WHAT IF Check report

This file was created 2013-07-12 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 pdb2tun.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 1.826
CA-only RMS fit for the two chains : 1.201

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 D

All-atom RMS fit for the two chains : 1.550
CA-only RMS fit for the two chains : 1.056

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and E

All-atom RMS fit for the two chains : 1.922
CA-only RMS fit for the two chains : 1.293

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and E

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and F

All-atom RMS fit for the two chains : 1.772
CA-only RMS fit for the two chains : 1.096

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and F

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 : 1.731
CA-only RMS fit for the two chains : 1.093

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

Administrative problems that can generate validation failures

Error: Overlapping residues removed

The pairs of residues listed in the table overlapped too much.

The left-hand residue has been removed, and the right hand residue has been kept for validation. Be aware that WHAT IF calls everything a residue. Two residues are defined as overlapping if the two smallest ellipsoids encompassing the two residues interpenetrate by 33% of the longest axis. Many artefacts can actually cause this problem. The most often observed reason is alternative residue conformations expressed by two residues that accidentally both got 1.0 occupancy for all atoms.

 327 ARG   (  32-)  C  -              326 ASN   (  30-)  C  -           2.7

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

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

Warning: What type of B-factor?

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

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

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

Warning: More than 2 percent of buried atoms has low B-factor

For protein structures determined at room temperature, no more than about 1 percent of the B factors of buried atoms is below 5.0.

Percentage of buried atoms with B less than 5 : 2.77

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 153 PRO   (   8-)  B      CD   N     1.58    7.6
 304 PRO   (   8-)  C      N    CA    1.40   -4.5
 304 PRO   (   8-)  C      CD   N     1.63   11.2
 453 THR   (   7-)  D      C    O     1.39    8.2
 453 THR   (   7-)  D      CA   CB    1.61    4.0
 518 THR   (  72-)  D      CA   CB    1.62    4.5
 519 HIS   (  73-)  D      CA   CB    1.62    4.6

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

 |  0.997048  0.000097  0.000250|
 |  0.000097  0.996236 -0.000251|
 |  0.000250 -0.000251  0.997202|
Proposed new scale matrix

 |  0.006041  0.003491  0.000000|
 |  0.000000  0.006982  0.000002|
 | -0.000003  0.000003  0.010702|
With corresponding cell

    A    = 165.523  B   = 165.407  C    =  93.441
    Alpha=  90.036  Beta=  89.978  Gamma= 120.019

The CRYST1 cell dimensions

    A    = 166.000  B   = 166.000  C    =  93.700
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 298.595
(Under-)estimated Z-score: 12.735

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.

   2 PRO   (   8-)  A      C    CA   CB  117.73    4.0
   3 SER   (   9-)  A     -C    N    CA  130.12    4.7
   4 ASP   (  10-)  A     -C    N    CA  129.36    4.3
   4 ASP   (  10-)  A      CA   CB   CG  117.71    5.1
  25 ARG   (  31-)  A     -C    N    CA  133.20    6.4
  26 ARG   (  32-)  A      CD   NE   CZ  129.69    4.4
  27 ALA   (  33-)  A     -C    N    CA  129.71    4.5
  33 ASN   (  39-)  A     -C    N    CA  130.21    4.7
  47 GLU   (  53-)  A      CA   CB   CG  122.40    4.1
  51 LEU   (  57-)  A      C    CA   CB  118.18    4.3
  58 PHE   (  64-)  A      CA   CB   CG  121.21    7.4
  65 SER   (  71-)  A      CA   C    O   128.03    4.3
  66 THR   (  72-)  A     -C    N    CA  133.67    6.7
  68 VAL   (  74-)  A     -C    N    CA  131.67    5.5
  69 LEU   (  75-)  A      N    CA   CB  102.29   -4.8
  76 ARG   (  82-)  A      CB   CG   CD  126.52    6.2
  76 ARG   (  82-)  A      CG   CD   NE  120.72    6.0
  96 GLN   ( 102-)  A      N    CA   C    99.74   -4.1
  96 GLN   ( 102-)  A      N    CA   CB  120.78    6.0
  96 GLN   ( 102-)  A      CB   CG   CD  105.46   -4.2
  97 ARG   ( 103-)  A     -C    N    CA  130.39    4.8
  97 ARG   ( 103-)  A      N    CA   CB  121.64    6.6
  97 ARG   ( 103-)  A      CA   CB   CG  128.70    7.3
 102 GLY   ( 108-)  A     -C    N    CA  129.62    5.3
 106 LYS   ( 112-)  A     -C    N    CA  130.20    4.7
And so on for a total of 264 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.

 153 PRO   (   8-)  B      N     -6.6   -24.07    -2.48
 304 PRO   (   8-)  C      N     46.8   151.10    -2.48
 406 ALA   ( 111-)  C      CA     8.6    45.04    34.09
 453 THR   (   7-)  D      C     -7.0   -10.23     0.30
 698 CYS   ( 101-)  E      CA     6.6    46.06    34.33
The average deviation= 1.202

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.

 407 LYS   ( 112-)  C    7.45
 349 GLY   (  54-)  C    7.04
 406 ALA   ( 111-)  C    5.96
 146 PHE   ( 152-)  A    5.81
 698 CYS   ( 101-)  E    5.61
 597 TYR   ( 151-)  D    5.53
 397 GLN   ( 102-)  C    5.26
 594 GLY   ( 148-)  D    5.08
 519 HIS   (  73-)  D    4.91
 732 GLU   ( 135-)  E    4.80
 181 LEU   (  36-)  B    4.73
 533 TYR   (  87-)  D    4.58
 401 PRO   ( 106-)  C    4.58
  96 GLN   ( 102-)  A    4.57
 557 ALA   ( 111-)  D    4.52
 258 PRO   ( 113-)  B    4.44
 247 GLN   ( 102-)  B    4.43
 308 PRO   (  12-)  C    4.42
 699 GLN   ( 102-)  E    4.40
 633 LEU   (  36-)  E    4.37
 246 CYS   ( 101-)  B    4.29
 703 PRO   ( 106-)  E    4.28
 895 SER   ( 147-)  F    4.27
  84 LYS   (  90-)  A    4.24
 894 GLU   ( 146-)  F    4.20
 861 PRO   ( 113-)  F    4.16
 245 PRO   ( 100-)  B    4.12
 292 SER   ( 147-)  B    4.10
 562 GLU   ( 116-)  D    4.08
 127 SER   ( 133-)  A    4.03
 503 LEU   (  57-)  D    4.03

Warning: High tau angle deviations

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

Tau angle RMS Z-score : 1.805

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -5.080

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.

 384 THR   (  89-)  C    -3.5
 518 THR   (  72-)  D    -3.4
 551 THR   ( 105-)  D    -3.4
  66 THR   (  72-)  A    -3.4
 702 THR   ( 105-)  E    -3.2
 250 THR   ( 105-)  B    -3.1
 552 PRO   ( 106-)  D    -3.1
 395 PRO   ( 100-)  C    -3.1
 401 PRO   ( 106-)  C    -3.1
 670 HIS   (  73-)  E    -3.0
 516 PRO   (  70-)  D    -2.9
 629 ARG   (  32-)  E    -2.9
 820 THR   (  72-)  F    -2.9
 367 THR   (  72-)  C    -2.8
 408 PRO   ( 113-)  C    -2.8
 100 PRO   ( 106-)  A    -2.8
 316 PRO   (  20-)  C    -2.8
  99 THR   ( 105-)  A    -2.7
 497 PRO   (  51-)  D    -2.6
 553 GLU   ( 107-)  D    -2.6
 853 THR   ( 105-)  F    -2.6
 823 LEU   (  75-)  F    -2.6
 477 ARG   (  31-)  D    -2.6
  68 VAL   (  74-)  A    -2.6
 748 TYR   ( 151-)  E    -2.5
And so on for a total of 121 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.

   3 SER   (   9-)  A  Poor phi/psi
  24 ASN   (  30-)  A  Poor phi/psi
  38 ARG   (  44-)  A  Poor phi/psi
  40 ASN   (  46-)  A  Poor phi/psi
  46 SER   (  52-)  A  Poor phi/psi
  47 GLU   (  53-)  A  Poor phi/psi
  64 PRO   (  70-)  A  Poor phi/psi
  66 THR   (  72-)  A  Poor phi/psi
  69 LEU   (  75-)  A  Poor phi/psi
  80 SER   (  86-)  A  Poor phi/psi
  82 GLN   (  88-)  A  Poor phi/psi
  97 ARG   ( 103-)  A  Poor phi/psi
  98 GLU   ( 104-)  A  Poor phi/psi
  99 THR   ( 105-)  A  Poor phi/psi
 101 GLU   ( 107-)  A  Poor phi/psi
 103 ALA   ( 109-)  A  Poor phi/psi
 104 GLU   ( 110-)  A  Poor phi/psi
 120 LEU   ( 126-)  A  Poor phi/psi
 155 ASP   (  10-)  B  Poor phi/psi
 167 ALA   (  22-)  B  Poor phi/psi
 176 ARG   (  31-)  B  Poor phi/psi
 178 ALA   (  33-)  B  Poor phi/psi
 183 ALA   (  38-)  B  Poor phi/psi
 185 GLY   (  40-)  B  Poor phi/psi
 189 ARG   (  44-)  B  Poor phi/psi
And so on for a total of 124 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 : -5.593

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!

   3 SER   (   9-)  A      0
   4 ASP   (  10-)  A      0
  15 GLN   (  21-)  A      0
  16 ALA   (  22-)  A      0
  17 GLU   (  23-)  A      0
  21 GLN   (  27-)  A      0
  24 ASN   (  30-)  A      0
  25 ARG   (  31-)  A      0
  26 ARG   (  32-)  A      0
  27 ALA   (  33-)  A      0
  28 ASN   (  34-)  A      0
  33 ASN   (  39-)  A      0
  38 ARG   (  44-)  A      0
  39 ASP   (  45-)  A      0
  40 ASN   (  46-)  A      0
  45 PRO   (  51-)  A      0
  46 SER   (  52-)  A      0
  47 GLU   (  53-)  A      0
  49 LEU   (  55-)  A      0
  61 GLN   (  67-)  A      0
  64 PRO   (  70-)  A      0
  65 SER   (  71-)  A      0
  66 THR   (  72-)  A      0
  67 HIS   (  73-)  A      0
  68 VAL   (  74-)  A      0
And so on for a total of 525 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.245

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!

 142 GLY   ( 148-)  A   1.92   26
 253 GLY   ( 108-)  B   1.87   19
 663 GLY   (  66-)  E   1.82   30
 417 GLY   ( 122-)  C   1.67   20
 870 GLY   ( 122-)  F   1.51   54

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

 183 ALA   (  38-)  B   1.68
 484 ALA   (  38-)  D   2.77
 556 GLU   ( 110-)  D   3.12

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]

 153 PRO   (   8-)  B    0.58 HIGH
 401 PRO   ( 106-)  C    0.48 HIGH
 408 PRO   ( 113-)  C    0.53 HIGH
 497 PRO   (  51-)  D    0.47 HIGH
 552 PRO   ( 106-)  D    0.51 HIGH
 710 PRO   ( 113-)  E    0.17 LOW
 818 PRO   (  70-)  F    0.16 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].

   2 PRO   (   8-)  A     8.0 envelop N (0 degrees)
 100 PRO   ( 106-)  A   -55.1 half-chair C-beta/C-alpha (-54 degrees)
 153 PRO   (   8-)  B  -163.0 half-chair N/C-delta (-162 degrees)
 196 PRO   (  51-)  B   -54.9 half-chair C-beta/C-alpha (-54 degrees)
 215 PRO   (  70-)  B   -65.0 envelop C-beta (-72 degrees)
 245 PRO   ( 100-)  B    27.7 envelop C-delta (36 degrees)
 258 PRO   ( 113-)  B    49.8 half-chair C-delta/C-gamma (54 degrees)
 262 PRO   ( 117-)  B   -41.5 envelop C-alpha (-36 degrees)
 284 PRO   ( 139-)  B    26.4 half-chair N/C-delta (18 degrees)
 304 PRO   (   8-)  C  -166.3 half-chair N/C-delta (-162 degrees)
 308 PRO   (  12-)  C    52.2 half-chair C-delta/C-gamma (54 degrees)
 316 PRO   (  20-)  C   -40.3 envelop C-alpha (-36 degrees)
 346 PRO   (  51-)  C    33.3 envelop C-delta (36 degrees)
 395 PRO   ( 100-)  C   125.4 half-chair C-beta/C-alpha (126 degrees)
 401 PRO   ( 106-)  C   118.1 half-chair C-beta/C-alpha (126 degrees)
 408 PRO   ( 113-)  C   160.9 half-chair C-alpha/N (162 degrees)
 412 PRO   ( 117-)  C   -44.6 envelop C-alpha (-36 degrees)
 454 PRO   (   8-)  D   105.2 envelop C-beta (108 degrees)
 516 PRO   (  70-)  D   -48.7 half-chair C-beta/C-alpha (-54 degrees)
 552 PRO   ( 106-)  D   147.4 envelop C-alpha (144 degrees)
 563 PRO   ( 117-)  D    15.4 half-chair N/C-delta (18 degrees)
 605 PRO   (   8-)  E   -63.7 envelop C-beta (-72 degrees)
 697 PRO   ( 100-)  E   -62.3 half-chair C-beta/C-alpha (-54 degrees)
 703 PRO   ( 106-)  E  -116.2 envelop C-gamma (-108 degrees)
 714 PRO   ( 117-)  E    27.3 envelop C-delta (36 degrees)
 760 PRO   (  12-)  F    28.6 envelop C-delta (36 degrees)
 768 PRO   (  20-)  F    40.3 envelop C-delta (36 degrees)
 848 PRO   ( 100-)  F   -64.0 envelop C-beta (-72 degrees)
 865 PRO   ( 117-)  F   -61.2 half-chair C-beta/C-alpha (-54 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.

  96 GLN   ( 102-)  A      NE2 <->  214 CYS   (  69-)  B      SG     0.64    2.66  INTRA
 214 CYS   (  69-)  B      CB  <->  249 GLU   ( 104-)  B      CB     0.47    2.73  INTRA
  21 GLN   (  27-)  A      NE2 <->   40 ASN   (  46-)  A      OD1    0.39    2.31  INTRA
 817 CYS   (  69-)  F      SG  <->  862 TRP   ( 114-)  F      NE1    0.35    2.95  INTRA
 622 GLN   (  25-)  E      OE1 <->  624 GLN   (  27-)  E      NE2    0.35    2.35  INTRA BL
  67 HIS   (  73-)  A      NE2 <->  258 PRO   ( 113-)  B      O      0.35    2.35  INTRA BF
 160 HIS   (  15-)  B      ND1 <->  204 TYR   (  59-)  B      OH     0.34    2.36  INTRA BL
 214 CYS   (  69-)  B      SG  <->  249 GLU   ( 104-)  B      CG     0.33    3.07  INTRA
 400 THR   ( 105-)  C      O   <->  402 GLU   ( 107-)  C      N      0.31    2.39  INTRA BF
 852 GLU   ( 104-)  F      O   <->  853 THR   ( 105-)  F      C      0.29    2.31  INTRA
 291 GLU   ( 146-)  B      CB  <->  292 SER   ( 147-)  B      N      0.29    2.41  INTRA BL
 291 GLU   ( 146-)  B      CG  <->  292 SER   ( 147-)  B      N      0.27    2.73  INTRA BL
 356 GLN   (  61-)  C      NE2 <->  413 ILE   ( 118-)  C      O      0.27    2.43  INTRA
 312 VAL   (  16-)  C      N   <->  447 PHE   ( 152-)  C      O      0.27    2.43  INTRA BL
 160 HIS   (  15-)  B      N   <->  181 LEU   (  36-)  B      O      0.26    2.44  INTRA
 702 THR   ( 105-)  E      N   <->  703 PRO   ( 106-)  E      CD     0.26    2.74  INTRA
 700 ARG   ( 103-)  E      CD  <->  701 GLU   ( 104-)  E      N      0.24    2.76  INTRA
 372 THR   (  77-)  C      N   <->  432 ASN   ( 137-)  C      OD1    0.24    2.46  INTRA
  92 LYS   (  98-)  A      NZ  <->  393 LYS   (  98-)  C      NZ     0.24    2.61  INTRA
 132 ARG   ( 138-)  A      NH2 <->  584 ARG   ( 138-)  D      NH2    0.24    2.61  INTRA
 484 ALA   (  38-)  D      CB  <->  485 ASN   (  39-)  D      N      0.24    2.46  INTRA B3
 829 SER   (  81-)  F      O   <->  881 SER   ( 133-)  F      N      0.24    2.46  INTRA BL
 360 LYS   (  65-)  C      N   <->  436 TYR   ( 141-)  C      O      0.23    2.47  INTRA BL
 707 GLU   ( 110-)  E      N   <->  708 ALA   ( 111-)  E      N      0.23    2.37  INTRA B3
 193 LEU   (  48-)  B      O   <->  277 LEU   ( 132-)  B      N      0.23    2.47  INTRA
And so on for a total of 247 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 700 ARG   ( 103-)  E      -7.66
 248 ARG   ( 103-)  B      -7.54
 166 GLN   (  21-)  B      -7.21
 851 ARG   ( 103-)  F      -6.92
 176 ARG   (  31-)  B      -6.69
  25 ARG   (  31-)  A      -6.68
  15 GLN   (  21-)  A      -6.64
 382 TYR   (  87-)  C      -6.55
 892 PHE   ( 144-)  F      -6.48
 779 ARG   (  31-)  F      -6.46
 769 GLN   (  21-)  F      -6.38
 549 ARG   ( 103-)  D      -6.32
 477 ARG   (  31-)  D      -6.31
 247 GLN   ( 102-)  B      -6.25
 773 GLN   (  25-)  F      -6.14
 398 ARG   ( 103-)  C      -6.10
 321 GLN   (  25-)  C      -5.98
 629 ARG   (  32-)  E      -5.76
 362 GLN   (  67-)  C      -5.73
 402 GLU   ( 107-)  C      -5.64
 699 GLN   ( 102-)  E      -5.63
  61 GLN   (  67-)  A      -5.49
 815 GLN   (  67-)  F      -5.41
 548 GLN   ( 102-)  D      -5.38
  97 ARG   ( 103-)  A      -5.32
 664 GLN   (  67-)  E      -5.31
 707 GLU   ( 110-)  E      -5.28
 319 GLU   (  23-)  C      -5.28
 407 LYS   ( 112-)  C      -5.27
 212 GLN   (  67-)  B      -5.26
 232 TYR   (  87-)  B      -5.22
 556 GLU   ( 110-)  D      -5.16
 405 GLU   ( 110-)  C      -5.09
 255 GLU   ( 110-)  B      -5.08
 620 GLU   (  23-)  E      -5.07
 622 GLN   (  25-)  E      -5.03

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

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

  96 GLN   ( 102-)  A        98 - GLU    104- ( A)         -4.94
 247 GLN   ( 102-)  B       249 - GLU    104- ( B)         -6.04
 397 GLN   ( 102-)  C       399 - GLU    104- ( C)         -5.14
 548 GLN   ( 102-)  D       550 - GLU    104- ( D)         -5.47
 699 GLN   ( 102-)  E       701 - GLU    104- ( E)         -5.95
 850 GLN   ( 102-)  F       852 - GLU    104- ( F)         -5.23

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

 395 PRO   ( 100-)  C   -3.11
 821 HIS   (  73-)  F   -3.08
 670 HIS   (  73-)  E   -2.92
 630 ALA   (  33-)  E   -2.90
 218 HIS   (  73-)  B   -2.63
 519 HIS   (  73-)  D   -2.62
  32 ALA   (  38-)  A   -2.59
 490 ARG   (  44-)  D   -2.59
  96 GLN   ( 102-)  A   -2.59

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.

  37 LEU   (  43-)  A     -   40 ASN   (  46-)  A        -1.80

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Water, ion, and hydrogenbond related checks

Error: 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.

  33 ASN   (  39-)  A
 119 GLN   ( 125-)  A
 164 ASN   (  19-)  B
 294 GLN   ( 149-)  B
 524 HIS   (  78-)  D
 627 ASN   (  30-)  E
 664 GLN   (  67-)  E
 670 HIS   (  73-)  E
 850 GLN   ( 102-)  F

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

  12 ALA   (  18-)  A      N
  20 LEU   (  26-)  A      N
  24 ASN   (  30-)  A      N
  24 ASN   (  30-)  A      ND2
  26 ARG   (  32-)  A      N
  37 LEU   (  43-)  A      N
  38 ARG   (  44-)  A      N
  39 ASP   (  45-)  A      N
  40 ASN   (  46-)  A      ND2
  44 VAL   (  50-)  A      N
  59 LYS   (  65-)  A      NZ
  63 CYS   (  69-)  A      N
  68 VAL   (  74-)  A      N
  69 LEU   (  75-)  A      N
  76 ARG   (  82-)  A      NE
  78 VAL   (  84-)  A      N
  86 ASN   (  92-)  A      ND2
  91 ILE   (  97-)  A      N
  93 SER   (  99-)  A      OG
  95 CYS   ( 101-)  A      N
 104 GLU   ( 110-)  A      N
 115 GLY   ( 121-)  A      N
 119 GLN   ( 125-)  A      N
 120 LEU   ( 126-)  A      N
 122 LYS   ( 128-)  A      N
And so on for a total of 177 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.

  72 HIS   (  78-)  A      ND1
 121 GLU   ( 127-)  A      OE1
 140 GLU   ( 146-)  A      OE1
 206 GLN   (  61-)  B      OE1
 223 HIS   (  78-)  B      ND1
 275 ASP   ( 130-)  B      OD1
 291 GLU   ( 146-)  B      OE2
 373 HIS   (  78-)  C      ND1
 387 ASN   (  92-)  C      OD1
 425 ASP   ( 130-)  C      OD1
 441 GLU   ( 146-)  C      OE2
 485 ASN   (  39-)  D      OD1
 519 HIS   (  73-)  D      NE2
 576 ASP   ( 130-)  D      OD1
 595 GLN   ( 149-)  D      OE1
 644 GLN   (  47-)  E      OE1
 658 GLN   (  61-)  E      OE1
 675 HIS   (  78-)  E      ND1
 699 GLN   ( 102-)  E      OE1
 727 ASP   ( 130-)  E      OD1
 737 ASP   ( 140-)  E      OD1
 743 GLU   ( 146-)  E      OE2
 746 GLN   ( 149-)  E      OE1
 763 HIS   (  15-)  F      NE2
 782 ASN   (  34-)  F      OD1
 795 GLN   (  47-)  F      OE1
 809 GLN   (  61-)  F      OE1
 840 ASN   (  92-)  F      OD1
 873 GLN   ( 125-)  F      OE1
 878 ASP   ( 130-)  F      OD1
 888 ASP   ( 140-)  F      OD1

Warning: No crystallisation information

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

Warning: Possible wrong residue type

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

 121 GLU   ( 127-)  A   H-bonding suggests Gln; but Alt-Rotamer
 187 GLU   (  42-)  B   H-bonding suggests Gln
 275 ASP   ( 130-)  B   H-bonding suggests Asn; but Alt-Rotamer
 291 GLU   ( 146-)  B   H-bonding suggests Gln
 422 GLU   ( 127-)  C   H-bonding suggests Gln
 488 GLU   (  42-)  D   H-bonding suggests Gln; but Alt-Rotamer
 556 GLU   ( 110-)  D   H-bonding suggests Gln
 562 GLU   ( 116-)  D   H-bonding suggests Gln; but Alt-Rotamer
 576 ASP   ( 130-)  D   H-bonding suggests Asn
 713 GLU   ( 116-)  E   H-bonding suggests Gln
 727 ASP   ( 130-)  E   H-bonding suggests Asn; but Alt-Rotamer
 743 GLU   ( 146-)  E   H-bonding suggests Gln
 878 ASP   ( 130-)  F   H-bonding suggests Asn; but Alt-Rotamer
 888 ASP   ( 140-)  F   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.799
  2nd generation packing quality :  -3.376 (poor)
  Ramachandran plot appearance   :  -5.080 (bad)
  chi-1/chi-2 rotamer normality  :  -5.593 (bad)
  Backbone conformation          :  -1.242

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.727
  Bond angles                    :   1.624
  Omega angle restraints         :   0.226 (tight)
  Side chain planarity           :   0.437 (tight)
  Improper dihedral distribution :   1.392
  B-factor distribution          :   1.037
  Inside/Outside distribution    :   0.989

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 : 3.10


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.6
  2nd generation packing quality :  -1.2
  Ramachandran plot appearance   :  -2.3
  chi-1/chi-2 rotamer normality  :  -3.0 (poor)
  Backbone conformation          :  -0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.727
  Bond angles                    :   1.624
  Omega angle restraints         :   0.226 (tight)
  Side chain planarity           :   0.437 (tight)
  Improper dihedral distribution :   1.392
  B-factor distribution          :   1.037
  Inside/Outside distribution    :   0.989
==============

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.