#============================================================================= # 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') # # The file check.def should either be in the directory where the program # is run or specified with the environment variable CHECKDEF # (e.g. setenv CHECKDEF /mnt/user/checkdef) # # - Validation output will be in the order as defined implicitly below # # - 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 # _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 A**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 #============================================================================= # >>> Definition of Notification Levels (4A8) (Pseudo ALERT) _000 A 0 0 0 0 ALERT_G ALERT_C ALERT_B ALERT_A #============================================================================= # >>> Listing header on file *.chk (Pseudo ALERT) _001 A 0 0 0 0 # PLATON/CHECK-(------) versus check.def version of 070515 #============================================================================= # >>> 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 0 5 A 1 0 0 0 No _iucr_refine_instructions_details in the CIF Please Do ! No 'refinement details' record was found. Acta Cryst. requires the inclusion of the last shelxl.res file (in case of a SHELXL or XL refinement) in the CIF embedded between records with semicolons in position 1, preceded by an '_iucr_refine_instructions_details' record. Note: SHELXL2014 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. #============================================================================= # >>> 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 0 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. will soon require the inclusion of the 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: SHELXL2014 will automatically include the .hkl as an embedded comment with the dataname '_shelx_hkl_file'. #============================================================================= # >>> _009 0 2 2 1 A 0 0 0 1 Reported radiation_type and wavelength differ .. Please Check The reported values for _diffrn_radiation_type and _diffrn_radiation_wavelength should be consistent. #============================================================================= # >>> 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_instructions_details record. SHELXL2014 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 _shelx_res_checksum _012 0 0 0 1 A 1 0 0 0 No _shelx_res_checksum found in CIF............. Please Check The CIF contains a _shelx_res_file record but not an associate _shelx_res_checksum record. #============================================================================= # >>> Check for _shelx_hkl_checksum _013 0 0 0 1 A 1 0 0 0 No _shelx_hkl_checksum found in CIF............. Please Check The CIF contains a _shelx_hkl_file record but not an associate _shelx_hkl_checksum record. #============================================================================= # >>> Check for _shelxl_fab_checksum _014 0 0 0 1 A 1 0 0 0 No _shelx_fab_checksum found in CIF............. Please Check The CIF contains a _shelx_fab_file record but not an associate _shelx_fab_checksum record. #============================================================================= # >>> 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 Consistency of Scattering Type $B for $A Check for the correct scattering type assignment to this atom. #============================================================================= # >>> Check _diffrn_measured_fraction_theta_max and full identical _018 0.00 0.00 2.00 1 A 0 0 0 0 _diffrn_measured_fraction_theta_max .NE. _full ! Check The reported value of _diffrn_measured_fraction_theta_full is not equal to the reported value of _diffrn_measured_fraction_theta_max with _diffrn_reflns_theta_max and _diffrn_reflns_theta_full reported as equal. #============================================================================= # >>> 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. #============================================================================= # >>> Check Rint _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 extinctions 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 Degree Check resolution of the data set. Alert is issued when sin(theta)/lambda < 0.6 #============================================================================= # >>> 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 weak data _026 50 60 70 3 A 0 1 0 0 Ratio Observed / Unique Reflections too Low .... $I % Check whether a sufficient fraction of the unique data is indeed above the 2 sigma level. #============================================================================= # >>> Check _diffrn_reflns_theta_full _027 .06 .07 .08 3 A 0 1 0 0 _diffrn_reflns_theta_full (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 Low ....... $F 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 Low ....... $F Note 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 ...... $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 su 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 su indicates that the experimental data do not support the determination of the absolute structure. This will generally be the case with light atom MoKa data where f" is nearly zero. Note: Use the TWIN & BASF 0.0 instructions in SHELXL97. The default FLACK parameter is not always reliable, in particular when strongly correlated with the position of the origin (e.g. along y in space-group P21). Please refer to Flack,H.D. & Bernardinelli, G. (1999) Acta Cryst. A55, 908-915 and (2000) J. Appl. Cryst., 33, 1143-1148. #============================================================================= # >>> Check Flack Parameter value _033 0.3 10.0 10.0 4 A 0 0 0 0 Flack x Value Deviates > 2*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 su < 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 No _chemical_absolute_configuration info 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 su _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 with 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. #============================================================================= #1>>> Check Reported and Calculated Z _045 0.0 1.0 1.0 1 A 0 0 0 1 Calculated and Reported Z Differ by ............ $F Ratio 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 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 ........................ Please Do ! 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. #============================================================================= # >>> 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 Likely 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 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 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 (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 1.0 1.0 1 A 0 0 0 1 Occupancy Parameter = 0.0 for .................. $A Check The CIF contains an atom with occupacy less than 0.0001 #============================================================================= # >>> 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 (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 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 S should in general be close to 1 at the end of a refinement with a proper weighting scheme. If not, there might be significant unresolved problems with the model. #============================================================================= # >>> 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 S should in general be close to 1 at the end of a refinement with a proper weighting scheme. If not, there might be significant unresolved problems with the model. #============================================================================= # >>> 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 10.0 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 10 for a quality determination for a structure containing heavy atoms with ZMAX greater than 17. This ratio can be improved by not refining C-H parameters other than riding on their carrier atom. #============================================================================= # >>> 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] _092 0 0 0 4 A 0 0 0 1 Check: Wavelength given is not Cu,Ga,Mo,Ag Ka .. $F Ang. The wavelength, specified in the CIF, is not CuKa = 1.5418A, GaKa = 1.3414A, MoKa = 0.71073A or AgKa = 0.71073A radiation within a tolerance of 0.0005A. Valid exceptions are Neutron and Synchrotron data. #============================================================================= # >>> Test for inconsistency 'mixed' versus 'no refined H positions' _093 0 0 0 1 I 0 0 0 1 No su'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 Residual density maximum larger than expected. This might be caused by residual absorption artefacts, unaccounted for twinning, wrongly assigned atom types and other model errors. #============================================================================= # >>> 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 Residual density minimum larger than expected. This might be caused by residual absorption artefacts, wrongly assigned atom types and other model errors. #============================================================================= # >>> Test for minimum residual density less 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. #============================================================================= # >>> Test for insufficient digits for special pos 1/3 & 2/3 in x-coord. _101 0 0 10 2 A 1 0 0 0 Limited Precision x-coordinate $A Suspect: $B Do ! 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). #============================================================================= # >>> Test for insufficient digits for special pos 1/3 & 2/3 in x-coord. _102 0 0 10 2 A 1 0 0 0 Limited Precision y-coordinate $A Suspect: $B Do ! 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). #============================================================================= # >>> Test for insufficient digits for special pos 1/3 & 2/3 in x-coord. _103 0 0 10 2 A 1 0 0 0 Limited Precision z-coordinate $A Suspect: $B Do ! 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). #============================================================================= # >>> 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 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 (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 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 50 100 2 A 0 0 0 1 ADDSYM Detects Additional (Pseudo) Symm. Elem... $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). This ALERT reports on potential additional (pseudo/real) rotation axes and mirrors. In addition, (pseudo/real) lattice centering/translations are reported as A, B, C, I, X, Y, Z, S. (Here S stands for special and not covered by the preceding types). Full details on the situation at hand should be gleaned from an actual PLATON/ADDSYM run. Chiral molecules are incompatible with an inversion centre or (glide)planes. Note: H-atoms and disordered atoms are not taken into account in the tests. #============================================================================= # >>> Report New space-group suggested by ADDSYM _113 90 95 99 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 % 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 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 SPGR $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 Absent '_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 ....... $A$B 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://www.kristall.ethz.ch/LFK/software/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 $A$B Check The reported Hall-symbol is found to be inconsistent with the one derived from the explicit symmetry operations. Alternatively, no Hall-symbol could be derived by PLATON for the explicit set of symmetry operations. This may be the case when an unusual origin is chosen. Refer to: S.R.Hall, Space Group Notation with an Explicit Origin; Acta Cryst. (1981), A37, 517-525. or: http://www.kristall.ethz.ch/LFK/software/sginfo/hall_symbols.html #============================================================================= # >>> 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. #============================================================================= # >>> 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 0 0 0 Rhombohedral: alpha, beta & gamma are Not All Equal Please Check Symmetry constraints on cell dimensions are checked. #============================================================================= #1>>> su on a - axis small or missing _141 0 10 10 4 A 1 0 0 0 su on a - Axis Small or Missing ................ $F Ang. The su on the a-axis is small or missing. The presence of su's (where required) and value are checked. Su's as given by the diffractometer software are often much smaller then realistic. #============================================================================= #1>>> su on b - axis small or missing _142 0 10 10 4 A 1 0 0 0 su on b - Axis Small or Missing ................ $F Ang. The su on the b-axis is small or missing. The presence of su's (where required) and value are checked. Su's as given by the diffractometer software are often much smaller then realistic. #============================================================================= #1>>> su on c - axis small or missing _143 0 10 10 4 A 1 0 0 0 su on c - Axis Small or Missing ................ $F Ang. The su on the c-axis is small or missing. The presence of su's (where required) and value are checked. Su's as given by the diffractometer software are often much smaller then realistic. #============================================================================= #1>>> su on alpha small or missing _144 0 10 10 4 A 1 0 0 0 su on alpha Small or Missing ................ $F Degree The su on alpha is small or missing. The presence of su's (where required) and value are checked. Su's as given by the diffractometer software are often much smaller then realistic. #============================================================================= #1>>> su on beta small or missing _145 0 10 10 4 A 1 0 0 0 su on beta Small or Missing ................ $F Degree The su on beta is small or missing. The presence of su's (where required) and value are checked. Su's as given by the diffractometer software are often much smaller then realistic. #============================================================================= #1>>> su on gamma small or missing _146 0 10 10 4 A 1 0 0 0 su on gamma Small or Missing ................ $F Degree The su on gamma is small or missing. The presence of su's (where required) and value are checked. Su's as given by the diffractometer software are often much smaller then realistic. #============================================================================= #1>>> su on symmetry restricted cell angle _147 0 10 10 1 A 0 1 0 0 su on Symmetry Constrained Cell Angle(s) ....... Please Check There should be no s.u. on symmetry constrained cell angles. Example: No su on alpha, beta and gamma for orthorhombic symmetry. #============================================================================= #1>>> su on a,b, or c - axis too large _148 0 10 10 3 A 0 1 0 0 su on the $A - Axis is (Too) Large ........ $F Ang. The su on the reported -axis is unexpectedly large. #============================================================================= #1>>> su on alpha, beta or gamma too large _149 0.10 0.20 10 3 A 0 1 0 0 su on the $A Angle is Too Large .......... $F Degree The su on the reported angle is too large. #============================================================================= #1>>> Check Volume _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 su (esd) Given on Volume .................... Please Do ! Missing s.u. on cell volume. #============================================================================= # >>> Check for consistency of su 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 su's incorrectly. The correct formula for triclinic, monoclinic and orthorhombic systems (based on the propagation of error expression) may be found in: M. Nardelli, Computer & Chemistry, (1983), 7, 95-98. or C. Giacovazzo ed. in 'Fundamentals of Crystallography', Second Edition, Oxford University Press, 2003, p135. 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 su's _153 0 10 10 1 I 0 0 0 1 The su's on the Cell Axes are Equal .......... $F Ang. The reported cell axes su's are reported equal. Please check whether this is correct or a software default value. #============================================================================= # >>> test for equal cell angle su's _154 0 10 10 1 I 0 0 0 1 The su's on the Cell Angles are Equal .......... $F Degree The reported cell angle su'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. #============================================================================= # >>> 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. #============================================================================= # >>> Missing x-coordinate su _161 0 10 10 4 A 0 0 0 1 Missing or Zero su (esd) on x-coordinate for ... $A Missing or Zero su (esd) on x-coordinate. Positional parameters for all non-hydrogen atoms in general positions are checked for the presence of a non-zero s.u. on them. This includes parameters fixed to fix the origin in polar space-groups which is no longer necessary when refinement is done with modern programs (e.g. SHELXL, XTAL). #============================================================================= # >>> Missing y-coordinate su _162 0 10 10 4 A 0 0 0 1 Missing or Zero su (esd) on y-coordinate for ... $A Missing or Zero su (esd) on y-coordinate. Positional parameters for all non-hydrogen atoms in general positions are checked for the presence of a non-zero s.u. on them. This includes parameters fixed to fix the origin in polar space-groups (e.g. P21) which is no longer necessary when refinement is done with modern programs (e.g. SHELXL, XTAL). #============================================================================= # >>> Missing z-coordinate su _163 0 10 10 4 A 0 0 0 1 Missing or Zero su (esd) on z-coordinate for ... $A Missing or Zero su (esd) on z-coordinate. Positional parameters for all non-hydrogen atoms in general positions are checked for the presence of a non-zero s.u. on them. This includes parameters fixed to fix the origin in polar space-groups (e.g. P41) which is no longer necessary when refinement is done with modern programs (e.g. SHELXL, XTAL). #============================================================================= # >>> 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 Report on restrained (riding) Non-Hydrogen atoms. Note: This may lead to non meaningfull bond and angle su's (ALERTS _751, _752). R-flagged atoms may arise unintentional being caused by an "AFIX 0" line being missing in a shelxl.ins file (SHELXL-97 refinement). Alternatively, the number of refined parameters may have been limited deliberately (e.g. by refinement of C-F with fixed known geometry, similar to C-H) in order to keep the data/parameter ratio acceptable. #============================================================================= # >>> 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 Calc-flagged atoms are not supposed to carry s.u.'s on their coordinates. #============================================================================= # >>> 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) n 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 It is unusual that more cell parameters end with a zero and the su is 10. This problem might be caused by the specification of insufficient 'meaningful' digits as compared to the reported su. see also: W.Clegg, Acta Cryst. (2003) E59, e2-e5. #============================================================================= # >>> 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. #============================================================================= # >>> 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 values. #============================================================================= # >>> Check for missing _cell_measurement_reflns_used datum _194 0 10 10 1 I 1 0 0 0 Missing _cell_measurement_reflns_used datum .... Please Do ! Please supply value for _cell_measurement_reflns_used #============================================================================= # >>> Check for missing _cell_measurement_theta_max datum _195 0 10 10 1 I 1 0 0 0 Missing _cell_measurement_theta_max datum .... Please Do ! Please supply value for _cell_measurement_theta_max #============================================================================= # >>> Check for missing _cell_measurement_theta_min datum _196 0 10 10 1 I 1 0 0 0 Missing _cell_measurement_theta_min datum .... Please Do ! Please supply value for _cell_measurement_theta_min #============================================================================= # >>> Test for specification of unitcell measurement temperature _197 0 0 0 1 I 1 0 0 0 Missing _cell_measurement_temperature Please Supply Please specify the temperature (Kelvin) at which the unit-cell was determined. #============================================================================= # >>> Test for specification of Datacollection temperature _198 0 0 0 1 A 1 0 0 0 Missing _diffrn_ambient_temperature Please Supply Please specify the temperature (Kelvin) at which the intensity data were collected. #============================================================================= # >>> Test for SHELXL Roomtemperature Default (Cell) _199 0 0 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 SHELXL to 293 K if the TEMP instruction is not used. The actual temperature is likely either slightly or significantly (for a low temperature data collection) different. #============================================================================= # >>> Test for SHELXL Roomtemperature Default (Datacollection) _200 0 0 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 SHELXL to 293 K if the TEMP instruction is not used. The actual temperature is likely either slightly or significantly (for a low temperature data collection) different. #============================================================================= # >>> 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 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 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 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 & Correct U(aniso) data for completeness etc. Do not use SHELX style '=' continuation line #============================================================================= # >>> 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 Large Non-Solvent $AUeq(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 Large Solv./Anion $AUeq(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 7.0 9.9 3 A 0 0 1 0 Large Non-Solvent H Uiso(max)/Uiso(min) ... $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 3.0 4.0 5.0 4 A 0 0 1 0 Large Solvent/Anion H Ueq(max)/Ueq(min) ..... $F Ratio This test reports on large ranges in displacement parameters for hydrogen atoms in the solvent/anion part of the structure. #============================================================================= # >>> Test for difference in implicit and explicit U(eq) _224 .002 .003 .005 1 A 0 0 1 0 Ueq(Rep) and Ueq(Calc) differ by$A Ang**2 . $B 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 su 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 su 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 su 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. #============================================================================= # >>> 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 su 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 Ueq as Compared to Neighbors for ..... $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 Ueq as Compared to Neighbors for ..... $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 AngSq 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 Average U(i,j) Tensor .... $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 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 Fixed Partial Occupancy _300 0 0 0 4 A 0 0 1 0 Atom Site Occupancy of $A is 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 ............ Percentage = $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 Disorder ............ Percentage = $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 H-Atom $A with # Connections $F Check Hydrogen atoms are generally connected to only one other atom. A hydrogen atom between two oxygen atoms is a special case. Investigate whether this hydrogen atom is better described with a disorder model with two partially occupied sites. A difference map might show a double-well density. #============================================================================= # >>> Test for non-integer number of atoms in residue _304 0 2 2 4 A 0 0 1 0 Non-Integer Number of Atoms ($A) in Resd. # $I 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 (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 (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) ........ $A Check Oxygen atom with three covalent bonds detected. Check for correct atom type assignment (e.g. N rather than O) Note: Exceptions are H3O+ (Oximium or Hydroxonium) and H5O2+ (Hydronium or aqua-hydroxonium) species. #============================================================================= # >>> Test for Metal-O-H angle of H2O _314 0 2 2 2 A 0 0 1 0 Check Small Angle for H2O: Metal-$A-$B $F Degree A water molecule coordinated to a metal is detected with an unusually small value of the Metal-Oxygen-Hydrogen Angle. #============================================================================= # >>> 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 Average Phenyl C-C _330 0.01 0.02 0.03 2 A 0 0 1 0 Large Average 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 Average 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 Check Large Av 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 Average Benzene C-C 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 Average Torsion Angle in cyclo-hexane ring _338 25.0 45.0 60.0 4 A 0 0 1 0 Small Average 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 su for X-Y bonds is tested (named bond-precision). X-Y will generally be C-C bonds, unless there are none. In the last case the su's of the lowest element numbers are considered (excluding hydrogen). There are three test ranges: one for structures with the largest element Z < 20, one for the largest Z in the range 20 to 39 and one for structures with Z(max) 40 or higher (_340, _341 and _342 respectively) #============================================================================= # >>> 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 su for X-Y bonds is tested (named bond-precision). X-Y will generally be C-C bonds, unless there are none. In the last case the su's of the lowest element numbers are considered (excluding hydrogen). There are three test ranges: one for structures with the largest element Z < 20, one for the largest Z in the range 20 to 39 and one for structures with Z(max) 40 or higher (_340, _341 and _342 respectively) #============================================================================= # >>> 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 su for X-Y bonds is tested (named bond-precision). X-Y will generally be C-C bonds, unless there are none. In the last case the su's of the lowest element numbers are considered (excluding hydrogen). There are three test ranges: one for structures with the largest element Z < 20, one for the largest Z in the range 20 to 39 and one for structures with Z(max) 40 or higher (_340, _341 and _342 respectively) #============================================================================= # >>> Hybridisation Problem on C in main residue(s) _343 0 0 0 2 A 0 0 1 0 Unusual $A Angle 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 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 0.0 0.0 0.0 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 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 X-O-Y Angle _395 20.0 40.0 70.0 2 A 0 0 0 1 Deviating X-O-Y Angle from 120 Deg for $A $F Degree The X-O-Y angle is significantly larger than the expected 120.0 Degrees. #============================================================================= # >>> Test Si-O-Si Angle _396 10.0 20.0 30.0 2 A 0 0 0 1 Deviating Si-O-Si Angle from 150 Deg for $A $F Degree The Si-O-Si angle is significantly larger than the expected 150.0 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 non-bonding intra D-H..H-X contact. #============================================================================= # >>> Test for short non-bonding inter D-H..H-X contacts _415 0.1 0.3 0.5 2 A 0 0 0 1 Short Inter D-H..H-X $A.. $B .. $F Ang. Short non-bonding inter D-H..H-X contact. #============================================================================= # >>> 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 without acceptor _420 0 1.5 99 2 A 0 0 0 1 D-H 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 on a calculated position 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 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. #============================================================================= # >>> 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 to $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 Structure Contains Solvent Accessible VOIDS of . $I Ang3 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 VERY LARGE 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 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 Structure Contains Solvent Accessible VOIDS of . $I A**3 Crystal structures in general do not contain large solvent accessible voids in the lattice. Most structures lose their long-range ordering when solvent molecules leave the crystal. Only when the remaining network is strongly bonded (e.g. zeolites and some hydrogen bonded networks) the crystal structure may survive. Residual voids in a structure may indicate the omission of (disordered) density from the model. Disordered density may go undetected when smeared since peak search programs are not designed to locate maxima on density ridges. The presence or absence of residual density in the void may be verified on a printed/plotted difference Fourier map or with PLATON/SQUEEZE. Voids of 40 Ang**3 may accommodate H2O. Small molecules such as Tetrahydrofuran have typical volumes in the 100 to 200 Ang**3 range. This test reports the volume of the largest solvent accessible void in the structure. A paper reporting a crystal structure with a significant solvent accessible void should at the least discuss the issue. Note: The use of PLATON/SQUEEZE was reported in the CIF #============================================================================= # >>> Test for TOO LARGE (Reported) solvent accessible voids _606 0 0 0 4 A 0 0 0 1 VERY LARGE Solvent Accessible VOID(S) in Structure ! Info This test reports on a solvent accessible void in the structure, too large or too time consuming for the current PLATON version for a more detailed analysis as part of the validation run. Use the SOLV option for more details. Such a warning might also indicate that the symmetry is incomplete e.g. should have been specified as P-1 and not P1, leaving out half of the unit cell content. #============================================================================= # >>> Test for consistency of Bonds and Coordinates in CIF _701 1.0 2.0 3.0 1 A 0 0 0 1 Bond Calc$X, Rep$Y, Dev.. $F Sigma Bond distances given in the CIF are cross-checked with corresponding values calculated from the coordinates. Alerts are set at 1,2 and 3 sigma deviation levels. Note: Default s.u.'s are used where no su given (e.g. for C-H) In general, all differences should be within the associated s.u. Small differences may arise from rounding. Very large deviation (or zero distance) normally indicate incorrectly specified symmetry operations on the associated atoms, or 'cut-and-pasting' of incompatible CIF's. #============================================================================= # >>> Test for consistency of Angles and Coordinates in CIF _702 1.0 2.0 3.0 1 A 0 0 0 1 Angle Calc$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 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 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 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 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 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 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 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 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 .......... $I Note Up to 4 Character Labels of the type C11, H101, N10A, i.e. chemical symbol + number + optional letter are to be preferred. #============================================================================= # >>> Test for consistency of Bonds and Coordinates in CIF _721 1.0 2.0 3.0 1 A 0 0 0 1 Bond Calc$X, Rep$Y Dev... $F Ang. Same as 701 but for distance without su (esd). Difference is tested in terms of Angstroms. #============================================================================= # >>> Test for consistency of Angles and Coordinates in CIF _722 1.0 2.0 3.0 1 A 0 0 0 1 Angle Calc$X, Rep$Y Dev... $F Degree Same as 702 but for angle without su (esd). Difference is tested in terms of Degrees. #============================================================================= # >>> Test for consistency of Torsions and Coordinates in CIF _723 1.0 999. 999. 1 A 0 0 0 1 Torsion Calc$X, Rep$Y Dev... $F Sigma Same as 703 but for torsion without su (esd). Difference is tested in terms of Degrees. #============================================================================= # >>> Test for consistency of Contact Distances and Coordinates in CIF _724 1.0 2.0 3.0 2 A 0 0 0 1 Contact Calc$X, Rep$Y Dev... $F Ang. Same as 704, but for distance without su (esd). Difference is tested in terms of Angstroms. #============================================================================= # >>> Test for consistency of H-Bond D-H distances and Coordinates in CIF _725 1.0 2.0 3.0 2 A 0 0 0 1 D-H Calc$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... $F Degree Same as ALERT 708 but for angle without s.u. (esd). Differences are tested in terms of Degrees. #============================================================================= # >>> Test for consistency of Bond su's and Coordinate su's in CIF _731 3.0 6.0 12.0 1 A 0 0 0 1 Bond Calc$X, Rep$Y ...... $I su-Ratio A large ratio of the reported and calculated bond s.u.'s is found. The use of a DFIX instruction might cause such a warning since calculated s.u.'s are based on reported variances only. Note_1: su's on the unit-cell dimensions are taken into account in the calculation of expected su's. This may result in large differences between expected and reported su's when this contribution is not included in the reported su's, in particular for inaccurate unit-cells. Note_2: Another source for the discrepancy between calculated and reported su's can be that the validation software has access only to the variances of the refined parameters as opposed to the full co-variance matrix used by e.g. SHELXL for the calculation of derived parameters with associated su's. Constrained/restrained refinement may cause large co-variances. #============================================================================= # >>> Test for consistency of Angles and Coordinates in CIF s.u.'s _732 2.0 4.0 8.0 1 A 0 0 0 1 Angle Calc$X, Rep$Y ...... $F su-Ratio A large ratio of the reported and calculated bond angle s.u.'s is found. This check should warn for erroneous rounding: E.g. 105.5(19) to 105.5(2) or 105.0(5) to 105(5) etc. Note: Large differences are possible when certain constraints/restraints were applied in the refinement (e.g. the FLAT option in SHELXL97). Note: su's on the unit-cell dimensions are taken into account in the calculation of expected su's. This may result in large differences between expected and reported su's when this contribution is not included in the reported su's, in particular for inaccurate unit-cells. Note_2: Another source for the discrepancy between calculated and reported su's can be that the validation software has access only to the variances of the refined parameters as opposed to the full co-variance matrix used by e.g. SHELXL for the calculation of derived parameters with associated su's. Constrained/restrained refinement may cause large co-variances. #============================================================================= # >>> Test for consistency of Torsions and Coordinates in CIF s.u's _733 4.0 6.0 8.0 1 A 0 0 0 1 Torsion Calc$X, Rep$Y ...... $F su-Ratio A large ratio of the reported and calculated torsion angle s.u.'s is found. This check should warn for erroneous rounding: E.g. 105.5(19) to 105.5(2) or 105.0(5) to 105(5) etc. Note: su's on the unit-cell dimensions are taken into account in the calculation of expected su's. This may result in large differences between expected and reported su's when this contribution is not included in the reported su's, in particular for inaccurate unit-cells. Note_2: Another source for the discrepancy between calculated and reported su's can be that the validation software has access only to the variances of the refined parameters as opposed to the full co-variance matrix used by e.g. SHELXL for the calculation of derived parameters with associated su's. Constrained/restrained refinement may cause large co-variances. #============================================================================= # >>> Test for consistency of Contact Distance s.u. and Coordinate s.u. in CIF _734 2.0 4.0 8.0 1 A 0 0 0 1 Contact Calc$X, Rep$Y ...... $F su-Ratio A large ratio of the reported and calculated contact distance s.u.'s is found. Note: su's on the unit-cell dimensions are taken into account in the calculation of expected su's. This may result in large differences between expected and reported su's when this contribution is not included in the reported su's, in particular for inaccurate unit-cells. #============================================================================= # >>> Test for consistency of H-Bond D-H distance s.u. and Coordinate s.u in CIF _735 2.0 4.0 8.0 1 A 0 0 0 1 D-H Calc$X, Rep$Y ...... $I su-Ratio A large ratio of the reported and calculated H-bond D-H distance s.u.'s is found. The use of a DFIX instruction might cause such a warning since calculated s.u.'s are based on reported variances only. Note: su's on the unit-cell dimensions are taken into account in the calculation of expected su's. This may result in large differences between expected and reported su's when this contribution is not included in the reported su's, in particular for inaccurate unit-cells. #============================================================================= # >>> Test for consistency of H-Bond H..A Distance s.u. and Coordinates in CIF _736 2.0 4.0 8.0 1 A 0 0 0 1 H...A Calc$X, Rep$Y ...... $F su-Ratio A large ratio of the reported and calculated H-bond H..A distance s.u.'s is found. Note: su's on the unit-cell dimensions are taken into account in the calculation of expected su's. This may result in large differences between expected and reported su's when this contribution is not included in the reported su's, in particular for inaccurate unit-cells. #============================================================================= # >>> Test for consistency of H-Bond D..A Distance s.u. and Coordinates in CIF _737 2.0 4.0 8.0 1 A 0 0 0 1 D...A Calc$X, Rep$Y ...... $F su-Ratio A large ratio of the reported and calculated H-Bond D...A distance s.u.'s is found. #============================================================================= # >>> Test for consistency of H-Bond D-H..A Angle and Coordinates in CIF s.u. _738 2.0 4.0 8.0 1 A 0 0 0 1 D-H..A Calc$X, Rep$Y ...... $F su-Ratio A large ratio of the reported and calculated H-Bond D-H..A angle s.u.'s is found. Note: su's on the unit-cell dimensions are taken into account in the calculation of expected su's. This may result in large differences between expected and reported su's when this contribution is not included in the reported su's, in particular for inaccurate unit-cells. #============================================================================= # >>> Test for missing Bond su in CIF _741 0.0 99.0 99.0 1 A 0 0 0 1 Bond Calc$X, Rep$Y ...... Missing su Likely missing s.u. on Bond in CIF. #============================================================================= # >>> Test for missing Angle s.u. in CIF _742 0.0 99.0 99.0 1 A 0 0 0 1 Angle Calc$X, Rep$Y ...... Missing su Likely missing s.u. on Bond angle in CIF. #============================================================================= # >>> Test for missing Torsion s.u. in CIF _743 0.0 99.0 99.0 1 A 0 0 0 1 Torsion Calc$X, Rep$Y ...... Missing su Likely missing s.u. on Torsion angle in CIF. #============================================================================= # >>> Test for missing Contact Distance s.u. in CIF _744 0.0 99.0 99.0 1 A 0 0 0 1 Contact Calc$X, Rep$Y ...... Missing su Likely missing s.u. on contact Distance in CIF. #============================================================================= # >>> Test for missing H-Bond D-H distance s.u. in CIF _745 0.0 99.0 99.0 1 A 0 0 0 1 D-H Calc$X, Rep$Y ...... Missing su Likely missing s.u. on H-Bond D-H distance in CIF. #============================================================================= # >>> Test for missing H-Bond H..A Distance s.u. in CIF _746 0.0 99.0 99.0 1 A 0 0 0 1 H...A Calc$X, Rep$Y ...... Missing su Likely missing s.u. on H-Bond H...A distance in CIF. #============================================================================= # >>> Test for missing H-Bond D..A Distance s.u. in CIF _747 0.0 99.0 99.0 1 A 0 0 0 1 D...A Calc$X, Rep$Y ...... Missing su Likely missing s.u. on H-Bond D...A distance in CIF. #============================================================================= # >>> Test for missing H-Bond D-H..A Angle s.u. in CIF _748 0.0 99.0 99.0 1 A 0 0 0 1 D-H..A Calc$X, Rep$Y ...... Missing su Likely missing s.u. on H-Bond D-H..A angle in CIF. #============================================================================= # >>> Test for senseless Bond s.u. in CIF _751 0.0 99.0 99.0 4 A 0 0 0 1 Bond Calc$X, Rep$Y ...... Senseless su An s.u. should not be given in the CIF for constrained distances. Please check for proper refinement status flags (e.g. R) #============================================================================= # >>> Test for senseless Angle s.u. in CIF _752 0.0 99.0 99.0 4 A 0 0 0 1 Angle Calc$X, Rep$Y ...... Senseless su An s.u. should not be given in the CIF for constrained angles. Please check for proper refinement status flags (e.g. R) #============================================================================= # >>> Test for senseless Torsion s.u. in CIF _753 0.0 99.0 99.0 4 A 0 0 0 1 Torsion Calc$X, Rep$Y ...... Senseless su An s.u. should not be given in the CIF for constrained torsion angles. Please check for proper refinement status flags (e.g. R) #============================================================================= # >>> Test for senseless Contact Distance s.u. in CIF _754 0.0 99.0 99.0 4 A 0 0 0 1 Contact Calc$X, Rep$Y ...... Senseless su An s.u. should not be given in the CIF for constrained contact distances. Please check for proper refinement status flags (e.g. R) #============================================================================= # >>> Test for senseless H-Bond D-H distance s.u. in CIF _755 0.0 99.0 99.0 4 A 0 0 0 1 D-H Calc$X, Rep$Y ...... Senseless su An s.u. should not be given in the CIF for constrained distances. Please check for proper refinement status flags (e.g. R) #============================================================================= # >>> Test for senseless H-Bond H..A Distance s.u. in CIF _756 0.0 99.0 99.0 4 A 0 0 0 1 H...A Calc$X, Rep$Y ...... Senseless su An s.u. should not be given in the CIF for constrained distances. Please check for proper refinement status flags (e.g. R) #============================================================================= # >>> Test for senseless H-Bond D..A Distance s.u. in CIF _757 0.0 99.0 99.0 4 A 0 0 0 1 D...A Calc$X, Rep$Y ...... Senseless su An s.u. should not be given in the CIF for constrained distances. Please check for proper refinement status flags (e.g. R) #============================================================================= # >>> Test for Senseless H-Bond D-H..A Angle s.u. in CIF _758 0.0 99.0 99.0 4 A 0 0 0 1 D-H..A Calc$X, Rep$Y ...... Senseless su 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 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 0.0 0.0 2 A 0 0 0 1 Suspect 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 Suspect 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 Suspect X-Y Cont 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 Suspect D-H Dist in CIF: $A-- $B .. $F Ang. Likely Erroneous D-H Entry. #============================================================================= # >>> 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 in CIF .... # $A Check 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 #============================================================================= # >>> 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 'chiral' spgr _791 0 0 0 4 I 0 0 0 1 The Model has Chirality at $A (Chiral SPGR) $B Verify This test addresses the consistency of the absolute configuration assignment in non-centrosymmetric structures with proper symmetry operations (i.e. all matrices with determinant = 1) only. Verify the (R/S) absolute configuration assignment of this atom and the consistency of the absolute configuration implicit in the CIF-data with that in the 'ORTEP' illustration. Torsion angles should have the correct sign. The absolute structure assignment should also be consistent with the lowest value of the Flack parameter and/or know absolute configuration. #============================================================================= # >>> Check the absolute configuration of chiral atom in 'non-chiral' spgr _792 0 0 0 1 I 0 0 0 1 The 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 centrosymmetric spgr _793 0 0 0 4 A 0 0 0 1 The 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 Note 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 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 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 n 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 ! 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 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 fot (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. #============================================================================= # >>> 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 #============================================================================= # >>> 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 and su .. $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 Use of an older SHELXL version _899 0 0 0 4 A 0 0 0 1 SHELXL97 is Deprecated and Succeeded by SHELXL $I Note A more recent SHELXL version is now available. Final refinement with the latest version is recommended. #============================================================================= # >>> Test for 'No-matching reflection file' _900 0 0 0 1 I 0 0 0 1 No Matching 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) [of F(obs)**2 equal F(calc)**2]. #============================================================================= # >>> 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 SHELX manual). For details see the Analysis-of-Variance Section in the '.ckf' file. #============================================================================= # >>> 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 % 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 Observed Data at Theta(Max) still $I % 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. #============================================================================= # >>> Test for missing reflections below Theta-Min _910 0 10 50 3 A 0 0 0 1 Missing # of FCF Reflection(s) Below Th(Min) ... $I Report Possible causes: Beamstop theta-min limit set too high, large unit-cell etc. A possible technical solution on CCD based equipment involves the collection of additional images with the detector at a larger distance from the crystal with the beamstop setting changed accordingly.. #============================================================================= # >>> Test for missing reflections between Theta-Min and sinth/lambda=0.6 _911 -1 5 999 3 A 0 0 0 1 Missing # FCF Refl Between THmin & STh/L=$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.) #============================================================================= # >>> 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.) #============================================================================= # >>> 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. #============================================================================= # >>> 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 10. 50. 100 3 A 0 0 0 1 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 1.0 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. #============================================================================= # >>> 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. 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. 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. 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. Note: The Reported and Calculated values may differ slightly due to a differing peak interpolation algorithm. #============================================================================= # >>> 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. Note: The Reported and Calculated values may differ slightly due to a differing peak interpolation algorithm. #============================================================================= # >>> 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. 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. 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 . $F Please check whether the S value that is reported in the CIF corresponds with the S value calculated from the parameters supplied in the CIF. This test is based on the observed reflection data in the FCF and reflection data that are calculated with the parameters (i.e. coordinates, displacement and weight parameters) taken from the CIF. #============================================================================= # >>> Test for interpretable weight parameters for R1,wR2 & S Comparison _929 0 10 10 5 A 0 0 0 1 No Weight Pars,Obs and Calc R1,wR2,S not checked ! Info SHELXL weight parameters are expected to be given in the format below: _refine_ls_weighting_details 'calc w=1/[\s^2^(Fo^2^)+(0.1000P)^2^+0.0000P] where P=(Fo^2^+2Fc^2^)/3' JANA style weight is expected to be given in the format: _refine_ls_weighting_details 'w=1/(\s^2^(I)+0.0016I^2^)' Do not edit this string or make it into a text block between ';'. #============================================================================= # >>> Test for Missed Twinning from FCF data _930 .00 .00 .80 2 A 0 0 1 0 Check Twin Law ($A)[$B] Estimated BASF $F Check the proposed Twin Law. The entry in () represents the proposed rotation axis in reciprocal space and the one in [] the corresponding rotation is direct space. The relevant Twin Matrix can be found in the file '.ckf'. Note: This analysis is based on Fo/Fc differences with Fc data given in the .fcf file (i.e. Fobs, Fcalc listing). ALERT-930 is expected to generate an related ALERT-931 as well. #============================================================================= # >>> Test for Missed Twinning from FCF/CIF data _931 .00 .00 .80 5 A 0 0 1 0 Found Twin Law ($A)[$B] Estimated 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 F(calc) values calculated with the data in the CIF. This ALERT can be ignored when twinning has been addressed in the refinement (As indicated by the Absence of ALERT 930). Please check whether twinning is mentioned in the write-up of the paper. #============================================================================= # >>> Report number of outliers _934 0 1 10 3 A 0 0 1 0 Number of (Iobs-Icalc)/SigmaW > 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 SHELXL optimizes two weight parameters to bring the S value close to 1.0. This ALERT reports the S value based on the supplied sigma(I) only. A large value of the last generally indicates the presence of large outliers in the data set. Examples are reflections 'measured' behind the beam stop. (See also ALERT_919). The latter are best left out with an OMIT instruction. #============================================================================= # >>> Test for wR2 refinement with all data _940 0 0 2 3 A 0 0 0 1 F**2 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. #============================================================================= # >>> 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(Fo^2) = 0 _962 0 0 1 5 A 0 0 0 1 Number of Input Relections with Sigma(Fo^2) = 0 $I Reflections with Sigma(Fo^2) = 0 are suspect and best left out of the refinement. This type of reflections will result in multiple R & S-value difference ALERTS. #============================================================================= # >>> Test for large positive calculated residual density _971 1.50 2.50 3.50 2 A 0 0 1 0 Check Calcd Residual Density$B From $A $F eA-3 Larger than expected residual density maximum outside metal atom locations. This might be caused by unaccounted for twinning, wrongly assigned atom types, unaccounted for solvent and other model errors. #============================================================================= # >>> Test for large negative calculated residual density _972 1.50 2.50 3.50 2 A 0 0 1 0 Check Calcd Residual Density$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. #============================================================================= # >>> Test for large positive density on metal atom _973 1.00 1.5 2.0 2 A 0 0 1 0 Check Calcd Positive Residual 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 Residual Density on $A $F eA-3 Larger than expected residual density minimum on metal atom location. This might be caused by unaccounted for twinning, wrongly assigned atom types and other model errors. Another cause may be a SHELXL 'DAMP 0 0' instruction for a non-converged refinement. #============================================================================= # >>> Test for positive density near N or O _975 0.30 1.5 2.0 2 A 0 0 1 0 Check Calcd Residual Density$B From $A $F eA-3 Positive density found in a difference density map at a position within bonding distance for a hydrogen atom from a nitrogen or oxygen atom. A possible reason can be a missing hydrogen atom. Also check for tautomerism. #============================================================================= # >>> Test for negative density near N or O _976 0.30 1.5 2.0 2 A 0 0 1 0 Check Calcd Residual Density$B From $A $F eA-3 Negative density found in a difference density map at a location within bonding distance for a hydrogen atom from a nitrogen or oxygen atom. A possible reason can be a misassigned hydrogen atom. Also check for tautomerism. #============================================================================= # >>> Test for non-zero number of anomalous scattering factors _980 0 0 999 1 A 0 0 0 1 No Anomalous Scattering Factors Found in CIF ... Please Check Check for missing anomalous scattering factors. #============================================================================= # >>> Test for non-zero f" anomalous scattering factor values _981 0 0 999 1 A 0 0 0 1 No non-zero f" Anomalous Scattering Values Found Please Check Check for non-zero f" anomalous scattering factor values in the CIF. Note: Zero values are correct for SHELXL MERG 4 refinements. #============================================================================= # >>> Test the anomalous scattering factor f' values against IT _982 0 0 999 1 A 0 0 0 1 The$A$F Deviates from the 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 the 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 or 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 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 this value deviates significantly from zero and the structure contains significant anomalous scatterers. #============================================================================= # >>> 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