CIF-VALIDATION DOCUMENTATION

(11-8-98)

This document should provide information on the CIF-validation tests as specified in the file 'check.def' and implemented in PLATON.

# check.def contains the tests, error thresholds and warning messages
# 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')
#
# - Test 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
#

------------------------------------------------------------------------------- _020 : Check on R(int) ------------------------------------------------------------------------------- R(int) should be well below 10% and in the order of magnitude of the reported R-values. R(int) may be relatively meaningless when based on a very limited number of averaged data.

------------------------------------------------------------------------------- _030 Check on meaningfully refined extinction parameter. ------------------------------------------------------------------------------- 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 it value is within 3.33 s.u.

------------------------------------------------------------------------------- _11x : ADDSYM Tests for missed symmetry (with an expanded MISSYM (C) clone) ------------------------------------------------------------------------------- These tests warn for missed or possible higher (pseudo) symmetry in the structural model (i.e. based on the coordinate data). Close examination of the situation at hand is indicated in order to prove/disprove the issue (usually in combination with the reflection data).

The tests are split-up in three classes of problems:

_110 Reports on potential (pseudo/real) lattice centering or cell halving.

_111 Reports on potential additional (pseudo/real) inversion centres.

_112 Reports on potential additional (pseudo/real) rotation axes and mirrors.

Note: Disordered atoms are not taken into account in the tests.

------------------------------------------------------------------------------- _12x : Tests for consistency and completeness of symmetry data items in CIF. ------------------------------------------------------------------------------- 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.

The tests done include (with some redundancy to point to the real problem)

_120 Test for consistency of the _symmetry_equiv_pos_as_xyz set with symmetry_space_group_name_H-M.

_121 Test for valid symmetry_space_group_name_H-M symbol.

_122 Test for missing (i.e. ?) symmetry_space_group_name_H-M symbol.

_123 Test for uninterpretable or inconsistent Spacegroup information.

------------------------------------------------------------------------------- _16x : Tests for missing s.u. on coordinates ------------------------------------------------------------------------------- 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).

_161 Missing or Zero su (esd) on x-coordinate.
_162 Missing or Zero su (esd) on x-coordinate.
_163 Missing or Zero su (esd) on x-coordinate.

------------------------------------------------------------------------------- _201 Test for isotropic non-hydrogen atoms in main residue (molecule) ------------------------------------------------------------------------------- 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.

------------------------------------------------------------------------------- _202 Test for isotropic non-hydrogen atoms in anion/solvent (small moiety) ------------------------------------------------------------------------------- This test reports on isotropically refined atoms in small moieties (usually anions or solvent)

------------------------------------------------------------------------------- _211 Test for NPD ADP's in main residue(s) ------------------------------------------------------------------------------- This test reports on non-positive definite (i.e. complex and unrealistic) anisotropic displacement parameters in the main residue.

------------------------------------------------------------------------------- _212 Test for NPD ADP's in small moieties (solvent/anions) ------------------------------------------------------------------------------- This test reports on non-positive definite (i.e. complex and unrealistic) anisotropic displacement parameters in small moieties (solvent/anion).

------------------------------------------------------------------------------- _213 ADP maximum/minimum ratio test for main residue ------------------------------------------------------------------------------- The maximum and minimum main axis ADP ratio (Angstrom Units) is tested for the main residue. Large values may indicate unresolved disorder.

------------------------------------------------------------------------------- _214 ADP maximum/minimum ratio test for small moiety ------------------------------------------------------------------------------- The maximum and minimum main axis ADP ratio (Angstrom Units) is tested for the minor residue(s). Large values may indicate unresolved disorder.

------------------------------------------------------------------------------- _220 Test Ueq(max)/Ueq(Min) range for non-H in main residue(s) ------------------------------------------------------------------------------- This test reports on a larger than usual U(eq) range for the non-hydrogen atoms. Too high or too low Ueq's may be an indication for falsely identified atomic species (i.e. Br versus Ag)

------------------------------------------------------------------------------- _221 Test Ueq(max)/Ueq(Min) range for non-H atoms in minor residue(s) ------------------------------------------------------------------------------- This test reports on a larger than usual U(eq) range for the non-hydrogen atoms. Too high or too low Ueq's may be an indication for falsely identified atomic species (i.e. Br versus Ag)

------------------------------------------------------------------------------- _222 Test Ueq(max)/Ueq(Min) range for H atoms in main residue(s) ------------------------------------------------------------------------------- This test reports on large ranges in displacement parameters for hydrogen atoms.

------------------------------------------------------------------------------- _223 Test Ueq(max)/Ueq(Min) range for H atoms in minor residues(s) ------------------------------------------------------------------------------ This test reports on large ranges in displacement parameters for hydrogen atoms.

------------------------------------------------------------------------------- _230 : Hirshfeld rigid bond test ------------------------------------------------------------------------------- Components of anisotropic displacement parameters along chemical bonds are assumed to be equal in magnitude. Large differences supposedly indicate contamination of these parameters with other (unresolved) effects such as disorder and/or overrefinement. Atom 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.

------------------------------------------------------------------------------- _301, _302 : Detection of Disorder ------------------------------------------------------------------------------- Atom sites that are not fully occupied are counted. A large fraction of disordered atoms may be both a signal for serious structure determination problems or less reliable/interesting results. A distinction is made for 'solvent molecules of less interest' (_302) and the 'main components' (_301)

------------------------------------------------------------------------------- _305 Test for 'Isolated' Hydrogen atoms ------------------------------------------------------------------------------- This test reports on hydrogen atoms that are not on bonding distance to any atom.

------------------------------------------------------------------------------- _306 Test for 'Isolated' Oxygen atoms ------------------------------------------------------------------------------- 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.

------------------------------------------------------------------------------- _310 Test for 'Too close' (symmetry related) full weight atoms. ------------------------------------------------------------------------------- This test identifies (very) short contacts between atoms that only becomes apparent after the application of symmetry on the primary coordinate set.

------------------------------------------------------------------------------- _320, _321 : Checks on Hybridisation of C atoms ------------------------------------------------------------------------------- This test is split up in two sections: the main molecule (_320) and solvent molecules (_321).

The test attempts to assign one of three hybridisations to C atoms: 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.

------------------------------------------------------------------------------- _350 : _373 : Test for Short/Long Bonds as compaired with standard values ------------------------------------------------------------------------------- Large deviations from generally accepted values may indicate model problems, overrefinement etc.

Default (X-Ray) values are from SHELXL (X-H) and 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.

------------------------------------------------------------------------------- _410, _411 : Tests for Short Intra and Intermolecular H...H Contacts ------------------------------------------------------------------------------- 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 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 intermolecular contacts, an alert is generated for contacts less than 2.4 Angstrom.

For intramolecular contacts alerts are generated for contacts less than 2.0 Angstrom.

Shorter intramolecular contacts may make sense for crowded configurations, in particular when hydrogen atoms are calculated in idealised positions.

------------------------------------------------------------------------------- _420 : Test for D-H without acceptor ------------------------------------------------------------------------------- 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.

------------------------------------------------------------------------------- _601, _602 : Solvent Accessible Void(s) Test(s) ------------------------------------------------------------------------------- Crystal structures in general do not contain large solvent accessible voids in the lattice. Most structures loose their long-range ordening 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 veryfied on a printed/plotted difference Fourier map or with PLATON/SQUEEZE.

Voids of 40 Ang**3 may accommodate H2O. Small molecules such as Tetrahydro Furane have typical volumes in the 100 to 200 Ang**3 range.

_601 : This test reports the volume of the largest solvent accessible void in the structure.

_602 : This test reports on a void, too large for the current PLATON version for more detailed analysis.