data validation procedures

PROC-NAME: FORMU01 Type_1/2

PURPOSE: To check that the total sum formulae derived from the _chemical_formula_sum _chemical_formula_moiety, _atom_site_ and _atom_type_ data all match.

PROCEDURE:

CALCULATE

(1). Sum formula derived from the _chemical_formula_moiety using the rules in the CIF-dictionary. Type_1
(2). Sum formula from the _atom_site_ items taking into account the _atom_site_occupancy and symmetry as appropriate. Type_1
(3). Sum formula from the _atom_type_ items (if present). Type_2

TEST

IF the atom count is > 0.01 atom, from that given by the _chemical_formula_sum
THEN issue a General ALERT
For (1)
"There is a discrepancy between the atom counts in the _chemical_formula_sum and _chemical_formula_moiety. This is usually due to the moiety formula being in the wrong format."

_chemical_formula_moiety has the identical format to _chemical_formula_sum, namely C, H, then alphabetical, with the exception that the individual unconnected independent entities in the structure are listed separately. A common mistake is to attempt to depict organometallic coordination with this entry. Such coordination can be given under _chemical_formula_structural or _chemical_formula_IUPAC if desired, but must never be given as _chemical_formula_moiety. Furthermore, do not use subscript formatting: C10 H20 is correct, C~10~ H~20~ is not. Nesting of parentheses is also not allowed.

Correct examples:
_chemical_formula_moiety   'C7 H4 Cl Hg N O3 S'
_chemical_formula_moiety   'C12 H17 N4 O S 1+, C6 H2 N3 O7 1-'
_chemical_formula_moiety   'C12 H16 N2 O6, 5(H2 O1)'
_chemical_formula_moiety   '(Cd 2+)3, (C6 N6 Cr 3-)2, 2(H2 O)'

Formulae like '[Co Re (C12 H22 P)2 (C O)6].0.5C H3 O H' and '(Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2' are INCORRECT for _chemical_formula_moiety.
However these can be given as:
_chemical_formula_IUPAC '[Co Re (C12 H22 P)2 (C O)6].0.5(C H3 O H)'
_chemical_formula_structural '(Pt (N H3)2 (C5 H7 N3 O)2) (Cl O4)2'

If _chemical_formula_moiety has been given in the correct style, then there is a discrepancy between the atom counts in one or more of the moieties and the total calculated over all moieties. Check that there is not a typographical error in _chemical_formula_moiety and _chemical_formula_sum and that the actual moieties present in the structure have been interpreted correctly.

Both _chemical_formula_moiety and _chemical_formula_sum must correspond with the true species present, including any solvent, and not the contents implied by the model if there are differences due to the omission of a few H atoms or solvent atoms.

If multiple moieties such as solvent are present, or one of the moieties possesses or is disordered about a crystallographic symmetry element, ensure that the correct ratio of moieties has been allowed for in the calculation of Z, _chemical_formula_moiety and _chemical_formula_sum.

For (2)
"There is a discrepancy between the atom counts in the _chemical_formula_sum and the formula from the _atom_type* data."

There is a discrepancy between the total number of each element in the unit cell calculated from Z * _chemical_formula_sum and that given in the loop structure:
loop_
   _atom_type_symbol
   _atom_type_description
   _atom_type_number_in_cell

Check that the entries under _cell_formula_units_Z, _chemical_formula_sum and in the above loop are given correctly and completely. _chemical_formula_sum must correspond with the true sum of all elements in all distinct moieties present, including any solvent and all H atoms, and not the contents implied by the model if there are differences due to the omission of a few H atoms or solvent atoms. Similarly, the atom_type_* loop must indicate the total number of each element type expected to be present in the entire unit cell, including all solvent and H atoms.

_chemical_formula_sum must also be in the correct format (e.g. do not use subscript formatting: C10 H20 is correct, C~10~ H~20~ is not).

For (3)
"There is a discrepancy between the atom counts in the _chemical_formula_sum and the formula from the _atom_site* data."

There is a difference between the atom count derived from _chemical_formula_sum and from the _atom_site_ list (i.e the list of atomic coordinates). Check that _chemical_formula_sum is given correctly and in the correct format (e.g. do not use subscript formatting: C10 H20 is correct, C~10~ H~20~ is not).

Of course, _chemical_formula_sum must correspond with the true sum of all elements in all distinct moieties present, including any solvent and all H atoms, and not the contents implied by the model if there are differences due to the omission of a few H atoms or solvent atoms. In this case, this message can be ignored. However, be sure that the model is indeed otherwise complete and that no elements have been misassigned.

However, this alert could also be an indication of overlooked errors in the model. Be sure that the model is indeed as complete as intended and that no elements have been misassigned.

Also check that the atom site occupancy is correct for the atomic coordinates otherwise a mismatch may be encountered [e.g an atom on a 2-fold axis normally has a site occupancy of 1.0 (but a multiplicity of 0.5)]. Furthermore, the site occupancy for disordered atomic sites should always sum to 1.0 when all of the alternative disordered sites are considered.

PROC-NAME: ABSMU01 Type_1

PURPOSE: To check that _exptl_absorpt_coefficient_mu value is consistent with the cell contents.

PROCEDURE:

SUMMATION

(1) match _atom_type_symbol with element symbol in table of atomic abs coefficients and extract the AMU value for _diffrn_radiation_type.

IF _diffrn_radiation_type is not identified, issue a General ALERT
"Calculation of _exptl_absorpt_correction_mu not performed for this radiation type."

Only Mo, Cu and Ag radiation is recognized by CHECKCIF for these purposes; wavelengths from other X-ray tubes, synchrotrons or neutrons will cause the calculation of _exptl_absorpt_correction_mu to be skipped.

If you are using Mo, Cu or Ag radiation, but this is not recognised, the format of your keyword entry for _diffrn_radiation_type may be incorrect. The correct format for _diffrn_radiation_type is 'Mo K\a', 'Cu K\a' or 'Ag K\a'.

[Attached are AMU values by Z for CuK\a, MoK\a and AgK\a]

>>> AMU for CuK\a in barn/atom (INT TAB VOL C P193-198)

[.0655, .194, .576, 1.66, 4.15, 8.99, 17.3, 30.4, 49.8, 76.8, 114., 161., 222., 297., 388., 497., 624., 772., 940., 1130., 1350., 1590., 1850., 2130., 2460., 2800., 3140., 476., 547., 629., 719., 819., 929., 1050., 1180., 1320., 1480., 1650., 1830., 2030., 2230., 2460., 2700., 2950., 3230., 3520., 3820., 4150., 4500., 4860., 5250., 5650., 6070., 6520., 7000., 7500., 8030., 8570., 9120., 9680., 10200., 10800., 11000., 10500., 8470., 9770., 3470., 3670., 3930., 4100., 4500., 4600., 4850., 5130., 5720., 5800., 6240., 6340., 6690., 6680., 7540., 7980., 8430., 8810., 8650., 9720., 10200., 10200., 14300., 11800., 10600., 11200.]

>>> AMU for MoK\a in barn/atom (INT TAB VOL C P193-198)

[.0624, .134, .228, .383, .661, 1.15, 1.96, 3.25, 5.15, 7.86, 11.6, 16.5, 22.9, 31., 41., 53.2, 67.8, 85.1, 105., 129., 156., 186., 220., 258., 302., 349., 401., 457., 518., 586., 660., 738., 822., 911., 1000., 1100., 1210., 1320., 1430., 247., 273., 300., 332., 364., 399., 436., 476., 518., 563., 611., 662., 716., 773., 834., 898., 965., 1040., 1110., 1190., 1270., 1350., 1440., 1540., 1630., 1740., 1840., 1950., 2070., 2190., 2310., 2440., 2580., 2720., 2860., 3010., 3160., 3310., 3480., 3650., 3820., 4010., 4190., 4380., 4580., 4070., 3980., 3220., 3300., 5400., 3700., 3870., 4030.]

>>> AMU for AgK\a in barn/atom (INT TAB VOL C P193-198)

[.0614, .128, .206, .313, .479, .745, 1.17, 1.82, 2.77, 4.12, 5.96, 8.42, 11.6, 15.6, 20.6, 26.7, 34.1, 42.9, 53.2, 65.2, 78.9, 94.7, 112., 133., 155., 180., 207., 238., 271., 307., 346., 387., 433., 482., 535., 592., 652., 715., 780., 847., 922., 1150., 1070., 192., 210., 230., 251., 273., 297., 323., 350., 378., 409., 441., 475., 511., 549., 588., 630., 674., 720., 768., 819., 872., 927., 985., 1040., 1110., 1170., 1240., 1310., 1390., 1460., 1540., 1620., 1710., 1800., 1890., 1990., 2090., 2190., 2290., 2400., 2510., 2620., 2730., 2850., 2980., 3110., 3230., 3420., 3500.]

(2) SUM
TOTAMU = AMU * <number of each type in cell>

(3) CALCULATE

MU = 10 * TOTAMU / _cell_volume (ie. mu/mm)

RMU = _exptl_absorpt_coefficient_mu / MU

TEST

IF RMU is 0.90 <> 1.10 issue ALERT A
   "Alert A The ratio of given/expected absorption coefficient lies outside the range 0.90 <> 1.10"
0.95 <> 1.05 issue ALERT B
   "Alert B The ratio of given/expected absorption coefficient lies outside the range 0.95 <> 1.05"
0.99 <> 1.01 issue ALERT C
   "Alert C The ratio of given/expected absorption coefficient lies outside the range 0.99 <> 1.01"

This alert does not imply that you need to apply an absorption correction or that your absorption correction is inappropriate in any way. It indicates that your value of the linear absorption coefficient (_exptl_absorpt_correction_mu) in the CIF does not agree with the value calculated from your given unit cell volume and the total number of each element type in the unit cell.

Small differences between your value and the predicted value may arise if your software uses an older (e.g. Int. Tables, Vol. IV, 1974) or a different source of the mass attenuation coefficients. CHECKCIF uses the photon interaction cross sections for the elements given in Int. Tables, Vol. C, 1992, Table 4.2.4.2, pp. 193-198.

Other differences between your value and the predicted value will arise if the unit cell volume, Z or _chemical_formula_sum in your CIF is different from that used to obtain your value of mu. Don't forget that _chemical_formula_sum must correspond with the true sum of all elements in all distinct moieties present, including any solvent and all H atoms, and not the contents implied by the model if there are differences due to the omission of a few H atoms or solvent atoms.

PROC-NAME: ABSTY01 Type_1

PURPOSE: To check that _exptl_absorpt_correction_type is one of the recognised keywords.

CHECKLIST:

none (none applied)
analytical (analytical from crystal shape)
integration (integration from crystal shape)
numerical (numerical from crystal shape)
gaussian (Gaussian from crystal shape)
empirical (psi-scan of intensities)
psi-scan (psi-scan of intensities)
multi-scan (symmetry-related measurements)
refdelf (refined from delta-F)
sphere (spherical)
cylinder (cylindrical)

Otherwise issue ALERT A
"Alert A The absorption correction doesn't match a standard keyword"

IF extra text has been entered issue General ALERT
"Extra text has been found in the _exptl_absorpt_correction_type field, which should be only a single keyword. A literature citation should be included in the _exptl_absorpt_process_details field."

Use ONLY one of the specified keywords and no other text under _exptl_absorpt_correction_type. Note that psi-scans should be indicated as 'psi-scan' and not as '\f-scan'. The citation should be in parentheses in the usual citation format.

Example:
_exptl_absorpt_correction_type psi-scan
_exptl_absorpt_process_details '(North et al., 1968)'

PROC-NAME: ABSTY02 Type_1

PURPOSE: To check that _exptl_absorpt_correction_type contains some reference text.

PROCEDURE:
TEST

IF _exptl_absorpt_correction_type !~ 'Ref:'
OR _exptl_absorpt_process_details is missing
issue ALERT C
"Alert C An _exptl_absorpt_correction_type has been given without a literature citation. This should be contained in the _exptl_absorpt_process_details field."

A literature citation to the absorption correction method must be provided. However, do not append this to the keyword given with _exptl_absorpt_correction_type. There is a separate data name entry for the citation which is _exptl_absorpt_process_details. The citation should be in parentheses in the usual citation format.

Example:
_exptl_absorpt_correction_type psi-scan
_exptl_absorpt_process_details '(North et al., 1968)'

PROC-NAME: CELLK01 Type_1

PURPOSE: To check that _cell_measurement_temperature has the correct units ie. Kelvin rather than Celsius.

PROCEDURE:
TEST

IF _cell_measurement_temperature < 25
issue ALERT C (may be in Celsius units).
"Alert C Check that the cell measurement temperature is in Kelvin."

Check that the temperature has been given in the correct units, i.e. Kelvin.

PROC-NAME: CELLT01 Type_1

PURPOSE: To check that _cell_measurement_theta_min is less than _cell_measurement_theta_max.

PROCEDURE:
TEST

IF _cell_measurement_theta_min >= _cell_measurement_theta_max
issue ALERT A
"Alert A The minimum theta value cannot exceed the maximum value."

The minimum theta value cannot exceed the maximum value. Either there is a typographical error or the values under _cell_measurement_theta_min and _cell_measurement_theta_max have accidentally been reversed.

PROC-NAME: CELLV01 Type_1

PURPOSE: To check that the _cell_volume matches _cell_length_ and _cell_angle_ values.

PROCEDURE:

CALCULATE

S = { _cell_angle_alpha + _cell_angle_beta + _cell_angle_gamma } / 2

VOL = _cell_length_a * _cell_length_b * _cell_length_c * 2 *
SQRT { SIN [S] * SIN [S - _cell_angle_alpha ] * SIN [S - _cell_angle_beta ] * SIN [S - _cell_angle_gamma ] }

RV = _cell_volume / VOL

TEST

IF RV is 0.999 <> 1.001 issue ALERT A
"Alert A The supplied cell volume differs from that calculated from the cell parameters. Ratio outside the range 0.999 < > 1.001"

There is a discrepancy between the unit cell volume given in the CIF and that calculated from the unit cell dimensions given in the CIF. Check the volume and cell dimensions for typographical errors.

PROC-NAME: CELLV02 Type_1

PURPOSE: To check that the _cell_volume su matches _cell_length_ and _cell_angle_ su values.

PROCEDURE: (Ref: Giacovazzo Fundamentals of Crystallography p.122)

CALCULATE

CSA = COSINE [ _cell_angle_alpha ]
CSB = COSINE [ _cell_angle_beta ]
CSG = COSINE [ _cell_angle_gamma ]

SA = SINE [ _cell_angle_alpha ]
SB = SINE [ _cell_angle_beta ]
SG = SINE [ _cell_angle_gamma ]

A1 = (su of a)/_cell_length_a
A2 = (su of b)/_cell_length_b
A3 = (su of c)/_cell_length_c

B1 = SA*(CSA-CSB*CSG)*(su of alpha)
B2 = SB*(CSB-CSA*CSG)*(su of beta)
B3 = SG*(CSG-CSA*CSB)*(su of gamma)

CV = [ ( _cell_length_a * _cell_length_b * _cell_length_c )**4 / (_cell_volume)**2 ]

SUVOL = SQRT {
(_cell_volume)**2 * (A1**2 + A2**2 + A3**2)
+ CV*(B1**2 + B2**2 +B3**2)}

DSUV = |{su of cell volume} - SUVOL |

TEST

IF DSUV > 8 issue ALERT A
   "Alert A The supplied cell volume s.u. differs from that calculated from the cell parameter s.u.'s by > 8"
DSUV > 4 issue ALERT B
   "Alert B The supplied cell volume s.u. differs from that calculated from the cell parameter s.u.'s by > 4"
DSUV > 2 issue ALERT C
   "Alert C The supplied cell volume s.u. differs from that calculated from the cell parameter s.u.'s by > 2"

There is a discrepancy between the standard uncertainty (s.u.) for the unit cell volume given in the CIF and that calculated from the s.u.s of the unit cell dimensions given in the CIF. Check the volume and cell dimension s.u.s for typographical errors (rule of '19' applies).

PROC-NAME: CELLZ01 Type_1

PURPOSE: To check that the cell contents calculated from _chemical_formula_sum and _cell_formula_units_Z matches that from the atom sites present in the _atom_site_ list and the _symmetry_ information.

PROCEDURE:

SUMMATION

(1) For each atomic species in the _chemical_formula_sum string, calculate the number of atoms in the cell using the _chemical_formula_sum counts and the _cell_formula_units_Z.

(2) For each atomic species in the _atom_site_ list, calculate, using the _atom_site_occupancy value and the symmetry site-multiplicity value (generated from NSYM), the number of atoms in the cell.

CALCULATE

DN = [cell contents from (1)] - [cell contents from (2)] for each atom type

SUMDN = sum of DN for ALL atom species

TEST

IF atom counts in (1) differ from those declared in the _atom_type_ list (if present) issue General ALERT
"WARNING: Cell contents from the formula and atom_type data differ!"

There is a discrepancy between the total number of each element in the unit cell calculated from Z * _chemical_formula_sum and that given in the loop structure:
loop_
_atom_type_symbol
_atom_type_description
_atom_type_number_in_cell

_chemical_formula_sum must also be in the correct format (e.g. do not use subscript formatting: C10 H20 is correct, C~10~ H~20~ is not).

IF H-M space group mismatches Hall symbol issue General ALERT
"Input H-M symbol mismatch with Hall symbol"

Check that the entries given under _symmetry_space_group_name_H-M and _symmetry_space_group_name_Hall refer to the same space group and setting and do not have typographical errors. Note that space group symbols under _symmetry_space_group_name_H-M should not have typesetting formatting included (e.g. subscripts).

Example:
The following is the strictly correct way to represent space group 14.
_symmetry_space_group_name_H-M 'P 1 21/c 1'

Also interpreted correctly by CHECKCIF is:
_symmetry_space_group_name_H-M 'P 21/c'

Incorrect are:
_symmetry_space_group_name_H-M 'P 2(1)/c'
_symmetry_space_group_name_H-M 'P 2~1~/c'

IF SUMDN > 0.05 issue the General ALERT
"Difference between formula and atom_site contents detected."

AND THEN

IF SUMDN < 0.5 issue the General ALERT
"ALERT: Check formula stoichiometry or atom site occupancies."

_chemical_formula_sum must also be in the correct format (e.g. do not use subscript formatting: C10 H20 is correct, C~10~ H~20~ is not).

IF DN for Hydrogen atoms > 0.5 issue the General ALERT
"WARNING: H atoms missing from atom site list. Is this intentional?"

H atoms must be included in the model as far as possible. Exceptions might be where the H atoms cannot be located and their positions cannot otherwise be calculated or predicted from geometrical considerations. For example, with solvent or coordinated water H atoms or in severely disordered groups or solvent molecules.

ELSE issue the General ALERT
"ALERT: Large difference may be due to symmetry error - see SYMMG tests."

PROC-NAME: CHEMS01 Type_1

PURPOSE: To check that the _chemical_formula_sum is properly constructed. i.e. C H followed by alphabetic.

PROCEDURE:

Read the _chemical_formula_sum and check that the formula is in the order, carbon count, hydrogen count followed by the other elements in alphabetic order.
IF _chemical_formula_sum contains an invalid character then issue ALERT B
   "Alert B The sum formula contains an invalid character."
IF _chemical_formula_sum contains more than one moiety then issue ALERT A
   "Alert A The sum formula contains more than one moiety."
IF _chemical_formula_sum contains an invalid element symbol then issue ALERT A
   "Alert A The sum formula contains an invalid element symbol."
IF _chemical_formula_sum contains elements in the wrong order then issue ALERT B
   "Alert B The sum formula contains elements in the wrong order. Sequence must be C, H, then alphabetical for organics or metal-organics."
OR
   "Alert B The sum formula contains elements in the wrong order. Sequence must alphabetical for inorganics."

The _chemical_formula_sum must contain just one sequence of elements (i.e. not separated into moieties) in the order C, H, then alphabetical. Do not use any special formatting characters, such as subscripts (e.g. C10 H20 is correct, C~10~ H~20~ is not). There is no space between an element and its count, but there is a space before the next element. Enclose the string in quotes.

Example:
_chemical_formula_sum 'C18 H19 N7 O8 S'

PROC-NAME: CHEMS02 Type_1

PURPOSE: To check that the stated category _publ_requested_category is consistent with the chemical formula of the compound.

PROCEDURE:

If compound contains no C then inorganic.
If compound contains C but no H, probably inorganic.
If compound contains C, H and a metal then metalorganic.
If compound contains C, H and no metal then organic.

IF the _publ_requested_category doesn't match the deduced category then issue a General ALERT for author to cross check
"Please check that you have entered the correct _publ_requested_category classification of your compound; FI or CI for inorganic; FM or CM for metal-organic; FO or CO for organic."

PROC-NAME: CHEMW01 Type_1

PURPOSE: To check that the _chemical_formula_weight matches that calculated for the _chemical_formula_sum .

PROCEDURE:

SUMMATION

(1) match the element symbols in _chemical_formula_sum
with values for _atom_type_symbol [NOT USED]

(2) multiply the number of atoms in _chemical_formula_sum
by the mass for this element

CALCULATE

RW = _chemical_formula_weight / SUM of (2)
DW = | _chemical_formula_weight - SUM of (2)|

TEST

IF RW
0.90 <> 1.10 issue ALERT A (> 10% difference)
   "Alert A The ratio of given/expected molecular weight as calculated from the _chemical_formula_sum lies outside the range 0.90 <> 1.10 "
0.95 <> 1.05 issue ALERT B (> 5% difference)
   "Alert B The ratio of given/expected molecular weight as calculated from the _chemical_formula_sum lies outside the range 0.95 <> 1.05 "
0.99 <> 1.01 issue ALERT C (> 1% difference)
   "Alert C The ratio of given/expected molecular weight as calculated from the _chemical_formula_sum lies outside the range 0.99 <> 1.01 "

IF DW > 1.0 and category is FO, FM, CO or CM
issue ALERT C
   "Alert C The difference between the given and expected weight for compound is greater 1 mass unit. Check that all hydrogen atoms have been taken into account."

The formula weight given in the CIF differs from that calculated using the formula in _chemical_formula_sum. Check that (a) you have calculated the formula weight correctly and (b) that _chemical_formula_sum is correctly and fully specified. Remember that _chemical_formula_sum and _chemical_formula_weight must correspond with the true sum of all elements in all distinct moieties present, including any solvent and all H atoms, and not the contents implied by the model if there are differences due to the omission of a few H atoms or solvent atoms.

_chemical_formula_sum must also be in the correct format (e.g. do not use subscript formatting: C10 H20 is correct, C~10~ H~20~ is not).

PROC-NAME: CHEMW03 Type_2

PURPOSE: To check that the _chemical_formula_weight matches that calculated for the atomic content data from the two lists, _atom_site_ and _atom_type_, using the number of formula units per cell and the number of symmetry equivalent positions {NSYM from procedure SM}.

PROCEDURE:

SUMMATION

(1) Match the element symbol with the _atom_site_label in the _atom_site_ list and sum the atomic weights for all sites, multiplying by the _atom_site_occupancy value and the symmetry site-multiplicity value (generated from NSYM).

(2) Additionally, if the _atom_type_ list is present in the CIF, sum the atomic weights for the _atom_type_number_in_cell for each element.

CALCULATE

XX = SUM of (1)[or (2)] / _cell_formula_units_Z

WT = XX * NSYM

RC = _chemical_formula_weight / WT

TEST

IF RC
0.90 <> 1.10 issue ALERT Level A (> 10% difference)
   "ALERT: The ratio of given/expected molecular weight as calculated from the _atom_site*(or type) data lies outside the range 0.90 <> 1.10"
0.95 <> 1.05 issue ALERT Level B (> 5% difference)
   "WARNING: The ratio of given/expected molecular weight as calculated from the _atom_site*(or type) data lies outside the range 0.95 <> 1.05 "
0.99 <> 1.01 issue ALERT Level C (> 1% difference)
   "The ratio of given/expected molecular weight as calculated from the _atom_site*(or type) data lies outside the range 0.99 <> 1.01"

The formula weight given in the CIF differs from that calculated using the _atom_site_ list (i.e. the list of atomic coordinates). Check that you have calculated the formula weight correctly and that it corresponds with the true sum of all elements in all distinct moieties present, including any solvent and all H atoms. This message can be ignored if the model is intentionally incomplete due to the omission of a few H atoms or solvent atoms.

However, this alert could also be an indication of overlooked errors in the model. Be sure that the model is indeed as complete as intended and that no elements have been misassigned.

Similarly, this alert could appear if you have given the following loop structure:

loop_
_atom_type_symbol
_atom_type_description
_atom_type_number_in_cell

A discrepancy between the formula weight derived from this list and the formula weight given under _chemical_formula_weight may mean that the atom counts in the loop are incorrect or that _chemical_formula_weight has been incorrectly specified. Once again, _atom_type_symbol and _atom_type_number_in_cell must correspond with the true contents of the unit cell, including any solvent and all H atoms.

PROC-NAME: CRYSC01 Type_1

PURPOSE: To check that _exptl_crystal_colour is consistent with expected colour code combinations.

PROCEDURE:
TEST
IF _exptl_crystal_colour != (qualifier)(intensity)(base-colour)
issue ALERT C
where allowed values are:

(qualifier)
blank, metallic, lusterous, translucent, fluorescent, clear

(intensity)
blank, dark, light, intense, pale

(base-colour)
white, black, blue, violet, red, pink, yellow, gold, silver, bronze, grey, orange, green, colourless, brown, purple

IF A word has been used that has not been identified as a standard identifier issue ALERT C
   "Alert C The word below has not been recognised as a standard identifier."
IF No recognised colour has been given for crystal colour issue ALERT C
   "Alert C No recognised colour has been given for crystal colour."
IF The identifiers are ordered incorrectly issue ALERT C
   "Alert C There is an ordering error in _exptl_crystal_colour. It should be (QUALIFIER) (INTENSITY) (BASE_COLOUR)."

_exptl_crystal_colour must be given as a set of specific keywords in the following specific order:

(QUALIFIER) (INTENSITY) (BASE_COLOUR)

where (QUALIFIER) and/or (INTENSITY) are optional. These keywords must be chosen from the following list:

(qualifier) blank, metallic, lustrous, translucent, fluorescent, clear

(intensity) blank, dark, light, intense, pale

(base-colour) white, black, blue, violet, red, pink, yellow, gold, silver, bronze, grey, orange, green, colourless, brown, purple

PROC-NAME: CRYSR01 Type_1

PURPOSE: To check that the radius of the crystal is given for a spherical or cylindrical crystal.

PROCEDURE:

(1) If the _exptl_crystal_description contains either 'cylinder' or 'sphere' check for a value of _exptl_crystal_size_rad
IF missing then issue ALERT C "Alert C _exptl_crystal_size_rad not in the CIF when expected."

_exptl_crystal_size_rad is not given in the CIF although _exptl_crystal_description is given as 'cylinder' or 'sphere'. Either give the cylinder or sphere radius or change _exptl_crystal_description to another type.

PROC-NAME: CRYSS01 Type_1

PURPOSE: To check that _exptl_crystal_size_min value is consistent with _exptl_crystal_size_mid and _exptl_crystal_size_max.

PROCEDURE:
TEST

IF _exptl_crystal_size_min > _exptl_crystal_size_mid
OR _exptl_crystal_size_mid > _exptl_crystal_size_max
issue ALERT B
"Alert B The magnitudes of the crystal dimensions do not match the min, mid and max definitions"

The magnitudes of the crystal dimensions do not match the min, mid and max definitions. This is usually caused by a typographical error when entering the crystal dimensions or assigning the greatest dimension to the _exptl_crystal_size_min entry and vice versa.

PROC-NAME: CRYSS02 Type_3

PURPOSE: To check that the values of _exptl_crystal_size_* are not larger than expected.

PROCEDURE:
(1) IF _exptl_crystal_size_min > 0.6 && _diffrn_radiation_type != neutron
issue ALERT B
   "Alert B The value of _exptl_crystal_size_min is > 0.6"
(2) IF _exptl_crystal_size_mid > 0.8 && _diffrn_radiation_type != neutron
issue ALERT B
   "Alert B The value of _exptl_crystal_size_mid is > 0.8"
(3) IF _exptl_crystal_size_max > 1.0 && _diffrn_radiation_type != neutron
issue ALERT B
   "Alert B The value of _exptl_crystal_size_max is > 1.0"

The crystal must be smaller than size of the incident beam at the crystal. For most diffractometers with fine-focus X-ray tubes and monochromated radiation, this size is unlikely to be much greater than 0.5 mm. Note that increasing the collimator diameter will not necessarily increase the size of the incident beam at the crystal. If the crystal used in the data collection is larger than the incident beam, then unpredictable errors in intensities will occur due to the varying amounts of the crystal in the beam for different reflection positions. If you obtain an alert about crystal size, then data should be collected with a smaller crystal. For the above reasons, it is recommended that crystals be generally smaller than 0.5 mm along any edge.

If you used neutrons and obtained an alert about the crystal size, then you have forgotten to set _diffrn_radiation_type 'neutron'.

PROC-NAME: DENSD01 Type_1

PURPOSE: To check that the _exptl_crystal_density_diffrn matches the _cell_volume and _chemical_formula_weight values

PROCEDURE:
CALCULATE

DEN = 1.66042 * _chemical_formula_weight * _cell_formula_units_Z / _cell_volume

RD = _exptl_crystal_density_diffrn / DEN

TEST
IF RD 0.9 <> 1.1 issue ALERT A
   "Alert A The ratio of the submitted crystal density and that calculated from the formula is outside the range 0.90 <> 1.10 "
RD 0.95 <> 1.05 issue ALERT B
   "Alert B The ratio of the submitted crystal density and that calculated from the formula is outside the range 0.95 <> 1.05 "
RD 0.99 <> 1.01 issue ALERT C
   "Alert C The ratio of the submitted crystal density and that calculated from the formula is outside the range 0.99 <> 1.01 "

The calculated density given in the CIF differs from that calculated using the specified formula weight and the stated number of formula units in the unit cell (Z). Check that (a) you have calculated the density correctly and (b) that _chemical_formula_weight and _cell_formula_units_Z are correctly specified. Remember that _chemical_formula_weight and the calculated density must correspond with the true sum of all elements in all distinct moieties present, including any solvent and all H atoms, and not the contents implied by the model if there are differences due to the omission of a few H atoms or solvent atoms.

PROC-NAME: DENSM01 Type_1

PURPOSE: To check that the _exptl_crystal_density_meas is supplied is the _exptl_crystal_density_method is present.

PROCEDURE: IF _exptl_crystal_density_method != 'none'
AND != 'not measured'
AND != '?'
AND _exptl_crystal_density_meas == '?'
issue ALERT B
"Alert B _exptl_crystal_density_method is given but no value of _exptl_crystal_density_meas is reported."

You have given the method used to determine the density of the crystal under _exptl_crystal_density_method, but have forgotten to specify the experimentally measured density under _exptl_crystal_density_meas. If you have not actually determined the density experimentally, then set _exptl_crystal_density_method to 'not measured'.

The experimentally measured density should not be confused with the calculated density derived from the unit cell volume and contents which should be specified under _exptl_crystal_density_diffrn.

PROC-NAME: DENSX01 Type_1

PURPOSE: To check that the _exptl_crystal_density_meas matches the _exptl_crystal_density_diffrn.

PROCEDURE:
CALCULATE

RD = _exptl_crystal_density_diffrn / _exptl_crystal_density_meas

TEST
IF RD is 0.80 <> 1.20 issue ALERT A
   "Alert A The ratio of the calculated to measured crystal density lies outside the range 0.80 <> 1.20"
RD is 0.90 <> 1.10 issue ALERT B
   "Alert B The ratio of the calculated to measured crystal density lies outside the range 0.90 <> 1.10"
RD is 0.95 <> 1.05 issue ALERT C
   "Alert C The ratio of the calculated to measured crystal density lies outside the range 0.95 <> 1.05"

The calculated density given in the CIF differs significantly from the experimentally measured density quoted in the CIF. Check that you have measured, calculated and entered the densities correctly and that in your calculations you have allowed correctly for all distinct moieties present, including any solvent and all H atoms, and not the contents implied by the model if there are differences due to the omission of a few H atoms or solvent atoms.

PROC-NAME: DIFMN01 Type_1

PURPOSE: To check that _refine_diff_density_min is less than _refine_diff_density_max.

PROCEDURE:
TEST
IF _refine_diff_density_min >= _refine_diff_density_max
issue ALERT A
"Alert A The minimum difference density cannot exceed the maximum difference density"

You have given the minimum residual electron density with a value greater than the maximum residual electron density. Check that you have not accidentally reversed these values, and that you have not forgotten the negative sign for the minimum residual electron density.

PROC-NAME: DIFMN02 Type_2

PURPOSE: To check that _refine_diff_density_min is within expected limits.

PROCEDURE:
DMIN = _refine_diff_density_min
DTEST = 0.1 * ZMAX

TEST

IF DMIN < -DTEST*2 issue ALERT A
   "Alert A The minimum difference density is < -0.1*ZMAX*2.00"
< -DTEST issue ALERT B
   "Alert B The minimum difference density is < -0.1*ZMAX*1.00"
< -DTEST*.75 issue ALERT C
   "Alert C The minimum difference density is < -0.1*ZMAX*0.75"

The minimum residual electron density is more negative than normally expected, even after making an allowance for the heaviest element in the structure. This is often an indication that (a) the absorption corrections are inadequate; (b) the overall quality of the data may be poor, leading to spurious peaks and holes of residual electron density; (c) there is twinning which has not been allowed for where overlap from the second twin domain (which may have been ignored in the data collection) causes errors in the intensities of some reflections; (d) the model is incorrect or incomplete in terms of incorrect element assignment, missing atoms or unmodelled or inadequately modelled disorder or solvent atoms.

If you believe you have eliminated all potential causes of this alert, but the minimum residual electron density still remains more negative than normally expected, you must specify the name of the nearest atom to this minimum and its distance from the minimum.

IF DMIN > 0.0 issue ALERT A
"Alert A The minimum difference density is > 0.0"

The minimum residual electron density should have a negative value. Have you forgotten the sign or reversed the minimum and maximum entries?

PROC-NAME: DIFMN03 Type_1

PURPOSE: To check that if _refine_diff_density_min is not within expected limits that the adjacent site is identified.

PROCEDURE:
DMIN = _refine_diff_density_min
DTEST = 0.1 * ZMAX

TEST
IF DMIN < -DTEST*.75 atom site should be identified.
Issue ALERT C
"Alert C The minimum difference density is < -0.1*ZMAX*0.75 The relevant atom site should be identified."

The minimum residual electron density is more negative than normally expected. Please specify the name of the nearest atom to this minimum and its distance from the minimum.

PROC-NAME: DIFMX01 Type_2

PURPOSE: To check that _refine_diff_density_max is within expected limits.

PROCEDURE:
DMAX = _refine_diff_density_max
DTEST = 0.1 * ZMAX

TEST

IF DMAX > DTEST*2 issue ALERT A
   "Alert A The maximum difference density is > 0.1*ZMAX*2.00"
> DTEST issue ALERT B
   "Alert B The maximum difference density is > 0.1*ZMAX*1.00"
> DTEST*.75 issue ALERT C
   "Alert C The maximum difference density is > 0.1*ZMAX*0.75"

The maximum residual electron density is larger than normally expected, even after making an allowance for the heaviest element in the structure. This is often an indication that (a) the absorption corrections are inadequate; (b) the overall quality of the data may be poor, leading to spurious peaks and holes of residual electron density; (c) there is twinning which has not been allowed for where overlap from the second twin domain (which may have been ignored in the data collection) causes errors in the intensities of some reflections; (d) the model is incorrect or incomplete in terms of incorrect element assignment, missing atoms or unmodelled or inadequately modelled disorder or solvent atoms.

If you believe you have eliminated all potential causes of this alert, but the maximum residual electron density still remains larger than normally expected, you must specify the name of the nearest atom to this minimum and its distance from the minimum.

IF DMAX < 0.0 issue ALERT A
"Alert A The maximum difference density is < 0.0"

The maximum residual electron density should have a positive value. Have you reversed the minimum and maximum entries?

PROC-NAME: DIFMX02 Type_1

PURPOSE: To check that if _refine_diff_density_max is not within expected limits that the adjacent site is identified.

PROCEDURE:
DMAX = _refine_diff_density_max
DTEST = 0.1 * ZMAX

TEST
IF DMAX > DTEST*.75 atom site should be identified.
Issue ALERT C
"Alert C The minimum difference density is > 0.1*ZMAX*0.75 The relevant atom site should be identified."

The maximum residual electron density is larger than normally expected. Please specify the name of the nearest atom to this maximum and its distance from the maximum.

PROC-NAME: FCOEF01 Type_1

PURPOSE: Check that the value of _refine_ls_structure_factor_coef is recognised.

CHECKLIST:

Inet (net intensity)
Fsqd (structure factor squared)
F (structure factor magnitude)

Otherwise issue ALERT A
"Alert A The absorption correction doesn't match a standard keyword"

_refine_ls_structure_factor_coef must ONLY be one of the following keywords (do not add extra text to this field - e.g. F-squared or F^2^ is not correct):

Inet
Fsqd
F

IF extra text is found in this field or the keyword is almost correct issue General ALERT
"Extra text has been found in the _refine_ls_structure_factor_coef field"

_refine_ls_structure_factor_coef must ONLY be one of the following keywords (do not add extra text to this field - e.g. F-squared or F^2^ is not correct):

Inet
Fsqd
F

PROC-NAME: GOODF01 Type_1/2

PURPOSE: To check that _refine_ls_goodness_of_fit_ref is within expected limits.

PROCEDURE:
TEST
(Type_2)
IF _refine_ls_goodness_of_fit_ref < 0.4 OR > 6.0 issue ALERT A
   "Alert A The least squares goodness of fit parameter lies outside the range 0.40 <> 6.00"
< 0.6 OR > 4.0 issue ALERT B
   "Alert B The least squares goodness of fit parameter lies outside the range 0.60 <> 4.00"
< 0.8 OR > 2.0 issue ALERT C
   "Alert C The least squares goodness of fit parameter lies outside the range 0.80 <> 2.00"

Ideally, the goodness of fit (or standard deviation of an observation of unit weight) should be as close to 1.0 as possible. Values that deviate significantly from 1.0 may be an indication of one of the following: (a) the model is incorrect or incomplete or has been inadequately developed to account for disorder or solvent; (b) the reflection data are poor or weak; (c) there is twinning which has not been allowed for where overlap from the second twin domain (which may have been ignored in the data collection) causes errors in the intensities of some reflections; (d) the absorption corrections are inadequate; (e) the weighting scheme is inappropriate.

Users of SHELXL should normally obtain goodness of fit values very close to 1.0 if none of the above features is relevant. If this is not the case, check that the weighting scheme co-efficients recommended by the program have been updated immediately prior to the last refinement run. If only the weights proposed when the model was in an early stage of development are used and not subsequently updated, the goodness of fit might deviate significantly from 1.0 and the weights should be updated.

Users of other refinement software, particularly older programs or with refinement on F, might routinely obtain values for the goodness of fit in the range 1.5-2.5. This is acceptable, but authors need to be satisfied that this range for the goodness of fit is normal for good structures determined in their laboratory. However, values for the goodness of fit that are significantly smaller than 1.0 are usually a symptom of other problems with the data or model.

IF _refine_ls_goodness_of_fit_obs has been used issue a General ALERT
"_refine_ls_goodness_of_fit_obs is an old dataname which has been superceded by _refine_ls_goodness_of_fit_ref" (Type_1)

You are using an "old-fashioned", but still legal data name: _refine_ls_goodness_of_fit_obs. Please update the item to match the currently preferred name of _refine_ls_goodness_of_fit_ref. To ease this problem for the future, it is recommended that you upgrade or modify your CIF generating software accordingly.

PROC-NAME: HYDTR01 Type_1

PURPOSE: Check that the value of _refine_ls_hydrogen_treatment is recognised.

CHECKLIST:

refall (all H parameters refined)
refxyz (only H coordinates refined)
refU (only H U values refined)
noref (no H parameters refined)
undef (H parameters not determined)
constr (H sites constrained by attached site)
none
mixed

Otherwise issue ALERT C
"Alert C The hydrogen treatment doesn't match a standard keyword"
n.b. "see text" and "riding" have been allowed even though these do not comply with the current CIF-dictionary.
IF extra text is found in the field (i.e. over and above the keyword) issue a General ALERT
"Extra text has been found in the _refine_ls_hydrogen_treatment field. Explanatory text should be in the _publ_section_refinement field."

_refine_ls_hydrogen_treatment must ONLY be one of the following keywords (do not add extra text to this field):

refall
refxyz
refU
noref
undef
constr
none
mixed

You cannot use multiple keywords to depict a variety of methods - use 'mixed' instead.

For a riding refinement, use 'constr'.

By default, SHELXL inserts 'mixed' in EVERY case. Please ensure that you edit this item to represent the actual H-atom treatment used.

Additional descriptive text, if required, should be placed in the _publ_section_exptl_refinement section.

PROC-NAME: RADNT01 Type_1

PURPOSE: Check that the radiation type is recognised.

PROCEDURE:

(1). Check that the _diffrn_radiation_type contains one of the
following.

CHECKLIST:

'Cu K\a'
'Mo K\a'
'Ag K\a'
neutron
synchrotron

Otherwise issue ALERT A
"Alert A The radiation type doesn't match a standard keyword"

_diffrn_radiation_type must ONLY be one of the following keywords (do not add extra text to this field and watch the formatting e.g. 'Cu K~\a~' and 'Cu Kalpha' are incorrect, the space before K should be present):
   'Cu K\a'
   'Mo K\a'
   'Ag K\a'
   'Ga K\a'
   neutron
   synchrotron

If you used a less common X-ray source, such as a gold X-ray tube, this alert can be ignored. The keyword 'synchrotron' should be used for all work carried out on a beam line.

PROC-NAME: RADNW01 Type_1

PURPOSE: To check that the _diffrn_radiation_wavelength matches the _diffrn_radiation_type.

PROCEDURE:
TEST
IF _diffrn_radiation_type == 'Cu K\a'
AND {
_diffrn_radiation_wavelength > 1.54180
OR _diffrn_radiation_wavelength < 1.54175 } issue ALERT C
   "Alert C The radiation wavelength lies outside the expected range for the supplied radiation type. Expected range 1.54175-1.54180"

IF _diffrn_radiation_type == 'Cu K\a'
AND {
_diffrn_radiation_wavelength > 1.54048
AND _diffrn_radiation_wavelength < 1.54057 } issue General ALERT
   "The radiation wavelength given implies that Cu K\a1 has been used. Please check that this is correct."

IF _diffrn_radiation_type == 'Mo K\a'
AND {
_diffrn_radiation_wavelength > 0.71075
OR _diffrn_radiation_wavelength < 0.71065 } issue ALERT C
   "Alert C The radiation wavelength lies outside the expected range for the supplied radiation type. Expected range 0.71075-0.71065"

IF _diffrn_radiation_type == 'Mo K\a'
AND {
_diffrn_radiation_wavelength > 0.70921
AND _diffrn_radiation_wavelength < 0.70931 } issue General ALERT
   "The radiation wavelength given implies that Mo K\a1 has been used. Please check that this is correct."

IF _diffrn_radiation_type == 'Ag K\a'
AND {
_diffrn_radiation_wavelength > 0.56085
OR _diffrn_radiation_wavelength < 0.56080 } issue ALERT C
   "Alert C The radiation wavelength lies outside the expected range for the supplied radiation type. Expected range 0.56085-0.56080"

IF _diffrn_radiation_type == 'Ag K\a'
AND {
_diffrn_radiation_wavelength > 0.55934
AND _diffrn_radiation_wavelength < 0.55938 } issue General ALERT
   "The radiation wavelength given implies that Ag K\a1 has been used. Please check that this is correct."

IF _diffrn_radiation_type == 'Ga K\a'
AND {
_diffrn_radiation_wavelength > 1.34150
OR _diffrn_radiation_wavelength < 1.34130 } issue ALERT C
   "Alert C The radiation wavelength lies outside the expected range for the supplied radiation type. Expected range 1.34130-1.34150"

Have you used the correct radiation symbol and the corresponding wavelength? Check for typographical errors, especially if you are hand editing an old CIF and changed the wavelength, but forgot the radiation symbol or vice-versa.
The K(alpha-bar) wavelength should be used.

PROC-NAME: REFLE01 Type_3

PURPOSE: To check that _reflns_threshold_expression contains a multiplier which is below the limit.

PROCEDURE:
TEST

IF _reflns_threshold_expression ~ 'I'
OR _reflns_threshold_expression ~ 'F^2^'
AND {
_reflns_threshold_expression >= '6' issue ALERT A
   "Alert A The _reflns_threshold_multiplier given is >= 6"
_reflns_threshold_expression >= '5' issue ALERT B
   "Alert B The _reflns_threshold_multiplier given is >= 5"
_reflns_threshold_expression >= '4' issue ALERT C}
   "Alert C The _reflns_threshold_multiplier given is >= 4"
OR
IF _reflns_threshold_expression ~ 'F'
AND {
_reflns_threshold_expression >= '12' issue ALERT A
   "Alert A The _reflns_threshold_multiplier given is >= 12"
_reflns_threshold_expression >= '10' issue ALERT B
   "Alert B The _reflns_threshold_multiplier given is >= 10"
_reflns_threshold_expression >= '8' issue ALERT C}
   "Alert C The _reflns_threshold_multiplier given is >= 8"

The multiplier in _reflns_threshold_expression is used to select the significantly intense reflections for use in the calculation of the regular R-factor given in _refile_ls_R_factor_gt. Older refinement programs, particularly those based on F, may use ONLY the intense reflections selected by this criterion. Therefore it is highly desirable to keep the multiplier in _reflns_threshold_expression as small as possible. Typically a value of 2 or less is used in the expressions 'I > 2\s(I)' or 'F^2^ > 2\s(F^2^)', or 4 or less in 'F > 4\s(F)'.

IF _reflns_threshold_expression is not present issue ALERT C
"Alert C Test not performed"

You have not specified _reflns_threshold_expression or the text cannot be interpreted. This item is compulsory and should be of the form 'I > x\s(I)' or 'F^2^ > x\s(F^2^)' or 'F > x\s(F)'.

The multiplier, x, is typically 2 or less. If you selected zero for the multiplier, you still must provide the expression for _reflns_threshold_expression; e.g. 'I > 0\s(I)'

IF _reflns_observed_criterion has been used issue a General ALERT
"_reflns_observed_criterion is an old dataname which has been superceded by _reflns_threshold_expression"

You are using an "old-fashioned", but still legal data name: _reflns_observed_criterion. Please update the item to match the currently preferred name of _reflns_threshold_expression. To ease this problem for the future, it is recommended that you upgrade or modify your CIF generating software accordingly.

PROC-NAME: REFLG01 Type_1

PURPOSE: To check that _reflns_number_gt less than or equal to the _diffrn_reflns_number.

PROCEDURE:
TEST

IF _reflns_number_gt > _diffrn_reflns_number
issue ALERT B
"Alert B The number of reflections greater than the sigma threshold cannot exceed the total number of reflections measured"

The total number of reflections measured originally by the diffractometer should be given under _diffrn_reflns_number. Any subsequent set of reflections derived from this must, logically, be a subset of the total reflections measured. Therefore, the reported number of reflections for _reflns_number_gt, i.e. those with intensity greater than the sigma threshold defined by _reflns_threshold_expression, must be less than (or possibly equal to) the number given under _diffrn_reflns_number.
Check for typographical errors.

IF _reflns_number_observed has been used issue General ALERT
"_reflns_number_observed is an old dataname which has been superceded by _reflns_number_gt"

You are using an "old-fashioned", but still legal data name: _reflns_number_observed. Please update the item to match the currently preferred name of _reflns_number_gt. To ease this problem for the future, it is recommended that you upgrade or modify your CIF generating software accordingly.

PROC-NAME: REFLL01 Type_1

PURPOSE: To check that _diffrn_reflns_limit_ values are in the correct order.

PROCEDURE:
TEST
IF _diffrn_reflns_limit_h_min >= _diffrn_reflns_limit_h_max issue ALERT B
   "Alert B The minimum h value cannot exceed the maximum h value"
IF _diffrn_reflns_limit_k_min >= _diffrn_reflns_limit_k_max issue ALERT B
   "Alert B The minimum h value cannot exceed the maximum k value"
IF _diffrn_reflns_limit_l_min >= _diffrn_reflns_limit_l_max issue ALERT B
   "Alert B The minimum h value cannot exceed the maximum l value"

Check that you have not accidentally mistyped or reversed one or more of the entries for the maximum and minimum values of h,k,l. Note that the limits for the reflection indices should correspond with the extremes used for the data collection and not those after the data have been merged.

PROC-NAME: REFLT01 Type_1

PURPOSE: To check that _reflns_number_total is less than or equal to the _diffrn_reflns_number.

PROCEDURE:
TEST

IF _reflns_number_total > _diffrn_reflns_number
issue ALERT B
"Alert B The number of symmetry-independent reflections cannot exceed the total number of reflections measured"

The total number of reflections measured originally by the diffractometer should be given under _diffrn_reflns_number. Any subsequent set of reflections derived from this must, logically, be a subset of the total reflections measured. Therefore, the reported number of unique reflections given with _reflns_number_total must be less than (or possibly equal to) the number given under _diffrn_reflns_number. Check for typographical errors.

PROC-NAME: REFLT02 Type_1

PURPOSE: To check that _reflns_number_total is greater than or equal to the _reflns_number_gt.

PROCEDURE:
TEST

IF _reflns_number_total < _reflns_number_gt
issue ALERT B
"Alert B The number of reflections greater than the sigma threshold cannot exceed the number of symmetry-independent reflections"

The total number of symmetry-unique reflections, including all reflections considered to be "unobserved", but excluding systematically absent reflections, should be given under _reflns_number_total. If Friedel-related reflections are being treated as independent observations in order to utilise the effects of anomalous dispersion, _reflns_number_total should correspond with the total number of these independent reflections. Normally, one uses just these independent reflections during refinement and any subsequent set of reflections derived from this must, logically, be a subset of the total unique reflections. Therefore, the reported number of reflections for _reflns_number_gt, i.e. those with intensity greater than the sigma threshold defined by _reflns_threshold_expression, must normally be less than (or possibly equal to) the number given under _reflns_number_total.

Check for typographical errors and/or that you have merged the equivalent reflections correctly before refinement.

An exception to this requirement may occur if data from a non-merohedrally twinned crystal is employed, as this may result in more than one entry in the reflection file for a given set of h,k,l indices (e.g. data read into SHELXL with HKLF 5). As a result, more reflections may be used in the refinement than the apparent number of unique reflections.

A second exception might be if you deliberately choose not to merge symmetry equivalent reflections before the refinement. This procedure is not recommended and its use should be specifically mentioned under _publ_section_exptl_refinement.

IF _reflns_number_observed has been used issue General ALERT
"_reflns_number_observed is an old dataname which has been superceded by _reflns_number_gt"

PROC-NAME: REFNR01 Type_3

PURPOSE: To check that the ratio of _refine_ls_number_reflns and _refine_ls_number_parameters is acceptable.

PROCEDURE:
CALCULATE

S = SIN [_diffrn_reflns_theta_max] / _diffrn_radiation_wavelength

RRRT = _refine_ls_number_reflns / _reflns_number_total

RRTP = _refine_ls_number_reflns / _refine_ls_number_parameters

TEST

IF S < 0.59 OR RRRT < 0.95

IF CENTROSYMMETRIC
RRTP < 10 issue ALERT C
   "Alert C Ratio of reflections to parameters is < 10 for a centrosymmetric structure"
RRTP < 8 issue ALERT B
   "Alert B Ratio of reflections to parameters is < 8 for a centrosymmetric structure"
RRTP < 6 issue ALERT A
   "Alert A Ratio of reflections to parameters is < 6 for a centrosymmetric structure"

IF NON-CENTROSYMMETRIC
IF ZMAX > 18
RRTP < 10 issue ALERT C
   "Alert C Ratio of reflections to parameters is < 10 for a non-centrosymmetric structure, where ZMAX > 18"
RRTP < 8 issue ALERT B
   "Alert B Ratio of reflections to parameters is < 8 for a non-centrosymmetric structure, where ZMAX > 18"
RRTP < 6 issue ALERT A
   "Alert A Ratio of reflections to parameters is < 6 for a non-centrosymmetric structure, where ZMAX > 18"
ELSE
RRTP < 8 issue ALERT C
   "Alert C Ratio of reflections to parameters is < 8 for a non-centrosymmetric structure, where ZMAX < 18"
RRTP < 6 issue ALERT B
   "Alert B Ratio of reflections to parameters is < 6 for a non-centrosymmetric structure, where ZMAX < 18"
RRTP < 4 issue ALERT A
   "Alert A Ratio of reflections to parameters is < 4 for a non-centrosymmetric structure, where ZMAX < 18"

The ratio of reflections used in the refinement to refined parameters (the r/p ratio) is important for ensuring precise atomic and geometric parameters. Higher r/p ratios generally improve the precision.

It is expected that for centrosymmetric space groups, the r/p ratio should be at least 10:1. This also applies for non-centrosymmetric space groups when an element heavier than chlorine is present, because the heavy atom usually improves the diffracting power of the sample to an extent that makes it worthwhile to collect additional high angle data and thereby obtain higher r/p ratios.

For non-centrosymmetric space groups when only elements lighter than argon are present, it is expected that the r/p ratio should be at least 8:1.

If you are having difficulty obtaining a suitable r/p ratio, consider the following:
(a) Was theta(max) set high enough for the measurement? A theta(max) of 25 deg. for Mo radiation or 67 deg. for Cu radiation is the minimum requirement, but use higher theta(max) values if the crystal diffracts sufficiently.
(b) Consider using a low temperature measurement to improve the diffracting power and then collect to a higher theta(max).
(c) Check that the data are complete to your chosen theta(max) and that segments of the unique reflections are not missing. If data completeness is an issue leading to a low r/p ratio, you will receive a separate validation alert about that.
(d) Check that you are using all (or as many as feasible) of your reflection data in the refinement. If weak reflections are being omitted with a sigma threshold cutoff, such as the criterion defined under _reflns_threshold_expression (this may be particularly relevant for refinements based on F), then you should consider reducing the cutoff threshold as far as possible, or, preferably, use all reflections in the refinement.
(e) Reduce the number of refined parameters by, for example, not refining H-atoms, using restraints or constraints, or refining highly disordered or ill-behaved atoms isotropically.

Note that if you have measured data to at least sin(theta)/lambda of 0.6 (theta(max) = 25 deg. for Mo radiation; theta(max) = 67 deg. for Cu radiation) and you have used all available unique reflections in the refinement, the reflection/parameter test is not applied, because it is considered that you have measured an appropriate quantity of data and that you have made the best possible use of that data.

Also note that with light atom non-centrosymmetric structures where anomalous dispersion effects are insignificant, it is unwise to attempt to use unmerged Friedel-related reflections simply to boost the r/p ratio.

PROC-NAME: RFACG01 Type_3

PURPOSE: To check that _refine_ls_R_factor_gt is within expected limits.

PROCEDURE:
TEST
IF _refine_ls_R_factor_gt > 0.20 issue ALERT A
   "Alert A The value of the R factor is > 0.20"
> 0.15 issue ALERT B
   "Alert B The value of the R factor is > 0.15"
> 0.10 issue ALERT C
   "Alert C The value of the R factor is > 0.10"

The value of _refine_ls_R_factor_gt is equivalent to the conventional R-factor and when calculated using a threshold of 2sigma(I) in _reflns_threshold_expression, values less than 0.07 are normally expected. Higher values should be accompanied by a suitable explanation in the _publ_section_exptl_refinement section. However, authors should first ensure that there are not overlooked problems associated with the data or the model. Elevated values for _refine_ls_R_factor_gt may be indicative of a need to recollect the data from a crystal of higher quality or to improve or correct the model. Consider the following:
(a) The absorption corrections are inadequate or inappropriate.
(b) The overall quality of the data may be poor due to the crystal quality.
(c) There is untreated twinning either in the form of unconsidered merohedral twinning or where overlap from the second twin domain in non-merohedral twins (which may have been ignored in the data collection) causes errors in the intensities of some reflections.
(d) The model is incorrect or incomplete in terms of incorrect element assignment, missing atoms or unmodelled or inadequately modelled disorder or solvent atoms.

IF _refine_ls_R_factor_obs has been used issue General ALERT
"_refine_ls_R_factor_obs is an old dataname which has been superceded by _refine_ls_R_factor_gt"

You are using an "old-fashioned", but still legal data name: _refine_ls_R_factor_obs. Please update the item to match the currently preferred name of _refine_ls_R_factor_gt. To ease this problem for the future, it is recommended that you upgrade or modify your CIF generating software accordingly.

IF neither _refine_ls_R_factor_gt or _refine_ls_R_factor_obs are present issue Gerneral ALERT
"Alert C Test not performed. _refine_ls_R_factor_gt is not present."

It is compulsory to report the conventional R-factor under the item _refine_ls_R_factor_gt. This data name is not present in your CIF or has not been assigned a value. Please insert the data item with an apropriate value.

PROC-NAME: RFACR01 Type_3

PURPOSE: To check that _refine_ls_wR_factor_ref is within expected limits.

PROCEDURE:

TEST

IF _refine_ls_wR_factor_ref > 0.45 issue ALERT A
   "Alert A The value of the weighted R factor is > 0.45"
> 0.35 issue ALERT B
   "Alert B The value of the weighted R factor is > 0.35"
> 0.25 issue ALERT C
   "Alert C The value of the weighted R factor is > 0.25"

The value of _refine_ls_wR_factor_ref should normally be considerably less than 0.20. Higher values should be accompanied by a suitable explanation in the _publ_section_exptl_refinement section. However, authors should first ensure that there are not overlooked problems associated with the data or the model. Elevated values for _refine_ls_wR_factor_ref may be indicative of a need to recollect the data from a crystal of higher quality or to improve or correct the model. Consider the following:
(a) The absorption corrections are inadequate or inappropriate.
(b) The overall quality of the data may be poor due to the crystal quality.
(c) The crystal is very weakly diffracting, so that a large proportion of essentially "unobserved" reflections are being used in the refinement. You should consider using a better crystal or a data collection at low temperature and/or, if the compound is organic, using Cu radiation.
(d) There is untreated twinning either in the form of unconsidered merohedral twinning or where overlap from the second twin domain in non-merohedral twins (which may have been ignored in the data collection) causes errors in the intensities of some reflections.
(e) The model is incorrect or incomplete in terms of incorrect element assignment, missing atoms or unmodelled or inadequately modelled disorder or solvent atoms.

IF _refine_ls_wR_factor_obs has been used issue a General ALERT
"_refine_ls_wR_factor_obs is an old dataname which has been superceded by _refine_ls_wR_factor_ref"

You are using an "old-fashioned", but still legal data name: _refine_ls_wR_factor_obs. Please update the item to match the currently preferred name of _refine_ls_wR_factor_ref. To ease this problem for the future, it is recommended that you upgrade or modify your CIF generating software accordingly.

IF neither _refine_ls_wR_factor_ref or _refine_ls_wR_factor_obs are present issue ALERT C
"Alert C Test not performed. _refine_ls_wR_factor_ref is not present."

It is compulsory to report the weighted R-factor under the item _refine_ls_wR_factor_ref. This data name is not present in your CIF or has not been assigned a value. Please insert the data item with an appropriate value.

PROC-NAME: RINTA01 Type_3

PURPOSE: To check that _diffrn_reflns_av_R_equivalents is within expected limits.

PROCEDURE:
TEST
IF _diffrn_reflns_av_R_equivalents > 0.20 issue ALERT A
   "Alert A The value of Rint is greater than 0.20"
> 0.15 issue ALERT B
   "Alert B The value of Rint is greater than 0.15"
> 0.10 issue ALERT C
   "Alert C The value of Rint is greater than 0.10"
< 0.0 issue ALERT A
   "Alert A The value of Rint is less than 0.0"

The value of _diffrn_reflns_av_R_equivalents should normally be considerably less than 0.10. Higher values should be accompanied by a suitable explanation in the _publ_section_exptl_refinement section. However, authors should first ensure that there are not overlooked problems associated with the data or the space group. Elevated values for _diffrn_reflns_av_R_equivalents may be indicative of a need to recollect the data from a crystal of higher quality or that there is a problem with the data treatment. Consider the following:
(a) The absorption corrections are inadequate or inappropriate.
(b) The overall quality of the data may be poor due to the crystal quality.
(c) The crystal is very weakly diffracting, so that a large proportion of essentially "unobserved" reflections are being used in the refinement. You should consider using a better crystal or a data collection at low temperature and/or, if the compound is organic, using Cu radiation. (d) You are working in the wrong crystal system or Laue group.
(e) You have only a very small number of equivalent reflections, which may lead to artificially high values of _diffrn_reflns_av_R_equivalents

Note that if _diffrn_reflns_av_sigmaI/netI is also large, the quality of the data should be considered to be suspect.

PROC-NAME: SHFSU01 Type_2

PURPOSE: To check that _refine_ls_shift/su_max is within expected limits.

PROCEDURE:
TEST
IF |_refine_ls_shift/su_max| > 0.20 issue ALERT A
   "Alert A The absolute value of parameter shift to su ratio > 0.20"
> 0.10 issue ALERT B
   "Alert B The absolute value of parameter shift to su ratio > 0.10"
> 0.05 issue ALERT C
   "Alert C The absolute value of parameter shift to su ratio > 0.05"

An elevated value for the largest parameter shift/s.u. is indicative that proper convergence of the refinement has not yet been achieved. Additional cycles of refinement are usually sufficient to achieve adequate convergence and remove this alert. In disordered or otherwise poorly behaved structures, many additional cycles may be required before a suitable level of convergence has been achieved. Any parameters that remain constantly oscillating should be detailed in the _publ_section_exptl_refinement section. You should also consider whether appropriate restraints might help to stabilise ill-defined and oscillating parameters.

IF _refine_ls_shift/esd_max has been used issue General ALERT
"_refine_ls_shift/esd_max is an old dataname which has been superceded by _refine_ls_shift/su_max"

You are using an "old-fashioned", but still legal data name: _refine_ls_shift/esd_max. Please update the item to match the currently preferred name of refine_ls_shift/su_max. To ease this problem for the future, it is recommended that you upgrade or modify your CIF generating software accordingly.

IF neither _refine_ls_shift/su_max or _refine_ls_shift/esd_max has been used issue ALERT C
"Alert C Test not performed. _refine_ls_shift/su_max is not present."

It is compulsory to report the largest parameter shift/s.u. value in the final refinement cycle under the item _refine_ls_shift/su_max. This data name is not present in your CIF or has not been assigned a value. Please insert the data item with an appropriate value.

PROC-NAME: STRDE01 Type_1

PURPOSE: To check that _refine_ls_abs_structure_details is present if necessary.

PROCEDURE:

(1) For NON-CENTROSYMMETRIC structures only, _refine_ls_abs_structure_details should be present if a Flack parameter is given.
Otherwise issue ALERT B
" Alert B A value for _refine_ls_abs_structure_flack has been given, without an explanation in the _refine_ls_abs_structure_details field."

You have entered a value for Flack's absolute structure parameter (or the software has automatically entered one for you because you have a non-centrosymmetric space group).

If the absolute structure parameter is meaningless because the compound is a weak anomalous scatterer (i.e. no atom heavier than Si is present), it is best to remove the absolute structure parameter from the CIF.

If the absolute structure parameter is meaningful, then you have forgotten to provide appropriate reference details under _refine_ls_abs_structure_details. For example:

_refine_ls_abs_structure_details 'Flack (1983), XXXX Friedel pairs'

and replace the XXXX with the actual number of Friedel pairs used in the refinement. [An easy way to determine the number of Friedel pairs is to look at the difference between the number of unique reflections used in SHELXL when a MERG2 and MERG 3 instruction is used (MERG 3 forces Friedel pairs to be merged before use).]

(2) For NON-CENTROSYMMETRIC structures only, _refine_ls_abs_structure_details should be present if a Rogers parameter is given.
Otherwise issue ALERT B
"Alert B A value for _refine_ls_abs_structure_rogers has been given, without an explanation in the _refine_ls_abs_structure_details field."

You have entered a value for Rogers' absolute structure parameter (or the software has automatically entered one for you because you have a non-centrosymmetric space group).

If the absolute structure parameter is meaningless because the compound is a weak anomalous scatterer, it is best to remove the absolute structure parameter from the CIF.

If the absolute structure parameter is meaningful, then you have forgotten to provide appropriate reference details under _refine_ls_abs_structure_details. For example:

_refine_ls_abs_structure_details 'Rogers (1981), XXXX Friedel pairs'

Note that the use of Rogers' absolute structure parameter cannot cope with merohedral twins or cases where there is a partial mix of enantiomers. It is recommended that you refine using Flack's absolute structure parameter instead.

PROC-NAME: STRVA01 Type_2/4

PURPOSE: To check that _refine_ls_abs_structure_flack is within expected limits.

PROCEDURE:
FLACK = _refine_ls_abs_structure_flack
SFLACK = su of _refine_ls_abs_structure_flack

TEST
IF FLACK > 0.7 issue ALERT C
"Alert C Chirality of atom sites is inverted?" Type_2

The correct absolute structure has been defined by the atomic coordinates if _refine_ls_abs_structure_flack is close to 0.0 (and the s.u. is sufficiently small). If _refine_ls_abs_structure_flack is close to 1.0, the incorrect enantiomer is being modelled and the atomic coordinates should be inverted and refined again.

In cases of intermediate values of _refine_ls_abs_structure_flack, and you believe that a merohedral twin or a partial mix of enantiomers is present, choose the configuration that gives the lowest value for _refine_ls_abs_structure_flack.

Note that if the s.u. of the Flack parameter is large, e.g. greater than or equal to 0.3, one cannot confidently derive the absolute structure from the data, because, within the 3sigma confidence limits, the full range of possible values of the Flack parameter are plausible. In such cases, even if the Flack parameter itself is close to 0.0, no conclusions about the absolute structure are justified. This will usually be the case if the compound is a weak anomalous scatterer (i.e. no atom heavier than Si is present). If a heavy atom is present, but the s.u. is still large, you should ensure that a significant fraction (ideally all) of the Friedel opposites of the symmetry unique reflections have been included in the data set.

If the absolute structure parameter is meaningless because the compound is a weak anomalous scatterer, it is best to remove the absolute structure parameter from the CIF.

If the absolute structure parameter is meaningful, please also provide appropriate reference details under _refine_ls_abs_structure_details. For example:

_refine_ls_abs_structure_details 'Flack (1983), XXXX Friedel pairs'

ELSE IF FLACK > 0.3 AND FLACK < 0.7 issue ALERT C
"Alert C Flack test results are ambiguous." Type_4

The correct absolute structure has been defined by the atomic coordinates if _refine_ls_abs_structure_flack is close to 0.0 (and the s.u. is sufficiently small).

In cases of intermediate values of _refine_ls_abs_structure_flack, a merohedral twin or a partial mix of enantiomers may be present and this fact should be discussed in the manuscript. However, intermediate values might also be obtained when the absolute structure parameter is essentially meaningless because the compound is a weak anomalous scatterer.

Note that if the s.u. of the Flack parameter is large, e.g. > 0.3, one cannot confidently derive the absolute structure from the data, because, within the 3sigma confidence limits, the full range of possible values of the Flack parameter are plausible. In such cases, even if the Flack parameter itself is close to 0.0, no conclusions about the absolute structure are justified. This will usually be the case if the compound is a weak anomalous scatterer (i.e. no atom heavier than Si is present). If a heavy atom is present, but the s.u. is still large, you should ensure that a significant fraction (ideally all) of the Friedel opposites of the symmetry unique reflections have been included in the data set.

If the absolute structure parameter is meaningless because the compound is a weak anomalous scatterer, it is best to remove the absolute structure parameter from the CIF.

If the absolute structure parameter is meaningful, please also provide appropriate reference details under _refine_ls_abs_structure_details. For example:

_refine_ls_abs_structure_details 'Flack (1983), XXXX Friedel pairs'

ELSE IF FLACK < -0.2 issue ALERT C
"Alert C Flack parameter is too small." Type_4

The value of _refine_ls_abs_structure_flack is well outside the expected range of 0.0-1.0. This may mean that there is some systematic error in the model or data, or that the absolute structure parameter is meaningless because the compound is a weak anomalous scatterer. In the latter case, the s.u. of the Flack parameter is also usually large and it is best to remove the absolute structure parameter from the CIF. If a heavy atom is present in the compound, you should ensure that a significant fraction (ideally all) of the Friedel opposites of the symmetry unique reflections have been included in the data set. If _refine_ls_abs_structure_flack is still out of range, the quality of the data and/or the correctness of the model could be checked carefully.

ELSE IF SFLACK > 0.5 issue ALERT C
"Alert C Flack test results are meaningless." Type_4

If the s.u. of the Flack parameter is large, e.g. > 0.3, one cannot confidently derive the absolute structure from the data, because, within the 3sigma confidence limits, the full range of possible values of the Flack parameter are plausible. In such cases, even if the Flack parameter itself is close to 0.0, no conclusions about the absolute structure are justified. This will usually be the case if the compound is a weak anomalous scatterer (i.e. no atom heavier than Si is present). If a heavy atom is present, but the s.u. is still large, you should ensure that a significant fraction (ideally all) of the Friedel opposites of the symmetry unique reflections have been included in the data set.

If the absolute structure parameter is meaningless because the compound is a weak anomalous scatterer, it is best to remove the absolute structure parameter from the CIF.

PROC-NAME: STRVA02 Type_2/3/4

PURPOSE: To check that _refine_ls_abs_structure_rogers is within expected limits.

PROCEDURE:
ROGERS = _refine_ls_abs_structure_rogers

TEST
IF ABS(ROGERS) > 1.2 issue ALERT C
"Alert C Rogers value is too large" Type_3

The value of _refine_ls_abs_structure_rogers is well outside the expected range of -1.0 to 1.0. This may mean that there is some systematic error in the model or data, or that the Rogers parameter is meaningless because the compound is a weak anomalous scatterer (i.e. no atom heavier than Si is present). In the latter case, it is best to remove the Rogers parameter from the CIF. If a heavy atom is present in the compound, you should ensure that a significant fraction (ideally all) of the Friedel opposites of the symmetry unique reflections have been included in the data set. If _refine_ls_abs_structure_rogers is still out of range, the quality of the data and/or the correctness of the model could be checked carefully.

IF ROGERS > -0.5 AND ROGERS < 0.5 issue ALERT C
"Alert C Rogers value is inconclusive" Type_4

The correct absolute structure has been defined by the atomic coordinates if _refine_ls_abs_structure_rogers is close to 1.0 (range -1.0 to 1.0)

In cases of intermediate values of _refine_ls_abs_structure_rogers, a merohedral twin or a partial mix of enantiomers may be present and this fact should be discussed in the manuscript. However, intermediate values might also be obtained when _refine_ls_abs_structure_rogers is essentially meaningless because the compound is a weak anomalous scatterer (i.e. no atom heavier than Si is present).

If the value for _refine_ls_abs_structure_rogers is meaningless because the compound is a weak anomalous scatterer, it is best to remove _refine_ls_abs_structure_rogers from the CIF. This will usually be the case if no atom heavier than Si is present.

If the value for _refine_ls_abs_structure_rogers is meaningful and a heavy atom is present, you should ensure that a significant fraction (ideally all) of the Friedel opposites of the symmetry unique reflections have been included in the data set. Please also provide appropriate reference details under _refine_ls_abs_structure_details. For example:

_refine_ls_abs_structure_details 'Rogers (1981), XXXX Friedel pairs'

IF ROGERS < -1.2 issue ALERT C
"Alert C Rogers value is too low" Type_3

IF ROGERS < -0.5 issue ALERT C
"Alert C Rogers value suggests reverse chirality" Type_2

The correct absolute structure has been defined by the atomic coordinates if _refine_ls_abs_structure_rogers is close to 1.0 (range -1.0 to 1.0). If _refine_ls_abs_structure_rogers is close to -1.0, the incorrect enantiomer is being modelled and the atomic coordinates should be inverted and refined again.

In cases of intermediate values of _refine_ls_abs_structure_rogers, a merohedral twin or a partial mix of enantiomers may be present and this fact should be discussed in the manuscript. Choose the configuration that gives the value of _refine_ls_abs_structure_rogers closest to 1.0. However, intermediate values might also be obtained when _refine_ls_abs_structure_rogers is essentially meaningless because the compound is a weak anomalous scatterer (i.e. no atom heavier than Si is present).

_refine_ls_abs_structure_details 'Rogers (1981), XXXX Friedel pairs'

PROC-NAME: SYMMG01 Type_1

PURPOSE: To check that the _symmetry_space_group_name_H-M value is recognised as a legitimate symmetry symbol.

PROCEDURE:
(1) ATTACH list of H-M symbols, in all settings (e.g. 'symmap' STAR-format file of R Grosse-Kunstleve)

(2) SEARCH for a match of _symmetry_space_group_name_H-M with an entry in the list.

(3) EXTRACT the space group number of the matched symbol.

(4) EXTRACT the number of symmetry equivalent positions.

TEST

IF (2) fails, issue ALERT A that symbol unrecognied.
"Alert A Unrecognised _symmetry_space_group_name_H-M"

IF the number from (3) != _symmetry_space_group_number,
issue an ALERT A of mismatch.
"Alert A _symmetry_space_group_number does not match H-M symbol"

The space group symbol given under _symmetry_space_group_name_H-M is missing, or it cannot be recognised and/or does not correspond with the space group number given under symmetry_space_group_number.

Note that this message usually means that you have incorrectly formatted the space group symbol. Do not insert subscript formatting or parentheses in the space group symbol. You must leave spaces between symbols referring to different axes.

Examples for _symmetry_space_group_name_H-M:

Correct	Incorrect
'P 21 21 21'	'P2~1~2~1~2~1~' or 'P212121'
'P 1 21/c 1' ['P21/c' allowed, but] [not strictly correct]	'P2(1)/c'
'P 2/n 2/n 2/n (origin at -1)'
'R -3 2/m'

Note that the H-M symbol does not necessarily contain complete information about the symmetry and the space-group origin. If used always supply the FULL symbol from International Tables for Crystallography, Vol. A (1992) and indicate the origin and the setting if it is not implicit. If there is any doubt that the equivalent positions can be uniquely deduced from this symbol specify the _symmetry_equiv_pos_as_xyz *_Hall data items as well.

PROC-NAME: SYMMG02 Type_1

PURPOSE: To check that the _symmetry_space_group_name_H-M given is consistent with the _symmetry_equiv_pos_as_xyz if given.

PROCEDURE:
(1). Search the symmap file to produce a Hall symbol from the H-M symbol. Generate the xyz from this and convert back into a H-M symbol via the Hall symbol and symmap file.
(2). Generate a H-M symbol from the xyz via the Hall symbol and symmap file.
(3). xcheck the H-M symbols generated from (1) and (2).
SUMMARY:
h-m --> (symmap) --> hall --> xyz --> hall --> (symmap) --> h-m
hall --> xyz --> hall --> (symmap) --> h-m
xyz --> hall --> (symmap) --> h-m

IF h-m and hall are inconsistent issue ALERT A
   "Alert A The _symmetry_equiv_pos_as_xyz values are in consistent with the H-M symbol given"

IF the number of _symmetry_equiv_pos_as_xyz positions does not match the number expected for the given space group issue ALERT A
   "Alert A The number of _symmetry_equiv_pos_as_xyz positions in the CIF does not match the number expected for this space group"

IF _symmetry_equiv_pos_as_xyz loop is not present issue ALERT A
   "Alert A _symmetry_equiv_pos_as_xyz not in the CIF"

IF _symmetry_equiv_pos_as_xyz loop is incorrectly formatted issue ALERT B
with an appropriate message, e.g.
   "Alert B The denominator for a fractional translation has been omitted."
   "Alert B More than one identity symop (x,y,z) detected."
etc,.....

The space group symbol given under _symmetry_space_group_name_H-M cannot be matched with the space group symmetry operators given under _symmetry_equiv_pos_as_xyz.

Check that you have fully and correctly specified and formatted both _symmetry_space_group_name_H-M and _symmetry_equiv_pos_as_xyz and that they both refer to the SAME space group and the SAME setting of the axes.

_symmetry_equiv_pos_as_xyz must include ALL symmetry operators for the space group concerned, including the identity x,y,z, all those related by a centre of inversion and all those related by a non-primitive lattice operation.

Example:
loop_
_symmetry_equiv_pos_as_xyz
   'x, y, z'
   '-x, y+1/2, -z+1/2'
   '-x, -y, -z'
   'x, -y+1/2, z+1/2'

The space group symbol must not include subscript formatting or parentheses. You must leave spaces between symbols referring to different axes.

Examples for _symmetry_space_group_name_H-M:

Correct	Incorrect
'P 21 21 21'	'P2~1~2~1~2~1~' or 'P212121'
'P 1 21/c 1' ['P21/c' allowed, but] [not strictly correct]	'P2(1)/c'
'P 2/n 2/n 2/n (origin at -1)'
'R -3 2/m'

PROC-NAME: SYMMS01 Type_1

PURPOSE: To check that the _symmetry_cell_setting matches one of the keywords.

CHECKLIST:

triclinic
monoclinic
orthorhombic
tetragonal
rhombohedral
trigonal
hexagonal
cubic

Otherwise issue ALERT B
"Alert B The _symmetry_cell_setting doesn't match one of the standard keywords"

_symmetry_cell_setting must ONLY be one of the following keywords (do not add extra text to this field - e.g. 'monoclinic C-centred' or 'rhombohedral - hexagonal setting' are incorrect):

triclinic
monoclinic
orthorhombic
tetragonal
rhombohedral
trigonal
hexagonal
cubic

PROC-NAME: SYMMS02 Type_1

PURPOSE: To check that the _symmetry_cell_setting is consistent with the _cell_length_ and _cell_angle_ values.

PROCEDURE:

IF _symmetry_cell_setting == 'triclinic'
AND { _cell_length_a == _cell_length_b
OR _cell_length_a == _cell_length_c
OR any _cell_angle values == 90. } issue ALERT B
   "Alert B The unit-cell lengths a and b should not be equal for a triclinic cell"
   "Alert B The unit-cell lengths a and c should not be equal for a triclinic cell"
   "Alert B No unit-cell angle should be equal to 90 for a triclinic cell"

IF _symmetry_cell_setting == 'monoclinic'
AND { _cell_length_a == _cell_length_b
OR _cell_length_a == _cell_length_c
OR all _cell_angle_ values == 90.
OR two _cell_angle_ values != 90. } issue ALERT B
   "Alert B The unit-cell lengths a and b should not be equal for a monoclinic cell"
   "Alert B The unit-cell lengths a and c should not be equal for a monoclinic cell"
   "Alert B All angles should not be 90 for a monoclinic cell"
   "Alert B Two angles should be 90 for a monoclinic cell"

IF _symmetry_cell_setting == 'orthorhombic'
AND { _cell_length_a == _cell_length_b
OR _cell_length_a == _cell_length_c
OR all _cell_angle_ values != 90. } issue ALERT B
   "Alert B The unit-cell lengths a and b should not be equal for a orthorhombic cell"
   "Alert B The unit-cell lengths a and c should not be equal for a orthorhombic cell"
   "Alert B At least one angle should be 90 for an orthorhombic cell"

IF _symmetry_cell_setting == 'tetragonal'
AND { _cell_length_a != _cell_length_b
OR all _cell_angle_ values != 90. } issue ALERT B
   "Alert B The unit-cell lengths a and b should be equal for a tetragonal cell"
   "Alert B All angles should be 90 for a tetragonal cell"

IF _symmetry_cell_setting == 'rhombohedral'
AND { _cell_length_a != _cell_length_b
OR _cell_length_a != _cell_length_c
OR _cell_angle_alpha != _cell_length_beta
OR _cell_angle_alpha != _cell_length_gamma
OR _cell_angle_ values == 90. } issue ALERT B
   "Alert B The unit-cell lengths a and b should be equal for a rhombohedral cell"
   "Alert B The unit-cell lengths a and c should be equal for a rhombohedral cell"
   "Alert B Cell angles alpha and beta should be equal for a rhombohedral cell"
   "Alert B Cell angles alpha and gamma should be equal for a rhombohedral cell"
   "Alert B All angles should not be 90 for a rhombohedral cell"

IF _symmetry_cell_setting == 'trigonal' OR 'hexagonal'
AND { _cell_length_a != _cell_length_b
OR _cell_angle_alpha != 90.
OR _cell_angle_beta != 90.
OR _cell_angle_gamma != 120. } issue ALERT B
   "Alert B The unit-cell lengths a and b should be equal for a trigonal/hexagonal cell"
   "Alert B Cell angla alpha should be 90 for a trigonal/hexagonal cell"
   "Alert B Cell angla beta should be 90 for a trigonal/hexagonal cell"
   "Alert B Cell angle gamma should be 120 for a trigonal/hexagonal cell"

IF _symmetry_cell_setting == 'cubic'
AND { _cell_length_a != _cell_length_b
OR _cell_length_a != _cell_length_c
OR all _cell_angle_ values != 90. } issue ALERT B
   "Alert B The unit-cell lengths a and b should be equal for a cubic cell"
   "Alert B The unit-cell lengths a and c should be equal for a cubic cell"
   "Alert B All angles should be 90 for a cubic cell"

The unit cell parameters do not seem to be consistent with the expected constraints implied by the crystal system specified under _symmetry_cell_setting. Check that the crystal system has been correctly specified and that the unit cell parameters have been constrained where necessary.

For example, a monoclinic unit cell should not be specified with an angle of 89.98 deg. for an angle that should be exactly 90 deg due to the symmetry requirements. Such unit cell parameters should be constrained to appropriate values during the unit cell refinement. Similarly, a tetragonal unit cell should have identical values for the lengths of the a and b axes.

Of course, it is possible that two unit cell axes coincidentally have virtually equal lengths in a low symmetry crystal system or that a monoclinic structure has a beta angle that is indistinguishable from 90.0 deg. In such cases, these alerts can be ignored.

PROC-NAME: SYMOP01 Type_1

PURPOSE: To check that the symmetry operators are given in the correct CIF format.

PROCEDURE:
EXTRACT the symmetry operators for each of the following datanames.
_geom_bond_site_symmetry_1, _geom_bond_site_symmetry_2
_geom_contact_site_symmetry_1, _geom_contact_site_symmetry_2
_geom_angle_site_symmetry_1, _geom_angle_site_symmetry_2, _geom_angle_site_symmetry_3
_geom_torsion_site_symmetry_1, _geom_torsion_site_symmetry_2, _geom_torsion_site_symmetry_3, _geom_torsion_site_symmetry_4
_geom_hbond_site_symmetry_D, _geom_hbond_site_symmetry_H, _geom_hbond_site_symmetry_A

TEST

If the symmetry operator is not of the form defined in the CIF dictionary (e.g. 1_555, 3) then
issue ALERT A
"Alert A Wrong symmetry operator for _geom_bond_site_symmetry_2"

The correct form for the symmetry code is described below. The most common error is the use of symmetry codes such as those used in PLATON (of the form 54502).
The symmetry code of each atom site as the symmetry-equivalent position number 'n' and the cell translation number 'klm'. These numbers are combined to form the code 'n klm' or n_klm. The character string n_klm is composed as follows:
n refers to the symmetry operation that is applied to the coordinates stored in _atom_site_fract_x, _atom_site_fract_y and _atom_site_fract_z. It must match a number given in _space_group_symop_id. k, l and m refer to the translations that are subsequently applied to the symmetry-transformed coordinates to generate the atom used in calculating the bond. These translations (x,y,z) are related to (k,l,m) by the relations k = 5 + x l = 5 + y m = 5 + z By adding 5 to the translations, the use of negative numbers is avoided.

Examples:

`.`	no symmetry or translation to site

`4`	4th symmetry operation applied

7_645 7th symm. posn.; +a on x; -b on y

PROC-NAME: THETM01 Type_3

PURPOSE: To check that _diffrn_reflns_theta_max is greater than expected limits.

PROCEDURE:
CALCULATE

S = SIN [_diffrn_reflns_theta_max] / _diffrn_radiation_wavelength

TEST

IF S < 0.55 issue ALERT A
   "Alert A The value of sine(theta_max)/wavelength is less than 0.550"
< 0.575 issue ALERT B
   "Alert B The value of sine(theta_max)/wavelength is less than 0.575"
< 0.59 issue ALERT C
   "Alert C The value of sine(theta_max)/wavelength is less than 0.590"

The Commission on Journals has determined that setting the maximum sin(theta)/lambda for measurements to at least 0.6 is both optimal and achievable for most structural studies. The extent of the data not only affects the ratio of measurements to refined parameters and hence the accuracy of the atomic and geometric parameters, but also the reliability of the angular dependent terms, such as Uijs.

It is unlikely that any submitted CIF which contains the results of a data collection with a lower theta(max) will be accepted for publication unless there are exceptional circumstances. Old data claimed to have been collected when less stringent criteria were in place will not be excepted.

You should routinely set your diffractometer so that a theta(max) of 25 deg. for Mo radiation or 67 deg. for Cu radiation is the minimum that is achieved. If the crystal diffracts sufficiently well, it is strongly recommended that theta(max) is set to an even higher value.

It is understood that there may be little point in collecting background "noise" when a weakly diffracting crystal gives no detectable diffraction above theta values well below our required limit. In such a case, you should first ensure that you have conscientiously undertaken all possible steps to ensure that the experiment has been able to extract the best diffracting power from your sample. To this end, all of the following options should have been exhausted:

(a) The best possible crystal has been sought and utilised for the data collection. If the crystal was small or of poor quality, are you sure that a better or bigger one cannot be obtained? The chosen crystal may have been the best one in the batch, but had enough effort and patience really been expended in the crystallisation attempt? Often, lack of experience, impatience or unwillingness to try another crystallisation technique or solvent leads to the experimentalist abandoning crystallisation attempts before the optimal conditions have been found. Before you blame the crystal quality, be sure that you have convinced yourself that nothing further can be done in this direction.

(b) Use low temperature measurements to enhance the reflection intensities and the extent of the "observed" data.

(c) For organic compounds, try data collection with Cu radiation, which significantly enhances the reflection intensities.

PROC-NAME: WEIGH01 Type_1

PURPOSE: Check that the value of _refine_ls_weighting_scheme is recognised.

CHECKLIST:

sigma (based on measured intensity su's)
calc (calculated weights applied)

issue ALERT A if scheme isn't recognised or is set to unit weights(*).
"Alert A The weighting scheme doesn't match one of the standard keywords"

_refine_ls_weighting_scheme must be included in the CIF. Use one of the following keywords (do not add extra text to this field - e.g. including the weighting equation is not correct):

sigma
calc

Note that although unit weights are allowed for in the CIF dictionary, structures refined with unit weights are not acceptable.

The equation for the weighting scheme must be given under _refine_ls_weighting_details.

Example:
_refine_ls_weighting_scheme calc
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0544P)^2^+0.1452P] where P=(Fo^2^+2Fc^2^)/3'

IF extra text is found in the field (i.e. over and above the keyword) issue an ALERT C
"Alert C Extra text has been found in the _refine_ls_weighting_scheme field. This should be in the _refine_ls_weighting_details field."

_refine_ls_weighting_scheme must be included in the CIF. Use one of the following keywords (do not add extra text to this field - e.g. including the weighting equation is not correct):

sigma
calc

The equation for the weighting scheme must be given under _refine_ls_weighting_details.

Example:
_refine_ls_weighting_scheme calc
_refine_ls_weighting_details
'w=1/[\s^2^(Fo^2^)+(0.0544P)^2^+0.1452P] where P=(Fo^2^+2Fc^2^)/3'

Note that although unit weights are allowed for in the CIF dictionary, structures refined with unit weights are not acceptable.

* Unit weights are legal in the CIF-dictionary but are not acceptable for Acta Crystallographica submissions.

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