WHAT IF Check report

This file was created 2011-12-22 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb1dlh.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.537
CA-only RMS fit for the two chains : 0.353

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and E

All-atom RMS fit for the two chains : 0.721
CA-only RMS fit for the two chains : 0.633

Note: Non crystallographic symmetry backbone difference plot

The plot shows the differences in backbone torsion angles between two similar chains on a residue-by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show high differences, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and E

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: C and F

All-atom RMS fit for the two chains : 0.383
CA-only RMS fit for the two chains : 0.143

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

 769 NDG   ( 512-)  B  -
 770 NDG   ( 521-)  B  -
 771 NDG   ( 512-)  E  -
 772 NDG   ( 521-)  E  -

Administrative problems that can generate validation failures

Warning: Strange inter-chain connections detected

The pairs of residues listed in the table below seem covalently bound while belonging to different chains in the PDB file.

Sometimes this is unavoidable (e.g. if two protein chains are covalently connected via a Cys-Cys or other bond). But if it can be avoided (e.g. often we observe sugars with one chain identifier connected to protein chains with another chain identifier), it should be avoided. WHAT IF and WHAT-CHECK try to deal with all exceptions thrown at it, but if you want these programs to work optimally (i.e. make as few false error messages as is possible) you should help them by getting as much of the administration correct as is humanly possible.

 116 ASN   ( 118-)  A  -   ND2  764 NAG   ( 511-)  B  -   C1
 497 ASN   ( 118-)  D  -   ND2  766 NAG   ( 511-)  E  -   C1

Warning: Strange inter-chain connections could NOT be corrected

Often inter-chain connections are simple administrative problems. In this case not. The observed inter-chain connection(s) either are real, or they are too strange for WHAT IF to correct. Human inspection seems required.

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 764 NAG   ( 511-)  B  -   O4  bound to  769 NDG   ( 512-)  B  -   C1
 766 NAG   ( 511-)  E  -   O4  bound to  771 NDG   ( 512-)  E  -   C1

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

  48 ARG   (  50-)  A  -   CG
  48 ARG   (  50-)  A  -   CD
  48 ARG   (  50-)  A  -   NE
  48 ARG   (  50-)  A  -   CZ
  48 ARG   (  50-)  A  -   NH1
  48 ARG   (  50-)  A  -   NH2
  53 GLU   (  55-)  A  -   CG
  53 GLU   (  55-)  A  -   CD
  53 GLU   (  55-)  A  -   OE1
  53 GLU   (  55-)  A  -   OE2
 237 GLU   (  59-)  B  -   CG
 237 GLU   (  59-)  B  -   CD
 237 GLU   (  59-)  B  -   OE1
 237 GLU   (  59-)  B  -   OE2
 365 GLU   ( 187-)  B  -   CG
 365 GLU   ( 187-)  B  -   CD
 365 GLU   ( 187-)  B  -   OE1
 365 GLU   ( 187-)  B  -   OE2
 367 ARG   ( 189-)  B  -   CG
 367 ARG   ( 189-)  B  -   CD
 367 ARG   ( 189-)  B  -   NE
 367 ARG   ( 189-)  B  -   CZ
 367 ARG   ( 189-)  B  -   NH1
 367 ARG   ( 189-)  B  -   NH2
 429 ARG   (  50-)  D  -   CG
 429 ARG   (  50-)  D  -   CD
 429 ARG   (  50-)  D  -   NE
 429 ARG   (  50-)  D  -   CZ
 429 ARG   (  50-)  D  -   NH1
 429 ARG   (  50-)  D  -   NH2
 434 GLU   (  55-)  D  -   CG
 434 GLU   (  55-)  D  -   CD
 434 GLU   (  55-)  D  -   OE1
 434 GLU   (  55-)  D  -   OE2
 618 GLU   (  59-)  E  -   CG
 618 GLU   (  59-)  E  -   CD
 618 GLU   (  59-)  E  -   OE1
 618 GLU   (  59-)  E  -   OE2
 746 GLU   ( 187-)  E  -   CG
 746 GLU   ( 187-)  E  -   CD
 746 GLU   ( 187-)  E  -   OE1
 746 GLU   ( 187-)  E  -   OE2
 748 ARG   ( 189-)  E  -   CG
 748 ARG   ( 189-)  E  -   CD
 748 ARG   ( 189-)  E  -   NE
 748 ARG   ( 189-)  E  -   CZ
 748 ARG   ( 189-)  E  -   NH1
 748 ARG   ( 189-)  E  -   NH2

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

 645 GLY   (  86-)  E  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Coordinate problems, unexpected atoms, B-factor and occupancy checks

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. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

 645 GLY   (  86-)  E      O

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

 243 LYS   (  65-)  B    High
 765 NAG   ( 501-)  D    High

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Geometric checks

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 sigmas 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 "-SG*", the disulphide bridge has a deviating length.

  32 VAL   (  34-)  A      CA   CB    1.61    4.2
 209 ILE   (  31-)  B      CA   CB    1.61    4.1
 544 VAL   ( 165-)  D      CA   CB    1.61    4.1
 739 VAL   ( 180-)  E      CA   CB    1.61    4.1

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 percent 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 the wavelength 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 restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  1.001412  0.000085 -0.000108|
 |  0.000085  1.001386  0.000054|
 | -0.000108  0.000054  1.001263|
Proposed new scale matrix

 |  0.010556  0.000000  0.000001|
 |  0.000000  0.010556  0.000000|
 |  0.000000  0.000000  0.004035|
With corresponding cell

    A    =  94.732  B   =  94.730  C    = 247.837
    Alpha=  90.002  Beta=  90.008  Gamma=  90.001

The CRYST1 cell dimensions

    A    =  94.600  B   =  94.600  C    = 247.500
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 49.316
(Under-)estimated Z-score: 5.176

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

   3 HIS   (   5-)  A      CG   ND1  CE1 109.76    4.2
   5 ILE   (   7-)  A      N    CA   C    98.27   -4.6
   7 GLN   (   9-)  A      N    CA   C    99.90   -4.0
  31 HIS   (  33-)  A      CG   ND1  CE1 109.62    4.0
 109 LYS   ( 111-)  A      N    CA   C   122.59    4.1
 118 THR   ( 120-)  A      C    CA   CB  102.38   -4.1
 141 HIS   ( 143-)  A      CG   ND1  CE1 109.95    4.3
 144 ARG   ( 146-)  A      CB   CG   CD  103.60   -5.3
 161 CYS   ( 163-)  A      N    CA   C    98.30   -4.6
 207 ARG   (  29-)  B      CB   CG   CD  105.06   -4.5
 207 ARG   (  29-)  B      CG   CD   NE  118.40    4.6
 273 VAL   (  95-)  B      N    CA   C    97.80   -4.8
 285 GLN   ( 107-)  B      C    CA   CB  101.44   -4.6
 301 TYR   ( 123-)  B      N    CA   C    99.86   -4.1
 342 VAL   ( 164-)  B      N    CA   C    97.93   -4.7
 386 ILE   (   7-)  D      N    CA   C    99.25   -4.3
 388 GLN   (   9-)  D      N    CA   C    96.40   -5.3
 471 LEU   (  92-)  D      N    CA   CB  103.43   -4.2
 525 ARG   ( 146-)  D      CB   CG   CD  103.43   -5.3
 542 CYS   ( 163-)  D      N    CA   C    97.55   -4.9
 556 HIS   ( 177-)  D      CG   ND1  CE1 111.47    5.9
 572 PHE   (  13-)  E      N    CA   C    99.62   -4.1
 575 HIS   (  16-)  E      CG   ND1  CE1 109.64    4.0
 579 GLY   (  20-)  E      N    CA   C    99.20   -4.6
 588 ARG   (  29-)  E      CG   CD   NE  118.07    4.5
 654 VAL   (  95-)  E      N    CA   C    97.81   -4.8
 670 HIS   ( 111-)  E      CG   ND1  CE1 109.62    4.0
 671 HIS   ( 112-)  E      CG   ND1  CE1 109.89    4.3
 682 TYR   ( 123-)  E      N    CA   C    98.90   -4.4
 723 VAL   ( 164-)  E      N    CA   C    96.15   -5.4
 725 ARG   ( 166-)  E      N    CA   C    96.97   -5.1

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

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 extra warning if the chirality for an atom is opposite to the expected value.

 200 GLU   (  22-)  B      C      8.2    11.83    -0.03
 581 GLU   (  22-)  E      C     -7.1   -10.28    -0.03
 682 TYR   ( 123-)  E      C     -7.0   -10.62     0.33
The average deviation= 1.820

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

 263 VAL   (  85-)  B    6.13
 109 LYS   ( 111-)  A    6.08
 490 LYS   ( 111-)  D    5.61
 725 ARG   ( 166-)  E    5.37
 723 VAL   ( 164-)  E    5.37
 388 GLN   (   9-)  D    5.28
 579 GLY   (  20-)  E    5.16
 542 CYS   ( 163-)  D    5.08
  87 VAL   (  89-)  A    5.02
 446 LYS   (  67-)  D    4.97
 452 MET   (  73-)  D    4.81
 161 CYS   ( 163-)  A    4.76
 273 VAL   (  95-)  B    4.73
 654 VAL   (  95-)  E    4.73
 682 TYR   ( 123-)  E    4.69
 342 VAL   ( 164-)  B    4.68
   5 ILE   (   7-)  A    4.62
  43 LEU   (  45-)  A    4.55
 175 HIS   ( 177-)  A    4.54
 601 SER   (  42-)  E    4.46
  54 ALA   (  56-)  A    4.43
 435 ALA   (  56-)  D    4.42
 277 VAL   (  99-)  B    4.37
 572 PHE   (  13-)  E    4.34
 301 TYR   ( 123-)  B    4.33
 386 ILE   (   7-)  D    4.18
 681 PHE   ( 122-)  E    4.17
  71 MET   (  73-)  A    4.16
 286 PRO   ( 108-)  B    4.11
 544 VAL   ( 165-)  D    4.10
 755 GLN   ( 311-)  F    4.08
 703 SER   ( 144-)  E    4.02

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.913

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.

 422 TRP   (  43-)  D      CB   5.72
 141 HIS   ( 143-)  A      CB   4.94
  41 TRP   (  43-)  A      CB   4.77
 557 TRP   ( 178-)  D      CB   4.76
 522 HIS   ( 143-)  D      CB   4.19
  52 PHE   (  54-)  A      CB   4.13
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -3.099

Torsion-related checks

Warning: Ramachandran Z-score low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is a bit low.

Ramachandran Z-score : -3.099

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.

 552 PRO   ( 173-)  D    -2.9
 171 PRO   ( 173-)  A    -2.8
 111 THR   ( 113-)  A    -2.6
 665 THR   ( 106-)  E    -2.6
 217 ARG   (  39-)  B    -2.6
 283 LYS   ( 105-)  B    -2.6
 653 ARG   (  94-)  E    -2.6
 469 THR   (  90-)  D    -2.6
 460 PRO   (  81-)  D    -2.5
 311 ARG   ( 133-)  B    -2.5
  91 THR   (  93-)  A    -2.5
 664 LYS   ( 105-)  E    -2.5
 492 THR   ( 113-)  D    -2.4
 272 ARG   (  94-)  B    -2.4
 234 PRO   (  56-)  B    -2.4
  88 THR   (  90-)  A    -2.3
 475 PRO   (  96-)  D    -2.3
 598 ARG   (  39-)  E    -2.3
 205 LEU   (  27-)  B    -2.3
 586 LEU   (  27-)  E    -2.2
 716 THR   ( 157-)  E    -2.2
 551 GLU   ( 172-)  D    -2.2
 479 ARG   ( 100-)  D    -2.2
 364 VAL   ( 186-)  B    -2.2
 199 THR   (  21-)  B    -2.2
And so on for a total of 53 lines.

Warning: Backbone evaluation reveals 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.

  13 ASN   (  15-)  A  PRO omega poor
  16 GLN   (  18-)  A  Poor phi/psi
  26 GLY   (  28-)  A  Poor phi/psi
  37 LYS   (  39-)  A  Poor phi/psi
  76 ASN   (  78-)  A  Poor phi/psi
  77 TYR   (  79-)  A  Poor phi/psi
  90 LEU   (  92-)  A  Poor phi/psi
  98 ARG   ( 100-)  A  Poor phi/psi
 111 THR   ( 113-)  A  PRO omega poor
 113 PRO   ( 115-)  A  Poor phi/psi
 122 ASN   ( 124-)  A  Poor phi/psi
 123 GLY   ( 125-)  A  Poor phi/psi
 141 HIS   ( 143-)  A  Poor phi/psi
 170 GLU   ( 172-)  A  Poor phi/psi
 171 PRO   ( 173-)  A  Poor phi/psi
 211 ASN   (  33-)  B  Poor phi/psi
 223 GLY   (  45-)  B  Poor phi/psi
 264 GLY   (  86-)  B  Poor phi/psi
 268 THR   (  90-)  B  Poor phi/psi
 283 LYS   ( 105-)  B  Poor phi/psi
 288 GLN   ( 110-)  B  Poor phi/psi
 301 TYR   ( 123-)  B  PRO omega poor
 313 GLY   ( 135-)  B  Poor phi/psi
 331 TRP   ( 153-)  B  Poor phi/psi
 394 ASN   (  15-)  D  PRO omega poor
 397 GLN   (  18-)  D  Poor phi/psi
 418 LYS   (  39-)  D  Poor phi/psi
 451 ILE   (  72-)  D  Poor phi/psi
 457 ASN   (  78-)  D  Poor phi/psi
 458 TYR   (  79-)  D  Poor phi/psi
 479 ARG   ( 100-)  D  Poor phi/psi
 490 LYS   ( 111-)  D  Poor phi/psi
 492 THR   ( 113-)  D  PRO omega poor
 494 PRO   ( 115-)  D  Poor phi/psi
 522 HIS   ( 143-)  D  Poor phi/psi
 551 GLU   ( 172-)  D  Poor phi/psi
 578 ASN   (  19-)  E  Poor phi/psi
 582 ARG   (  23-)  E  Poor phi/psi
 592 ASN   (  33-)  E  Poor phi/psi
 640 HIS   (  81-)  E  Poor phi/psi
 649 THR   (  90-)  E  Poor phi/psi
 664 LYS   ( 105-)  E  Poor phi/psi
 669 GLN   ( 110-)  E  Poor phi/psi
 682 TYR   ( 123-)  E  PRO omega poor
 693 ASN   ( 134-)  E  Poor phi/psi
 712 TRP   ( 153-)  E  Poor phi/psi
 727 GLY   ( 168-)  E  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.093

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 correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -4.093

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring 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 centre.

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!

   9 GLU   (  11-)  A      0
  13 ASN   (  15-)  A      0
  15 ASP   (  17-)  A      0
  16 GLN   (  18-)  A      0
  17 SER   (  19-)  A      0
  24 PHE   (  26-)  A      0
  29 ILE   (  31-)  A      0
  30 PHE   (  32-)  A      0
  31 HIS   (  33-)  A      0
  48 ARG   (  50-)  A      0
  49 PHE   (  51-)  A      0
  75 SER   (  77-)  A      0
  76 ASN   (  78-)  A      0
  77 TYR   (  79-)  A      0
  86 GLU   (  88-)  A      0
  90 LEU   (  92-)  A      0
  92 ASN   (  94-)  A      0
  97 LEU   (  99-)  A      0
  98 ARG   ( 100-)  A      0
 108 ASP   ( 110-)  A      0
 109 LYS   ( 111-)  A      0
 110 PHE   ( 112-)  A      0
 111 THR   ( 113-)  A      0
 112 PRO   ( 114-)  A      0
 113 PRO   ( 115-)  A      0
And so on for a total of 324 lines.

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 restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 2.249

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 restraining on the neighbouring 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!

 303 GLY   ( 125-)  B   1.51   44

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. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

  14 PRO   (  16-)  A    0.46 HIGH
  94 PRO   (  96-)  A    0.47 HIGH
 125 PRO   ( 127-)  A    0.47 HIGH
 137 PRO   ( 139-)  A    0.45 HIGH
 286 PRO   ( 108-)  B    0.45 HIGH
 395 PRO   (  16-)  D    0.45 HIGH
 506 PRO   ( 127-)  D    0.46 HIGH
 742 PRO   ( 183-)  E    0.45 HIGH

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. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

  79 PRO   (  81-)  A   -41.7 envelop C-alpha (-36 degrees)
 171 PRO   ( 173-)  A   121.3 half-chair C-beta/C-alpha (126 degrees)
 361 PRO   ( 183-)  B  -126.0 half-chair C-delta/C-gamma (-126 degrees)
 369 PRO   ( 306-)  C  -116.5 envelop C-gamma (-108 degrees)
 460 PRO   (  81-)  D   -55.0 half-chair C-beta/C-alpha (-54 degrees)
 552 PRO   ( 173-)  D   142.2 envelop C-alpha (144 degrees)
 667 PRO   ( 108-)  E    42.3 envelop C-delta (36 degrees)
 683 PRO   ( 124-)  E    52.9 half-chair C-delta/C-gamma (54 degrees)
 742 PRO   ( 183-)  E  -116.3 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short distance; each bump is listed in only one direction,

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 centres 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 criterion 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 are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

 578 ASN   (  19-)  E      ND2  <->   772 NDG   ( 521-)  E      C1   1.21    1.49  INTRA BF
 578 ASN   (  19-)  E      CG   <->   772 NDG   ( 521-)  E      C1   0.73    2.47  INTRA
 602 ASP   (  43-)  E      N    <->   777 HOH   ( 546 )  E      O    0.59    2.11  INTRA
  48 ARG   (  50-)  A      N    <->   773 HOH   ( 528 )  A      O    0.56    2.14  INTRA BF
 186 LEU   (   8-)  B      N    <->   774 HOH   ( 556 )  B      O    0.55    2.15  INTRA BL
  49 PHE   (  51-)  A      N    <->   773 HOH   ( 528 )  A      O    0.51    2.19  INTRA BF
 181 THR   (   3-)  B      CG2  <->   184 ARG   (   6-)  B      NH2  0.50    2.60  INTRA
 562 THR   (   3-)  E      CG2  <->   563 ARG   (   4-)  E      NH1  0.49    2.61  INTRA BF
 581 GLU   (  22-)  E      N    <->   777 HOH   ( 526 )  E      O    0.48    2.22  INTRA
 585 LEU   (  26-)  E      CD1  <->   638 CYS   (  79-)  E      SG   0.47    2.93  INTRA
 204 LEU   (  26-)  B      CD1  <->   257 CYS   (  79-)  B      SG   0.46    2.94  INTRA
 562 THR   (   3-)  E      CG2  <->   565 ARG   (   6-)  E      NH2  0.45    2.65  INTRA BF
 197 ASN   (  19-)  B      ND2  <->   770 NDG   ( 521-)  B      C7   0.45    2.65  INTRA BF
  17 SER   (  19-)  A      N    <->   773 HOH   ( 535 )  A      O    0.44    2.26  INTRA
 664 LYS   ( 105-)  E      NZ   <->   777 HOH   ( 539 )  E      O    0.43    2.27  INTRA BF
 181 THR   (   3-)  B      CG2  <->   182 ARG   (   4-)  B      NH1  0.43    2.67  INTRA BF
 344 ARG   ( 166-)  B      NE   <->   774 HOH   ( 536 )  B      O    0.42    2.28  INTRA BF
 194 HIS   (  16-)  B      N    <->   774 HOH   ( 550 )  B      O    0.40    2.30  INTRA BL
 756 ASN   ( 312-)  F      ND2  <->   778 HOH   ( 133 )  F      O    0.40    2.30  INTRA
 556 HIS   ( 177-)  D      ND1  <->   774 HOH   ( 545 )  B      O    0.39    2.31  INTRA BL
  46 PHE   (  48-)  A      C    <->   773 HOH   ( 528 )  A      O    0.37    2.43  INTRA
 174 LYS   ( 176-)  A      NZ   <->   773 HOH   ( 517 )  A      O    0.37    2.33  INTRA BF
 203 ARG   (  25-)  B      N    <->   774 HOH   ( 550 )  B      O    0.36    2.34  INTRA BL
 101 ASN   ( 103-)  A      N    <->   773 HOH   ( 529 )  A      O    0.35    2.35  INTRA
 201 ARG   (  23-)  B      NH2  <->   774 HOH   ( 526 )  B      O    0.35    2.35  INTRA BF
And so on for a total of 319 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

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.

 748 ARG   ( 189-)  E      -7.26
 367 ARG   ( 189-)  B      -6.41
  98 ARG   ( 100-)  A      -6.30
 479 ARG   ( 100-)  D      -5.81
 698 LYS   ( 139-)  E      -5.66
 563 ARG   (   4-)  E      -5.49
 182 ARG   (   4-)  B      -5.42
 668 LEU   ( 109-)  E      -5.36
 317 LYS   ( 139-)  B      -5.36
  48 ARG   (  50-)  A      -5.32
  16 GLN   (  18-)  A      -5.28

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. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.

 287 LEU   ( 109-)  B       289 - HIS    111- ( B)         -4.33

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: B

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: C

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: D

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: E

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: F

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 packing 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.

 222 VAL   (  44-)  B   -2.82
 211 ASN   (  33-)  B   -2.65

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Water, ion, and hydrogenbond related checks

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

 773 HOH   ( 527 )  A      O
 774 HOH   ( 523 )  B      O
 774 HOH   ( 535 )  B      O
 777 HOH   ( 524 )  E      O
Bound group on Asn; dont flip   76 ASN  (  78-) A
Bound to:  763 NAG  ( 501-) A
Bound group on Asn; dont flip  116 ASN  ( 118-) A
Bound to:  764 NAG  ( 511-) B
Bound group on Asn; dont flip  197 ASN  (  19-) B
Bound to:  770 NDG  ( 521-) B
Bound group on Asn; dont flip  457 ASN  (  78-) D
Bound to:  765 NAG  ( 501-) D
Bound group on Asn; dont flip  497 ASN  ( 118-) D
Bound to:  766 NAG  ( 511-) E
Bound group on Asn; dont flip  578 ASN  (  19-) E
Bound to:  772 NDG  ( 521-) E

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 favourable 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. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

 288 GLN   ( 110-)  B
 334 GLN   ( 156-)  B
 352 GLN   ( 174-)  B
 666 GLN   ( 107-)  E
 733 GLN   ( 174-)  E
 755 GLN   ( 311-)  F

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.

Waters are not listed by this option.

  36 LYS   (  38-)  A      N
  42 ARG   (  44-)  A      NH2
  43 LEU   (  45-)  A      N
  53 GLU   (  55-)  A      N
  57 ALA   (  59-)  A      N
 109 LYS   ( 111-)  A      N
 119 TRP   ( 121-)  A      NE1
 141 HIS   ( 143-)  A      NE2
 166 TRP   ( 168-)  A      N
 184 ARG   (   6-)  B      NH2
 198 GLY   (  20-)  B      N
 207 ARG   (  29-)  B      NE
 207 ARG   (  29-)  B      NH1
 224 GLU   (  46-)  B      N
 235 ASP   (  57-)  B      N
 249 ARG   (  71-)  B      NH2
 253 VAL   (  75-)  B      N
 264 GLY   (  86-)  B      N
 289 HIS   ( 111-)  B      N
 308 ARG   ( 130-)  B      NH1
 331 TRP   ( 153-)  B      N
 375 ASN   ( 312-)  C      N
 396 ASP   (  17-)  D      N
 417 LYS   (  38-)  D      N
 423 ARG   (  44-)  D      NH2
 424 LEU   (  45-)  D      N
 426 GLU   (  47-)  D      N
 434 GLU   (  55-)  D      N
 438 ALA   (  59-)  D      N
 472 THR   (  93-)  D      OG1
 489 ASP   ( 110-)  D      N
 490 LYS   ( 111-)  D      N
 500 TRP   ( 121-)  D      NE1
 515 VAL   ( 136-)  D      N
 547 TRP   ( 168-)  D      N
 565 ARG   (   6-)  E      NH2
 580 THR   (  21-)  E      OG1
 588 ARG   (  29-)  E      NE
 588 ARG   (  29-)  E      NH1
 596 SER   (  37-)  E      OG
 616 ASP   (  57-)  E      N
 630 ARG   (  71-)  E      NH2
 634 VAL   (  75-)  E      N
 641 ASN   (  82-)  E      ND2
 672 ASN   ( 113-)  E      ND2
 755 GLN   ( 311-)  F      NE2

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

   9 GLU   (  11-)  A      OE1
  64 ASP   (  66-)  A      OD2
 147 HIS   ( 149-)  A      ND1
 211 ASN   (  33-)  B      OD1
 230 GLU   (  52-)  B      OE2
 374 GLN   ( 311-)  C      OE1
 390 GLU   (  11-)  D      OE1
 445 ASP   (  66-)  D      OD2
 480 GLU   ( 101-)  D      OE2
 528 HIS   ( 149-)  D      ND1
 541 ASP   ( 162-)  D      OD1
 569 GLN   (  10-)  E      OE1
 575 HIS   (  16-)  E      NE2
 600 ASP   (  41-)  E      OD1
 611 GLU   (  52-)  E      OE2
 709 ASN   ( 150-)  E      OD1
 715 GLN   ( 156-)  E      OE1

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

  19 GLU   (  21-)  A   H-bonding suggests Gln
  23 ASP   (  25-)  A   H-bonding suggests Asn
  64 ASP   (  66-)  A   H-bonding suggests Asn
 156 GLU   ( 158-)  A   H-bonding suggests Gln
 160 ASP   ( 162-)  A   H-bonding suggests Asn
 230 GLU   (  52-)  B   H-bonding suggests Gln
 400 GLU   (  21-)  D   H-bonding suggests Gln
 445 ASP   (  66-)  D   H-bonding suggests Asn; but Alt-Rotamer
 541 ASP   ( 162-)  D   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.286
  2nd generation packing quality :  -1.481
  Ramachandran plot appearance   :  -3.099 (poor)
  chi-1/chi-2 rotamer normality  :  -4.093 (bad)
  Backbone conformation          :  -0.556

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.869
  Bond angles                    :   1.053
  Omega angle restraints         :   0.409 (tight)
  Side chain planarity           :   0.954
  Improper dihedral distribution :   1.505 (loose)
  B-factor distribution          :   1.290
  Inside/Outside distribution    :   1.033

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.0
  2nd generation packing quality :   0.1
  Ramachandran plot appearance   :  -0.6
  chi-1/chi-2 rotamer normality  :  -1.8
  Backbone conformation          :   0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.869
  Bond angles                    :   1.053
  Omega angle restraints         :   0.409 (tight)
  Side chain planarity           :   0.954
  Improper dihedral distribution :   1.505 (loose)
  B-factor distribution          :   1.290
  Inside/Outside distribution    :   1.033
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.