WHAT IF Check report

This file was created 2011-12-18 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 pdb1t75.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 : 0.850
CA-only RMS fit for the two chains : 0.432

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 : 0.911
CA-only RMS fit for the two chains : 0.546

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 : 1.006
CA-only RMS fit for the two chains : 0.541

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: B and D

All-atom RMS fit for the two chains : 0.912
CA-only RMS fit for the two chains : 0.498

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

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and E

All-atom RMS fit for the two chains : 0.924
CA-only RMS fit for the two chains : 0.555

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: B and E

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: D

Note: Ramachandran plot

Chain identifier: E

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

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 4

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

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Nomenclature related problems

Warning: Tyrosine convention problem

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

  98 TYR   (  99-)  A
 312 TYR   (  99-)  B
 394 TYR   ( 181-)  B
 526 TYR   (  99-)  D
 608 TYR   ( 181-)  D
 740 TYR   (  99-)  E
 822 TYR   ( 181-)  E

Warning: Phenylalanine convention problem

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

  24 PHE   (  25-)  A
  25 PHE   (  26-)  A
 127 PHE   ( 128-)  A
 239 PHE   (  26-)  B
 341 PHE   ( 128-)  B
 453 PHE   (  26-)  D
 555 PHE   ( 128-)  D
 666 PHE   (  25-)  E
 667 PHE   (  26-)  E
 769 PHE   ( 128-)  E

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.

 143 ASP   ( 144-)  A
 357 ASP   ( 144-)  B
 571 ASP   ( 144-)  D
 785 ASP   ( 144-)  E

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.

  19 GLU   (  20-)  A
  88 GLU   (  89-)  A
 108 GLU   ( 109-)  A
 135 GLU   ( 136-)  A
 198 GLU   ( 199-)  A
 201 GLU   ( 202-)  A
 240 GLU   (  27-)  B
 269 GLU   (  56-)  B
 325 GLU   ( 112-)  B
 483 GLU   (  56-)  D
 486 GLU   (  59-)  D
 516 GLU   (  89-)  D
 661 GLU   (  20-)  E
 730 GLU   (  89-)  E
 777 GLU   ( 136-)  E

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.

  18 VAL   (  19-)  A      CA   C     1.41   -5.6
  26 GLU   (  27-)  A      CB   CG    1.34   -6.1
  26 GLU   (  27-)  A      N   -C     1.20   -6.4
  62 HIS   (  63-)  A      CB   CG    1.57    4.9
 229 LYS   (  16-)  B      N   -C     1.02  -15.2

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

 |  0.999511 -0.000286 -0.000272|
 | -0.000286  0.998471 -0.000181|
 | -0.000272 -0.000181  0.998217|
Proposed new scale matrix

 |  0.009058  0.000003  0.000002|
 |  0.000003  0.009068  0.000002|
 |  0.000002  0.000001  0.006163|
With corresponding cell

    A    = 110.394  B   = 110.280  C    = 162.259
    Alpha=  90.021  Beta=  90.031  Gamma=  90.033

The CRYST1 cell dimensions

    A    = 110.447  B   = 110.447  C    = 162.536
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 51.831
(Under-)estimated Z-score: 5.306

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.

  18 VAL   (  19-)  A      C    CA   CB   99.69   -5.5
  19 GLU   (  20-)  A     -C    N    CA  111.03   -5.9
  19 GLU   (  20-)  A      C    CA   CB  119.80    5.1
  19 GLU   (  20-)  A      CA   CB   CG  126.37    6.1
  19 GLU   (  20-)  A      CB   CG   CD  105.68   -4.1
  21 ASP   (  22-)  A      CA   CB   CG  117.64    5.0
  22 PRO   (  23-)  A      CD   N    CA   97.00  -10.7
  23 GLY   (  24-)  A     -C    N    CA  128.01    4.4
  26 GLU   (  27-)  A     -C    N    CA  109.39   -6.8
  26 GLU   (  27-)  A      CA   CB   CG  135.23   10.6
  26 GLU   (  27-)  A      CB   CG   CD  126.39    8.1
  30 GLN   (  31-)  A     -C    N    CA  113.75   -4.4
  30 GLN   (  31-)  A      CG   CD   NE2 126.08    6.5
  30 GLN   (  31-)  A      NE2  CD   OE1 112.79   -9.8
  32 GLN   (  33-)  A      CG   CD   NE2 126.39    6.7
  32 GLN   (  33-)  A      NE2  CD   OE1 112.83   -9.8
  34 PRO   (  35-)  A      N    CA   CB  109.14    5.6
  34 PRO   (  35-)  A      CD   N    CA   83.26  -20.5
  47 PRO   (  48-)  A      CD   N    CA   90.91  -15.1
  69 VAL   (  70-)  A      C    CA   CB  118.14    4.2
 121 HIS   ( 122-)  A      CG   ND1  CE1 109.95    4.3
 176 HIS   ( 177-)  A      CG   ND1  CE1 109.64    4.0
 202 GLN   ( 203-)  A      CG   CD   NE2 126.41    6.7
 202 GLN   ( 203-)  A      NE2  CD   OE1 112.82   -9.8
 213 LEU   ( 214-)  A     -C    N    CA  114.36   -4.1
 229 LYS   (  16-)  B     -CA  -C    N   106.54   -4.8
 229 LYS   (  16-)  B     -C    N    CA  104.72   -9.4
 236 PRO   (  23-)  B     -C    N    CD  103.70   -5.2
 236 PRO   (  23-)  B      N    CA   C   122.44    4.3
 236 PRO   (  23-)  B      CD   N    CA   90.01  -15.7
 238 PHE   (  25-)  B      N    CA   CB  103.03   -4.4
 238 PHE   (  25-)  B      CA   CB   CG  119.12    5.3
 244 GLN   (  31-)  B     -C    N    CA  110.27   -6.3
 244 GLN   (  31-)  B      C    CA   CB  125.06    7.9
 244 GLN   (  31-)  B      CG   CD   NE2 126.99    7.1
 244 GLN   (  31-)  B      NE2  CD   OE1 113.51   -9.1
 246 GLN   (  33-)  B      CB   CG   CD  120.59    4.7
 246 GLN   (  33-)  B      CG   CD   NE2 125.97    6.4
 246 GLN   (  33-)  B      NE2  CD   OE1 112.62  -10.0
 613 GLY   ( 186-)  D     -C    N    CA  129.17    5.0
 739 HIS   (  98-)  E      CG   ND1  CE1 109.74    4.1
 825 HIS   ( 184-)  E      CG   ND1  CE1 109.68    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.

  19 GLU   (  20-)  A
  88 GLU   (  89-)  A
 108 GLU   ( 109-)  A
 135 GLU   ( 136-)  A
 143 ASP   ( 144-)  A
 198 GLU   ( 199-)  A
 201 GLU   ( 202-)  A
 240 GLU   (  27-)  B
 269 GLU   (  56-)  B
 325 GLU   ( 112-)  B
 357 ASP   ( 144-)  B
 483 GLU   (  56-)  D
 486 GLU   (  59-)  D
 516 GLU   (  89-)  D
 571 ASP   ( 144-)  D
 661 GLU   (  20-)  E
 730 GLU   (  89-)  E
 777 GLU   ( 136-)  E
 785 ASP   ( 144-)  E

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.

  22 PRO   (  23-)  A      N     -8.4   -29.87    -2.48
  34 PRO   (  35-)  A      N    -11.2   -39.32    -2.48
  47 PRO   (  48-)  A      N     -9.6   -34.06    -2.48
 228 SER   (  15-)  B      C     -7.3   -11.63     0.37
 236 PRO   (  23-)  B      N    -15.7   -53.98    -2.48
The average deviation= 0.983

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.

 217 ILE   (   4-)  B    6.37
 487 LEU   (  60-)  D    4.48
 772 SER   ( 131-)  E    4.37
  20 GLU   (  21-)  A    4.23

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.

 484 PRO   (  57-)  D    -2.7
 824 ILE   ( 183-)  E    -2.6
 661 GLU   (  20-)  E    -2.5
  44 SER   (  45-)  A    -2.5
 302 GLU   (  89-)  B    -2.4
 757 ILE   ( 116-)  E    -2.4
  67 ASN   (  68-)  A    -2.3
 516 GLU   (  89-)  D    -2.3
 472 SER   (  45-)  D    -2.3
 115 ILE   ( 116-)  A    -2.2
 286 THR   (  73-)  B    -2.2
 130 SER   ( 131-)  A    -2.2
 281 ASN   (  68-)  B    -2.2
 196 ASN   ( 197-)  A    -2.2
  23 GLY   (  24-)  A    -2.1
  22 PRO   (  23-)  A    -2.1
  65 VAL   (  66-)  A    -2.1
 605 GLY   ( 178-)  D    -2.1
 329 ILE   ( 116-)  B    -2.1
 619 ASP   ( 192-)  D    -2.0
 258 SER   (  45-)  B    -2.0
 448 GLU   (  21-)  D    -2.0
 427 LEU   ( 214-)  B    -2.0
 191 ASP   ( 192-)  A    -2.0
 543 ILE   ( 116-)  D    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  22 PRO   (  23-)  A  Poor phi/psi
  23 GLY   (  24-)  A  Poor phi/psi
  24 PHE   (  25-)  A  Poor phi/psi
  25 PHE   (  26-)  A  omega poor
  31 ALA   (  32-)  A  Poor phi/psi
  66 ALA   (  67-)  A  Poor phi/psi
 109 ASN   ( 110-)  A  Poor phi/psi
 184 ASP   ( 185-)  A  Poor phi/psi
 191 ASP   ( 192-)  A  Poor phi/psi
 228 SER   (  15-)  B  Poor phi/psi
 245 ALA   (  32-)  B  Poor phi/psi
 265 LEU   (  52-)  B  omega poor
 273 LEU   (  60-)  B  omega poor
 280 ALA   (  67-)  B  Poor phi/psi
 285 HIS   (  72-)  B  omega poor
 302 GLU   (  89-)  B  Poor phi/psi
 327 GLY   ( 114-)  B  omega poor
 398 ASP   ( 185-)  B  Poor phi/psi
 402 ARG   ( 189-)  B  omega poor
 404 LEU   ( 191-)  B  omega poor
 405 ASP   ( 192-)  B  Poor phi/psi
 424 ASN   ( 211-)  B  omega poor
 426 LYS   ( 213-)  B  omega poor
 427 LEU   ( 214-)  B  Poor phi/psi
 447 GLU   (  20-)  D  omega poor
 459 ALA   (  32-)  D  Poor phi/psi
 494 ALA   (  67-)  D  Poor phi/psi
 613 GLY   ( 186-)  D  Poor phi/psi
 618 LEU   ( 191-)  D  omega poor
 619 ASP   ( 192-)  D  Poor phi/psi
 625 ARG   ( 198-)  D  omega poor
 662 GLU   (  21-)  E  Poor phi/psi, omega poor
 673 ALA   (  32-)  E  Poor phi/psi
 708 ALA   (  67-)  E  Poor phi/psi
 755 GLY   ( 114-)  E  omega poor
 832 LEU   ( 191-)  E  omega poor
 833 ASP   ( 192-)  E  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.259

Warning: chi-1/chi-2 angle correlation Z-score low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is a bit low.

chi-1/chi-2 correlation Z-score : -3.259

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.

  14 SER   (  15-)  A    0.39
 559 SER   ( 132-)  D    0.39
 345 SER   ( 132-)  B    0.39
 650 SER   (   9-)  E    0.39

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

  21 ASP   (  22-)  A      0
  31 ALA   (  32-)  A      0
  34 PRO   (  35-)  A      0
  43 ASP   (  44-)  A      0
  44 SER   (  45-)  A      0
  45 ARG   (  46-)  A      0
  56 PRO   (  57-)  A      0
  58 GLU   (  59-)  A      0
  64 ASN   (  65-)  A      0
  65 VAL   (  66-)  A      0
  66 ALA   (  67-)  A      0
  67 ASN   (  68-)  A      0
  70 ILE   (  71-)  A      0
  71 HIS   (  72-)  A      0
  72 THR   (  73-)  A      0
  85 ASP   (  86-)  A      0
  87 LEU   (  88-)  A      0
  88 GLU   (  89-)  A      0
  98 TYR   (  99-)  A      0
 114 LEU   ( 115-)  A      0
 136 MET   ( 137-)  A      0
 178 TRP   ( 179-)  A      0
 191 ASP   ( 192-)  A      0
 192 VAL   ( 193-)  A      0
 193 THR   ( 194-)  A      0
And so on for a total of 274 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!

 658 MET   (  17-)  E   1.75   35

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]

  22 PRO   (  23-)  A    0.51 HIGH
  34 PRO   (  35-)  A    0.64 HIGH
  47 PRO   (  48-)  A    0.59 HIGH
 236 PRO   (  23-)  B    0.60 HIGH
 538 PRO   ( 111-)  D    0.11 LOW
 779 PRO   ( 138-)  E    0.19 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].

  22 PRO   (  23-)  A   164.1 half-chair C-alpha/N (162 degrees)
  34 PRO   (  35-)  A  -168.3 half-chair N/C-delta (-162 degrees)
  47 PRO   (  48-)  A  -178.3 envelop N (180 degrees)
  56 PRO   (  57-)  A  -120.9 half-chair C-delta/C-gamma (-126 degrees)
 236 PRO   (  23-)  B  -174.9 envelop N (180 degrees)
 270 PRO   (  57-)  B   105.8 envelop C-beta (108 degrees)
 484 PRO   (  57-)  D  -141.5 envelop C-delta (-144 degrees)
 565 PRO   ( 138-)  D  -123.4 half-chair C-delta/C-gamma (-126 degrees)
 698 PRO   (  57-)  E  -133.7 half-chair C-delta/C-gamma (-126 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

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

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

 215 LYS   (   2-)  B      CE   <->   862 HOH   ( 277 )  B      O    1.58    1.22  INTRA BF
 215 LYS   (   2-)  B      NZ   <->   862 HOH   ( 277 )  B      O    1.37    1.33  INTRA BF
 232 VAL   (  19-)  B      O    <->   236 PRO   (  23-)  B      CG   0.92    1.88  INTRA BF
 612 ASP   ( 185-)  D      O    <->   667 PHE   (  26-)  E      CZ   0.91    1.89  INTRA BF
 232 VAL   (  19-)  B      O    <->   236 PRO   (  23-)  B      CD   0.77    2.03  INTRA BF
 215 LYS   (   2-)  B      NZ   <->   862 HOH   ( 278 )  B      O    0.66    2.04  INTRA BF
 226 LEU   (  13-)  B      O    <->   230 MET   (  17-)  B      CG   0.63    2.17  INTRA BF
  21 ASP   (  22-)  A      O    <->    23 GLY   (  24-)  A      N    0.56    2.14  INTRA BF
 612 ASP   ( 185-)  D      C    <->   667 PHE   (  26-)  E      CZ   0.53    2.67  INTRA BF
  24 PHE   (  25-)  A      CD1  <->    25 PHE   (  26-)  A      CD1  0.52    2.68  INTRA BF
 155 TYR   ( 156-)  A      OH   <->   201 GLU   ( 202-)  A      OE1  0.52    1.88  INTRA BF
 612 ASP   ( 185-)  D      O    <->   667 PHE   (  26-)  E      CE2  0.52    2.28  INTRA BF
 216 ASP   (   3-)  B      OD1  <->   217 ILE   (   4-)  B      N    0.46    2.14  INTRA BF
 354 ARG   ( 141-)  B      CD   <->   862 HOH   ( 248 )  B      O    0.46    2.34  INTRA BF
  24 PHE   (  25-)  A      CE1  <->    25 PHE   (  26-)  A      CE1  0.46    2.74  INTRA BF
 232 VAL   (  19-)  B      C    <->   236 PRO   (  23-)  B      CD   0.42    2.78  INTRA BF
 215 LYS   (   2-)  B      CD   <->   862 HOH   ( 277 )  B      O    0.40    2.40  INTRA BF
 604 HIS   ( 177-)  D      ND1  <->   863 HOH   ( 257 )  D      O    0.38    2.32  INTRA
 305 HIS   (  92-)  B      ND1  <->   390 HIS   ( 177-)  B      NE2  0.35    2.65  INTRA BL
  24 PHE   (  25-)  A      CD1  <->    25 PHE   (  26-)  A      CE1  0.34    2.86  INTRA BF
 232 VAL   (  19-)  B      CG2  <->   239 PHE   (  26-)  B      CE2  0.32    2.88  INTRA BF
 228 SER   (  15-)  B      C    <->   229 LYS   (  16-)  B      CA   0.30    2.00  INTRA BF
  21 ASP   (  22-)  A      C    <->    23 GLY   (  24-)  A      N    0.30    2.60  INTRA BF
 140 ARG   ( 141-)  A      NH1  <->   214 LYS   ( 215-)  A      NZ   0.30    2.55  INTRA BF
 801 HIS   ( 160-)  E      NE2  <->   843 GLU   ( 202-)  E      OE2  0.29    2.41  INTRA BL
And so on for a total of 140 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: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

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.

  32 GLN   (  33-)  A      -6.55
 674 GLN   (  33-)  E      -6.31
 460 GLN   (  33-)  D      -6.26
 611 HIS   ( 184-)  D      -6.24
 473 ARG   (  46-)  D      -6.23
 246 GLN   (  33-)  B      -6.06
 183 HIS   ( 184-)  A      -6.06
 687 ARG   (  46-)  E      -6.05
 397 HIS   ( 184-)  B      -6.02
  45 ARG   (  46-)  A      -5.94
 259 ARG   (  46-)  B      -5.78
 753 GLU   ( 112-)  E      -5.71
 373 HIS   ( 160-)  B      -5.54
 587 HIS   ( 160-)  D      -5.54
 825 HIS   ( 184-)  E      -5.53
 325 GLU   ( 112-)  B      -5.44
 801 HIS   ( 160-)  E      -5.43
 111 GLU   ( 112-)  A      -5.42
 159 HIS   ( 160-)  A      -5.37
 539 GLU   ( 112-)  D      -5.25
 427 LEU   ( 214-)  B      -5.12
 322 GLU   ( 109-)  B      -5.10
 750 GLU   ( 109-)  E      -5.09
 108 GLU   ( 109-)  A      -5.08
 536 GLU   ( 109-)  D      -5.07
  20 GLU   (  21-)  A      -5.06
 234 GLU   (  21-)  B      -5.02
 448 GLU   (  21-)  D      -5.02

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: 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: 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: D

Note: Second generation quality Z-score plot

Chain identifier: E

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

 862 HOH   ( 258 )  B      O     81.77   44.50  123.97

Error: Water molecules without hydrogen bonds

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

 861 HOH   ( 240 )  A      O
 861 HOH   ( 241 )  A      O
 861 HOH   ( 245 )  A      O
 862 HOH   ( 239 )  B      O
 862 HOH   ( 240 )  B      O
 862 HOH   ( 258 )  B      O
 862 HOH   ( 281 )  B      O
 864 HOH   ( 227 )  E      O
 864 HOH   ( 232 )  E      O
 864 HOH   ( 240 )  E      O
 864 HOH   ( 242 )  E      O
 864 HOH   ( 272 )  E      O
Metal-coordinating Histidine residue  97 fixed to   1
Metal-coordinating Histidine residue 311 fixed to   1
Metal-coordinating Histidine residue 525 fixed to   1
Metal-coordinating Histidine residue 739 fixed to   1

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.

  10 ASN   (  11-)  A
 206 HIS   ( 207-)  A
 420 HIS   ( 207-)  B
 848 HIS   ( 207-)  E

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.

   3 ILE   (   4-)  A      N
  19 GLU   (  20-)  A      N
  25 PHE   (  26-)  A      N
  50 ARG   (  51-)  A      N
  67 ASN   (  68-)  A      N
 138 GLN   ( 139-)  A      N
 139 GLU   ( 140-)  A      N
 164 GLN   ( 165-)  A      NE2
 183 HIS   ( 184-)  A      N
 193 THR   ( 194-)  A      N
 213 LEU   ( 214-)  A      N
 218 ASP   (   5-)  B      N
 220 LEU   (   7-)  B      N
 227 TRP   (  14-)  B      NE1
 244 GLN   (  31-)  B      N
 246 GLN   (  33-)  B      N
 264 ARG   (  51-)  B      NE
 340 TRP   ( 127-)  B      NE1
 397 HIS   ( 184-)  B      N
 407 THR   ( 194-)  B      N
 430 ASP   (   3-)  D      N
 432 ASP   (   5-)  D      N
 441 TRP   (  14-)  D      NE1
 476 ALA   (  49-)  D      N
 483 GLU   (  56-)  D      N
 525 HIS   (  98-)  D      ND1
 566 GLN   ( 139-)  D      N
 567 GLU   ( 140-)  D      N
 570 LEU   ( 143-)  D      N
 571 ASP   ( 144-)  D      N
 590 ILE   ( 163-)  D      N
 612 ASP   ( 185-)  D      N
 613 GLY   ( 186-)  D      N
 614 LEU   ( 187-)  D      N
 621 THR   ( 194-)  D      N
 626 GLU   ( 199-)  D      N
 660 VAL   (  19-)  E      N
 667 PHE   (  26-)  E      N
 701 LEU   (  60-)  E      N
 713 HIS   (  72-)  E      N
 714 THR   (  73-)  E      N
 781 GLU   ( 140-)  E      N
 804 ILE   ( 163-)  E      N
 806 GLN   ( 165-)  E      NE2
 820 TRP   ( 179-)  E      NE1
 839 ARG   ( 198-)  E      N
 840 GLU   ( 199-)  E      N
Only metal coordination for   97 HIS  (  98-) A      NE2
Only metal coordination for  311 HIS  (  98-) B      NE2
Only metal coordination for  525 HIS  (  98-) D      NE2
Only metal coordination for  739 HIS  (  98-) E      NE2

Warning: Buried unsatisfied hydrogen bond acceptors

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

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

Waters are not listed by this option.

 235 ASP   (  22-)  B      OD1
 235 ASP   (  22-)  B      OD2
 289 ASN   (  76-)  B      OD1
 503 ASN   (  76-)  D      OD1
 634 HIS   ( 207-)  D      ND1
 662 GLU   (  21-)  E      OE2
 717 ASN   (  76-)  E      OD1

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.

 235 ASP   (  22-)  B   H-bonding suggests Asn; but Alt-Rotamer
 338 ASP   ( 125-)  B   H-bonding suggests Asn; but Alt-Rotamer
 552 ASP   ( 125-)  D   H-bonding suggests Asn
 644 ASP   (   3-)  E   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.219
  2nd generation packing quality :  -1.849
  Ramachandran plot appearance   :  -2.032
  chi-1/chi-2 rotamer normality  :  -3.259 (poor)
  Backbone conformation          :  -0.191

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.655 (tight)
  Bond angles                    :   0.915
  Omega angle restraints         :   1.064
  Side chain planarity           :   0.597 (tight)
  Improper dihedral distribution :   0.917
  B-factor distribution          :   0.414
  Inside/Outside distribution    :   0.940

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.8
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :  -0.1
  chi-1/chi-2 rotamer normality  :  -1.4
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.655 (tight)
  Bond angles                    :   0.915
  Omega angle restraints         :   1.064
  Side chain planarity           :   0.597 (tight)
  Improper dihedral distribution :   0.917
  B-factor distribution          :   0.414
  Inside/Outside distribution    :   0.940
==============

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.