WHAT IF Check report

This file was created 2012-03-13 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 pdb4gtu.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 : 0.964
CA-only RMS fit for the two chains : 0.559

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.918
CA-only RMS fit for the two chains : 0.452

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.913
CA-only RMS fit for the two chains : 0.530

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 : 0.902
CA-only RMS fit for the two chains : 0.458

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 : 0.941
CA-only RMS fit for the two chains : 0.524

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

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: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

 340 LYS   ( 123-)  B
 350 MET   ( 133-)  B
1597 TYR   (  78-)  H

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:

Crystal temperature (K) :289.000

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 : 3.81

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

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.

1375 ASN   (  73-)  G      N   -C     1.24   -4.3

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.999184  0.000254  0.000023|
 |  0.000254  0.998194  0.000075|
 |  0.000023  0.000075  0.999248|
Proposed new scale matrix

 |  0.019624 -0.000005  0.002547|
 | -0.000001  0.004644  0.000000|
 |  0.000000  0.000000  0.010672|
With corresponding cell

    A    =  50.958  B   = 215.314  C    =  94.489
    Alpha=  90.006  Beta=  97.397  Gamma=  89.970

The CRYST1 cell dimensions

    A    =  51.000  B   = 215.700  C    =  94.560
    Alpha=  90.000  Beta=  97.400  Gamma=  90.000

Variance: 80.765
(Under-)estimated Z-score: 6.623

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.

 300 HIS   (  83-)  B      CG   ND1  CE1 109.61    4.0
1586 HIS   (  67-)  H      CG   ND1  CE1 109.61    4.0

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.

  49 LYS   (  49-)  A    5.82
1591 SER   (  72-)  H    5.76
1131 LEU   (  46-)  F    5.40
1707 GLU   ( 188-)  H    4.72
1258 CYS   ( 173-)  F    4.69
 606 ASN   ( 172-)  C    4.60
1345 SER   (  43-)  G    4.57
 289 SER   (  72-)  B    4.50
1128 SER   (  43-)  F    4.42
 613 ASN   ( 179-)  C    4.35
1009 LEU   ( 141-)  E    4.34
 998 LEU   ( 130-)  E    4.33
 324 SER   ( 107-)  B    4.26
 477 SER   (  43-)  C    4.26
 110 LEU   ( 110-)  A    4.14
1276 GLU   ( 191-)  F    4.12
 483 LYS   (  49-)  C    4.10

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 : -4.165

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.

 223 TYR   (   6-)  B    -3.1
 874 TYR   (   6-)  E    -3.0
 605 PRO   ( 171-)  C    -3.0
 855 PRO   ( 204-)  D    -2.9
1508 PRO   ( 206-)  G    -2.8
 421 PRO   ( 204-)  B    -2.8
1131 LEU   (  46-)  F    -2.7
1359 PRO   (  57-)  G    -2.7
1142 PRO   (  57-)  F    -2.7
 440 TYR   (   6-)  C    -2.6
1145 PRO   (  60-)  F    -2.6
 315 ILE   (  98-)  B    -2.6
 506 SER   (  72-)  C    -2.6
 723 SER   (  72-)  D    -2.6
1374 SER   (  72-)  G    -2.5
  57 PRO   (  57-)  A    -2.5
1204 PHE   ( 119-)  F    -2.5
1421 PHE   ( 119-)  G    -2.5
   6 TYR   (   6-)  A    -2.5
 657 TYR   (   6-)  D    -2.4
1039 PRO   ( 171-)  E    -2.4
 491 PRO   (  57-)  C    -2.4
 674 THR   (  23-)  D    -2.4
  72 SER   (  72-)  A    -2.4
 287 THR   (  70-)  B    -2.4
And so on for a total of 91 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.

  11 GLY   (  11-)  A  Poor phi/psi
  24 ASP   (  24-)  A  Poor phi/psi
  36 ASP   (  36-)  A  Poor phi/psi
  37 ALA   (  37-)  A  Poor phi/psi
  49 LYS   (  49-)  A  Poor phi/psi
  59 LEU   (  59-)  A  PRO omega poor
  71 GLN   (  71-)  A  Poor phi/psi
 176 ALA   ( 176-)  A  Poor phi/psi
 205 LYS   ( 205-)  A  PRO omega poor
 210 ARG   ( 210-)  A  Poor phi/psi
 211 VAL   ( 211-)  A  Poor phi/psi
 223 TYR   (   6-)  B  Poor phi/psi
 253 ASP   (  36-)  B  Poor phi/psi
 254 ALA   (  37-)  B  Poor phi/psi
 275 ASN   (  58-)  B  Poor phi/psi
 276 LEU   (  59-)  B  PRO omega poor
 287 THR   (  70-)  B  Poor phi/psi
 300 HIS   (  83-)  B  Poor phi/psi
 301 ASN   (  84-)  B  Poor phi/psi
 336 PHE   ( 119-)  B  Poor phi/psi
 364 PHE   ( 147-)  B  Poor phi/psi
 389 ASN   ( 172-)  B  Poor phi/psi
 422 LYS   ( 205-)  B  PRO omega poor
 440 TYR   (   6-)  C  Poor phi/psi
 445 GLY   (  11-)  C  Poor phi/psi
And so on for a total of 97 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

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

chi-1/chi-2 correlation Z-score : -4.127

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.

 185 SER   ( 185-)  A    0.35
 758 SER   ( 107-)  D    0.35
1006 SER   ( 138-)  E    0.36
1425 LYS   ( 123-)  G    0.37
 123 LYS   ( 123-)  A    0.38

Warning: Unusual backbone conformations

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

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

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

   6 TYR   (   6-)  A      0
   7 TRP   (   7-)  A      0
   8 ASP   (   8-)  A      0
  10 ARG   (  10-)  A      0
  12 LEU   (  12-)  A      0
  23 THR   (  23-)  A      0
  26 SER   (  26-)  A      0
  36 ASP   (  36-)  A      0
  37 ALA   (  37-)  A      0
  38 PRO   (  38-)  A      0
  41 ASP   (  41-)  A      0
  42 ARG   (  42-)  A      0
  49 LYS   (  49-)  A      0
  52 LEU   (  52-)  A      0
  55 ASP   (  55-)  A      0
  56 PHE   (  56-)  A      0
  57 PRO   (  57-)  A      0
  58 ASN   (  58-)  A      0
  59 LEU   (  59-)  A      0
  64 ASP   (  64-)  A      0
  66 ALA   (  66-)  A      0
  67 HIS   (  67-)  A      0
  70 THR   (  70-)  A      0
  71 GLN   (  71-)  A      0
  85 LEU   (  85-)  A      0
And so on for a total of 583 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 : 1.012

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!

 903 GLY   (  35-)  E   1.55   18

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...

 288 GLN   (  71-)  B   1.69

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]

1216 PRO   ( 131-)  F    0.45 HIGH
1643 PRO   ( 124-)  H    0.45 HIGH

Warning: Unusual PRO puckering phases

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

 388 PRO   ( 171-)  B  -115.3 envelop C-gamma (-108 degrees)
 421 PRO   ( 204-)  B    50.4 half-chair C-delta/C-gamma (54 degrees)
 605 PRO   ( 171-)  C  -116.9 envelop C-gamma (-108 degrees)
 855 PRO   ( 204-)  D    48.6 half-chair C-delta/C-gamma (54 degrees)
 925 PRO   (  57-)  E  -118.2 half-chair C-delta/C-gamma (-126 degrees)
1723 PRO   ( 204-)  H    41.6 envelop C-delta (36 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 948 ALA   (  80-)  E      CB  <->  954 CYS   (  86-)  E      SG     0.45    2.95  INTRA BL
 765 CYS   ( 114-)  D      SG  <->  865 TRP   ( 214-)  D      CE3    0.39    3.01  INTRA
 173 CYS   ( 173-)  A      SG  <->  174 LEU   ( 174-)  A      N      0.39    2.81  INTRA
 568 MET   ( 134-)  C      SD  <->  608 LEU   ( 174-)  C      CD1    0.36    3.04  INTRA
 414 MET   ( 197-)  B      SD  <->  419 PHE   ( 202-)  B      CZ     0.36    3.04  INTRA
 331 CYS   ( 114-)  B      SG  <->  431 TRP   ( 214-)  B      CE3    0.34    3.06  INTRA
 114 CYS   ( 114-)  A      SG  <->  214 TRP   ( 214-)  A      CE3    0.33    3.07  INTRA
1225 PHE   ( 140-)  F      O   <-> 1229 ARG   ( 144-)  F      NH1    0.32    2.38  INTRA BL
 114 CYS   ( 114-)  A      SG  <->  214 TRP   ( 214-)  A      CB     0.31    3.09  INTRA
 514 ALA   (  80-)  C      CB  <->  520 CYS   (  86-)  C      SG     0.27    3.13  INTRA BL
 262 TRP   (  45-)  B      CH2 <->  278 TYR   (  61-)  B      CE2    0.26    2.94  INTRA BL
 529 ARG   (  95-)  C      NH1 <->  574 PHE   ( 140-)  C      CE2    0.25    2.85  INTRA BL
  58 ASN   (  58-)  A      CG  <->   59 LEU   (  59-)  A      N      0.25    2.75  INTRA BL
1514 ALA   ( 212-)  G      O   <-> 1518 ASN   ( 216-)  G      ND2    0.24    2.46  INTRA
 349 THR   ( 132-)  B      O   <->  353 HIS   ( 136-)  B      ND1    0.23    2.47  INTRA
 429 ALA   ( 212-)  B      O   <->  433 ASN   ( 216-)  B      ND2    0.22    2.48  INTRA
 607 CYS   ( 173-)  C      SG  <->  608 LEU   ( 174-)  C      N      0.22    2.98  INTRA
 447 ALA   (  13-)  C      O   <->  449 ALA   (  15-)  C      N      0.21    2.49  INTRA BL
1255 GLU   ( 170-)  F      O   <-> 1258 CYS   ( 173-)  F      SG     0.21    2.64  INTRA
1223 SER   ( 138-)  F      O   <-> 1264 ASN   ( 179-)  F      ND2    0.21    2.49  INTRA BL
1231 TRP   ( 146-)  F      O   <-> 1234 GLY   ( 149-)  F      N      0.20    2.50  INTRA BL
1657 SER   ( 138-)  H      OG  <-> 1698 ASN   ( 179-)  H      ND2    0.20    2.50  INTRA BL
 384 ARG   ( 167-)  B      NH2 <->  401 ILE   ( 184-)  B      CG2    0.20    2.90  INTRA BL
1304 MET   (   2-)  G      O   <-> 1330 GLU   (  28-)  G      N      0.20    2.50  INTRA
1421 PHE   ( 119-)  G      CZ  <-> 1516 TRP   ( 214-)  G      CD1    0.20    3.00  INTRA
And so on for a total of 242 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

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.

 577 LYS   ( 143-)  C      -6.62
1011 LYS   ( 143-)  E      -6.52
 856 LYS   ( 205-)  D      -6.17
1507 LYS   ( 205-)  G      -6.00
 422 LYS   ( 205-)  B      -5.88
1662 LYS   ( 143-)  H      -5.87
 360 LYS   ( 143-)  B      -5.83
1073 LYS   ( 205-)  E      -5.80
1724 LYS   ( 205-)  H      -5.79
1290 LYS   ( 205-)  F      -5.76
1228 LYS   ( 143-)  F      -5.75
1445 LYS   ( 143-)  G      -5.68
 143 LYS   ( 143-)  A      -5.63
 205 LYS   ( 205-)  A      -5.61
 701 PHE   (  50-)  D      -5.58
 794 LYS   ( 143-)  D      -5.45
 639 LYS   ( 205-)  C      -5.42

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

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.

1505 LEU   ( 203-)  G   -2.59

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

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.

 166 HIS   ( 166-)  A
 389 ASN   ( 172-)  B
 396 ASN   ( 179-)  B
 478 GLN   (  44-)  C
 492 ASN   (  58-)  C
 542 ASN   ( 108-)  C
 665 HIS   (  14-)  D
 830 ASN   ( 179-)  D
 912 GLN   (  44-)  E
1040 ASN   ( 172-)  E
1047 ASN   ( 179-)  E
1654 GLN   ( 135-)  H
1655 HIS   ( 136-)  H
1698 ASN   ( 179-)  H

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.

   7 TRP   (   7-)  A      N
   9 ILE   (   9-)  A      N
  17 ARG   (  17-)  A      NH1
  32 TYR   (  32-)  A      OH
  50 PHE   (  50-)  A      N
  56 PHE   (  56-)  A      N
  58 ASN   (  58-)  A      N
  59 LEU   (  59-)  A      N
  67 HIS   (  67-)  A      N
  70 THR   (  70-)  A      N
  81 ARG   (  81-)  A      NH1
  86 CYS   (  86-)  A      N
 148 VAL   ( 148-)  A      N
 151 LYS   ( 151-)  A      N
 155 VAL   ( 155-)  A      N
 167 ARG   ( 167-)  A      NH1
 172 ASN   ( 172-)  A      N
 175 ASP   ( 175-)  A      N
 176 ALA   ( 176-)  A      N
 205 LYS   ( 205-)  A      N
 210 ARG   ( 210-)  A      N
 211 VAL   ( 211-)  A      N
 216 ASN   ( 216-)  A      N
 220 THR   (   3-)  B      OG1
 224 TRP   (   7-)  B      N
And so on for a total of 214 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.

  29 GLU   (  29-)  A      OE2
  73 ASN   (  73-)  A      OD1
  90 GLU   (  90-)  A      OE2
 246 GLU   (  29-)  B      OE2
 290 ASN   (  73-)  B      OD1
 307 GLU   (  90-)  B      OE2
 383 HIS   ( 166-)  B      ND1
 507 ASN   (  73-)  C      OD1
 524 GLU   (  90-)  C      OE2
 570 HIS   ( 136-)  C      ND1
 600 HIS   ( 166-)  C      ND1
 665 HIS   (  14-)  D      NE2
 724 ASN   (  73-)  D      OD1
 751 GLU   ( 100-)  D      OE1
 941 ASN   (  73-)  E      OD1
 958 GLU   (  90-)  E      OE1
 970 GLN   ( 102-)  E      OE1
1024 ASP   ( 156-)  E      OD1
1158 ASN   (  73-)  F      OD1
1375 ASN   (  73-)  G      OD1
1621 GLN   ( 102-)  H      OE1
1628 GLN   ( 109-)  H      OE1
1685 HIS   ( 166-)  H      ND1

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.

  24 ASP   (  24-)  A   H-bonding suggests Asn
 156 ASP   ( 156-)  A   H-bonding suggests Asn
 182 ASP   ( 182-)  A   H-bonding suggests Asn
 314 ASP   (  97-)  B   H-bonding suggests Asn; but Alt-Rotamer
 442 ASP   (   8-)  C   H-bonding suggests Asn
 531 ASP   (  97-)  C   H-bonding suggests Asn
 659 ASP   (   8-)  D   H-bonding suggests Asn
 779 GLU   ( 128-)  D   H-bonding suggests Gln
 780 GLU   ( 129-)  D   H-bonding suggests Gln
 833 ASP   ( 182-)  D   H-bonding suggests Asn; but Alt-Rotamer
1050 ASP   ( 182-)  E   H-bonding suggests Asn
1093 ASP   (   8-)  F   H-bonding suggests Asn; but Alt-Rotamer
1210 GLU   ( 125-)  F   H-bonding suggests Gln
1214 GLU   ( 129-)  F   H-bonding suggests Gln
1326 ASP   (  24-)  G   H-bonding suggests Asn
1399 ASP   (  97-)  G   H-bonding suggests Asn
1427 GLU   ( 125-)  G   H-bonding suggests Gln
1431 GLU   ( 129-)  G   H-bonding suggests Gln; but Alt-Rotamer
1458 ASP   ( 156-)  G   H-bonding suggests Asn
1527 ASP   (   8-)  H   H-bonding suggests Asn
1624 ASP   ( 105-)  H   H-bonding suggests Asn; but Alt-Rotamer
1648 GLU   ( 129-)  H   H-bonding suggests Gln

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 :  -1.008
  2nd generation packing quality :  -2.135
  Ramachandran plot appearance   :  -4.165 (bad)
  chi-1/chi-2 rotamer normality  :  -4.127 (bad)
  Backbone conformation          :  -0.791

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.352 (tight)
  Bond angles                    :   0.613 (tight)
  Omega angle restraints         :   0.184 (tight)
  Side chain planarity           :   0.431 (tight)
  Improper dihedral distribution :   0.764
  B-factor distribution          :   1.115
  Inside/Outside distribution    :   0.959

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 : 3.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :   0.0
  Ramachandran plot appearance   :  -1.2
  chi-1/chi-2 rotamer normality  :  -1.7
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.352 (tight)
  Bond angles                    :   0.613 (tight)
  Omega angle restraints         :   0.184 (tight)
  Side chain planarity           :   0.431 (tight)
  Improper dihedral distribution :   0.764
  B-factor distribution          :   1.115
  Inside/Outside distribution    :   0.959
==============

WHAT IF
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      WHAT IF: a molecular modelling and drug design program,
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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.