Bijvoet centre for biomolecular research, vakgroep kristal- en structuurchemie, university of utrecht

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_053 Test for specification xtal_dimension_min

_054 Test for specification xtal_dimension_mid

_055 Test for specification xtal_dimension_max

_056  Test for specification xtal_radius

_057 Test for absorption correction needed

_058 Test for Tmax specified

_059 Test for Tmin specified

_060 RR Test

_061 RR' Test

_062 Rescale Tmin & Tmax

_063 Test crystal size

Alert for crystals with at least one dimension probably too large for the

homogeneous part of the Xray beam when used for data collection using

crystal monochromated radiation. An exception will be datacollection using

a beta-filter and a sufficiently large collimator.

_064 Test for T(max) .GE. T(min)

_065 Test for applicability of (semi-)empirical abs.corr.

_070 Test for duplicate atom labels

_071 Uninterpretable label 

This alert relates to unintelligable labels on input and are deleted from

the model & checking.

_080 Test maximum shift/error

_081 Test for maximum shift/error given

_082 Test for reasonable R1 value

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_084 Test for reasonable R2 value

R2 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.

_086, _087 Test for reasonable S value

S should in general be close to 1 at the end of a refinement with a proper

weighting scheme. If not, there might be significant unresolved problems

with the model.

_088 Test for reasonable Data / parameter ratio  (centro)

_089 Test for reasonable Data / parameter ratio  (non-centrosymmetric)

_095 Test for residual density maximum given

_096 Test for residual density maximum given

_097 Test maximum residual density

_098 Test for minimum residual density

_099 Test for minimum residual density less zero

_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.

_113 Report New spacegroup suggested by ADDSYM

 

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

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

CIF.

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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.

_124 Test for uninterpretable or absent explicit symmetry records.

_130 - _140 : Test for symmetry restrictions on cell-parameters.

Symmetry restrictions on cell dimensions are checked.

_141 - _146 : Test Su's on cell parameters

The presence of su's (where required) and value are checked. Su's as given

by the diffractometer software are often much smaller than realistic.

_150 Check Reported versus Calculated volume

An alert is issued when the reported unit cell volume differs significantly

from the volume calculated on the basis of the supplied cell dimensions.

_16x : Tests for missing s.u. on coordinates or refined C-H

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. 

_164 Refined C-H H-atoms in heavy-atom structure (warning) 

 

Such H-atoms are better refined at calculated positions riding on the atoms

they are attached to.

_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)

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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, _233 : 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.

_241, _242 Test for too high/low U(eq) as compaired to neighbours

The U(eq) value of an atom is compaired 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).

 

_301, _302 : Detection of Disorder

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