The value of Rint (i.e. _diffrn_reflns_av_R_equivalents) should normally be
considerably less than 0.12 and in the order of magnitude of the reported
R-values. Rint may be relatively meaningless when based on a very limited
number of averaged data. 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.
The expected number of reflections corresponds to that in the asymmetric unit of the Laue group. Expected ratio: less-or-equal 1 for centro symmetric structures and less than 2 for non-centrosymmetric structures. Reasons to exceed those numbers can be: 1 - Systematic extinctions not omitted from the obsd data count. 2 - Refinement with redundant (i.e. not merged/unique) data set.
Test for data completeness. The ratio of the reported number of unique reflections and expected number of reflections for the resolution given is reported. The ratio can be low due to a missing cusp of data when collected with a 2D-detector. Alternatively, the wrong asymmetric part of reciprocal space was collected on a serial detector system.
Check resolution of the data set. Alert is issued when sin(theta)/lambda < 0.6
Averaging of Friedel pairs is strongly advised when indicated by a large su on the Flack parameter. Large su values indicate that the anomalous scattering power is too small in combination with the data quality at hand to merit refinement with a non-averaged dataset. This will generally be the case with MoKa datasets for structures containing atoms not heavier than Si. The value of the Flack parameter will be largely meaningless anyway for large su values. Use MERG 3 or MERG 4 in case of refinement with the SHELXL97 program. Non-compliance with the above for valid scientific reasons should be discussed in detail in the experimental section of the paper.
Check reported h,k,l - range with calculated range based on reported theta-max.
Check whether a sufficient fraction of the unique data is indeed above the 2 sigma level.
Ideally (and a requirement for publication in Acta Crystallographica),
the dataset should be essentially complete, as defined by
-diffrn-measured-fraction-theta-full (close to 1.0), up to
sin(theta)/lambda = 0.6 (i.e. 25.24 degrees MoKa).
The three major causes of incomplete data sets are:
1 - A missing cusp of data due to data collection by rotation around
the spindle axis only (standard on some image-plate systems).
Cure: collect an additional data set after remounting the crystal.
2 - The DENZO image processing package has problems with certain strong
reflections. They are often excluded from the data set.
Cure: Add an additional scan at lower power setting in order to
include strong low order reflections.
3 - Incomplete scans.
Ideally, the reported '_diffrn_measured_fraction_theta_max' value, corresponding to theta-max, should be close to 1.0.
Ideally (and a requirement for publication in Acta Crystallographica),
this fraction should be close to 1.0 for theta-full greater or equal
to sin(theta/lambda) = 0.6 (i.e. 25.24 degrees for MoKa and 67.7 degrees
for CuKa radiation).
The three major causes of incomplete data sets are:
1 - A missing cusp of data due to data collection by rotation around
the spindle axis only (standard on some image-plate systems).
Cure: collect an additional data set after remounting the crystal.
2 - The DENZO imageprocessing package has problems with certain strong
reflections. They are often excluded from the data set.
Cure: Add an additional scan at lower power setting in order to
include strong low order reflections.
3 - Incomplete scans, possibly based on erroneously assumed higher than
actual symmetry.
Note: The default value of _diffrn_measured_fraction_theta_full that
is automatically calculated and inserted in the CIF by SHELXL-97 might
generate A-level ALERTS when significant numbers of reflections are
missing at higher theta values. In order to avoid such an ALERT,
substitute the values calculated with the SHELXL instruction 'ACTA 50'
for _diffrn_reflns_theta_full and _diffrn_measured_fraction_theta_full
respectively. For Mo-radiation, corresponding values of 25 degees (or
higher) and 0.99 (or higher) are expected.
PLATON may be used to analyse the case at hand (by invoking either the
'FCF-VALIDATION' mode or the 'ASYM-VIEW' mode).
The number of measured reflections should be equal or greater than the number of unique reflections.
This test checks whether a refined extinction parameter is meaningful i.e. whether its value is significantly larger than its corresponding s.u. If not, this parameter should be removed from the model and the structure refined without this meaningless additional parameter. The current default gives a warning when its value is within 3.33 s.u. SHELXL97-2 will not allow negative values leading to ill-convergence and non-zero maximum shift/error values: remove extinction parameter from the refinement.
Check the validity of the absolute structure determination. A high su indicates that the experimental data do not support the determination of the absolute structure. This will generally be the case with light atom MoKa data where f" is nearly zero. Note: Use the TWIN & BASF 0.0 instructions in SHELXL97. The default FLACK parameter is not always reliable, in particular when strongly correlated with the position of the origin (e.g. along y in space-group P21). Please refer to Flack,H.D. & Bernardinelli, G. (1999) Acta Cryst. A55, 908-915 and (2000) J. Appl. Cryst., 33, 1143-1148.
Check the relevance/validity of the absolute structure determination. Please refer to Flack,H.D. & Bernardinelli, G. (1999) Acta Cryst. A55, 908-915 and (2000) J. Appl. Cryst., 33, 1143-1148. A value of the Flack parameter that deviates significantly from zero (taking into account the associated s.u.) might indicate that the absolute structure should be inverted in case of a value closer to 1.0 than to zero. A value close to 0.5 may be indicative of an inversion twin or a missed centre of inversion. For valid absolute structure assignments, abs(x) should be less thans 2 * su, with su < 0.04. For enantiopure compounds, su should be less than 0.1.
No Flack parameter value given for non-centrosymmetric structure with heaviest atom Z > Si. This might be intentional.
Options are 'rm', 'ad', 'rmad', 'syn', 'unk' or '.'
rm : absolute configuration established by the structure determination
of a compound containing a chiral reference molecule of known
absolute configuration.
ad : absolute configuration established by anomalous dispersion effects
in diffraction measurements on the crystal.
rmad : absolute configuration established by the structure determination
of a compound containing a chiral reference molecule of known
absolute configuration and confirmed by anomalous dispersion
effects in diffraction measurements on the crystal.
syn : absolute configuration has not been established by anomalous
dispersion effects in diffraction measurements on the crystal.
The enantiomer has been assigned by reference to an unchanging
chiral centre in the synthetic procedure.
unk : absolute configuration is unknown, there being no firm chemical
evidence for its assignment to hand and it having not been
established by anomalous dispersion effects in diffraction
measurements on the crystal. An arbitrary choice of enantiomer
has been made.
. : inapplicable.
No standard uncertainty found for the Flack parameter. When the structure refinement was done with SHELXL97-2, the likely reason for this is a missing BASF instruction. This applies in particular when the associated Flack parameter has the value 0.000. No valid conclusions on the absolute structure can be drawn.
No information is given about the theta value for which the dataset is complete, subject to the percentage given with the dataname _diffrn_measured_fraction_theta_full.
This fraction should be specified in combination with the theta value given with the dataname _diffrn_reflns_theta_full.
This fraction should be specified in combination with the value for theta-max.
Alert for 'no H-atoms' in CIF. This is unusual for carbon containing compounds, but may be correct.
In the ideal case, both SumFormula strings (reported and calculated) should be identical. If not, the reason for the difference should be clear. Examples are cases where populations do not add up to integer numbers, or when solvent molecules have been SQUEEZED. Note: SHELXL97 reports population parameters in the CIF with two decimals only. This may lead to non-integer atom counts in cases of disorder due to rounding. Note: Alerts _041, _042 & _045 can probably be ignored when the relevant values differ by the same factor.
In the ideal case, the MoietyFormula string as reported should be identical to the MoietyFormula string calculated from the data in the CIF. If not, the reason should be clear. Examples are cases where there is no separating space between two element names or cases where populations do not add up to integer numbers or when moieties are separated by '.' instead of ','. Example: NO3 should be given as N O3 Note: Alerts _041, _042 & _045 can probably be ignored when the relevant values differ by the same factor.
Note: atomic weights used in the calculation of the molecular weight are taken from Inorg. Chim. Acta 217 (1994) 217-218 which deviate in a few cases slightly from the older values used in SHELXL97-2.
In the ideal case, both data items should be the same within a small tolerance. If not, the reason should be clear.
In the ideal case, both data items (Z(calc) & Z(reported)) should be the same. If not, the reason for the difference should be clear. An example is the situation where PLATON gives Z = 1 when the program cannot work out a proper Z. Note: Alerts _041, _042 & _045 can probably be ignored when the relevant values differ by the same factor.
D(calc) as calculated from the reported Z and MW is compared for consistency with the reported d(calc).
The Sumformula, corresponding with the Moietyformula, should be given.
The Moiety formula (i.e. the specification of the various species in the structure) should be given in the CIF. Example: '(Cd 2+)3, (C6 N6Cr 3-)2, 2(H2 O)'
The calculated density will with a few exceptions be larger than 1.0. A smaller value may indicate either an incomplete model or incorrect symmetry. (e.g. a missing 'bar' in P-1 etc.)
The linear absorption coefficient corresponding to the Sumformula should be given.
In the ideal case, both data items should be the same within a small tolerance. If not, the reason should be clear.
The treatment/method of absorption(correction) should be given explicitly. Set _exptl_absorpt_correction_type to 'none when no correction is done. Other recognized values are 'psi-scan', 'empirical', 'multi-scan', 'refdelf', 'analytical', 'numerical', 'gaussian'.
The smallest crystal dimension should be supplied in the CIF. The expected value should be a real number (i.e. not 0.35mm)
The medium crystal dimension should be supplied in the CIF. The expected value should be a real number (i.e. not 0.35mm)
The largest crystal dimension should be supplied in the CIF. The expected value should be a real number (i.e. not 0.35mm)
You have indicated that an absorption correction has not been applied. (_exptl_absorpt_correction_type 'none'). However, the predicted values of Tmin & Tmax, based on the crystal dimensions given in the CIF, are sufficiently unequal that absorption effects appear to be significant. Therefore, the application of a suitable absorption correction would appear to be required. Also check that the crystal dimensions given in the CIF do represent the actual crystal dimensions as closely as possible. Inaccuracies here can lead to a poor prediction of Tmin & Tmax and give rise to these alerts. It should normally be possible to estimate the crystal dimensions to 2 decimal places. Rough estimates to only 1 decimal place may be too inaccurate to provide reliable estimates of Tmin & Tmax.
The Maximum transmission factor should be specified in the case a correction for absorption was done. This is NOT the value that is calculated automatically with SHELXL when a SIZE instruction is given in the SHELXL instruction file. The values reported by SHELXL represent the EXPECTED correction range. Some correction packages (e.g. SADABS) will provide only one 'relative- correction-factor'. In such cases, Tmax should be given as Tmax-expected and Tmin = relative-correction-factor * Tmax.
The Minimum transmission factor should be specified in case a correction for absorption was done. This is NOT the value that is calculated automatically with SHELXL when a SIZE instruction is given in the SHELXL instruction file. The values reported by SHELXL represent the EXPECTED correction range. Some correction packages (e.g. SADABS) will provide only one 'relative-correction-factor'. In such cases, Tmax should be given as Tmax-expected and Tmin = relative-correction-factor * Tmax.
see IUCR WEB-Pages
see IUCR WEB-Pages
Some (empirical) correction packages (e.g. SADABS) will provide only one 'relative-correction-factor'. In such cases, Tmax should be given as Tmax-expected (as calculated from the crystal dimensions) and Tmin = relative-correction-factor * Tmax.
Alert for crystals with at least one dimension probably too large for the homogeneous part of the X-ray beam when used for datacollection using crystal monochromated radiation. An exception will be datacollection using a beta-filter and a sufficiently large collimator. See also: C.H.Gorbitz (1999), Acta Cryst. B55, 1090-1098.
Check that the values entered under _exptl_correction_T_min and _exptl_correction_T_max have not been reversed or if there is a typographical error for one of these two items.
For high mu * r values, numerical absorption correction procedures are recommended.
The predicted and reported transmission ranges are found to be identical which is not to be expected. CIF's generated with SHELXL97 report transmission ranges based on the crystal dimensions supplied on the SIZE card. Those values have nothing to do with the actual corrections for absorption as applied to the data: they just report the EXPECTED range. Some correction packages (e.g. SADABS) will provide only one 'relative-correction-factor'. In such cases, Tmax should be given as Tmax-expected and Tmin = relative-correction-factor * Tmax.
Minimum an Maximum dimensions are likely exchanged in the CIF.
In the ideal case, both data items should have the same value. If not, the reason should be clear. A reason might be the output by SHELXL-97 of population parameters to the CIF with only two decimals. Note: SHELXL counts the number of electrons in the unit cell. The result will in general be an integer. This is also the number checked for here. The official definition calls for 'The effective number of electrons in the crystal unit cell contributing to F(000)'. It may contain dispersion contributions and is calculated as: F(000) = [ (sum f~r~)^2^ + (sum f~i~)^2^ ]^1/2^ f~r~ = real part of the scattering factors at theta = 0 f~i~ = imaginary part of the scattering factors at theta = 0
The CIF contains duplicate labels posing interpretation problems for PLATON/CHECK. Derived geometry ALERTS may have their origin in this problem.
The CIF contains labels posing problems for PLATON/CHECK. Example: label HN1 with no scattering type information supplied. Validation is aborted.
The first parameter on the SHELXL weighting line has an exceptionally large value. This may indicate either improper reflection s.u.'s or an unresolved problem such as missed twinning.
The structure contains refined hydrogen atoms. However the data item _refine_ls_hydrogen_treatment has the value 'constr'. The value 'mixed' is more appropriate.
The CIF contains an atom with occupacy less than 0.0001
The CIF contains an atom with Occupancy greater than 1.0.
The CIF contains an atom sitting on a special position with occupancy specified as less than 1.0. This is often an error and the result of the confusion of the notions 'occupancy' and 'population parameter'. The first should be 1.0 for a fully occupied site. The latter multiplies the site-symmetry with the occupancy. Thus, for a fully occupied site on a mirror plane the site-symmetry will be 0.5 * 1.0 = 0.5. Note: a wrong occupancy number will lead to an incorrect expected chemical formula.
The unit-cell contains a non-integer number of atoms of a given atom type. Valid reasons include partially occupied (solvent) sites and substitutional disorder.
The structure contains no hydrogen atoms. However the data item _atom_sites_solution_hydrogen had the value 'geom'. This value is likely the SHELXL default and should be replaced by '.'.
The structure contains no hydrogen atoms. However the data item _refine_ls_hydrogen_treatment has the value 'mixed'. This value is likely the SHELXL default and should be replaced by '.'.
Convergence of the refinement is proven with a close to zero shift/error value for all refined parameters. Such a convergence is easily achieved with a few additional refinement cycles at little cost. Note: Some SHELXL-97 versions do not allow for negative Flack parameter values. Convergence in such a case may be never reached because the Flack parameter value is reset to zero.
A higher than usual R1 indicates either an insufficient model or poor quality data.
The second parameter on the SHELXL weighting line has an exceptionally large value. This may indicate either improper reflection s.u.'s or an unresolved problem such as missed twinning.
wR2 will in general have a value twice of that of R1 with refinement on F**2. Significantly larger values usually indicate a poor refinement model. Also check for unaccounted for twinning.
The weighting scheme is found to be left at the SHELXL default.
S should in general be close to 1 at the end of a refinement with a proper weighting scheme. If not, there might be significant unresolved problems with the model.
S should in general be close to 1 at the end of a refinement with a proper weighting scheme. If not, there might be significant unresolved problems with the model.
The data/parameter ratio should in general be higher than 10 for a quality structure determination. This ratio can be improved by not refining C-H parameters other than riding on their carrier atom.
The data/parameter ratio should in general be higher than 8 for a quality determination of a structure containing atoms with Z less than 18. This ratio can be improved by not refining C-H parameters other than riding on their carrier atom. 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.
The data/parameter ratio should in general be higher than 10 for a quality determination for a structure containing heavy atoms with ZMAX greater than 17. This ratio can be improved by not refining C-H parameters other than riding on their carrier atom.
No Wavelength specification found in the CIF.
Warning: specified wavelength is not Cu,Mo or Ag Ka radiation. Valid exceptions are Neutron and Synchrotron data.
The 'mixed' type Hydrogen atom refinement is reported (SHELXL-97 default). However, no Hydrogen atoms with freely refined positions are found in the CIF. Likely, the value 'constr' for '_refine_ls_hydrogen_treatment' will be more appropriate (e.g. when all Hydrogen atoms have been refined in the riding mode on their carrier atom).
The ratio of the maximum and minimum residual density excursions is unusual. This might indicate unaccounted for twinning or missing atoms (e.g. associated with disordered solvent).
No residual electron density maximum given in CIF.
No residual electron density minimum given in CIF.
Residual density maximum larger than expected. This might be caused by residual absorption artefacts, unaccounted for twinning, wrongly assigned atom types and other model errors.
Residual density minimum larger than expected. This might be caused by residual absorption artefacts, wrongly assigned atom types and other model errors.
Likely interchanged maximum and minimum values. Alternatively, the minimum residual density has the (unlikely) value zero.
Tests for missed symmetry are done with ADDSYM, an expanded MISSYM (C) clone. These tests warn for missed or possible higher (pseudo) symmetry in the structural model (i.e. based on the coordinate data). Close examination of the situation at hand is indicated in order to prove/disprove the issue (usually in combination with the reflection data). Report on potential (pseudo/real) lattice centering or cell halving. Note: H-atoms and disordered atoms are not taken into account in the tests.
Tests for missed symmetry are done with ADDSYM, an expanded MISSYM (C) clone. These tests warn for missed or possible higher (pseudo) symmetry in the structural model (i.e. based on the coordinate data). Close examination of the situation at hand is indicated in order to prove/disprove the issue (usually in combination with the reflection data). This ALERT reports on a potential additional (pseudo/real) inversion centre. A pseudo-centre may be incompatible with existing symmetry elements. Chiral molecules are incompatible with an inversion centre. Note: H-atoms and disordered atoms are not taken into account in the test.
Tests for missed symmetry are done with ADDSYM, an expanded MISSYM (C) clone. These tests warn for missed or possible higher (pseudo) symmetry in the structural model (i.e. based on the coordinate data). Close examination of the situation at hand is indicated in order to prove/disprove the issue (usually in combination with the reflection data). This ALERT reports on potential additional (pseudo/real) rotation axes and mirrors. In addition, (pseudo/real) lattice centering/translations are reported as A, B, C, I, X, Y, Z, S. (Here S stands for special and not covered by the preceding types). Full details on the situation at hand should be gleaned from an actual PLATON/ADDSYM run. Chiral molecules are incompatible with an inversion centre or (glide)planes. Note: H-atoms and disordered atoms are not taken into account in the tests.
Tests for missed symmetry are done with ADDSYM, an extended MISSYM (C) clone.
These tests warn for missed or possible higher (pseudo) symmetry in the
structural model (i.e. based on the coordinate data). Close examination of
the situation at hand is indicated in order to prove/disprove the issue
(usually in combination with the reflection data).
Chiral molecules are incompatible with an inversion centre or (glide)planes.
For an example of reported pseudo-symmetry see I.A.Guzei et al, (2002).
Acta Cryst. C58, m141-m143.
Note: H-atoms and disordered atoms (i.e. atoms with population less
than 1.0) are not taken into account in the tests. This may artificially
lead to a symmetry higher than the actual one.
Note: Atoms are treated as having the same atom type in order to catch
certain types of disorder or incorrect atom type assignment.
ADDSYM has problems to reconstruct a space-group from the symmetry operation found in the symmetry expanded coordinate set. The reason being either intricate additionally detected pseudo-symmetry or serious errors in the data set.
Tests for missed symmetry are done with ADDSYM, an expanded MISSYM (C) clone. This ALERT reports on local inversion symmetry, not compatible with the reported space-group symmetry. Note: H-atoms and disordered atoms are not taken into account in the test.
A symmetry operation should be specified in the CIF either without spaces or between quotes.
Space-group symmetry should be provided in the CIF both explicitly with a _symmetry_equiv_pos_as_xyz loop and implicitly with _symmetry_space_group_name-H-M. An unusual (non-standard) choice of origin may also raise this ALERT. Please check and Explain.
Symmetry in the CIF should be provided both explicitly with a _symmetry_equiv_pos_as_xyz loop and implicitly with _symmetry_space_group_name_H-M. Test for valid _symmetry_space_group_name_H-M symbol.
Symmetry in the CIF should be provided both explicitly with a _symmetry_equiv_pos_as_xyz loop and implicitly with _symmetry_space_group_name_H-M. Test for missing (i.e. ?) _symmetry_space_group_name_H-M symbol.
Symmetry in the CIF should be provided in the CIF both explicitly with a _symmetry_equiv_pos_as_xyz loop and implicitly with _symmetry_space_group_name_H-M. Test for uninterpretable or inconsistent Space-group information.
Symmetry in the CIF should be provided in the CIF both explicitly with a _symmetry_equiv_pos_as_xyz loop and implicitly with _symmetry_space_group_name_H-M. Test for uninterpretable or absent explicit symmetry records
Optionally specify the Hall symbol. The Hall symbol provides an
unambiguous definition of the space-group symmetry where the Hermann-
Mauguin symbol leaves room for alternative choices of the origin.
E.g. for space-group P21, the screw axis is in general taken to coincide
with the b-axis. However, sometimes it is chosen to be shifted by 1/4
in the c-axis direction to bring out the relation with P21/c. The Hall
symbols will be 'P 2yb' and 'P 2ybc' respectively.
Refer to: S.R.Hall, Space-Group Notation with an Explicit Origin;
Acta Cryst. (1981), A37, 517-525.
or: http://www.kristall.ethz.ch/LFK/software/sginfo/hall_symbols.html
The reported Hall-symbol is found to be in error or uninterpretable.
Refer to: S.R.Hall, Space-Group Notation with an Explicit Origin;
Acta Cryst. (1981), A37, 517-525.
or: http://www.kristall.ethz.ch/LFK/software/sginfo/hall_symbols.html
The reported Hall-symbol is found to be inconsistent with the one derived
from the explicit symmetry operations.
Alternatively, no Hall-symbol could be derived by PLATON for the explicit
set of symmetry operations. This may be the case when an unusual origin
is chosen.
Refer to: S.R.Hall, Space-Group Notation with an Explicit Origin;
Acta Cryst. (1981), A37, 517-525.
or: http://www.kristall.ethz.ch/LFK/software/sginfo/hall_symbols.html
The reported monoclinic space-group is in a non-standard setting. Transformation to the conventional setting is indicated unless there is a good (scientific) reason not to do so.
The reported space-group name is unusual.
Symmetry constraints on cell dimensions are checked.
Symmetry constraints on cell dimensions are checked.
Symmetry constraints on cell dimensions are checked.
Symmetry constraints on cell dimensions are checked.
Symmetry constraints on cell dimensions are checked.
Symmetry constraints on cell dimensions are checked.
Symmetry constraints on cell dimensions are checked.
Symmetry constraints on cell dimensions are checked.
Symmetry constraints on cell dimensions are checked.
Symmetry constraints on cell dimensions are checked.
Symmetry constraints on cell dimensions are checked.
The su on the a-axis is small or missing. The presence of su's (where required) and value are checked. Su's as given by the diffractometer software are often much smaller then realistic.
The su on the b-axis is small or missing. The presence of su's (where required) and value are checked. Su's as given by the diffractometer software are often much smaller then realistic.
The su on the c-axis is small or missing. The presence of su's (where required) and value are checked. Su's as given by the diffractometer software are often much smaller then realistic.
The su on alpha is small or missing. The presence of su's (where required) and value are checked. Su's as given by the diffractometer software are often much smaller then realistic.
The su on beta is small or missing. The presence of su's (where required) and value are checked. Su's as given by the diffractometer software are often much smaller then realistic.
The su on gamma is small or missing. The presence of su's (where required) and value are checked. Su's as given by the diffractometer software are often much smaller then realistic.
There should be no s.u. on symmetry constrained cell angles. Example: No su on alpha, beta and gamma for orthorhombic symmetry.
The su on the reported -axis is unexpectedly large.
The su on the reported angle is too large.
An ALERT is issued when the reported unit cell volume differs significantly from the volume calculated on the basis of the supplied cell dimensions.
Missing s.u. on cell volume.
Some software packages calculate Volume su's incorrectly. The correct formula for triclinic, monoclinic and orthorhombic systems (based on the propagation of error expression) may be found in: M. Nardelli, Computer & Chemistry, (1983), 7, 95-98. or C. Giacovazzo ed. in 'Fundamentals of Crystallography', Second Edition, Oxford University Press, 2003, p135.
The reported cell axes su's are reported equal. Please check whether this is correct or a software default value.
The reported cell angle su's are reported equal. Please check whether this is correct or a software default value.
Unless for special reasons related to the structure/content, a unit-cell and structure is best reported with reference to the Niggli Reduced Cell. This ALERT may originate also from a failure to order the axes from small to large.
The axial order should be from small to large in the triclinic cell.
By convention, the Monoclinic beta angle is always chosen to be larger than 90.0 Degrees. A trivial transformation (1 0 0/0 -1 0/0 0 -1) should be applied to the data.
Unless for special reasons related to the structure/content, a unit-cell and structure is best reported with reference to the Niggli Reduced Cell.
Missing or Zero su (esd) on x-coordinate. Positional parameters for all non-hydrogen atoms in general positions are checked for the presence of a non-zero s.u. on them. This includes parameters fixed to fix the origin in polar space-groups which is no longer necessary when refinement is done with modern programs (e.g. SHELXL, XTAL).
Missing or Zero su (esd) on y-coordinate. Positional parameters for all non-hydrogen atoms in general positions are checked for the presence of a non-zero s.u. on them. This includes parameters fixed to fix the origin in polar space-groups (e.g. P21) which is no longer necessary when refinement is done with modern programs (e.g. SHELXL, XTAL).
Missing or Zero su (esd) on z-coordinate. Positional parameters for all non-hydrogen atoms in general positions are checked for the presence of a non-zero s.u. on them. This includes parameters fixed to fix the origin in polar space-groups (e.g. P41) which is no longer necessary when refinement is done with modern programs (e.g. SHELXL, XTAL).
Warning: Refined C-H H-atoms in heavy-atom structure (i.e. containing an element beyond element #18). Such H-atoms are in general better refined at calculated positions riding on the atoms they are attached to. A better data over parameter ratio will be achieved.
Report on restrained (riding) Non-Hydrogen atoms. Note: This may lead to non meaningfull bond and angle su's (ALERTS _751, _752). R-flagged atoms may arise unintentional being caused by an "AFIX 0" line being missing in a shelxl.ins file (SHELXL-97 refinement). Alternatively, the number of refined parameters may have been limited deliberately (e.g. by refinement of C-F with fixed known geometry, similar to C-H) in order to keep the data/parameter ratio acceptable.
Calc-flagged atoms are not supposed to carry s.u.'s on their coordinates.
Insufficient data encountered in coordinate loop. A possible cause might be the use of a SHELX style '=' continuation line.
It is unusual that more cell parameters end with a zero and the su is 10. This problem might be caused by the specification of insufficient 'meaningful' digits as compared to the reported su. see also: W.Clegg, Acta Cryst. (2003) E59, e2-e5.
The reported _cell_measurement_temperature deviates from the reported _diffrn_ambient_temperature values.
Please supply value for _cell_measurement_reflns_used
Please supply value for _cell_measurement_theta_max
Please supply value for _cell_measurement_theta_min
Please specify the temperature (Kelvin) at which the unit-cell was determined.
Please specify the temperature (Kelvin) at which the intensity data were collected.
The cell determination temperature is set in the CIF by default by SHELXL to 293 K if the TEMP instruction is not used. The actual temperature is likely either slightly or significantly (for a low temperature data collection) different.
The data collection temperature is set in the CIF by default by SHELXL to 293 K if the TEMP instruction is not used. The actual temperature is likely either slightly or significantly (for a low temperature data collection) different.
This test reports on non-hydrogen atoms that were refined with isotropic displacement parameters only in the main residue. Such a practice is unusual by modern standards and only needed for minor disorder modelling.
This test reports on isotropically refined atoms in small moieties (usually anions or solvent).
No anisotropically refined atoms in CIF ?
This test reports on non-positive definite (i.e. complex and unrealistic) anisotropic displacement parameters in the main residue.
This test reports on non-positive definite (i.e. complex and unrealistic) anisotropic displacement parameters in an anion or solvent residue.
The maximum and minimum main axis ADP ratio (Angstrom Units) is tested for the main residue. Large values may indicate unresolved disorder.
The maximum and minimum main axis ADP ratio (Angstrom Units) is tested for the minor residue(s). Large values may indicate unresolved disorder.
The maximum and minimum main axis ADP ratio (Angstrom Units) is tested for the main residue. Large values may indicate unresolved disorder.
The maximum and minimum main axis ADP ratio (Angstrom Units) is tested for the minor residue(s). Large values may indicate unresolved disorder.
Check & Correct U(aniso) data for completeness etc. Do not use SHELX style '=' continuation line
This test reports on a larger than usual U(eq) range for the specified element type in the non-solvent/anion part of the structure. Too high or too low Ueq's may be an indication for incorrectly identified atomic species (i.e. O versus N).
This test reports on a larger than usual U(eq) range for the non-hydrogen atoms solvent/anion. Too high or too low Ueq's may be an indication for incorrectly identified atomic species (i.e. Br versus Ag).
This test reports on a larger than usual range of U(eq) values for hydrogen
atoms in the non-solvent/anion part of the structure.
Possible causes are:
1 - disorder, e.g. in t-butyl moieties.
2 - poor data, not adequate for the refinement of individual displacement
parameters.
3 - Misplaced hydrogen atoms (i.e. there is no density at the position
where one of the H-atoms is positioned).
This test reports on large ranges in displacement parameters for hydrogen atoms in the solvent/anion part of the structure.
This test reports on a large difference between Ueq in the CIF and the Ueq calculated from the 6 reported Uij values. .
The components of the anisotropic displacement parameters along chemical bonds are assumed to be equal in magnitude. Large differences supposedly indicate contamination of these parameters with other (unresolved) effects such as (substitutional) disorder, model or data errors and/or over refinement. Atomic sites assigned the wrong scattering type (e.g. Ag versus Br) should generate 'problem signals' with this test. Data sets corrected for absorption effects with DELREF techniques (e.g. DIFABS, SHELXA, XABS2) often show large DELU values for bonds involving the heaviest atom. Note: The original 'Hirshfeld-test' was defined in absolute terms (see F.L.Hirshfeld, Acta Cryst. (1976). A32, 239-244). The current test is with reference to the associated standard uncertainty.
The components of the anisotropic displacement parameters along chemical bonds are assumed to be equal in magnitude. Large differences supposedly indicate contamination of these parameters with other (unresolved) effects such as (substitutional) disorder, model or data errors and/or over refinement. Atomic sites assigned the wrong scattering type (e.g. Ag versus Br) should generate 'problem signals' with this test. Data sets corrected for absorption effects with DELREF techniques (e.g. DIFABS, SHELXA, XABS2) often show large DELU values for bonds involving the heaviest atom. Note: The original 'Hirshfeld-test' was defined in absolute terms (see F.L.Hirshfeld, Acta Cryst. (1976). A32, 239-244). The current test is with reference to the associated standard uncertainty.
The components of the anisotropic displacement parameters along chemical bonds are assumed to be equal in magnitude. Large differences supposedly indicate contamination of these parameters with other (unresolved) effects such as (substitutional) disorder, model or data errors and/or over-refinement. Atomic sites assigned the wrong scattering type (e.g. Ag versus Br) should generate 'problem signals' with this test. Data sets corrected for absorption effects with DELREF techniques (e.g. DIFABS, SHELXA, XABS2) often show large DELU values for bonds involving the heaviest atom. A special case are M-C=O type of systems that generally show significant differences for the M-C bond. See D.Braga & T.F. Koetzle (1988), Acta Cryst. B44, 151-155). Note: The original 'Hirshfeld-test' was defined in absolute terms (see F.L.Hirshfeld, Acta Cryst. (1976). A32, 239-244). The current test is with reference to the associated standard uncertainty.
The components of the anisotropic displacement parameters along chemical bonds are assumed to be equal in magnitude. Large differences supposedly indicate contamination of these parameters with other (unresolved) effects such as (substitutional) disorder, model or data errors and/or over refinement. Atomic sites assigned the wrong scattering type (e.g. Ag versus Br) should generate 'problem signals' with this test. Data sets corrected for absorption effects with DELREF techniques (e.g. DIFABS, SHELXA, XABS2) often show large DELU values for bonds involving the heaviest atom. Note: The original 'Hirshfeld-test' was defined in absolute terms (see F.L.Hirshfeld, Acta Cryst. (1976). A32, 239-244). The current test is with reference to the associated standard uncertainty.
The components of the anisotropic displacement parameters along chemical bonds are assumed to be equal in magnitude. Large differences supposedly indicate contamination of these parameters with other (unresolved) effects such as (substitutional) disorder, model or data errors and/or over refinement. Atomic sites assigned the wrong scattering type (e.g. Ag versus Br) should generate 'problem signals' with this test. Data sets corrected for absorption effects with DELREF techniques (e.g. DIFABS, SHELXA, XABS2) often show large DELU values for bonds involving the heaviest atom. Note: The original 'Hirshfeld-test' was defined in absolute terms (see F.L. Hirshfeld, Acta Cryst. (1976). A32, 239-244).
The U(eq) value of an atom is compared with the average U(eq) for to non-hydrogen atoms bonded to it. Large differences may indicate that the wrong atom type was assigned (e.g. N instead of O).
The U(eq) value of an atom is compared with the average U(eq) for non-hydrogen atoms bonded to it. Large differences may indicate that the wrong atom type was assigned (e.g. N instead of O). False alarms may occur for terminal groups such as the t-butyl moiety.
The U(eq) value of an atom in the solvent or ion is compared with the average U(eq) for non-hydrogen atoms bonded to it. Large differences may indicate that the wrong atom type was assigned (e.g. N instead of O).
The U(eq) value of an atom in the solvent or ion is compared with the average U(eq) for non-hydrogen atoms bonded to it. Large differences may indicate that the wrong atom type was assigned (e.g. N instead of O). False alarms may occur for terminal groups such as the t-butyl moiety.
U(iso) of a hydrogen atom is generally expected to be greater than the
U(eq) of the non-hydrogen atom it is attached to.
An average value of the U(i,j) tensor of the asymmetric unit of a residue is calculated. An ALERT is generated when the corresponding U3/U1 ratio deviates significantly from 1.0. Large values of this ratio should be taken as an indication of possible systematic errors in the data or errors in the model. Visual inspection of an ORTEP plot will show that many displacement ellipsoids have their major axis pointing in the same direction.
Atom sites that are not fully occupied are counted. A large fraction of disordered atoms may be both a signal for serious structure analysis problems or less reliable/interesting results.
Atom sites that are not fully occupied are counted. A large fraction of
Hydrogen atoms are generally connected to only one other atom. A hydrogen atom between two oxygen atoms is a special case. Investigate whether this hydrogen atom is better described with a disorder model with two partially occupied sites. A difference map might show a double-well density.
This test reports on hydrogen atoms that are not on bonding distance to any atom. This ALERT may indicate that the hydrogen atom refined to a non-bonding position or needs a symmetry operation to bring it to bonding distance. It also may indicate a problem with incompatible population parameters (e.g. C - H with population 0.8 and 0.9 respectively).
This test reports on oxygen atoms that are not within bonding distance to any other atom in the structure. A common reason may be that no hydrogen atoms are given for a water molecule. Attempts should be made to locate those hydrogen atoms from a difference map.
This test reports on metal atoms that are not bonded or at coordination distance of other atoms. Isolated ions are very unusual (or non-existent ?)
This test reports on single bonded (coordinated) metal atoms/ions. This represents a very unusual situation. There are literature examples where such a 'single bonded metal' was shown to be a halogen.
Single bonded Oxygen with C-O .GT. 1.3 Angstrom. Missing H-Atom ?
This test identifies (very) short contacts between atoms that only becomes apparent after the application of symmetry on the primary coordinate set.
This test reports on oxygen atoms (not full weight) that are not within bonding distance to any other atom in the structure. A common reason may be that no hydrogen atoms are given for a water molecule.
Strange C-O-H geometry with C-O .LT. 1.25 Angstrom detected. Misplaced H-Atom ?
Oxygen atom with three covalent bonds detected. Check for correct atom type
assignment (e.g. N rather than O)
Note: Exceptions are H3O+ (Oximium or Hydroxonium) and
H5O2+ (Hydronium or aqua-hydroxonium) species.
A water molecule coordinated to a metal is detected with an unusually small value of the Metal-Oxygen-Hydrogen Angle.
An sp3 hybridized C was detected as part of a C=N moiety. Only one attached H atom in sp2 configuration is expected and not two. In SHELXL terms this corresponds with an erroneous AFIX 23 rather than an AFIX 43 type of H atom position generation and refinement.
An sp3 hybridized C was detected as part of a C=N moiety. Only one attached H atom in sp2 configuration is expected and not two. In SHELXL terms this corresponds with an erroneous AFIX 23 rather than an AFIX 43 type of H atom position generation and refinement.
The test attempts to assign one of three hybridisations to N atoms in main residue: sp, sp2 or sp3 on the basis of the angles around N. This ALERT may indicate a mis-assigned H atom position (e.g. an atom placed in a sp2 position instead of sp3).
The test attempts to assign one of three hybridisations to N atoms in main residue: sp, sp2 or sp3 on the basis of the angles around N. This ALERT may indicate a mis-assigned H atom position (e.g. an atom placed in a sp2 position instead of sp3).
The test attempts to assign one of three hybridisations to C atoms in main residue: sp, sp2 or sp3 on the basis of the angles around C. In this way, missing H atoms or too many H-atoms on a carbon atom should be detected.
The test attempts to assign one of three hybridisations to C atoms in solven/anion: sp, sp2 or sp3 on the basis of the angles around C. In this way missing H atoms or too many H-atoms on a carbon atom should be detected.
The test attempts to assign one of three hybridisations to a non-C atom in the main residue: sp, sp2 or sp3 on the basis of the angles around the non-C atom. In this way, missing H atoms or too many H-atoms should be detected.
The test attempts to assign one of three hybridisations to a non-C atom in the solvent/anion: sp, sp2 or sp3 on the basis of the angles around the non-C atom. In this way, missing H atoms or too many H-atoms should be detected.
Check for possibly missing Hydrogen atom on Nitrogen coordinating to a metal in the main residue.
Check for possibly missing Hydrogen atom on Nitrogen coordinating to a metal in the solvent/anion.
Check for possibly missing Hydrogen atom on Carbon with sp3-like geometry in the main residue.
Check for possibly missing Hydrogen atom on Carbon with sp3-like geometry in the solvent/anion.
Check for a possibly missing Hydrogen atom on Phosphorus with sp3-like geometry.
The standard average C-C bond distance in a phenyl ring is 1.395 Angstrom. The actual average ring distance may be larger than expected due to systematic errors in the cell dimensions (e.g. use of incorrect wavelength value for the determination of the cell parameters).
The standard average C-C bond distance in a phenyl ring is 1.395 Angstrom. The average ring distance may be smaller due to large thermal motion or incorrect cell dimensions.
The standard average C-C in a phenyl ring is 1.395 Angstrom. Bond distances in the ring are expected to vary only slightly due to thermal motion or substituent effects. Large deviations are likely due to data or model errors.
The standard average C-C bond distance in a flat six carbon atom containing aromatic ring is 1.395 Angstrom. The actual average ring distance may be larger than expected due to substituents such as =O, single bonds or systematic errors in the cell dimensions (E.g. when the wrong wavelength is used in the derivation of the cell parameters).
The standard average C-C bond distance in a benzene ring is 1.395 Angstrom. The average ring distance may be smaller due to large thermal motion, substituents such as =O or incorrect cell dimensions.
The standard average C-C bond distance in a benzene ring is 1.395 Angstrom. Bond distances in the ring are expected to vary only slightly when due to substituent effects (exceptions include =O substituents). Large deviations may indicate data or model errors.
Cyclohexane moieties should have be significantly puckered as measured by the average torsion angle tau. Unresolved disorder generally results in flattened rings and elongated displacement ellipsoids. A disorder model should be included in the calculations.
The average su for X-Y bonds is tested (named bond-precision). X-Y will generally be C-C bonds, unless there are none. In the last case the su's of the lowest element numbers are considered (excluding hydrogen). There are three test ranges: one for structures with the largest element Z < 20, one for the largest Z in the range 20 to 39 and one for structures with Z(max) 40 or higher (_340, _341 and _342 respectively)
The average su for X-Y bonds is tested (named bond-precision). X-Y will generally be C-C bonds, unless there are none. In the last case the su's of the lowest element numbers are considered (excluding hydrogen). There are three test ranges: one for structures with the largest element Z < 20, one for the largest Z in the range 20 to 39 and one for structures with Z(max) 40 or higher (_340, _341 and _342 respectively)
The average su for X-Y bonds is tested (named bond-precision). X-Y will generally be C-C bonds, unless there are none. In the last case the su's of the lowest element numbers are considered (excluding hydrogen). There are three test ranges: one for structures with the largest element Z < 20, one for the largest Z in the range 20 to 39 and one for structures with Z(max) 40 or higher (_340, _341 and _342 respectively)
The angle range is larger than usual for the tentatively assigned hybridisation of the reported atom in the main residue.
The angle range is larger than usual for the tentatively assigned hybridisation of the reported atom in the solven/anion.
Large deviations from generally accepted values may indicate model problems, over refinement etc. Default C-H = 0.96 Ang. (X-Ray) value from SHELXL.
Large deviations from generally accepted values may indicate model problems, over refinement etc. Default C-H = 0.96 Ang. (X-Ray) value from SHELXL.
Large deviations from generally accepted values may indicate model problems, over refinement etc. Default N-H = 0.87 Ang. (X-Ray) value from SHELXL.
Large deviations from generally accepted values may indicate model problems, over refinement etc. Default N-H = 0.87 Ang. (X-Ray) value from SHELXL.
Large deviations from generally accepted values may indicate model problems, over refinement etc. Default O-H = 0.82 Ang. (X-Ray) value from SHELXL.
Large deviations from generally accepted values may indicate model problems, over refinement etc. Default O-H = 0.82 Ang. (X-Ray) value from SHELXL.
Large deviations from generally accepted values may indicate model problems, over refinement etc. Default C4-C4 = 1.54 Ang. (X-Ray) value from Ladd & Palmer, Structure Determination by Xray Crystallography (1985). Note: - C4-C4 indicates a bond between atoms with 4 bonds each.
Large deviations from generally accepted values may indicate model problems, over refinement etc. Default C4-C4 = 1.54 Ang. (X-Ray) value from Ladd & Palmer, Structure Determination by Xray Crystallography (1985). Note: - C4-C4 indicates a bond between atoms with 4 bonds each.
Large deviations from generally accepted values may indicate model problems, over refinement etc. Default C4-C3 = 1.52 Ang. (X-Ray) value from Ladd & Palmer, Structure Determination by Xray Crystallography (1985). Note: - C4-C3 indicates a bond between an atom with 4 bonds and one with 3 bonds. - Conjugated systems may cause some 'false alarm' messages.
Large deviations from generally accepted values may indicate model problems, over refinement etc. Default C4-C3 = 1.52 Ang. (X-Ray) value from Ladd & Palmer, Structure Determination by Xray Crystallography (1985). Note: - C4-C3 indicates a bond between an atom with 4 bonds and one with 3 bonds. - Conjugated systems may cause some 'false alarm' messages.
Large deviations from generally accepted values may indicate model problems, over refinement etc. Default C4-C2 = 1.46 Ang. (X-Ray) value from Ladd & Palmer, Structure Determination by Xray Crystallography (1985). Note: - C4-C2 indicates a bond between an atom with 4 bonds and one with 2 bonds. - Conjugated systems may cause some 'false alarm' messages.
Large deviations from generally accepted values may indicate model problems, over refinement etc. Default C4-C2 = 1.46 Ang. (X-Ray) value from Ladd & Palmer, Structure Determination by Xray Crystallography (1985). Note: - C4-C2 indicates a bond between an atom with 4 bonds and one with 2 bonds. - Conjugated systems may cause some 'false alarm' messages.
Large deviations from generally accepted values may indicate model problems, over refinement etc. Default C?-C? = 1.50 Ang. (X-Ray) value from Ladd & Palmer, Structure Determination by Xray Crystallography (1985). This ALERT may also arise when the hybridisation at least one atom is not recognized.
Large deviations from generally accepted values may indicate model problems, over refinement etc. Default C?-C? = 1.50 Ang. (X-Ray) value from Ladd & Palmer, Structure Determination by Xray Crystallography (1985).
Large deviations from generally accepted values may indicate model problems, over refinement etc. Default C3-C3 = 1.34 Ang. (X-Ray) value from Ladd & Palmer, Structure Determination by Xray Crystallography (1985). Note: - C3-C3 indicates a bond between atoms with 3 bonds each. - Conjugated systems may cause some 'false alarm' messages.
Large deviations from generally accepted values may indicate model problems,
over refinement etc. Default C3-C3 = 1.34 Ang. (X-Ray) value from
Ladd & Palmer, Structure Determination by Xray Crystallography (1985).
Note:
- C3-C3 indicates a bond between atoms with 4 with 3 bonds each.
- Conjugated systems may cause some 'false alarm' messages.
- A notable exception is the C-C bond in -C(=O)-C(=O)- systems with an
observed mean value of 1.54 Angstrom.
Large deviations from generally accepted values may indicate model problems, over refinement etc. Default C3-C2 = 1.31 Ang. (X-Ray) value from Ladd & Palmer, Structure Determination by Xray Crystallography (1985). Note: - C3-C2 indicates a bond between an atom with 3 bonds and one with 2 bonds. - Conjugated systems may cause some 'false alarm' messages.
Large deviations from generally accepted values may indicate model problems, over refinement etc. Default C3-C2 = 1.31 Ang. (X-Ray) value from Ladd & Palmer, Structure Determination by Xray Crystallography (1985). Note: - C3-C2 indicates a bond between an atom with 3 bonds and one with 2 bonds. - Conjugated systems may cause some 'false alarm' messages.
Large deviations from generally accepted values may indicate model problems, over refinement etc. Default C2-C2 = 1.25 Ang. (X-Ray) value from Ladd & Palmer, Structure Determination by Xray Crystallography (1985). Note: - C2-C2 indicates a bond between atoms with 2 bonds each. - Conjugated systems may cause some 'false alarm' messages.
Large deviations from generally accepted values may indicate model problems, over refinement etc. Default C2-C2 = 1.25 Ang. (X-Ray) value from Ladd & Palmer, Structure Determination by Xray Crystallography (1985). Note: - C2-C2 indicates a bond between atoms with 2 bonds each. - Conjugated systems may cause some 'false alarm' messages.
Large deviations from generally observed bond distances may indicate model problems, over-refinement etc. Check for wrong atom-type assignments. For an example see: Acta Cryst. (2003) E59, m710-m712.
This test alerts for possible incorrectly oriented CH3 moieties. (E.g. AFIX 33 instead of AFIX 137 etc. within the SHELXL realm)
Unusual Methyl Moiety X-C-H Angle (Ideally 109 Degrees for 4-bonded C).
Unusual Methyl Moiety H-C-H Angle (ideally 109 Degrees).
The X-O-Y angle is significantly larger than the expected 120.0 Degrees.
The Si-O-Si angle is significantly larger than the expected 150.0 Degrees.
Short intramolecular contacts may arise when H-atoms are in (false) calculated positions. Short intramolecular contacts may also be a sign for a false structure with the molecule sitting on a site with improper site symmetry (e.g. '2' instead of '-1') which may happen when a lattice translation is missed. Short contacts are defined using a van der Waals radius of 1.2 Angstrom. For intramolecular contacts alerts are generated for contacts less than 2.0 Angstrom.
Short intermolecular H..H contacts may indicate incorrectly determined structures (i.e. wrong symmetry, missed translation symmetry, wrong position with reference to the symmetry elements, hydrogen atoms on atoms where there should not be any etc..) Short intermolecular contacts may be indicative for inconsistent symmetry data (e.g. coordinates for space-group P43 and symmetry specified as P41 or P21/n & P21/c confusions). Short contacts are defined using a van der Waals radius of 1.2 Angstrom. For intermolecular contacts, an alert is generated for contacts less than 2.4 Angstrom.
Short intramolecular contacts may arise when H-atoms are in (false) calculated positions. Short intramolecular contacts may also be a sign for a false structure with the molecule sitting on a site with improper site symmetry (e.g. '2' instead of '-1') which may happen when a lattice translation is missed. Short contacts are defined using a van der Waals radius of 1.2 Angstrom. Short H .. H contact involving CH3 H-atoms are often hampered by the fact that they involve H atoms at not optimal calculated positions.
Short intermolecular H..H contacts may indicate incorrectly determined structures (i.e. wrong symmetry, missed translation symmetry, wrong position with reference to the symmetry elements, hydrogen atoms on atoms where there should not be any etc..). Short intermolecular contacts may be indicative for inconsistent symmetry data (e.g. coordinates for space-group P43 and symmetry specified as P41 or P21/n & P21/c confusions). Short contacts are defined using a van der Waals radius of 1.2 Angstrom. Short H .. H contact involving CH3 H-atoms are often hampered by the fact that they involve H atoms at not optimal calculated positions.
Short non-bonding intra D-H..H-X contact.
Short non-bonding inter D-H..H-X contact.
Short non-bonding intra D-H..H-D contacts may be related to disordered or misplaced H-atoms.
Short non-bonding inter D-H..H-D contacts may be related to disordered or misplaced H-atoms. Experience has shown that any intermolecular H...H separation of less than 1.8 Angstroms between unit-occupancy H atoms is a clear indicator that one or both of these H atoms may be wrongly placed.
Potential hydrogen bond donors are checked for the presence of suitable acceptors using commonly used (Jeffrey) H-bond criteria. As a general rule there should be an acceptor for each donor. Exceptions are very rare for O-H and more common for -NH and -NH2. A common error is an -OH on a calculated position pointing in the wrong direction.
This test alerts for possibly missed Hydrogen bonds as indicated by short (i.e. shorter than sum of the van der Waals radii - 0.2 Angstrom) Donor - Acceptor distances. Note: Short C=O .. O=C are observed sometimes when part of three-centre O-H, N-H or C-H O..O bridging.
This test reports on short intermolecular Halogen .. Donor/Acceptor atom-type distances.
This test raised an ALERT for short intermolecular contacts. In general, intermolecular contact distances should be not much smaller than the sum of the associated van der Waals Radii. More often than not, such short contacts can be a warning sign for errors. All short contacts should therefore be examined in some detail. Interesting exceptions are carbonyl- carbonyl interactions that often feature short O...C contacts (see Allen et al. (1998) B54, 320-329, short NO2 O...O interactions and BF4(-) to (aromatic) carbon contacts.
This test raised an ALERT for short intermolecular contacts between minor disorder components. In general, intermolecular contact distances should be not much smaller than the sum of the associated van der Waals Radii. More often than not, such short contacts can be a warning sign for errors. All short contacts should therefore examined in some detail. Interesting exceptions are carbonyl-carbonyl interactions that often feature short O...C contacts (see Allen et al. (1998) B54, 320-329.
Check this (unrealistically) long reported H..A contact. Jeffrey criterium: Contact .LT. vdWR(H) + vdWR(A) - 0.12 Angstrom.
Check this (unrealistically) long reported D..A contact. Jeffrey criterium: Contact .LT. vdWR(D) + vdWR(A) + 0.50 Angstrom.
Check this unrealistically small reported D-H..A Angle. Jeffrey criterium: D-H..A Angle .GT. 100 degrees.
Crystal structures in general do not contain large solvent accessible voids in the lattice. Most structures lose their long-range ordering when solvent molecules leave the crystal. Only when the remaining network is strongly bonded (e.g. zeolites and some hydrogen bonded networks) the crystal structure may survive. Residual voids in a structure may indicate the omission of (disordered) density from the model. Disordered density may go undetected when smeared since peak search programs are not designed to locate maxima on density ridges. The presence or absence of residual density in the void may be verified on a printed/plotted difference Fourier map or with PLATON/SQUEEZE. Voids of 40 Ang**3 may accommodate H2O. Small molecules such as Tetrahydrofuran have typical volumes in the 100 to 200 Ang**3 range. This test reports the volume of the largest solvent accessible void in the structure. A paper reporting a crystal structure with a significant solvent accessible void should at the least discuss the issue.
This test reports on a solvent accessible void in the structure, too large or too time consuming for the current PLATON version for a more detailed analysis as part of the validation run. Use the SOLV option for more details. Such a warning might also indicate that the symmetry is incomplete e.g. should have been specified as P-1 and not P1, leaving out half of the unit cell content.
No search for solvent accessible VOIDS done as part of VALIDATION in view of large unit-cell.
Too many solvent accessible VOIDS.
Crystal structures in general do not contain large solvent accessible voids in the lattice. Most structures lose their long-range ordering when solvent molecules leave the crystal. Only when the remaining network is strongly bonded (e.g. zeolites and some hydrogen bonded networks) the crystal structure may survive. Residual voids in a structure may indicate the omission of (disordered) density from the model. Disordered density may go undetected when smeared since peak search programs are not designed to locate maxima on density ridges. The presence or absence of residual density in the void may be verified on a printed/plotted difference Fourier map or with PLATON/SQUEEZE. Voids of 40 Ang**3 may accommodate H2O. Small molecules such as Tetrahydrofuran have typical volumes in the 100 to 200 Ang**3 range. This test reports the volume of the largest solvent accessible void in the structure. A paper reporting a crystal structure with a significant solvent accessible void should at the least discuss the issue. Note: The use of PLATON/SQUEEZE was reported in the CIF
This test reports on a solvent accessible void in the structure, too large or too time consuming for the current PLATON version for a more detailed analysis as part of the validation run. Use the SOLV option for more details. Such a warning might also indicate that the symmetry is incomplete e.g. should have been specified as P-1 and not P1, leaving out half of the unit cell content.
Bond distances given in the CIF are cross-checked with corresponding values calculated from the coordinates. Alerts are set at 1,2 and 3 sigma deviation levels. Note: Default s.u.'s are used where no su given (e.g. for C-H) In general, all differences should be within the associated s.u. Small differences may arise from rounding. Very large deviation (or zero distance) normally indicate incorrectly specified symmetry operations on the associated atoms, or 'cut-and-pasting' of incompatible CIF's.
Bond Angles given in the CIF are cross-checked with corresponding values calculated from the coordinates. Alerts are set at 1,2 and 3 sigma deviation levels. In general, all differences should be within the associated s.u. Small differences may arise from rounding. Very large deviations normally indicate incorrectly specified symmetry operations on the associated atoms, or 'cut-and-pasting' of incompatible CIF's.
Torsion angles given in the CIF are cross-checked with corresponding values calculated from the coordinates. Alerts are set at 1,2 and 3 sigma deviation levels. In general, all differences should be within the associated s.u. Small differences may arise from rounding. Very large deviations normally indicate incorrectly specified symmetry operations on the associated atoms, or 'cut-and-pasting' of incompatible CIF's.
Intermolecular contacts listed in the CIF are checked against the coordinates in the CIF. Alerts are set at 1,2 and 3 sigma deviation levels.
Hydrogen-Bond D-H listed in the CIF is checked. Alerts are set at 1,2 and 3 sigma deviation levels.
Hydrogen-Bond H..A listed in the CIF is checked. Alerts are set at 1,2 and 3 sigma deviation levels. This ALERT is generally related to incorrect symmetry codes. The symmetry number s in the symmetry code s_pqr should correspond to the expression for s in the CIF. Those expressions can be different for different software packages. E.g. pasting H-bond table data generated with PLATON into a CIF generated with SHELXL may raise this ALERT. Manual correction of the symmetry code should be trivial.
Hydrogen-Bond D..A listed in the CIF is checked. Alerts are set at 1,2 and 3 sigma deviation levels. This ALERT is generally related to incorrect symmetry codes. The symmetry number s in the symmetry code s_pqr should correspond to the expression for s in the CIF. Those expressions can be different for different software packages. E.g. pasting H-bond table data generated with PLATON into a CIF generated with SHELXL may raise this ALERT. Manual correction of the symmetry code should be trivial.
Hydrogen-Bond Angle D-H..A listed in the CIF is checked. Alerts are set at 1,2 and 3 sigma deviation levels. This ALERT is generally related to incorrect symmetry codes. The symmetry number s in the symmetry code s_pqr should correspond to the expression for s in the CIF. Those expressions can be different for different software packages. E.g. pasting H-bond table data generated with PLATON into a CIF generated with SHELXL may raise this ALERT. Manual correction of the symmetry code should be trivial.
Torsion angles specified in the CIF are checked for the 'linear variety' where one or both of the 1-2-3 and 2-3-4 bond angles are close to 180 Deg. SHELXL97 will generate those 'torsions' for molecules containing linear moieties (E.g. Metal-C=O).
When labels are found on geometry items (bonds, angles etc.) that are not in the coordinate list, and alert _71n is issued, related to alert _70n.
When labels are found on geometry items (bonds, angles etc.) that are not in the coordinate list, and alert _71n is issued, related to alert _70n.
When labels are found on geometry items (bonds, angles etc.) that are not in the coordinate list, and alert _71n is issued, related to alert _70n.
When labels are found on geometry items (bonds, angles etc.) that are not in the coordinate list, and alert _71n is issued, related to alert _70n.
When labels are found on geometry items (bonds, angles etc.) that are not in the coordinate list, and alert _71n is issued, related to alert _70n.
When labels are found on geometry items (bonds, angles etc.) that are not in the coordinate list, and alert _71n is issued, related to alert _70n.
When labels are found on geometry items (bonds, angles etc.) that are not in the coordinate list, and alert _71n is issued, related to alert _70n.
When labels are found on geometry items (bonds, angles etc.) that are not in the coordinate list, and alert _71n is issued, related to alert _70n.
Up to 4 Character Labels of the type C11, H101, N10A, i.e. chemical symbol + number + optional letter are to be preferred.
Same as 701 but for distance without su (esd). Difference is tested in terms of Angstroms.
Same as 702 but for angle without su (esd). Difference is tested in terms of Degrees.
Same as 703 but for torsion without su (esd). Difference is tested in terms of Degrees.
Same as 704, but for distance without su (esd). Difference is tested in terms of Angstroms.
Same as 705 but for distance without s.u. (esd). Differences are tested in terms of Angstrom.
Same as 706 but for distance without s.u. (esd). Differences are tested in terms of Angstrom.
Same as 707 but for distance without s.u. (esd). Differences are tested in terms of Angstrom.
Same as 708 but for angle without s.u. (esd). Differences are tested in terms of Degrees.
A large ratio of the reported and calculated bond s.u.'s is found. The use of a DFIX instruction might cause such a warning since calculated s.u.'s are based on reported variances only. Note_1: su's on the unit-cell dimensions are taken into account in the calculation of expected su's. This may result in large differences between expected and reported su's when this contribution is not included in the reported su's, in particular for inaccurate unit-cells. Note_2: Another source for the discrepancy between calculated and reported su's can be that the validation software has access only to the variances of the refined parameters as opposed to the full co-variance matrix used by e.g. SHELXL for the calculation of derived parameters with associated su's. Constrained/restrained refinement may cause largei co-variances.
A large ratio of the reported and calculated bond angle s.u.'s is found. This check should warn for erroneous rounding: E.g. 105.5(19) to 105.5(2) or 105.0(5) to 105(5) etc. Note: Large differences are possible when certain constraints/restraints were applied in the refinement (e.g. the FLAT option in SHELXL97). Note: su's on the unit-cell dimensions are taken into account in the calculation of expected su's. This may result in large differences between expected and reported su's when this contribution is not included in the reported su's, in particular for inaccurate unit-cells. Note_2: Another source for the discrepancy between calculated and reported su's can be that the validation software has access only to the variances of the refined parameters as opposed to the full co-variance matrix used by e.g. SHELXL for the calculation of derived parameters with associated su's. Constrained/restrained refinement may cause large co-variances.
A large ratio of the reported and calculated torsion angle s.u.'s is found. This check should warn for erroneous rounding: E.g. 105.5(19) to 105.5(2) or 105.0(5) to 105(5) etc. Note: su's on the unit-cell dimensions are taken into account in the calculation of expected su's. This may result in large differences between expected and reported su's when this contribution is not included in the reported su's, in particular for inaccurate unit-cells. Note_2: Another source for the discrepancy between calculated and reported su's can be that the validation software has access only to the variances of the refined parameters as opposed to the full co-variance matrix used by e.g. SHELXL for the calculation of derived parameters with associated su's. Constrained/restrained refinement may cause large co-variances.
A large ratio of the reported and calculated contact distance s.u.'s is found. Note: su's on the unit-cell dimensions are taken into account in the calculation of expected su's. This may result in large differences between expected and reported su's when this contribution is not included in the reported su's, in particular for inaccurate unit-cells.
A large ratio of the reported and calculated H-bond D-H distance s.u.'s is found. The use of a DFIX instruction might cause such a warning since calculated s.u.'s are based on reported variances only. Note: su's on the unit-cell dimensions are taken into account in the calculation of expected su's. This may result in large differences between expected and reported su's when this contribution is not included in the reported su's, in particular for inaccurate unit-cells.
A large ratio of the reported and calculated H-bond H..A distance s.u.'s is found. Note: su's on the unit-cell dimensions are taken into account in the calculation of expected su's. This may result in large differences between expected and reported su's when this contribution is not included in the reported su's, in particular for inaccurate unit-cells.
A large ratio of the reported and calculated H-Bond D...A distance s.u.'s is found.
A large ratio of the reported and calculated H-Bond D-H..A angle s.u.'s is found. Note: su's on the unit-cell dimensions are taken into account in the calculation of expected su's. This may result in large differences between expected and reported su's when this contribution is not included in the reported su's, in particular for inaccurate unit-cells.
Likely missing s.u. on Bond in CIF.
Likely missing s.u. on Bond angle in CIF.
Likely missing s.u. on Torsion angle in CIF.
Likely missing s.u. on contact Distance in CIF.
Likely missing s.u. on H-Bond D-H distance in CIF.
Likely missing s.u. on H-Bond H...A distance in CIF.
Likely missing s.u. on H-Bond D...A distance in CIF.
Likely missing s.u. on H-Bond D-H..A angle in CIF.
An s.u. should not be given in the CIF for constrained distances. Please check for proper refinement status flags (e.g. R)
An s.u. should not be given in the CIF for constrained angles. Please check for proper refinement status flags (e.g. R)
An s.u. should not be given in the CIF for constrained torsion angles. Please check for proper refinement status flags (e.g. R)
An s.u. should not be given in the CIF for constrained contact distances. Please check for proper refinement status flags (e.g. R)
An s.u. should not be given in the CIF for constrained distances. Please check for proper refinement status flags (e.g. R)
An s.u. should not be given in the CIF for constrained distances. Please check for proper refinement status flags (e.g. R)
An s.u. should not be given in the CIF for constrained distances. Please check for proper refinement status flags (e.g. R)
An s.u. should not be given in the CIF for constrained angles. Please check for proper refinement status flags (e.g. R)
The CIF contains no X-H Bonds. This might be caused by not using the SHELXL instruction BOND $H Inclusion is required by Acta Cryst. but not necessarily so by other journals.
The CIF contains no X-Y-H or H-Y-H bond angles. This might be caused by not using the SHELXL instruction BOND $H. Those data should also be supplied when H-atoms are introduced on calculated positions and/or refined riding on their carrier atom. Inclusion is required by Acta Cryst. but not necessarily so by other journals.
Bond list in CIF likely incomplete.
The CIF contains more bonds than the unique set, indicating redundancy. An example is redundancy due to the inclusion of symmetry related bonds.
Report on unusual C-H bonds not caught in other tests.
Report on unusual N-H bonds not caught in other tests.
Report on unusual O-H bonds not caught in other tests.
Note: Exceptions can be H-atoms in acid O..H..O bridges or in H5O2+
(Hydronium) species.
Report on unusual C-C bonds, possibly not caught in other tests. Exceptions include C-C distances of around 1.75 Ang. in e.g. 1,2-dicarba-closo-dodecaborane.
Likely Erroneous Bond Entry
Likely Erroneous Contact Entry
Likely Erroneous D-H Entry
Possibly erroneous (Bond)angle less than 45 degree. The angle might be considered for elimination from the CIF when irrelevant. This ALERT can also be triggered when the assigned occupancy factors are incorrect.
Atoms given in a CIF should form a 'connected set', i.e. no symmetry operations are needed to get atoms in a bonding position. A connected set of atoms is not needed for the least squares refinement (unless hydrogen atoms are to be added at calculated positions). Geometry listings (bonds, angles, torsions & H-bonds) become unwieldy for non-connected atom sets.
A Flack parameter value is erroneously given for a structure reported in a centrosymmetric space-group.
The geometry of the reported moiety appears to be unusual/inconsistent. The C-O bond distances in C-CO2 are expected to add up to about 2.5 The N-O bond distances in C-NO2 are expected to add up to about 2.4
Unless for a good reason, molecular species should be transformed (by symmetry and/or translation) so that their centres of gravity are close to or within the unit-cell bounds. This is a strict rule for the main species. Deviations from this general rule are for smaller additional species when relevant for intermolecular interactions with the main species.
This test addresses the consistency of the absolute configuration assignment in non-centrosymmetric structures with proper symmetry operations (i.e. all matrices with determinant = 1) only. Verify the (R/S) absolute configuration assignment of this atom and the consistency of the absolute configuration implicit in the CIF-data with that in the 'ORTEP' illustration. Torsion angles should have the correct sign. The absolute structure assignment should also be consistent with the lowest value of the Flack parameter and/or know absolute configuration.
This test addresses the consistency of the absolute structure assignment (i.e. polarity etc.) in non-centrosymmetric structures in space groups that include improper symmetry operations (e.g. mirror planes). Check the (R/S) absolute configuration assignment of this atom and the consistency of the absolute configuration implicit in the CIF-data with that in the 'ORTEP' illustration.
This test addresses the consistency of the absolute configuration assignment of molecules in the reported asymmetric unit among coordinates, molecular presentations and chemical diagrams. Check the (R/S) absolute configuration assignment of this atom and the consistency of the absolute configuration implicit in the CIF-data with that in the 'ORTEP' illustration.
This test reports the valency of an atom as predicted by the Valence
Bond Model. See:
N.E. Brese & M. O'Keeffe (1991) Acta Cryst. B47, 192-197.
I.D. Brown (2002). The Chemical Bond in Inorganic Chemistry:
The Bond Valence Model. Oxford University Press.
More explicit info on the calculations can be obtained by running the
calculations explicitly with the PLATON option BondValence.
Note: The underlying theory is empirical and might not apply to the
case at hand (e.g. charged species).
Atom labels are generally not a number (i.e. starting with one or two characters indicating the atom type). Labels can be erroneously numeric due to typing errors (e.g. 'Oxygen' typed as 'zero').
Atom labels are generally not a number (i.e. starting with one or two characters indicating the atom type). Labels can be erroneously numeric due to typing errors (e.g. 'Oxygen' typed as 'zero').
PLATON has a problem with the Cell data. The possible reason can be that the cell data are missing, incomplete or out-of-sequence. PLATON/CHECK wishes to see the cell and symmetry data before any coordinates are given. PLATON expects the values of all six cell parameters.
The CIF contains records longer than 80 characters. Not all software will read beyond column 80. The CIF-1.1 definition specifies a maximum of 2048 character per record.
Fatal Problem: Check loop data names and data for errors. There are likely too many or to few data in the loop.
Problem: ARU representations turn out to be needed outside the ORTEP style -5:5 unit-cell translation range. The Analysis might be incomplete. The problem often occurs for structures with aliphatic chains stretching over many unitcells or network structures. Transformation of the unitcell content to a symmetry related position might solve the problem.
Check Coordinate Data Loop.
Check UIJ Data Loop.
PLATON can handle up to 7000 atoms in the (expanded) ATOM list. This might happen with disordered or network structures in high symmetry space groups. Deletion of the symmetry information might solve part of the problem and provide a partial validation. Alternatively, clicking on 'NOSYMM' on the PLATON menu before invoking validation might address the problem.
The software did not succeed in finding/analyzing a parsable weighting scheme. SHELXL style weight parameters are expected to be given in the format: _refine_ls_weighting_details 'calc w=1/[\s^2^(Fo^2^)+(0.1000P)^2^+0.0000P] where P=(Fo^2^+2Fc^2^)/3' JANA style weight is expected to be given in the format: _refine_ls_weighting_details 'w=1/(\s^2^(I)+0.0016I^2^)' Do not edit this string or make it into a text block between ';'.
The software did not succeed in Parsing SHELXL style weighting scheme. The string might have been edited.
Analysis for missing reflections may be incomplete due to an out-of-memory problem.
The ADDSYM test for missed symmetry is not executed for structures with too many disordered atoms.
Internal PLATON Problem. Please refer problem to author at a.l.spek@uu.nl
This G_ALERT can be ignored in the case that the so-called 'on-the-cheap' Flack parameter is reported as determined with SHELXL. Exactly zero values are possible but may also be a software artefact. The following should be checked: Problem #1: Some SHELXL97 versions do not allow negative values of the Flack parameter when determined using the BASF/TWIN instructions. Negative values are set to 0.00001. Refinement may not converge completely. Problem #2: Some SHELXL97 versions put meaningless values in the CIF for the Flack parameter when 'TWIN -1 0 0 0 -1 0 0 0 -1 2 / BASF' instructions (i.e. an explicit matrix is specified on the TWIN instruction) are used. Please check the value of BASF (in the list output) against the Flack parameter in the CIF.
The use of restraints used in the refinement should be explained in the write-up of a structure analysis. Note: An exception are restraints for floating origins (e.g. in P21).
ALERTS related to twinning effects that can not (yet) be accounted for as part of the VALIDATION algorithms have been suppressed.
ALERTS related to the use of radiation other than AgKa, MoKa, CuKa have been suppressed.
Likely cause: Dataset names on CIF and FCF differ. Note: FCF Validation is Skipped for this Entry.
Likely causes: Wrong Dataset, CIF or FCF Parameters Edited inconsistently. Note: FCF Validation is Skipped for this Entry.
Either no reflections in FCF or uninterpretable due to unknown format or editing. Note: FCF Validation is Skipped for this Entry.
A low maximum percentage of reflections with I .gt. 2*s(I) may
indicate:
1 - Missed translation symmetry. E.g. all reflections hkl weak
for l = 2n +1
2 - Pseudo-merohedral twinning, index .gt. 1. (e.g. non-spacegroup
extinctions.
3 - Very weak observed data.
This ALERT Reports on whether there is still a significant level of observed data beyond the Theta cutoff of the Dataset. There should be a good reason for a cutoff below sin(theta)/lambda = 0.6.
Possible causes: Beamstop theta-min limit set too high, large unit-cell etc. A possible technical solution on CCD based equipment involves the collection of additional images with the detector at a larger distance from the crystal with the beamstop setting changed accordingly..
Possible causes: Missing cusp of data (due to rotation about one axis), deleted (overflow) reflections or improper strategy (orthorhombic for monoclinic crystal etc.)
Possible causes: Missing cusp of data (due to rotation about one axis), deleted (overflow) reflections or improper strategy (orthorhombic for monoclinic crystal etc.)
This ALERT reports the number of missing reflections with Fc**2 values greater than the largest Fc**2 value in the FCF. Possible causes: Missing cusp of data (due to rotation about one axis), deleted (overflow) reflections or improper strategy (orthorhombic for monoclinic crystal etc.) or behind the beamstop.
This ALERT reflects the notion that a dataset should contain a sufficient number of Bijvoet (Friedel) pairs for the reliable determination of the absolute structure of a non-centrosymmetric crystal structure. This test is invoked when a Flack parameter value is specified. Note: SHELXL97 will calculate/report a Flack parameter value even for refinement against Friedel merged data. Remove the Flack entry from the CIF.
This ALERT reflects the notion that a dataset should contain a sufficient number of Bijvoet (Friedel) pairs for the reliable determination of the absolute structure of a non-centrosymmetric crystal structure. A Friedel coverage that deviates significantly from 100 percent may bias/invalidate the value of the Flack parameter.
The Hooft y Parameter is calculated independently from the Bijvoet differences and should have a value similar (observing the s.u.'s) to that of the Flack x Parameter. See: Hooft, R.W.W, Straver, L.H. & Spek,A.L. (2008). J. Appl, Cryst. 41, 96-103. Thompson,A.L. & Watkin, D.J. (2009). Tetrahedron: Asymmetry, doi:10.1016/j.tetasy.2009.02.025 Large differences may arise in cases where the Flack parameter was not done with BASF/TWIN or with essentially centrosymmetric data. See: Flack, H.D., Bernardinelli, G, Clemente, D.A., Linden, A. Spek, A.L. (2006) Acta Cryst. B62, 695-701.
The contribution of F(-h,-k,-l) to F(h,k,l) is likely not included in the FCF file. This usually indicates that the Flack parameter was NOT determined with a BASF/TWIN type of refinement.
This ALERT reports on the number of reflections with (Fo**2 - Fc**2) / Sigma(Fo**2) < - 100.0. Those reflections are better removed from the final refinement since they are in systematic error. Of course, a valid reason for this problem should be found.
This ALERT reports the number of reflections with intensities seriously effected by the beamstop. Reflections are counted for which theta < 3 Degrees and (Fo**2 - Fc**2) / sqrt(weight) < - 10.0. Those reflections are better removed from the final refinement since they are in systematic error.
Check reflection statistics of the data in the FCF for consistency with the data reported in the CIF. A difference usually indicates an edited CIF or an FCF file that was not created in the same SHELXL run where the CIF was created.
Please check whether the supplied FCF corresponds with the CIF produced in the same least squares refinement job. The test is based on the observed and calculated F**2 in the FCF and de weight parameters taken from the CIF.
Please check whether the supplied FCF corresponds with the CIF produced in the same least squares refinement job. The test is based on the observed and calculated F**2 in the FCF and de weight parameters taken from the CIF.
Please check whether the supplied FCF corresponds with the CIF produced in the same least squares refinement job. The test is based on the observed and calculated F**2 in the FCF and de weight parameters taken from the CIF.
Check & Explain why the Reported Rho(min) differs significantly from the value calculated on the basis of the reported structure. Note: The Reported and Calculated values may differ slightly due to a differing peak interpolation algorithm.
Check & Explain why the Reported Rho(max) differs significantly from the value calculated on the basis of the reported structure. Note: The Reported and Calculated values may differ slightly due to a differing peak interpolation algorithm.
Please check whether the R1 value that is reported in the CIF corresponds with the R1 value calculated from the parameters supplied in the CIF. This test is based on the observed reflection data in the FCF and reflection data that are calculated with the parameters (i.e. coordinates, displacement and weight parameters) taken from the CIF.
Please check whether the wR2 value that is reported in the CIF corresponds with the wR2 value calculated from the parameters supplied in the CIF. This test is based on the observed reflection data in the FCF and reflection data that are calculated with the parameters (i.e. coordinates, displacement and weight parameters) taken from the CIF.
Please check whether the S value that is reported in the CIF corresponds with the S value calculated from the parameters supplied in the CIF. This test is based on the observed reflection data in the FCF and reflection data that are calculated with the parameters (i.e. coordinates, displacement and weight parameters) taken from the CIF.
SHELXL weight parameters are expected to be given in the format below: _refine_ls_weighting_details 'calc w=1/[\s^2^(Fo^2^)+(0.1000P)^2^+0.0000P] where P=(Fo^2^+2Fc^2^)/3' JANA style weight is expected to be given in the format: _refine_ls_weighting_details 'w=1/(\s^2^(I)+0.0016I^2^)' Do not edit this string or make it into a text block between ';'.
Check the proposed Twin Law. The entry in () represents the proposed rotation axis in reciprocal space and the one in [] the corresponding rotation is direct space. The relevant Twin Matrix can be found in the file '.ckf'. Note: This analysis is based on Fo/Fc differences with Fc data given in the .fcf file (i.e. Fobs, Fcalc listing). ALERT-930 is expected to generate an related ALERT-931 as well.
Check the proposed Twin Law. The entry in () represents the proposed rotation axis in reciprocal space and the one in [] the corresponding rotation is direct space. The relevant Twin Matrix can be found in the file '.fck'. Note: This test is based on F(calc) values calculated with the data in the CIF. This ALERT can be ignored when twinning has been addressed in the refinement (As indicated by the Absence of ALERT 930). Please check whether twinning is mentioned in the write-up of the paper.
This ALERT reports on the number of reflections for which I(obs) and I(calc) differ more that 10 times SigmaW. (The latter being the square root of the weight for that reflection in the L.S. refinement). The reason for those deviations should be investigated. When shown to be systematic errors, those reflections are best removed from the refinement and their omission from the refinement reported in the experimental section of an associated paper.
Both significantly positive and significantly negative values should invoke a search for a likely cause and a corrective action.
Apparently, observed data with I > n * sigma(I) were used in the F**2 least squares refinement, rather than all observed data.
Reported and Calculated Max(Hmax,-Hmin) values differ by more than one unit. Check the consistency of wavelength and reported resolution data.
Reported and Calculated Max(Kmax,-Kmin) values differ by more than one unit. Check the consistency of wavelength and reported resolution data.
Reported and Calculated Max(Lmax,-Lmin) values differ by more than one unit. Check the consistency of wavelength and reported resolution data.
Reported (in the CIF) and Actual (in the FCF) Max(Hmax,-Hmin) values differ by more than one unit. Check for data set truncation.
Reported (in the CIF) and Actual (in the FCF) Max(Kmax,-Kmin) values differ by more than one unit. Check for data set truncation.
Reported (in the CIF) and Actual (in the FCF) Max(Lmax,-Lmin) values differ by more than one unit. Check for data set truncation.
Multiple strongly negative intensities may be indicative for poor integration of the diffraction images. Too many negative intensities may result in higher than usual wR2 values.
Larger than expected residual density maximum outside heavy atom locations. This might be caused by unaccounted for twinning, wrongly assigned atom types and other model errors.
Larger than expected residual density minimum outside heavy atom locations. This might be caused by unaccounted for twinning, wrongly assigned atom types and other model errors.
Larger than expected residual density maximum on heavy atom location. This might be caused by unaccounted for twinning, wrongly assigned atom types and other model errors. Another cause may be a SHELXL 'DAMP 0 0' instruction for a non-converged refinement.
Larger than expected residual density minimum on heavy atom location. This might be caused by unaccounted for twinning, wrongly assigned atom types and other model errors. Another cause may be a SHELXL 'DAMP 0 0' instruction for a non-converged refinement.
Check for missing anomalous scattering factors.
Check for non-zero f" anomalous scattering factor values in the CIF. Note: Zero values are correct for SHELXL MERG 4 refinements.
Check the anomalous scattering factor values.
Check the anomalous scattering factor values.