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 pdb1pmm.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    =  90.780  B   =  91.406  C    =  93.686
    Alpha=  76.800  Beta=  77.100  Gamma=  78.240

Dimensions of a reduced cell

    A    =  90.780  B   =  91.406  C    =  93.686
    Alpha=  76.800  Beta=  77.100  Gamma=  78.240

Dimensions of the conventional cell

    A    = 141.345  B   = 114.951  C    =  93.686
    Alpha=  89.698  Beta= 106.921  Gamma=  90.402

Transformation to conventional cell

 |  1.000000  1.000000  0.000000|
 |  1.000000 -1.000000  0.000000|
 |  0.000000  0.000000 -1.000000|

Crystal class of the cell: TRICLINIC

Crystal class of the conventional CELL: MONOCLINIC

Space group name: P 1

Bravais type of conventional cell is: 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 B

All-atom RMS fit for the two chains : 0.528
CA-only RMS fit for the two chains : 0.221

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 : 0.490
CA-only RMS fit for the two chains : 0.106

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 : 0.540
CA-only RMS fit for the two chains : 0.237

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 : 0.448
CA-only RMS fit for the two chains : 0.150

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 : 0.530
CA-only RMS fit for the two chains : 0.230

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

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

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.

2699 PLP   ( 500-)  A  -
2700 ACY   (5518-)  A  -
2701 PLP   ( 500-)  B  -
2702 ACY   (6518-)  B  -
2703 PLP   ( 501-)  C  -
2704 ACY   (8518-)  C  -
2705 PLP   ( 501-)  D  -
2706 ACY   (7518-)  D  -
2707 PLP   ( 502-)  E  -
2708 ACY   (9518-)  E  -
2709 PLP   ( 502-)  F  -
2710 ACY   (9519-)  E  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 274 LYS   ( 276-)  A  -   NZ  bound to 2699 PLP   ( 500-)  A  -   C4A
 724 LYS   ( 276-)  B  -   NZ  bound to 2701 PLP   ( 500-)  B  -   C4A
1173 LYS   ( 276-)  C  -   NZ  bound to 2703 PLP   ( 501-)  C  -   C4A
1623 LYS   ( 276-)  D  -   NZ  bound to 2705 PLP   ( 501-)  D  -   C4A
2072 LYS   ( 276-)  E  -   NZ  bound to 2707 PLP   ( 502-)  E  -   C4A
2522 LYS   ( 276-)  F  -   NZ  bound to 2709 PLP   ( 502-)  F  -   C4A

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

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

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

 872 MET   ( 424-)  B    0.80
1321 MET   ( 424-)  C    0.80

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) : 90.000

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

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

 |  0.998713 -0.000048 -0.000047|
 | -0.000048  0.998608 -0.000048|
 | -0.000047 -0.000048  0.998734|
Proposed new scale matrix

 |  0.011030 -0.002296 -0.002125|
 |  0.000000  0.011190 -0.002184|
 |  0.000000  0.000000  0.011171|
With corresponding cell

    A    =  90.662  B   =  91.276  C    =  93.566
    Alpha=  76.804  Beta=  77.103  Gamma=  78.243

The CRYST1 cell dimensions

    A    =  90.780  B   =  91.406  C    =  93.686
    Alpha=  76.800  Beta=  77.100  Gamma=  78.240

Variance: 156.470
(Under-)estimated Z-score: 9.219

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.

 216 GLU   ( 218-)  A      N    CA   C    96.15   -5.4
 666 GLU   ( 218-)  B      N    CA   C    95.78   -5.5
1115 GLU   ( 218-)  C      N    CA   C    96.74   -5.2
1565 GLU   ( 218-)  D      N    CA   C    96.36   -5.3
2014 GLU   ( 218-)  E      N    CA   C    96.39   -5.3
2464 GLU   ( 218-)  F      N    CA   C    96.24   -5.3

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.

  12 LEU   (  14-)  A    5.54
 911 LEU   (  14-)  C    5.38
 666 GLU   ( 218-)  B    5.34
 216 GLU   ( 218-)  A    5.22
2464 GLU   ( 218-)  F    5.19
1565 GLU   ( 218-)  D    5.15
2014 GLU   ( 218-)  E    5.13
1810 LEU   (  14-)  E    5.11
1361 LEU   (  14-)  D    5.11
 462 LEU   (  14-)  B    5.09
1115 GLU   ( 218-)  C    5.02
2339 SER   (  93-)  F    4.56
2260 LEU   (  14-)  F    4.46
 541 SER   (  93-)  B    4.32
1440 SER   (  93-)  D    4.29
  91 SER   (  93-)  A    4.25
 990 SER   (  93-)  C    4.16
2487 HIS   ( 241-)  F    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.

1061 ILE   ( 164-)  C    -2.5
 612 ILE   ( 164-)  B    -2.4
 162 ILE   ( 164-)  A    -2.4
1960 ILE   ( 164-)  E    -2.4
2005 PHE   ( 209-)  E    -2.4
2331 ILE   (  85-)  F    -2.4
2455 PHE   ( 209-)  F    -2.4
2410 ILE   ( 164-)  F    -2.4
1106 PHE   ( 209-)  C    -2.3
1556 PHE   ( 209-)  D    -2.3
 657 PHE   ( 209-)  B    -2.3
1432 ILE   (  85-)  D    -2.3
 207 PHE   ( 209-)  A    -2.3
1980 PRO   ( 184-)  E    -2.3
1511 ILE   ( 164-)  D    -2.3
2430 PRO   ( 184-)  F    -2.2
 658 GLY   ( 210-)  B    -2.2
1557 GLY   ( 210-)  D    -2.2
2456 GLY   ( 210-)  F    -2.2
1107 GLY   ( 210-)  C    -2.2
 208 GLY   ( 210-)  A    -2.2
  83 ILE   (  85-)  A    -2.2
2006 GLY   ( 210-)  E    -2.2
 761 PHE   ( 313-)  B    -2.2
1210 PHE   ( 313-)  C    -2.1
 982 ILE   (  85-)  C    -2.1
 311 PHE   ( 313-)  A    -2.1
1660 PHE   ( 313-)  D    -2.1
2109 PHE   ( 313-)  E    -2.1
1917 THR   ( 121-)  E    -2.1
 533 ILE   (  85-)  B    -2.1
2559 PHE   ( 313-)  F    -2.1
 119 THR   ( 121-)  A    -2.1
1018 THR   ( 121-)  C    -2.1
 182 PRO   ( 184-)  A    -2.1
1468 THR   ( 121-)  D    -2.1
2095 LEU   ( 299-)  E    -2.1
1881 ILE   (  85-)  E    -2.1
 569 THR   ( 121-)  B    -2.1
1776 PHE   ( 429-)  D    -2.0
 500 LEU   (  52-)  B    -2.0
1848 LEU   (  52-)  E    -2.0
2367 THR   ( 121-)  F    -2.0
 949 LEU   (  52-)  C    -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.

 107 HIS   ( 109-)  A  Poor phi/psi
 159 PRO   ( 161-)  A  Poor phi/psi
 259 ASP   ( 261-)  A  Poor phi/psi
 274 LYS   ( 276-)  A  Poor phi/psi
 277 LEU   ( 279-)  A  Poor phi/psi
 281 GLY   ( 283-)  A  Poor phi/psi
 315 PHE   ( 317-)  A  Poor phi/psi
 557 HIS   ( 109-)  B  Poor phi/psi
 709 ASP   ( 261-)  B  Poor phi/psi
 724 LYS   ( 276-)  B  Poor phi/psi
 727 LEU   ( 279-)  B  Poor phi/psi
 731 GLY   ( 283-)  B  Poor phi/psi
 765 PHE   ( 317-)  B  Poor phi/psi
 767 ARG   ( 319-)  B  Poor phi/psi
1006 HIS   ( 109-)  C  Poor phi/psi
1058 PRO   ( 161-)  C  Poor phi/psi
1158 ASP   ( 261-)  C  Poor phi/psi
1173 LYS   ( 276-)  C  Poor phi/psi
1176 LEU   ( 279-)  C  Poor phi/psi
1180 GLY   ( 283-)  C  Poor phi/psi
1214 PHE   ( 317-)  C  Poor phi/psi
1273 PRO   ( 376-)  C  Poor phi/psi
1456 HIS   ( 109-)  D  Poor phi/psi
1608 ASP   ( 261-)  D  Poor phi/psi
1623 LYS   ( 276-)  D  Poor phi/psi
1626 LEU   ( 279-)  D  Poor phi/psi
1630 GLY   ( 283-)  D  Poor phi/psi
1664 PHE   ( 317-)  D  Poor phi/psi
1905 HIS   ( 109-)  E  Poor phi/psi
1957 PRO   ( 161-)  E  Poor phi/psi
2056 TRP   ( 260-)  E  Poor phi/psi
2057 ASP   ( 261-)  E  Poor phi/psi
2072 LYS   ( 276-)  E  Poor phi/psi
2075 LEU   ( 279-)  E  Poor phi/psi
2079 GLY   ( 283-)  E  Poor phi/psi
2113 PHE   ( 317-)  E  Poor phi/psi
2355 HIS   ( 109-)  F  Poor phi/psi
2507 ASP   ( 261-)  F  Poor phi/psi
2522 LYS   ( 276-)  F  Poor phi/psi
2525 LEU   ( 279-)  F  Poor phi/psi
2529 GLY   ( 283-)  F  Poor phi/psi
2563 PHE   ( 317-)  F  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -0.454

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.

1889 SER   (  93-)  E    0.34
1743 SER   ( 396-)  D    0.35
 442 SER   ( 444-)  A    0.35
 844 SER   ( 396-)  B    0.36
2240 SER   ( 444-)  E    0.36
 990 SER   (  93-)  C    0.36
1243 SER   ( 346-)  C    0.36
1293 SER   ( 396-)  C    0.36
2192 SER   ( 396-)  E    0.38
 394 SER   ( 396-)  A    0.39
 892 SER   ( 444-)  B    0.39
 908 SER   (  11-)  C    0.40
2642 SER   ( 396-)  F    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!

  21 ILE   (  23-)  A      0
  26 GLU   (  28-)  A      0
  27 SER   (  29-)  A      0
  28 LYS   (  30-)  A      0
  29 ARG   (  31-)  A      0
  32 LEU   (  34-)  A      0
  33 HIS   (  35-)  A      0
  35 MET   (  37-)  A      0
  36 ARG   (  38-)  A      0
  49 TYR   (  51-)  A      0
  51 ASP   (  53-)  A      0
  61 PHE   (  63-)  A      0
  65 TRP   (  67-)  A      0
  82 TRP   (  84-)  A      0
  83 ILE   (  85-)  A      0
  88 TYR   (  90-)  A      0
 106 TRP   ( 108-)  A      0
 107 HIS   ( 109-)  A      0
 108 ALA   ( 110-)  A      0
 112 LYS   ( 114-)  A      0
 117 VAL   ( 119-)  A      0
 120 ASN   ( 122-)  A      0
 122 ILE   ( 124-)  A      0
 150 THR   ( 152-)  A      0
 151 ASP   ( 153-)  A      0
And so on for a total of 969 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 : 1.317

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!

1088 PRO   ( 191-)  C   1.73   13
1538 PRO   ( 191-)  D   1.72   17
 189 PRO   ( 191-)  A   1.65   14
1987 PRO   ( 191-)  E   1.65   14

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.

2522 LYS   ( 276-)  F      NZ  <-> 2709 PLP   ( 502-)  F      C4A    1.37    1.33  INTRA B3
2522 LYS   ( 276-)  F      CE  <-> 2709 PLP   ( 502-)  F      C4A    0.75    2.45  INTRA
 141 LYS   ( 143-)  A      NZ  <->  296 GLU   ( 298-)  A      OE2    0.37    2.33  INTRA
 169 ARG   ( 171-)  A      NH1 <->  746 GLU   ( 298-)  B      O      0.28    2.42  INTRA
2594 GLN   ( 348-)  F      NE2 <-> 2677 MET   ( 431-)  F      CE     0.26    2.84  INTRA BL
2246 ASP   ( 450-)  E      C   <-> 2247 HIS   ( 451-)  E      ND1    0.25    2.75  INTRA BF
 898 ASP   ( 450-)  B      C   <->  899 HIS   ( 451-)  B      ND1    0.24    2.76  INTRA BF
2385 TRP   ( 139-)  F      CE3 <-> 2388 ARG   ( 142-)  F      NH2    0.23    2.87  INTRA BL
 273 HIS   ( 275-)  A      ND1 <->  281 GLY   ( 283-)  A      N      0.21    2.79  INTRA BL
1497 LYS   ( 150-)  D      NZ  <-> 1547 GLU   ( 200-)  D      OE1    0.21    2.49  INTRA BL
 181 ARG   ( 183-)  A      NH2 <->  184 GLN   ( 186-)  A      OE1    0.21    2.49  INTRA
2385 TRP   ( 139-)  F      NE1 <-> 2389 LYS   ( 143-)  F      CE     0.21    2.89  INTRA BL
1039 ARG   ( 142-)  C      NH2 <-> 1521 ASP   ( 174-)  D      OD2    0.19    2.51  INTRA
1172 HIS   ( 275-)  C      NE2 <-> 2703 PLP   ( 501-)  C      O1P    0.19    2.51  INTRA BL
2429 ARG   ( 183-)  F      NH2 <-> 2432 GLN   ( 186-)  F      OE1    0.18    2.52  INTRA
2429 ARG   ( 183-)  F      NE  <-> 2432 GLN   ( 186-)  F      OE1    0.18    2.52  INTRA
1295 ARG   ( 398-)  C      NH1 <-> 1344 TYR   ( 447-)  C      CD1    0.18    2.92  INTRA
 598 LYS   ( 150-)  B      NZ  <->  648 GLU   ( 200-)  B      OE1    0.17    2.53  INTRA BL
1530 ARG   ( 183-)  D      NH2 <-> 1533 GLN   ( 186-)  D      OE1    0.17    2.53  INTRA
 273 HIS   ( 275-)  A      NE2 <-> 2699 PLP   ( 500-)  A      O1P    0.17    2.53  INTRA BL
 689 HIS   ( 241-)  B      ND1 <->  717 SER   ( 269-)  B      OG     0.16    2.54  INTRA BL
 222 HIS   ( 224-)  A      NE2 <->  264 ARG   ( 266-)  A      N      0.16    2.84  INTRA BL
1622 HIS   ( 275-)  D      NE2 <-> 2705 PLP   ( 501-)  D      O1P    0.16    2.54  INTRA BL
1545 CYS   ( 198-)  D      O   <-> 2714 HOH   (7709 )  D      O      0.15    2.25  INTRA BL
2696 ASP   ( 450-)  F      C   <-> 2697 HIS   ( 451-)  F      ND1    0.15    2.85  INTRA BF
And so on for a total of 274 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Warning: Abnormal packing environment for some residues

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

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

 304 LEU   ( 306-)  A      -6.52
1653 LEU   ( 306-)  D      -6.46
 754 LEU   ( 306-)  B      -6.43
1203 LEU   ( 306-)  C      -6.42
2102 LEU   ( 306-)  E      -6.41
1011 LYS   ( 114-)  C      -6.37
 562 LYS   ( 114-)  B      -6.29
 112 LYS   ( 114-)  A      -6.28
1910 LYS   ( 114-)  E      -6.27
1461 LYS   ( 114-)  D      -6.21
2360 LYS   ( 114-)  F      -6.21
2459 TYR   ( 213-)  F      -6.13
 661 TYR   ( 213-)  B      -6.06
2009 TYR   ( 213-)  E      -6.06
 211 TYR   ( 213-)  A      -6.00
2552 LEU   ( 306-)  F      -5.95
1110 TYR   ( 213-)  C      -5.80
1560 TYR   ( 213-)  D      -5.78
2086 ARG   ( 290-)  E      -5.71
1637 ARG   ( 290-)  D      -5.62
 288 ARG   ( 290-)  A      -5.59
2536 ARG   ( 290-)  F      -5.58
 388 TYR   ( 390-)  A      -5.53
1187 ARG   ( 290-)  C      -5.46
 479 ARG   (  31-)  B      -5.44
2277 ARG   (  31-)  F      -5.43
2648 ARG   ( 402-)  F      -5.37
2186 TYR   ( 390-)  E      -5.28
 928 ARG   (  31-)  C      -5.19
1287 TYR   ( 390-)  C      -5.15
  29 ARG   (  31-)  A      -5.08

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Warning: Low packing Z-score for some residues

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

 977 ILE   (  80-)  C   -2.85
1876 ILE   (  80-)  E   -2.83
 528 ILE   (  80-)  B   -2.83
  78 ILE   (  80-)  A   -2.82
2326 ILE   (  80-)  F   -2.82
1427 ILE   (  80-)  D   -2.80
1361 LEU   (  14-)  D   -2.73
2298 LEU   (  52-)  F   -2.68
 462 LEU   (  14-)  B   -2.63
1810 LEU   (  14-)  E   -2.63
 500 LEU   (  52-)  B   -2.61
2260 LEU   (  14-)  F   -2.60
  12 LEU   (  14-)  A   -2.59
 949 LEU   (  52-)  C   -2.57
 911 LEU   (  14-)  C   -2.56
  50 LEU   (  52-)  A   -2.52

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Water, ion, and hydrogenbond related checks

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.

2712 HOH   (6728 )  B      O     29.53  -49.62  -34.86
2712 HOH   (6777 )  B      O    -15.14  -32.71   42.17
2714 HOH   (7810 )  D      O     65.22  -25.25   -1.47
2716 HOH   ( 602 )  F      O    -31.98  -22.20   53.49
2716 HOH   ( 637 )  F      O    -37.05   38.68  -15.18
2716 HOH   ( 721 )  F      O    -32.74  -19.46   52.05

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.

 792 ASN   ( 344-)  B
1548 ASN   ( 201-)  D
2140 ASN   ( 344-)  E

Warning: Buried unsatisfied hydrogen bond donors

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

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

Waters are not listed by this option.

  23 THR   (  25-)  A      N
  56 GLN   (  58-)  A      NE2
  65 TRP   (  67-)  A      N
  81 ASN   (  83-)  A      N
  81 ASN   (  83-)  A      ND2
 123 GLY   ( 125-)  A      N
 124 SER   ( 126-)  A      N
 125 SER   ( 127-)  A      N
 186 PHE   ( 188-)  A      N
 202 GLY   ( 204-)  A      N
 244 SER   ( 246-)  A    A OG
 259 ASP   ( 261-)  A      N
 273 HIS   ( 275-)  A      NE2
 276 GLY   ( 278-)  A      N
 289 ASP   ( 291-)  A      N
 296 GLU   ( 298-)  A      N
 316 SER   ( 318-)  A      N
 454 VAL   (   6-)  B      N
 473 THR   (  25-)  B      N
 506 GLN   (  58-)  B      NE2
 515 TRP   (  67-)  B      N
 531 ASN   (  83-)  B      N
 531 ASN   (  83-)  B      ND2
 574 SER   ( 126-)  B      N
 575 SER   ( 127-)  B      N
And so on for a total of 110 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.

  34 GLU   (  36-)  A      OE2
  84 ASP   (  86-)  A      OD2
 484 GLU   (  36-)  B      OE2
 534 ASP   (  86-)  B      OD2
1882 ASP   (  86-)  E      OD2
2282 GLU   (  36-)  F      OE1
2332 ASP   (  86-)  F      OD2
2660 GLU   ( 414-)  F      OE2
2676 GLU   ( 430-)  F      OE2

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.

2715 HOH   (9725 )  E      O  1.14  K  4
2715 HOH   (9775 )  E      O  1.00  K  4 ION-B

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.

  13 ASP   (  15-)  A   H-bonding suggests Asn
  66 ASP   (  68-)  A   H-bonding suggests Asn; but Alt-Rotamer
  84 ASP   (  86-)  A   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
  86 GLU   (  88-)  A   H-bonding suggests Gln
 177 GLU   ( 179-)  A   H-bonding suggests Gln; but Alt-Rotamer
 226 ASP   ( 228-)  A   H-bonding suggests Asn
 428 GLU   ( 430-)  A   H-bonding suggests Gln
 456 ASP   (   8-)  B   H-bonding suggests Asn
 463 ASP   (  15-)  B   H-bonding suggests Asn
 534 ASP   (  86-)  B   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
 681 ASP   ( 233-)  B   H-bonding suggests Asn
 878 GLU   ( 430-)  B   H-bonding suggests Gln
 898 ASP   ( 450-)  B   H-bonding suggests Asn
 905 ASP   (   8-)  C   H-bonding suggests Asn
 912 ASP   (  15-)  C   H-bonding suggests Asn
 983 ASP   (  86-)  C   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
1122 ASP   ( 225-)  C   H-bonding suggests Asn
1327 GLU   ( 430-)  C   H-bonding suggests Gln
1347 ASP   ( 450-)  C   H-bonding suggests Asn
1355 ASP   (   8-)  D   H-bonding suggests Asn
1415 ASP   (  68-)  D   H-bonding suggests Asn; but Alt-Rotamer
1433 ASP   (  86-)  D   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
1777 GLU   ( 430-)  D   H-bonding suggests Gln
1797 ASP   ( 450-)  D   H-bonding suggests Asn
1804 ASP   (   8-)  E   H-bonding suggests Asn
1811 ASP   (  15-)  E   H-bonding suggests Asn
1864 ASP   (  68-)  E   H-bonding suggests Asn; but Alt-Rotamer
1882 ASP   (  86-)  E   H-bonding suggests Asn; Ligand-contact
1884 GLU   (  88-)  E   H-bonding suggests Gln
2182 GLU   ( 386-)  E   H-bonding suggests Gln
2226 GLU   ( 430-)  E   H-bonding suggests Gln
2254 ASP   (   8-)  F   H-bonding suggests Asn
2332 ASP   (  86-)  F   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
2610 GLU   ( 364-)  F   H-bonding suggests Gln; but Alt-Rotamer
2676 GLU   ( 430-)  F   H-bonding suggests Gln
2696 ASP   ( 450-)  F   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.132
  2nd generation packing quality :  -0.853
  Ramachandran plot appearance   :  -0.327
  chi-1/chi-2 rotamer normality  :  -0.454
  Backbone conformation          :  -0.332

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.251 (tight)
  Bond angles                    :   0.584 (tight)
  Omega angle restraints         :   0.240 (tight)
  Side chain planarity           :   0.246 (tight)
  Improper dihedral distribution :   0.568
  B-factor distribution          :   0.326
  Inside/Outside distribution    :   1.002

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 : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.2
  2nd generation packing quality :  -0.6
  Ramachandran plot appearance   :   0.2
  chi-1/chi-2 rotamer normality  :   0.3
  Backbone conformation          :  -0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.251 (tight)
  Bond angles                    :   0.584 (tight)
  Omega angle restraints         :   0.240 (tight)
  Side chain planarity           :   0.246 (tight)
  Improper dihedral distribution :   0.568
  B-factor distribution          :   0.326
  Inside/Outside distribution    :   1.002
==============

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.