WHAT IF Check report

This file was created 2012-01-31 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 pdb5tsw.ent

Checks that need to be done early-on in validation

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    =  94.170  B   =  94.560  C    =  95.890
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    =  94.170  B   =  94.560  C    =  95.890
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    =  94.560  B   =  94.170  C    =  95.890
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

 |  0.000000 -1.000000  0.000000|
 |  1.000000  0.000000  0.000000|
 |  0.000000  0.000000  1.000000|

Crystal class of the cell: ORTHORHOMBIC

Crystal class of the conventional CELL: TETRAGONAL

Space group name: P 21 21 21

Bravais type of conventional cell is: P

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 B

All-atom RMS fit for the two chains : 1.005
CA-only RMS fit for the two chains : 0.731

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 B

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 C

All-atom RMS fit for the two chains : 0.961
CA-only RMS fit for the two chains : 0.578

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 C

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 : 0.850
CA-only RMS fit for the two chains : 0.543

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: A and E

All-atom RMS fit for the two chains : 1.020
CA-only RMS fit for the two chains : 0.750

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 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: A and F

All-atom RMS fit for the two chains : 1.096
CA-only RMS fit for the two chains : 0.764

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 F

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.

Administrative problems that can generate validation failures

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.

 149 LEU   ( 157-)  A  -
 298 LEU   ( 157-)  B  -
 447 LEU   ( 157-)  C  -
 596 LEU   ( 157-)  D  -
 745 LEU   ( 157-)  E  -
 894 LEU   ( 157-)  F  -

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'.

   1 SER   (   9-)  A      OG
   2 ASP   (  10-)  A      CG
   2 ASP   (  10-)  A      OD1
   2 ASP   (  10-)  A      OD2
  15 GLU   (  23-)  A      CG
  15 GLU   (  23-)  A      CD
  15 GLU   (  23-)  A      OE1
  15 GLU   (  23-)  A      OE2
  17 GLN   (  25-)  A      CG
  17 GLN   (  25-)  A      CD
  17 GLN   (  25-)  A      OE1
  17 GLN   (  25-)  A      NE2
  79 TYR   (  87-)  A      CG
  79 TYR   (  87-)  A      CD1
  79 TYR   (  87-)  A      CD2
  79 TYR   (  87-)  A      CE1
  79 TYR   (  87-)  A      CE2
  79 TYR   (  87-)  A      CZ
  79 TYR   (  87-)  A      OH
  80 GLN   (  88-)  A      CG
  80 GLN   (  88-)  A      CD
  80 GLN   (  88-)  A      OE1
  80 GLN   (  88-)  A      NE2
  95 ARG   ( 103-)  A      CG
  95 ARG   ( 103-)  A      CD
And so on for a total of 264 lines.

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:

Crystal temperature (K) :298.000

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

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

 483 ARG   (  44-)  D
 632 ARG   (  44-)  E

Warning: Tyrosine convention problem

The tyrosine residues listed in the table below have their chi-2 not between -90.0 and 90.0

  51 TYR   (  59-)  A
 107 TYR   ( 115-)  A
 111 TYR   ( 119-)  A
 133 TYR   ( 141-)  A
 282 TYR   ( 141-)  B
 292 TYR   ( 151-)  B
 409 TYR   ( 119-)  C
 431 TYR   ( 141-)  C
 441 TYR   ( 151-)  C
 580 TYR   ( 141-)  D
 590 TYR   ( 151-)  D
 647 TYR   (  59-)  E
 703 TYR   ( 115-)  E
 729 TYR   ( 141-)  E
 739 TYR   ( 151-)  E
 856 TYR   ( 119-)  F
 878 TYR   ( 141-)  F
 888 TYR   ( 151-)  F

Warning: Phenylalanine convention problem

The phenylalanine residues listed in the table below have their chi-2 not between -90.0 and 90.0.

  48 PHE   (  56-)  A
  56 PHE   (  64-)  A
 136 PHE   ( 144-)  A
 144 PHE   ( 152-)  A
 205 PHE   (  64-)  B
 265 PHE   ( 124-)  B
 293 PHE   ( 152-)  B
 354 PHE   (  64-)  C
 442 PHE   ( 152-)  C
 503 PHE   (  64-)  D
 591 PHE   ( 152-)  D
 652 PHE   (  64-)  E
 740 PHE   ( 152-)  E
 801 PHE   (  64-)  F
 889 PHE   ( 152-)  F

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, or their proton on OD1 instead of OD2.

  37 ASP   (  45-)  A
 135 ASP   ( 143-)  A
 186 ASP   (  45-)  B
 284 ASP   ( 143-)  B
 335 ASP   (  45-)  C
 433 ASP   ( 143-)  C
 484 ASP   (  45-)  D
 582 ASP   ( 143-)  D
 633 ASP   (  45-)  E
 731 ASP   ( 143-)  E
 782 ASP   (  45-)  F
 880 ASP   ( 143-)  F

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  34 GLU   (  42-)  A
  45 GLU   (  53-)  A
 108 GLU   ( 116-)  A
 119 GLU   ( 127-)  A
 257 GLU   ( 116-)  B
 268 GLU   ( 127-)  B
 332 GLU   (  42-)  C
 406 GLU   ( 116-)  C
 417 GLU   ( 127-)  C
 436 GLU   ( 146-)  C
 492 GLU   (  53-)  D
 555 GLU   ( 116-)  D
 704 GLU   ( 116-)  E
 715 GLU   ( 127-)  E
 779 GLU   (  42-)  F
 853 GLU   ( 116-)  F
 864 GLU   ( 127-)  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.

  65 HIS   (  73-)  A      N   -C     1.24   -4.2
  81 THR   (  89-)  A      N   -C     1.11  -11.1
 230 THR   (  89-)  B      N   -C     1.21   -6.2
 252 ALA   ( 111-)  B      N   -C     1.18   -7.5
 379 THR   (  89-)  C      N   -C     1.19   -7.0
 395 THR   ( 105-)  C      N   -C     1.43    4.9
 510 SER   (  71-)  D      N   -C     1.13  -10.0
 528 THR   (  89-)  D      N   -C     1.22   -5.6
 659 SER   (  71-)  E      N   -C     1.16   -8.7
 661 HIS   (  73-)  E      N   -C     1.42    4.5
 673 VAL   (  85-)  E      N   -C     1.05  -13.8
 693 THR   ( 105-)  E      N   -C     1.47    7.3
 826 THR   (  89-)  F      N   -C     1.24   -4.5
 848 ALA   ( 111-)  F      N   -C     1.24   -4.4
 895 LEU   ( 157-)  A      SG  -SG*   2.47   10.7
 895 LEU   ( 157-)  A      SG  -SG*   2.47   10.7
 895 LEU   ( 157-)  A      SG  -SG*   2.47   10.8
 895 LEU   ( 157-)  A      SG  -SG*   2.47   10.8
 657 CYS   (  69-)  E      SG  -SG*   2.24    5.1
 689 CYS   ( 101-)  E      SG  -SG*   2.24    5.1
 689 CYS   ( 101-)  E      SG  -SG*   2.45   10.1
 689 CYS   ( 101-)  E      SG  -SG*   2.45   10.1

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

 |  0.999036  0.000482 -0.000040|
 |  0.000482  0.998220 -0.000011|
 | -0.000040 -0.000011  0.999192|
Proposed new scale matrix

 |  0.010629 -0.000005  0.000000|
 | -0.000005  0.010594  0.000000|
 |  0.000000  0.000000  0.010437|
With corresponding cell

    A    =  94.080  B   =  94.394  C    =  95.809
    Alpha=  90.001  Beta=  90.001  Gamma=  89.945

The CRYST1 cell dimensions

    A    =  94.170  B   =  94.560  C    =  95.890
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 42.402
(Under-)estimated Z-score: 4.799

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.

  70 HIS   (  78-)  A      CG   ND1  CE1 109.64    4.0
  77 VAL   (  85-)  A     -O   -C    N   113.77   -5.8
  77 VAL   (  85-)  A     -C    N    CA  133.47    6.5
  81 THR   (  89-)  A     -C    N    CA  134.99    7.4
 103 ALA   ( 111-)  A     -C    N    CA  129.12    4.1
 246 THR   ( 105-)  B     -O   -C    N   105.67  -10.8
 246 THR   ( 105-)  B     -CA  -C    N   124.66    4.2
 252 ALA   ( 111-)  B     -C    N    CA  136.26    8.1
 305 HIS   (  15-)  C      CG   ND1  CE1 109.68    4.1
 361 SER   (  71-)  C     -O   -C    N   111.65   -7.1
 375 VAL   (  85-)  C     -O   -C    N   115.94   -4.4
 379 THR   (  89-)  C     -O   -C    N   115.63   -4.6
 379 THR   (  89-)  C     -C    N    CA  130.91    5.1
 401 ALA   ( 111-)  C     -C    N    CA  129.33    4.2
 424 ALA   ( 134-)  C      N    CA   C    96.62   -5.2
 476 LEU   (  37-)  D      N    CA   C    99.05   -4.3
 524 VAL   (  85-)  D     -O   -C    N   112.01   -6.9
 524 VAL   (  85-)  D     -C    N    CA  131.00    5.2
 528 THR   (  89-)  D     -C    N    CA  129.83    4.5
 544 THR   ( 105-)  D     -O   -C    N   115.92   -4.4
 550 ALA   ( 111-)  D     -C    N    CA  136.55    8.3
 810 HIS   (  73-)  F      CG   ND1  CE1 109.61    4.0
 822 VAL   (  85-)  F     -C    N    CA  129.04    4.1

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  34 GLU   (  42-)  A
  37 ASP   (  45-)  A
  45 GLU   (  53-)  A
 108 GLU   ( 116-)  A
 119 GLU   ( 127-)  A
 135 ASP   ( 143-)  A
 186 ASP   (  45-)  B
 257 GLU   ( 116-)  B
 268 GLU   ( 127-)  B
 284 ASP   ( 143-)  B
 332 GLU   (  42-)  C
 335 ASP   (  45-)  C
 406 GLU   ( 116-)  C
 417 GLU   ( 127-)  C
 433 ASP   ( 143-)  C
 436 GLU   ( 146-)  C
 483 ARG   (  44-)  D
 484 ASP   (  45-)  D
 492 GLU   (  53-)  D
 555 GLU   ( 116-)  D
 582 ASP   ( 143-)  D
 632 ARG   (  44-)  E
 633 ASP   (  45-)  E
 704 GLU   ( 116-)  E
 715 GLU   ( 127-)  E
 731 ASP   ( 143-)  E
 779 GLU   (  42-)  F
 782 ASP   (  45-)  F
 853 GLU   ( 116-)  F
 864 GLU   ( 127-)  F
 880 ASP   ( 143-)  F

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.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

  62 PRO   (  70-)  A      C      6.6    10.77     0.42
  76 ALA   (  84-)  A      C      8.7    13.45     0.08
 211 PRO   (  70-)  B      C    -10.7   -16.41     0.42
 245 GLU   ( 104-)  B      C    -13.9   -20.12    -0.03
 360 PRO   (  70-)  C      C     12.3    19.86     0.42
 374 ALA   (  84-)  C      C     17.1    26.30     0.08
 394 GLU   ( 104-)  C      C      7.0    10.12    -0.03
 523 ALA   (  84-)  D      C     11.7    17.94     0.08
 543 GLU   ( 104-)  D      C     -8.1   -11.71    -0.03
 660 THR   (  72-)  E      C     -6.6    -9.67     0.30
 692 GLU   ( 104-)  E      C     -7.7   -11.23    -0.03
 807 PRO   (  70-)  F      C     -8.2   -12.59     0.42
The average deviation= 1.451

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.

 424 ALA   ( 134-)  C    5.46
 476 LEU   (  37-)  D    4.48
 276 GLU   ( 135-)  B    4.26
 358 GLY   (  68-)  C    4.19
 514 LEU   (  75-)  D    4.12
  78 SER   (  86-)  A    4.10
 894 LEU   ( 157-)  F    4.01
 525 SER   (  86-)  D    4.01

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 : 1.509

Torsion-related checks

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.

 362 THR   (  72-)  C    -3.5
 660 THR   (  72-)  E    -3.4
 677 THR   (  89-)  E    -2.9
 211 PRO   (  70-)  B    -2.8
 395 THR   ( 105-)  C    -2.8
 525 SER   (  86-)  D    -2.7
 673 VAL   (  85-)  E    -2.6
 227 SER   (  86-)  B    -2.6
 732 PHE   ( 144-)  E    -2.6
 884 SER   ( 147-)  F    -2.5
 659 SER   (  71-)  E    -2.5
 632 ARG   (  44-)  E    -2.5
  71 THR   (  79-)  A    -2.5
 147 ILE   ( 155-)  A    -2.4
 434 PHE   ( 144-)  C    -2.4
  77 VAL   (  85-)  A    -2.4
 888 TYR   ( 151-)  F    -2.4
 296 ILE   ( 155-)  B    -2.4
 210 CYS   (  69-)  B    -2.4
 425 GLU   ( 135-)  C    -2.3
 670 ARG   (  82-)  E    -2.3
 806 CYS   (  69-)  F    -2.3
 693 THR   ( 105-)  E    -2.3
 658 PRO   (  70-)  E    -2.3
 528 THR   (  89-)  D    -2.2
And so on for a total of 71 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.

  26 ASN   (  34-)  A  Poor phi/psi
  29 LEU   (  37-)  A  Poor phi/psi
  37 ASP   (  45-)  A  Poor phi/psi
  38 ASN   (  46-)  A  Poor phi/psi
  62 PRO   (  70-)  A  Poor phi/psi
  63 SER   (  71-)  A  Poor phi/psi
  64 THR   (  72-)  A  Poor phi/psi
  76 ALA   (  84-)  A  Poor phi/psi
  77 VAL   (  85-)  A  Poor phi/psi
  79 TYR   (  87-)  A  Poor phi/psi
  80 GLN   (  88-)  A  Poor phi/psi
  96 GLU   ( 104-)  A  Poor phi/psi
 100 GLY   ( 108-)  A  Poor phi/psi
 101 ALA   ( 109-)  A  Poor phi/psi
 103 ALA   ( 111-)  A  Poor phi/psi
 104 LYS   ( 112-)  A  Poor phi/psi
 139 SER   ( 147-)  A  Poor phi/psi
 175 ASN   (  34-)  B  Poor phi/psi
 180 ASN   (  39-)  B  Poor phi/psi
 186 ASP   (  45-)  B  Poor phi/psi
 187 ASN   (  46-)  B  Poor phi/psi
 201 SER   (  60-)  B  Poor phi/psi
 211 PRO   (  70-)  B  Poor phi/psi
 212 SER   (  71-)  B  Poor phi/psi
 213 THR   (  72-)  B  Poor phi/psi
And so on for a total of 86 lines.

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 : -4.122

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!

  15 GLU   (  23-)  A      0
  22 ASN   (  30-)  A      0
  23 ARG   (  31-)  A      0
  25 ALA   (  33-)  A      0
  26 ASN   (  34-)  A      0
  27 ALA   (  35-)  A      0
  28 LEU   (  36-)  A      0
  29 LEU   (  37-)  A      0
  30 ALA   (  38-)  A      0
  31 ASN   (  39-)  A      0
  36 ARG   (  44-)  A      0
  37 ASP   (  45-)  A      0
  38 ASN   (  46-)  A      0
  39 GLN   (  47-)  A      0
  45 GLU   (  53-)  A      0
  47 LEU   (  55-)  A      0
  51 TYR   (  59-)  A      0
  57 LYS   (  65-)  A      0
  59 GLN   (  67-)  A      0
  63 SER   (  71-)  A      0
  64 THR   (  72-)  A      0
  76 ALA   (  84-)  A      0
  77 VAL   (  85-)  A      0
  78 SER   (  86-)  A      0
  79 TYR   (  87-)  A      0
And so on for a total of 471 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 : 2.172

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]

 241 PRO   ( 100-)  B    0.47 HIGH

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic 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. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. 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). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 508 CYS   (  69-)  D      SG  <->  540 CYS   ( 101-)  D      SG     0.91    2.54  INTRA
 210 CYS   (  69-)  B      SG  <->  242 CYS   ( 101-)  B      SG     0.86    2.59  INTRA BF
 672 ALA   (  84-)  E      O   <->  674 SER   (  86-)  E      N      0.55    2.15  INTRA BF
 508 CYS   (  69-)  D      CB  <->  540 CYS   ( 101-)  D      SG     0.45    2.95  INTRA
  61 CYS   (  69-)  A      O   <->   63 SER   (  71-)  A      N      0.43    2.27  INTRA BF
 436 GLU   ( 146-)  C      CD  <->  511 THR   (  72-)  D      N      0.40    2.70  INTRA BF
 210 CYS   (  69-)  B      CB  <->  242 CYS   ( 101-)  B      SG     0.40    3.00  INTRA BF
 436 GLU   ( 146-)  C      OE1 <->  511 THR   (  72-)  D      N      0.37    2.33  INTRA BF
 229 GLN   (  88-)  B      C   <->  506 GLN   (  67-)  D      OE1    0.36    2.44  INTRA BF
 508 CYS   (  69-)  D      O   <->  510 SER   (  71-)  D      N      0.35    2.35  INTRA BF
 657 CYS   (  69-)  E      O   <->  659 SER   (  71-)  E      N      0.32    2.38  INTRA BF
 210 CYS   (  69-)  B      O   <->  212 SER   (  71-)  B      N      0.27    2.43  INTRA BF
 658 PRO   (  70-)  E      O   <->  659 SER   (  71-)  E      C      0.26    2.34  INTRA BF
  37 ASP   (  45-)  A      CG  <->  123 ARG   ( 131-)  A      NH2    0.24    2.86  INTRA
 491 ILE   (  52-)  D      CG1 <->  492 GLU   (  53-)  D      N      0.23    2.77  INTRA
 820 ILE   (  83-)  F      CD1 <->  824 TYR   (  87-)  F      CA     0.21    2.99  INTRA BF
 752 HIS   (  15-)  F      ND1 <->  796 TYR   (  59-)  F      OH     0.21    2.49  INTRA BL
 449 ASP   (  10-)  D      C   <->  478 ASN   (  39-)  D      ND2    0.20    2.90  INTRA
 224 ILE   (  83-)  B      CD1 <->  228 TYR   (  87-)  B      CA     0.20    3.00  INTRA BF
 436 GLU   ( 146-)  C      OE1 <->  511 THR   (  72-)  D      CA     0.19    2.61  INTRA
 699 ALA   ( 111-)  E      CB  <->  905 HOH   (1543 )  E      O      0.19    2.61  INTRA BF
 521 ARG   (  82-)  D      NH2 <->  569 ASP   ( 130-)  D      OD2    0.19    2.51  INTRA BL
 363 HIS   (  73-)  C      CE1 <->  392 GLN   ( 102-)  C      O      0.18    2.62  INTRA BF
 140 GLY   ( 148-)  A      O   <->  385 SER   (  95-)  C      N      0.18    2.52  INTRA BL
 660 THR   (  72-)  E      O   <->  905 HOH   ( 302 )  E      O      0.18    2.22  INTRA
And so on for a total of 162 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.

 609 GLN   (  21-)  E      -7.37
 321 ARG   (  31-)  C      -7.35
 172 ARG   (  31-)  B      -7.25
 619 ARG   (  31-)  E      -7.06
 690 GLN   ( 102-)  E      -6.86
  13 GLN   (  21-)  A      -6.80
 392 GLN   ( 102-)  C      -6.77
 758 GLN   (  21-)  F      -6.75
 162 GLN   (  21-)  B      -6.73
 470 ARG   (  31-)  D      -6.73
 311 GLN   (  21-)  C      -6.71
  23 ARG   (  31-)  A      -6.53
 460 GLN   (  21-)  D      -6.47
  94 GLN   ( 102-)  A      -6.36
 541 GLN   ( 102-)  D      -6.35
 839 GLN   ( 102-)  F      -6.34
 243 GLN   ( 102-)  B      -6.13
 768 ARG   (  31-)  F      -6.06
 804 GLN   (  67-)  F      -5.94
 655 GLN   (  67-)  E      -5.55
  59 GLN   (  67-)  A      -5.46
  96 GLU   ( 104-)  A      -5.40
 208 GLN   (  67-)  B      -5.23
 193 ILE   (  52-)  B      -5.12
 822 VAL   (  85-)  F      -5.10
 544 THR   ( 105-)  D      -5.10
 842 THR   ( 105-)  F      -5.09
 789 ILE   (  52-)  F      -5.09
 693 THR   ( 105-)  E      -5.09
 395 THR   ( 105-)  C      -5.09
  77 VAL   (  85-)  A      -5.03

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.

  96 GLU   ( 104-)  A        98 - PRO    106- ( A)         -4.80

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.

 526 TYR   (  87-)  D   -3.14
 824 TYR   (  87-)  F   -3.04
 676 GLN   (  88-)  E   -2.95
 527 GLN   (  88-)  D   -2.85
 840 ARG   ( 103-)  F   -2.76
  95 ARG   ( 103-)  A   -2.74
 542 ARG   ( 103-)  D   -2.73
 810 HIS   (  73-)  F   -2.73
 377 TYR   (  87-)  C   -2.72
 244 ARG   ( 103-)  B   -2.71
 692 GLU   ( 104-)  E   -2.68
 549 GLU   ( 110-)  D   -2.67
  79 TYR   (  87-)  A   -2.66
 825 GLN   (  88-)  F   -2.64
 543 GLU   ( 104-)  D   -2.64
 691 ARG   ( 103-)  E   -2.64
 251 GLU   ( 110-)  B   -2.63
 393 ARG   ( 103-)  C   -2.62
 546 GLU   ( 107-)  D   -2.60
  80 GLN   (  88-)  A   -2.59
 675 TYR   (  87-)  E   -2.55
 228 TYR   (  87-)  B   -2.54
  17 GLN   (  25-)  A   -2.54
 661 HIS   (  73-)  E   -2.54
 725 ASN   ( 137-)  E   -2.52
 245 GLU   ( 104-)  B   -2.52

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.

 320 ASN   (  30-)  C     -  323 ALA   (  33-)  C        -1.60

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

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. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

 901 HOH   ( 164 )  A      O     -0.31   71.77   12.93
 901 HOH   ( 197 )  A      O      2.35   66.59   15.73
 901 HOH   ( 208 )  A      O    -19.80   45.24   19.64
 902 HOH   ( 218 )  B      O    -26.33   32.67   14.10
 902 HOH   ( 219 )  B      O    -24.59   38.63   10.32
 903 HOH   ( 201 )  C      O     -5.61   30.13   23.96
 904 HOH   ( 167 )  D      O    -18.91    5.04   25.33
 905 HOH   ( 239 )  E      O    -21.86   -0.91   -1.76
 905 HOH   (1537 )  E      O    -21.20   -2.56    2.27
 906 HOH   ( 304 )  F      O     17.99    1.22  -10.08
 906 HOH   (1534 )  F      O     -5.47  -21.81   -8.55

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.

 901 HOH   ( 167 )  A      O
 901 HOH   ( 173 )  A      O
 901 HOH   ( 197 )  A      O
 901 HOH   ( 204 )  A      O
 901 HOH   ( 205 )  A      O
 901 HOH   ( 207 )  A      O
 901 HOH   ( 211 )  A      O
 902 HOH   ( 159 )  B      O
 902 HOH   ( 187 )  B      O
 902 HOH   ( 203 )  B      O
 902 HOH   ( 221 )  B      O
 903 HOH   ( 166 )  C      O
 903 HOH   ( 168 )  C      O
 903 HOH   ( 209 )  C      O
 903 HOH   ( 212 )  C      O
 904 HOH   ( 167 )  D      O
 904 HOH   ( 191 )  D      O
 904 HOH   ( 200 )  D      O
 904 HOH   ( 202 )  D      O
 905 HOH   ( 167 )  E      O
 905 HOH   ( 216 )  E      O
 905 HOH   ( 219 )  E      O
 905 HOH   (1541 )  E      O
 905 HOH   (1543 )  E      O
 906 HOH   ( 222 )  F      O
 906 HOH   ( 303 )  F      O
 906 HOH   ( 304 )  F      O
 906 HOH   (1532 )  F      O

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.

  65 HIS   (  73-)  A
  70 HIS   (  78-)  A
 460 GLN   (  21-)  D
 517 HIS   (  78-)  D
 661 HIS   (  73-)  E
 784 GLN   (  47-)  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.

  17 GLN   (  25-)  A      N
  24 ARG   (  32-)  A      N
  39 GLN   (  47-)  A      N
  44 ILE   (  52-)  A      N
  55 LEU   (  63-)  A      N
  61 CYS   (  69-)  A      N
  78 SER   (  86-)  A      N
  80 GLN   (  88-)  A      N
  81 THR   (  89-)  A      N
  89 ILE   (  97-)  A      N
  97 THR   ( 105-)  A      N
 104 LYS   ( 112-)  A      N
 130 ARG   ( 138-)  A      N
 138 GLU   ( 146-)  A      N
 139 SER   ( 147-)  A      OG
 140 GLY   ( 148-)  A      N
 141 GLN   ( 149-)  A      NE2
 173 ARG   (  32-)  B      N
 182 VAL   (  41-)  B      N
 193 ILE   (  52-)  B      N
 204 LEU   (  63-)  B      N
 215 VAL   (  74-)  B      N
 238 ILE   (  97-)  B      N
 242 CYS   ( 101-)  B      N
 253 LYS   ( 112-)  B      N
And so on for a total of 77 lines.

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.

 219 HIS   (  78-)  B      ND1
 368 HIS   (  78-)  C      ND1
 517 HIS   (  78-)  D      ND1
 541 GLN   ( 102-)  D      OE1
 666 HIS   (  78-)  E      ND1
 815 HIS   (  78-)  F      ND1

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.

 332 GLU   (  42-)  C   H-bonding suggests Gln
 425 GLU   ( 135-)  C   H-bonding suggests Gln
 867 ASP   ( 130-)  F   H-bonding suggests Asn; but Alt-Rotamer

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 :  -0.403
  2nd generation packing quality :  -2.717
  Ramachandran plot appearance   :  -2.472
  chi-1/chi-2 rotamer normality  :  -4.122 (bad)
  Backbone conformation          :  -0.486

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.602 (tight)
  Bond angles                    :   0.858
  Omega angle restraints         :   0.395 (tight)
  Side chain planarity           :   0.559 (tight)
  Improper dihedral distribution :   1.376
  B-factor distribution          :   1.228
  Inside/Outside distribution    :   0.975

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 : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.6
  2nd generation packing quality :  -1.2
  Ramachandran plot appearance   :  -0.4
  chi-1/chi-2 rotamer normality  :  -2.1
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.602 (tight)
  Bond angles                    :   0.858
  Omega angle restraints         :   0.395 (tight)
  Side chain planarity           :   0.559 (tight)
  Improper dihedral distribution :   1.376
  B-factor distribution          :   1.228
  Inside/Outside distribution    :   0.975
==============

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.