checkCIF/PLATON page 2

# checkCIF (basic structural check) running

Checking for embedded fcf data in CIF ...
Found embedded fcf data in CIF. Extracting fcf data from uploaded CIF, please wait . . . . .

# checkCIF/PLATON (basic structural check)

Structure factors have been supplied for datablock(s) cu_BruecknerJK_153F40_0m

THIS REPORT IS FOR GUIDANCE ONLY. IF USED AS PART OF A REVIEW PROCEDURE FOR PUBLICATION, IT SHOULD NOT REPLACE THE EXPERTISE OF AN EXPERIENCED CRYSTALLOGRAPHIC REFEREE.

    No syntax errors found. CIF dictionary
    Please wait while processing ....  Interpreting this report

Structure factor report
Datablock: cu_BruecknerJK_153F40_0m

`Bond precision:` | `C-C = 0.0031 A` | `Wavelength=1.54178`

`Cell:` | `a=19.678(3)` | `b=37.0229(9)` | `c=4.7720(4)`
| `alpha=90` | `beta=90` | `gamma=90`
`Temperature:` | `102 K` | `` | ``

`` | `Calculated` | `Reported`
`Volume` | `3476.6(6)` | `3476.6(7)`
`Space group` | `P 21 21 2` | `P 21 21 2`
`Hall group` | `P 2 2ab` | `P 2 2ab`
`Moiety formula` | `2(C38 H38 O12), C H4 O` | `?`
`Sum formula` | `C77 H80 O25` | `C38.50 H40 O12.50`
`Mr` | `1405.41` | `702.70`
`Dx,g cm-3` | `1.343` | `1.343`
`Z` | `2` | `4`
`Mu (mm-1)` | `0.838` | `0.838`
`F000` | `1484.0` | `1484.0`
`F000'` | `1489.09` | ``
`h,k,lmax` | `25,47,6` | `24,47,5`
`Nref` | `7449[ 4339]` | `7338`
`Tmin,Tmax` | `0.904,0.967` | `0.770,0.929`
`Tmin'` | `0.832` | ``

`Correction method= # Reported T Limits: Tmin=0.770 Tmax=0.929 AbsCorr = MULTI-SCAN` | ``

`Data completeness= 1.69/0.99` | `Theta(max)= 78.476`

`R(reflections)= 0.0364( 7290)` | `wR2(reflections)= 0.0919( 7338)`
`S = 1.198` | `Npar= 479`

    The following ALERTS were generated. Each ALERT has the format
           test-name_ALERT_alert-type_alert-level.
    Click on the hyperlinks for more details of the test.
    Alert level C
    PLAT413_ALERT_2_C Short Inter XH3 .. XHn     H13      ..H19B     .       2.14 Ang.
                                                       x,y,-1+z  =      1_554 Check
    PLAT911_ALERT_3_C Missing FCF Refl Between Thmin & STh/L=    0.600          3 Report
    Alert level G
    PLAT007_ALERT_5_G Number of Unrefined Donor-H Atoms ..............          1 Report
    PLAT045_ALERT_1_G Calculated and Reported Z Differ by a Factor ...      0.500 Check
    PLAT187_ALERT_4_G The CIF-Embedded .res File Contains RIGU Records          1 Report
    PLAT300_ALERT_4_G Atom Site Occupancy of O13        Constrained at        0.5 Check
    And 5 other PLAT300 Alerts
    PLAT300_ALERT_4_G Atom Site Occupancy of C39        Constrained at        0.5 Check
    PLAT300_ALERT_4_G Atom Site Occupancy of H13A       Constrained at        0.5 Check
    PLAT300_ALERT_4_G Atom Site Occupancy of H39A       Constrained at        0.5 Check
    PLAT300_ALERT_4_G Atom Site Occupancy of H39B       Constrained at        0.5 Check
    PLAT300_ALERT_4_G Atom Site Occupancy of H39C       Constrained at        0.5 Check
    PLAT302_ALERT_4_G Anion/Solvent/Minor-Residue Disorder (Resd  2  )       100% Note
    PLAT398_ALERT_2_G Deviating  C-O-C   Angle From 120 for O3       .      109.2 Degree
    PLAT432_ALERT_2_G Short Inter X...Y Contact  O2       ..C17      .       2.91 Ang.
                                                -1/2+x,1/2-y,-z  =      4_455 Check
    PLAT789_ALERT_4_G Atoms with Negative _atom_site_disorder_group  #          6 Check
    PLAT822_ALERT_4_G CIF-embedded .res Contains Negative PART Numbers          1 Check
    PLAT860_ALERT_3_G Number of Least-Squares Restraints .............          5 Note
    PLAT912_ALERT_4_G Missing # of FCF Reflections Above STh/L=  0.600         16 Note
    PLAT913_ALERT_3_G Missing # of Very Strong Reflections in FCF ....          1 Note
    PLAT978_ALERT_2_G Number C-C Bonds with Positive Residual Density.         23 Info
       0 ALERT level A = Most likely a serious problem - resolve or explain
       0 ALERT level B = A potentially serious problem, consider carefully
       2 ALERT level C = Check. Ensure it is not caused by an omission or oversight
      18 ALERT level G = General information/check it is not something unexpected

       1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
       4 ALERT type 2 Indicator that the structure model may be wrong or deficient
       3 ALERT type 3 Indicator that the structure quality may be low
      11 ALERT type 4 Improvement, methodology, query or suggestion
       1 ALERT type 5 Informative message, check

Validation response form

Please find below a validation response form (VRF) that can be filled in and pasted into your CIF.

    # start Validation Reply Form
    _vrf_PLAT413_cu_BruecknerJK_153F40_0m
    ;
    PROBLEM: Short Inter XH3 .. XHn     H13      ..H19B     .       2.14 Ang.
    RESPONSE: ...
    ;
    _vrf_PLAT911_cu_BruecknerJK_153F40_0m
    ;
    PROBLEM: Missing FCF Refl Between Thmin & STh/L=    0.600          3 Report
    RESPONSE: ...
    ;
    # end Validation Reply Form

It is advisable to attempt to resolve as many as possible of the alerts in all categories. Often the minor alerts point to easily fixed oversights, errors and omissions in your CIF or refinement strategy, so attention to these fine details can be worthwhile. In order to resolve some of the more serious problems it may be necessary to carry out additional measurements or structure refinements. However, the purpose of your study may justify the reported deviations and the more serious of these should normally be commented upon in the discussion or experimental section of a paper or in the "special_details" fields of the CIF. checkCIF was carefully designed to identify outliers and unusual parameters, but every test has its limitations and alerts that are not important in a particular case may appear. Conversely, the absence of alerts does not guarantee there are no aspects of the results needing attention. It is up to the individual to critically assess their own results and, if necessary, seek expert advice. Publication of your CIF in IUCr journals A basic structural check has been run on your CIF. These basic checks will be run on all CIFs submitted for publication in IUCr journals (Acta Crystallographica, Journal of Applied Crystallography, Journal of Synchrotron Radiation); however, if you intend to submit to Acta Crystallographica Section C or E or IUCrData, you should make sure that full publication checks are run on the final version of your CIF prior to submission. Publication of your CIF in other journals Please refer to the Notes for Authors of the relevant journal for any special instructions relating to CIF submission.

PLATON version of 06/07/2023; check.def file version of 30/06/2023

Datablock cu_BruecknerJK_153F40_0m - ellipsoid plot

Download CIF editor (publCIF) from the IUCr
Download CIF editor (enCIFer) from the CCDC
Test a new CIF entry