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum           .   0
                                  0   0
    _item_type.code               int
     save_

save__phasing_MIR_der.reflns_anomalous
    _item_description.description
;              The number of anomalous reflections used in phasing for this
               derivative.
;
    _item.name                  '_phasing_MIR_der.reflns_anomalous'
    _item.category_id             phasing_MIR_der
    _item.mandatory_code          no
    _item_aliases.alias_name    '_phasing_MIR_der.ebi_reflns_anomalous'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum           .   0
                                  0   0
    _item_type.code               int
     save_

save__phasing_MIR_der.reflns_centric
    _item_description.description
;              The number of centric reflections used in phasing for this
               derivative.
;
    _item.name                  '_phasing_MIR_der.reflns_centric'
    _item.category_id             phasing_MIR_der
    _item.mandatory_code          no
    _item_aliases.alias_name    '_phasing_MIR_der.ebi_reflns_centric'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum           .   0
                                  0   0
    _item_type.code               int
     save_

##########################
## PHASING_MIR_DER_SITE ##
##########################
#
############################################################
## proposed additional data items in an existing category ##
############################################################
#
#########################################
## Submitted by Kim Henrick            ##
## Content review by Paula Fitzgerald  ##
## Editorial review by HB, JW and PMDF ##
#########################################

save__phasing_MIR_der_site.occupancy_anom
    _item_description.description
;              The relative anomalous occupancy of the atom type
               present at this heavy-atom site in a given derivative.
               This atom occupancy will probably be on an arbitrary scale.
;
    _item.name                  '_phasing_MIR_der_site.occupancy_anom'
    _item.category_id             phasing_MIR_der_site
    _item.mandatory_code          no
    _item_aliases.alias_name    '_phasing_MIR_der_site.ebi_occupancy_anom'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
    _item_related.related_name  '_phasing_MIR_der_site.occupancy_anom_esd'
    _item_related.function_code   associated_esd
    _item_type.code               float
    _item_type_conditions.code    esd
     save_

save__phasing_MIR_der_site.occupancy_anom_esd
    _item_description.description
;              The standard uncertainty (e.s.d.) of
               _phasing_MIR_der_site.occupancy_anom.
;
    _item.name                  '_phasing_MIR_der_site.occupancy_anom_esd'
    _item.category_id             phasing_MIR_der_site
    _item.mandatory_code          no
    _item_aliases.alias_name    '_phasing_MIR_der_site.ebi_occupancy_anom_esd'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
    _item_default.value           0.0
    _item_related.related_name  '_phasing_MIR_der_site.occupancy_anom'
    _item_related.function_code   associated_value
    _item_type.code               float
     save_

save__phasing_MIR_der_site.occupancy_iso
    _item_description.description
;              The relative real isotropic occupancy of the atom type
               present at this heavy-atom site in a given derivative.
               This atom occupancy will probably be on an arbitrary scale.
;
    _item.name                  '_phasing_MIR_der_site.occupancy_iso'
    _item.category_id             phasing_MIR_der_site
    _item.mandatory_code          no
    _item_aliases.alias_name    '_phasing_MIR_der_site.ebi_occupancy_iso'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
    _item_related.related_name  '_phasing_MIR_der_site.occupancy_iso_esd'
    _item_related.function_code   associated_esd
    _item_type.code               float
    _item_type_conditions.code    esd
     save_

save__phasing_MIR_der_site.occupancy_iso_esd
    _item_description.description
;              The standard uncertainty (e.s.d.) of
               _phasing_MIR_der_site.occupancy_iso.
;
    _item.name                  '_phasing_MIR_der_site.occupancy_iso_esd'
    _item.category_id             phasing_MIR_der_site
    _item.mandatory_code          no
    _item_aliases.alias_name    '_phasing_MIR_der_site.ebi_occupancy_iso_esd'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
    _item_default.value           0.0
    _item_related.related_name  '_phasing_MIR_der_site.occupancy_iso'
    _item_related.function_code   associated_value
    _item_type.code               float
     save_

#######################
## PHASING_MIR_SHELL ##
#######################
#
############################################################
## proposed additional data items in an existing category ##
############################################################
#
#########################################
## Submitted by Kim Henrick            ##
## Content review by Paula Fitzgerald  ##
## Editorial review by HB, JW and PMDF ##
#########################################

save__phasing_MIR_shell.fom_acentric
    _item_description.description
;              The mean value of the figure of merit m for acentric reflections
               in this shell.

                   int P~alpha~ exp(i*alpha) dalpha
               m = --------------------------------
                         int P~alpha~ dalpha

               P~a~ = the probability that phase angle a is correct

               int is taken over the range alpha = 0 to 2 pi.
;
    _item.name                  '_phasing_MIR_shell.fom_acentric'
    _item.category_id             phasing_MIR_shell
    _item.mandatory_code          no
    _item_aliases.alias_name    '_phasing_MIR_shell.ebi_fom_acentric'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum            .    0.0
                                  0.0   0.0
    _item_type.code               float
     save_

save__phasing_MIR_shell.fom_centric
    _item_description.description
;              The mean value of the figure of merit m for centric reflections
               in this shell.

                   int P~alpha~ exp(i*alpha) dalpha
               m = --------------------------------
                         int P~alpha~ dalpha

               P~a~ = the probability that phase angle a is correct

               int is taken over the range alpha = 0 to 2 pi.
;
    _item.name                  '_phasing_MIR_shell.fom_centric'
    _item.category_id             phasing_MIR_shell
    _item.mandatory_code          no
    _item_aliases.alias_name    '_phasing_MIR_shell.ebi_fom_centric'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum            .    0.0
                                  0.0   0.0
    _item_type.code               float
     save_

save__phasing_MIR_shell.reflns_acentric
    _item_description.description
;              The number of acentric reflections in this shell.
;
    _item.name                  '_phasing_MIR_shell.reflns_acentric'
    _item.category_id             phasing_mir_shell
    _item.mandatory_code          no
    _item_aliases.alias_name    '_phasing_MIR_shell.ebi_reflns_acentric'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum           .   0
                                  0   0
    _item_type.code               int
     save_

save__phasing_MIR_shell.reflns_anomalous
    _item_description.description
;              The number of anomalous reflections in this shell.
;
    _item.name                  '_phasing_MIR_shell.reflns_anomalous'
    _item.category_id             phasing_mir_shell
    _item.mandatory_code          no
#   _item_aliases.alias_name    '_phasing_MIR_shell.ebi_reflns_anomalous'
#   _item_aliases.dictionary      ebi_extensions
#   _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum           .   0
                                  0   0
    _item_type.code               int
     save_

save__phasing_MIR_shell.reflns_centric
    _item_description.description
;              The number of centric reflections in this shell.
;
    _item.name                  '_phasing_MIR_shell.reflns_centric'
    _item.category_id             phasing_mir_shell
    _item.mandatory_code          no
    _item_aliases.alias_name    '_phasing_MIR_shell.ebi_reflns_centric'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum           .   0
                                  0   0
    _item_type.code               int
     save_

############
## REFINE ##
############
#
############################################################
## proposed additional data items in an existing category ##
############################################################
#
###################################################
## Submitted by Kim Henrick                      ##
## Content review by Dale Tronrud - Mar 19, 1988 ##
## Editorial review by HB, JW and PMDF           ##
###################################################

save__refine.correlation_coeff_Fo_to_Fc
    _item_description.description
;              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>)
  R~corr~ = ------------------------------------------------------------
            SQRT{sum~i~(Fo~i~)^2^-<Fo>^2^} SQRT{sum~i~(Fc~i~)^2^-<Fc>^2^}

               Fo = observed structure factors
               Fc = calculated structure factors
               <> = denotes average value of data

               summation is over reflections included in the refinement
;
    _item.name                  '_refine.correlation_coeff_Fo_to_Fc'
    _item.category_id             refine
    _item.mandatory_code          no
    _item_aliases.alias_name    '_refine.ebi_Correlation_coeff_Fo_to_Fc'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
    _item_type.code               float
     save_

save__refine.correlation_coeff_Fo_to_Fc_free
    _item_description.description
;              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>)
  R~corr~ = ------------------------------------------------------------
            SQRT{sum~i~(Fo~i~)^2^-<Fo>^2^} SQRT{sum~i~(Fc~i~)^2^-<Fc>^2^}

                Fo  = observed structure factors
                Fc  = calculated structure factors
                <>  = denotes average value of data

                summation is over reflections not included (free reflections)
                in the refinement
;
    _item.name                  '_refine.correlation_coeff_Fo_to_Fc_free'
    _item.category_id             refine
    _item.mandatory_code          no
    _item_aliases.alias_name    '_refine.ebi_Correlation_coeff_Fo_to_Fc_free'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
    _item_type.code               float
     save_

save__refine.overall_ESU_B
    _item_description.description
;              The overall standard uncertainty (e.s.d.) of the thermal
               parameters based on a maximum likelihood residual.

               The overall ESU (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
    (sigma~B~)^2  = 8 ----------------------------------------------
                      sum~i~ {(1/Sigma - (E_o)^2 (1-m^2)(SUM_AS)s^4}

               SUM_AS         = (sigma_A)^2/Sigma^2)
               N_a            = number of atoms
               Sigma          = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2)
               E_o            = normalized structure factors
               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              = is form factor of atoms
               delta_x        = expected error
               m              = is figure of merit of phases of reflection
                                included in summation delta_x expected error
               s              = reciprocal space vector
               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.

                    (ESU ML estimation) "Simplified error estimation a la
                    Cruickshank in macromolecular crystallography",
                    Murshudov G. N. & Dodson E. J. (1997). CCP4 Newsletter,
                    no. 33. http://www.dl.ac.uk/CCP/CCP4/newsletter33/
;
    _item.name                  '_refine.overall_ESU_B'
    _item.category_id             refine
    _item.mandatory_code          no
    _item_aliases.alias_name    '_refine.ebi_Overall_ESU_B'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
    _item_type.code               float
     save_

save__refine.overall_ESU_ML
    _item_description.description
;              The overall standard uncertainty (e.s.d.) of the positional
               parameters based on a maximum likelihood residual.

               The overall ESU (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
    (sigma~X~)^2  = -----------------------------------------------------
                    8 pi^2 sum~i~ {(1/Sigma - (E_o)^2 (1-m^2)(SUM_AS)s^2}
  
               SUM_AS         = (sigma_A)^2/Sigma^2)
               N_a            = number of atoms
               Sigma          = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2)
               E_o            = normalized structure factors

               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              = is formfactor of atoms
               delta_x        = expected error
               m              = is figure of merit of phases of reflection
                                included in summation delta_x expected error
               s              = reciprocal space vector
               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.

                    (ESU ML estimation) "Simplified error estimation a la
                    Cruickshank in macromolecular crystallography",
                    Murshudov G. N. & Dodson E. J. (1997). CCP4 Newsletter,
                    no. 33. http://www.dl.ac.uk/CCP/CCP4/newsletter33/
;
    _item.name                  '_refine.overall_ESU_ML'
    _item.category_id             refine
    _item.mandatory_code          no
    _item_aliases.alias_name    '_refine.ebi_Overall_ESU_ML'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
    _item_type.code               float
     save_

save__refine.overall_ESU_R_Cruickshank_DPI
    _item_description.description
;              The overall standard uncertainty (e.s.d.) of the thermal
               parameters based on the crystallographic R value, expressed
               in a formalism known as the dispersion precisions indicator
               (DPI).

               The overall ESU (sigma~B~) 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
               (sigma_B)^2  = 0.65 --------- (R_value)^2 (D_min)^2 C^(-2/3)
                                   (N_o-N_p)


               N_a      = number of atoms
               N_o      = number of reflections included in refinement
               N_p      = number of refined parameters
               R_value  = conventional crystallographic R-value
               D_min    = maximum resolution
               C        = completeness of data

               Ref: Cruickshank, D. W. (1997). "Refinement of macromolecular
                    structures". Proc. CCP4 study weekend.

                    "Simplified error estimation a la Cruickshank in
                    macromolecular crystallography", Murshudov G. N. &
                    Dodson E. J. (1997). CCP4 Newsletter, no. 33.
                    http://www.dl.ac.uk/CCP/CCP4/newsletter33/

;
    _item.name                  '_refine.overall_ESU_R_Cruickshank_DPI'
    _item.category_id             refine
    _item.mandatory_code          no
    _item_aliases.alias_name    '_refine.ebi_Overall_ESU_R_Cruickshanks_DPI'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
    _item_type.code               float
     save_

save__refine.overall_ESU_R_free
    _item_description.description
;              The overall standard uncertainty (e.s.d.) of the thermal
               parameters based on the free R value.

               The overall ESU 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
               (sigma_B)^2  = 0.65 ----- (R_free)^2 (D_min)^2 C^(-2/3)
                                    N_o

               N_a    = number of atoms
               N_o    = number of reflections included in refinement
               N_p    = number of refined parameters
               R_free = conventional free crystallographic R-value calculated
                        using reflections not included in refinement
               D_min  = maximum resolution
               C      = completeness of data

               Ref: Cruickshank, D. W. (1997). "Refinement of macromolecular
                    structures". Proc. CCP4 study weekend.

                    "Simplified error estimation a la Cruickshank in
                    macromolecular crystallography", Murshudov G. N. &
                    Dodson E. J. (1997). CCP4 Newsletter, no. 33.
                    http://www.dl.ac.uk/CCP/CCP4/newsletter33/
;
    _item.name                  '_refine.overall_ESU_R_free'
    _item.category_id             refine
    _item.mandatory_code          no
    _item_aliases.alias_name    '_refine.ebi_Overall_ESU_Rfree'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
    _item_type.code               float
     save_

save__refine.overall_FOM_free_R_set
    _item_description.description
;              Average figure of merit of phases of reflections not included
               in the refinement.

               This value is derived from the likelihood function.

               fom           = I_1(X)/I_0(X)
               I_0, I_1      = zero- and first-order modified Bessel function
                               of the first kind
               X             = sigma_A |E_o| |E_c|/SIGMA
               E_o, E_c      = normalized observed and calculated 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             = formfactor of atoms
               delta_x       = expected error
               SIGMA         = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2)
               sigma_{E;exp} = uncertainties of normalized observed structure
                               factors
               epsilon       = multiplicity of diffracting plane

               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.
;
    _item.name                  '_refine.overall_FOM_free_R_set'
    _item.category_id             refine
    _item.mandatory_code          no
    _item_aliases.alias_name    '_refine.ebi_overall_FOM_free_Rset'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
    _item_type.code               float
     save_

save__refine.overall_FOM_work_R_set
    _item_description.description
;              Average figure of merit of phases of reflections included in
               the refinement.

               This value is derived from the likelihood function.

               fom           = I_1(X)/I_0(X)

               I_0, I_1      = zero- and first-order modified Bessel function
                               of the first kind
               X             = sigma_A |E_o| |E_c|/SIGMA
               E_o, E_c      = normalized observed and calculated 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             = is formfactor of atoms
               delta_x       = expected error
               SIGMA         = (sigma_{E;exp})^2 + epsilon (1-{sigma_A)^2)
               sigma_{E;exp} = uncertainties of normalized observed
                               structure factors
               epsilon       = multiplicity of diffracting plane

               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.
;
    _item.name                  '_refine.overall_FOM_work_R_set'
    _item.category_id             refine
    _item.mandatory_code          no
    _item_aliases.alias_name    '_refine.ebi_overall_FOM_work_Rset'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
    _item_type.code               float
     save_

####################
## REFINE_ANALYZE ##
####################
#
############################################################
## proposed additional data items in an existing category ##
############################################################
#
###################################################
## Submitted by Kim Henrick                      ##
## Content review by Dale Tronrud - Jan 13, 1998 ##
## Editorial review by HB, JW and PMDF           ##
###################################################

save__refine_analyze.RG_d_res_high
    _item_description.description
;              The value of the high-resolution cutoff in angstroms
               used in calculation of the Hamilton generalized
               R factor (RG) stored in refine_analyze.RG_work and
               _refine_analyze.RG_free.

               Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510.
;
    _item.name                  '_refine_analyze.RG_d_res_high'
    _item.category_id             refine_analyze
    _item.mandatory_code          no
    _item_aliases.alias_name    '_refine_analyze.ebi_RG_d_res_high'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum            .    0.0
                                  0.0   0.0
    _item_type.code               float
    _item_units.code              angstroms
     save_

save__refine_analyze.RG_d_res_low
    _item_description.description
;              The value of the low-resolution cutoff in angstroms
	       used in calculation of the Hamilton generalized
               R factor (RG) stored in refine_analyze.RG_work and
               _refine_analyze.RG_free.

               Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510.
;
    _item.name                  '_refine_analyze.RG_d_res_low'
    _item.category_id             refine_analyze
    _item.mandatory_code          no
    _item_aliases.alias_name    '_refine_analyze.ebi_RG_d_res_low'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum            .    0.0
                                  0.0   0.0
    _item_type.code               float
    _item_units.code              angstroms
     save_

save__refine_analyze.RG_free
    _item_description.description
;              The Hamilton generalized R factor for all reflections that
               satisfy the resolution limits established by
               _refine_analyze.RG_d_res_high and
               _refine_analyze.RG_d_res_low for the free R set of
               reflections that were excluded from the refinement.

             sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j)
 Rg = Sqrt( ----------------------------------------------------------------- )
                          sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j               

               where

               |Fobs|  = the observed structure factor amplitudes
               |Fcalc| = the calculated structure factor amplitudes
               G       = the scale factor which puts |Fcalc| on the
                         same scale as |Fobs|
               w_{i,j} = the weight for the combination of the reflections
                         i and j.

               sum_i and sum_j are taken over the specified reflections

               When the covariance of the amplitude of reflection i and
               reflection j is zero (i.e. the reflections are independent)
               w{i,i} can be redefined as  w_i and the nested sums collapsed
               into one.

                           sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2 
               Rg = Sqrt( ----------------------------------- )
                                  sum_i w_i |Fobs|_i^2       

               Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510.
;
    _item.name                  '_refine_analyze.RG_free'
    _item.category_id             refine
    _item.mandatory_code          no
    _item_aliases.alias_name    '_refine_analyze.ebi_RG_free'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum            .    0.0
                                  0.0   0.0
    _item_type.code               float
     save_

save__refine_analyze.RG_work
    _item_description.description
;              The Hamilton generalized R factor for all reflections
               that satisfy the resolution limits established by
               _refine_analyze.RG_d_res_high and
               _refine_analyze.RG_d_res_low  and for those
               reflections included in the working set when a free R set
               of reflections are omitted from the refinement.

             sum_i sum_j w_{i,j}(|Fobs|_i - G|Fcalc|_i)(|Fobs|_j - G|Fcalc|_j)
 Rg = Sqrt( ----------------------------------------------------------------- )
                          sum_i sum_j w_{i,j} |Fobs|_i |Fobs|_j               

               where

               |Fobs|  = the observed structure factor amplitudes
               |Fcalc| = the calculated structure factor amplitudes
               G       = the scale factor which puts |Fcalc| on the
                         same scale as |Fobs|
               w_{i,j} = the weight for the combination of the reflections
                         i and j.

               sum_i and sum_j are taken over the specified reflections

               When the covariance of the amplitude of reflection i and
               reflection j is zero (i.e. the reflections are independent)
               w{i,i} can be redefined as w_i and the nested sums collapsed
               into one.

                           sum_i w_i(|Fobs|_i - G|Fcalc|_i)^2 
               Rg = Sqrt( ----------------------------------- )
                                  sum_i w_i |Fobs|_i^2        

               Ref: Hamilton, W. C. (1965). Acta Cryst. 18, 502-510.
;
    _item.name                  '_refine_analyze.RG_work'
    _item.category_id             refine
    _item.mandatory_code          no
    _item_aliases.alias_name    '_refine_analyze.ebi_RG_work'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum            .    0.0
                                  0.0   0.0
    _item_type.code               float
     save_

save__refine_analyze.RG_free_work_ratio
    _item_description.description
:              The observed ratio of RGfree to RGwork. The expected RG ratio
               is the value that should be achievable at the end of a structure
               refinement when only random uncorrelated errors exist in data
               and model provided that the observations are properly weighted.
               When compared with the observed RG ratio it may indicate that a
               structure has not reached convergence or a model has been
               over-refined with no corresponding improvement in the model.

               In an unrestrained refinement the ratio of RGfree/RGwork with
               only random uncorrelated errors at convergence depends only
               on the number of reflections and the number of parameters as:

                                 sqrt[(f + m) / (f - m) ]

               where f = number of included structure amplitudes and
                         target distances, and
                     m = number of parameters being refined.

               In the restrained case, RGfree is calculated from a random
               selection of residuals including both structure amplitudes
               and restraints.  When restraints are included in refinement
               the RG ratio requires a term for the contribution to the
               minimized residual at convergence, Drest, due to those
               restraints:

                        Drest = r - sum (w_i . (a_i)^t . (H)^-1 a_i

               where

               r is the number of geometrical, temperature factor and
                 other restraints
               H is the (m,m) normal matrix given by A^t.W.A
               W is the (n,n) symmetric weight matrix of the included
                 observations
               A is the least-squares design matrix of derivatives of 
                 order (n,m)
               a_i is the ith row of A

              Then the expected RGratio becomes

                     sqrt [ (f + (m - r + Drest))/ (f - (m - r + Drest)) ]

              The expected RGfree/RGwork is not yet included in the mmCIF
              dictionary.


               Ref: "Rfree and the Rfree ratio. Part I: derivation of expected
                    values of cross-validation residuals used in macromolecular
                    least-squares refinement". Tickle, I. J., Laskowski, R. A.
                    & Moss, D.S. (1998). Acta Cryst. D, in the press.
                    
;
    _item.name                  '_refine_analyze.RG_free_work_ratio'
    _item.category_id             refine_analyze
    _item.mandatory_code          no
    _item_aliases.alias_name    '_refine_analyze.ebi_RG_work_free_ratio'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum            .    0.0
                                  0.0   0.0
    _item_type.code               float
     save_

###############################
## REFINE_FUNCT_MINIMIZED    ##
###############################
#
###########################
## proposed new category ##
###########################
#
###################################################
## Submitted by Kim Henrick                      ##
## Content review by Dale Tronrud - Jan 13, 1998 ##
## Editorial review by HB, JW and PMDF           ##
###################################################

save_REFINE_FUNCT_MINIMIZED
    _category.description
;              Data items in the REFINE_FUNCT_MINIMIZED category record
               details about the individual terms of the function minimized
               during refinement.
;
    _category.id                 refine_funct_minimized
    _category.mandatory_code     no
    _category_key.name          '_refine_funct_minimized.type'
     loop_
    _category_group.id           'inclusive_group'
                                 'refine_group'
     loop_
    _category_examples.detail
    _category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
    Example 1 - based on RESTRAIN refinement for the CCP4 text data set
                toxd.
;
;
     loop_
    _refine_funct_minimized.type
    _refine_funct_minimized.number_terms
    _refine_funct_minimized.residual
    'sum(W*Delta(Amplitude)^2'               3009      1621.3
    'sum(W*Delta(Plane+Rigid)^2'               85       56.68
    'sum(W*Delta(Distance)^2'                1219      163.59
    'sum(W*Delta(U-tempfactors)^2'           1192      69.338
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     save_

save__refine_funct_minimized.number_terms
    _item_description.description
;              The number of observations in this term.  For example, if the
               term is a residual of the X-ray data this item would contain
               the number of reflections used in the refinement.
;
    _item.name                  '_refine_funct_minimized.number_terms'
    _item.category_id             refine_funct_minimized
    _item.mandatory_code          no
    _item_aliases.alias_name    '_ebi_refine_funct_minimized.NumTerms'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum           .   0
                                  0   0
    _item_type.code               int
     save_

save__refine_funct_minimized.residual
    _item_description.description
;              The residual for this term of the function which was minimized
               in refinement.
;
    _item.name                  '_refine_funct_minimized.residual'
    _item.category_id             refine_funct_minimized
    _item.mandatory_code          no
    _item_aliases.alias_name    '_ebi_refine_funct_minimized.Residual'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_range.maximum
    _item_range.minimum            .    0.0
                                  0.0   0.0
    _item_type.code               float
     save_

save__refine_funct_minimized.type
    _item_description.description
;              The type of the function being minimized.
;
    _item.name                  '_refine_funct_minimized.type'
    _item.category_id             refine_funct_minimized
    _item.mandatory_code          yes
    _item_aliases.alias_name    '_ebi_refine_funct_minimized.type'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
    _item_type.code               line
     save_

save__refine_funct_minimized.weight
    _item_description.description
;              The weight applied to this term of the function which was
               minimized in the refinement.
;
    _item.name                  '_refine_funct_minimized.weight'
    _item.category_id             refine_funct_minimized
    _item.mandatory_code          no
    _item_aliases.alias_name    '_ebi_refine_funct_minimized.weight'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
    _item_type.code               float
     save_

#####################
## REFINE_LS_RESTR ##
#####################
#
###################################################
## proposed elaboration of an existing data item ##
###################################################
#
####################################################
## Submitted by Kim Henrick                       ##
## Content review by John Westbrook               ##
## Kim Henrick approval of changes - Jan 22, 1998 ##
## Editorial review by HB, JW and PMDF            ##
####################################################

save__refine_ls_restr.type
    _item_description.description
;              The type of the parameter being restrained.

               An explicit set of data values is provided for the programs
               Protin/ Prolsq (beginning with p_) and X-plor (beginning with
               x_). As computer programs will evolve, these data values
               are given as examples, and not as an enumeration list. Computer
               programs converting a data block to a refinement table will
               expect the exact form of the data values given here to be used.
;
     loop_
    _item.name
    _item.category_id
    _item.mandatory_code
        '_refine_ls_restr.type'       refine_ls_restr        yes
        '_refine_ls_restr_type.type'  refine_ls_restr_type   yes
     loop_
    _item_linked.child_name
    _item_linked.parent_name
               '_refine_ls_restr_type.type'  '_refine_ls_restr.type'
    _item_type.code               line
     loop_
    _item_examples.case
    _item_examples.detail        'p_bond_d'
                                 'bond distance'
                                 'p_angle_d'
                                 'bond angle expressed as a distance'
                                 'p_planar_d'
                                 'planar 1,4 distance'
                                 'p_xhbond_d'
                                 'x-h bond distance'
                                 'p_xhangle_d'
                                 'x-h bond angle expressed as a distance'
                                 'p_hydrog_d'
                                 'hydrogen distance'
                                 'p_special_d'
                                 'special distance'
                                 'p_planar'
                                 'planes'
                                 'p_chiral'
                                 'chiral centers'
                                 'p_singtor_nbd'
                                 'single-torsion non-bonded contact'
                                 'p_multtor_nbd'
                                 'multiple-torsion non-bonded contact'
                                 'p_xyhbond_nbd'
                                 'possible (x...y) hydrogen-bond'
                                 'p_xhyhbond_nbd'
                                 'possible (x-h...y) hydrogen-bond'
                                 'p_special_tor'
                                 'special torsion angle'
                                 'p_planar_tor'
                                 'planar torsion angle'
                                 'p_staggered_tor'
                                 'staggered torsion angle'
                                 'p_orthonormal_tor'
                                 'orthonormal torsion angle'
                                 'p_mcbond_it'
                                 'main-chain bond isotropic thermal factor'
                                 'p_mcangle_it'
                                 'main-chain angle isotropic thermal factor'
                                 'p_scbond_it'
                                 'side-chain bond isotropic thermal factor'
                                 'p_scangle_it'
                                 'side-chain angle isotropic thermal factor'
                                 'p_xhbond_it'
                                 'x-h bond isotropic thermal factor'
                                 'p_xhangle_it'
                                 'x-h angle isotropic thermal factor'
                                 'p_special_it'
                                 'special isotropic thermal factor'
    'RESTRAIN_Distances < 2.12'
;  For the program RESTRAIN, the root-mean-square deviation
   of the difference between the values calculated from the structures
   used to compile the restraints dictionary parameters and the dictionary
   values themselves in the distance range less than 2.12 Angtroms.
;
    'RESTRAIN_Distances 2.12 < D < 2.625'
;  For the program RESTRAIN, the root-mean-square deviation
   of the difference between the values calculated from the structures
   used to compile the restraints dictionary parameters and the dictionary
   values themselves in the distance range 2.12 - 2.625 Angtroms.
;
    'RESTRAIN_Distances > 2.625'
;  For the program RESTRAIN, the root-mean-square deviation
   of the difference between the values calculated from the structures
   used to compile the restraints dictionary parameters and the dictionary
   values themselves in the distance range greater than 2.625 Angtroms.
;
    'RESTRAIN_Peptide Planes'
;  For the program RESTRAIN, the root-mean-square deviation
   of the difference between the values calculated from the structures
   used to compile the restraints dictionary parameters and the dictionary
   values themselves for peptide planes.
;
    'RESTRAIN_Ring and other planes'
;  For the program RESTRAIN, the root-mean-square deviation
   of the difference between the values calculated from the structures
   used to compile the restraints dictionary parameters and the dictionary
   values themselves for rings and planes other than peptide planes.
;
    'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.2-1.4'
    .
    'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.4-1.6'
    .
    'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.8-2.0'
    .
    'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.0-2.2'
    .
    'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.2-2.4'
    .
    'RESTRAIN_r.m.s. diffs for Uiso atoms at dist >2.4'
    .
     save_

###########################
## REFINE_LS_RESTR_TYPE  ##
###########################
#
###########################
## proposed new category ##
###########################
#
####################################################
## Submitted by Kim Henrick                       ##
## Content review by John Westbrook               ##
## Kim Henrick approval of changes - Jan 22, 1998 ##
## Editorial review by HB, JW and PMDF            ##
####################################################

save_REFINE_LS_RESTR_TYPE
    _category.description
;              Data items in the REFINE_LS_RESTR_TYPE category record details
               about the restraints types used in the least-squares refinement.
;
    _category.id                  refine_ls_restr_type
    _category.mandatory_code      no
    _category_key.name          '_refine_ls_restr_type.type'
     loop_
    _category_group.id           'inclusive_group'
                                 'refine_group'
     loop_
    _category_examples.detail
    _category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
    Example 1 - based on RESTRAIN refinement for the CCP4 text data set
                toxd.
;
;
loop_
_refine_ls_restr.type
_refine_ls_restr.number
_refine_ls_restr.dev_ideal
_refine_ls_restr.dev_ideal_target
 'RESTRAIN_Distances < 2.12'                               509     0.005 0.022
 'RESTRAIN_Distances 2.12 < D < 2.625'                     671     0.016 0.037
 'RESTRAIN_Distances > 2.625'                              39      0.034 0.043
 'RESTRAIN_Peptide Planes'                                 59      0.002 0.010
 'RESTRAIN_Ring and other planes'                          26      0.014 0.010
 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.2-1.4'    212     0.106     .
 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.4-1.6'    288     0.101     .
 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.8-2.0'    6       0.077     .
 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.0-2.2'    10      0.114     .
 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.2-2.4'    215     0.119     .
 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist >2.4'       461     0.106     .

loop_
_refine_ls_restr_type.type
_refine_ls_restr_type.distance_cutoff_low
_refine_ls_restr_type.distance_cutoff_high
_refine_ls_restr_type.U_sigma_weights
 'RESTRAIN_Distances < 2.12'                              .     2.12       .
 'RESTRAIN_Distances 2.12 < D < 2.625'                    2.12  2.625      .
 'RESTRAIN_Distances > 2.625'                             2.625 .          .
 'RESTRAIN_Peptide Planes'                                .     .          .
 'RESTRAIN_Ring and other planes'                         .     .          .
 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.2-1.4'   1.2   1.4        1.800



 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.4-1.6'   1.4   1.6        1.800



 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 1.8-2.0'   1.8   2.0        1.800



 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.0-2.2'   2.0   2.2        1.800



 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist 2.2-2.4'   2.2   2.4        1.800



 'RESTRAIN_r.m.s. diffs for Uiso atoms at dist >2.4'      2.4   .          1.800



;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     save_

save__refine_ls_restr_type.distance_cutoff_high
    _item_description.description
;              The upper limit in angstroms of the distance range applied to
               the current restraint type.
;
    _item.name                  '_refine_ls_restr_type.distance_cutoff_high'
    _item.category_id             refine_ls_restr_type
    _item.mandatory_code          no
     loop_
    _item_range.maximum
    _item_range.minimum            .    0.0
                                  0.0   0.0
    _item_type.code               float
    _item_units.code              angstroms
     save_

save__refine_ls_restr_type.distance_cutoff_low
    _item_description.description
;              The lower limit in angstroms of the distance range applied to
               the current restraint type.
;
    _item.name                  '_refine_ls_restr_type.distance_cutoff_low'
    _item.category_id             refine_ls_restr_type
    _item.mandatory_code          no
     loop_
    _item_range.maximum
    _item_range.minimum            .    0.0
                                  0.0   0.0
    _item_type.code               float
    _item_units.code              angstroms
     save_

save__refine_ls_restr_type.type
    _item_description.description
;              This data item is a pointer to _refine_ls_restr.type in the
               REFINE_LS_RESTR category.
;

    _item.name                  '_refine_ls_restr_type.type'
    _item.category_id             refine_ls_restr_type
    _item.mandatory_code          yes
    _item_type.code               line
     save_

###################
## REFLN_SYS_ABS ##
###################
#
###########################
## proposed new category ##
###########################
#
#########################################
## Submitted by Kim Henrick            ##
## Content review by Paula Fitzgerald  ##
## Editorial review by HB, JW and PMDF ##
#########################################

save_REFLN_SYS_ABS
    _category.description
;              Data items in the REFLN_SYS_ABS category record details about
               the reflection data that should be systematically absent,
               given the designated space group.
;
    _category.id                  refln_sys_abs
    _category.mandatory_code      no
     loop_
    _category_key.name          '_refln_sys_abs.index_h'
                                '_refln_sys_abs.index_k'
                                '_refln_sys_abs.index_l'
     loop_
    _category_group.id           'inclusive_group'
                                 'refln_group'
     loop_
    _category_examples.detail
    _category_examples.case
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
;
    Example 1 - completely arbitrary
;
;
     loop_
    _refln_sys_abs.index_h
    _refln_sys_abs.index_k
    _refln_sys_abs.index_l
    _refln_sys_abs.I
    _refln_sys_abs.sigmaI
    _refln_sys_abs.I_over_sigmaI
     0  3  0   28.32  22.95  1.23
     0  5  0   14.11  16.38  0.86
     0  7  0  114.81  20.22  5.67
     0  9  0   32.99  24.51  1.35
;
# - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
     save_

save__refln_sys_abs.I
    _item_description.description
;              The measured value of the intensity in arbitrary units.
;
    _item.name                  '_refln_sys_abs.I'
    _item.category_id             refln_sys_abs
    _item.mandatory_code          no
    _item_aliases.alias_name    '_ebi_refln_sys_abs.I'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_related.related_name
    _item_related.function_code '_refln_sys_abs.sigmaI'
                                  associated_esd
    _item_type.code               float
    _item_type_conditions.code    esd
    _item_units.code              arbitrary
     save_

save__refln_sys_abs.I_over_sigmaI
    _item_description.description
;              The ratio of _refln_sys_abs.I to _refln_sys_abs.sigmaI.  Used
               to evaluate whether a reflection that should be systematically
               absent according to the designated space group is in fact
               absent.
;
    _item.name                  '_refln_sys_abs.I_over_sigmaI'
    _item.category_id             refln_sys_abs
    _item_aliases.alias_name    '_ebi_refln_sys_abs.I_over_sigma'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
    _item.mandatory_code          no
    _item_type.code               float
     save_

save__refln_sys_abs.index_h
    _item_description.description
;              Miller index h of the reflection. The values of the Miller
               indices in the REFLN_SYS_ABS category must correspond to
               the cell defined by cell lengths and cell angles in the CELL
               category.
;
    _item.name                  '_refln_sys_abs.index_h'
    _item.category_id             refln_sys_abs
    _item.mandatory_code          yes
    _item_aliases.alias_name    '_ebi_refln_sys_abs.h'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_dependent.dependent_name
                                '_refln_sys_abs.index_k'
                                '_refln_sys_abs.index_l'
    _item_sub_category.id         miller_index
    _item_type.code               int
     save_

save__refln_sys_abs.index_k
    _item_description.description
;              Miller index k of the reflection. The values of the Miller
               indices in the REFLN_SYS_ABS category must correspond to the
               cell defined by cell lengths and cell angles in the CELL
               category.
;
    _item.name                  '_refln_sys_abs.index_k'
    _item.category_id             refln_sys_abs
    _item.mandatory_code          yes
    _item_aliases.alias_name    '_ebi_refln_sys_abs.k'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_dependent.dependent_name
                                '_refln_sys_abs.index_h'
                                '_refln_sys_abs.index_l'
    _item_sub_category.id         miller_index
    _item_type.code               int
save_

save__refln_sys_abs.index_l
    _item_description.description
;              Miller index l of the reflection. The values of the Miller
               indices in the REFLN_SYS_ABS category must correspond to the
               cell defined by cell lengths and cell angles in the CELL
               category.
;
    _item.name                  '_refln_sys_abs.index_l'
    _item.category_id             refln_sys_abs
    _item.mandatory_code          yes
    _item_aliases.alias_name    '_ebi_refln_sys_abs.l'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_dependent.dependent_name
                                '_refln_sys_abs.index_h'
                                '_refln_sys_abs.index_k'
    _item_sub_category.id         miller_index
    _item_type.code               int
     save_

save__refln_sys_abs.sigmaI
    _item_description.description
;              The standard uncertainty (e.s.d.) of _refln_sys_abs.I, in
               arbitrary units.
;
    _item.name                  '_refln_sys_abs.sigmaI'
    _item.category_id             refln_sys_abs
    _item.mandatory_code          no
    _item_aliases.alias_name    '_ebi_refln_sys_abs.sigmaI'
    _item_aliases.dictionary      ebi_extensions
    _item_aliases.version         1.0
     loop_
    _item_related.related_name
    _item_related.function_code '_ebi_refln_sys_abs.I'
                                  associated_value
    _item_type.code               float
    _item_units.code              arbitrary
     save_

####
******************************************************************
  John Westbrook                                   
  Rutgers, The State University of New Jersey      
  Department of Chemistry                          
  610 Taylor Road                                  
  Piscataway, NJ 08854-8087      
  e-mail: jwest@rcsb.rutgers.edu                    
  Ph:  (732) 445-4290  Fax: (732) 445-4320         
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