WHAT IF Check report

This file was created 2011-12-13 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 pdb3ax2.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 C

All-atom RMS fit for the two chains : 0.890
CA-only RMS fit for the two chains : 0.444

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and E

All-atom RMS fit for the two chains : 1.247
CA-only RMS fit for the two chains : 0.894

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 G

All-atom RMS fit for the two chains : 2.161
CA-only RMS fit for the two chains : 1.671

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 G

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 : 2.866
CA-only RMS fit for the two chains : 2.132

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 F

All-atom RMS fit for the two chains : 0.422
CA-only RMS fit for the two chains : 0.189

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 F

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

 338 PO4   (   2-)  B  -
 339 PO4   (   1-)  D  -

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

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

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

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) : 95.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

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

  80 TYR   (  21-)  B
 165 TYR   (  21-)  D
 245 TYR   (  21-)  F
 276 TYR   (  86-)  G
 324 TYR   (  21-)  H

Warning: Phenylalanine convention problem

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

  13 PHE   (  69-)  A
  98 PHE   (  69-)  C
 178 PHE   (  69-)  E
 259 PHE   (  69-)  G

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.

   6 ASP   (  62-)  A
  29 ASP   (  85-)  A
  35 ASP   (  91-)  A
  91 ASP   (  62-)  C
 114 ASP   (  85-)  C
 120 ASP   (  91-)  C
 171 ASP   (  62-)  E
 194 ASP   (  85-)  E
 200 ASP   (  91-)  E
 275 ASP   (  85-)  G

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.

  16 GLU   (  72-)  A
  17 GLU   (  73-)  A
 101 GLU   (  72-)  C
 102 GLU   (  73-)  C
 107 GLU   (  78-)  C
 108 GLU   (  79-)  C
 182 GLU   (  73-)  E
 254 GLU   (  64-)  G
 262 GLU   (  72-)  G
 263 GLU   (  73-)  G
 269 GLU   (  79-)  G

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.

  22 GLU   (  78-)  A      CB   CG    1.36   -5.2
  70 LEU   ( 126-)  A      CA   C     1.61    4.2
 115 TYR   (  86-)  C      CD1  CE1   1.50    4.0
 135 LEU   ( 106-)  C      CG   CD1   1.66    4.1
 137 GLN   ( 108-)  C      CB   CG    1.65    4.2
 187 GLU   (  78-)  E      CB   CG    1.39   -4.4
 210 GLY   ( 101-)  E      N    CA    1.52    4.2
 213 GLN   ( 104-)  E      CG   CD    1.64    4.9
 291 GLY   ( 101-)  G      N    CA    1.52    4.5

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

 |  0.993228  0.000555 -0.000672|
 |  0.000555  0.994366  0.001352|
 | -0.000672  0.001352  0.991898|
Proposed new scale matrix

 |  0.016369  0.009433 -0.000002|
 | -0.000011  0.018885 -0.000026|
 |  0.000007 -0.000014  0.010252|
With corresponding cell

    A    =  61.073  B   =  61.095  C    =  97.542
    Alpha=  89.826  Beta=  90.078  Gamma= 119.922

The CRYST1 cell dimensions

    A    =  61.490  B   =  61.490  C    =  98.341
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 484.601
(Under-)estimated Z-score: 16.224

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.

  36 HIS   (  92-)  A      CG   ND1  CE1 110.03    4.4
  70 LEU   ( 126-)  A     -C    N    CA  131.77    5.6
 123 THR   (  94-)  C      CG2  CB   OG1 118.00    4.3
 165 TYR   (  21-)  D      CA   CB   CG  105.33   -4.4
 183 ILE   (  74-)  E      CB   CG1  CD1 104.54   -4.4
 201 HIS   (  92-)  E      CG   ND1  CE1 109.67    4.1
 238 ARG   (  14-)  F      CG   CD   NE  102.95   -4.4
 282 HIS   (  92-)  G      CG   ND1  CE1 109.76    4.2

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.

   6 ASP   (  62-)  A
  16 GLU   (  72-)  A
  17 GLU   (  73-)  A
  29 ASP   (  85-)  A
  35 ASP   (  91-)  A
  91 ASP   (  62-)  C
 101 GLU   (  72-)  C
 102 GLU   (  73-)  C
 107 GLU   (  78-)  C
 108 GLU   (  79-)  C
 114 ASP   (  85-)  C
 120 ASP   (  91-)  C
 171 ASP   (  62-)  E
 182 GLU   (  73-)  E
 194 ASP   (  85-)  E
 200 ASP   (  91-)  E
 254 GLU   (  64-)  G
 262 GLU   (  72-)  G
 263 GLU   (  73-)  G
 269 GLU   (  79-)  G
 275 ASP   (  85-)  G

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.

 244 SER   (  20-)  F    5.81
 187 GLU   (  78-)  E    4.00

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 134 GLN   ( 105-)  C    5.44

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.

 293 PRO   ( 103-)  G    -2.8
 212 PRO   ( 103-)  E    -2.7
  47 PRO   ( 103-)  A    -2.7
 132 PRO   ( 103-)  C    -2.4
 157 PRO   (  13-)  D    -2.3
 305 PRO   ( 115-)  G    -2.3
 237 PRO   (  13-)  F    -2.2
 154 LYS   ( 125-)  C    -2.1

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.

 323 SER   (  20-)  H    0.36

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!

  27 GLN   (  83-)  A      0
  30 TYR   (  86-)  A      0
  46 GLN   ( 102-)  A      0
  57 THR   ( 113-)  A      0
  69 LYS   ( 125-)  A      0
  70 LEU   ( 126-)  A      0
  71 GLY   (  12-)  B      0
  72 PRO   (  13-)  B      0
  73 ARG   (  14-)  B      0
  83 SER   (  24-)  B      0
  84 GLY   (  25-)  B      0
  85 CYS   (  26-)  B      0
  86 GLY   (  57-)  C      0
  87 SER   (  58-)  C      0
 112 GLN   (  83-)  C      0
 115 TYR   (  86-)  C      0
 131 GLN   ( 102-)  C      0
 142 THR   ( 113-)  C      0
 154 LYS   ( 125-)  C      0
 155 LEU   ( 126-)  C      0
 156 GLY   (  12-)  D      0
 157 PRO   (  13-)  D      0
 158 ARG   (  14-)  D      0
 168 SER   (  24-)  D      0
 169 GLY   (  25-)  D      0
And so on for a total of 65 lines.

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

 145 PRO   ( 116-)  C    0.47 HIGH
 146 PRO   ( 117-)  C    0.20 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].

  72 PRO   (  13-)  B   -54.1 half-chair C-beta/C-alpha (-54 degrees)
 237 PRO   (  13-)  F    25.2 half-chair N/C-delta (18 degrees)
 293 PRO   ( 103-)  G   -55.0 half-chair C-beta/C-alpha (-54 degrees)
 305 PRO   ( 115-)  G   101.3 envelop C-beta (108 degrees)
 306 PRO   ( 116-)  G   124.8 half-chair C-beta/C-alpha (126 degrees)
 307 PRO   ( 117-)  G   -29.1 envelop C-alpha (-36 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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.

  23 GLU   (  79-)  A      OE2  <->   238 ARG   (  14-)  F      NH1  0.75    1.95  INTRA
  71 GLY   (  12-)  B      N    <->   338 PO4   (   2-)  B      O2   0.42    2.28  INTRA BF
   1 GLY   (  57-)  A      N    <->     4 LEU   (  60-)  A      CD2  0.42    2.68  INTRA
 131 GLN   ( 102-)  C      NE2  <->   342 HOH   ( 156 )  C      O    0.40    2.30  INTRA
 184 GLN   (  75-)  E      OE1  <->   344 HOH   ( 157 )  E      O    0.39    2.01  INTRA
 181 GLU   (  72-)  E      CD   <->   344 HOH   ( 156 )  E      O    0.31    2.49  INTRA
 161 ARG   (  17-)  D      NH1  <->   339 PO4   (   1-)  D      O3   0.16    2.54  INTRA
 188 GLU   (  79-)  E      CG   <->   192 GLN   (  83-)  E      NE2  0.16    2.94  INTRA
  76 ARG   (  17-)  B      NH1  <->   338 PO4   (   2-)  B      O2   0.16    2.54  INTRA
 263 GLU   (  73-)  G      OE1  <->   282 HIS   (  92-)  G      ND1  0.15    2.55  INTRA BL
  20 LEU   (  76-)  A      CD1  <->   340 HOH   (  52 )  A      O    0.15    2.65  INTRA
 235 LEU   ( 126-)  E      CD1  <->   344 HOH   ( 130 )  E      O    0.14    2.66  INTRA BF
  16 GLU   (  72-)  A      OE1  <->   340 HOH   ( 146 )  A      O    0.14    2.26  INTRA
 182 GLU   (  73-)  E      OE1  <->   201 HIS   (  92-)  E      ND1  0.13    2.57  INTRA BL
 304 LEU   ( 114-)  G      O    <->   305 PRO   ( 115-)  G      C    0.13    2.47  INTRA BF
 296 LEU   ( 106-)  G      N    <->   347 HOH   ( 133 )  H      O    0.08    2.62  INTRA
 304 LEU   ( 114-)  G      C    <->   305 PRO   ( 115-)  G      C    0.08    2.72  INTRA BF
  57 THR   ( 113-)  A      CG2  <->   242 LEU   (  18-)  F      CD1  0.08    3.12  INTRA
  97 LYS   (  68-)  C      NZ   <->   342 HOH   ( 146 )  C      O    0.08    2.62  INTRA
  22 GLU   (  78-)  A      OE2  <->   240 SER   (  16-)  F      N    0.06    2.64  INTRA
 305 PRO   ( 115-)  G      C    <->   307 PRO   ( 117-)  G      CD   0.06    3.14  INTRA BF
 282 HIS   (  92-)  G      NE2  <->   346 HOH   (  16 )  G      O    0.05    2.65  INTRA
  60 PRO   ( 116-)  A      N    <->    61 PRO   ( 117-)  A      CD   0.05    2.95  INTRA
 313 LEU   ( 123-)  G      C    <->   315 LYS   ( 125-)  G      N    0.03    2.87  INTRA BF
 309 PHE   ( 119-)  G      CE2  <->   313 LEU   ( 123-)  G      CD2  0.03    3.17  INTRA BF
  44 CYS   ( 100-)  A      SG   <->    47 PRO   ( 103-)  A      CA   0.03    3.37  INTRA BL
  17 GLU   (  73-)  A      OE1  <->    36 HIS   (  92-)  A      ND1  0.02    2.68  INTRA BL
 235 LEU   ( 126-)  E      CB   <->   344 HOH   ( 130 )  E      O    0.01    2.79  INTRA BF
   2 SER   (  58-)  A      N    <->     3 ASP   (  59-)  A      N    0.01    2.59  INTRA B3
   4 LEU   (  60-)  A      O    <->     8 GLU   (  64-)  A      N    0.01    2.69  INTRA BL
  96 GLN   (  67-)  C      NE2  <->   162 LEU   (  18-)  D      CD2  0.01    3.09  INTRA
 137 GLN   ( 108-)  C      NE2  <->   263 GLU   (  73-)  G      OE2  0.01    2.69  INTRA BL

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

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

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

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: G

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: H

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

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

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.

 343 HOH   (  84 )  D      O     41.59  -20.20   22.48

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.

 131 GLN   ( 102-)  C
 220 GLN   ( 111-)  E
 257 GLN   (  67-)  G
 294 GLN   ( 104-)  G

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.

   4 LEU   (  60-)  A      N
  48 GLN   ( 104-)  A      NE2
  73 ARG   (  14-)  B      N
  76 ARG   (  17-)  B      NH1
 292 GLN   ( 102-)  G      N

Warning: Unusual water packing

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

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

 343 HOH   (  28 )  D      O  1.01  K  5

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.

   6 ASP   (  62-)  A   H-bonding suggests Asn; but Alt-Rotamer
  91 ASP   (  62-)  C   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.545
  2nd generation packing quality :   0.176
  Ramachandran plot appearance   :   0.642
  chi-1/chi-2 rotamer normality  :  -0.499
  Backbone conformation          :   1.925

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.180
  Bond angles                    :   1.019
  Omega angle restraints         :   0.937
  Side chain planarity           :   1.499
  Improper dihedral distribution :   1.269
  B-factor distribution          :   0.752
  Inside/Outside distribution    :   0.984

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 1.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :   2.1
  2nd generation packing quality :  -0.2
  Ramachandran plot appearance   :   1.1
  chi-1/chi-2 rotamer normality  :   0.1
  Backbone conformation          :   1.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.180
  Bond angles                    :   1.019
  Omega angle restraints         :   0.937
  Side chain planarity           :   1.499
  Improper dihedral distribution :   1.269
  B-factor distribution          :   0.752
  Inside/Outside distribution    :   0.984
==============

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.