WHAT IF Check report

This file was created 2013-12-10 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 pdb4ai6.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    = 174.886  B   = 119.175  C    = 193.974
    Alpha=  90.000  Beta=  90.180  Gamma=  90.000

Dimensions of a reduced cell

    A    = 119.175  B   = 174.886  C    = 193.974
    Alpha=  90.180  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    = 119.175  B   = 174.886  C    = 193.974
    Alpha=  89.820  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: MONOCLINIC

Crystal class of the conventional CELL: ORTHORHOMBIC

Space group name: P 1 21 1

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 : 1.998
CA-only RMS fit for the two chains : 1.942

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

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: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: P 1 21 1
Number of matrices in space group: 2
Highest polymer chain multiplicity in structure: 2
Highest polymer chain multiplicity according to SEQRES: 1
Warning: one pair of SEQRES sequences is sneakingly different
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 4
Polymer chain multiplicity and SEQRES multiplicity disagree 2 1
Z and NCS seem to support the 3D multiplicity

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.

5301 ADP   (5402-)  A  -
5303 ATP   (5400-)  B  -
5304 ADP   (5401-)  B  -
5305 ADP   (5402-)  B  -
5309 ATP   (5400-)  A  -
5310 ADP   (5401-)  A  -

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

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   (   1-)  A      OG
   2 PRO   (   2-)  A      CG
   2 PRO   (   2-)  A      CD
   3 ILE   (   3-)  A      CG1
   3 ILE   (   3-)  A      CG2
   3 ILE   (   3-)  A      CD1
   4 LEU   (   4-)  A      CG
   4 LEU   (   4-)  A      CD1
   4 LEU   (   4-)  A      CD2
   6 TYR   (   6-)  A      CG
   6 TYR   (   6-)  A      CD1
   6 TYR   (   6-)  A      CD2
   6 TYR   (   6-)  A      CE1
   6 TYR   (   6-)  A      CE2
   6 TYR   (   6-)  A      CZ
   6 TYR   (   6-)  A      OH
   7 TRP   (   7-)  A      CG
   7 TRP   (   7-)  A      CD1
   7 TRP   (   7-)  A      CD2
   7 TRP   (   7-)  A      NE1
   7 TRP   (   7-)  A      CE2
   7 TRP   (   7-)  A      CE3
   7 TRP   (   7-)  A      CZ2
   7 TRP   (   7-)  A      CZ3
   7 TRP   (   7-)  A      CH2
And so on for a total of 1422 lines.

Warning: B-factors outside the range 0.0 - 100.0

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

   1 SER   (   1-)  A    High
   2 PRO   (   2-)  A    High
   3 ILE   (   3-)  A    High
   4 LEU   (   4-)  A    High
   5 GLY   (   5-)  A    High
   6 TYR   (   6-)  A    High
   7 TRP   (   7-)  A    High
   8 LYS   (   8-)  A    High
   9 ILE   (   9-)  A    High
  10 LYS   (  10-)  A    High
  11 GLY   (  11-)  A    High
  12 LEU   (  12-)  A    High
  13 VAL   (  13-)  A    High
  14 GLN   (  14-)  A    High
  15 PRO   (  15-)  A    High
  16 THR   (  16-)  A    High
  17 ARG   (  17-)  A    High
  18 LEU   (  18-)  A    High
  19 LEU   (  19-)  A    High
  20 LEU   (  20-)  A    High
  21 GLU   (  21-)  A    High
  22 TYR   (  22-)  A    High
  23 LEU   (  23-)  A    High
  24 GLU   (  24-)  A    High
  25 GLU   (  25-)  A    High
And so on for a total of 5300 lines.

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

2049 ILE   (3481-)  A    0.50
4699 ILE   (3481-)  B    0.50

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

Crystal temperature (K) :100.000

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

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.

 388 ARG   (1536-)  A
1380 ARG   (2528-)  A
1798 ARG   (2962-)  A
1810 ARG   (2974-)  A
1833 ARG   (2997-)  A
1873 ARG   (3305-)  A
1908 ARG   (3340-)  A
1910 ARG   (3342-)  A
1933 ARG   (3365-)  A
2013 ARG   (3445-)  A
2032 ARG   (3464-)  A
2113 ARG   (3545-)  A
2350 ARG   (3792-)  A
2586 ARG   (4028-)  A
3038 ARG   (1536-)  B
4030 ARG   (2528-)  B
4363 ARG   (2861-)  B
4448 ARG   (2962-)  B
4460 ARG   (2974-)  B
4483 ARG   (2997-)  B
4523 ARG   (3305-)  B
4558 ARG   (3340-)  B
4560 ARG   (3342-)  B
4583 ARG   (3365-)  B
4663 ARG   (3445-)  B
4682 ARG   (3464-)  B
4763 ARG   (3545-)  B
5000 ARG   (3792-)  B
5236 ARG   (4028-)  B

Warning: Tyrosine convention problem

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

 272 TYR   (1420-)  A
 273 TYR   (1421-)  A
 557 TYR   (1705-)  A
 610 TYR   (1758-)  A
 954 TYR   (2102-)  A
2264 TYR   (3706-)  A
2343 TYR   (3785-)  A
2513 TYR   (3955-)  A
2922 TYR   (1420-)  B
2923 TYR   (1421-)  B
3145 TYR   (1643-)  B
3260 TYR   (1758-)  B
3604 TYR   (2102-)  B
3966 TYR   (2464-)  B
4493 TYR   (3007-)  B
4639 TYR   (3421-)  B
4993 TYR   (3785-)  B
5202 TYR   (3994-)  B

Warning: Phenylalanine convention problem

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

 229 PHE   (1377-)  A
 389 PHE   (1537-)  A
 791 PHE   (1939-)  A
 912 PHE   (2060-)  A
 946 PHE   (2094-)  A
1042 PHE   (2190-)  A
1067 PHE   (2215-)  A
1198 PHE   (2346-)  A
2217 PHE   (3649-)  A
2261 PHE   (3703-)  A
2356 PHE   (3798-)  A
2879 PHE   (1377-)  B
3039 PHE   (1537-)  B
3068 PHE   (1566-)  B
3297 PHE   (1795-)  B
3328 PHE   (1826-)  B
3397 PHE   (1895-)  B
3441 PHE   (1939-)  B
3596 PHE   (2094-)  B
3692 PHE   (2190-)  B
3696 PHE   (2194-)  B
4087 PHE   (2585-)  B
4222 PHE   (2720-)  B
4462 PHE   (2976-)  B
4624 PHE   (3406-)  B
4847 PHE   (3629-)  B
4867 PHE   (3649-)  B
4994 PHE   (3786-)  B

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.

 675 ASP   (1823-)  A
1720 ASP   (2868-)  A
2051 ASP   (3483-)  A
2340 ASP   (3782-)  A
3325 ASP   (1823-)  B
4990 ASP   (3782-)  B

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.

 236 GLU   (1384-)  A
 249 GLU   (1397-)  A
 440 GLU   (1588-)  A
 466 GLU   (1614-)  A
 510 GLU   (1658-)  A
 575 GLU   (1723-)  A
 707 GLU   (1855-)  A
 783 GLU   (1931-)  A
 838 GLU   (1986-)  A
1047 GLU   (2195-)  A
1204 GLU   (2352-)  A
1304 GLU   (2452-)  A
1517 GLU   (2665-)  A
1699 GLU   (2847-)  A
1791 GLU   (2939-)  A
1870 GLU   (3302-)  A
1907 GLU   (3339-)  A
2001 GLU   (3433-)  A
2002 GLU   (3434-)  A
2009 GLU   (3441-)  A
2024 GLU   (3456-)  A
2104 GLU   (3536-)  A
2108 GLU   (3540-)  A
2136 GLU   (3568-)  A
2147 GLU   (3579-)  A
And so on for a total of 57 lines.

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.

 115 GLU   ( 115-)  A      N    CA    1.55    4.6
 115 GLU   ( 115-)  A      CA   CB    1.62    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

 |  0.997855 -0.000260  0.000330|
 | -0.000260  0.998413  0.000093|
 |  0.000330  0.000093  0.997709|
Proposed new scale matrix

 |  0.005730  0.000001  0.000016|
 |  0.000002  0.008404  0.000000|
 | -0.000002  0.000000  0.005167|
With corresponding cell

    A    = 174.511  B   = 118.986  C    = 193.543
    Alpha=  90.002  Beta=  90.143  Gamma=  90.030

The CRYST1 cell dimensions

    A    = 174.886  B   = 119.175  C    = 193.974
    Alpha=  90.000  Beta=  90.180  Gamma=  90.000

Variance: 700.626
(Under-)estimated Z-score: 19.508

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.

 115 GLU   ( 115-)  A      N    CA   CB  117.96    4.4
 201 PRO   ( 201-)  A     -C    N    CA  146.22    4.7
 315 LEU   (1463-)  A      CA   CB   CG  130.55    4.1
 559 HIS   (1707-)  A      CG   ND1  CE1 109.63    4.0
 646 PHE   (1794-)  A      N    CA   CB  120.09    5.6
 734 LEU   (1882-)  A      CA   CB   CG  131.09    4.2
 781 ILE   (1929-)  A      N    CA   CB  117.71    4.2
 819 HIS   (1967-)  A      CG   ND1  CE1 109.60    4.0
1080 HIS   (2228-)  A      CG   ND1  CE1 109.88    4.3
1086 TYR   (2234-)  A      CA   CB   CG  121.52    4.2
1252 HIS   (2400-)  A      CG   ND1  CE1 109.61    4.0
1359 ARG   (2507-)  A      CG   CD   NE  119.62    5.4
1466 HIS   (2614-)  A      CG   ND1  CE1 109.61    4.0
1872 GLU   (3304-)  A     -C    N    CA  112.36   -5.2
2254 MET   (3696-)  A      CB   CG   SD   99.31   -4.5
2286 GLU   (3728-)  A     -C    N    CA  112.93   -4.9
2458 ILE   (3900-)  A      C    CA   CB  102.23   -4.1
2851 PRO   ( 201-)  B     -C    N    CA  144.89    4.5
3296 PHE   (1794-)  B      N    CA   CB  118.61    4.8
3338 VAL   (1836-)  B      C    CA   CB  118.17    4.2
3440 GLY   (1938-)  B      N    CA   C   100.03   -4.3
3635 ILE   (2133-)  B      N    CA   CB  117.97    4.4
3637 ARG   (2135-)  B      CB   CG   CD  106.04   -4.0
3637 ARG   (2135-)  B      CG   CD   NE  117.34    4.0
3892 ILE   (2390-)  B      C    CA   CB  118.20    4.3
3957 LEU   (2455-)  B      CB   CG   CD1  97.38   -4.4
3965 ASN   (2463-)  B      N    CA   CB  103.16   -4.3
3974 THR   (2472-)  B      CG2  CB   OG1  99.36   -5.0
4020 THR   (2518-)  B      C    CA   CB  117.78    4.0
4046 ILE   (2544-)  B     -C    N    CA  128.99    4.0
5221 HIS   (4013-)  B      CG   ND1  CE1 109.66    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.

 236 GLU   (1384-)  A
 249 GLU   (1397-)  A
 388 ARG   (1536-)  A
 440 GLU   (1588-)  A
 466 GLU   (1614-)  A
 510 GLU   (1658-)  A
 575 GLU   (1723-)  A
 675 ASP   (1823-)  A
 707 GLU   (1855-)  A
 783 GLU   (1931-)  A
 838 GLU   (1986-)  A
1047 GLU   (2195-)  A
1204 GLU   (2352-)  A
1304 GLU   (2452-)  A
1380 ARG   (2528-)  A
1517 GLU   (2665-)  A
1699 GLU   (2847-)  A
1720 ASP   (2868-)  A
1791 GLU   (2939-)  A
1798 ARG   (2962-)  A
1810 ARG   (2974-)  A
1833 ARG   (2997-)  A
1870 GLU   (3302-)  A
1873 ARG   (3305-)  A
1907 GLU   (3339-)  A
And so on for a total of 92 lines.

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.

 646 PHE   (1794-)  A      CA    -7.6    21.76    33.98
 880 PRO   (2028-)  A      N     -6.0   -22.24    -2.48
2581 ILE   (4023-)  A      CB     6.7    41.07    32.31
3296 PHE   (1794-)  B      CA    -7.6    21.84    33.98
3530 PRO   (2028-)  B      N     -6.3   -23.15    -2.48
5223 PHE   (4015-)  B      CA    -6.7    23.31    33.98
The average deviation= 0.932

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.

3440 GLY   (1938-)  B    6.96
3835 GLU   (2333-)  B    6.16
  14 GLN   (  14-)  A    5.77
3042 LEU   (1540-)  B    5.29
3357 GLU   (1855-)  B    5.19
1185 GLU   (2333-)  A    5.04
2184 GLU   (3616-)  A    4.90
 790 GLY   (1938-)  A    4.79
2548 ALA   (3990-)  A    4.65
4369 LEU   (2867-)  B    4.41
 855 LEU   (2003-)  A    4.32
1816 MET   (2980-)  A    4.26
3510 ASP   (2008-)  B    4.21
5190 TRP   (3982-)  B    4.14
 392 LEU   (1540-)  A    4.08
4257 HIS   (2755-)  B    4.03
2250 LYS   (3692-)  A    4.00

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.

1414 PRO   (2562-)  A    -3.0
4064 PRO   (2562-)  B    -3.0
3530 PRO   (2028-)  B    -2.9
1128 LEU   (2276-)  A    -2.8
3778 LEU   (2276-)  B    -2.7
5188 ILE   (3980-)  B    -2.7
5070 THR   (3862-)  B    -2.6
4065 SER   (2563-)  B    -2.6
1541 ILE   (2689-)  A    -2.6
4191 ILE   (2689-)  B    -2.6
 360 THR   (1508-)  A    -2.6
1048 THR   (2196-)  A    -2.6
1636 PRO   (2784-)  A    -2.6
1027 ILE   (2175-)  A    -2.6
3774 LEU   (2272-)  B    -2.5
2420 THR   (3862-)  A    -2.5
3677 ILE   (2175-)  B    -2.5
1213 ILE   (2361-)  A    -2.5
3071 ILE   (1569-)  B    -2.5
2899 GLU   (1397-)  B    -2.5
3724 ILE   (2222-)  B    -2.5
1415 SER   (2563-)  A    -2.5
4118 LEU   (2616-)  B    -2.5
 243 GLY   (1391-)  A    -2.5
4684 ILE   (3466-)  B    -2.5
And so on for a total of 142 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.

   2 PRO   (   2-)  A  omega poor
  11 GLY   (  11-)  A  Poor phi/psi
  13 VAL   (  13-)  A  omega poor
  24 GLU   (  24-)  A  Poor phi/psi
  53 ASN   (  53-)  A  Poor phi/psi
  54 LEU   (  54-)  A  PRO omega poor
  59 ASP   (  59-)  A  Poor phi/psi
  61 ASP   (  61-)  A  Poor phi/psi
  64 LEU   (  64-)  A  omega poor
  66 GLN   (  66-)  A  Poor phi/psi
 138 HIS   ( 138-)  A  Poor phi/psi
 140 THR   ( 140-)  A  omega poor
 197 TYR   ( 197-)  A  omega poor
 200 TRP   ( 200-)  A  PRO omega poor
 213 ASP   ( 213-)  A  omega poor
 243 GLY   (1391-)  A  Poor phi/psi, omega poor
 249 GLU   (1397-)  A  Poor phi/psi
 250 TRP   (1398-)  A  omega poor
 346 ASP   (1494-)  A  Poor phi/psi
 407 HIS   (1555-)  A  Poor phi/psi
 426 PHE   (1574-)  A  omega poor
 428 GLU   (1576-)  A  Poor phi/psi
 453 SER   (1601-)  A  Poor phi/psi
 485 GLY   (1633-)  A  Poor phi/psi
 519 ASN   (1667-)  A  Poor phi/psi
And so on for a total of 266 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 : -4.429

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.

5276 GLU   (4068-)  B    0.33
3143 SER   (1641-)  B    0.34
2219 SER   (3651-)  A    0.35
 376 SER   (1524-)  A    0.35
4613 SER   (3395-)  B    0.35
2079 SER   (3511-)  A    0.36
4306 SER   (2804-)  B    0.36
4098 SER   (2596-)  B    0.36
3459 SER   (1957-)  B    0.36
 123 SER   ( 123-)  A    0.36
 222 SER   (1370-)  A    0.36
1778 SER   (2926-)  A    0.36
2773 SER   ( 123-)  B    0.36
3287 SER   (1785-)  B    0.36
3756 SER   (2254-)  B    0.36
4364 SER   (2862-)  B    0.37
 809 SER   (1957-)  A    0.37
3026 SER   (1524-)  B    0.37
2627 SER   (4069-)  A    0.37
2491 SER   (3933-)  A    0.37
5141 SER   (3933-)  B    0.37
2642 SER   (4084-)  A    0.38
1448 SER   (2596-)  A    0.38
 714 SER   (1862-)  A    0.38
1418 SER   (2566-)  A    0.38
2768 LYS   ( 118-)  B    0.38
3449 SER   (1947-)  B    0.38
2316 SER   (3758-)  A    0.39
 637 SER   (1785-)  A    0.39
4068 SER   (2566-)  B    0.40

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 TYR   (   6-)  A      0
   7 TRP   (   7-)  A      0
   8 LYS   (   8-)  A      0
   9 ILE   (   9-)  A      0
  10 LYS   (  10-)  A      0
  12 LEU   (  12-)  A      0
  13 VAL   (  13-)  A      0
  26 LYS   (  26-)  A      0
  27 TYR   (  27-)  A      0
  33 GLU   (  33-)  A      0
  35 ASP   (  35-)  A      0
  36 GLU   (  36-)  A      0
  46 GLU   (  46-)  A      0
  49 LEU   (  49-)  A      0
  50 GLU   (  50-)  A      0
  51 PHE   (  51-)  A      0
  52 PRO   (  52-)  A      0
  53 ASN   (  53-)  A      0
  54 LEU   (  54-)  A      0
  59 ASP   (  59-)  A      0
  65 THR   (  65-)  A      0
  66 GLN   (  66-)  A      0
  79 ASN   (  79-)  A      0
  80 MET   (  80-)  A      0
  81 LEU   (  81-)  A      0
And so on for a total of 1480 lines.

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

1612 GLY   (2760-)  A   3.20   10
2476 GLY   (3918-)  A   2.02   18
3630 GLY   (2128-)  B   1.91   10
 100 ASP   ( 100-)  A   1.66   14
 666 GLY   (1814-)  A   1.53   80
2583 PRO   (4025-)  A   1.52   10

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]

   2 PRO   (   2-)  A    0.00 LOW
  15 PRO   (  15-)  A    0.00 LOW
  52 PRO   (  52-)  A    0.00 LOW
  55 PRO   (  55-)  A    0.00 LOW
  85 PRO   (  85-)  A    0.00 LOW
 126 PRO   ( 126-)  A    0.00 LOW
 150 PRO   ( 150-)  A    0.00 LOW
 166 PRO   ( 166-)  A    0.00 LOW
 173 PRO   ( 173-)  A    0.00 LOW
 186 PRO   ( 186-)  A    0.00 LOW
 201 PRO   ( 201-)  A    0.00 LOW
 215 PRO   ( 215-)  A    0.00 LOW
 216 PRO   ( 216-)  A    0.00 LOW
 649 PRO   (1797-)  A    0.18 LOW
 776 PRO   (1924-)  A    0.15 LOW
1272 PRO   (2420-)  A    0.16 LOW
2459 PRO   (3901-)  A    0.18 LOW
2652 PRO   (   2-)  B    0.00 LOW
2665 PRO   (  15-)  B    0.00 LOW
2702 PRO   (  52-)  B    0.00 LOW
2705 PRO   (  55-)  B    0.00 LOW
2735 PRO   (  85-)  B    0.00 LOW
2776 PRO   ( 126-)  B    0.00 LOW
2800 PRO   ( 150-)  B    0.00 LOW
2816 PRO   ( 166-)  B    0.00 LOW
2823 PRO   ( 173-)  B    0.00 LOW
2836 PRO   ( 186-)  B    0.00 LOW
2851 PRO   ( 201-)  B    0.00 LOW
2865 PRO   ( 215-)  B    0.00 LOW
2866 PRO   ( 216-)  B    0.00 LOW
4121 PRO   (2619-)  B    0.46 HIGH

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

 322 PRO   (1470-)  A   -13.3 half-chair C-alpha/N (-18 degrees)
 752 PRO   (1900-)  A   -63.5 envelop C-beta (-72 degrees)
 761 PRO   (1909-)  A   100.3 envelop C-beta (108 degrees)
1240 PRO   (2388-)  A  -114.0 envelop C-gamma (-108 degrees)
1245 PRO   (2393-)  A  -115.4 envelop C-gamma (-108 degrees)
1327 PRO   (2475-)  A   -32.6 envelop C-alpha (-36 degrees)
1371 PRO   (2519-)  A    -3.4 envelop N (0 degrees)
1389 PRO   (2537-)  A    99.8 envelop C-beta (108 degrees)
1390 PRO   (2538-)  A   -63.8 envelop C-beta (-72 degrees)
1414 PRO   (2562-)  A   -56.5 half-chair C-beta/C-alpha (-54 degrees)
1534 PRO   (2682-)  A    47.7 half-chair C-delta/C-gamma (54 degrees)
1583 PRO   (2731-)  A    10.2 half-chair N/C-delta (18 degrees)
1636 PRO   (2784-)  A   105.9 envelop C-beta (108 degrees)
1822 PRO   (2986-)  A   -58.2 half-chair C-beta/C-alpha (-54 degrees)
1825 PRO   (2989-)  A  -115.2 envelop C-gamma (-108 degrees)
1973 PRO   (3405-)  A   -14.5 half-chair C-alpha/N (-18 degrees)
2069 PRO   (3501-)  A    42.9 envelop C-delta (36 degrees)
2445 PRO   (3887-)  A  -117.8 half-chair C-delta/C-gamma (-126 degrees)
2505 PRO   (3947-)  A   -64.6 envelop C-beta (-72 degrees)
2588 PRO   (4030-)  A    22.8 half-chair N/C-delta (18 degrees)
2613 PRO   (4055-)  A    44.7 envelop C-delta (36 degrees)
2972 PRO   (1470-)  B   -39.3 envelop C-alpha (-36 degrees)
3402 PRO   (1900-)  B   -21.9 half-chair C-alpha/N (-18 degrees)
3411 PRO   (1909-)  B   118.3 half-chair C-beta/C-alpha (126 degrees)
3878 PRO   (2376-)  B  -113.7 envelop C-gamma (-108 degrees)
3977 PRO   (2475-)  B   -34.3 envelop C-alpha (-36 degrees)
4021 PRO   (2519-)  B   -22.8 half-chair C-alpha/N (-18 degrees)
4233 PRO   (2731-)  B    29.9 envelop C-delta (36 degrees)
4286 PRO   (2784-)  B   101.8 envelop C-beta (108 degrees)
4343 PRO   (2841-)  B   116.1 envelop C-beta (108 degrees)
4408 PRO   (2906-)  B  -118.3 half-chair C-delta/C-gamma (-126 degrees)
4475 PRO   (2989-)  B  -118.6 half-chair C-delta/C-gamma (-126 degrees)
4623 PRO   (3405-)  B   -20.5 half-chair C-alpha/N (-18 degrees)
4719 PRO   (3501-)  B    33.4 envelop C-delta (36 degrees)
5093 PRO   (3885-)  B  -118.0 half-chair C-delta/C-gamma (-126 degrees)
5095 PRO   (3887-)  B  -116.8 envelop C-gamma (-108 degrees)
5109 PRO   (3901-)  B   -29.7 envelop C-alpha (-36 degrees)
5238 PRO   (4030-)  B    26.3 half-chair N/C-delta (18 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.

4234 MET   (2732-)  B      CE  <-> 4270 ILE   (2768-)  B      CG2    0.94    2.26  INTRA BF
 217 PHE   (1365-)  A      CE2 <->  218 VAL   (1366-)  A      CG2    0.94    2.26  INTRA BF
2867 PHE   (1365-)  B      CD1 <-> 2868 VAL   (1366-)  B      CG2    0.90    2.30  INTRA BF
3975 LEU   (2473-)  B      CD2 <-> 3977 PRO   (2475-)  B      CD     0.87    2.33  INTRA BF
4234 MET   (2732-)  B      CB  <-> 5305 ADP   (5402-)  B      C6     0.86    2.34  INTRA BF
4235 VAL   (2733-)  B      N   <-> 5305 ADP   (5402-)  B      N1     0.78    2.22  INTRA BF
4752 LEU   (3534-)  B      CD1 <-> 4836 TYR   (3618-)  B      CE2    0.76    2.44  INTRA BF
2867 PHE   (1365-)  B      CE1 <-> 2868 VAL   (1366-)  B      CG2    0.75    2.45  INTRA BF
2923 TYR   (1421-)  B      CE2 <-> 2927 GLU   (1425-)  B      CG     0.74    2.46  INTRA BF
2102 LEU   (3534-)  A      CD1 <-> 2186 TYR   (3618-)  A      CE2    0.71    2.49  INTRA BL
2335 VAL   (3777-)  A      CG1 <-> 2453 PHE   (3895-)  A      CE1    0.69    2.51  INTRA BF
1369 LYS   (2517-)  A      CE  <-> 1376 VAL   (2524-)  A      CG2    0.69    2.51  INTRA BF
3122 PHE   (1620-)  B      CD1 <-> 3262 PHE   (1760-)  B      CZ     0.69    2.51  INTRA BF
1276 LYS   (2424-)  A      NZ  <-> 5310 ADP   (5401-)  A      PB     0.69    2.61  INTRA BL
 472 PHE   (1620-)  A      CD1 <->  612 PHE   (1760-)  A      CZ     0.67    2.53  INTRA BF
1472 ARG   (2620-)  A      NH2 <-> 5310 ADP   (5401-)  A      PA     0.66    2.64  INTRA BF
3880 VAL   (2378-)  B      CG2 <-> 3882 LEU   (2380-)  B      CD1    0.66    2.54  INTRA BF
1874 TRP   (3306-)  A      CH2 <-> 2162 ALA   (3594-)  A      CB     0.66    2.54  INTRA BF
4234 MET   (2732-)  B      CB  <-> 5305 ADP   (5402-)  B      C5     0.64    2.56  INTRA BF
3582 LYS   (2080-)  B      NZ  <-> 4051 ARG   (2549-)  B      NH2    0.64    2.21  INTRA BF
3882 LEU   (2380-)  B      CD2 <-> 3892 ILE   (2390-)  B      CD1    0.63    2.57  INTRA BF
3132 ILE   (1630-)  B      CG2 <-> 3157 MET   (1655-)  B      SD     0.62    2.78  INTRA BF
3888 MET   (2386-)  B      CB  <-> 4129 ARG   (2627-)  B      CD     0.61    2.59  INTRA BF
2867 PHE   (1365-)  B      CD1 <-> 2868 VAL   (1366-)  B      N      0.60    2.40  INTRA BF
3888 MET   (2386-)  B      CG  <-> 4129 ARG   (2627-)  B      CD     0.60    2.60  INTRA BF
And so on for a total of 985 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

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.

 754 TYR   (1902-)  A      -9.22
3404 TYR   (1902-)  B      -9.18
1823 ARG   (2987-)  A      -7.34
4140 ARG   (2638-)  B      -7.34
4473 ARG   (2987-)  B      -7.19
1413 TYR   (2561-)  A      -6.87
1615 ARG   (2763-)  A      -6.61
4265 ARG   (2763-)  B      -6.59
3888 MET   (2386-)  B      -6.58
1490 ARG   (2638-)  A      -6.45
 353 HIS   (1501-)  A      -6.38
3003 HIS   (1501-)  B      -6.35
3531 LEU   (2029-)  B      -6.33
5272 GLN   (4064-)  B      -6.27
1554 LEU   (2702-)  A      -6.25
1238 MET   (2386-)  A      -6.20
3870 PHE   (2368-)  B      -6.18
4063 TYR   (2561-)  B      -6.12
3868 LEU   (2366-)  B      -6.12
1349 TYR   (2497-)  A      -6.10
2622 GLN   (4064-)  A      -6.10
1218 LEU   (2366-)  A      -6.02
1792 PHE   (2940-)  A      -6.00
1348 LYS   (2496-)  A      -5.99
4204 LEU   (2702-)  B      -5.95
And so on for a total of 110 lines.

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.

 210 GLY   ( 210-)  A       212 - GLY    212- ( A)         -4.76
1816 MET   (2980-)  A      1818 - VAL   2982- ( A)         -4.99
2860 GLY   ( 210-)  B      2862 - GLY    212- ( B)         -4.73
3911 ASN   (2409-)  B      3913 - LYS   2411- ( B)         -4.43

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

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.

 197 TYR   ( 197-)  A   -3.41
 139 LYS   ( 139-)  A   -3.29
 167 MET   ( 167-)  A   -3.29
2699 LEU   (  49-)  B   -3.26
2817 MET   ( 167-)  B   -3.23
2791 TYR   ( 141-)  B   -3.22
2658 LYS   (   8-)  B   -3.21
2789 LYS   ( 139-)  B   -3.14
   8 LYS   (   8-)  A   -3.11
  49 LEU   (  49-)  A   -3.08
  51 PHE   (  51-)  A   -3.06
 141 TYR   ( 141-)  A   -3.03
2730 MET   (  80-)  B   -2.98
2659 ILE   (   9-)  B   -2.95
2728 HIS   (  78-)  B   -2.94
2684 ARG   (  34-)  B   -2.92
   9 ILE   (   9-)  A   -2.90
  34 ARG   (  34-)  A   -2.89
2792 LEU   ( 142-)  B   -2.89
2847 TYR   ( 197-)  B   -2.87
2591 LEU   (4033-)  A   -2.86
 164 MET   ( 164-)  A   -2.83
2694 LYS   (  44-)  B   -2.82
  80 MET   (  80-)  A   -2.82
4230 LEU   (2728-)  B   -2.80
  32 TYR   (  32-)  A   -2.80
1695 LEU   (2843-)  A   -2.75
2850 TRP   ( 200-)  B   -2.71
2859 PHE   ( 209-)  B   -2.67
2713 LYS   (  63-)  B   -2.66
 109 ALA   ( 109-)  A   -2.65
4345 LEU   (2843-)  B   -2.63
3993 LEU   (2491-)  B   -2.62
1343 LEU   (2491-)  A   -2.62
  44 LYS   (  44-)  A   -2.60
 209 PHE   ( 209-)  A   -2.60
1489 PRO   (2637-)  A   -2.56
2660 LYS   (  10-)  B   -2.55
2676 LYS   (  26-)  B   -2.55
2824 LYS   ( 174-)  B   -2.55
 169 LEU   ( 169-)  A   -2.54
2853 GLN   ( 203-)  B   -2.54
2693 LYS   (  43-)  B   -2.54
  33 GLU   (  33-)  A   -2.53
 174 LYS   ( 174-)  A   -2.53
2701 PHE   (  51-)  B   -2.52
2697 LEU   (  47-)  B   -2.52
  47 LEU   (  47-)  A   -2.51
 172 PHE   ( 172-)  A   -2.51

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.

   7 TRP   (   7-)  A     -   10 LYS   (  10-)  A        -2.51
  11 GLY   (  11-)  A     -   14 GLN   (  14-)  A        -1.81
  24 GLU   (  24-)  A     -   27 TYR   (  27-)  A        -2.15
  31 LEU   (  31-)  A     -   34 ARG   (  34-)  A        -2.48
  42 ASN   (  42-)  A     -   47 LEU   (  47-)  A        -2.19
  52 PRO   (  52-)  A     -   55 PRO   (  55-)  A        -1.97
  60 GLY   (  60-)  A     -   63 LYS   (  63-)  A        -1.88
 106 SER   ( 106-)  A     -  110 TYR   ( 110-)  A        -1.72
 134 ASP   ( 134-)  A     -  137 CYS   ( 137-)  A        -1.83
 140 THR   ( 140-)  A     -  143 ASN   ( 143-)  A        -2.14
 161 VAL   ( 161-)  A     -  170 ASP   ( 170-)  A        -2.09
 195 SER   ( 195-)  A     -  198 ILE   ( 198-)  A        -2.20
 200 TRP   ( 200-)  A     -  203 GLN   ( 203-)  A        -2.06
1577 ASP   (2725-)  A     - 1582 VAL   (2730-)  A        -1.56
2657 TRP   (   7-)  B     - 2660 LYS   (  10-)  B        -2.59
2672 TYR   (  22-)  B     - 2677 TYR   (  27-)  B        -2.16
2692 ASN   (  42-)  B     - 2697 LEU   (  47-)  B        -2.19
2700 GLU   (  50-)  B     - 2705 PRO   (  55-)  B        -2.10
2784 ASP   ( 134-)  B     - 2787 CYS   ( 137-)  B        -1.88
2790 THR   ( 140-)  B     - 2793 ASN   ( 143-)  B        -2.27
2814 MET   ( 164-)  B     - 2819 LEU   ( 169-)  B        -2.10
2845 SER   ( 195-)  B     - 2848 ILE   ( 198-)  B        -2.07
2849 ALA   ( 199-)  B     - 2853 GLN   ( 203-)  B        -2.01
4228 GLU   (2726-)  B     - 4232 VAL   (2730-)  B        -2.05

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

Water, ion, and hydrogenbond related checks

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.

 294 GLN   (1442-)  A
 318 GLN   (1466-)  A
 344 GLN   (1492-)  A
 474 GLN   (1622-)  A
 517 GLN   (1665-)  A
 569 ASN   (1717-)  A
 609 GLN   (1757-)  A
 831 ASN   (1979-)  A
 882 ASN   (2030-)  A
 919 GLN   (2067-)  A
 951 ASN   (2099-)  A
1091 ASN   (2239-)  A
1134 ASN   (2282-)  A
1187 GLN   (2335-)  A
1192 GLN   (2340-)  A
1305 HIS   (2453-)  A
1311 HIS   (2459-)  A
1738 HIS   (2886-)  A
1803 ASN   (2967-)  A
1807 HIS   (2971-)  A
1844 GLN   (3008-)  A
2052 HIS   (3484-)  A
2120 ASN   (3552-)  A
2142 GLN   (3574-)  A
2156 ASN   (3588-)  A
And so on for a total of 56 lines.

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.

  45 PHE   (  45-)  A      N
 148 THR   ( 148-)  A      N
 219 ILE   (1367-)  A      N
 233 ALA   (1381-)  A      N
 242 SER   (1390-)  A      N
 245 LYS   (1393-)  A      N
 247 VAL   (1395-)  A      N
 252 VAL   (1400-)  A      N
 270 SER   (1418-)  A      N
 273 TYR   (1421-)  A      N
 277 GLU   (1425-)  A      N
 313 GLU   (1461-)  A      N
 317 ILE   (1465-)  A      N
 318 GLN   (1466-)  A      N
 324 GLU   (1472-)  A      N
 349 ILE   (1497-)  A      N
 350 GLU   (1498-)  A      N
 359 THR   (1507-)  A      N
 383 ARG   (1531-)  A      NH1
 388 ARG   (1536-)  A      N
 390 TYR   (1538-)  A      N
 390 TYR   (1538-)  A      OH
 396 ASP   (1544-)  A      N
 409 GLN   (1557-)  A      N
 415 LYS   (1563-)  A      N
And so on for a total of 667 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.

 240 HIS   (1388-)  A      ND1
 316 ASP   (1464-)  A      OD1
 358 ASP   (1506-)  A      OD1
 561 ASN   (1709-)  A      OD1
 603 GLN   (1751-)  A      OE1
 904 GLU   (2052-)  A      OE2
1126 HIS   (2274-)  A      ND1
1134 ASN   (2282-)  A      OD1
1145 HIS   (2293-)  A      ND1
1181 ASP   (2329-)  A      OD2
1281 ASN   (2429-)  A      OD1
1340 GLU   (2488-)  A      OE1
1352 GLN   (2500-)  A      OE1
1738 HIS   (2886-)  A      ND1
1779 GLN   (2927-)  A      OE1
1899 GLU   (3331-)  A      OE1
1977 ASP   (3409-)  A      OD1
2055 ASP   (3487-)  A      OD1
2085 HIS   (3517-)  A      ND1
2148 ASN   (3580-)  A      OD1
2161 GLU   (3593-)  A      OE1
2192 HIS   (3624-)  A      ND1
2243 GLN   (3685-)  A      OE1
2328 ASP   (3770-)  A      OD1
2401 ASN   (3843-)  A      OD1
And so on for a total of 56 lines.

Warning: No crystallisation information

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

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

5302  MG   (5404-)  B   -.-  -.-  Low probability ion. B= 97.0
5307  MG   (5404-)  A   -.-  -.-  Low probability ion. B=107.5
Since there are no waters, the water check has been skipped.

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.

 260 ASP   (1408-)  A   H-bonding suggests Asn; but Alt-Rotamer
 262 GLU   (1410-)  A   H-bonding suggests Gln
 277 GLU   (1425-)  A   H-bonding suggests Gln
 316 ASP   (1464-)  A   H-bonding suggests Asn; but Alt-Rotamer
 346 ASP   (1494-)  A   H-bonding suggests Asn
 366 ASP   (1514-)  A   H-bonding suggests Asn; but Alt-Rotamer
 408 ASP   (1556-)  A   H-bonding suggests Asn
 438 GLU   (1586-)  A   H-bonding suggests Gln
 537 ASP   (1685-)  A   H-bonding suggests Asn
 591 ASP   (1739-)  A   H-bonding suggests Asn; but Alt-Rotamer
 675 ASP   (1823-)  A   H-bonding suggests Asn
 892 ASP   (2040-)  A   H-bonding suggests Asn
 992 ASP   (2140-)  A   H-bonding suggests Asn
1023 ASP   (2171-)  A   H-bonding suggests Asn
1099 ASP   (2247-)  A   H-bonding suggests Asn; but Alt-Rotamer
1103 ASP   (2251-)  A   H-bonding suggests Asn; but Alt-Rotamer
1107 ASP   (2255-)  A   H-bonding suggests Asn
1123 ASP   (2271-)  A   H-bonding suggests Asn
1164 ASP   (2312-)  A   H-bonding suggests Asn; but Alt-Rotamer
1181 ASP   (2329-)  A   H-bonding suggests Asn
1216 ASP   (2364-)  A   H-bonding suggests Asn; but Alt-Rotamer
1258 ASP   (2406-)  A   H-bonding suggests Asn
1330 ASP   (2478-)  A   H-bonding suggests Asn
1473 GLU   (2621-)  A   H-bonding suggests Gln; but Alt-Rotamer
1517 GLU   (2665-)  A   H-bonding suggests Gln; but Alt-Rotamer
And so on for a total of 91 lines.

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 :  -0.511
  2nd generation packing quality :  -2.391
  Ramachandran plot appearance   :  -2.421
  chi-1/chi-2 rotamer normality  :  -4.429 (bad)
  Backbone conformation          :  -0.379

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.512 (tight)
  Bond angles                    :   0.761
  Omega angle restraints         :   1.094
  Side chain planarity           :   0.524 (tight)
  Improper dihedral distribution :   0.823
  B-factor distribution          :   1.322
  Inside/Outside distribution    :   1.065

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 : 3.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.9
  2nd generation packing quality :  -0.2
  Ramachandran plot appearance   :   0.5
  chi-1/chi-2 rotamer normality  :  -1.9
  Backbone conformation          :   0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.512 (tight)
  Bond angles                    :   0.761
  Omega angle restraints         :   1.094
  Side chain planarity           :   0.524 (tight)
  Improper dihedral distribution :   0.823
  B-factor distribution          :   1.322
  Inside/Outside distribution    :   1.065
==============

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.