WHAT IF Check report

This file was created 2011-12-17 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 pdb3p9k.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 1.237
CA-only RMS fit for the two chains : 1.053

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 : 0.668
CA-only RMS fit for the two chains : 0.456

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 : 1.247
CA-only RMS fit for the two chains : 1.051

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: B and C

All-atom RMS fit for the two chains : 1.091
CA-only RMS fit for the two chains : 0.886

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 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: B and D

All-atom RMS fit for the two chains : 0.764
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: B and D

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.

1426 SAH   ( 401-)  A  -
1427 CIY   ( 601-)  A  -
1428 SAH   ( 402-)  B  -
1429 CIY   ( 602-)  B  -
1430 SAH   ( 403-)  C  -
1431 CIY   ( 603-)  C  -
1432 CIY   ( 604-)  D  -
1433 SAH   ( 404-)  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

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

 652 VAL   ( 299-)  B      CG1
 652 VAL   ( 299-)  B      CG2
 657 ASN   ( 304-)  B      CG
 657 ASN   ( 304-)  B      OD1
 657 ASN   ( 304-)  B      ND2
 717 ASP   (   7-)  C      CG
 717 ASP   (   7-)  C      OD1
 717 ASP   (   7-)  C      OD2
 718 MET   (   8-)  C      CG
 718 MET   (   8-)  C      SD
 718 MET   (   8-)  C      CE

Warning: B-factors outside the range 0.0 - 100.0

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

 655 GLU   ( 302-)  B    High
 656 ALA   ( 303-)  B    High
 657 ASN   ( 304-)  B    High
 658 PRO   ( 305-)  B    High

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) :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: C

Note: B-factor plot

Chain identifier: D

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

 135 TYR   ( 138-)  A
 278 TYR   ( 281-)  A
 634 TYR   ( 281-)  B
 991 TYR   ( 281-)  C
1342 TYR   ( 281-)  D

Warning: Phenylalanine convention problem

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

 148 PHE   ( 151-)  A
 157 PHE   ( 160-)  A
 861 PHE   ( 151-)  C
 905 PHE   ( 195-)  C
1256 PHE   ( 195-)  D

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.

  93 ASP   (  96-)  A
 806 ASP   (  96-)  C
1264 ASP   ( 203-)  D
1289 ASP   ( 228-)  D

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.

 354 GLU   ( 357-)  A
 549 GLU   ( 196-)  B
 588 GLU   ( 235-)  B
 724 GLU   (  14-)  C
 802 GLU   (  92-)  C
1118 GLU   (  57-)  D
1313 GLU   ( 252-)  D

Geometric checks

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

 |  0.999285  0.000093 -0.000311|
 |  0.000093  0.998118 -0.000312|
 | -0.000311 -0.000312  0.999644|
Proposed new scale matrix

 |  0.010494  0.000000  0.004188|
 | -0.000001  0.011778  0.000004|
 |  0.000003  0.000003  0.010925|
With corresponding cell

    A    =  95.306  B   =  84.903  C    =  98.566
    Alpha=  90.038  Beta= 111.773  Gamma=  89.988

The CRYST1 cell dimensions

    A    =  95.375  B   =  85.062  C    =  98.586
    Alpha=  90.000  Beta= 111.750  Gamma=  90.000

Variance: 53.434
(Under-)estimated Z-score: 5.387

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.

1354 VAL   ( 293-)  D      N    CA   C    99.82   -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.

  93 ASP   (  96-)  A
 354 GLU   ( 357-)  A
 549 GLU   ( 196-)  B
 588 GLU   ( 235-)  B
 724 GLU   (  14-)  C
 802 GLU   (  92-)  C
 806 ASP   (  96-)  C
1118 GLU   (  57-)  D
1264 ASP   ( 203-)  D
1289 ASP   ( 228-)  D
1313 GLU   ( 252-)  D

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.

1030 HIS   ( 320-)  C    4.87
 673 HIS   ( 320-)  B    4.66
 317 HIS   ( 320-)  A    4.66
1381 HIS   ( 320-)  D    4.49
 188 LEU   ( 191-)  A    4.37
  99 SER   ( 102-)  A    4.29
1354 VAL   ( 293-)  D    4.06

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.

 654 PRO   ( 301-)  B    -3.0
 616 TRP   ( 263-)  B    -2.7
 773 PRO   (  63-)  C    -2.7
 260 TRP   ( 263-)  A    -2.7
1324 TRP   ( 263-)  D    -2.6
 973 TRP   ( 263-)  C    -2.6
 219 ILE   ( 222-)  A    -2.3
  60 PRO   (  63-)  A    -2.3
 227 PRO   ( 230-)  A    -2.2
 552 GLY   ( 199-)  B    -2.0
  90 GLU   (  93-)  A    -2.0
 196 GLY   ( 199-)  A    -2.0
1363 GLU   ( 302-)  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.

  60 PRO   (  63-)  A  Poor phi/psi
  82 ASN   (  85-)  A  Poor phi/psi
 249 GLU   ( 252-)  A  Poor phi/psi
 319 PRO   ( 322-)  A  Poor phi/psi
 347 TYR   ( 350-)  A  Poor phi/psi
 349 ASN   ( 352-)  A  Poor phi/psi
 416 PRO   (  63-)  B  Poor phi/psi
 438 ASN   (  85-)  B  Poor phi/psi
 616 TRP   ( 263-)  B  Poor phi/psi
 653 ASN   ( 300-)  B  Poor phi/psi
 654 PRO   ( 301-)  B  Poor phi/psi
 655 GLU   ( 302-)  B  Poor phi/psi
 675 PRO   ( 322-)  B  Poor phi/psi
 705 ASN   ( 352-)  B  Poor phi/psi
 795 ASN   (  85-)  C  Poor phi/psi
 962 GLU   ( 252-)  C  Poor phi/psi
 973 TRP   ( 263-)  C  Poor phi/psi
1060 TYR   ( 350-)  C  Poor phi/psi
1062 ASN   ( 352-)  C  Poor phi/psi
1146 ASN   (  85-)  D  Poor phi/psi
1324 TRP   ( 263-)  D  Poor phi/psi
1364 ALA   ( 303-)  D  Poor phi/psi
1383 PRO   ( 322-)  D  Poor phi/psi
1411 TYR   ( 350-)  D  Poor phi/psi
1413 ASN   ( 352-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.780

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.

1367 SER   ( 306-)  D    0.38
   8 SER   (  11-)  A    0.40

Warning: Unusual backbone conformations

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

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

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

  22 SER   (  25-)  A      0
  23 SER   (  26-)  A      0
  38 LEU   (  41-)  A      0
  60 PRO   (  63-)  A      0
  61 SER   (  64-)  A      0
  82 ASN   (  85-)  A      0
  83 VAL   (  86-)  A      0
  89 GLU   (  92-)  A      0
 109 LEU   ( 112-)  A      0
 113 GLU   ( 116-)  A      0
 116 VAL   ( 119-)  A      0
 118 MET   ( 121-)  A      0
 143 ASP   ( 146-)  A      0
 146 ILE   ( 149-)  A      0
 152 TYR   ( 155-)  A      0
 162 THR   ( 165-)  A      0
 188 LEU   ( 191-)  A      0
 193 GLU   ( 196-)  A      0
 197 THR   ( 200-)  A      0
 201 VAL   ( 204-)  A      0
 205 VAL   ( 208-)  A      0
 237 PRO   ( 240-)  A      0
 245 ASP   ( 248-)  A      0
 246 MET   ( 249-)  A      0
 249 GLU   ( 252-)  A      0
And so on for a total of 344 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 : 1.158

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!

  47 GLY   (  50-)  A   1.96   21
 403 GLY   (  50-)  B   1.86   22
 760 GLY   (  50-)  C   1.63   13
1111 GLY   (  50-)  D   1.56   19

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]

 298 PRO   ( 301-)  A    0.45 HIGH

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.

1355 GLN   ( 294-)  D      NE2 <-> 1437 HOH   (1113 )  D      O      0.39    2.31  INTRA BL
  15 MET   (  18-)  A      CE  <->  705 ASN   ( 352-)  B      ND2    0.30    2.80  INTRA BF
   1 THR   (   4-)  A      O   <->    5 MET   (   8-)  A      N      0.29    2.41  INTRA BF
1430 SAH   ( 403-)  C      SD  <-> 1431 CIY   ( 603-)  C      C3M    0.25    3.15  INTRA
  15 MET   (  18-)  A      CE  <->  705 ASN   ( 352-)  B      CG     0.25    2.95  INTRA BF
 647 GLN   ( 294-)  B      NE2 <-> 1435 HOH   (1040 )  B      O      0.25    2.45  INTRA BF
1027 MET   ( 317-)  C      SD  <-> 1031 ASN   ( 321-)  C      ND2    0.24    3.06  INTRA BL
1426 SAH   ( 401-)  A      SD  <-> 1427 CIY   ( 601-)  A      C3M    0.24    3.16  INTRA
 314 MET   ( 317-)  A      SD  <->  318 ASN   ( 321-)  A      ND2    0.24    3.06  INTRA
 196 GLY   ( 199-)  A      O   <->  220 LYS   ( 223-)  A      N      0.23    2.47  INTRA BF
1071 ALA   (  10-)  D      O   <-> 1075 GLU   (  14-)  D      N      0.23    2.47  INTRA BF
 177 HIS   ( 180-)  A      ND1 <->  259 LYS   ( 262-)  A      NZ     0.22    2.78  INTRA
1432 CIY   ( 604-)  D      C3M <-> 1433 SAH   ( 404-)  D      SD     0.20    3.20  INTRA BL
 246 MET   ( 249-)  A      N   <-> 1426 SAH   ( 401-)  A      N1     0.19    2.81  INTRA BL
1004 GLN   ( 294-)  C      NE2 <-> 1436 HOH   (1074 )  C      O      0.19    2.51  INTRA BF
1260 GLY   ( 199-)  D      O   <-> 1284 LYS   ( 223-)  D      N      0.18    2.52  INTRA
   1 THR   (   4-)  A      O   <->    4 ASP   (   7-)  A      N      0.18    2.52  INTRA BF
 881 ARG   ( 171-)  C      NH1 <-> 1436 HOH   (1298 )  C      O      0.16    2.54  INTRA BF
 309 HIS   ( 312-)  A      NE2 <->  437 TYR   (  84-)  B      OH     0.16    2.54  INTRA BL
 552 GLY   ( 199-)  B      O   <->  576 LYS   ( 223-)  B      N      0.16    2.54  INTRA BF
 581 ASP   ( 228-)  B      OD1 <->  582 LEU   ( 229-)  B      N      0.15    2.45  INTRA BF
 225 ASP   ( 228-)  A      OD1 <->  226 LEU   ( 229-)  A      N      0.15    2.45  INTRA BL
1388 ARG   ( 327-)  D      N   <-> 1437 HOH   (1042 )  D      O      0.15    2.55  INTRA BL
  63 ALA   (  66-)  A      N   <-> 1434 HOH   (1064 )  A      O      0.15    2.55  INTRA BF
 602 MET   ( 249-)  B      N   <-> 1428 SAH   ( 402-)  B      N1     0.14    2.86  INTRA BL
And so on for a total of 148 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

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.

  92 LYS   (  95-)  A      -6.70
1299 GLN   ( 238-)  D      -6.69
 591 GLN   ( 238-)  B      -6.69
 235 GLN   ( 238-)  A      -6.52
 948 GLN   ( 238-)  C      -6.40
 805 LYS   (  95-)  C      -6.36
1156 LYS   (  95-)  D      -6.32
 448 LYS   (  95-)  B      -6.28
 653 ASN   ( 300-)  B      -5.92
 928 HIS   ( 218-)  C      -5.87
1279 HIS   ( 218-)  D      -5.87
 571 HIS   ( 218-)  B      -5.81
 215 HIS   ( 218-)  A      -5.76
 113 GLU   ( 116-)  A      -5.63
1177 GLU   ( 116-)  D      -5.62
 640 HIS   ( 287-)  B      -5.61
 469 GLU   ( 116-)  B      -5.56
1348 HIS   ( 287-)  D      -5.55
 997 HIS   ( 287-)  C      -5.54
 826 GLU   ( 116-)  C      -5.52
 284 HIS   ( 287-)  A      -5.46
 317 HIS   ( 320-)  A      -5.34
 655 GLU   ( 302-)  B      -5.34
1030 HIS   ( 320-)  C      -5.29
1381 HIS   ( 320-)  D      -5.24
1009 VAL   ( 299-)  C      -5.20
1411 TYR   ( 350-)  D      -5.16
 296 VAL   ( 299-)  A      -5.11
 673 HIS   ( 320-)  B      -5.10
1360 VAL   ( 299-)  D      -5.04

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

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.

 547 GLY   ( 194-)  B   -2.81
 191 GLY   ( 194-)  A   -2.72
1384 GLY   ( 323-)  D   -2.71
 320 GLY   ( 323-)  A   -2.66
1033 GLY   ( 323-)  C   -2.64
 676 GLY   ( 323-)  B   -2.63

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

Water, ion, and hydrogenbond related checks

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.

1435 HOH   (1122 )  B      O
1437 HOH   (1767 )  D      O

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.

 862 ASN   ( 152-)  C
1332 GLN   ( 271-)  D

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.

  51 THR   (  54-)  A      OG1
  64 ASN   (  67-)  A      ND2
  84 VAL   (  87-)  A      N
  95 ARG   (  98-)  A      NE
 114 ASP   ( 117-)  A      N
 125 ASN   ( 128-)  A      ND2
 154 MET   ( 157-)  A      N
 157 PHE   ( 160-)  A      N
 178 SER   ( 181-)  A      OG
 192 PHE   ( 195-)  A      N
 195 LEU   ( 198-)  A      N
 196 GLY   ( 199-)  A      N
 246 MET   ( 249-)  A      N
 259 LYS   ( 262-)  A      NZ
 291 GLN   ( 294-)  A      NE2
 318 ASN   ( 321-)  A      ND2
 440 VAL   (  87-)  B      N
 451 ARG   (  98-)  B      N
 477 LEU   ( 124-)  B      N
 481 ASN   ( 128-)  B      ND2
 495 ASP   ( 142-)  B      N
 510 MET   ( 157-)  B      N
 513 PHE   ( 160-)  B      N
 545 TYR   ( 192-)  B      OH
 548 PHE   ( 195-)  B      N
And so on for a total of 62 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.

 215 HIS   ( 218-)  A      ND1
 263 HIS   ( 266-)  A      NE2
 264 ASP   ( 267-)  A      OD1
 571 HIS   ( 218-)  B      ND1
 579 ASN   ( 226-)  B      OD1
 619 HIS   ( 266-)  B      NE2
 976 HIS   ( 266-)  C      NE2
1178 ASP   ( 117-)  D      OD2
1279 HIS   ( 218-)  D      ND1
1287 ASN   ( 226-)  D      OD1
1327 HIS   ( 266-)  D      NE2
1328 ASP   ( 267-)  D      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.

  10 ASP   (  13-)  A   H-bonding suggests Asn; but Alt-Rotamer
  12 ASP   (  15-)  A   H-bonding suggests Asn
  93 ASP   (  96-)  A   H-bonding suggests Asn; but Alt-Rotamer
 232 GLU   ( 235-)  A   H-bonding suggests Gln
 264 ASP   ( 267-)  A   H-bonding suggests Asn; Ligand-contact
 368 ASP   (  15-)  B   H-bonding suggests Asn
 556 ASP   ( 203-)  B   H-bonding suggests Asn; but Alt-Rotamer
 620 ASP   ( 267-)  B   H-bonding suggests Asn; Ligand-contact
 913 ASP   ( 203-)  C   H-bonding suggests Asn; but Alt-Rotamer
 977 ASP   ( 267-)  C   H-bonding suggests Asn; Ligand-contact
 992 ASP   ( 282-)  C   H-bonding suggests Asn
1076 ASP   (  15-)  D   H-bonding suggests Asn; but Alt-Rotamer
1153 GLU   (  92-)  D   H-bonding suggests Gln
1264 ASP   ( 203-)  D   H-bonding suggests Asn; but Alt-Rotamer
1296 GLU   ( 235-)  D   H-bonding suggests Gln; but Alt-Rotamer
1328 ASP   ( 267-)  D   H-bonding suggests Asn; Ligand-contact

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 :   0.341
  2nd generation packing quality :  -0.941
  Ramachandran plot appearance   :  -0.862
  chi-1/chi-2 rotamer normality  :  -0.780
  Backbone conformation          :   0.926

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.293 (tight)
  Bond angles                    :   0.595 (tight)
  Omega angle restraints         :   0.210 (tight)
  Side chain planarity           :   0.245 (tight)
  Improper dihedral distribution :   0.562
  B-factor distribution          :   0.680
  Inside/Outside distribution    :   0.971

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 : 2.25


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.9
  2nd generation packing quality :  -1.0
  Ramachandran plot appearance   :   0.1
  chi-1/chi-2 rotamer normality  :   0.4
  Backbone conformation          :   1.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.293 (tight)
  Bond angles                    :   0.595 (tight)
  Omega angle restraints         :   0.210 (tight)
  Side chain planarity           :   0.245 (tight)
  Improper dihedral distribution :   0.562
  B-factor distribution          :   0.680
  Inside/Outside distribution    :   0.971
==============

WHAT IF
    G.Vriend,
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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.