!check.def version 240105 =================================================== # check.def contains the tests, error thresholds, short warning messages # and text offering some explanation and advise issued by # the program PLATON when run in the 'VALIDATION' mode # # This file is read when PLATON is called with the '-u' switch # (e.g. 'platon -u sk1500.cif') # # - Validation output will be in the order as defined implicitly below, # subject to being split-up in ALERT A, B, C & G section # # - Tests are identified with three-digit numbers # _0xx - general # _1xx - cell/symmetry # _2xx - adp-related # _3xx - intra geometry # _4xx - inter geometry # _5xx - coordination geometry # _6xx - void tests & varia # _7xx - varia # _8xx - (Fatal) Software Errors/Problems # _9xx - Reflection data issues # # - All tests are defined as two line stanzas # The first line gives the test-number and thresholds (A4, 3A5) # E.g. _klm crit_1 crit_2 crit_3 # The second line defines the message (A55). # E.g. 'Structure contains solvent accessible Voids of $F Ang**3' # # $I defines where (optionally) an 'integer' threshold/value will be placed # $F defines where (optionally) a 'real' threshold/value will be placed # $A defines where an atom label is inserted (first) # $B defines where an atom label is inserted (second) # $X defines where bond,angle,torsion (calculated) is inserted # $Y defines where bond,angle,torsion (reported) is inserted # # Tests (value > crit) are done from right to left (ie crit_3 crit_2 crit_1) # # ALERT_Level_A = Could Indicate a Serious Problem - Consider Carefully. # ALERT_Level_B = Might Indicate a Potentially Serious Problem. # ALERT_Level_C = Check to Ensure it is OK and not Because of an Oversight. # ALERT_Level_G = General Info. Check that it is not Something Unexpected. # # ALERT_Type_1 = CIF Construction/Syntax Error, Inconsistent or Missing Data. # ALERT_Type_2 = Indicator that the Structure Model may be Wrong or Deficient. # ALERT_Type_3 = Indicator that the Structure Quality may be Low. # ALERT_Type_4 = Cosmetic improvement, Methodology, Query or Suggestion. # ALERT_Type_5 = Informative Message, Check. # # NOTES: - Validation runs invoked with the '-u' option will provide textual # information and HELP on the reported ALERTS (and -U without) # - The -G option provides for 'Chem-Mode' (i.e. without Acta # specific ALERTS) # - Actual ALERTS start at _002 (Others are pseudo ALERTS) # - Coding on criteria line: A = All, I = IUCr only, O = Obsolete # - Four numbers (0 or 1) indicate (and used for counting) respectively # - Missing Experimental Info Issues # - Experimental Data Related Issues # - Structural Model Related Issues # - Unresolved or to be Checked Issues #============================================================================= # >>> Check for '_shelx_res_file' refinement instruction file _001 0 2 3 1 C 1 0 0 0 No _shelx_res_file DataName Found in SHELXL CIF Please Do ! SHELXL20xy and later will automatically include the final .res in the CIF as an embedded comment preceded by the dataname '_shelx_res_file'. That dataname should not be renamed into _iucr_refine_instructions_details. #============================================================================= # >>> Report number of atom sites with distance/angle restraints _002 0 0 0 2 A 0 0 1 0 Number of Distance or Angle Restraints on AtSite $I Note This ALERT reports the number of atomic sites that are flagged as distance or angle restrained (D-Flag). #============================================================================= # >>> Report number of non-H atoms with Uiso or Uij restraints _003 0 0 0 2 A 0 0 1 0 Number of Uiso or Uij Restrained non-H Atoms ... $I Report This ALERT reports the number of non-H atoms that are flagged as handled with Uiso or Uij restraints (U-Flag). #============================================================================= # >>> Report Dimensionality of polymer _004 0 0 0 5 A 0 0 0 0 Polymeric Structure Found with Maximum Dimension $I Info This ALERT reports on polymeric networks and their dimensionality as found in the crystal structure. Note: Polymeric structures can be legitimate or due to an erroneous structure analysis. #============================================================================= # >>> Check for refinement instruction file _005 0 0 1 5 A 1 0 0 0 No Embedded Refinement Details Found in the CIF Please Do ! No embedded 'refinement details' records were found in the CIF. Acta Cryst. requires the inclusion of the last shelxl.res file (in case of a SHELXL or XL refinement or similar for non-SHELXL refinement programs) in the CIF, embedded between records with semicolons in position 1, preceded by an '_iucr_refine_instructions_details' record. Note: SHELXL20xy will automatically include the final .res as an embedded comment with the dataname '_shelx_res_file'. #============================================================================= # >>> Check for Extinction parameter refinement _006 0 0 0 5 A 0 0 0 0 Note: Extinction Parameter Refined = $A ! Info This ALERT reports the refinement of an extinction parameter. SHELXL corrects Fobs values in the FCF for Extinction. JANA not. Note: Large values of this parameter may be caused by other factors than extinction (e.g. twinning, systematically under or over-estimated intensities and other systematic errors). #============================================================================= # >>> Report on unrefined D-H atoms _007 0 0 0 5 A 0 0 1 0 Number of Unrefined Donor-H Atoms .............. $I Report It is standard practice to refine Hydrogen atoms on hetero atoms as proof of their correct assignment. #============================================================================= # >>> Check for refinement reflections details _008 0 0 2 5 A 1 0 0 0 No _iucr_refine_reflections_details in the CIF Please Do ! No reflection records were found in the CIF. Acta Cryst. and 'FAIR' require the inclusion of the unmerged reflection file used in the final refinement (shelxl.hkl in case of a SHELXL or XL refinement) in the CIF, embedded between records with semicolons in position 1 and preceded by an '_iucr_refine_instructions_details' record. Note: SHELXL20xy will automatically include the .hkl as an embedded comment with the dataname '_shelx_hkl_file'. #============================================================================= # >>> Check for potential Radiation type and standard wavelenght conflict _009 0 2 2 1 A 0 0 0 1 Reported Radiation_type and Wavelength Conflict? Please Check The reported values for _diffrn_radiation_type and _diffrn_radiation_wavelength should be consistent. This ALERT should catch possible cases such as where a synchrotron based dataset is erroneously refined with one of the standard wavelengths such as MoKa = 0.71073. #============================================================================= # >>> Test for Reflection Data for Validation and Archival _010 0 0 0 1 A 1 0 0 0 No Suitable (Embedded) Reflection Data Supplied Please Do ! Validation is not complete without the availability of the diffraction data. Deposited reflection data are preferably the set of reflections that were used in the final refinement and embedded in the CIF between records with semicolons in position 1 and preceded by an _iucr_refine_reflections_details record. SHELXL20xy will do that automatically. Alternatively, an external file with final observed, calculated and sigma reflection data will be the minimum for validation and archival. #============================================================================= # >>> Test for any ATOMS found in CIF _011 0 0 0 1 A 0 0 0 0 No Atoms Found in the Supplied CIF ............. Please Check No atom coordinates were detected in the CIF prior to the U(i,j) loop. #============================================================================= # >>> Check for valid _shelx_res_checksum _012 0 0 1.0 1 A 1 0 0 0 $A_shelx_res_checksum Found in CIF ...... Please Check The supplied CIF contains a '_shelx_res_file' record but not a valid associated '_shelx_res_checksum' record. A valid pair of embedded .res and .hkl files allows the automatic creation of a .fcf file with SHELXL20xy to be used for a detailed analysis of the refinement result. A file is valid when the calculated and reported checksums are identical. Only characters with an ASCII value higher than 32 contribute to the checksum. An embedded .res file might be broken, either due to tranfer errors or to deliberate or accidental post-refinement editing of its content. #============================================================================= # >>> Check for _shelx_hkl_checksum _013 0 0 1.0 1 A 1 0 0 0 $A_shelx_hkl_checksum Found in CIF ...... Please Check The supplied CIF contains a '_shelx_hkl_file' record but not a valid associated '_shelx_hkl_checksum' record. A valid pair of embedded .res and .hkl files allows the automatic creation of a .fcf file with SHELXL20xy to be used for a detailed analysis of the refinement result. A file is valid when the calculated and reported checksums are identical. Only characters with an ASCII value higher than 32 contribute to the checksum. An embedded .res file might be broken, either due to tranfer errors or to deliberate or accidental post-refinement editing of its content. #============================================================================= # >>> Check for _shelxl_fab_checksum _014 0 0 1.0 1 A 1 0 0 0 $A_shelx_fab_checksum Found in CIF ...... Please Check The supplied CIF contains a '_shelx_fab_file' record but not a valid associated '_shelx_fab_checksum' record. A valid pair of embedded .res and .hkl files allows the automatic creation of a .fcf file with SHELXL20xy to be used for a detailed analysis of the refinement result. A file is valid when the calculated and reported checksums are identical. Only characters with an ASCII value higher than 32 contribute to the checksum. An embedded .res file might be broken, either due to tranfer errors or to deliberate or accidental post-refinement editing of its content. #============================================================================= # >>> Check for refinement reflections details (SHELXL20xy) _015 0 0 0 5 A 1 0 0 0 No _shelx_hkl_file Record in SHELXL20xy CIF .... Please Do ! No embedded reflection record was found in the CIF file that was created with SHELXL20xy (or XL). SHELXL20xy automatically includes the '.hkl' file that was used in the refinement (along with the final '.res' file) as an embedded comment with the dataname '_shelx_hkl_file'. Do not change this dataname in _iucr_refine_reflections_details. Such a record is useful for archival and follow-up calculations. #============================================================================= # >>> Check for refinement FAB file (SHELXL20xy) _016 0 0 0 5 A 1 0 0 0 No _shelx_fab_file Record in SHELXL20xy CIF .... Please Supply No embedded .fab record was found in the CIF file that was created with SHELXL20xy (or XL). SHELXL20xy automatically includes the '.fab' file that was used in the refinement (along with the final '.res' & '.hkl' files) as an embedded comment with the dataname '_shelx_fab_file'. Do not change this dataname. Such a record is useful for archival and follow-up calculations. #============================================================================= # >>> Check the Consistency of Scattering Type _017 0.00 0.00 0.00 1 A 0 0 1 0 Check Scattering Type Consistency of $Aas $B Check for the correct scattering type assignment to this atom. #============================================================================= # >>> Check _diffrn_measured_fraction_theta_max and *_full equality _018 0.00 1.00 2.00 1 A 0 0 0 0 _diffrn_measured_fraction_theta_max .NE. *_full ! Check The values of '_diffrn_reflns_theta_max' and '_diffrn_reflns_theta_full' are reported as equal. However, the associated reported values of '_diffrn_measured_fraction_theta_max' and '_diffrn_measured_fraction_theta_full' are not equal. This is inconsistent. CIF Dataname Definitions: _diffrn_measured_fraction_theta_max: Fraction of unique (symmetry-independent) reflections measured out to '_diffrn_reflns_theta_max'. _diffrn_measured_fraction_theta_full: Fraction of unique (symmetry-independent) reflections measured out to '_diffrn_reflns_theta_full'. _diffrn_reflns_theta_max: Maximum theta angle in degrees for the measured intensities. The fraction of unique reflections measured out to this angle is given by '_diffrn_measured_fraction_theta_max'. -diffrn_reflns_theta_full: The theta angle (in degrees) at which the measured reflection count is close to complete. The fraction of unique reflections measured out to this angle is given by '_diffrn_measured_fraction_theta_full'. #============================================================================= # >>> Check _diffrn_measured_fraction_theta_max/full consistency _019 0.00 0.02 1.00 1 A 0 1 0 0 _diffrn_measured_fraction_theta_full/*_max < 1.0 $F Report The reported value of _diffrn_measured_fraction_theta_full is less than the reported value of _diffrn_measured_fraction_theta_max. Their ratio is reported when less than 1.0. When theta_full is less than theta_max such a value indicates that there are relatively more reflections missing at lower resolution. The measured fraction (completeness) is expected to be higher at a lower theta_full value. Usually, a theta_full value corresponding to sin(theta)/lambda = 0.6 should give a satisfactory data completeness value. CIF Dataname Definitions: _diffrn_measured_fraction_theta_max: Fraction of unique (symmetry-independent) reflections measured out to out to '_diffrn_reflns_theta_max'. _diffrn_measured_fraction_theta_full: Fraction of unique (symmetry-independent) reflections measured out to out to '_diffrn_reflns_theta_full'. _diffrn_reflns_theta_max: Maximum theta angle in degrees for the measured intensities. The fraction of unique reflections measured out to this angle is given by '_diffrn_measured_fraction_theta_max'. -diffrn_reflns_theta_full: The theta angle (in degrees) at which the measured reflection count is close to complete. The fraction of unique reflections measured out to this angle is given by '_diffrn_measured_fraction_theta_full'. #============================================================================= # >>> Check for unusually high Rint value _020 0.12 0.18 0.25 3 A 0 1 0 0 The Value of Rint is Greater Than 0.12 ......... $F Report 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. #============================================================================= # >>> Check Expected number of Reflections (Max = 1 Centro, 2 - non-centro) _021 0.01 0.05 100. 4 A 0 1 0 0 Ratio Unique / Expected Reflections too High ... $F 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 absencies not omitted from the observed data count. 2 - Refinement with redundant (i.e. not merged/unique) data set. 3 - SHELXL HKLF 5 Refinement #============================================================================= # >>> Check Expected number of Reflections (completeness) _022 0.05 0.10 0.15 3 A 0 1 0 0 Ratio Unique / Expected Reflections (too) Low .. $F 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 Theta-Max _023 .010 .025 0.05 3 A 0 1 0 0 Resolution (too) Low [sin(theta)/Lambda < 0.6].. $F Ang-1 Check resolution of the data set. This alert is issued when sin(theta)/lambda < 0.6 (i.e. theta < 25.24 degree for MoKa or 67.7 degree for CuKa radiation). In principle, all observed data should be included in the refinement. Alternatively, a sin(theta)/Lambda cutoff value can be used at a value where average(I/sigma(I)) < 2 in order not to refine on noise. #============================================================================= # >>> Check for required Friedel pair averaging Z<=Si (Obsolete 1/1/2011) _024 0 2 2 4 A 0 0 0 0 Merging of Friedel Pairs is Indicated .......... ! (No longer imposed) #============================================================================= # >>> Check for Hmin..Lmax _025 .000 .000 2.00 1 A 1 0 0 0 Hmin..Lmax Data Incomplete or Missing .......... Please Check Check reported h,k,l - range with calculated range based on reported theta-max. #============================================================================= # >>> Check for a weak data set _026 50 60 70 3 A 0 1 0 0 Ratio Observed / Unique Reflections (too) Low ..$I% Check Check whether a sufficient fraction of the unique data set is indeed above the 2 * sigma(I) level. All reflection data are included in this test. Check whether this low ratio is caused by weak data beyond sin(theta)/lambda > 0.5 (i.e. low resolution). #============================================================================= # >>> Check _diffrn_reflns_theta_full _027 .06 .07 .08 3 A 0 1 0 0 _diffrn_reflns_theta_full value (too) Low ...... $F Degree 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. #============================================================================= # >>> Check the reported _diffrn_measured_fraction_theta_max _028 .050 .100 0.15 3 A 0 1 0 0 _diffrn_measured_fraction_theta_max Value Low .. $F Why? Ideally, the reported '_diffrn_measured_fraction_theta_max' value, corresponding to theta-max, should be close to 1.0. #============================================================================= # >>> Check the reported _diffrn_measured_fraction_theta_full _029 .020 .040 .060 3 A 0 1 0 0 _diffrn_measured_fraction_theta_full value Low . $F Why? 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. (See SHELXL manual). PLATON may be used to analyse the case at hand (by invoking either the 'FCF-VALIDATION' mode or the 'ASYM-VIEW' mode). #============================================================================= # >>> Check _diffrn_reflns_number >= reflns_number_total _030 0 2 2 1 A 0 0 0 0 _diffrn_reflns_number < _reflns_number_total Please Check The number of measured reflections should be equal or greater than the number of unique reflections. #============================================================================= # >>> Check need for Extinction Correction Parameter _031 0.3 0.4 1.0 4 A 0 1 0 0 Refined Extinction Parameter Within Range of ... $F Sigma 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 s.u. Flack Parameter _032 0.2 10.0 10.0 4 A 0 0 0 0 Std. Uncertainty on Flack Parameter Value High . $F Report Check the validity of the absolute structure determination. A high s.u. 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 Flack Parameter value _033 0.3 10.0 10.0 4 A 0 0 0 0 Flack x Value Deviates > 3.0 * sigma from Zero . $F Note 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 than 2 * s.u., with s.u. < 0.04. For enantiopure compounds, s.u. should be less than 0.1. #============================================================================= # >>> Check for Flack parameter value specified Z>Si, non-centro _034 0 2 2 1 A 0 0 0 0 No Flack Parameter Given. Z > Si, NonCentro .... Please Do ! No Flack parameter value given for non-centrosymmetric structure with heaviest atom Z > Si. This might be intentional. #============================================================================= # >>> Check for _chemical_absolute_configuration _035 0 0 2 1 A 1 0 0 0 _chemical_absolute_configuration Info Not Given Please Do ! 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. #============================================================================= # >>> Check for missing Flack Parameter s.u. _036 0.5 2.0 2.0 1 A 1 0 0 0 No s.u. Given for Flack Parameter .............. Please Do ! 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 in that case. #============================================================================= # >>> Check _diffrn_reflns_theta_full _037 0 0 0 1 I 1 0 0 0 _diffrn_reflns_theta_full ............ Not Given Please Do ! 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. #============================================================================= # >>> Check _diffrn_measured_fraction_theta_max _038 0 0 0 1 I 1 0 0 0 _diffrn_measured_fraction_theta_max Not Given . Please Do ! This fraction should be specified in combination with the theta value given with the dataname _diffrn_reflns_theta_full. #============================================================================= # >>> Check _diffrn_measured_fraction_theta_full _039 0 0 0 1 I 1 0 0 0 _diffrn_measured_fraction_theta_full Not Given . Please Do ! This fraction should be specified in combination with the value for _diffrn_reflns_theta_max. #============================================================================= # >>> Test for H-atoms [0,1] _040 0.0 99.0 99.0 1 A 0 0 1 0 No H-atoms in this Carbon Containing Compound .. Please Check Alert for 'no H-atoms' in CIF. This is unusual for carbon containing compounds, but may be correct. #============================================================================= # >>> Test SumFormula _041 0.0 99.0 99.0 1 A 0 0 0 1 Calc. and Reported SumFormula Strings Differ Please Check 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. #============================================================================= # >>> Test MoietyFormula _042 0.0 99.0 99.0 1 I 0 0 0 1 Calc. and Reported MoietyFormula Strings Differ Please Check 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. #============================================================================= #1>>> Test for MolWeight _043 0.1 1.0 10.0 1 A 0 0 0 1 Calculated and Reported Mol. Weight Differ by .. $F Check 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. Note: The tabulated atomic weights that are used may deviate from the actual value in case of special isotopes of e.g. Uranium or Plutonium. #============================================================================= #1>>> Check Reported against calculated density _044 1.0 5.0 10.0 1 A 0 0 0 1 Calculated and Reported Density Dx Differ by .. $F Check In the ideal case, both data items should be the same within a small tolerance. If not, the reason should be clear. Check also whether the density value is reported in the CIF. #============================================================================= #1>>> Check Reported and Calculated Z _045 0.0 0.0 0.0 1 A 0 0 0 1 Calculated and Reported Z Differ by a Factor ... $A Check 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. #============================================================================= #1>>> Check Reported Density with calculated density from Z*MW _046 1.0 5.0 10.0 1 A 0 0 0 1 Reported Z, MW and D(calc) are Inconsistent .... $F Check D(calc) as calculated from the reported Z and MW is compared for consistency with the reported d(calc). #============================================================================= #1>>> Test SumFormula Given _047 0.0 0.0 0.0 1 A 1 0 0 0 SumFormula Not Given ........................... Please Do ! The Sumformula, corresponding with the Moietyformula, should be given. #============================================================================= #1>>> Test MoietyFormula Given _048 0.0 99.0 99.0 1 I 1 0 0 0 MoietyFormula Not Given (or Incomplete) ........ Please Check 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)' #============================================================================= # >>> Check Calculated Density .GT. 1.0 _049 0.0 0.0 1.0 1 A 0 0 0 1 Calculated Density Less Than 1.0 gcm-3 ......... $F Check 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.) #============================================================================= # >>> Test for mu given [0,1] _050 0.0 0.0 0.0 1 A 1 0 0 0 Absorption Coefficient mu Not Given ............ Please Do ! The linear absorption coefficient corresponding to the Sumformula should be given. #============================================================================= # >>> Test for difference mu(cif) with mu(calc) [%] _051 1 5 10 1 A 0 0 0 1 Mu(calc) and Mu(CIF) Ratio Differs from 1.0 by . $F % In the ideal case, both data items should be the same within a small tolerance. If not, the reason should be clear. Note: A significant difference may occur when no elemental mu values are specified on SHELXL .ins DISP records in case of synchrotron based data. #============================================================================= # >>> Test for specification absorption correction method [0,1] _052 0.0 99.0 99.0 1 A 1 0 0 0 Info on Absorption Correction Method Not Given Please Do ! 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'. #============================================================================= # >>> Test for specification xtal_dimension_min [0,1] _053 0.0 2.0 2.0 1 I 1 0 0 0 Minimum Crystal Dimension Missing (or Error) ... Please Check The smallest crystal dimension should be supplied in the CIF. The expected value should be a real number (i.e. not 0.35mm) #============================================================================= # >>> Test for specification xtal_dimension_mid [0,1] _054 0.0 2.0 2.0 1 I 1 0 0 0 Medium Crystal Dimension Missing (or Error) ... Please Check The medium crystal dimension should be supplied in the CIF. The expected value should be a real number (i.e. not 0.35mm) #============================================================================= # >>> Test for specification xtal_dimension_max [0,1] _055 0.0 2.0 2.0 1 I 1 0 0 0 Maximum Crystal Dimension Missing (or Error) ... Please Check The largest crystal dimension should be supplied in the CIF. The expected value should be a real number (i.e. not 0.35mm) #============================================================================= # >>> Test for specification xtal_radius [0,1] _056 0.0 0.0 0.0 1 I 1 0 0 0 Crystal Radius Missing for Spherical Correction Please Do ! Spherical correction for absorption is reported. The radius used is not supplied. #============================================================================= # >>> Test for correction for absorption needed _057 1.1 1.2 1.3 3 A 0 1 0 0 Correction for Absorption Required RT(exp) ... $F Do ! 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. #============================================================================= # >>> Test for specification Tmax [0,1] _058 0.5 0.5 0.5 1 A 1 0 0 0 Maximum Transmission Factor Missing ............ ? 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. #============================================================================= # >>> Test for specification Tmin [0,1] _059 0.5 0.5 0.5 1 A 1 0 0 0 Minimum Transmission Factor Missing ............ ? 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. #============================================================================= # >>> RR Test _060 1.10 1.50 2.00 4 I O 0 0 0 0 Ratio Tmax/Tmin (Exp-to-Rep) (too) Large ....... $F see IUCR WEB-Pages #============================================================================= # >>> RR' Test _061 0.10 0.25 0.50 4 I O 0 0 0 0 Tmax/Tmin Range Test RR' too Large ............. $F see IUCR WEB-Pages #============================================================================= # >>> Rescale Tmin & Tmax _062 0 2 2 4 I O 0 0 0 0 Rescale T(min) & T(max) by ..................... $F 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. #============================================================================= # >>> Test for Crystal Size _063 0.6 0.6 5.0 4 I 0 0 0 1 Crystal Size Possibly too Large for Beam Size .. $F mm 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. #============================================================================= # >>> Test for T(max) .GE. T(min) _064 0.0 0.0 0.0 1 A 0 0 0 0 Reported T(min) is Greater than Reported T(max) . ! 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. #============================================================================= # >>> Test for applicability of (semi-)empirical abs.corr. [0,1] _065 3.0 3.0 3.0 3 A O 0 0 0 0 Numerical Correction Might be Beneficial: mu*mid $F Note For high mu * mid values, numerical absorption correction procedures are recommended (either based on Gaussian integration or analytical) in case of homogeneous beam profiles and crystals small enough to fit within the homogeneous part of the X-ray beam. In case of in-homogeneous beams, a combination of numerical crystal face based correction and multi-scan correction is recommended. #============================================================================= # >>> Test whether Predicted and Reported Transmission Ranges are Identical _066 0.0 2.0 2.0 1 I 0 0 0 0 Predicted and Reported Tmin&Tmax Range Identical ? Check 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. #============================================================================= # >>> Insure that minimum dimension less max dimension _067 0.0 0.0 0.0 1 I 0 0 0 1 Maximum Dimension Less Min. Xtal Dimension ..... Please Check Minimum an Maximum dimensions are likely exchanged in the CIF. #============================================================================= # >>> Test for F000 Calc/Reported difference _068 0.01 10.0 10.0 1 I 0 0 0 1 Reported F000 Differs from Calcd (or Missing)... Please Check 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 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 #============================================================================= # >>> Test for label without numerical part _069 0.0 2.0 2.0 1 I 0 0 0 1 Atom Label Without Numerical Part .............. $A Do ! Acta Cryst. Notes for Authors requires atom labels to contain a numerical part. E.g. A label of the type 'O' should be given as 'O1'. This is not necessarily a requirement for other journals. #============================================================================= # >>> Test for duplicate labels _070 0.0 0.0 0.0 1 A 0 0 0 1 Duplicate Atomic Label on INPUT ................ $A Note The CIF contains duplicate labels posing interpretation problems for PLATON/CHECK. Derived geometry ALERTS may have their origin in this problem. #============================================================================= # >>> Test for uninterpretable labels _071 0 0 0 1 A 0 0 0 1 Uninterpretable Atom Label on Input ............ $A Note The CIF contains labels posing problems for PLATON/CHECK. Example: label HN1 with no scattering type information supplied. Validation is aborted. #============================================================================= # >>> Test for extreme first weighting parameter value (SHELXL) _072 0.1 0.2 0.3 2 A 0 0 0 1 SHELXL First Parameter in WGHT Unusually Large $F Report 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. #============================================================================= # >>> Test for inconsistency 'constr' versus 'H-Atoms refined' _073 0 0 0 1 I 0 0 0 1 H-atoms ref, but _hydrogen_treatment Reported as $A Check The structure contains refined hydrogen atoms. However the data item _refine_ls_hydrogen_treatment has the value 'constr'. The value 'mixed' is more appropriate. #============================================================================= # >>> Test for Occupancy equal 0.0 _074 0.0 0.0 0.0 1 A 0 0 0 1 Occupancy Parameter = 0.0 for .................. $A Check The CIF contains an atom with occupacy less than 0.0001 Please check whether the zero occupancy specification is intended. #============================================================================= # >>> Test for Occupancy greater than 1.0 _075 0.0 0.0 0.0 1 A 0 0 0 1 Occupancy $F Greater Than 1.0 for ...... $A The CIF contains an atom with Occupancy greater than 1.0. #============================================================================= # >>> Test for Occupancy less than 1.0 for atom on special position _076 0.0 1.0 1.0 1 A 0 0 0 1 Occupancy $F Less Than 1.0 for Sp.pos . $A 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. #============================================================================= # >>> Test for Non-Integral # of atoms in Unit Cell _077 0.0 1.0 1.0 4 A 0 0 0 1 Unitcell Contains Non-integer Number of Atoms .. Please Check 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. #============================================================================= # >>> Test for inconsistency 'geom' versus 'no H-Atoms' _078 0 0 0 1 I 0 0 0 1 No H-atoms, but _solution_hydrogens Reported as $A Check 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 '.'. #============================================================================= # >>> Test for inconsistency 'mixed' versus 'no H-Atoms' _079 0 0 0 1 I 0 0 0 1 No H-atoms, but _hydrogen_treatment Reported as $A Check 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 '.'. #============================================================================= # >>> Test maximum shift/error _080 0.05 0.10 0.20 2 A 0 0 1 0 Maximum Shift/Error ............................ $F Why ? Convergence of the refinement is proved 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. #============================================================================= # >>> Test for maximum shift/error given _081 0.00 0.00 0.00 1 A 0 0 0 1 No Maximum Shift/Error Given ................... Please Do ! A maximum shift/error should be specified in order to judge convergence. #============================================================================= # >>> Test for reasonable R1 _082 0.10 0.15 0.20 2 A 0 0 1 0 High R1 Value .................................. $F Report A higher than usual R1 indicates either an insufficient model or poor quality data. #============================================================================= # >>> Test for extreme second weighting parameter value (SHELXL) _083 5.0 25.0 50.0 2 A 0 0 0 1 SHELXL Second Parameter in WGHT Unusually Large $F Why ? 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. #============================================================================= # >>> Test for reasonable wR2 _084 0.25 0.35 0.45 3 A 0 0 1 0 High wR2 Value (i.e. > 0.25) ................... $F Report 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. #============================================================================= # >>> Test for default SHELXL weighting scheme _085 0 10 10 2 A 0 0 0 1 SHELXL Default Weighting Scheme is not Optimized Please Check The weighting scheme is found to be left at the SHELXL default. This default value is recommended for the preliminary structure refinement. It is uncommon that this unoptimized weight gives the best final refinement result. #============================================================================= # >>> Test for reasonable S (Too Low) _086 0.4 0.6 0.8 2 A 0 0 0 1 Unsatisfactory S Value (Too Low or Not Given) .. $F Check The Goodness-of-Fit value 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 refinement model or reflection data. #============================================================================= # >>> Test for reasonable S (Too High) _087 2.0 4.0 6.0 2 A 0 0 0 1 Unsatisfactory S value (Too High) .............. $F Check The Goodness-of-Fit value 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 refinement model or reflection data. #============================================================================= # >>> Test for reasonable Data / parameter ratio (centro) _088 10.0 12.5 16.7 3 A 0 0 1 0 Poor Data / Parameter Ratio .................... $F Note 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. #============================================================================= # >>> Test for reasonable Data / parameter ratio (non-centro) (Zmax < 18) _089 13.5 18.0 25.0 3 A 0 0 1 0 Poor Data / Parameter Ratio (Zmax < 18) ........ $F Note The data/parameter ratio should in general be higher than 7 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: The number of reflections used in this ratio is the number obtained by Laue group averaging. #============================================================================= # >>> Test for reasonable Data / parameter ratio (non-centro) (ZMAX > 18) _090 12.5 16.5 25.0 3 A 0 0 1 0 Poor Data / Parameter Ratio (Zmax > 18) ........ $F Note The data/parameter ratio should in general be higher than 8 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. The number of reflections used for this ratio is the Laue averaged number of reflections. The validation criteria used are expected to be met with a dataset complete with a resolution sin(theta)/lambda .GE. 0.6 Ang-1. #============================================================================= # >>> Test for 'No-wavelength given' _091 0 0 0 1 A 1 0 0 0 No Wavelength Found in CIF - 0.71073 Ang Assumed Please Check No Wavelength specification found in the CIF. #============================================================================= # >>> Test for wavelength type [Cu,Ga,Mo,Ag,In Ka] _092 0 0 0 4 A 0 0 0 1 Check: Wavelength Given is not Cu,Ga,Mo,Ag,In Ka $F Ang. The wavelength, specified in the CIF, is not CuKa = 1.5418A, GaKa = 1.3414A, MoKa = 0.71073A, AgKa = 0.56086A or InKa = 0.51359A radiation within a tolerance of 0.0005A. Valid exceptions are Kb, Neutron and Synchrotron data. #============================================================================= # >>> Test for inconsistency 'mixed' versus 'no refined H positions' _093 0 0 0 1 I 0 0 0 1 No s.u.'s on H-positions, Refinement Reported as $A Check 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' or 'refU' 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). #============================================================================= # >>> Test for maximum/minimum residual density ratio _094 2.0 4.0 8.0 2 A 0 0 1 0 Ratio of Maximum / Minimum Residual Density .... $F Report 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). #============================================================================= # >>> Test for residual density maximum given [0,1] _095 0 0 0 1 A 1 0 0 0 No Residual Density Maximum Given .............. Please Do ! No residual electron density maximum given in CIF. #============================================================================= # >>> Test for residual density minimum given [0,1] _096 0 0 0 1 A 1 0 0 0 No Residual Density Minimum Given .............. Please Do ! No residual electron density minimum given in CIF. #============================================================================= # >>> Test maximum residual density (Reported) _097 0.75 1.0 2.0 2 A 0 0 1 0 Large Reported Max. (Positive) Residual Density $F eA-3 A residual density maximum larger than expected is reported. This might be caused by residual absorption artefacts, unaccounted for twinning, disorder, wrongly assigned atom types, missing hydrogen atoms and other model errors. #============================================================================= # >>> Test for minimum residual density (Reported) _098 0.75 1.0 2.0 2 A 0 0 1 0 Large Reported Min. (Negative) Residual Density $F eA-3 A residual density minimum larger than expected is reported. This might be caused by residual absorption artefacts, disorder, wrongly assigned atom types and other model errors. #============================================================================= # >>> Test for minimum residual density greater zero [0, 1] _099 0.0 0.0 0.0 1 A 0 0 0 1 Minimum (Negative) Residual Density .GE. 0 !!... $F eA-3 Likely interchanged maximum and minimum values. Alternatively, the minimum residual density has the (unlikely) value zero. #========================================================================== # >>> Report non-integer reported Z-value in CIF _100 0 0 0 5 A 0 0 0 1 A Non-Integer Z value Reported in the CIF ...... $F Check The norm is integer. The CIF-definition for _cell_formula_units_Z specifies Z values as 1 -> infinity. SHELXL may report in certain cases a real number (E.g. Z = 0.67). In such a case, check whether really more decimals are intended and edit accordingly, i.e. 0.67 => 0.66667. #========================================================================== # >>> Test for insufficient digits for special position 1/3 & 2/3 in x-coord. _101 0 0 10 2 A 1 0 0 0 Limited Precision x-Coordinate $A For ... $B Check Fractions of the type (+/-)1/3 and (+/-)2/3 for the positional parameters of atoms in special positions should be provided with sufficient digits. (i.e. 0.66667 and 0.33333). Check whether exact 1/3 etc. is intended. #============================================================================= # >>> Test for insufficient digits for special position 1/3 & 2/3 in y-coord. _102 0 0 10 2 A 1 0 0 0 Limited Precision y-Coordinate $A For ... $B Check Fractions of the type (+/-)1/3 and (+/-)2/3 for the positional parameters of atoms in special positions should be provided with sufficient digits. (i.e. 0.66667 and 0.33333). Check whether exact 1/3 etc. is intended. #============================================================================= # >>> Test for insufficient digits for special position 1/3 & 2/3 in z-coord. _103 0 0 10 2 A 1 0 0 0 Limited Precision z-Coordinate $A For ... $B Check Fractions of the type (+/-)1/3 and i(+/-)2/3 for the positional parameters of atoms in special positions should be provided with sufficient digits. (i.e. 0.66667 and 0.33333). Check whether exact 1/3 etc. is intended. #============================================================================= # >>> Test for additional translational symmetry [0, 1] _104 0 0 0 1 A 0 0 0 1 The Reported Crystal System is Inconsistent with $A Check Check the reported crystal system against the reported space group. Alternatively, no crystal system was reported. #============================================================================= # >>> Test validity of inversion twinning operation _107 0 0 99 2 A 0 1 0 0 Twinning Matrix Invalid in Centrosymmetric SPGR ? Check Inversion twinning is meaningless in centrosymmetric spacegroup. #============================================================================= # >>> Test validity of the twinning operation _108 1 1 1 2 A 0 1 0 0 Twinning Matrix is inverted Laue group operation ? Check The SHELXL TWIN instruction matrix corresponds to a symmetry operation of the non-centrosymmetric Laue group of the crystal structure. This is not a valid twin operation. #============================================================================= # >>> Test the twinning operation as alternate inversion twinning _109 1 1 1 2 A 0 1 0 0 Twinning Matrix = Alternate Inversion Twinning . ? Check The SHELXL TWIN instruction matrix corresponds to an inverted non-centrosymmetric pointgroup operation belonging to the corresponding centrosymmetric Laue group. The reported twinning factor is actually the Flack x value. The close to zero CIF reported Flack parameter value is meaningless. Please re-refine with the TWIN instruction replaced by 'TWIN' (i.e. without numerical data). #============================================================================= # >>> Test for additional translational symmetry [0, 1] _110 0.5 0.5 999 2 A 0 0 0 1 ADDSYM Detects Potential Lattice Translation ... ? Check 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). Report on potential (pseudo/real) lattice centering or cell halving. Note: H-atoms and disordered atoms are not taken into account in the tests. #============================================================================= # >>> Test for additional centre of symmetry [0, 100] _111 90 95 100 2 A 0 0 0 1 ADDSYM Detects New (Pseudo) Centre of Symmetry . $I %Fit 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 with PLATON/ADDSYM 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. #============================================================================= # >>> Test for additional symmetry [0, 1] _112 50 95 100 2 A 0 0 0 1 ADDSYM Detects New (Pseudo) Symm. Elem $A $I %Fit 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). 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. Note: Atom types are treated in this test as EQUAL for structures with less than 250 atoms in the asymmetric unit in order to detect cases of misassigned atom types. 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. #============================================================================= # >>> Report New space-group suggested by ADDSYM _113 90 95 100 2 A 0 0 0 1 ADDSYM Suggests Possible Pseudo/New Space Group $A Check Tests for missed symmetry are done with ADDSYM, an extended MISSYM (C) clone. These tests warn for missed or possible higher (pseudo) symmetry in the structural model (i.e. based on the coordinate data). Close examination of the situation at hand is indicated in order to prove/disprove the issue (usually in combination with the reflection data). Chiral molecules are incompatible with an inversion centre or (glide)planes. For an example of reported pseudo-symmetry see I.A.Guzei et al, (2002). Acta Cryst. C58, m141-m143. Note: H-atoms and disordered atoms (i.e. atoms with population less than 1.0) are not taken into account in the tests. This may artificially lead to a symmetry higher than the actual one. Note: Atoms are treated as having the same atom type in order to catch certain types of disorder or incorrect atom type assignment. #============================================================================= # >>> Report on ADDSYM problem _114 0 2 2 2 A 0 0 0 1 ADDSYM Could not (Re)Construct Proper Spacegroup Please Check ADDSYM has problems to reconstruct a space group from the symmetry operation found in the symmetry expanded coordinate set. The reason being either intricate additionally detected pseudo-symmetry or serious errors in the data set. #============================================================================= # >>> Test for non-crystallographic centre of symmetry [0, 100] _115 50 100 100 5 A 0 0 0 1 ADDSYM Detects Noncrystallographic Inversion ...$I% Check 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. #============================================================================= # >>> Report implemented (Pseudo) Lattice Translation _116 0 1 2 2 A 0 0 0 1 ADDSYM Included (Pseudo) Lattice Translation ... Please Check A (Pseudo) Lattice translation was detected and implemented before the current ADDSYM analysis. #============================================================================= # >>> Report Problem with symmetry operator syntax _119 0 0 0 1 A 0 0 0 1 Problem with the Syntax of a Symmetry Operation. $A Check A symmetry operation should be specified in the CIF either without spaces or between quotes. #============================================================================= # >>> Test for consistent _symmetry_space_group_name_H-M and Symm Opp _120 0 10 10 1 A 0 0 0 1 Reported $A Inconsistent with Explicit $B Check 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. #============================================================================= # >>> Test for valid _symmetry_space_group_name_H-M _121 0 10 10 1 A 1 0 0 0 Invalid _symmetry_space_group_name_H-M ......... $A Check 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. #============================================================================= # >>> Test for ? _symmetry_space_group_name_H-M _122 0 0 0 1 A 1 0 0 0 No _symmetry_space_group_name_H-M Given ........ Please Do ! 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. #============================================================================= # >>> Test for Interpretable Space Group Symmetry _123 0 0 0 1 A 1 0 0 0 Uninterpretable or Inconsistent Space Group Info Please Check 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 or _symmetry_space_group_name_H-M_alt. Test for uninterpretable or inconsistent Space group information. #============================================================================= # >>> Test for _symmetry_equiv_pos_as_xyz present _124 0 0 0 1 A 1 0 0 0 Uninterpretable or No _symmetry_equiv_pos_as_xyz ? Check 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. #============================================================================= # >>> Test for ? _symmetry_space_group_name_Hall _125 0 10 10 4 I 1 0 0 0 No '_symmetry_space_group_name_Hall' Given ..... Please Do ! 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 #============================================================================= # >>> Test for _symmetry_space_group_name_Hall error _126 0 10 10 1 A 0 0 0 1 Error in or Uninterpretable Hall Symbol ....... $A Check 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://cci.lbl.gov/sginfo/hall_symbols.html #============================================================================= # >>> Test for _symmetry_space_group_name_Hall consistency _127 0 10 10 1 A 0 0 0 1 Implicit Hall Symbol Inconsistent with Explicit $A Check The reported Hall-symbol is not identical to the one internally tabulated for the space group as derived from the explicitly supplied symmetry operations. As an example, the Hall symbols '-P 2yn' and '-P 2yabc' both correspond with space group 'P21/n'. Alternatively, no Hall-symbol could be derived by PLATON for the explicit set of symmetry operations. This may be the case when an unusual origin is chosen. Refer to: S.R.Hall, Space Group Notation with an Explicit Origin; Acta Cryst. (1981), A37, 517-525. or: http://cci.lbl.gov/sginfo/hall_symbols.html #============================================================================= # >>> Test for non-standard space_group settings _128 0 10 10 4 A 0 0 0 1 Alternate Setting for Input Space Group$A $B Note P21/n and I2/a etc. settings are often preferred over P21/c and C2/c when that leads to a closer to 90 degrees beta angle. Standard choice of origin is to be preferred. A non-standard origin choice might be useful for for the comparison of related structures. #============================================================================= # >>> Test for unusual non-standard Space group name _129 0 0 0 4 A 0 0 0 1 Unusual Space Group Specified .................. $A Check The reported space-group name is unusual. #============================================================================= # >>> Test for Cubic: a = b = c _130 0 0 0 1 A 0 1 0 0 Cubic : a, b & c Dimensions Differ ........... Please Check Symmetry constraints on cell dimensions are checked. #============================================================================= # >>> Test for Cubic: alpha = beta = gamma = 90 _131 0 0 0 1 A 0 1 0 0 Cubic : alpha, beta and gamma should be 90 Deg Exact Please Check Symmetry constraints on cell dimensions are checked. #============================================================================= # >>> Test for Trigonal/Hexagonal : a = b _132 0 0 0 1 A 0 1 0 0 Trigonal/Hexagonal a and b Differ .............. Please Check Symmetry constraints on cell dimensions are checked. #============================================================================= # >>> Test for Trigonal/Hexagonal : alpha = beta = 90 _133 0 0 0 1 A 0 1 0 0 Trigonal/Hexagonal alpha and beta Should be 90 Deg Please Check Symmetry constraints on cell dimensions are checked. #============================================================================= # >>> Test for Trigonal/Hexagonal : gamma = 120 _134 0 0 0 1 A 0 1 0 0 Trigonal/Hexagonal gamma Should be 120 Deg Exact Please Check Symmetry constraints on cell dimensions are checked. #============================================================================= # >>> Test for Tetragonal: a = b _135 0 0 0 1 A 0 1 0 0 Tetragonal: a and b Should be Equal ........... Please Check Symmetry constraints on cell dimensions are checked. #============================================================================= # >>> Test for Tetragonal: alpha = beta = gamma = 90 _136 0 0 0 1 A 0 1 0 0 Tetragonal: alpha, beta & gamma Should be 90 Deg Please Check Symmetry constraints on cell dimensions are checked. #============================================================================= # >>> Test for Orthorhombic: alpha = beta = gamma = 90 _137 0 0 0 1 A 0 1 0 0 Orthorhombic: alpha, beta & gamma Should be 90 Deg Please Check Symmetry constraints on cell dimensions are checked. #============================================================================= # >>> Test for Monoclinic more than 1 angle off 90 degrees _138 0 0 0 1 A 0 1 0 0 Monoclinic: More than one Angle Unequal 90.0 ... Please Check Symmetry constraints on cell dimensions are checked. #============================================================================= # >>> Test for Rhombohedral a = b = c _139 0 0 0 1 A 0 1 0 0 Rhombohedral: a, b & c are not all Exactly Equal Please Check Symmetry constraints on cell dimensions are checked. #============================================================================= # >>> Test for Rhombohedral alpha = beta = gamma _140 0 0 0 1 A 0 1 0 0 Rhombohedral: alpha, beta & gamma are Not All Equal Please Check Symmetry constraints on cell dimensions are checked. #============================================================================= #1>>> s.u. on a - axis small or missing _141 0 10 10 4 A 1 0 0 0 s.u. on a - Axis Small or Missing .............. $F Ang. The s.u. on the a-axis is small or missing. The presence of s.u.'s (where required) and value are checked. S.u.'s as given by the diffractometer software are often much smaller then realistic. #============================================================================= #1>>> s.u. on b - axis small or missing _142 0 10 10 4 A 1 0 0 0 s.u. on b - Axis Small or Missing .............. $F Ang. The s.u. on the b-axis is small or missing. The presence of s.u.'s (where required) and value are checked. Su's as given by the diffractometer software are often much smaller then realistic. #============================================================================= #1>>> s.u. on c - axis small or missing _143 0 10 10 4 A 1 0 0 0 s.u. on c - Axis Small or Missing .............. $F Ang. The s.u. on the c-axis is small or missing. The presence of s.u.'s (where required) and value are checked. Su's as given by the diffractometer software are often much smaller then realistic. #============================================================================= #1>>> s.u. on alpha small or missing _144 0 10 10 4 A 1 0 0 0 s.u. on alpha Small or Missing .............. $F Degree The s.u. on alpha is small or missing. The presence of s.u.'s (where required) and value are checked. Su's as given by the diffractometer software are often much smaller then realistic. #============================================================================= #1>>> s.u. on beta small or missing _145 0 10 10 4 A 1 0 0 0 s.u. on beta Small or Missing .............. $F Degree The s.u. on beta is small or missing. The presence of s.u.'s (where required) and value are checked. Su's as given by the diffractometer software are often much smaller then realistic. #============================================================================= #1>>> s.u. on gamma small or missing _146 0 10 10 4 A 1 0 0 0 s.u. on gamma Small or Missing .............. $F Degree The s.u. on gamma is small or missing. The presence of s.u.'s (where required) and value are checked. Su's as given by the diffractometer software are often much smaller then realistic. #============================================================================= #1>>> s.u. on symmetry restricted cell angle _147 0 10 10 1 A 0 1 0 0 s.u. on Symmetry Constrained Cell Angle(s) ..... Please Check There should be no s.u. on symmetry constrained cell angles. Example: No s.u. on alpha, beta and gamma for orthorhombic symmetry. #============================================================================= #1>>> s.u. on a,b, or c - axis too large _148 0 10 10 3 A 0 1 0 0 s.u. on the $A - Axis is (Too) Large .... $F Ang. The s.u. on the reported -axis is unexpectedly large. #============================================================================= #1>>> s.u. on alpha, beta or gamma too large _149 0.10 0.20 10 3 A 0 1 0 0 s.u. on the $A Angle is Too Large ....... $F Degree The s.u. on the reported angle is too large. #============================================================================= #1>>> Check reported unit cell Volume value _150 0.5 1.0 1.0 1 A 1 0 0 0 Volume as Calculated Differs from that Given ... $F Ang-3 An ALERT is issued when the reported unit cell volume differs significantly from the volume calculated on the basis of the supplied cell dimensions. #============================================================================= # >>> Check for s.u. on Volume _151 0 10 10 1 A 1 0 0 0 No s.u. (esd) Given on Volume .................. Please Do ! Missing s.u. on cell volume. #============================================================================= # >>> Check for consistency of s.u. on Volume and cell parameters _152 1 99 99 1 I 0 0 0 0 The Supplied and Calc. Volume s.u. Differ by ... $I Units Some software packages calculate Volume s.u.'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. Also note that several cell parameters for higher symmetry cells are no longer independent. S.u. calculations need special treatment in those cases. #============================================================================= # >>> test for equal axial s.u.'s _153 0 10 10 1 I 0 0 0 1 The s.u.'s on the Cell Axes are Equal ..(Note) $F Ang. The reported cell axes s.u.'s are reported equal. Please check whether this is correct or a software default value. #============================================================================= # >>> test for equal cell angle s.u.'s _154 0 10 10 1 I 0 0 0 1 The s.u.'s on the Cell Angles are Equal ..(Note) $F Degree The reported cell angle s.u.'s are reported equal. Please check whether this is correct or a software default value. #============================================================================= # >>> Check for reduced cell aP _155 0 10 10 4 A 0 0 0 1 The Triclinic Unitcell is NOT Reduced .......... Please Do ! 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 dimension. #============================================================================= # >>> Check for non-standard axial order _156 0 10 10 4 A 0 0 0 1 Axial System Input Cell not Standard ........... Please Do ! The axial order should be from small to large in the triclinic cell. #============================================================================= # >>> Check for non-standard monoclinic beta angle less 90 Degrees. _157 0.0 10. 10. 4 A 0 0 0 1 Non-standard Monoclinic Beta Angle less 90 Deg $F Degree 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. #============================================================================= # >>> Check for standard reduced cell _158 0 10 10 4 A 0 0 0 1 The Input Unitcell is NOT Standard/Reduced ..... Please Check Unless for special reasons related to the structure/content, a unit-cell and structure is best reported with reference to the Niggli Reduced Cell. #============================================================================= # >>> Check Beta-Angle value for Monoclinic c _159 0 0 0 1 A 0 1 0 0 The Beta Angle Deviates from 90 for Monoclinic-c Please Check Only the Gamma angle may have a value not equal to 90 degrees. #============================================================================= # >>> Missing x-coordinate s.u. _161 0 10 10 4 A 0 0 0 1 Missing or Zero s.u. (esd) on x-coordinate for . $A Check Missing or Zero s.u. (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 y-coordinate s.u. _162 0 10 10 4 A 0 0 0 1 Missing or Zero s.u. (esd) on y-coordinate for . $A Check Missing or Zero s.u. (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 z-coordinate s.u. _163 0 10 10 4 A 0 0 0 1 Missing or Zero s.u. (esd) on z-coordinate for . $A Check Missing or Zero s.u. (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). #============================================================================= # >>> Check for Refined C-H H-Atoms _164 0 10 10 4 A 0 0 1 0 Nr. of Refined C-H H-Atoms in Heavy-Atom Struct. $I Note 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. #============================================================================= # >>> Check for R-flagged Non-H Atoms _165 0 10 10 3 A 0 0 0 1 Nr. of Status R Flagged Non-Hydrogen Atoms ..... $I Note Report on restrained (riding) Non-Hydrogen atoms. Note: This may lead to non meaningfull bond and angle s.u.'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. #============================================================================= # >>> Check for calc flagged atoms with s.u.'s on coordinates _166 0 10 10 4 A 0 0 0 1 S.U's Given on Coordinates for Calc-flagged .... $A Note Calc-flagged atoms are not supposed to carry s.u.'s on their coordinates. #============================================================================= # >>> Test DANG restraint value in CIF-Embedded .res file _167 0 0 0 3 A 0 0 1 0 A Non-default DANG Restraint Value has been used $F Report SHELXL applies a default effective standard deviation value of 0.04 Ang for the DANG restraints. The use of a much stronger restraint, with a lower value of those parameters, may hide serious problems with a structure. #============================================================================= # >>> Check for EXYZ Record(s) in CIF-Embedded shelxl.res _168 0 0 0 4 A 0 0 0 1 The CIF-Embedded .res File Contains EXYZ Records $I Report The use of EXYZ record(s) in the SHELXL .res file should be documented in the experimental section of the associated publication. #============================================================================= # >>> Check for AFIX 1 Record(s) in CIF-Embedded shelxl.res _169 0 0 0 4 A 0 0 0 1 The CIF-Embedded .res File Contains AFIX 1 Recds $I Report The use of 'AFIX 1' record(s) in the SHELXL .res file should be documented in the experimental section of the associated publication. #============================================================================= # >>> Check for sufficient data in in Atom data loop _170 0 0 0 4 A 0 0 0 1 Insufficient Data in Coordinate Loop ........... $A Insufficient data encountered in coordinate loop. A possible cause might be the use of a SHELX style '=' continuation line. #============================================================================= # >>> Check for EADP Record(s) in CIF-Embedded shelxl.res _171 0 0 0 4 A 0 0 0 1 The CIF-Embedded .res File Contains EADP Records $I Report The use of EADP record(s) in the SHELXL .res file should be documented in the experimental section of the associated publication. #============================================================================= # >>> Check for DFIX Record(s) in CIF-Embedded shelxl.res _172 0 0 0 4 A 0 0 0 1 The CIF-Embedded .res File Contains DFIX Records $I Report The use of DFIX record(s) should be documented in the experimental section of the associated publication. #============================================================================= # >>> Check for DANG Record(s) in CIF-Embedded shelxl.res _173 0 0 0 4 A 0 0 0 1 The CIF-Embedded .res File Contains DANG Records $I Report The use of DANG record(s) should be documented in the experimental section of the associated publication. #============================================================================= # >>> Check for FLAT Record(s) in CIF-Embedded shelxl.res _174 0 0 0 4 A 0 0 0 1 The CIF-Embedded .res File Contains FLAT Records $I Report The use of FLAT record(s) should be documented in the experimental section of the associated publication. #============================================================================= # >>> Check for SAME Record(s) in CIF-Embedded shelxl.res _175 0 0 0 4 A 0 0 0 1 The CIF-Embedded .res File Contains SAME Records $I Report The use of SAME record(s) in the SHELXL .res file should be documented in the experimental section of the associated publication. #============================================================================= # >>> Check for SADI Record(s) in CIF-Embedded shelxl.res _176 0 0 0 4 A 0 0 0 1 The CIF-Embedded .res File Contains SADI Records $I Report The use of SADI record(s) in the SHELXL .res file should be documented in the experimental section of the associated publication. #============================================================================= # >>> Check for DELU Record(s) in CIF-Embedded shelxl.res _177 0 0 0 4 A 0 0 0 1 The CIF-Embedded .res File Contains DELU Records $I Report The use of DELU record(s) in the SHELXL .res file should be documented in the experimental section of the associated publication. #============================================================================= # >>> Check for SIMU Record(s) in CIF-Embedded shelxl.res _178 0 0 0 4 A 0 0 0 1 The CIF-Embedded .res File Contains SIMU Records $I Report The use of SIMU record(s) in the SHELXL .res file should be documented in the experimental section of the associated publication. #============================================================================= # >>> Check for CHIV Record(s) in CIF-Embedded shelxl.res _179 0 0 0 4 A 0 0 0 1 The CIF-Embedded .res File Contains CHIV Records $I Report The use of CHIV record(s) in the SHELXL .res file should be documented in the experimental section of the associated publication. #============================================================================= # >>> Check Rounding of Cell Axes and Angles _180 0 0 0 4 I 0 1 0 0 Check Cell Rounding: # of Values Ending with 0 = $I Note It is unusual that more cell parameters end with a zero and the s.u. is 10. This problem might be caused by the specification of insufficient 'meaningful' digits as compared to the reported s.u. see also: W.Clegg, Acta Cryst. (2003) E59, e2-e5. #============================================================================= # >>> Check for all angles exactly 90 degrees in monoclinic _181 0 0 2 1 A 1 0 0 0 All Angles Exactly 90 Degrees in Monoclinic Cell Please Check One of the angles in a monoclinic cell is expected to be not exactly 90 degrees. #============================================================================= # >>> Check for at least one s.u. greater than zero in monoclinic _182 0 0 2 1 A 1 0 0 0 All Angles with zero s.u. in Monoclinic Cell ... Please Check One angle should have an s.u. greater than zero in a monoclinic cell. #============================================================================= # >>> Check for _cell_measured_reflns_used value reported _183 0 0 0 1 A 1 0 0 0 Missing _cell_measurement_reflns_used Value .... Please Do ! Please supply the value for _cell_measurement_reflns_used. #============================================================================= # >>> Check for _cell_measured_theta_min value reported _184 0 0 0 1 A 1 0 0 0 Missing _cell_measurement_theta_min Value ...... Please Do ! Please supply the value for _cell_measurement_theta_min. #============================================================================= # >>> Check for _cell_measured_theta_max value reported _185 0 0 0 1 A 1 0 0 0 Missing _cell_measurement_theta_max Value ...... Please Do ! Please supply the value for _cell_measurement_theta_max. #============================================================================= # >>> Check for ISOR Record(s) in CIF-Embedded shelxl.res _186 0 0 0 4 A 0 0 0 1 The CIF-Embedded .res File Contains ISOR Records $I Report The use of ISOR record(s) in the SHELXL .res file should be documented in the experimental section of the associated publication. #============================================================================= # >>> Check for RIGU Record(s) in CIF-Embedded shelxl.res _187 0 0 0 4 A 0 0 0 1 The CIF-Embedded .res File Contains RIGU Records $I Report The use of RIGU record(s) in the SHELXL .res file should be documented in the experimental section of the associated publication. #============================================================================= # >>> Test SIMU restraint value in CIF-Embedded .res file _188 0 0 0 3 A 0 0 1 A Non-default SIMU Restraint Value has been used $F Report SHELXL applies a default effective standard deviation value of 0.04 for the SIMU restraint. The use of a much stronger restraint with a lower value of that parameter may hide serious problems with a structure such as wrong atom type assignments. #============================================================================= # >>> Test SAME restraint value in CIF-Embedded .res file _189 0 0 0 3 A 0 0 1 0 A Non-default SAME Restraint Value for $A $F Report SHELXL applies a default effective standard deviation value of 0.02 Ang for the SAME 1,2 or 1,3 bond restraints. The use of a much stronger restraint, with a lower value of those parameters, may hide serious problems with a structure. #============================================================================= # >>> Test RIGU restraint value in CIF-Embedded .res file _190 0 0 0 3 A 0 0 1 0 A Non-default RIGU Restraint Value for $A $F Report SHELXL applies a default effective standard deviation value of 0.004 for the RIGU restraint. The use of a much stronger restraint with a lower value of that parameter may hide serious problems with a structure such as wrong atom type assignments. #============================================================================= # >>> Test SADI restraint value in CIF-Embedded .res file _191 0 0 0 3 A 0 0 1 0 A Non-default SADI Restraint Value has been used $F Report SHELXL applies a default effective standard deviation value of 0.02 Ang for the SADI bond restraints. The use of a much stronger restraint, with a lower value of those parameters, may hide serious problems with a structure. #============================================================================= # >>> Test DELU restraint value in CIF-Embedded .res file _192 0 0 0 3 A 0 0 1 0 A Non-default DELU Restraint Value for $A $F Report SHELXL applies a default effective standard deviation value of 0.01 Ang for the DELU restraints. The use of a much stronger restraint, with a lower value of those parameters, may hide serious problems with a structure. #============================================================================= # >>> Test for consistency of cell & diffraction temperatures _193 0 5 10 1 I 0 1 0 0 Cell and Diffraction Temperatures Differ by .... $I Degree The reported _cell_measurement_temperature deviates from the reported _diffrn_ambient_temperature value. The relevant set of cell parameter values are those at the datacollection temperature (i.e. ambient temperature at the crystal) because the derived geometry parameter values will be correct and meaningfull only when those cell paarameter values are used. When relevant, cell parameter values at temperatures differing from the _diffrn_ambient_temperature are best archived as comment value under _cell_special_details. #============================================================================= # >>> Report on non-default DEFS restraint values in CIF-Embedded .res file _194 0 0 0 3 A 0 0 1 0 A Non-default DEFS Restraint Value set $A $F Note! Non-default DEFS parameter values in CIF-Embedded .res file. See SHELXL manual. #============================================================================= # >>> Test DFIX restraint value in CIF-Embedded .res file _195 0 0 0 3 A 0 0 1 0 A Non-default DFIX Restraint Value has been used $F Report SHELXL applies a default effective standard deviation value of 0.02 Ang for the DFIX restraints. The use of a much stronger restraint, with a lower value of those parameters, may hide serious problems with a structure. #============================================================================= # >>> Test for Measurement temperature not equal 293K and no TEMP Record _196 0 0 2.0 1 I 1 0 0 0 No TEMP record and _measurement_temperature .NE. $I Degree SHELXL places Hydrogen atoms at calculated positions with default distance values to their parent atoms depending on the temperature reported in the TEMP record. When the TEMP record is absent in the embedded .res file a default temperature of 293K is assumed. An ALERT is issued when the CIF reported _measurement_temperature differs from that value. #============================================================================= # >>> Test for specification of unitcell measurement temperature _197 0 0 0 1 I 1 0 0 0 Missing _cell_measurement_temperature Datum .... Please Add Please specify the temperature (Kelvin) at which the unit-cell parameters were determined. That temperature should be generally identical to the temperature value specified with _diffrn_ambient_temperature (the temperature of the crystal during data-collection) in order to make sense when used in the calculation of derived geometry parameter values (i.e. bond distances, bond angles etc.). #============================================================================= # >>> Test for specification of Datacollection temperature _198 0 0 0 1 A 1 0 0 0 Missing _diffrn_ambient_temperature Datum .... Please Add Please specify the temperature (Kelvin) at which the intensity data were collected. The reported cell parameter values should be those at this temperature to make sense of the derived geometry parameter values. #============================================================================= # >>> Test for SHELXL Roomtemperature Default (Cell) _199 0 1.0 2.0 1 I 0 0 0 1 Reported _cell_measurement_temperature ..... (K) $I Check The cell determination temperature is set in the CIF by default by SHELXL97 to 293 K when the TEMP instruction is not used. The actual temperature is likely either slightly or significantly (in case of a low temperature data collection) different. A likely erroneous temperature of 273K (0C) is also flagged. #============================================================================= # >>> Test for SHELXL Roomtemperature Default (Datacollection) _200 0 1.0 2.0 1 I 0 0 0 1 Reported _diffrn_ambient_temperature ..... (K) $I Check The data collection temperature is set in the CIF by default by SHELXL97 to 293 K if the TEMP instruction is not used. A likely erroneous temperature of 273K (0C) is also flagged. The actual temperature is likely either slightly or significantly (for a low temperature data collection) different. #============================================================================= # >>> Test for isotropic non-H atoms in main residue(s) _201 0 0 10 2 A 0 0 1 0 Isotropic non-H Atoms in Main Residue(s) ....... $I Report 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. #============================================================================= # >>> Test for isotropic non-H atoms in anion ? or solvent ? _202 0 50 50 3 A 0 0 1 0 Isotropic non-H Atoms in Anion/Solvent ......... $I Check This test reports on isotropically refined atoms in small moieties (usually anions or solvent). #============================================================================= # >>> Test for negative non-Hydrogen U(iso) _203 0 0 0 2 A 0 0 1 0 Negative Isotropic ADP for $A ........... $F Report Isotropic U(iso) values are expected to have a positive value. #============================================================================= # >>> Test for 'all-isotropic adp(s) _210 0 0 10 3 A 0 0 1 0 No Anisotropic ADP's Found in CIF .............. Please Check No anisotropically refined atoms in CIF ? #============================================================================= # >>> Test for NPD ADP's (1.0) in main residue(s) _211 0 0 0.5 2 A 0 0 1 0 ADP of Atom $A is N.P.D. or (nearly) 2D . Please Check This test reports on non-positive definite (i.e. complex and unrealistic) anisotropic displacement parameters in the main residue. #============================================================================= # >>> Test for NPD ADP's in anion? & solvent ? [0, 1] _212 0 0.5 99 2 A 0 0 1 0 ADP of Atom $A is N.P.D. or (nearly) 2D . Please Check This test reports on non-positive definite (i.e. complex and unrealistic) anisotropic displacement parameters in an anion or solvent residue. #============================================================================= # >>> Test ratio adp max/min in main residue(s) _213 3.0 4.0 5.0 2 A 0 0 1 0 Atom $A has ADP max/min Ratio ..... $F $B The main axes values of the ADP(S) of the main residue(s) are determined and ordered: U1 < U2 < U3. The value of SQRT(U3/U1) main axis ADP ratio (Angstrom Units) is tested for the main residue(s). Large values may indicate unresolved disorder. Oblate criterium: U3 - U2 < U2 - U1. Prolate otherwise. #============================================================================= # >>> Test ratio adp max/min in anion ? or solvent ? _214 4.0 5.0 6.0 2 A 0 0 1 0 Atom $A (Anion/Solvent) ADP max/min Ratio $F $B The main axes values of the ADP(S) of the minor residue(s) are determined and ordered: U1 < U2 < U3. The value of SQRT(U3/U1) main axis ADP ratio (Angstrom Units) is tested for the main residue(s). Large values may indicate unresolved disorder. Oblate criterium: U3 - U2 < U2 - U1. Prolate otherwise. #============================================================================= # >>> Test for unusual disordered atom ADP in main residue _215 3.0 4.0 5.0 3 I 0 0 1 0 Disordered $A has ADP max/min Ratio ..... $F Note The maximum and minimum main axis ADP ratio (Angstrom Units) is tested for the main residue. Large values may indicate unresolved disorder. #============================================================================= # >>> Test for unusual disordered atom ADP in minor residue _216 5.0 7.0 9.0 3 I 0 0 1 0 Disordered $A (An/Solv) ADP max/min Ratio $F Note The maximum and minimum main axis ADP ratio (Angstrom Units) is tested for the minor residue(s). Large values may indicate unresolved disorder. #============================================================================= # >>> Test for Incomplete UIJ data _217 0.0 0.0 0.0 1 A 1 0 0 0 Incomplete U(aniso) Data for ................... $A Check Check & Correct U(aniso) data for completeness etc. Do not use SHELX style '=' continuation line. #============================================================================= # >>> Test for Constrained Uij's _218 0 2 2 3 A 1 0 0 0 Constrained U(ij) Components(s) for $A . $I Check Uij components have been constrained (i.e. without s.u.) in the refinement. #============================================================================= # >>> Test Ueq(max)/Ueq(Min) range for non-H atoms in non-solvent _220 3.0 6.0 10.0 2 I 0 0 1 0 NonSolvent Resd$Aeq(max)/Ueq(min) Range $F Ratio This test reports on a larger than usual U(eq) range for the specified element type in the non-solvent/anion part of the structure. Too high or too low Ueq's may be an indication for incorrectly identified atomic species (i.e. O versus N). #============================================================================= # >>> Test Ueq(max)/Ueq(Min) range for non-H atoms in solvent _221 4.0 8.0 12.0 2 A 0 0 1 0 Solv./Anion Resd$Aeq(max)/Ueq(min) Range $F Ratio This test reports on a larger than usual U(eq) range for the non-hydrogen atoms solvent/anion. Too high or too low Ueq's may be an indication for incorrectly identified atomic species (i.e. Br versus Ag). #============================================================================= # >>> Test Uiso(max)/Uiso(Min) range for H atoms in non-solvent _222 4.0 10.0 99.9 3 A 0 0 1 0 NonSolvent Resd$Aiso(max)/Uiso(min) Range $F Ratio This test reports on a larger than usual range of U(eq) values for hydrogen atoms in the non-solvent/anion part of the structure. Possible causes are: 1 - disorder, e.g. in t-butyl moieties. 2 - poor data, not adequate for the refinement of individual displacement parameters. 3 - Misplaced hydrogen atoms (i.e. there is no density at the position where one of the H-atoms is positioned). #============================================================================= # >>> Test Ueq(max)/Ueq(Min) range for H atoms in solvent _223 4.0 10.0 99.9 4 A 0 0 1 0 Solv./Anion Resd$Aeq(max)/Ueq(min) Range $F Ratio This test reports on large ranges in displacement parameters for hydrogen atoms in the solvent/anion part of the structure. #============================================================================= # >>> Test for difference in implicit and explicit U(eq) _224 .002 .003 .005 1 A 0 0 1 0 Ueq(Rep) and Ueq(Calc) Differ by$A Ang**2 $B Check This test reports on a large difference between Ueq in the CIF and the Ueq calculated from the 6 reported Uij values. . #============================================================================= # >>> Hirshfeld Rigid-Bond Test (Acta Cryst (1976),A32,239-244 _230 5.0 7.0 99.0 2 A 0 0 1 0 Hirshfeld Test Diff for $A--$B. $F s.u. The components of the anisotropic displacement parameters along chemical bonds are assumed to be equal in magnitude. Large differences might 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. #============================================================================= # >>> Hirshfeld Rigid-Bond Test (Acta Cryst (1976),A32,239-244 _231 5.0 9.0 99.0 4 A 0 0 1 0 Hirshfeld Test (Solvent) $A--$B. $F s.u. The components of the anisotropic displacement parameters along chemical bonds are assumed to be equal in magnitude. Large differences might indicate the 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. #============================================================================= # >>> Hirshfeld Rigid-Bond Test (Metal-X) (Acta Cryst (1976),A32,239-244 _232 5.0 10.0 99.0 2 A 0 0 1 0 Hirshfeld Test Diff (M-X) $A--$B. $F s.u. The components of the anisotropic displacement parameters along chemical bonds are assumed to be equal in magnitude. Large differences might 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. Note: The 'Hirshfeld-test' ALERTS are suppressed for polymeric or disordered structures. #============================================================================= # >>> Hirshfeld Rigid-Bond Test (Metal-X) (Acta Cryst (1976),A32,239-244 _233 10.0 15.0 99.0 4 A 0 0 1 0 Hirshfeld (M-X Solvent) $A--$B. $F s.u. The components of the anisotropic displacement parameters along chemical bonds are assumed to be equal in magnitude. Large differences might 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. #============================================================================= # >>> Hirshfeld Rigid-Bond Test (Acta Cryst (1976),A32,239-244 _234 0.15 0.25 0.3 4 A 0 0 1 0 Large Hirshfeld Difference $A--$B. $F Ang. The components of the anisotropic displacement parameters along chemical bonds are assumed to be equal in magnitude. Large differences might 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). #============================================================================= # >>> Test for unusually high U(eq) as compared with bonded neighbors _241 .015 0.05 0.15 2 A 0 0 1 0 High 'MainMol' Ueq as Compared to Neighbors of $A Check 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). #============================================================================= # >>> Test for Unusually Low U(eq) as compared with bonded neighbors _242 .015 0.05 0.15 2 A 0 0 1 0 Low 'MainMol' Ueq as Compared to Neighbors of $A Check 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. #============================================================================= # >>> Test for unusually high solvent U(eq) as compared with bonded neighbors _243 .015 1.00 1.00 4 A 0 0 1 0 High 'Solvent' Ueq as Compared to Neighbors of $A Check 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). #============================================================================= # >>> Test for unusually low solvent U(eq) as compared with bonded neighbors _244 .015 1.00 1.00 4 A 0 0 1 0 Low 'Solvent' Ueq as Compared to Neighbors of $A Check 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. #============================================================================= # >>> Test for unusually low H-U(eq) as compared with bonded atom _245 0.01 0.05 0.10 2 A 0 0 1 0 U(iso) $A Smaller than U(eq) $B by $F Ang**2 U(iso) of a hydrogen atom is generally expected to be greater than the U(eq) of the non-hydrogen atom it is attached to. #============================================================================= # >>> Test for unusual anisotropic average UIJ _250 2.00 4.00 9.00 2 A 0 0 1 0 Large U3/U1 Ratio for Tensor($A) $F Note 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 main axis 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. #============================================================================= # >>> Test for high average Ueq for residue _260 .100 0.30 1.00 2 A 0 0 3 0 Large Average Ueq of Residue Including $A $F Check A large average Ueq value for a residue may indicate refinement with a too high (possibly fixed) population parameter value. #============================================================================= # >>> Test for Fixed Partial Occupancy _300 0 0 0 4 A 0 0 1 0 Atom Site Occupancy of $A Constrained at $F Check This site is expected to be fully occupied but has been constrained (e.g. with a SHELXL FVAR variable) or fixed at a value less than 1.0. Please check for incomplete (substitutional) disorder handling. #============================================================================= # >>> Test for main residue(s) disorder % _301 0 0 0 3 A 0 0 1 0 Main Residue Disorder ..............($A)$I% Note Atom sites that are not fully occupied are counted. A large fraction of disordered atoms may be both a signal for serious structure analysis problems or less reliable/interesting results. #============================================================================= # >>> Test for (anion/solvent) disorder % _302 0 0 0 4 A 0 0 1 0 Anion/Solvent/Minor-Residue Disorder ($A)$I% Note Atom sites that are not fully occupied are counted. #============================================================================= # >>> Test for more than 1 connection to Hydrogen Atoms _303 1 2 3 2 A 0 0 1 0 Full Occupancy Atom $A with # Connections $F Check Hydrogen atoms are generally connected to only one other atom. A hydrogen atom between two oxygen atoms is a special case. Investigate whether this hydrogen atom is better described with a disorder model with two partially occupied sites. A difference map might show a double-well density. #============================================================================= # >>> Test for non-integer number of atoms in residue _304 0 2 2 4 A 0 0 1 0 Non-Integer Number of Atoms in ..... ($B) $F Check A non-integer number of atoms has been found in a residue. #============================================================================= # >>> Test for isolated Hydrogen Atoms _305 0 0 0 2 A 0 0 1 0 Isolated Hydrogen Atom (Outside Bond Range ??) $A Check 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). #============================================================================= # >>> Test for isolated Oxygen Atoms _306 0 0 2 2 A 0 0 1 0 Isolated Oxygen Atom (H-atoms Missing ?) ....... $A Check 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. #============================================================================= # >>> Test for isolated Metal Atoms _307 0 0 0 2 A 0 0 1 0 Isolated Metal Atom found in Structure (Unusual) $A Check 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 ?) #============================================================================= # >>> Test for single bonded Metal Atoms _308 0 0 0 2 A 0 0 1 0 Single Bonded Metal Atom in Structure (Unusual) $A Check 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. #============================================================================= # >>> Test for single bonded Oxygen Atoms _309 0 99 99 2 A 0 0 1 0 Single Bonded Oxygen (C-O > 1.3 Ang) ........... $A Check Single bonded Oxygen with C-O > 1.3 Angstrom. Missing H-Atom ? Check #============================================================================= # >>> Test for 'too close' (symmetry related) full weight atoms _310 0 0 0 2 A 0 0 1 0 $A Deleted (Close to $B) Dist ... $F Ang. This test identifies (very) short contacts between atoms that only becomes apparent after the application of symmetry on the primary coordinate set. #============================================================================= # >>> Test for isolated Disordered Oxygen Atoms _311 0 10 10 2 A 0 0 1 0 Isolated Disordered Oxygen Atom (No H's ?) ..... $A Check 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. #============================================================================= # >>> Test for C=O-H _312 0 0.02 0.05 2 A 0 0 1 0 Strange C-O-H Geometry (C-O < 1.25 Ang) ..... $A Check Strange C-O-H geometry with C-O < 1.25 Angstrom detected. Misplaced H-Atom ? #============================================================================= # >>> Test for O with three covalent bonds _313 0 2 2 2 A 0 0 1 0 Oxygen with Three Covalent Bonds (rare) ........ $A Check Oxygen atom with three covalent bonds detected. Check for correct atom type assignment (e.g. N rather than O) Note: Exceptions are H3O+ (Oximium or Hydroxonium) and H5O2+ (Hydronium or aqua-hydroxonium) species. #============================================================================= # >>> Test for Metal-O-H angle of H2O _314 0 2 2 2 A 0 0 1 0 Small Angle for H2O: Metal-$A-$B . $F Degree A water molecule coordinated to a metal is detected with an unusually small value of the Metal-Oxygen-Hydrogen Angle. #============================================================================= # >>> Test for single bonded Carbon atom _315 0 0 2 2 A 0 0 1 0 Singly Bonded Carbon Detected (H-atoms Missing). $A Check Check for missing H-atoms. #============================================================================= # >>> Check for too many H's on C in C=N bond in main residue(s) _316 0 0 0 2 A 0 0 1 0 Too many H on C in C=N Moiety in Main Residue .. $A Check 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. #============================================================================= # >>> Check for too many H's on C in C=N bond in Solvent/Ion (s) _317 0 10 10 2 A 0 0 1 0 Too many H on C in C=N Moiety in Solvent/Ion ... $A Check 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. #============================================================================= # >>> Hybridisation Problem on N in main residue(s) _318 0 99 99 2 A 0 0 1 0 Hybridisation of $A in Main Residue ..... Please Check 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). #============================================================================= # >>> Hybridisation Problem on N in solvent/ion _319 0 99 99 2 A 0 0 1 0 Hybridisation of $A in Solvent/Ion ...... Please Check 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). #============================================================================= # >>> Hybridisation Problem on C in main residue(s) _320 0 99 99 2 A 0 0 1 0 Hybridisation of $A in Main Residue ..... Please Check 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. #============================================================================= # >>> Hybridisation Problem on C in solvent/ion _321 0 99 99 2 A 0 0 1 0 Hybridisation of $A in Solvent/Ion ...... Please Check 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. #============================================================================= # >>> Hybridisation Problem on non-C in main residue(s) _322 0 99 99 2 A 0 0 1 0 Hybridisation of $A in Main Residue ..... Please Check 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. #============================================================================= # >>> Hybridisation Problem on non-C in Solvent/Ion _323 0 99 99 2 A 0 0 1 0 Hybridisation of $A in Solvent/Ion ...... Please Check 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 H on coordinating X-N-X in main residue _324 0 99 99 2 A 0 0 1 0 Check for Possibly Missing H on Coordinating.... $A Check Check for possibly missing Hydrogen atom on Nitrogen coordinating to a metal in the main residue. #============================================================================= # >>> Check for possibly missing H on coordinating X-N-X in solvent/anion _325 0 99 99 2 A 0 0 1 0 Check for Possibly Missing H on Coordinating.... $A Check Check for possibly missing Hydrogen atom on Nitrogen coordinating to a metal in the solvent/anion. #============================================================================= # >>> Check for possibly missing H on potentially sp3 Carbon _326 0 0 99 2 A 0 0 1 0 Possible Missing H on sp3? Carbon .............. $A Check Check for possibly missing Hydrogen atom on Carbon with sp3-like geometry in the main residue. #============================================================================= # >>> Check for possibly missing H on potentially sp3 Carbon _327 0 0 99 2 A 0 0 1 0 Possible Missing H on sp3? Carbon .............. $A Check Check for possibly missing Hydrogen atom on Carbon with sp3-like geometry in the solvent/anion. #============================================================================= # >>> Check for a possibly missing H on potentially sp3 Phosphorus _328 0 99 99 4 A 0 0 1 0 Possible Missing H on sp3? Phosphorus .......... $A Check Check for a possibly missing Hydrogen atom on Phosphorus with sp3-like geometry. #============================================================================= # >>> Check for unclear Carbon Atom Hybridisation _329 0 99 99 4 A 0 0 1 0 Carbon Atom Hybridisation Unclear for .......... $A Check The hybridisation of this calbon atom could not be established from the number of substituents and their geometry. Check for missing hydrogen atoms and/or poor geometry. #============================================================================= # >>> Check Average Phenyl C-C _330 0.01 0.02 0.03 2 A 0 0 1 0 Large Aver Phenyl C-C Dist $A--$B. $F Ang. 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). #============================================================================= # >>> Check Average Phenyl C-C _331 0.02 0.03 0.04 2 A 0 0 1 0 Small Aver Phenyl C-C Dist $A--$B. $F Ang. 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. #============================================================================= # >>> Check Phenyl C-C Range _332 0.15 0.25 0.35 2 A 0 0 1 0 Large Phenyl C-C Range $A -$B. $F Ang. 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. #============================================================================= # >>> Check Average in Multiple Substituted Benzene Type C-C _333 0.03 0.06 0.09 2 A 0 0 1 0 Large Aver C6-Ring C-C Dist $A-$B. $F Ang. 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). #============================================================================= # >>> Check Average in Multiple Substituted Benzene Type C-C _334 0.03 0.06 0.09 2 A 0 0 1 0 Small Benzene Dist. $A-$B. $F Ang. 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. #============================================================================= # >>> Check Multiple Substituted Benzene Type C-C Range _335 0.15 0.25 0.35 2 A 0 0 1 0 Check Large C6 Ring C-C Range $A-$B$F Ang. 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. #============================================================================= # >>> Check Unusual Bond Distance _336 0.0 2.0 2.0 2 A 0 0 1 0 Long Bond Distance for ..... $A-$B $F Ang. Check this bond distance. #============================================================================= # >>> Check Average Torsion Angle in cyclo-hexane ring _338 25.0 45.0 60.0 4 A 0 0 1 0 Small Aver Tau in Cyclohexane $A-$B$F Degree 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. #============================================================================= # >>> Check Bond Precision for C-C in Light Atom Structures (Z(max) < 20) _340 .004 0.01 0.05 3 A 0 0 1 0 Low Bond Precision on C-C Bonds ............... $F Ang. The average s.u. 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 s.u.'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). #============================================================================= # >>> Check Bond Precision for C-C in Structures (19 < Z(max) < 40) _341 .006 .015 .075 3 A 0 0 1 0 Low Bond Precision on C-C Bonds ............... $F Ang. The average s.u. 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 s.u.'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). #============================================================================= # >>> Check Bond Precision for C-C in Structures (Z(max) > 39) _342 .008 .020 .100 3 A 0 0 1 0 Low Bond Precision on C-C Bonds ............... $F Ang. The average s.u. 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 s.u.'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). #============================================================================= # >>> Hybridisation Problem on C in main residue(s) _343 0 0 0 2 A 0 0 1 0 Unusual $AAngle Range in Main Residue for $B Check The angle range is larger than usual for the tentatively assigned hybridisation of the reported atom in the main residue. #============================================================================= # >>> Hybridisation Problem on C in solvent/ion _344 0 0 0 2 A 0 0 1 0 Unusual $A Angle Range in Solvent/Ion for $B Check The angle range is larger than usual for the tentatively assigned hybridisation of the reported atom in the solven/anion. #============================================================================= # >>> Test for short C - H (Angstrom Difference) XRAY: 0.96 NEUT 1.08 _350 0.11 0.2 0.3 3 A 0 0 1 0 Short C-H (X0.96,N1.08A) $A -$B . $F Ang. Large deviations from generally accepted values may indicate model problems, over refinement etc. Default C-H = 0.96 Ang. (X-Ray) value from SHELXL. #============================================================================= # >>> Test for long C - H (Angstrom Difference) XRAY: 0.96 NEUT 1.08 _351 0.14 0.2 0.3 3 A 0 0 1 0 Long C-H (X0.96,N1.08A) $A -$B . $F Ang. Large deviations from generally accepted values may indicate model problems, over refinement etc. Default C-H = 0.96 Ang. (X-Ray) value from SHELXL. #============================================================================= # >>> Test for short N - H (Angstrom Difference) XRAY: 0.87 NEUT 1.009 _352 0.1 0.2 0.3 3 A 0 0 1 0 Short N-H (X0.87,N1.01A) $A -$B . $F Ang. Large deviations from generally accepted values may indicate model problems, over refinement etc. Default N-H = 0.87 Ang. (X-Ray) value from SHELXL. #============================================================================= # >>> Test for long N - H (Angstrom Difference) XRAY: 0.87 NEUT 1.009 _353 0.13 0.2 0.3 3 A 0 0 1 0 Long N-H (N0.87,N1.01A) $A -$B . $F Ang. Large deviations from generally accepted values may indicate model problems, over refinement etc. Default N-H = 0.87 Ang. (X-Ray) value from SHELXL. #============================================================================= # >>> Test for short O - H (Angstrom Difference) XRAY: 0.82 NEUT 0.983 _354 0.1 0.2 0.3 3 A 0 0 1 0 Short O-H (X0.82,N0.98A) $A -$B . $F Ang. Large deviations from generally accepted values may indicate model problems, over refinement etc. Default O-H = 0.82 Ang. (X-Ray) value from SHELXL. #============================================================================= # >>> Test for long O - H (Angstrom Difference) XRAY: 0.82 NEUT 0.983 _355 0.18 0.25 0.3 3 A 0 0 1 0 Long O-H (X0.82,N0.98A) $A -$B . $F Ang. Large deviations from generally accepted values may indicate model problems, over refinement etc. Default O-H = 0.82 Ang. (X-Ray) value from SHELXL. #============================================================================= # >>> Test for short B-H distance in X-BH3 Moiety _356 0.05 0.16 0.25 3 A 0 0 1 0 Short X-BH3 Distance $A -$B $F Ang. A short B-H distance may be due to fixing that distance to a wrong value, e.g. to that of the C-H distance in a CH3 group. #============================================================================= # >>> Test for long B-H distance in X-BH3 Moiety _357 0.10 0.20 0.30 3 A 0 0 1 0 Long X-BH3 Distance $A -$B $F Ang. Check the long reported B-H bond distance (B-H is expected to have a value around 1.16 Ang in a X-BH3 group) #============================================================================= # >>> Test for short B-H distance in (X,Y,Z)-B-H Moiety _358 0.05 0.16 0.25 3 A 0 0 1 0 Short (X,Y,Z)-B-H Distance $A -$B $F Ang. A short B-H distance may be due to fixing that distance to a wrong value., e.g. to that of the C-H distance. #============================================================================= # >>> Test for long B-H distance in (X,Y,Z)-B-H Moiety _359 0.10 0.20 0.30 3 A 0 0 1 0 Long (X,Y,Z)-B-H Distance $A -$B $F Ang. Check the long reported B-H bond distance (B-H is expected to have a value around 1.06 Ang in a (X,Y,Z)-B-H moiety). #============================================================================= # >>> Test for short C4 - C4 (Angstrom Difference) XRAY: 1.54 _360 0.1 0.2 0.3 2 A 0 0 1 0 Short C(sp3)-C(sp3) Bond $A -$B . $F Ang. 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. #============================================================================= # >>> Test for long C4 - C4 (Angstrom Difference) XRAY: 1.54 _361 0.1 0.2 0.3 2 A 0 0 1 0 Long C(sp3)-C(sp3) Bond $A -$B . $F Ang. 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. #============================================================================= # >>> Test for short C4 - C3 (Angstrom Difference) XRAY: 1.52 _362 0.1 0.2 0.3 2 A 0 0 1 0 Short C(sp3)-C(sp2) Bond $A -$B . $F Ang. 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. #============================================================================= # >>> Test for long C4 - C3 (Angstrom Difference) XRAY: 1.52 _363 0.1 0.2 0.3 2 A 0 0 1 0 Long C(sp3)-C(sp2) Bond $A -$B . $F Ang. 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. #============================================================================= # >>> Test for short C4 - C2 (Angstrom Difference) XRAY: 1.46 _364 0.1 0.2 0.3 2 A 0 0 1 0 Short C(sp3)-C(sp) Bond $A -$B . $F Ang. 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. #============================================================================= # >>> Test for long C4 - C2 (Angstrom Difference) XRAY: 1.46 _365 0.1 0.2 0.3 2 A 0 0 1 0 Long C(sp3)-C(sp) Bond $A -$B . $F Ang. 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. #============================================================================= # >>> Test for short C? - C? (Angstrom Difference) XRAY: 1.50 _366 0.35 0.5 1.0 2 A 0 0 1 0 Short? C(sp?)-C(sp?) Bond $A -$B . $F Ang. The hybridisation of at least one carbon atom is not recognized. Large deviations from generally accepted values for a C-C bond may indicate model problems, unresolved disorder, over_refinement etc. The C-C bond is tested to be not shorter than 1.15 Angstrom. #============================================================================= # >>> Test for long C? - C? (Angstrom Difference) XRAY: 1.50 _367 0.05 0.2 0.3 2 A 0 0 1 0 Long? C(sp?)-C(sp?) Bond $A -$B . $F Ang. 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). #============================================================================= # >>> Test for short C3 - C3 (Angstrom Difference) XRAY: 1.34 _368 0.1 0.2 0.3 2 A 0 0 1 0 Short C(sp2)-C(sp2) Bond $A -$B . $F Ang. 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. #============================================================================= # >>> Test for long C3 - C3 (Angstrom Difference) XRAY: 1.34 _369 0.18 0.22 0.3 2 A 0 0 1 0 Long C(sp2)-C(sp2) Bond $A -$B . $F Ang. 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. #============================================================================= # >>> Test for short C3 - C2 (Angstrom Difference) XRAY: 1.31 _370 0.1 0.2 0.3 2 A 0 0 1 0 Short C(sp2)-C(sp1) Bond $A -$B . $F Ang. 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. #============================================================================= # >>> Test for long C3 - C2 (Angstrom Difference) XRAY: 1.31 _371 0.1 0.2 0.3 2 A 0 0 1 0 Long C(sp2)-C(sp1) Bond $A -$B . $F Ang. 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. #============================================================================= # >>> Test for short C2 - C2 (Angstrom Difference) XRAY: 1.25 _372 0.1 0.2 0.3 2 A 0 0 1 0 Short C(sp)-C(sp) Bond $A -$B . $F Ang. 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. #============================================================================= # >>> Test for long C2 - C2 (Angstrom Difference) XRAY: 1.25 _373 0.1 0.2 0.3 2 A 0 0 1 0 Long C(sp)-C(sp) Bond $A -$B . $F Ang. 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. #============================================================================= # >>> Test for long N - N Bond (> 1.45 Angstrom) _374 0.05 0.15 0.25 2 A 0 0 1 0 Long N - N Bond $A -$B . $F Ang. 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. #============================================================================= # >>> Test for C-O-H with large C-O Distance _375 0 0.02 0.05 2 A 0 0 1 0 Strange C-O-H Geometry (C-O > 1.45 Ang) ..... $A Check Strange C-O-H geometry with C-O > 1.45 Angstrom detected. Wrong Atom Type ? #============================================================================= # >>> Test for incorrectly Oriented Methyl Moiety _380 0.0 10.0 10.0 4 A 0 0 1 0 Incorrectly? Oriented X(sp2)-Methyl Moiety ..... $A Check This test alerts for possible incorrectly oriented CH3 moieties. (E.g. AFIX 33 instead of AFIX 137 etc. within the SHELXL realm). #============================================================================= # >>> Test Methyl Moiety X-C-H Bond Angle _390 6.5 9.5 50.0 3 A 0 0 1 0 Deviating Methyl $A X-C-H Bond Angle .... $I Degree Unusual Methyl Moiety X-C-H Angle (Ideally 109 Degrees for 4-bonded C). #============================================================================= # >>> Test Methyl Moiety H-C-H Bond Angle _391 7.5 9.5 50.0 3 A 0 0 1 0 Deviating Methyl $A H-C-H Bond Angle .... $I Degree Unusual Methyl Moiety H-C-H Angle (ideally 109 Degrees). #============================================================================= # >>> Test general X-O-Y Angle Value _395 10.0 180. 180. 2 A 0 0 0 1 Deviating $BAngle From 120 for $A. $F Degree The X-O-Y angle value differs from the common ~120.0 Degrees. #============================================================================= # >>> Test Si-O-Si Angle Value _396 10.0 180. 180. 2 A 0 0 0 1 Deviating $BAngle From 150 for $A. $F Degree The Si-O-Si angle value differs from the common ~150.0 Degrees. #============================================================================= # >>> Test B-O-B Angle Value _397 10.0 180. 180. 2 A 0 0 0 1 Deviating $B Angle From 120 for $A $F Degree The B-O-B angle differs significantly from 120.0 degrees. This is just a notice: B-O-B angles vary widely depending on what is bonded to the Boron atoms. #============================================================================= # >>> Test C-O-C Angle Value _398 10.0 180. 180. 2 A 0 0 0 1 Deviating $BAngle From 120 for $A. $F Degree The C-O-C angle value differs from the common ~120.0 Degrees. #============================================================================= # >>> Test for short non-bonding intra H..H contacts _410 0.4 0.5 0.6 2 A 0 0 0 1 Short Intra H...H Contact $A..$B. $F Ang. 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. #============================================================================= # >>> Test for short non-bonding inter H..H contacts _411 0 0.4 0.6 2 A 0 0 0 1 Short Inter H...H Contact $A..$B. $F Ang. 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. #============================================================================= # >>> Test for short non-bonding intra H..H contacts (involving XH3) _412 0.5 0.6 0.7 2 A 0 0 0 1 Short Intra XH3 .. XHn $A..$B. $F Ang. 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. #============================================================================= # >>> Test for short non-bonding inter H..H contacts (involving XH3) _413 0.0 0.4 0.5 2 A 0 0 0 1 Short Inter XH3 .. XHn $A..$B. $F Ang. 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. #============================================================================= # >>> Test for short non-bonding intra D-H..H-X contacts _414 0.4 0.5 0.6 2 A 0 0 0 1 Short Intra D-H..H-X $A..$B. $F Ang. Short intra D-H..H-X contact. This might be a di-hydrogen bond of the type B-H..H-O. See Crabtree et al. Acc. Chem. Res. 1996, 29, 348-354. #============================================================================= # >>> Test for short non-bonding inter D-H..H-X contacts _415 0.1 0.4 0.5 2 A 0 0 0 1 Short Inter D-H..H-X $A..$B. $F Ang. Short inter D-H..H-X contact. This might be a di-hydrogen bond of the type B-H..H-O. See: Crabtree et al. Acc. Chem. Res. 1996, 29, 348-354. #============================================================================= # >>> Test for short non-bonding intra D-H..H-D contacts _416 0.4 0.5 2.5 2 A 0 0 0 1 Short Intra D-H..H-D $A..$B. $F Ang. Short non-bonding intra D-H..H-D contacts may be related to disordered or misplaced H-atoms. #============================================================================= # >>> Test for short non-bonding inter D-H..H-D contacts _417 0 0.3 0.6 2 A 0 0 0 1 Short Inter D-H..H-D $A..$B. $F Ang. 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. #============================================================================= # >>> Test for D-H bonds without acceptor _420 0 1.5 99 2 A 0 0 0 1 D-H Bond Without Acceptor $A--$B. Please Check 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 with Hydrogen atom on a calculated position with O-H pointing in the wrong direction. #============================================================================= # >>> Test for short non-bonding inter D...A contacts _430 0 0.19 0.50 2 A 0 0 0 1 Short Inter D...A Contact $A..$B. $F Ang. 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 atom 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. #============================================================================= # >>> Test for short non-bonding inter HL...A contacts _431 0.10 0.30 0.50 2 A 0 0 0 1 Short Inter HL..A Contact $A..$B. $F Ang. This test reports on short intermolecular Halogen .. Donor/Acceptor atom-type distances. #============================================================================= # >>> Test for short non-bonding inter X...Y contacts _432 0.2 0.30 0.50 2 A 0 0 0 1 Short Inter X...Y Contact $A..$B. $F Ang. 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. #============================================================================= # >>> Test for short non-bonding minor..minor inter X...Y contacts _433 0.5 0.85 1.00 4 A 0 0 0 1 Short Inter X...Y Contact $A..$B. $F Ang. 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. #============================================================================= # >>> Test for short non-bonding inter HL...HL contacts _434 0.10 0.45 0.70 2 A 0 0 0 1 Short Inter HL..HL Contact $A..$B. $F Ang. This test reports on short intermolecular Halogen .. Halogen type distances. Note: Bridging I- ions in a X-I...I-...I-Y chain may invoke level B ALERTs. #============================================================================= # >>> Test for too large H...A _480 -.12 0.25 0.5 4 A 0 0 0 1 Long H...A H-Bond Reported $A..$B. $F Ang. Check this (unrealistically) long reported H..A contact. Jeffrey criterium: Contact < vdWR(H) + vdWR(A) - 0.12 Angstrom. #============================================================================= # >>> Test for too large D...A _481 0.5 1.0 2.0 4 A 0 0 0 1 Long D...A H-Bond Reported $A..$B. $F Ang. Check this (unrealistically) long reported D..A contact. Jeffrey criterium: Contact < vdWR(D) + vdWR(A) + 0.50 Angstrom. #============================================================================= # >>> Test for too small D-H...A Angle _482 80. 90.0 100. 4 A 0 0 0 1 Small D-H..A Angle Rep for $A..$B. $F Degree Check this unrealistically small reported D-H..A Angle. Jeffrey criterium: D-H..A Angle > 100 degrees. #============================================================================= # >>> Test for not rounded D-H...A Angle _484 0 2 2 4 I 0 0 0 1 Round D-H..A Angle Rep for $A..$B. $I Degree D-H..A angles without s.u. should be rounded to integer values for publication purposes (Required for Acta Cryst.). #============================================================================= # >>> Test for (Unreported) solvent accessible voids _601 30 100 200 2 A 0 0 0 1 Unit Cell Contains Solvent Accessible VOIDS of . $I Ang**3 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. #============================================================================= # >>> Test for TOO LARGE (Unreported) solvent accessible voids _602 0 0 0 2 A 0 0 0 1 Solvent Accessible VOID(S) in Structure ........ ! Check 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. #============================================================================= # >>> Test for TOO LARGE Unit Cell for VOID search _603 0 0 0 4 A 0 0 0 1 Unit Cell TOO large for VOID SEARCH in Structure ! Info No search for solvent accessible VOIDS done as part of VALIDATION in view of large unit-cell. #============================================================================= # >>> Test for TOO Many VOIDS _604 0 0 0 4 A 0 0 0 1 Too Many VOIDS Detected in Structure ............. ! Info Too many solvent accessible VOIDS. # ============================================================================ # >>> Test for (Reported) solvent accessible voids _605 0 0 0 4 A 0 0 0 1 Largest Solvent Accessible VOID in the Structure $I A**3 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. #============================================================================= # >>> Test for TOO LARGE (Reported) solvent accessible voids _606 0 0 0 4 A 0 0 0 1 Solvent Accessible VOID(S) in Structure ........ ! Info 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. #============================================================================= # >>> Test for Skipped VOID Test _607 0 0 0 4 A 0 0 0 1 VOID Test Skipped Due to Severe Disorder ....... ! Info Void test Skipped. #============================================================================= # >>> Test for too many atoms for ADDSYM test as part of CheckCIF _608 0 0 0 4 A 0 0 0 1 ADDSYM Test Skipped (Too Time-consuming) ....... ! Info The ADDSYM test is skipped as part of the checkCIF run when the symmetry generated cell content gets too large and the calculation too time consiming. The calculation can still be done via the ADDSYM tool in PLATON. #============================================================================= # >>> Check for Missing SQUEEZE or MASK Info _609 0 0 0 4 A 0 0 0 1 SQUEEZE or MASK Info missing, given ABIN Record ! Check The presence of an ABIN instruction in the SHELXL .ins file implies the use of the PLATON/SQUEEZE or OLEX2/MASK tool to take into account the disordered solvent contribution to the calculated structure factors. The corresponding procedure details, generated by those programs, appear to be absent from or incorrectly modified as part of the CIF embedded .fab file. #============================================================================= # >>> Report the use of the SHELXL/SWAT Instruction _650 0 0 0 4 A 0 0 0 1 SWAT Instruction Used to Model Solvent Disorder ! Report This test reports the use of the SHELXL/SWAT instruction for the modelling of the disordered solvent contribution to the calculated structure factors. #============================================================================= # >>> Test for radiation type specification _660 0 0 0 1 A 1 0 0 0 No Valid _diffrn_radiation_type Value Reported . Please Do ! Examples of expected values are 'MoKa', 'synchrotron', 'neutron', 'electron' #============================================================================= # >>> Check for BLANK records in embedded hkl file _697 0 0 0 1 A 1 0 0 0 Number of Blank Records in CIF embedded hkl File $I Check A number of blank records interspersed in the CIF embedded hkl file have been removed. #============================================================================= # >>> Check for _shelx_include_file_checksum _698 0 0 0 1 A 1 0 0 0 $A_shelx_include_file_checksum in CIF ... Please Check The supplied CIF contains a '_shelx_include_file' record but not a valid associated '_shelx_include_file_checksum' record or valid value.. This include file is called from .ins and is needed for the refinement and re-creation of the associated .fcf file (used for a detailed analysis of the refinement result). The calculated and reported checksums should be identical. Only characters with an ASCII value higher than 32 contribute to the checksum. An embedded include file might be broken, either due to tranfer errors or to deliberate or accidental post-refinement editing of its content. #============================================================================= # >>> Test for _exptl_crystal_description value _699 0 0 0 1 A 1 0 0 0 Missing _exptl_crystal_description Value ....... Please Do ! Examples of expected values are 'block', 'needle', 'plate', 'sphere', 'cylinder'. In case of 'cylinder' or 'sphere' also provide a value for '_exptl_size_rad'. #============================================================================= # >>> Test for consistency of Bonds and Coordinates in CIF _701 1.0 2.0 3.0 1 A 0 0 0 1 Bond Calc$X, Rep$Y, Dev.. $F Sigma Bond distances given in the CIF are cross-checked with corresponding values calculated from the coordinates. Alerts are set at 1,2 and 3 sigma deviation levels. Note: Default s.u.'s are used where no s.u. given (e.g. for C-H) In general, all differences should be within the associated s.u. Small differences may arise from rounding. Very large deviation (or zero distance) normally indicate incorrectly specified symmetry operations on the associated atoms, or 'cut-and-pasting' of incompatible CIF's. #============================================================================= # >>> Test for consistency of Angles and Coordinates in CIF _702 1.0 2.0 3.0 1 A 0 0 0 1 Angle Calc$X, Rep$Y, Dev.. $F Sigma Bond Angles given in the CIF are cross-checked with corresponding values calculated from the coordinates. Alerts are set at 1,2 and 3 sigma deviation levels. In general, all differences should be within the associated s.u. Small differences may arise from rounding. Very large deviations normally indicate incorrectly specified symmetry operations on the associated atoms, or 'cut-and-pasting' of incompatible CIF's. #============================================================================= # >>> Test for consistency of Torsions and Coordinates in CIF _703 1.0 2.0 3.0 1 A 0 0 0 1 Torsion Calc$X, Rep$Y, Dev.. $F Sigma Torsion angles given in the CIF are cross-checked with corresponding values calculated from the coordinates. Alerts are set at 1,2 and 3 sigma deviation levels. In general, all differences should be within the associated s.u. Small differences may arise from rounding. Very large deviations normally indicate incorrectly specified symmetry operations on the associated atoms, or 'cut-and-pasting' of incompatible CIF's. #============================================================================= # >>> Test for consistency of Contact Distances and Coordinates in CIF _704 1.0 2.0 3.0 1 A 0 0 0 1 Contact Calc$X, Rep$Y, Dev.. $F Sigma Intermolecular contacts listed in the CIF are checked against the coordinates in the CIF. Alerts are set at 1,2 and 3 sigma deviation levels. #============================================================================= # >>> Test for consistency of H-Bond D-H distances and Coordinates in CIF _705 1.0 2.0 3.0 1 A 0 0 0 1 D-H Calc$X, Rep$Y, Dev.. $F Sigma Hydrogen-Bond D-H listed in the CIF is checked. Alerts are set at 1,2 and 3 sigma deviation levels. #============================================================================= # >>> Test for consistency of H-Bond H..A Distances and Coordinates in CIF _706 1.0 2.0 3.0 1 A 0 0 0 1 H...A Calc$X, Rep$Y, Dev.. $F Sigma Hydrogen-Bond H..A listed in the CIF is checked. Alerts are set at 1,2 and 3 sigma deviation levels. This ALERT is generally related to incorrect symmetry codes. The symmetry number s in the symmetry code s_pqr should correspond to the expression for s in the CIF. Those expressions can be different for different software packages. E.g. pasting H-bond table data generated with PLATON into a CIF generated with SHELXL may raise this ALERT. Manual correction of the symmetry code should be trivial. #============================================================================= # >>> Test for consistency of H-Bond D..A Distances and Coordinates in CIF _707 1.0 2.0 3.0 1 A 0 0 0 1 D...A Calc$X, Rep$Y, Dev.. $F Sigma Hydrogen-Bond D..A listed in the CIF is checked. Alerts are set at 1,2 and 3 sigma deviation levels. This ALERT is generally related to incorrect symmetry codes. The symmetry number s in the symmetry code s_pqr should correspond to the expression for s in the CIF. Those expressions can be different for different software packages. E.g. pasting H-bond table data generated with PLATON into a CIF generated with SHELXL may raise this ALERT. Manual correction of the symmetry code should be trivial. #============================================================================= # >>> Test for consistency of H-Bond D-H..A Angles and Coordinates in CIF _708 1.0 2.0 3.0 1 A 0 0 0 1 D-H..A Calc$X, Rep$Y, Dev.. $F Sigma 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. #============================================================================= # >>> Test for Linear Torsions in CIF _710 0 0 0 4 I 0 0 0 1 Delete 1-2-3 or 2-3-4 Linear Torsion Angle ... # $A Do ! 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). #============================================================================= # >>> Test for label problems for Bonds in CIF _711 0 99 99 1 A 0 0 0 1 BOND Unknown or Inconsistent Label .......... $A Check 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. #============================================================================= # >>> Test for label problem for Angles in CIF _712 0 99 99 1 A 0 0 0 1 ANGLE Unknown or Inconsistent Label .......... $A Check 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. #============================================================================= # >>> Test for label problem for Torsions in CIF _713 0 99 99 1 A 0 0 0 1 TORSION Unknown or Inconsistent Label .......... $A Check 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. #============================================================================= # >>> Test for label problem for Contact Distances in CIF _714 0 99 99 1 A 0 0 0 1 CONTACT Unknown or Inconsistent Label .......... $A Check 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. #============================================================================= # >>> Test for label problem for H-Bond D-H distances in CIF _715 0 99 99 1 A 0 0 0 1 D-H Unknown or Inconsistent Label .......... $A Check 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. #============================================================================= # >>> Test for label problem for H-Bond H..A Distances in CIF _716 0 99 99 1 A 0 0 0 1 H...A Unknown or Inconsistent Label .......... $A Check 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. #============================================================================= # >>> Test for label problem for H-Bond D..A Distances in CIF _717 0 99 99 1 A 0 0 0 1 D...A Unknown or Inconsistent Label .......... $A Check 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. #============================================================================= # >>> Test for label problem for H-Bond D-H..A Angles in CIF _718 0 99 99 1 A 0 0 0 1 D-H..A Unknown or Inconsistent Label .......... $A Check 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. #============================================================================= # >>> Test for Unusual Labels _720 0 2 2 4 I 0 0 0 1 Number of Unusual/Non-Standard Labels .......... $I Note Up to 4 Character Labels of the type C11, H101, N10A, i.e. chemical symbol + number + optional letter are to be preferred. Note: SHELXL based refinements may use labels up to 7 characters (Including residue and or disorder information). #============================================================================= # >>> Test for consistency of Bonds and Coordinates in CIF _721 1.0 2.0 3.0 1 A 0 0 0 1 Bond Calc$X, Rep$Y Dev... $F Ang. Same as 701 but for distance without s.u. (esd). Difference is tested in terms of Angstroms. #============================================================================= # >>> Test for consistency of Angles and Coordinates in CIF _722 1.0 2.0 3.0 1 A 0 0 0 1 Angle Calc$X, Rep$Y Dev... $F Degree Same as 702 but for angle without s.u. (esd). Difference is tested in terms of Degrees. #============================================================================= # >>> Test for consistency of Torsions and Coordinates in CIF _723 1.0 999. 999. 1 A 0 0 0 1 Torsion Calc$X, Rep$Y Dev... $F Sigma Same as 703 but for torsion without s.u. (esd). Difference is tested in terms of Degrees. #============================================================================= # >>> Test for consistency of Contact Distances and Coordinates in CIF _724 1.0 2.0 3.0 2 A 0 0 0 1 Contact Calc$X, Rep$Y Dev... $F Ang. Same as 704, but for distance without s.u. (esd). Difference is tested in terms of Angstroms. #============================================================================= # >>> Test for consistency of H-Bond D-H distances and Coordinates in CIF _725 1.0 2.0 3.0 2 A 0 0 0 1 D-H Calc$X, Rep$Y Dev... $F Ang. Same as 705 but for distance without s.u. (esd). Differences are tested in terms of Angstrom. #============================================================================= # >>> Test for consistency of H-Bond H..A Distances and Coordinates in CIF _726 1.0 2.0 3.0 2 A 0 0 0 1 H...A Calc$X, Rep$Y Dev... $F Ang. Same as 706 but for distance without s.u. (esd). Differences are tested in terms of Angstrom. #============================================================================= # >>> Test for consistency of H-Bond D..A Distances and Coordinates in CIF _727 1.0 2.0 3.0 1 A 0 0 0 1 D...A Calc$X, Rep$Y Dev... $F Ang. Same as 707 but for distance without s.u. (esd). Differences are tested in terms of Angstrom. #============================================================================= # >>> Test for consistency of H-Bond D-H..A Angles and Coordinates in CIF _728 1.0 2.0 3.0 1 A 0 0 0 1 D-H..A Calc$X, Rep$Y Dev... $F Degree Same as ALERT 708 but for angle without s.u. (esd). Differences are tested in terms of Degrees. #============================================================================= # >>> Test for consistency of Bond s.u.'s and Coordinate s.u.'s in CIF _731 3.0 6.0 12.0 1 A 0 0 0 1 Bond Calc$X, Rep$Y ...... $I su-Rat A large ratio of the reported and calculated bond s.u.'s is found. The use of a DFIX instruction might cause such a warning since calculated s.u.'s are based on reported variances only. Note_1: s.u.'s on the unit-cell dimensions are taken into account in the calculation of expected s.u.'s. This may result in large differences between expected and reported s.u.'s when this contribution is not included in the reported s.u.'s, in particular for inaccurate unit-cells. Note_2: Another source for the discrepancy between calculated and reported s.u.'s can be that the validation software has access only to the variances of the refined parameters as opposed to the full co-variance matrix used by e.g. SHELXL for the calculation of derived parameters with associated s.u.'s. Constrained/restrained refinement may cause large co-variances. #============================================================================= # >>> Test for consistency of Angles and Coordinates in CIF s.u.'s _732 2.0 4.0 8.0 1 A 0 0 0 1 Angle Calc$X, Rep$Y ...... $F s.u.-Rat A large ratio of the reported and calculated bond angle s.u.'s is found. This check should warn for erroneous rounding: E.g. 105.5(19) to 105.5(2) or 105.0(5) to 105(5) etc. Note: Large differences are possible when certain constraints/restraints were applied in the refinement (e.g. the FLAT option in SHELXL97). Note_1: s.u.'s on the unit-cell dimensions are taken into account in the calculation of expected s.u.'s. This may result in large differences between expected and reported s.u.'s when this contribution is not included in the reported s.u.'s, in particular for inaccurate unit-cells. Note_2: Another source for the discrepancy between calculated and reported s.u.'s can be that the validation software has access only to the variances of the refined parameters as opposed to the full co-variance matrix used by e.g. SHELXL for the calculation of derived parameters with associated s.u.'s. Constrained/restrained refinement may cause large co-variances. #============================================================================= # >>> Test for consistency of Torsions and Coordinates in CIF s.u's _733 4.0 6.0 8.0 1 A 0 0 0 1 Torsion Calc$X, Rep$Y ...... $F s.u.-Rat A large ratio of the reported and calculated torsion angle s.u.'s is found. This check should warn for erroneous rounding: E.g. 105.5(19) to 105.5(2) or 105.0(5) to 105(5) etc. Note_1: s.u.'s on the unit-cell dimensions are taken into account in the calculation of expected s.u.'s. This may result in large differences between expected and reported s.u.'s when this contribution is not included in the reported s.u.'s, in particular for inaccurate unit-cells. Note_2: Another source for the discrepancy between calculated and reported s.u.'s can be that the validation software has access only to the variances of the refined parameters as opposed to the full co-variance matrix used by e.g. SHELXL for the calculation of derived parameters with associated s.u.'s. Constrained/restrained refinement may cause large co-variances. #============================================================================= # >>> Test for consistency of Contact Distance s.u. and Coordinate s.u. in CIF _734 2.0 4.0 8.0 1 A 0 0 0 1 Contact Calc$X, Rep$Y ...... $F s.u.-Rat A large ratio of the reported and calculated contact distance s.u.'s is found. Note: s.u.'s on the unit-cell dimensions are taken into account in the calculation of expected s.u.'s. This may result in large differences between expected and reported s.u.'s when this contribution is not included in the reported s.u.'s, in particular for inaccurate unit-cells. #============================================================================= # >>> Test for consistency of H-Bond D-H distance s.u. and Coordinate s.u in CIF _735 2.0 4.0 8.0 1 A 0 0 0 1 D-H Calc$X, Rep$Y ...... $I s.u.-Rat A large ratio of the reported and calculated H-bond D-H distance s.u.'s is found. The use of a DFIX instruction might cause such a warning since calculated s.u.'s are based on reported variances only. Note: s.u.'s on the unit-cell dimensions are taken into account in the calculation of expected s.u.'s. This may result in large differences between expected and reported s.u.'s when this contribution is not included in the reported s.u.'s, in particular for inaccurate unit-cells. #============================================================================= # >>> Test for consistency of H-Bond H..A Distance s.u. and Coordinates in CIF _736 2.0 4.0 8.0 1 A 0 0 0 1 H...A Calc$X, Rep$Y ...... $F s.u.-Rat A large ratio of the reported and calculated H-bond H..A distance s.u.'s is found. Note: s.u.'s on the unit-cell dimensions are taken into account in the calculation of expected s.u.'s. This may result in large differences between expected and reported s.u.'s when this contribution is not included in the reported s.u.'s, in particular for inaccurate unit-cells. #============================================================================= # >>> Test for consistency of H-Bond D..A Distance s.u. and Coordinates in CIF _737 2.0 4.0 8.0 1 A 0 0 0 1 D...A Calc$X, Rep$Y ...... $F s.u.-Rat A large ratio of the reported and calculated H-Bond D...A distance s.u.'s is found. #============================================================================= # >>> Test for consistency of H-Bond D-H..A Angle and Coordinates in CIF s.u. _738 2.0 4.0 8.0 1 A 0 0 0 1 D-H..A Calc$X, Rep$Y ...... $F s.u.-Rat A large ratio of the reported and calculated H-Bond D-H..A angle s.u.'s is found. Note: s.u.'s on the unit-cell dimensions are taken into account in the calculation of expected s.u.'s. This may result in large differences between expected and reported s.u.'s when this contribution is not included in the reported s.u.'s, in particular for inaccurate unit-cells. #============================================================================= # >>> Test for missing Bond s.u. in CIF _741 0.0 99.0 99.0 1 A 0 0 0 1 Bond Calc$X, Rep$Y ...... Missing s.u. Likely Missing s.u. on Bond in CIF. #============================================================================= # >>> Test for missing Angle s.u. in CIF _742 0.0 99.0 99.0 1 A 0 0 0 1 Angle Calc$X, Rep$Y ...... Missing s.u. Likely Missing s.u. on Bond angle in CIF. #============================================================================= # >>> Test for missing Torsion s.u. in CIF _743 0.0 99.0 99.0 1 A 0 0 0 1 Torsion Calc$X, Rep$Y ...... Missing s.u. Likely Missing s.u. on Torsion angle in CIF. #============================================================================= # >>> Test for missing Contact Distance s.u. in CIF _744 0.0 99.0 99.0 1 A 0 0 0 1 Contact Calc$X, Rep$Y ...... Missing s.u. Likely missing s.u. on contact Distance in CIF. #============================================================================= # >>> Test for missing H-Bond D-H distance s.u. in CIF _745 0.0 99.0 99.0 1 A 0 0 0 1 D-H Calc$X, Rep$Y ...... Missing s.u. Likely missing s.u. on H-Bond D-H distance in CIF. #============================================================================= # >>> Test for missing H-Bond H..A Distance s.u. in CIF _746 0.0 99.0 99.0 1 A 0 0 0 1 H...A Calc$X, Rep$Y ...... Missing s.u. Likely missing s.u. on H-Bond H...A distance in CIF. #============================================================================= # >>> Test for missing H-Bond D..A Distance s.u. in CIF _747 0.0 99.0 99.0 1 A 0 0 0 1 D...A Calc$X, Rep$Y ...... Missing s.u. Likely missing s.u. on H-Bond D...A distance in CIF. #============================================================================= # >>> Test for missing H-Bond D-H..A Angle s.u. in CIF _748 0.0 99.0 99.0 1 A 0 0 0 1 D-H..A Calc$X, Rep$Y ...... Missing s.u. Likely missing s.u. on H-Bond D-H..A angle in CIF. #============================================================================= # >>> Test for senseless Bond s.u. in CIF _751 0.0 99.0 99.0 4 A 0 0 0 1 Bond Calc$X, Rep$Y ...... Senseless s.u. An s.u. should not be given in the CIF for constrained distances. Please check for proper refinement status flags (e.g. R) #============================================================================= # >>> Test for senseless Angle s.u. in CIF _752 0.0 99.0 99.0 4 A 0 0 0 1 Angle Calc$X, Rep$Y ...... Senseless s.u. An s.u. should not be given in the CIF for constrained angles. Please check for proper refinement status flags (e.g. R) #============================================================================= # >>> Test for senseless Torsion s.u. in CIF _753 0.0 99.0 99.0 4 A 0 0 0 1 Torsion Calc$X, Rep$Y ...... Senseless s.u. An s.u. should not be given in the CIF for constrained torsion angles. Please check for proper refinement status flags (e.g. R) #============================================================================= # >>> Test for senseless Contact Distance s.u. in CIF _754 0.0 99.0 99.0 4 A 0 0 0 1 Contact Calc$X, Rep$Y ...... Senseless s.u. An s.u. should not be given in the CIF for constrained contact distances. Please check for proper refinement status flags (e.g. R) #============================================================================= # >>> Test for senseless H-Bond D-H distance s.u. in CIF _755 0.0 99.0 99.0 4 A 0 0 0 1 D-H Calc$X, Rep$Y ...... Senseless s.u. An s.u. should not be given in the CIF for constrained distances. Please check for proper refinement status flags (e.g. R). #============================================================================= # >>> Test for senseless H-Bond H..A Distance s.u. in CIF _756 0.0 99.0 99.0 4 A 0 0 0 1 H...A Calc$X, Rep$Y ...... Senseless s.u. An s.u. should not be given in the CIF for constrained distances. Please check for proper refinement status flags (e.g. R). #============================================================================= # >>> Test for senseless H-Bond D..A Distance s.u. in CIF _757 0.0 99.0 99.0 4 A 0 0 0 1 D...A Calc$X, Rep$Y ...... Senseless s.u. An s.u. should not be given in the CIF for constrained distances. Please check for proper refinement status flags (e.g. R). #============================================================================= # >>> Test for Senseless H-Bond D-H..A Angle s.u. in CIF _758 0.0 99.0 99.0 4 A 0 0 0 1 D-H..A Calc$X, Rep$Y ...... Senseless s.u. An s.u. should not be given in the CIF for constrained angles. Please check for proper refinement status flags (e.g. R) #============================================================================= # >>> Test for the presence of at least one torsion angle in the CIF _760 0 2 2 1 I 0 0 0 1 CIF Contains no Torsion Angles ................. ? Info The CIF contains no torsion angle entries. This might be accomplished with the SHELXL instruction CONF. Inclusion is encouraged by Acta Cryst. but not necessarily so by other journals. #============================================================================= # >>> Test for the presence of at least one X-H in the CIF _761 0 2 2 1 I 0 0 0 1 CIF Contains no X-H Bonds ...................... Please Check 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. #============================================================================= # >>> Test for at least one X-Y-H or H-Y-H entry in the CIF _762 0 2 2 1 I 0 0 0 1 CIF Contains no X-Y-H or H-Y-H Angles .......... Please Check 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. #============================================================================= # >>> Test for missing bonds in CIF _763 0.01 0.1 5.0 1 I 0 0 0 1 Incomplete CIF Bond list Detected (Rep/Expd) ... $F Ratio Bond list in CIF likely incomplete. #============================================================================= # >>> Test for overcomplete bonds in CIF _764 0.0 5.0 5.0 4 I 0 0 0 1 Overcomplete CIF Bond List Detected (Rep/Expd) . $F Ratio The CIF contains more bonds than the unique set, indicating redundancy. An example is redundancy due to the inclusion of symmetry related bonds. #============================================================================= # >>> TEST for ERRONEOUS LIST 8 INSTRUCTION IN EMBEDDED .INSTRUCTION _766 0.0 2.0 2.0 4 I 0 0 0 1 INS Embedded LIST 8 Instruction Should be LIST 4 Please Check The final .fcf associated with the .cif should have been created with the LIST 4 instruction (or just left out because already implicit with the ACTA instruction). The LIST 8 instruction will create an FCF file where the observed data are detwinned making the generated .fcf unsuitable for checking for missed (additional) twinning and validation. #============================================================================= # >>> TEST for ERRONEOUS LIST 6 INSTRUCTION IN EMBEDDED .INSTRUCTION _767 0.0 2.0 2.0 4 I 0 0 0 1 INS Embedded LIST 6 Instruction Should be LIST 4 Please Check The .fcf associated with the .cif should have been created with the LIST 4 instruction (or left out because already implicit with the ACTA instruction). LIST 6 will create an FCF file where the observed data are corrected for anomalous/resonant scattering, making the generated .fcf unsuitable for post refinement absolute structure analysis and validation. #============================================================================= # >>> TEST for CIF/RES embedded explicit scattering factor values _768 0.0 0.0 0.0 4 I 0 0 0 1 Embedded RES Explicitly Supplied Scattering Data Please Note The supplied CIF includes explicit atomic scattering factor date in the embedded .res file. Those values may or may not be identical to the standard values as included in current versions of SHELXL. It should be noted that those values will not be present as CIF data items in CIF's created with SHELXL. PLATON/checkCIF will use its own build-in scattering factors, that are identical to those used by default by SHELXL for common wavelengths, for its validation calculations. #============================================================================= # >>> TEST for CIF embedded explicit scattering factor values _769 0.0 0.0 0.0 4 I 0 0 0 1 CIF Embedded Explicitly Supplied Scattering Data Please Note The supplied CIF contains explicit scattering factor data as values of their corresponding CIF datanames. Those scattering factor data are used by PLATON/checkCIF for its validation calculations as opposed to using the neutral scattering factor data that are stored in PLATON (which are identical to those in stored in SHELXL). Those CIF reported values should be identical to those provided in the embedded *.ins file. Current SHELXL versions do not copy scattering factor data that are explicitly included in the *.ins instruction file into corresponding CIF data items. A reason for the use of non-standard scattering factors can be the modelling of charged atoms in the refinement. #============================================================================= # >>> Test for suspect C-H bonds in CIF (Not caught otherwise) _770 0.0 0.0 0.0 2 A 0 0 0 1 Suspect C-H Bond in CIF: $A--$B . $F Ang. Report on unusual C-H bonds not caught in other tests. #============================================================================= # >>> Test for suspect N-H bonds in CIF (Not caught otherwise) _771 0.0 1.4 1.5 2 A 0 0 0 1 Check N-H Bond in CIF: $A--$B .. $F Ang. Report on unusual N-H bonds not caught in other tests. #============================================================================= # >>> Test for suspect O-H bonds in CIF (Not caught otherwise) _772 0.0 1.4 1.5 2 A 0 0 0 1 Suspect O-H Bond in CIF: $A--$B .. $F Ang. 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. #============================================================================= # >>> Test for suspect C-C bonds in CIF (Not caught otherwise) _773 0.0 0.0 0.0 2 A 0 0 0 1 Check long C-C Bond in CIF: $A--$B $F Ang. 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. #============================================================================= # >>> Test for too large / erroneous bond distance _774 3.5 4.0 99.0 1 A 0 0 0 1 Check X-Y Bond in CIF: $A--$B .. $F Ang. Likely Erroneous Bond Entry. #============================================================================= # >>> Test for too large / erroneous Contact distance _775 4.0 6.0 99.0 1 A 0 0 0 1 Check X-Y Contact in CIF: $A--$B $F Ang. Likely Erroneous Contact Entry. #============================================================================= # >>> Test for too large / erroneous H-Bond D-H distance _776 1.3 1.5 2.0 1 A 0 0 0 1 Check D-H Dist in CIF: $A--$B .. $F Ang. Likely Erroneous D-H Entry. #============================================================================= # >>> Check for N..H..X+ bonds in CIF _777 0.0 0.0 0.0 2 A 0 0 0 1 Check N..H..X Bond in CIF: $A--$B $F Ang. Report N-H distance in special N..H..X+ bonds. The N .. X distance is expected to be shorter than in a standard hydrogen bond. #============================================================================= # >>> Check for O..H..X+ bonds in CIF _778 0.0 0.0 0.0 2 A 0 0 0 1 Check O..H..X Bond in CIF: $A--$B $F Ang. Report O-H distance in special O..H..X+ bonds. The O .. X distance is expected to be shorter than in a standard hydrogen bond. #============================================================================= # >>> Test for suspect Angle in CIF (Not caught otherwise) _779 0.0 0.0 0.0 4 I 0 0 0 1 Suspect or Irrelevant (Bond) Angle(s) in CIF ... $A Deg. 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. #============================================================================= # >>> Test whether coordinates form a connected set _780 0 0 1.0 1 A 0 1 0 0 Coordinates do not Form a Properly Connected Set Please Do ! 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. #============================================================================= # >>> Test for Flack x value for Centrosymmetric space-group _781 0 0 0 1 A 0 0 0 1 Flack Parameter is Given for Centro Space Group. ? Error A Flack parameter value is erroneously given for a structure reported in a centrosymmetric space-group. #============================================================================= # >>> Test for Unusual C-NO2 an C-CO2 moiety Bond geometry _782 0 1.0 2.0 2 A 0 0 1 0 Unusual Bond Geometry for $A Moiety Around $B Check Warning for a possible misassignment of C-NO2 and C-CO2 moieties. 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 Test Criteria: ALERT for C-O bond sum < 2.48 and C-C < 1.48 Angstrom The N-O bond distances in C-NO2 are expected to add up to about 2.4 Test Criteria: ALERT for N-O bond sum > 2.48 and C-C > 1.48 Angstrom #============================================================================= # >>> Test for El1 in SumFormula _787 0 99.0 99.0 4 A 0 0 0 1 Change $A into $B in SumFormula .. Please Do The numerical part for an element in the SumFormula should be dropped when '1'. #============================================================================= # >>> Test for El1 in MoietyFormula _788 0 99.0 99.0 4 A 0 0 0 1 Change $A into $B in MoietyFormula Please Do The numerical part for an element in the MoietyFormula should be dropped when '1'. #============================================================================= # >>> Report the number of atoms with negative _atom_site_disorder_group # _789 0 0 0 4 I 0 0 0 1 Atoms with Negative _atom_site_disorder_group # $I Check A negative value of the _atom_site_disorder_group number of an atom indicates whether that atom is part of a group disordered over a symmetry element. Check whether this negative sign assignment applies. #============================================================================= # >>> Test Whether C.G. Residue in Unitcell Box _790 0 2 2 4 I 0 0 0 1 Centre of Gravity not Within Unit Cell: Resd. # $I Note 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. #============================================================================= # >>> Check the absolute configuration of chiral atom in Sohnke spgr _791 0 0 0 4 I 0 0 0 1 Model has Chirality at $A (Sohnke SpGr) $B Verify A tentative (R/S) assignment is done on the basis of the geometrical and atom type data in the CIF. A correct assignment depends on the algorithm used to automatically detect double and triple bonds. For that reason it is important that the molecule is complete (i.e. all hydrogen atoms should be included). In case of a chiral molecule in a centro-symmetric spacegroup, it is essential that the coordinate set used and the associated molecular (ORTEP) illustration are consistent. This can be verified by checking the identical signs of relevant torsion angles. The absolute structure assignment should also be consistent with the lowest value of the Flack parameter and/or known absolute configuration. #============================================================================= # >>> Check the absolute configuration of chiral atom in a polar non-Sohnke spgr _792 0 0 0 1 I 0 0 0 1 Model has Chirality at $A (Polar SPGR) $B Verify 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. #============================================================================= # >>> Check the absolute configuration of chiral atom in a centrosymmetric SpGr _793 0 0 0 4 A 0 0 0 1 Model has Chirality at $A (Centro SPGR) $B Verify 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. #============================================================================= # >>> Report the calculated 'Valence Bond' valency for metals _794 0 0 0 5 A 0 0 0 1 Tentative Bond Valency for $A $B . $F Info 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). #============================================================================= # >>> Test for C-atom Labels Ordered _795 0.0 0.0 0.0 4 I 0 0 0 1 C-Atom in CIF Coordinate List Out-of-Sequence .. $A Note Atoms in the CIF are not given in logical order (i.e. C1, C2 etc.) The recommended procedure is to sort the atom list in some logical order before the final refinement cycles. #============================================================================= # >>> Test for O-atom Labels Ordered _796 0.0 2.0 2.0 4 I 0 0 0 1 O-Atom in CIF Coordinate List Out-of-Sequence .. $A Note Atoms in the CIF are not given in logical order (i.e. O1, O2 etc.) The recommended procedure is to sort the atom list in some logical order before the final refinement cycles. #============================================================================= # >>> Test for N-atom Labels Ordered _797 0.0 2.0 2.0 4 I 0 0 0 1 N-Atom in CIF Coordinate List Out-of-Sequence .. $A Note Atoms in the CIF are not given in logical order (i.e. N1, N2 etc.) The recommended procedure is to sort the atom list in some logical order before the final refinement cycles. #============================================================================= # >>> Test for Alphanumeric Label on coordinate record _798 0.0 2.0 2.0 4 A 0 0 0 1 Numeric Atom Label on Coordinate Par. Record ... $A Check 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'). #============================================================================= # >>> Test for Alphanumeric Label on displacement par. record _799 0.0 2.0 2.0 4 A 0 0 0 1 Numeric Label on Displacement Par. Record ...... $A Check 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'). #============================================================================= # >>> Test for out-of-order symmetry data _800 0.0 0.0 0.0 4 A 1 0 0 0 Symmetry Specification Should Precede Cell Data. Please Do! Symmetry data (i.e. space group, symmetry operations etc.) are expected to be given in the CIF prior to the cell dimensions and coordinate data. #============================================================================= # >>> Test for missing, incomplete or out-of-order Cell data _801 0.0 0.0 0.0 4 A 1 0 0 0 Cell Data Missing, Incomplete or Out-of-Order .. Please Check PLATON/CheckCIF has a problem with the Cell data. A possible reason can be that the cell data are missing, incomplete or out-of-sequence. PLATON/CheckCIF wishes to encounter the cell and symmetry data before any coordinates are given. PLATON expects the values of all six cell parameters. #============================================================================= # >>> Test for Input lines longer than 80 Characters _802 0 10 10 4 I 0 0 0 1 CIF Input Record(s) with more than 80 Characters $I Info 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. #============================================================================= # >>> Test for Loop problem in CIF-Read _803 0.0 0.0 0.0 1 A 0 0 0 1 Loop Problem in CIF-Reading (Too Many loop Items) Please Check Fatal Problem: Check loop data names and data for errors. There are likely too many or to few data in the loop. #============================================================================= # >>> Test for ARU-Pack Problem(s) in PLATON _804 0 1 1 5 I 0 0 0 1 Number of ARU-Code Packing Problem(s) in PLATON $I Info 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. #============================================================================= # >>> Test for insufficient 'coordinate data' _805 0 0 0 1 A 0 0 0 1 Fatal Problem: Insufficient Data in Atom Loop .. Please Check Check Coordinate Data Loop. #============================================================================= # >>> Test for insufficient 'UIJ data' _806 0 2 2 4 A 1 0 0 1 Fatal Problem: Insufficient Data in UIJ Loop ... Please Check Check UIJ Data Loop. #============================================================================= # >>> Test for Maximum number of ATOMS Exceeded Problem _807 0 0 100 5 A 0 0 0 1 Fatal Problem: Maximum Number of Atoms Exceeded. ! Info PLATON can handle up to 'NP1' 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. #============================================================================= # >>> Test for Parseable SHELXL style Weighting scheme _808 0 0 0 5 A 0 0 0 1 No Parseable SHELXL Style Weighting Scheme Found Please Check The validation 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 ';'. #============================================================================= # >>> Test the SHELXL style Weighting scheme _809 0 0 0 1 A 0 0 0 1 Can not Parse the SHELXL Weighting Scheme String Please Check The software did not succeed in Parsing the SHELXL style weighting scheme. The string might have been edited or of the more than 2 parameter variety (see SHELXL manual). #============================================================================= # >>> Test for Out-of-Memory Problem _810 0 0 0 5 A 0 0 0 1 Out-of-Memory Problem in PLATON/ASYM ........... ! Info Analysis for missing reflections may be incomplete due to an out-of-memory problem. #============================================================================= # >>> Test for No ADDSYM Analysis _811 0 2 2 5 A 0 0 0 1 No ADDSYM Analysis: Too Many Excluded Atoms .... ! Info The ADDSYM test for missed symmetry is not executed for structures with too many disordered atoms. #============================================================================= # >>> Test for ALIAS OVERFLOW _812 0 0 2 5 A 0 0 0 1 PLATON problem - Too Many Aliased Atoms. Max = $I Non-standard labels are aliased into acceptable labels. The maximum number of aliases is reached. #============================================================================= # >>> Test for insufficient data on HKLF record in CIF _813 0 0 0 1 A 0 0 0 1 No Numerical Data in HKLF (.res) Record in CIF . Please Check Check the HKLF record in the SHELXL style .res is embedded in the CIF. This Record should show either 'HKLF 4' or 'HKLF 5'. The information in this record is used to establish that a twinning model was refined. #============================================================================= # >>> Test for (In)Commensurate Structure CIF _814 0 0 0 5 A 0 0 0 1 No Validation of (In)commensurate Structure CIFs Note PLATON/CheckCIF can not validate the CIFs associated with (in)commensurate structure reports. #============================================================================= # >>> Test for number of population parameter overflow _815 0 0 0 5 A 0 0 0 1 PLATON Issue: Population Parameter Overflow .... Fatal PLATON/checkCIF is currently dimensioned for up to 255 population parameters. Please contact the author at a.l.spek@uu.nl #============================================================================= # >>> Test for final refinement with detwinned HKLF 4 data _816 0 0 0 5 A 0 0 0 1 Likely Final Refinement with Detwinned Data .... $A Check The CIF includes a loop with twin matrices. The embedded .res file however points to a HKLF 4 file with likely detwinned intensities. #============================================================================= # >>> Report Read Problem in PLATON/PLA230 _820 0 0 0 5 A 0 0 0 1 Internal PLATON Read Problem with ALERT Number . $A Internal PLATON Problem. Please refer problem to author at a.l.spek@uu.nl #============================================================================= # >>> Check for Negative PART Record(s) in CIF-Embedded shelxl.res _822 0 0 0 4 A 0 0 0 1 CIF-embedded .res Contains Negative PART Numbers $I Check Please check the validity of the negative PART numbers in the CIF-embedded SHELXL .res file. Their use may obscure disorder model errors. #============================================================================= # >>> Test for BASF/TWIN Problem in SHELXL _850 0.0 2.0 2.0 4 A 0 0 0 1 Check Flack Parameter Exact Value 0.00 with s.u. $F Check 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. #============================================================================= # >>> Test for restraints used in refinement _860 0 0 0 3 I 0 0 1 0 Number of Least-Squares Restraints ............. $I Note The use of restraints used in the refinement should be explained in the write-up of a structure analysis. It is also recommended to include the refinement instructions in the CIF (e.g. the final .res of a SHELXL refinement) as a comment: _iucr_refine_instructions_details ; TITL .. (etc.) ; Note: An exception are restraints for floating origins (e.g. in P21). #============================================================================= # >>> Report the Suppression of Olex2/_smtbx_masks use Related ALERTS _868 0 0 0 4 A 0 0 0 1 ALERTS Due to the Use of _smtbx_masks Suppressed ! Info ALERTS related to the use of Olex2/_smtbx_masks that can not (yet) be accounted for as part of the VALIDATION algorithms have been suppressed. #============================================================================= # >>> Report the Suppression of SQUEEZE use Related ALERTS _869 0 0 0 4 A 0 0 0 1 ALERTS Related to the Use of SQUEEZE Suppressed ! Info ALERTS related to the use of PLATON/SQUEEZE that can not (yet) be accounted for as part of the VALIDATION algorithms have been suppressed. #============================================================================= # >>> Report the Suppression of some Twinning Related ALERTS _870 0 0 0 4 A 0 0 0 1 ALERTS Related to Twinning Effects Suppressed .. ! Info ALERTS related to twinning effects that can not (yet) be accounted for as part of the VALIDATION algorithms have been suppressed. #============================================================================= # >>> Report the Suppression of some Laue technique related ALERTS _871 0 0 0 4 A 0 0 0 1 Laue Technique Related ALERTS are Suppressed ... ! Info ALERTS related to the use of the Laue technique with a wavelength range have been suppressed. #============================================================================= # >>> Report the Suppression of anharmonic refinement Related ALERTS _872 0 0 0 4 A 0 0 0 1 ALERTS Related to Anharmonic Refine Suppressed ! Info ALERTS related to anharmonic refinement have been suppressed. This generally concerns XD and some OLEX2 refinement based CIF's. Internally calculated structure factors are based on the reported harmonic displacement parameters only. #============================================================================= # >>> Report missing datum for _diffrn_reflns_number _880 0 0 0 1 A 1 0 0 0 No datum for _diffrn_reflns_number supplied .... Please Do ! The total number of measured reflections is not reported. #============================================================================= # >>> Report missing datum for _diffrn_reflns_av_R_equivalents _881 0 0 0 1 A 1 0 0 0 No Datum for _diffrn_reflns_av_R_equivalents ... Please Do ! The merging R-factor for equivalent reflections is missing in the CIF. A value of 0.0 usually indicates that merging has been done outside the program that created the CIF. A proper value should be included as reported by the external merging program. Note: modern hardware will generally produce redundant reflection data. #============================================================================= # >>> Report missing datum for __diffrn_reflns_av_unetI/netI _882 0 0 0 1 A 1 0 0 0 No Datum for _diffrn_reflns_av_unetI/netI ...... Please Do ! No value reported for either _diffrn_reflns_av_unetI/netI or the older/superseded _diffrn_reflns_av_sigmaI/netI CIF item. #============================================================================= # >>> Report missing datum for _atom_sites_solution_primary _883 0 0 0 1 I 1 0 0 0 No Info/Value for _atom_sites_solution_primary . Please Do ! Please supply the proper info for _atom_site_solution_primary. Values must be one of the following: difmap, vecmap, heavy, direct, geom, disper, isomor, notdet, dual, iterative, other. #============================================================================= # >>> Check for duplicate H-M space group symbol _898 0.0 0.0 0.0 4 A 0 0 0 1 Second Reported H-M Symbol in CIF Ignored ...... ! Check A second specification of the H-M symbol is found in the CIF. Only the first one encountered is retained. #============================================================================= # >>> Report the Use of an older SHELXL version _899 0 0 0 4 A 0 0 0 1 $B is Deprecated and Succeeded by SHELXL $A Note A more recent SHELXL version is now available. Final refinement with the latest version is recommended since (IUCr)checkCIF is run against the latest SHELXL version for the re-creation of the FCF. #============================================================================= # >>> Test for 'No-matching reflection file' _900 0 0 0 1 I 0 0 0 1 No Matching Fo/Fc Reflection File (FCF) Found .. Please Check Likely cause: Dataset names in the CIF and FCF differ. Note: FCF Validation is Skipped for this Entry. #============================================================================= # >>> Test for CIF & FCF CELL Not Matching _901 0 0 0 1 I 0 0 0 1 Cell Parameters in CIF and FCF do not Match .... ! Error Possible causes: wrong dataset, CIF or FCF parameters edited inconsistently or cell parameters for transformed cell (e.g. P21/n <-> P21/c). Note: FCF Validation is Skipped for this Entry. #============================================================================= # >>> Test for non-zero number of recognised reflections in FCF _902 0 0 0 1 I 0 0 0 1 No (Interpretable) Reflections Found in FCF .... Please Check Either no reflections are found in the FCF or the FCF is uninterpretable due to unknown format or editing. Note: FCF Validation is Skipped for this Entry. #============================================================================= # >>> Test for Fobs=Fcalc in FCF _903 0 0 0 1 I 0 0 0 1 F(obs) and F(calc) Values are Identical in FCF . Please Check Check the FCF file for F(obs) equal F(calc) [or F(obs)**2 equal F(calc)**2]. The FCF is obviously not created as the result of a refinement with regular observed data. #============================================================================= # >>> Test for NREF .GT. NPAR in the CIF _904 0 0 0 1 I 0 0 0 1 Number of Reflections is < Number of Parameters $I The number of reflections found in the reflection file is less than the number of parameters reported in the CIF. #============================================================================= # >>> Report Negative K values in the Analysis of Variance _905 0.0 1.0 2.0 3 I 0 0 1 0 Negative K value in the Analysis of Variance ... $F Report Scale Factors (i.e. K = Mean[Fo**2] / Mean [Fc**2]) for selected groups of reflections, as listed in the Analysis of Variance Section #7 of the FCF validation report, are expected to have a value of about 1.000. Strong deviations should be investigated, acted upon or explained. (see also SHELXL manual). A reason can be meaningless (weak) high order data where a cut-back of the resolution might be indicated. Incorrect background treatment can lead to numerous negative observed intensities for weak reflections (i.e. F(calc) close to zero. For details see the Analysis-of-Variance Section in the '.ckf' file. #============================================================================= # >>> Report Large K values in the Analysis of Variance _906 0.0 1.0 2.0 3 I 0 0 1 0 Large K Value in the Analysis of Variance ...... $F Check Scale Factors (i.e. K = Mean[Fo**2] / Mean [Fc**2]) for selected groups of reflections, as listed in the Analysis of Variance Section #7 of the FCF validation report, are expected to have a value of about 1.000. Strong deviations should be investigated, acted upon or explained. (see also SHELXL manual). For details see the Analysis-of-Variance Section in the '.ckf' file. #============================================================================= # >>> Check whether the structure needs to be inverted _907 0.5 10.0 10.0 2 A 0 0 1 0 Flack x > 0.5, Structure Needs to be Inverted? . $F Check A Flack x value generally indicates that the structure needs to be inverted. Check whether the Flack x value is unreliable due to a weak anomalous dispersion signal, systematic errors or weak data and against know absolute structure. #============================================================================= # >>> Report on Max Observed data in any Resolution Shell _908 0 0 0 2 A 0 0 0 1 Max. Perc. Data with I > 2*s(I) per Res.Shell . $F% Note A low maximum percentage of reflections with I > 2*s(I) may indicate: 1 - Missed translation symmetry. E.g. all reflections hkl weak for l = 2n +1 2 - Pseudo-merohedral twinning, index > 1. (e.g. non-spacegroup extinctions. 3 - Very weak observed data. #============================================================================= # >>> Report of Observed data at Theta Cutoff _909 0 0 0 3 A 0 1 0 0 Percentage of I>2sig(I) Data at Theta(Max) Still$I% Note 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. Reflection data beyond that value should not be removed when significantly above the noise level. E.g. they may be very relevant in case of pseudo- symmetry and (non)centrosymmetry refinement. #============================================================================= # >>> Test for number of missing reflections below Theta(Min) _910 0 10 50 3 A 0 0 0 1 Missing # of FCF Reflection(s) Below Theta(Min). $I Note Possible causes: Experimental beamstop Theta(min) limit set too high; A large unit-cell causing reflections effected by the beamstop. A possible technical solution on CCD based equipment involves the collection of additional images with the detector at a larger distance from the crystal with the beamstop setting changed accordingly. Alternatively, a large number of low-order 'outlier' reflections might have been 'Omitted' deliberately from the (final) least-squares refinement. The test is against the actual Theta(Min) of the reflections in the *.fcf file. See the *.ckf file for details of the missing reflections. Good quality low order reflections might be relevant for SQUEEZE and similar solvent modelling refinement techniques. #============================================================================= # >>> Test for missing reflections between Theta(Min)and sinth/lambda=0.6 _911 -1 5 999 3 A 0 0 0 1 Missing FCF Refl Between Thmin & STh/L=$A $I Report Possible causes: Missing cusp of data (due to rotation about one axis), deleted (overflow) reflections or improper strategy (orthorhombic for monoclinic crystal etc.) See the .ckf file for details. #============================================================================= # >>> Test for missing reflections above Sin(TH)/Lambda = 0.6 _912 -1 100 999 4 A 0 0 0 1 Missing # of FCF Reflections Above STh/L= 0.600 $I Note Possible causes: Missing cusp of data (due to rotation about one axis), deleted (overflow) reflections or improper strategy (orthorhombic for monoclinic crystal etc.) See the .ckf file for details. #============================================================================= # >>> Test for missing strong reflections _913 0 100 999 3 A 0 0 0 1 Missing # of Very Strong Reflections in FCF .... $I Note 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. See the .ckf file for details. #============================================================================= # >>> Test for absence of Bijvoet Pairs in non-centro structure _914 0 2 2 3 A 0 0 0 1 No Bijvoet Pairs in FCF for Non-centro Structure Please Check 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. #============================================================================= # >>> Test for low Friedel Pair Coverage in non-centro structure _915 20. 50. 100 3 A 0 0 0 1 No Flack x Check Done: Low Friedel Pair Coverage $I % 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. #============================================================================= # >>> Test for differing Flack x and Hooft y Parameter values _916 0.1 0.2 0.3 2 A 0 0 0 1 Hooft y and Flack x Parameter Values Differ by . $F Check 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. #============================================================================= # >>> Test/Report whether FCF is based on a BASF/TWIN refinement _917 0.0 0.0 0.0 2 A 0 0 0 1 The FCF is Likely NOT Based on a BASF/TWIN Flack Please Check 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. #============================================================================= # >>> Test for reflections with I(obs) << I(calc) _918 0 999 999 3 A 0 0 0 1 Reflection(s) with I(obs) much Smaller I(calc) . $I Check This ALERT reports on the number of reflections with (Fo**2 - Fc**2) / Sigma(Fo**2) < - 100.0. In case of strong reflections this might be due to extinction (to be addressed with the refinement of an extinction parameter. Otherwise 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. #============================================================================= # >>> Test for reflections effected by the beamstop _919 0 0 999 3 A 0 0 0 1 Reflection # Likely Affected by the Beamstop ... $I Check 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. #============================================================================= # >>> Test for TH(Max) Consistency between CIF & FCF _920 .10 .50 99.0 1 A 0 0 0 1 Theta(Max) in CIF and FCF Differ by ........... $F Degree 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. In rare cases this ALERT may point to using a SHELXL TWIN instruction for handling a non-merohedral twin. #============================================================================= # >>> Test for R1 Consistency between CIF & FCF(Reported) _921 .001 .005 .050 1 A 0 0 0 1 R1 in the CIF and FCF Differ by ............... $F Check Please check whether the supplied FCF corresponds with the CIF produced in the same least squares refinement job. See at the end of Section #10 in the .ckf report file for details. The test is based on the observed and calculated F**2 in the FCF and de weight parameters taken from the CIF. #============================================================================= # >>> Test for wR2 Consistency between CIF & FCF(Reported) _922 .001 .005 .050 1 A 0 0 0 1 wR2 in the CIF and FCF Differ by ............... $F Check Please check whether the supplied FCF corresponds with the CIF produced in the same least squares refinement job. See at the end of Section #10 in the .ckf report file for details. The test is based on the observed and calculated F**2 in the FCF and de weight parameters taken from the CIF. #============================================================================= # >>> Test for S Consistency between CIF & FCF(Reported) _923 .01 .50 1.0 1 A 0 0 0 1 S Values in the CIF and FCF Differ by ....... $F Check Please check whether the supplied FCF corresponds with the CIF produced in the same least squares refinement job. See at the end of Section #10 in the .ckf report file for details. The test is based on the observed and calculated F**2 in the FCF and de weight parameters taken from the CIF. #============================================================================= # >>> Test for Consistency of the Reported & Calculated Rho(min) _924 1.0 2.0 3.0 1 A 0 0 0 1 The Reported and Calculated Rho(min) Differ by . $F eA-3 Check & Explain why the Reported Rho(min) differs significantly from the value calculated on the basis of the reported structure (using the AIM model) Note: The Reported and Calculated values may differ slightly due to a differing peak interpolation algorithm, or significantly when the refinement is based on a non-spherical atom model. #============================================================================= # >>> Test for Consistency of the Reported & Calculated Rho(max) _925 1.0 2.0 3.0 1 A 0 0 0 1 The Reported and Calculated Rho(max) Differ by . $F eA-3 Check & Explain why the Reported Rho(max) differs significantly from the value calculated on the basis of the reported structure (using the AIM model) Note: The Reported and Calculated values may differ slightly due to a differing peak interpolation algorithm, or significantly when the refinement is based on a non-spherical atom model. #============================================================================= # >>> Test for R1 Consistency between CIF & FCF(Calculated) _926 .001 .005 .050 1 A 0 0 0 1 Reported and Calculated R1 Differ by ......... $F Check 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. See at the end of Section #10 in the .ckf report file for details. 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. #============================================================================= # >>> Test for wR2 Consistency between CIF & FCF(Calculated) _927 .001 .005 .050 1 A 0 0 0 1 Reported and Calculated wR2 Differ by ......... $F Check 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. See at the end of Section #10 in the .ckf report file for details. 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. #============================================================================= # >>> Test for S Consistency between CIF & FCF(Calculated) _928 .10 .20 2.00 1 A 0 0 0 1 Reported and Calculated S value Differ by . $F Check Please check whether the S value that is reported in the CIF corresponds with the S value calculated from the parameters supplied in the CIF. See at the end of Section #10 in the .ckf report file for details. This test is based on the observed reflection data in the FCF and reflection data that are calculated with the parameters (i.e. coordinates, displacement and weight parameters) taken from the CIF. #============================================================================= # >>> Test for interpretable weight parameters for R1,wR2 & S Comparison _929 0 10 10 5 A 0 0 0 1 No Weight Pars,Obs and Calc R1,wR2,S not Checked ! Info SHELXL weight parameters are expected to be given in the format below: _refine_ls_weighting_details 'calc w=1/[\s^2^(Fo^2^)+(0.1000P)^2^+0.0000P] where P=(Fo^2^+2Fc^2^)/3' JANA style weight is expected to be given in the format: _refine_ls_weighting_details 'w=1/(\s^2^(I)+0.0016I^2^)' Do not edit this string or make it into a text block between ';'. #============================================================================= # >>> Test for Missed Twinning from FCF data _930 .00 .00 .80 2 A 0 0 1 0 FCF-based Twin Law$A$BEst.d BASF $F Check Check the proposed Twin Law. The entry in () represents the proposed rotation axis in reciprocal space and the one in [] the corresponding rotation is direct space. The relevant Twin Matrix can be found in the file '.ckf'. Note: This analysis is based on Fobs**2/Fcalc**2 differences with Fcalc**2 data taken from the .fcf file (i.e. Fobs, Fcalc listing). ALERT-930 is expected to generate an related ALERT-931 as well. #============================================================================= # >>> Test for Missed Twinning from FCF/CIF data _931 .00 .00 .80 5 A 0 0 1 0 CIFcalcFCF Twin Law$A$BEst.d BASF $F Check 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 test is based on Fcalc**2 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 make sure that twinning is mentioned in the write-up of the structure report and paper. #============================================================================= # >>> Report number of OMIT records in embedded .res _933 0 0 0 2 A 0 0 1 0 Number of HKL-OMIT Records in Embedded .res File $I Note This ALERT reports on the number of 'OMIT h k l' records (Reflections omitted from the least-squares refinement) in the CIF embedded .res file. Generally, there should be a good reason for excluding those observed experimental data point such as (partial) obscuration by the beam stop. #============================================================================= # >>> Report number of outliers in the FCF file _934 0 1 10 3 A 0 0 1 0 Number of (Iobs-Icalc)/Sigma(W) > 10 Outliers .. $I Check 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 1.0/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. #============================================================================= # >>> Pseudo Extinction Parameter Test _935 .05 1.00 2.00 2 A 0 0 0 0 Large Value of Calc. Pseudo Extinction Parameter $F Both significantly positive and significantly negative values should invoke a search for a likely cause and a corrective action. #============================================================================= # >>> Test for DAMP instruction in embedded .res _936 0 0.5 1 2 A 0 0 1 0 The Embedded .res File Includes a DAMP Command . $F Report The reason for the use of a DAMP instruction in the final refinement job should be discussed/reported. 'DAMP 0.0' should not be used for small molecule refinement since it masks non-convergence. #============================================================================= # >>> Report Exponential Term in SHELXL weight expression _937 0 10.0 20.0 4 A 0 0 1 0 Weight Expression Contains Exponential Term .... $F Report The use of an exponential term in the SHELXL weight expression is not recommended in the final refinement stage (i.e. the third parameter in the SHELXL WGHT record). #============================================================================= # >>> Test for high not weight optimized S value _939 10.0 100. 500. 3 A 0 0 0 1 Large Value of Not (SHELXL) Weight Optimized S . $F Check SHELXL suggests/optimizes two weight parameters aiming at bringing the S value (Goodness-of-Fit) close to 1.0. This 939_ALERT reports the S value when based on the supplied sigma(I) values only. A large value of this not weight optimized S generally indicates the presence of large outliers in the data set. Examples are reflections (partially) 'measured' behind the beam stop. (See also ALERT_919). The latter low order reflections are best left out from the final refinement with an OMIT hkl instruction. #============================================================================= # >>> Test for wR2 refinement with all data _940 0 0 2 3 A 0 0 0 1 Fsqd Refinement With I > n * Sigma(I) Only ..... Please Check Apparently, observed data with I > n * sigma(I) were used in the F**2 least squares refinement, rather than all observed data. Please ignore when the dataset is essentially complete (and all reflections used in the refinement 'observed'. #============================================================================= # >>> Test fit Low Measured hkl Multiplicity _941 0.0 5.0 5.0 3 A 0 1 0 0 Average HKL Measurement Multiplicity ........... $F Low Multiple hkl measurements are advised, either of symmetry related reflections and/or at differen psi angle values around the diffrection vector normal to the diffracting plane. A good multiplicity is needed for a meaningful multi-scan based correction for absorption. Details can be found in the ckf file. #============================================================================= # >>> Test for Poisson type Intensity Sigma Distribution _949 0 0 0 5 A 0 1 0 0 Unusual Experimental Reflection Sigma(I)'s ..... Please Check Check the validity of the observed reflection data. #============================================================================= # >>> Test for Reported and Calculated Hmax Difference (From CIF Data) _950 0 100 200 5 I 0 0 0 1 Calculated (ThMax) and CIF-Reported Hmax Differ $I Units Reported (in the CIF) and Calculated (from Theta-max in CIF) Max(Hmax,-Hmin) values differ by at least one unit. Check the consistency of wavelength and reported resolution data items. #============================================================================= # >>> Test for Reported and Calculated Kmax Difference (From CIF Data) _951 0 100 200 5 I 0 0 0 1 Calculated (ThMax) and CIF-Reported Kmax Differ $I Units Reported (in the CIF) and Calculated (from Theta-max in CIF) Max(Kmax,-Kmin) values differ by at least one unit. Check the consistency of wavelength and reported resolution data items. #============================================================================= # >>> Test for Reported and Calculated Lmax Difference (From CIF Data) _952 0 100 200 5 I 0 0 0 1 Calculated (ThMax) and CIF-Reported Lmax Differ. $I Units Reported (in the CIF) and Calculated (from Theta-max in CIF) Max(Lmax,-Lmin) values differ by at least one unit. Check the consistency of wavelength and reported resolution data items. #============================================================================= # >>> Test for Reported (in CIF) and Actual Hmax Difference in the FCF File _953 1 999 999 1 I 0 0 0 1 Reported (CIF) and Actual (FCF) Hmax Differ by . $I Units Reported (in the CIF) and Actual (in the FCF) Max(Hmax,-Hmin) values differ by more than one unit. Check for data set truncation. #============================================================================= # >>> Test for Reported (in CIF) and Actual Kmax Difference in the FCF File _954 1 999 999 1 I 0 0 0 1 Reported (CIF) and Actual (FCF) Kmax Differ by . $I Units Reported (in the CIF) and Actual (in the FCF) Max(Kmax,-Kmin) values differ by more than one unit. Check for data set truncation. #============================================================================= # >>> Test for Reported (in CIF) and Actual Lmax Difference in the FCF file _955 1 999 999 1 I 0 0 0 1 Reported (CIF) and Actual (FCF) Lmax Differ by . $I Units Reported (in the CIF) and Actual (in the FCF) Max(Lmax,-Lmin) values differ by more than one unit. Check for data set truncation. #============================================================================= # >>> Test for Calculated (Theta-max) and Actual Hmax Difference in the FCF File _956 1 999 999 1 I 0 0 0 1 Calculated (ThMax) and Actual (FCF) Hmax Differ $I Units Calculated (From Theta-Max in the CIF) and Actual (in the FCF) Max(Hmax,-Hmin) values differ by more than one unit. Check for data set truncation. #============================================================================= # >>> Test for Calculated (Theta-max) and Actual Kmax Difference in the FCF File _957 1 999 999 1 I 0 0 0 1 Calculated (ThMax) and Actual (FCF) Kmax Differ $I Units Calculated (From Theta-Max in the CIF) and Actual (in the FCF) Max(Kmax,-Kmin) values differ by more than one unit. Check for data set truncation. #============================================================================= # >>> Test for Calculated (Theta-max) and Actual Lmax Difference in the FCF file _958 1 999 999 1 I 0 0 0 1 Calculated (ThMax) and Actual (FCF) Lmax Differ. $I Units Calculated (From Theta-max in the CIF) and Actual (in the FCF) Max(Lmax,-Lmin) values differ by more than one unit. Check for data set truncation. #============================================================================= # >>> Test for reflections with I < - 2 sigma _960 0 0 999 3 A 0 0 0 1 Number of Intensities with I < - 2*sig(I) ... $I Check 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. #============================================================================= # >>> Test for absence of negative observed intensities _961 0 0 0 5 A 0 0 0 1 Dataset Contains no Negative Intensities ....... Please Check Generally, both positive and slightly negative intensities are expected in a data set. Resetting negative intensities to zero may bias the refinement results and the 'analysis-of-variance' as reported e.g. in the SHELXL output listing. #============================================================================= # >>> Test for Input Reflections with Sig(I) = 0.0 _962 0 0 1 5 A 0 0 0 1 Number $A Relections with Sigma(I) = 0.0 $I Note Reflections with Sigma(I) = 0.0 are suspect and best left out of the refinement. This type of reflections will result in multiple R & S-value difference ALERTS. Note: Sometimes such a 0.00 value may be related to the limited number of reported decimals in the FCF file as opposed to those in the unscaled unmerged HKL file. #============================================================================= # >>> Test for both weighting parameter values zero (SHELXL) _963 0.0 0.0 0.0 2 A 0 0 0 1 Both SHELXL WEIGHT Parameter Values Zero ....... Please Check Check unusual reported/refined zero SHELXL weight parameter values. Note: SHELXL will not refine to negative values. #============================================================================= # >>> Test for consistency of SHELXL weight parameters in CIF & embedded RES _964 0.0 0.0 1.0 2 A 0 0 0 1 SHELXL WEIGHT Par. Values in CIF & RES Differ .. Please Check Two weight parameter values reported in the CIF weight expression string (_refine_ls_weighting_details) are found to differ from those archived in the WGHT parameter value list in the embedded RES file. The latter values are assumed to be the correct ones as part of the final refinement. Recreation of the FCF from the embedded .ins & .hkl will result in inconsistent wR2 and S values and associated ALERTS in the checkCIF report when those weight parameter values differ. Please also check the proper format of the SHELXL weight expression string. #============================================================================= # >>> Test whether the SHELXL weight optimisation has converged _965 0.0 0.0 0.0 2 A 0 0 0 1 The SHELXL WEIGHT Optimisation has not Converged Please Check Additional refinement cycles are advised using the (SHELXL) suggested new WGHT parameter values. #============================================================================= # >>> Test/Report omit threshold criterium value _966 0 0 0 5 A 0 0 0 1 Note: Non-Standard (i.e. 2.0) OMIT Threshold of $F Sig(I) The conventional OMIT threshold is I>2\s(I). This ALERT reports the use of a deviating value effecting e.g. the reported R1 value. #============================================================================= # >>> Report theta cutoff (OMIT) record in embedded .res _967 0 0 0 5 A 0 0 0 1 Note: Two-Theta Cutoff Value in Embedded .res .. $F Degree In general refinement with all experimental reflection data is advised. A theta value cutoff may be considered to avoid refinement on noise for resolution shells with < 2*sigma. #============================================================================= # >>> Report 'Henn et al.' Predicted and R-factor-gap values _969 0 0 0 5 A 0 0 0 1 The 'Henn et al.' R-Factor-gap value ........... $F Note Report on predicted wR2, based on counting statistics, or SHELXL style weighting as compared to the actual refined wR2. See: J.Henn & A.Schonleber, Acta Cryst. (2013) A69, 549-558. #============================================================================= # >>> Test/Report Electron Diffraction _970 0 0 0 5 A 0 0 0 1 Refinement Requires Electron Scattering Factors Please Check A structure based on electron diffraction is reported. Please check for the use of proper electron scattering factors in the refinement. X-ray scattering factors are not appropriate for a SHELXL based refinement. #============================================================================= # >>> Test for large positive calculated residual density _971 1.50 2.50 3.50 2 A 0 0 1 0 Check Calcd Resid. Dens.$B From $A $F eA-3 Larger than expected residual density maximum outside metal atom locations. This might be caused by unaccounted for twinning, wrongly assigned atom types, unaccounted for solvent and other model errors. Note: This value is based on an AIM calculation and may differ significantly for a refinement using a non-spherical atom model. #============================================================================= # >>> Test for large negative calculated residual density _972 1.50 2.50 3.50 2 A 0 0 1 0 Check Calcd Resid. Dens.$B From $A $F eA-3 Larger than expected residual density minimum outside metal atom locations. This might be caused by unaccounted for twinning, wrongly assigned atom types and other model errors. Note: This value is based on an AIM calculation and may differ significantly for a refinement using a non-spherical atom model. #============================================================================= # >>> Test for large positive density on metal atom _973 1.00 1.5 2.0 2 A 0 0 1 0 Check Calcd Positive Resid. Density on $A $F eA-3 Larger than expected residual density maximum on metal 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. #============================================================================= # >>> Test for large negative density close to metal atom _974 1.00 1.5 2.0 2 A 0 0 1 0 Check Calcd Negative Resid. Density on $A $F eA-3 Larger than expected residual density minimum on metal atom location. This might be caused by unaccounted for twinning, wrongly assigned atom types and other model errors. Another cause may be a SHELXL 'DAMP 0 0' instruction for a non-converged refinement. #============================================================================= # >>> Test for positive density near N or O _975 0.30 1.5 2.0 2 A 0 0 1 0 Check Calcd Resid. Dens.$B From $A $F eA-3 Positive density found in a difference density map at a position within bonding distance for a hydrogen atom from a nitrogen or oxygen atom. A possible reason can be a missing hydrogen atom. Also check for tautomerism. #============================================================================= # >>> Test for negative density near N or O _976 0.30 1.5 2.0 2 A 0 0 1 0 Check Calcd Resid. Dens.$B From $A $F eA-3 Negative density found in a difference density map at a location within bonding distance for a hydrogen atom from a nitrogen or oxygen atom. A possible reason can be a misassigned hydrogen atom. Also check for tautomerism. #============================================================================= # >>> Test for negative density on H-atom positions _977 0.30 1.5 2.0 2 A 0 0 1 0 Check Negative Difference Density on $A . $F eA-3 Negative density found in a difference density map at a H-atom location. A reason might be an incorrect AFIX instruction. #============================================================================= # >>> Report number of cases with positive density on C-C bonds _978 0 2 2 2 A 0 0 1 0 Number C-C Bonds with Positive Residual Density. $I Info Difference density maps generally show residual densities on C-C bonds. A significant number of those may indicate good data. Cases where this number is zero should be investigated for a reason. The use of aspherical scattering factors in the refinement model may be one. #============================================================================= # >>> Report the use of NoSpherA2 scattering factors _979 0 0 999 1 A 0 0 0 1 NoSpherA2 Scattering Factors Used .............. Please Note Non-spherical scattering factors were used in the refinement. Some ALERTS that assume spherical scattering factors are suppressed. #============================================================================= # >>> Test for non-zero number of anomalous scattering factors _980 0 0 999 1 A 0 0 0 1 No Anomalous Scattering Factors Found in CIF ... Please Check Check for missing anomalous scattering factors. #============================================================================= # >>> Test for non-zero f" anomalous scattering factor values _981 0 0 999 1 A 0 0 0 1 No non-zero f" Anomalous Scattering Values Found Please Check Check for non-zero f" anomalous scattering factor values in the CIF. Note: Zero values are correct for SHELXL MERG 4 refinements. #============================================================================= # >>> Test the anomalous scattering factor f' values against IT _982 0 0 999 1 A 0 0 0 1 The$A$F Deviates from IT-value = $B Check Check the supplied anomalous scattering factor f' value against those in the International Tables. #============================================================================= # >>> Test the anomalous scattering factor f" values against IT _983 0 0 999 1 A 0 0 0 1 The$A$F Deviates from IT-Value = $B Check Check the supplied anomalous scattering factor f'' value against those in the International Tables. #============================================================================= # >>> Test the anomalous scattering factor f' values against B&C _984 0 0 999 1 A 0 0 0 1 The$A$F Deviates from the B&C-Value $B Check Check the supplied anomalous scattering factor f' value for the non Cu, Mo, or Ag wavelength against those of Brennan & Cowan. #============================================================================= # >>> Test the anomalous scattering factor f" values against B&C _985 0 0 999 1 A 0 0 0 1 The$A$F Deviates from the B&C-Value $B Check Check the supplied anomalous scattering factor f'' value for the non Cu, Mo, Ag wavelength against those of Brennan & Cowan. #============================================================================= # >>> Test for non-zero f' anomalous scattering factor values _986 0 0 999 1 A 0 0 0 1 No non-zero f' Anomalous Scattering Values Found Please Check Check for non-zero f' anomalous scattering factor values in the CIF. #============================================================================= # >>> Test for the need of a TWIN/BASF refinement _987 0 1.0 999 1 A 0 0 0 1 The Flack x is >> 0 - Do a BASF/TWIN Refinement Please Check A BASF/TWIN refinement of the Flack x parameter is indicated when its value deviates significantly from zero as measured against its associated s.u. value. This applies in particular for structures containing significant anomalous scatterers. With a default SHELXL refinement, the Flack x parameter value is not taken into account in the refinement model as part of the calculation of F(calc) and the creation of the FCF file. Inclusion of a Flack x in the refinement model that deviates significantly from zero will lead to lower R-values and a better model. #============================================================================= # >>> Report the use of supplied f' for missing internaly calculated value _988 0 0 999 1 A 0 0 0 1 The CIF Supplied $Avalue Used in Validation $F Note Check the supplied anomalous scattering factor f' value for the reported wavelength. (No internally calculated value available). #============================================================================= # >>> Report the use of supplied f'' for missing internaly calculated value _989 0 0 999 1 A 0 0 0 1 The CIF Supplied $Avalue Used in Validation $F Note Check the supplied anomalous scattering factor f'' value for the reported wavelength. (No internally calculated value available). #============================================================================= # >>> Report Deprecated .res file based SQUEEZE job _990 0 0 999 1 A 0 0 0 1 Deprecated .res/.hkl Input Style SQUEEZE Job ... ! Note SQUEEZE jobs should as of the availability of SHELXL20xy be based on the use of a CIF+FCF created in a SHELXL20xy refinement. See A.L.Spek (2015) Acta Cryst. C71, 9-18. #============================================================================= # >>> Report on generated hkl data _991 0 0 0 5 A 0 0 0 1 HKL data created with PLATON/generate .......... ! Note Warning that the reflection data are not experimental. #============================================================================= # >>> Report difference between reported and actual _reflns_number_gt values _992 10 50 100 5 A 0 0 0 1 Repd & Actual _reflns_number_gt Values Differ by $I Check CIF Reported and actual (in FCF) '_reflns_number_gt' values are found to differ. R1 values are calculated by checkCIF for cross-checking with the R1 value as reported in the CIF. The number of 'observed' reflections that goes into that calculation is based on the criterium I > 2.0 * sigma(I). A refinement program like SHELXL uses F(obs) > 4.0 * sigma(F(obs)) as 'observed' criterium in its calculation of R1. Both numbers may differ slightly for numerical reasons. Large differences may point to inconsistencies between the CIF and FCF to be investigated. #============================================================================= # >>> Report Missing .bodd Include File _993 0 0 999 1 A 0 0 0 1 No .bodd Include File with BEDE & LONE records . ! Note The CIF-embedded .res file includes a call for a .bodd include file. Such a file is not found externally or CIF-embedded. Without this file, the details of the refinement are not complete and no .fcf can be created. #============================================================================= # >>> Report Missing SHELXL/MERG instruction _994 0 0 999 1 A 0 0 0 1 SHELXL .ins Contains no MERG Instruction ....... ! Note A SHELXL job generally includes a MERG instruction. If not, the refinement and LIST 4 FCF will include redundant reflections (i.e. refinement on more than the unique set of reflections.) #============================================================================= # >>> Report Problem with recreating FCF with SHELXL _995 0 0 2 1 A 0 0 0 1 Can not Recreate .fcf from Embedded .res & .hkl ! Check There is a problem with the recreation of a .fcf from the CIF embedded .res and .hkl data with SHELXL20xx. Note: SHELXL (or xl) must be in the PATH or set with the environment variable SHLEXE (e.g. to C:\bn\SXTL\xl.exe) Please inspect the SHELXL terminal logfile for error messages. #============================================================================= # >>> Test validity of SHELXL Style LIST 4 Fo/Fc FCF File _996 0 0 0 1 A 0 0 0 1 Non-Standard SHELXL LIST 4 Style FCF Supplied .. ! Check A SHELXL LIST 4 Style FCF File should comply with the SHELXL Format. This implies that an FCF should include only a unique set of reflections. For non-centrosymmetric structures, Friedel pairs should be included. #============================================================================= # >>> Test for Acceptable CIF/FCF file Combination for SHELXL _997 0 0 0 1 A 0 0 0 1 Unsuitable CIF/FCF File Combination with SHELXL CIF ! Error The CIF file reports refinement with SHELXL whereas the supplied reflection file is not of the SHELXL LIST 4 or LIST 8 type. Proper FCF validation is not possible with the alternative LIST options. #============================================================================= # >>> Test for LIST3 _998 0 0 0 1 A 0 0 0 1 SHELXL LIST 3 Fo/Fc Unsuitable for FCF-Validation ! Error IUCr CheckCIF validation requires SHELXL/LIST 4, LIST 8 or Equivalent Fo**2,Fc**2, sigma(Fo**2) reflection files. #============================================================================= # >>> Test for LIST6 _999 0 0 0 1 A 0 0 0 1 SHELXL LIST 6 Fo/Fc Unsuitable for FCF-Validation ! Error IUCr CheckCIF validation requires SHELXL/LIST 4, LIST 8 or Equivalent Fo**2,Fc**2, sigma(Fo**2) reflection files. #============================================================================= $ END-OF-SECTION