This document aims to help practical crystallographers decide what to do if certain "errors" or "warnings" are issued:
So here goes for the list of possible error and warning messages as it exists today (4 July, 1997). Note that these are my personal opinions (they are all mine and, no, you can't have them, and you don't have to agree with them, so there !). Comments, suggestions, fan-mail and hate-mail can be E-mailed. Useful comments may be added to this page (let me know in case you specifically do not want this to happen with your comments when you mail them).
The format of this page is simple - each entry consists of:
Click on an error or warning message or note in the list below to go to the comment and example:
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Symmetry related problems Error: Missing unit cell information No SCALE matrix is given in the PDB file. ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: Non-triclinic spacegroup-symbol is missing The CRYST1 card present in the PDB file gives a valid non-triclinic cell, but the space group symbol is not given. The CRYST1 cell dimensions A = 73.380 B = 80.259 C = 95.121 Alpha= 90.000 Beta= 90.000 Gamma= 90.000 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: C-unique setting for "P 21" The space group symbol on the CRYST1 card of the PDB file is ``P 21'' (monoclinic), but the cell setting is C-unique. The CRYST1 cell dimensions A = 52.230 B = 70.290 C = 95.470 Alpha= 90.000 Beta= 90.000 Gamma= 99.590 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: C-unique setting for "B 2" The space group symbol on the CRYST1 card of the PDB file is ``B 2'' (monoclinic), which is a non-standard c-unique setting for ``C 2''. The CRYST1 cell dimensions A = 185.500 B = 72.000 C = 73.000 Alpha= 90.000 Beta= 90.000 Gamma= 77.700 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Cell is non-standard The unit cell in the CRYST1 card of the PDB file contains angles outside the range 60-120 degrees. A conventional cell has angles within these limits. The CRYST1 cell dimensions A = 41.690 B = 34.620 C = 32.130 Alpha= 90.000 Beta= 127.600 Gamma= 90.000 Space group name: P 21 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Triclinic cell with mixed acute and obtuse angles The crystallographic unit cell does not conform to the convention that a triclinic cell should be specified as having either three obtuse (type II) or three acute angles (type I). The CRYST1 cell dimensions A = 32.100 B = 46.200 C = 25.400 Alpha= 105.900 Beta= 113.300 Gamma= 69.700 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Non-triclinic cell with acute angle The crystallographic unit cell does not conform to the convention that all non-orthogonal angles in a non-triclinic cell should be obtuse. The CRYST1 cell dimensions A = 185.500 B = 72.000 C = 73.000 Alpha= 90.000 Beta= 90.000 Gamma= 77.700 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Unconventional orthorhombic cell The primitive P 2 2 2 or P 21 21 21 cell specified does not conform to the convention that the axes should be given in order of increasing length. The CRYST1 cell dimensions A = 116.700 B = 103.900 C = 48.340 Alpha= 90.000 Beta= 90.000 Gamma= 90.000 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Class of conventional cell differs from CRYST1 cell The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment. The CRYST1 cell dimensions A = 85.070 B = 77.980 C = 88.860 Alpha= 90.000 Beta= 118.630 Gamma= 90.000 Dimensions of a reduced cell A = 77.980 B = 85.070 C = 88.819 Alpha= 118.582 Beta= 90.000 Gamma= 90.000 Dimensions of the conventional cell A = 85.070 B = 155.991 C = 77.980 Alpha= 90.000 Beta= 90.000 Gamma= 89.969 Transformation to conventional cell | 1.000000 0.000000 0.000000| | -1.000000 0.000000 -2.000000| | 0.000000 1.000000 0.000000| Crystal class of the cell: MONOCLINIC Crystal class of the conventional CELL: ORTHORHOMBIC Space group name: P 21 Bravais type of conventional cell is: C ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Unconventional cell on CRYST1 The derived ``conventional cell'' is different from the cell given on the CRYST1 card. The CRYST1 cell dimensions A = 55.300 B = 59.400 C = 42.500 Alpha= 90.000 Beta= 99.100 Gamma= 90.000 Dimensions of a reduced cell A = 42.500 B = 55.300 C = 59.400 Alpha= 90.000 Beta= 90.000 Gamma= 99.100 Dimensions of the conventional cell A = 42.500 B = 59.400 C = 55.300 Alpha= 90.000 Beta= 99.100 Gamma= 90.000 Transformation to conventional cell | 0.000000 0.000000 1.000000| | 0.000000 -1.000000 0.000000| | 1.000000 0.000000 0.000000| ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: Matthews Coefficient (Vm) very high The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that. Numbers this high are almost always caused by giving the wrong value for Z on the CRYST1 card. Molecular weight of all polymer chains: 65310.648 Volume of the Unit Cell V= 31006604.0 Cell multiplicity: 2 Matthews coefficient for observed atoms Vm= 237.378 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: Duplicate specification of SCALE cards There is more than one "SCALE" matrix present in the PDB file. ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: Invalid SCALE matrix The SCALE matrix contains elements larger than 0.5. This matrix represents a very small cell. Possible cause: Probably one or more of the values is mistyped, or the SCALE cards do not conform to the FORMAT given in the PDB specification. ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: The SCALE matrix gives a left handed axis system The SCALE matrix given in the PDB file represents a left handed axis system for the cell. This can cause weird problems (such as negative cell volumes). Scale matrix as derived from SCALE | 0.007435 0.010515 0.010515| | 0.007435 0.000000 0.010515| | -0.011641 0.000000 0.000000| ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Comment from Gert Vriend (Gert.Vriend@EMBL-Heidelberg.de),
EMBL, at 19980719:
Dear Gerard,
I was looking at your 'judgement' of the WHAT_CHECK checks. It must have
been a lot of work puting that whole file on the web...
However, there are some problems with the remarks you make.
For example, you write about most CRYST/SCALE problems that they
are unlikely to happen now that we have AUTODEP. However, see below
Enrique's quote:
"Dear Gert,
Your test for SCALE and CRYST is superior to what we do. All that we
do is to calculate a matrix based on the CRYST info and to compare this
with the SCALE matrix. Differences greater than some criteria are returned
to the depositor.
enrique"
That means that AUTODEP will not be able to deal with alternative
settings etc., that can be 'encoded' in the SCALE matrix. Further, our
checks do not only detect problems, but in roughly 50% of all cases
give suggestions for improvements. And there are more things to say...
I think that, although it would cost you some time, you should be a bit
more careful in the 'judgement' of WHAT_CHECK checks. I would say, try
to be just as careful as we are in detecting the 'errors'.
Greetings
Gert Vriend
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: Scale matrix represents wrong crystal class The crystal class for the unit cell on the CRYST1 card is different from the crystal class derived from the SCALE matrix. The cell on the CRYST1 card is compatible with the SPACE group. The CRYST1 cell dimensions A = 58.850 B = 58.850 C = 259.220 Alpha= 90.000 Beta= 90.000 Gamma= 90.000 Cell as derived from the SCALE matrix A = 58.851 B = 58.851 C = 260.793 Alpha= 90.000 Beta= 83.666 Gamma= 90.000 Space group name: P 43 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: Negated value in scale matrix One or more of the values of the scale matrix are wrong. Possible cause: Comparison with the matrix derived from the CRYST1 card reveals that values have been inverted in sign. SCALE matrices (as given and from CRYST1) 0.019685 0.000000 -0.002977 0.019685 0.000000 0.002977 0.000000 0.009355 0.000000 0.000000 0.009355 0.000000 0.000000 0.000000 0.027861 0.000000 0.000000 0.027861 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: The SCALE matrix is nonstandard The SCALE matrix given in the PDB file represents a crystallographic unit cell in which one or more angles are outside the range 60-120 degrees. The CRYST1 card does not contain such values. Possible cause: Values in the SCALE cards are wrong, or the PDB file format is not strictly adhered to. SCALE matrices (as given and from CRYST1) 0.007435 0.010515 0.010515 0.007435 0.000000 0.000000 0.007435 0.000000 0.010515 0.000000 0.007435 0.000000 -0.011641 0.000000 0.000000 0.000000 0.000000 0.011641 The CRYST1 cell dimensions A = 134.500 B = 134.500 C = 85.900 Alpha= 90.000 Beta= 90.000 Gamma= 90.000 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: Value in first row of scale matrix mistyped The SCALE matrix is incompatible with the CRYST1 cell. Possible cause: one or more of the values in the first row of the SCALE matrix are wrong. Scale matrix as derived from SCALE | 0.023558 0.000000 0.002855| | 0.000000 0.013193 0.000000| | 0.000000 0.000000 0.023554| ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: Inconsistent SCALE and CRYST1 cards The SCALE matrix and CRYST1 cards from the PDB file are inconsistent. Possible cause: A simple element by element comparison of the matrices can not locate an obvious cause. The CRYST1 cell dimensions A = 439.800 B = 426.900 C = 421.200 Alpha= 90.000 Beta= 90.000 Gamma= 90.000 Cell as derived from the SCALE matrix A = 441.301 B = 427.306 C = 421.932 Alpha= 89.999 Beta= 89.952 Gamma= 90.001 SCALE matrices (as given and from CRYST1) 0.001454 0.000011 0.001738 0.002274 0.000000 0.000000 0.000017 0.002340 -0.000029 0.000000 0.002342 0.000000 -0.001819 0.000032 0.001519 0.000000 0.000000 0.002374 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Note: Symmetry information inconsistent The SCALE and CRYST1 information disagree. Possible cause: The CRYST1 dimensions were rounded. The CRYST1 cell dimensions A = 380.100 B = 379.300 C = 350.900 Alpha= 90.000 Beta= 90.000 Gamma= 90.000 Cell as derived from the SCALE matrix A = 380.041 B = 379.290 C = 350.904 Alpha= 89.982 Beta= 90.013 Gamma= 89.997 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: New symmetry found In the conventional cell, independent molecules in the asymmetric unit seemingly become symmetry relatives. This fact needs manual checking. ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Conventional cell is pseudo-cell The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry. ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Determinant of MTRIX is not exactly 1 The Determinant of a matrix given on a set of MTRIX cards differs from 1 by more than 0.002 Matrix | -0.498700 0.866700 0.012480| | -0.865900 -0.498800 0.037820| | 0.039000 0.008050 0.992100| ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: MTRIX is not a pure rotation matrix The matrix given on a set of MTRIX cards is not a pure rotation matrix. Matrix | 0.373740 -0.056207 0.940855| | -0.073400 -0.996800 -0.033512| | 0.909789 -0.054363 -0.376740| ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Missing atoms The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Some checks (notably packing quality) will give worse results if the atoms are missing than when they would have been modelled first. 1 ASN ( 2 ) CB 1 ASN ( 2 ) CG 1 ASN ( 2 ) OD1 1 ASN ( 2 ) ND2 305 LYS ( 306 ) CB 305 LYS ( 306 ) CG 305 LYS ( 306 ) CD 305 LYS ( 306 ) CE 305 LYS ( 306 ) NZ ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: C-terminal oxygen atoms missing The C-atoms listed in the table below belong to a C-terminal residue in a protein chain, but the C-terminal oxygen ("O2" or "OXT") that it should be bound to was not found. 162 LYS ( 162 ) C ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: C-terminal groups where they should not be The C-atoms listed in the table below belong to a non-C-terminal residue in a protein chain, but nevertheless a terminating group was found for them. 121 PRO ( 129 ) C ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Duplicate atoms encountered. While reading the PDB file, at least one atom was encountered twice. This might be caused by missing alternate-conformation flags, or sometimes by naming the second C-terminal oxygen O instead of OXT or O2. The duplicates have been discarded. ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Unexpected atoms encountered While reading the PDB file, at least one atom was encountered that was not expected in the residue. This might be caused by a naming convention problem. The unexpected atoms have been discarded. ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Rounded coordinates detected At least two atoms were detected with all three coordinates rounded to 1 decimal place. Since this is highly unlikely to occur accidentally, the atoms listed in the table below were probably not refined. It could also be that ALL atomic coordinates were rounded to 1 or 2 decimal places (resulting in considerable loss of accuracy). 361 HOH (HOH ) 597 28.000 28.000 0.000 361 HOH (HOH ) 598 26.000 26.000 0.000 361 HOH (HOH ) 612 26.800 0.000 0.000 361 HOH (HOH ) 614 15.500 0.000 0.000 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Aspartic acid convention problem The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0. 24 ASP ( 24 ) A 46 ASP ( 46 ) A 80 ASP ( 24 ) B 102 ASP ( 46 ) B ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: Isoleucine nomenclature problem The isoleucine residues listed in the table below have their C-delta-1 attached to the wrong C-gamma. 99 ILE ( 99 ) A ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Chirality deviations detected The atoms listed in the table below have an improper dihedral value that is deviating from expected values. Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks. Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extrawarning if the chirality for an atom is opposite to the expected value. 40 ASN ( 40 ) CA -4.6 22.6 33.8 94 ALA ( 93 ) CA -4.0 26.8 34.4 107 MET ( 106 ) CA -4.6 23.8 34.1 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: High improper dihedral angle deviations The RMS Z-score for the improper dihedrals in the structure is high. For well refined structures this number is expected to be around 1.0. The fact that it is higher than 1.5 in this structure could be an indication of overrefinement. Improper dihedral Z-score : 1.775 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: Weights outside the 0.0 -- 1.0 range The atoms listed in the table below have their weight outside the 0.0--1.0 range. This problem is not hampering proper WHAT IF functioning, but it is indicative of problems with the X-ray refinement. 108 ALA ( 124 ) C 1.07 108 ALA ( 124 ) CB 1.07 108 ALA ( 124 ) O 1.07 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: Chain names not unique The chain names listed below are given for more than one protein/DNA molecule in the structure. Chain identifier(s): D, E, F ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: Water clusters without contacts with non-water atoms The water molecules listed in the table below are part of water molecule clusters that do not make contacts with non-waters. These water molecules are part of clusters that have a distance at least 1 Angstrom larger than the sum of the Van der Waals radii to the nearest non-solvent atom. Because these kinds of water clusters usually are not observed with X-ray diffraction their presence could indicate a refinement artifact. The number in brackets is the identifier of the water molecule in the input file. 804 HOH (HOH ) A 162 805 HOH (HOH ) A 286 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Water molecules need moving The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given. The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. 25 HOH (HOH ) 45 2.846 24.342 15.050 26 HOH (HOH ) 56 11.843 13.097 5.059 28 HOH (HOH ) 51 19.230 32.397 17.970 28 HOH (HOH ) 54 19.389 29.689 16.110 31 HOH (HOH ) 25 14.785 30.653 19.485 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Temperature factors given as "U", not as "B" The average temperature factor found is very low. Probably they are given as "U" values, and not as "B" values. Values will be multiplied by 8-pi-squared for the analysis of B-factors. ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Average B-factor problem The average B-factor for all buried protein atoms normally lies between 10--20. Values around 3--5 are expected for X-ray studies performed at liquid nitrogen temperature. Because of the extreme value for the average B-factor, no further analysis of the B-factors is performed. Average B-factor for buried atoms : 35.144 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: More than 5\% of buried atoms has low B-factor For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal of overrefined B-factors, constaints to too-low values, misuse of the B-factor field in the PDB file, or a scaling problem. If the average B factor is low too, it is probably a low temperature structure determination. Percentage of buried atoms with B less than 5 : 31.84 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: The B-factors of bonded atoms show signs of over-refinement For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors. RMS Z-score : 1.903 over 2783 bonds Average difference in B over a bond : 4.24 RMS difference in B over a bond : 5.54 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: Atoms too close to symmetry axes The atoms listed in the table below are closer than 0.77 Angstrom to a proper symmetry axis. This creates a bump between the atom and its symmetry relative(s). It is likely that these represent refinement artefacts. 2366 HOH (HOH ) 169 2366 HOH (HOH ) 1125 2366 HOH (HOH ) 1166 2366 HOH (HOH ) 1835 2368 HOH (HOH ) 81 2368 HOH (HOH ) 95 2368 HOH (HOH ) 106 2368 HOH (HOH ) 1175 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Comment from Kim Henrick (henrick@ebi.ac.uk), EBI, at 19971209: the program fails for PQR coordinates and for authors who submit coordinates in an unusual coordinate frame then the atoms first need to be re-orthogonalised, or WHATIF will be "unhappy" about the bump test.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: Abnormally short interatomic distances The pairs of atoms listed in the table below have an unusually short distance. The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centers of the two atoms. The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. If the final column contains the text 'HB', the bump criterium was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1--3 and 1--4 interactions (listed as 'B2' and 'B3', respectively). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably aren't there anyway. Bumps between atoms for which the sum of their occupancies is lower than one are not reported. In any case, each bump is listed in only one direction. 20 MET ( 20 ) SD -- 133 HOH (HOH ) 175 0.315 2.535 INTRA HB 45 ASN ( 45 ) ND2 -- 110 GLY ( 110 ) N 0.210 2.790 INTER 122 VAL ( 122 ) CB -- 134 HOH (HOH ) 157 0.061 2.739 INTRA 15 ASN ( 15 ) ND2 -- 83 ILE ( 83 ) CD1 0.024 3.076 INTER ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Unusual bond lengths The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigma for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given. Atom names starting with "<" belong to the previous residue in the chain. If the second atom name is "--SS", the disulphide bridge has a deviating length. 12 G ( 14 ) B C8 N7 1.281 -4.0 15 A ( 17 ) B O4* C1* 1.463 4.1 17 A ( 21 ) B O4* C1* 1.463 4.1 19 C ( 23 ) B C1* C2* 1.480 -4.8 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: High bond length deviations Bond lengths were found to deviate more than normal from the mean standard bond lengths (standard values for protein residues were taken from Engh and Huber [REF], for DNA/RNA these values were taken from Parkinson et al [REF]). The RMS Z-score given below is expected to be around 1.0 for a normally restrained data set. The fact that it is higher than 1.5 in this structure might indicate that the constraints used in the refinement were not strong enough. This will also occur if a different bond length dictionary is used. Z-score for bond lengths: 1.764 RMS-deviation in bond distances: 0.037 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Low bond length variability Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be around 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong constraints have been used in the refinement. This can only be a problem for high resolution X-ray structures. Z-score for bond lengths: 0.433 RMS-deviation in bond distances: 0.010 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Comment from Kim Henrick (henrick@ebi.ac.uk), EBI, at 19971209: I disagree with this. The problem doesn't come from an individaul wavelenght being unknown nor using the first or an average of the cells obtained in data reduction. This comes from wavelenght drift or the same beam having more than one wavelength perpendicular to each other so that data collected at one orientation is collected at a wavelength different to a following orientation. The effect is real only on sync data collection, however, no known program can or tries to correct for this observation. The WHATIF test is pointing out the fact one may have collected anisotropic wavelenght at different times in the same data collection, but the explanation is poor, and the correction is fairly meaningless as symmetry is broken to satisfy an isotropic distribution of bond lengths and angles. In some cases, the corrected cell dimensions are far off symmetry requirements and any attempt to use this cell to look at images and fit diffraction spots will be hopeless.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Possible cell scaling problem Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99\% confidence level) There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of lambda used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion. Please note that the proposed scale matrix has NOT been constrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination. Unit Cell deformation matrix | 0.998473 0.000049 0.000017| | 0.000049 0.998579 -0.000039| | 0.000017 -0.000039 0.998875| Proposed new scale matrix | 0.020398 -0.000001 0.004782| | -0.000001 0.013212 0.000001| | 0.000000 0.000000 0.011068| With corresponding cell A = 49.024 B = 75.690 C = 92.796 Alpha= 90.006 Beta= 103.193 Gamma= 89.994 The CRYST1 cell dimensions A = 49.100 B = 75.800 C = 92.900 Alpha= 90.000 Beta= 103.200 Gamma= 90.000 Variance: 42.888 (Under-)estimated Z-score: 4.827 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Directionality in bond lengths Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] standard values for DNA/RNA shows a significant systematic deviation. If this is not an XRAY structure this effect is hard to explain. Otherwise you will have seen symmetry problems earlier. Please correct these and rerun this check to see the possible implications on the cell axes. ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Unusual PRO puckering amplitudes The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. 7 PRO ( 244 ) A 0.46 HIGH ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Unusual PRO puckering phases The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. 1 PRO ( 238 ) A -58.1 half-chair C-beta/C-alpha (-54 degrees) 10 PRO ( 247 ) A 156.9 half-chair C-alpha/N (162 degrees) 34 PRO ( 271 ) A -47.0 half-chair C-beta/C-alpha (-54 degrees) 54 PRO ( 291 ) A 25.6 half-chair N/C-delta (18 degrees) 137 PRO ( 374 ) A 51.0 half-chair C-delta/C-gamma (54 degrees) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Torsion angle evaluation shows unusual residues The residues listed in the table below contain bad or abnormal torsion angles. These scores give an impression of how ``normal'' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position. 229 TYR ( 9 ) B -3.0211 8 TYR ( 9 ) A -3.0211 81 TYR ( 82 ) A -2.6449 302 TYR ( 82 ) B -2.6449 426 PRO ( 206 ) B -2.5862 205 PRO ( 206 ) A -2.5862 9 PHE ( 10 ) A -2.0385 230 PHE ( 10 ) B -2.0385 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: Ramachandran Z-score very low The score expressing how well the backbone conformations of all residues are corresponding to the known allowed areas in the Ramachandran plot is very low. Ramachandran Z-score : -7.127 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Omega angles too tightly restrained The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly constrained. This seems to be the case with the current structure, as the observed standard deviation is below 4.0 degrees. Standard deviation of omega values : 1.426 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: chi-1/chi-2 angle correlation Z-score very low The score expressing how well the chi-1/chi-2 angles of all residues are corresponding to the populated areas in the database is very low. chi-1/chi-2 correlation Z-score : -5.141 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Backbone torsion angle evaluation shows unusual conformations The residues listed in the table below have abnormal backbone torsion angles. Residues with ``forbidden'' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations. 25 SER ( 29 ) PRO omega poor 26 PRO ( 30 ) Poor PRO-phi 60 HIS ( 64 ) Poor phi/psi 61 ALA ( 65 ) Poor phi/psi 71 ASP ( 75 ) Poor phi/psi 107 LYS ( 111 ) Poor phi/psi 124 GLY ( 129 ) Poor phi/psi 173 ASN ( 178 ) Poor phi/psi 190 PRO ( 195 ) Poor PRO-phi 196 PRO ( 201 ) PRO omega poor 197 PRO ( 202 ) Poor phi/psi 210 PRO ( 215 ) Poor PRO-phi 248 ASN ( 253 ) Poor phi/psi ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: Side chain planarity problems The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value (0.0). 40 ASN ( 40 ) 7.152 72 ASP ( 72 ) 6.482 53 ASN ( 53 ) 5.524 89 ASP ( 89 ) 5.386 116 ASN ( 116 ) 4.235 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: Connections to aromatic rings out of plane The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane. For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures. 300 HIS ( 218 ) 2 CB 5.019 146 HIS ( 218 ) 1 CB 4.313 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Inside/Outside residue distribution unusual The distribution of residue types over the inside and the outside of the protein is unusual. Normal values for the RMS Z-score below are between 0.84 and 1.16. The fact that it is higher in this structure could be caused by transmembrane helices, by the fact that it is part of a multimeric active unit, or by mistraced segments in the density. RMS inside/outside Z-score : 1.401 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Abnormal packing environment for some residues The residues listed in the table below have an unusual packing environment. The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue. 103 GLU ( 103 ) -6.18 101 LYS ( 101 ) -6.13 100 LEU ( 100 ) -5.59 115 ASN ( 115 ) -5.33 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Abnormal packing environment for sequential residues A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop, but might also be an indication of misthreading. The table below lists the first and last residue in each stretch found, as well as the average residue score of the series. 751 MET ( 325 ) B --- 754 GLY ( 328 ) B -5.57 756 GLY ( 332 ) B --- 759 SER ( 335 ) B -4.68 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: Abnormal average packing environment The average quality control value for the structure is very low. A molecule is certain to be incorrect if the average quality score is below -3.0. Poorly refined molecules, very well energy minimized misthreaded molecules and low homology models give values between -2.0 and -3.0. The average quality of 200 highly refined Xray structures was -0.5+/-0.4 [REF]. Average for range 1 - 187 : -2.472 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Low packing Z-score for some residues The residues listed in the table below have an unusual packing environment according to the 2nd generation quality check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the "unusual" residues in the structure, so it will be interesting to take a special look at them. 169 ALA ( 181 ) -2.97 14 LEU ( 26 ) -2.93 396 LEU ( 408 ) -2.62 16 LEU ( 28 ) -2.59 336 ARG ( 348 ) -2.59 28 LYS ( 40 ) -2.54 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Abnormal packing Z-score for sequential residues A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading. The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series. 9 LYS ( 9 ) O --- 12 GLY ( 12 ) O -2.40 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: Abnormal structural average packing Z-score The quality control Z-score for the structure is very low. A molecule is certain to be incorrect if the Z-score is below -5.0. Poorly refined molecules, very well energy minimized misthreaded molecules and low homology models give values between -2.0 and -5.0. The average quality of properly refined Xray structures is 0.0+/-1.0. All contacts : Average = -1.409 Z-score = -7.19 BB-BB contacts : Average = -0.762 Z-score = -4.22 BB-SC contacts : Average = -1.344 Z-score = -8.22 SC-BB contacts : Average = -0.546 Z-score = -2.55 SC-SC contacts : Average = -1.005 Z-score = -5.01 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Backbone oxygen evaluation The residues listed in the table below have an unusual backbone oxygen position. For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some constraints on the neighboring backbone oxygens. In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking! 558 GLY ( 558 ) 2.88 14 180 GLY ( 180 ) 1.92 10 677 THR ( 677 ) 1.56 17 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Unusual rotamers The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.66. No value will be given if insufficient hits are found in the database. It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it. 117 SER ( 117 ) 0.39 108 GLU ( 108 ) 0.39 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Unusual backbone conformations For the residues listed in the table below, the backbone formed by itself and two neighboring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the center. For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions. A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at! 101 LYS ( 101 ) 0 126 ASP ( 126 ) 2 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: Backbone conformation Z-score very low A comparison of the backbone conformation with database proteins shows that the backbone fold in this structure is very unusual. Backbone conformation Z-score : -17.463 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Error: HIS, ASN, GLN side chain flips Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favorable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. If a residue is marked ``flexible'' the flipped conformation is only slightly better than the non-flipped conformation. 115 ASN ( 115 ) ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Comment from Kim Henrick (henrick@ebi.ac.uk), EBI, at 19971209: If a residue is burried then, according to WHATIF, it must have all H-bonds satisfied - if it is exposed it doesn't - but waters are not used in both steps. In one case, a Tyr has all H-bonds satisfied, some to water, some not. It is exposed with no water included in the accesible surface calculation, but is buried if water is used. WHATIF says for this example that the side chain is buried and that un-satisfied H-bonds are present - now one can't use water to bury the side chain and then exclude the water in looking for H-bonds. Rob Hooft told me that it shouldn't have been considered buried as its relative ASA is 0.7% - therefore it is exposed. This is a very confusing test.
----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- Warning: Buried unsatisfied hydrogen bond donors The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network. Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero. 7 ASN ( 91 ) A ND2 17 ASN ( 101 ) A N 54 THR ( 138 ) A N 81 GLN ( 165 ) A NE2 96 ALA ( 180 ) A N [...] 701 GLN ( 422 ) B N 720 ASN ( 441 ) B ND2 ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE ----- EXAMPLE -----
Latest update at 19 July, 1998.