WHAT IF Check report

This file was created 2011-12-15 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 pdb3gxi.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    = 110.050  B   =  91.713  C    = 152.283
    Alpha=  90.000  Beta= 111.130  Gamma=  90.000

Dimensions of a reduced cell

    A    =  91.713  B   = 110.050  C    = 152.283
    Alpha= 111.130  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    = 110.050  B   = 284.089  C    =  91.713
    Alpha=  90.000  Beta=  90.000  Gamma=  89.948

Transformation to conventional cell

 |  1.000000  0.000000  0.000000|
 |  1.000000  0.000000  2.000000|
 |  0.000000 -1.000000  0.000000|

Crystal class of the cell: MONOCLINIC

Crystal class of the conventional CELL: ORTHORHOMBIC

Space group name: P 1 21 1

Bravais type of conventional cell is: 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 B

All-atom RMS fit for the two chains : 1.303
CA-only RMS fit for the two chains : 0.835

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 : 0.483
CA-only RMS fit for the two chains : 0.148

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 : 1.287
CA-only RMS fit for the two chains : 0.859

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 C

All-atom RMS fit for the two chains : 1.289
CA-only RMS fit for the two chains : 0.810

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 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: B and D

All-atom RMS fit for the two chains : 0.476
CA-only RMS fit for the two chains : 0.151

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 D

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.

Warning: Chain identifier inconsistency

WHAT IF believes that certain residue(s) have the wrong chain identifier. It has corrected these chain identifiers as indicated in the table. In this table the residues (ligands, drugs, lipids, ions, sugars, etc) that got their chain identifier corrected are listed with the new chain identifier that is used throughout this validation report. WHAT IF does not care about the chain identifiers of water molecules.

2036 PO4   ( 506-)  B  C

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.

1997 PO4   ( 499-)  A  -
1998 PO4   ( 500-)  A  -
1999 PO4   ( 501-)  A  -
2000 PO4   ( 502-)  A  -
2001 PO4   ( 503-)  A  -
2002 PO4   ( 504-)  A  -
2003 PO4   ( 505-)  A  -
2004 PO4   ( 506-)  A  -
2005 PO4   ( 507-)  A  -
2006 PO4   ( 508-)  A  -
2007 PO4   ( 509-)  A  -
2008 PO4   ( 510-)  A  -
2009 PO4   ( 511-)  A  -
2010 PO4   ( 512-)  A  -
2011 PO4   ( 513-)  A  -
2012 PO4   ( 514-)  A  -
2013 PO4   ( 515-)  A  -
2014 PO4   ( 516-)  A  -
2015 PO4   ( 517-)  A  -
2016 PO4   ( 499-)  B  -
2017 PO4   ( 500-)  B  -
2018 PO4   ( 501-)  B  -
2019 PO4   ( 502-)  B  -
2020 PO4   ( 503-)  B  -
2021 PO4   ( 504-)  B  -
And so on for a total of 63 lines.

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

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

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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while 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:


Number of TLS groups mentione in PDB file header: 0

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

Nomenclature related problems

Warning: Tyrosine convention problem

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

  11 TYR   (  11-)  A
  22 TYR   (  22-)  A
 108 TYR   ( 108-)  A
 116 TYR   ( 116-)  A
 135 TYR   ( 135-)  A
 205 TYR   ( 205-)  A
 212 TYR   ( 212-)  A
 304 TYR   ( 304-)  A
 313 TYR   ( 313-)  A
 373 TYR   ( 373-)  A
 412 TYR   ( 412-)  A
 418 TYR   ( 418-)  A
 487 TYR   ( 487-)  A
 508 TYR   (  11-)  B
 519 TYR   (  22-)  B
 605 TYR   ( 108-)  B
 613 TYR   ( 116-)  B
 630 TYR   ( 133-)  B
 632 TYR   ( 135-)  B
 709 TYR   ( 212-)  B
 801 TYR   ( 304-)  B
 870 TYR   ( 373-)  B
 909 TYR   ( 412-)  B
 915 TYR   ( 418-)  B
 984 TYR   ( 487-)  B
And so on for a total of 51 lines.

Warning: Phenylalanine convention problem

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

  26 PHE   (  26-)  A
  75 PHE   (  75-)  A
 109 PHE   ( 109-)  A
 128 PHE   ( 128-)  A
 142 PHE   ( 142-)  A
 147 PHE   ( 147-)  A
 246 PHE   ( 246-)  A
 331 PHE   ( 331-)  A
 337 PHE   ( 337-)  A
 411 PHE   ( 411-)  A
 417 PHE   ( 417-)  A
 426 PHE   ( 426-)  A
 523 PHE   (  26-)  B
 572 PHE   (  75-)  B
 606 PHE   ( 109-)  B
 625 PHE   ( 128-)  B
 639 PHE   ( 142-)  B
 644 PHE   ( 147-)  B
 828 PHE   ( 331-)  B
 908 PHE   ( 411-)  B
 914 PHE   ( 417-)  B
 923 PHE   ( 426-)  B
1020 PHE   (  26-)  C
1069 PHE   (  75-)  C
1103 PHE   ( 109-)  C
1122 PHE   ( 128-)  C
1136 PHE   ( 142-)  C
1141 PHE   ( 147-)  C
1240 PHE   ( 246-)  C
1310 PHE   ( 316-)  C
1325 PHE   ( 331-)  C
1341 PHE   ( 347-)  C
1391 PHE   ( 397-)  C
1405 PHE   ( 411-)  C
1420 PHE   ( 426-)  C
1517 PHE   (  26-)  D
1522 PHE   (  31-)  D
1566 PHE   (  75-)  D
1600 PHE   ( 109-)  D
1619 PHE   ( 128-)  D
1633 PHE   ( 142-)  D
1638 PHE   ( 147-)  D
1822 PHE   ( 331-)  D
1888 PHE   ( 397-)  D
1902 PHE   ( 411-)  D
1908 PHE   ( 417-)  D
1917 PHE   ( 426-)  D

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.

 153 ASP   ( 153-)  A
 443 ASP   ( 443-)  A
 650 ASP   ( 153-)  B
1147 ASP   ( 153-)  C
1644 ASP   ( 153-)  D
1806 ASP   ( 315-)  D

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.

 151 GLU   ( 151-)  A
 388 GLU   ( 388-)  A
 547 GLU   (  50-)  B
 609 GLU   ( 112-)  B
 648 GLU   ( 151-)  B
 797 GLU   ( 300-)  B
1541 GLU   (  50-)  D
1563 GLU   (  72-)  D
1642 GLU   ( 151-)  D
1840 GLU   ( 349-)  D

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.

 615 ILE   ( 118-)  B      CG1  CD1   1.35   -4.1
1051 GLN   (  57-)  C      CB   CG    1.65    4.3

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

 |  0.995977 -0.000503 -0.000303|
 | -0.000503  0.996026  0.000041|
 | -0.000303  0.000041  0.996664|
Proposed new scale matrix

 |  0.009125  0.000004  0.003527|
 |  0.000006  0.010948  0.000000|
 |  0.000002  0.000000  0.007064|
With corresponding cell

    A    = 109.605  B   =  91.345  C    = 151.795
    Alpha=  89.981  Beta= 111.148  Gamma=  90.057

The CRYST1 cell dimensions

    A    = 110.050  B   =  91.713  C    = 152.283
    Alpha=  90.000  Beta= 111.130  Gamma=  90.000

Variance: 981.115
(Under-)estimated Z-score: 23.085

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.

  44 ARG   (  44-)  A      CG   CD   NE  118.33    4.6
 162 HIS   ( 162-)  A      CG   ND1  CE1 109.80    4.2
 255 HIS   ( 255-)  A      CG   ND1  CE1 109.64    4.0
 306 HIS   ( 306-)  A      CG   ND1  CE1 109.64    4.0
 328 HIS   ( 328-)  A      CG   ND1  CE1 109.70    4.1
 343 VAL   ( 343-)  A      C    CA   CB  118.77    4.6
 433 ARG   ( 433-)  A      CG   CD   NE   99.13   -6.7
 451 HIS   ( 451-)  A      CG   ND1  CE1 109.66    4.1
 541 ARG   (  44-)  B      CB   CG   CD  104.45   -4.8
 559 GLY   (  62-)  B      N    CA   C   129.84    6.0
 659 HIS   ( 162-)  B      CG   ND1  CE1 109.64    4.0
 770 HIS   ( 273-)  B      CG   ND1  CE1 109.81    4.2
 783 LEU   ( 286-)  B      CA   CB   CG  132.92    4.7
 787 HIS   ( 290-)  B      CG   ND1  CE1 109.71    4.1
 878 TRP   ( 381-)  B      C    CA   CB  118.26    4.3
 992 HIS   ( 495-)  B      CG   ND1  CE1 109.78    4.2
1038 ARG   (  44-)  C      CB   CG   CD  102.28   -5.9
1067 GLN   (  73-)  C      CA   CB   CG  123.17    4.5
1156 HIS   ( 162-)  C      CG   ND1  CE1 109.76    4.2
1279 ARG   ( 285-)  C      CB   CG   CD  105.11   -4.5
1280 LEU   ( 286-)  C      CA   CB   CG  133.11    4.8
1300 HIS   ( 306-)  C      CG   ND1  CE1 109.60    4.0
1338 GLY   ( 344-)  C     -C    N    CA  127.79    4.2
1416 HIS   ( 422-)  C      CG   ND1  CE1 109.85    4.2
1427 ARG   ( 433-)  C      CG   CD   NE  101.07   -5.5
1535 ARG   (  44-)  D      CB   CG   CD  105.93   -4.1
1764 HIS   ( 273-)  D      CG   ND1  CE1 109.80    4.2
1797 HIS   ( 306-)  D      CG   ND1  CE1 109.61    4.0
1820 ARG   ( 329-)  D      CG   CD   NE  117.55    4.1
1837 LYS   ( 346-)  D     -C    N    CA  133.45    6.5
1837 LYS   ( 346-)  D      N    CA   CB  117.64    4.2
1838 PHE   ( 347-)  D     -C    N    CA  129.51    4.3
1838 PHE   ( 347-)  D      N    CA   C    91.09   -7.2
1844 ARG   ( 353-)  D      CB   CG   CD  104.46   -4.8
1844 ARG   ( 353-)  D      CG   CD   NE  117.39    4.1
1986 HIS   ( 495-)  D      CG   ND1  CE1 109.64    4.0

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.

 151 GLU   ( 151-)  A
 153 ASP   ( 153-)  A
 388 GLU   ( 388-)  A
 443 ASP   ( 443-)  A
 547 GLU   (  50-)  B
 609 GLU   ( 112-)  B
 648 GLU   ( 151-)  B
 650 ASP   ( 153-)  B
 797 GLU   ( 300-)  B
1147 ASP   ( 153-)  C
1541 GLU   (  50-)  D
1563 GLU   (  72-)  D
1642 GLU   ( 151-)  D
1644 ASP   ( 153-)  D
1806 ASP   ( 315-)  D
1840 GLU   ( 349-)  D

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.

 343 VAL   ( 343-)  A      CA    -6.2    24.18    33.23
1063 LEU   (  69-)  C      CG     9.0   -17.25   -33.01
The average deviation= 1.141

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.

1838 PHE   ( 347-)  D    7.76
 559 GLY   (  62-)  B    5.84
1837 LYS   ( 346-)  D    4.10

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.

1838 PHE   ( 347-)  D    -3.8
 560 THR   (  63-)  B    -3.6
1476 THR   ( 482-)  C    -2.7
 979 THR   ( 482-)  B    -2.7
1973 THR   ( 482-)  D    -2.7
1961 LEU   ( 470-)  D    -2.6
 842 SER   ( 345-)  B    -2.6
 482 THR   ( 482-)  A    -2.6
 814 LEU   ( 317-)  B    -2.6
1391 PHE   ( 397-)  C    -2.5
 406 ILE   ( 406-)  A    -2.4
1496 ILE   (   5-)  D    -2.4
1837 LYS   ( 346-)  D    -2.3
 130 ILE   ( 130-)  A    -2.3
 556 ASN   (  59-)  B    -2.3
1554 THR   (  63-)  D    -2.2
  13 SER   (  13-)  A    -2.1
1338 GLY   ( 344-)  C    -2.1
 967 LEU   ( 470-)  B    -2.1
 397 PHE   ( 397-)  A    -2.1
 845 TRP   ( 348-)  B    -2.1
1940 LEU   ( 449-)  D    -2.1
 647 PRO   ( 150-)  B    -2.1
1441 VAL   ( 447-)  C    -2.0
1889 VAL   ( 398-)  D    -2.0
 895 VAL   ( 398-)  B    -2.0
 816 PRO   ( 319-)  B    -2.0
1275 LEU   ( 281-)  C    -2.0

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.

   4 CYS   (   4-)  A  omega poor
  19 ASN   (  19-)  A  Poor phi/psi
  22 TYR   (  22-)  A  omega poor
  55 PRO   (  55-)  A  omega poor
  56 ILE   (  56-)  A  omega poor
  75 PHE   (  75-)  A  Poor phi/psi
 108 TYR   ( 108-)  A  omega poor
 124 ALA   ( 124-)  A  Poor phi/psi
 126 CYS   ( 126-)  A  Poor phi/psi
 133 TYR   ( 133-)  A  omega poor
 140 ASP   ( 140-)  A  Poor phi/psi
 144 LEU   ( 144-)  A  Poor phi/psi
 192 ASN   ( 192-)  A  Poor phi/psi
 224 LYS   ( 224-)  A  Poor phi/psi
 233 GLU   ( 233-)  A  Poor phi/psi
 281 LEU   ( 281-)  A  Poor phi/psi
 282 ASP   ( 282-)  A  Poor phi/psi
 288 LEU   ( 288-)  A  PRO omega poor
 295 VAL   ( 295-)  A  omega poor
 343 VAL   ( 343-)  A  omega poor
 373 TYR   ( 373-)  A  omega poor
 374 HIS   ( 374-)  A  Poor phi/psi
 378 TRP   ( 378-)  A  omega poor
 379 THR   ( 379-)  A  omega poor
 381 TRP   ( 381-)  A  Poor phi/psi
And so on for a total of 129 lines.

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

 230 VAL   ( 230-)  A    0.33
1224 VAL   ( 230-)  C    0.33
1857 SER   ( 366-)  D    0.36
 863 SER   ( 366-)  B    0.36
1721 VAL   ( 230-)  D    0.38
1358 SER   ( 364-)  C    0.39

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!

   6 PRO   (   6-)  A      0
   9 PHE   (   9-)  A      0
  11 TYR   (  11-)  A      0
  12 SER   (  12-)  A      0
  18 CYS   (  18-)  A      0
  22 TYR   (  22-)  A      0
  23 CYS   (  23-)  A      0
  24 ASP   (  24-)  A      0
  26 PHE   (  26-)  A      0
  29 PRO   (  29-)  A      0
  33 ALA   (  33-)  A      0
  34 LEU   (  34-)  A      0
  45 SER   (  45-)  A      0
  48 ARG   (  48-)  A      0
  49 MET   (  49-)  A      0
  57 GLN   (  57-)  A      0
  59 ASN   (  59-)  A      0
  60 HIS   (  60-)  A      0
  65 LEU   (  65-)  A      0
  70 GLN   (  70-)  A      0
  73 GLN   (  73-)  A      0
  75 PHE   (  75-)  A      0
  79 LYS   (  79-)  A      0
  81 PHE   (  81-)  A      0
  85 MET   (  85-)  A      0
And so on for a total of 864 lines.

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]

 253 PRO   ( 253-)  A    0.17 LOW
 898 PRO   ( 401-)  B    0.46 HIGH
1463 PRO   ( 469-)  C    0.14 LOW
1744 PRO   ( 253-)  D    0.16 LOW
1892 PRO   ( 401-)  D    0.47 HIGH
1919 PRO   ( 428-)  D    0.18 LOW

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].

  55 PRO   (  55-)  A   -59.0 half-chair C-beta/C-alpha (-54 degrees)
 178 PRO   ( 178-)  A   -42.9 envelop C-alpha (-36 degrees)
 182 PRO   ( 182-)  A   105.3 envelop C-beta (108 degrees)
 201 PRO   ( 201-)  A   107.8 envelop C-beta (108 degrees)
 529 PRO   (  32-)  B   -61.3 half-chair C-beta/C-alpha (-54 degrees)
 675 PRO   ( 178-)  B   -65.0 envelop C-beta (-72 degrees)
 733 PRO   ( 236-)  B  -112.3 envelop C-gamma (-108 degrees)
 750 PRO   ( 253-)  B  -115.7 envelop C-gamma (-108 degrees)
 816 PRO   ( 319-)  B    -8.9 envelop N (0 degrees)
1000 PRO   (   6-)  C   -65.7 envelop C-beta (-72 degrees)
1049 PRO   (  55-)  C   -47.5 half-chair C-beta/C-alpha (-54 degrees)
1172 PRO   ( 178-)  C   -35.1 envelop C-alpha (-36 degrees)
1176 PRO   ( 182-)  C   108.8 envelop C-beta (108 degrees)
1230 PRO   ( 236-)  C  -112.5 envelop C-gamma (-108 degrees)
1669 PRO   ( 178-)  D   -52.1 half-chair C-beta/C-alpha (-54 degrees)
1790 PRO   ( 299-)  D  -112.7 envelop C-gamma (-108 degrees)
1810 PRO   ( 319-)  D   -28.6 envelop C-alpha (-36 degrees)

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.

 623 CYS   ( 126-)  B      SG  <-> 2061 HOH   ( 757 )  B      O      1.12    1.88  INTRA
1373 THR   ( 379-)  C      CB  <-> 2062 HOH   ( 766 )  C      O      1.04    1.76  INTRA
  44 ARG   (  44-)  A      NE  <-> 2060 HOH   ( 763 )  A      O      0.91    1.79  INTRA
  44 ARG   (  44-)  A      NH1 <-> 2000 PO4   ( 502-)  A      P      0.86    2.44  INTRA BF
  44 ARG   (  44-)  A      NH1 <-> 2000 PO4   ( 502-)  A      O2     0.83    1.87  INTRA BF
  44 ARG   (  44-)  A      NH2 <-> 2060 HOH   ( 763 )  A      O      0.75    1.95  INTRA
  44 ARG   (  44-)  A      CZ  <-> 2060 HOH   ( 763 )  A      O      0.69    2.11  INTRA
 759 ARG   ( 262-)  B      NE  <-> 2061 HOH   (1056 )  B      O      0.67    2.03  INTRA
1201 GLN   ( 207-)  C      NE2 <-> 1257 ASP   ( 263-)  C      OD1    0.64    2.06  INTRA
 207 GLN   ( 207-)  A      NE2 <->  263 ASP   ( 263-)  A      OD1    0.62    2.08  INTRA
 704 GLN   ( 207-)  B      NE2 <->  760 ASP   ( 263-)  B      OD1    0.54    2.16  INTRA BL
1698 GLN   ( 207-)  D      NE2 <-> 1754 ASP   ( 263-)  D      OD1    0.53    2.17  INTRA BL
 262 ARG   ( 262-)  A      NH1 <-> 2060 HOH   (1321 )  A      O      0.53    2.17  INTRA BF
 262 ARG   ( 262-)  A      NE  <-> 2060 HOH   (1178 )  A      O      0.53    2.17  INTRA BF
 544 ARG   (  47-)  B      NE  <-> 2061 HOH   (1170 )  B      O      0.47    2.23  INTRA
 508 TYR   (  11-)  B      CE1 <-> 2061 HOH   ( 734 )  B      O      0.44    2.36  INTRA BF
 536 ARG   (  39-)  B      CD  <-> 2061 HOH   ( 712 )  B      O      0.42    2.38  INTRA
 206 HIS   ( 206-)  A      NE2 <->  255 HIS   ( 255-)  A      NE2    0.40    2.60  INTRA
1697 HIS   ( 206-)  D      NE2 <-> 1746 HIS   ( 255-)  D      NE2    0.39    2.61  INTRA BL
1038 ARG   (  44-)  C      CD  <-> 2031 PO4   ( 501-)  C      O1     0.38    2.42  INTRA
1051 GLN   (  57-)  C      CG  <-> 1052 ALA   (  58-)  C      N      0.37    2.63  INTRA
1491 GLN   ( 497-)  C      NE2 <-> 2062 HOH   (1131 )  C      O      0.36    2.34  INTRA
1753 ARG   ( 262-)  D      NH1 <-> 2063 HOH   ( 683 )  D      O      0.36    2.34  INTRA BF
1200 HIS   ( 206-)  C      NE2 <-> 1249 HIS   ( 255-)  C      NE2    0.36    2.64  INTRA
 871 HIS   ( 374-)  B      ND1 <-> 2061 HOH   (1419 )  B      O      0.35    2.35  INTRA
And so on for a total of 366 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

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.

 169 GLN   ( 169-)  A      -7.05
 666 GLN   ( 169-)  B      -6.75
1932 LYS   ( 441-)  D      -6.68
 938 LYS   ( 441-)  B      -6.67
 441 LYS   ( 441-)  A      -6.59
1435 LYS   ( 441-)  C      -6.59
1163 GLN   ( 169-)  C      -6.43
1660 GLN   ( 169-)  D      -6.29
1691 GLN   ( 200-)  D      -6.12
1194 GLN   ( 200-)  C      -6.04
 697 GLN   ( 200-)  B      -5.98
 200 GLN   ( 200-)  A      -5.86
1841 GLN   ( 350-)  D      -5.62
 759 ARG   ( 262-)  B      -5.55
1025 PHE   (  31-)  C      -5.54
 847 GLN   ( 350-)  B      -5.50
 262 ARG   ( 262-)  A      -5.50
1256 ARG   ( 262-)  C      -5.49
1987 ARG   ( 496-)  D      -5.48
 993 ARG   ( 496-)  B      -5.47
1753 ARG   ( 262-)  D      -5.44
1522 PHE   (  31-)  D      -5.43
1264 ASN   ( 270-)  C      -5.34
  44 ARG   (  44-)  A      -5.25
 496 ARG   ( 496-)  A      -5.24
 528 PHE   (  31-)  B      -5.22
  31 PHE   (  31-)  A      -5.18
1551 HIS   (  60-)  D      -5.16
 814 LEU   ( 317-)  B      -5.13
 557 HIS   (  60-)  B      -5.13
1490 ARG   ( 496-)  C      -5.12
1038 ARG   (  44-)  C      -5.10
 541 ARG   (  44-)  B      -5.08
1535 ARG   (  44-)  D      -5.06
 531 LEU   (  34-)  B      -5.01
 350 GLN   ( 350-)  A      -5.01

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.

1550 ASN   (  59-)  D      1552 - THR     61- ( D)         -4.68

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

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.

  62 GLY   (  62-)  A   -2.80
1837 LYS   ( 346-)  D   -2.71
1661 ARG   ( 170-)  D   -2.61
 406 ILE   ( 406-)  A   -2.60
 476 ALA   ( 476-)  A   -2.58
 170 ARG   ( 170-)  A   -2.52
1470 ALA   ( 476-)  C   -2.52

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

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.

2060 HOH   ( 768 )  A      O    -12.99  -66.92   34.17
2062 HOH   ( 782 )  C      O     -8.73   27.64   66.14

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.

2060 HOH   (1063 )  A      O
2060 HOH   (1092 )  A      O
2061 HOH   ( 719 )  B      O
2061 HOH   ( 720 )  B      O
2061 HOH   ( 901 )  B      O
2061 HOH   (1210 )  B      O
2062 HOH   ( 860 )  C      O
2062 HOH   (1043 )  C      O
2062 HOH   (1114 )  C      O
2063 HOH   ( 699 )  D      O
2063 HOH   ( 994 )  D      O
2063 HOH   (1100 )  D      O
Bound group on Asn; dont flip   19 ASN  (  19-) A
Bound to: 1989 NAG  ( 498-) A
Bound group on Asn; dont flip  516 ASN  (  19-) B
Bound to: 1990 NAG  ( 498-) B
Bound group on Asn; dont flip 1013 ASN  (  19-) C
Bound to: 1991 NAG  ( 498-) C
Bound group on Asn; dont flip 1510 ASN  (  19-) D
Bound to: 1992 NAG  ( 498-) D

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.

  57 GLN   (  57-)  A
 274 HIS   ( 274-)  A
 328 HIS   ( 328-)  A
 557 HIS   (  60-)  B
 659 HIS   ( 162-)  B
 704 GLN   ( 207-)  B
 781 GLN   ( 284-)  B
 825 HIS   ( 328-)  B
 859 GLN   ( 362-)  B
 893 ASN   ( 396-)  B
1551 HIS   (  60-)  D

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.

  12 SER   (  12-)  A      OG
  43 THR   (  43-)  A      OG1
  44 ARG   (  44-)  A      NH1
 131 ARG   ( 131-)  A      N
 141 ASP   ( 141-)  A      N
 170 ARG   ( 170-)  A      NE
 184 TRP   ( 184-)  A      N
 194 LYS   ( 194-)  A      N
 205 TYR   ( 205-)  A      N
 211 ARG   ( 211-)  A      NE
 211 ARG   ( 211-)  A      NH1
 228 TRP   ( 228-)  A      NE1
 233 GLU   ( 233-)  A      N
 246 PHE   ( 246-)  A      N
 322 ALA   ( 322-)  A      N
 348 TRP   ( 348-)  A      N
 353 ARG   ( 353-)  A      NE
 366 SER   ( 366-)  A      OG
 377 GLY   ( 377-)  A      N
 382 ASN   ( 382-)  A      ND2
 384 ALA   ( 384-)  A      N
 410 THR   ( 410-)  A      OG1
 414 GLN   ( 414-)  A      NE2
 440 GLN   ( 440-)  A      N
 442 ASN   ( 442-)  A      ND2
And so on for a total of 108 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.

  87 ASP   (  87-)  A      OD1
 112 GLU   ( 112-)  A      OE1
 263 ASP   ( 263-)  A      OD1
 273 HIS   ( 273-)  A      ND1
 306 HIS   ( 306-)  A      ND1
 419 HIS   ( 419-)  A      NE2
 648 GLU   ( 151-)  B      OE1
 648 GLU   ( 151-)  B      OE2
 704 GLN   ( 207-)  B      OE1
 760 ASP   ( 263-)  B      OD1
 916 HIS   ( 419-)  B      NE2
 978 GLU   ( 481-)  B      OE1
1257 ASP   ( 263-)  C      OD1
1267 HIS   ( 273-)  C      ND1
1413 HIS   ( 419-)  C      NE2
1636 HIS   ( 145-)  D      NE2
1642 GLU   ( 151-)  D      OE1
1642 GLU   ( 151-)  D      OE2
1754 ASP   ( 263-)  D      OD1
1764 HIS   ( 273-)  D      ND1
1781 HIS   ( 290-)  D      ND1
1797 HIS   ( 306-)  D      ND1
1802 HIS   ( 311-)  D      ND1
1806 ASP   ( 315-)  D      OD1
1910 HIS   ( 419-)  D      NE2
1972 GLU   ( 481-)  D      OE1

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

2060 HOH   ( 727 )  A      O  0.98  K  4 Ion-B
2061 HOH   ( 595 )  B      O  0.98  K  4
2062 HOH   (1381 )  C      O  0.86  K  4
2062 HOH   (1436 )  C      O  1.00  K  4 Ion-B
2063 HOH   ( 713 )  D      O  0.89  K  4
2063 HOH   ( 865 )  D      O  0.95  K  4

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.

 112 GLU   ( 112-)  A   H-bonding suggests Gln
 203 ASP   ( 203-)  A   H-bonding suggests Asn; but Alt-Rotamer
 218 ASP   ( 218-)  A   H-bonding suggests Asn
 233 GLU   ( 233-)  A   H-bonding suggests Gln
 380 ASP   ( 380-)  A   H-bonding suggests Asn; but Alt-Rotamer
 634 ASP   ( 137-)  B   H-bonding suggests Asn
 700 ASP   ( 203-)  B   H-bonding suggests Asn
 715 ASP   ( 218-)  B   H-bonding suggests Asn; but Alt-Rotamer
 730 GLU   ( 233-)  B   H-bonding suggests Gln
 877 ASP   ( 380-)  B   H-bonding suggests Asn; but Alt-Rotamer
1131 ASP   ( 137-)  C   H-bonding suggests Asn
1197 ASP   ( 203-)  C   H-bonding suggests Asn; but Alt-Rotamer
1212 ASP   ( 218-)  C   H-bonding suggests Asn; but Alt-Rotamer
1227 GLU   ( 233-)  C   H-bonding suggests Gln
1374 ASP   ( 380-)  C   H-bonding suggests Asn; but Alt-Rotamer
1603 GLU   ( 112-)  D   H-bonding suggests Gln
1628 ASP   ( 137-)  D   H-bonding suggests Asn
1694 ASP   ( 203-)  D   H-bonding suggests Asn; but Alt-Rotamer
1724 GLU   ( 233-)  D   H-bonding suggests Gln
1806 ASP   ( 315-)  D   H-bonding suggests Asn
1871 ASP   ( 380-)  D   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 :  -0.145
  2nd generation packing quality :  -1.586
  Ramachandran plot appearance   :  -0.792
  chi-1/chi-2 rotamer normality  :  -1.798
  Backbone conformation          :  -0.499

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.748
  Bond angles                    :   0.847
  Omega angle restraints         :   1.262
  Side chain planarity           :   0.832
  Improper dihedral distribution :   0.953
  B-factor distribution          :   0.512
  Inside/Outside distribution    :   1.019

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 : 1.84


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.2
  2nd generation packing quality :  -1.3
  Ramachandran plot appearance   :  -0.7
  chi-1/chi-2 rotamer normality  :  -1.4
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.748
  Bond angles                    :   0.847
  Omega angle restraints         :   1.262
  Side chain planarity           :   0.832
  Improper dihedral distribution :   0.953
  B-factor distribution          :   0.512
  Inside/Outside distribution    :   1.019
==============

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.