WHAT IF Check report

This file was created 2014-04-17 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 pdb2hox.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 : 0.653
CA-only RMS fit for the two chains : 0.258

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 : 0.524
CA-only RMS fit for the two chains : 0.267

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 : 0.748
CA-only RMS fit for the two chains : 0.328

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 : 0.618
CA-only RMS fit for the two chains : 0.281

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 : 0.589
CA-only RMS fit for the two chains : 0.323

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.

1726 BMA   ( 503-)  A  -
1727 BMA   ( 505-)  A  -
1729 P1T   (6001-)  A  -
1731 P1T   (6002-)  B  -
1733 P1T   (6003-)  C  -
1735 P1T   (6004-)  D  -
1736 BMA   ( 503-)  C  -
1737 XYP   ( 504-)  A  -

Administrative problems that can generate validation failures

Warning: Strange inter-chain connections detected

The pairs of residues listed in the table below seem covalently bound while belonging to different chains in the PDB file.

Sometimes this is unavoidable (e.g. if two protein chains are covalently connected via a Cys-Cys or other bond). But if it can be avoided (e.g. often we observe sugars with one chain identifier connected to protein chains with another chain identifier), it should be avoided. WHAT IF and WHAT-CHECK try to deal with all exceptions thrown at it, but if you want these programs to work optimally (i.e. make as few false error messages as is possible) you should help them by getting as much of the administration correct as is humanly possible.

   2 MET   (   2-)  A  -   CE   427 MET   (   2-)  B  -   SD
   2 MET   (   2-)  A  -   CE   427 MET   (   2-)  B  -   CE

Warning: Strange inter-chain connections could NOT be corrected

Often inter-chain connections are simple administrative problems. In this case not. The observed inter-chain connection(s) either are real, or they are too strange for WHAT IF to correct. Human inspection seems required.

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.

1705 NAG   ( 500-)  A  -   O4  bound to 1707 NAG   ( 502-)  A  -   C1
1707 NAG   ( 502-)  A  -   O4  bound to 1726 BMA   ( 503-)  A  -   C1
1716 NAG   ( 500-)  C  -   O4  bound to 1718 NAG   ( 502-)  C  -   C1
1718 NAG   ( 502-)  C  -   O4  bound to 1736 BMA   ( 503-)  C  -   C1
1721 NAG   ( 500-)  D  -   O4  bound to 1723 NAG   ( 502-)  D  -   C1
1724 NAG   ( 503-)  D  -   O4  bound to 1725 NAG   ( 504-)  D  -   C1

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: 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.

1709 NAG   ( 507-)  A    High
1714 NAG   ( 503-)  B    High

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.

   2 MET   (   2-)  A    0.50
 427 MET   (   2-)  B    0.50
1147 LYS   ( 295-)  C    0.16

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :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: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

 684 ARG   ( 259-)  B
 737 ARG   ( 312-)  B
1536 ARG   ( 259-)  D
1589 ARG   ( 312-)  D

Warning: Tyrosine convention problem

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

  92 TYR   (  92-)  A
 417 TYR   ( 417-)  A
 470 TYR   (  45-)  B
 517 TYR   (  92-)  B
 774 TYR   ( 349-)  B
 841 TYR   ( 416-)  B
 944 TYR   (  92-)  C
1269 TYR   ( 417-)  C
1369 TYR   (  92-)  D
1626 TYR   ( 349-)  D

Warning: Phenylalanine convention problem

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

 519 PHE   (  94-)  B
 946 PHE   (  94-)  C
1380 PHE   ( 103-)  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.

  49 ASP   (  49-)  A
 337 ASP   ( 337-)  A
 692 ASP   ( 267-)  B
 845 ASP   ( 420-)  B
1189 ASP   ( 337-)  C
1544 ASP   ( 267-)  D
1614 ASP   ( 337-)  D
1697 ASP   ( 420-)  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.

 209 GLU   ( 209-)  A
 343 GLU   ( 343-)  A
 348 GLU   ( 348-)  A
 372 GLU   ( 372-)  A
 773 GLU   ( 348-)  B
 797 GLU   ( 372-)  B
 886 GLU   (  34-)  C
1061 GLU   ( 209-)  C
1224 GLU   ( 372-)  C
1432 GLU   ( 155-)  D
1447 GLU   ( 170-)  D
1601 GLU   ( 324-)  D
1620 GLU   ( 343-)  D
1649 GLU   ( 372-)  D

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.

 717 ARG   ( 292-)  B      CG   CD    1.40   -4.1
1569 ARG   ( 292-)  D      CG   CD    1.38   -4.8

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

 |  0.999834  0.000905 -0.002284|
 |  0.000905  1.000956  0.002384|
 | -0.002284  0.002384  0.997469|
Proposed new scale matrix

 |  0.014786 -0.000018  0.001932|
 | -0.000007  0.007874 -0.000019|
 |  0.000023 -0.000023  0.009845|
With corresponding cell

    A    =  67.653  B   = 127.009  C    = 102.469
    Alpha=  89.742  Beta=  97.574  Gamma=  89.897

The CRYST1 cell dimensions

    A    =  67.665  B   = 126.892  C    = 102.664
    Alpha=  90.000  Beta=  97.300  Gamma=  90.000

Variance: 243.462
(Under-)estimated Z-score: 11.500

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.

 208 PRO   ( 208-)  A      N    CA   C   122.27    4.2
1111 ARG   ( 259-)  C      CD   NE   CZ  129.87    4.5
1509 HIS   ( 232-)  D      C    CA   CB  102.08   -4.2

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  49 ASP   (  49-)  A
 209 GLU   ( 209-)  A
 337 ASP   ( 337-)  A
 343 GLU   ( 343-)  A
 348 GLU   ( 348-)  A
 372 GLU   ( 372-)  A
 684 ARG   ( 259-)  B
 692 ASP   ( 267-)  B
 737 ARG   ( 312-)  B
 773 GLU   ( 348-)  B
 797 GLU   ( 372-)  B
 845 ASP   ( 420-)  B
 886 GLU   (  34-)  C
1061 GLU   ( 209-)  C
1189 ASP   ( 337-)  C
1224 GLU   ( 372-)  C
1432 GLU   ( 155-)  D
1447 GLU   ( 170-)  D
1536 ARG   ( 259-)  D
1544 ASP   ( 267-)  D
1589 ARG   ( 312-)  D
1601 GLU   ( 324-)  D
1614 ASP   ( 337-)  D
1620 GLU   ( 343-)  D
1649 GLU   ( 372-)  D
1697 ASP   ( 420-)  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.

 505 SER   (  80-)  B    4.24

Error: Side chain planarity problems

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

1084 HIS   ( 232-)  C    8.99
1509 HIS   ( 232-)  D    6.57
 232 HIS   ( 232-)  A    6.04
 657 HIS   ( 232-)  B    5.91
1619 GLN   ( 342-)  D    4.94
1628 ASN   ( 351-)  D    4.14

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.

1323 THR   (  46-)  D    -3.0
 898 THR   (  46-)  C    -2.9
 471 THR   (  46-)  B    -2.9
  46 THR   (  46-)  A    -2.7
1377 PHE   ( 100-)  D    -2.7
 952 PHE   ( 100-)  C    -2.5
1311 GLU   (  34-)  D    -2.5
1635 PRO   ( 358-)  D    -2.5
1111 ARG   ( 259-)  C    -2.5
 100 PHE   ( 100-)  A    -2.5
1536 ARG   ( 259-)  D    -2.5
 259 ARG   ( 259-)  A    -2.4
 684 ARG   ( 259-)  B    -2.4
 234 THR   ( 234-)  A    -2.4
 525 PHE   ( 100-)  B    -2.4
1511 THR   ( 234-)  D    -2.4
 208 PRO   ( 208-)  A    -2.3
1081 TYR   ( 229-)  C    -2.3
 358 PRO   ( 358-)  A    -2.3
 654 TYR   ( 229-)  B    -2.3
 659 THR   ( 234-)  B    -2.3
1210 PRO   ( 358-)  C    -2.3
1086 THR   ( 234-)  C    -2.2
 783 PRO   ( 358-)  B    -2.2
1299 GLU   (  22-)  D    -2.2
1236 ARG   ( 384-)  C    -2.2
1506 TYR   ( 229-)  D    -2.2
 809 ARG   ( 384-)  B    -2.2
1485 PRO   ( 208-)  D    -2.1
1060 PRO   ( 208-)  C    -2.1
 633 PRO   ( 208-)  B    -2.1
 459 GLU   (  34-)  B    -2.1
 446 SER   (  21-)  B    -2.1
  25 ARG   (  25-)  A    -2.1
 229 TYR   ( 229-)  A    -2.1
 450 ARG   (  25-)  B    -2.0
 877 ARG   (  25-)  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.

   3 THR   (   3-)  A  Poor phi/psi
  20 CYS   (  20-)  A  omega poor
  21 SER   (  21-)  A  Poor phi/psi
  40 GLU   (  40-)  A  omega poor
  44 CYS   (  44-)  A  Poor phi/psi
  50 CYS   (  50-)  A  Poor phi/psi
  66 GLY   (  66-)  A  Poor phi/psi
  91 SER   (  91-)  A  omega poor
  92 TYR   (  92-)  A  omega poor
  93 PHE   (  93-)  A  omega poor
  95 ASN   (  95-)  A  PRO omega poor
  99 ASN   (  99-)  A  Poor phi/psi
 100 PHE   ( 100-)  A  Poor phi/psi
 162 ALA   ( 162-)  A  PRO omega poor
 204 SER   ( 204-)  A  PRO omega poor
 207 ASN   ( 207-)  A  PRO omega poor
 208 PRO   ( 208-)  A  omega poor
 232 HIS   ( 232-)  A  omega poor
 255 HIS   ( 255-)  A  Poor phi/psi
 354 ARG   ( 354-)  A  Poor phi/psi
 363 TYR   ( 363-)  A  omega poor
 365 TRP   ( 365-)  A  omega poor
 384 ARG   ( 384-)  A  Poor phi/psi
 387 THR   ( 387-)  A  omega poor
 394 GLU   ( 394-)  A  Poor phi/psi, omega poor
And so on for a total of 113 lines.

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.

1252 VAL   ( 400-)  C    0.36

Warning: Unusual backbone conformations

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

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

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

   3 THR   (   3-)  A      0
   4 TRP   (   4-)  A      0
  18 ILE   (  18-)  A      0
  20 CYS   (  20-)  A      0
  21 SER   (  21-)  A      0
  22 GLU   (  22-)  A      0
  23 HIS   (  23-)  A      0
  29 ASP   (  29-)  A      0
  33 SER   (  33-)  A      0
  42 ASN   (  42-)  A      0
  43 THR   (  43-)  A      0
  44 CYS   (  44-)  A      0
  46 THR   (  46-)  A      0
  50 CYS   (  50-)  A      0
  55 GLN   (  55-)  A      0
  60 ASP   (  60-)  A      0
  61 VAL   (  61-)  A      0
  62 ALA   (  62-)  A      0
  87 TRP   (  87-)  A      0
  88 HIS   (  88-)  A      0
  89 ARG   (  89-)  A      0
  90 MET   (  90-)  A      0
  94 PHE   (  94-)  A      0
  95 ASN   (  95-)  A      0
  96 PRO   (  96-)  A      0
And so on for a total of 697 lines.

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

1363 PRO   (  86-)  D   1.83   10
  86 PRO   (  86-)  A   1.62   10
 938 PRO   (  86-)  C   1.56   10

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]

 462 PRO   (  37-)  B    0.07 LOW
 900 PRO   (  48-)  C    0.16 LOW
1211 PRO   ( 359-)  C    0.17 LOW
1636 PRO   ( 359-)  D    0.15 LOW

Warning: Unusual PRO puckering phases

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

 151 PRO   ( 151-)  A    46.7 half-chair C-delta/C-gamma (54 degrees)
 208 PRO   ( 208-)  A   -60.8 half-chair C-beta/C-alpha (-54 degrees)
 358 PRO   ( 358-)  A   -60.9 half-chair C-beta/C-alpha (-54 degrees)
 576 PRO   ( 151-)  B    45.6 half-chair C-delta/C-gamma (54 degrees)
 783 PRO   ( 358-)  B   -66.0 envelop C-beta (-72 degrees)
1325 PRO   (  48-)  D   100.4 envelop C-beta (108 degrees)
1485 PRO   ( 208-)  D   -61.8 half-chair C-beta/C-alpha (-54 degrees)
1635 PRO   ( 358-)  D   -65.6 envelop C-beta (-72 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

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

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

1318 CYS   (  41-)  D      SG   <->  1741 HOH   (6250 )  D      O    1.06    1.94  INTRA
1726 BMA   ( 503-)  A      O2   <->  1737 XYP   ( 504-)  A      C1B  0.97    1.43  INTRA B3
1718 NAG   ( 502-)  C      O4   <->  1736 BMA   ( 503-)  C      C1   0.94    1.46  INTRA BF
1129 TYR   ( 277-)  C      CE2  <->  1740 HOH   (6486 )  C      O    0.82    1.98  INTRA
1726 BMA   ( 503-)  A      C2   <->  1737 XYP   ( 504-)  A      C1B  0.80    2.40  INTRA BL
1129 TYR   ( 277-)  C      CZ   <->  1740 HOH   (6486 )  C      O    0.78    2.02  INTRA
1718 NAG   ( 502-)  C      C4   <->  1736 BMA   ( 503-)  C      C1   0.69    2.51  INTRA
1129 TYR   ( 277-)  C      OH   <->  1740 HOH   (6486 )  C      O    0.55    1.85  INTRA
 753 ASN   ( 328-)  B      ND2  <->  1713 NAG   ( 502-)  B      C1   0.53    2.57  INTRA BF
 502 LYS   (  77-)  B      NZ   <->  1739 HOH   (6682 )  B      O    0.51    2.19  INTRA BF
1738 HOH   (6516 )  A      O    <->  1738 HOH   (6720 )  A      O    0.49    1.71  INTRA
 871 ASN   (  19-)  C      CG   <->  1740 HOH   (6742 )  C      O    0.47    2.33  INTRA BF
1740 HOH   (6008 )  C      O    <->  1740 HOH   (6677 )  C      O    0.45    1.75  INTRA
1738 HOH   (6631 )  A      O    <->  1738 HOH   (6720 )  A      O    0.40    1.80  INTRA
1715 NAG   (3500-)  B      O3   <->  1739 HOH   (6270 )  B      O    0.39    2.01  INTRA BF
1589 ARG   ( 312-)  D      CD   <->  1741 HOH   (6417 )  D      O    0.39    2.41  INTRA
 562 HIS   ( 137-)  B      CD2  <->  1739 HOH   (6599 )  B      O    0.39    2.41  INTRA
1400 ASP   ( 123-)  D      O    <->  1741 HOH   (6449 )  D      O    0.39    2.01  INTRA BF
 176 ASP   ( 176-)  A      CG   <->  1738 HOH   (6408 )  A      O    0.36    2.44  INTRA BF
1740 HOH   (6135 )  C      O    <->  1740 HOH   (6744 )  C      O    0.36    1.84  INTRA
 989 HIS   ( 137-)  C      CE1  <->  1029 LYS   ( 177-)  C      NZ   0.35    2.75  INTRA
 470 TYR   (  45-)  B      CE2  <->   478 LYS   (  53-)  B      CD   0.35    2.85  INTRA
 480 GLN   (  55-)  B      O    <->  1739 HOH   (6653 )  B      O    0.35    2.05  INTRA
1084 HIS   ( 232-)  C      CG   <->  1740 HOH   (6387 )  C      O    0.34    2.46  INTRA
 720 LYS   ( 295-)  B      NZ   <->  1739 HOH   (6089 )  B      O    0.33    2.37  INTRA
And so on for a total of 224 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.

 851 ARG   ( 426-)  B      -6.95
1703 ARG   ( 426-)  D      -6.88
1623 GLN   ( 346-)  D      -6.47
 907 GLN   (  55-)  C      -6.41
 771 GLN   ( 346-)  B      -6.33
1198 GLN   ( 346-)  C      -6.23
  55 GLN   (  55-)  A      -6.13
1332 GLN   (  55-)  D      -6.04
 346 GLN   ( 346-)  A      -5.95
1206 ARG   ( 354-)  C      -5.91
 779 ARG   ( 354-)  B      -5.84
 480 GLN   (  55-)  B      -5.76
 354 ARG   ( 354-)  A      -5.62
1195 GLU   ( 343-)  C      -5.61
1702 LYS   ( 425-)  D      -5.56
1490 ARG   ( 213-)  D      -5.45
 343 GLU   ( 343-)  A      -5.43
1631 ARG   ( 354-)  D      -5.42
 874 GLU   (  22-)  C      -5.38
 213 ARG   ( 213-)  A      -5.34
1065 ARG   ( 213-)  C      -5.31
 638 ARG   ( 213-)  B      -5.24
1299 GLU   (  22-)  D      -5.22
1089 LYS   ( 237-)  C      -5.11
1620 GLU   ( 343-)  D      -5.06
  22 GLU   (  22-)  A      -5.01
 237 LYS   ( 237-)  A      -5.00

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.

 212 LEU   ( 212-)  A       214 - HIS    214- ( A)         -4.74
 637 LEU   ( 212-)  B       639 - HIS    214- ( B)         -4.81
1064 LEU   ( 212-)  C      1066 - HIS    214- ( C)         -4.79
1489 LEU   ( 212-)  D      1491 - HIS    214- ( D)         -4.87

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.

 480 GLN   (  55-)  B   -2.88
1090 TYR   ( 238-)  C   -2.77
 238 TYR   ( 238-)  A   -2.72
 816 VAL   ( 391-)  B   -2.68
1042 VAL   ( 190-)  C   -2.67
1631 ARG   ( 354-)  D   -2.67
1668 VAL   ( 391-)  D   -2.64
1243 VAL   ( 391-)  C   -2.59
 391 VAL   ( 391-)  A   -2.59
 769 LEU   ( 344-)  B   -2.53
1621 LEU   ( 344-)  D   -2.52
 344 LEU   ( 344-)  A   -2.50

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

 766 TYR   ( 341-)  B     -  769 LEU   ( 344-)  B        -1.84
 777 TYR   ( 352-)  B     -  780 ARG   ( 355-)  B        -1.71
1205 PHE   ( 353-)  C     - 1208 MET   ( 356-)  C        -1.80

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

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.

1738 HOH   (6299 )  A      O     72.24  -35.43   14.62
1738 HOH   (6400 )  A      O      5.46   25.99   19.20
1738 HOH   (6417 )  A      O     41.67   24.07    1.56
1738 HOH   (6487 )  A      O     74.26  -37.29   15.87
1738 HOH   (6492 )  A      O     71.97  -12.53   33.32
1738 HOH   (6507 )  A      O     51.07   28.10   15.17
1738 HOH   (6522 )  A      O     54.30    4.37    5.07
1738 HOH   (6529 )  A      O     74.69  -31.47   24.37
1738 HOH   (6543 )  A      O     72.85  -39.04   17.13
1738 HOH   (6551 )  A      O     70.85  -36.21   16.96
1738 HOH   (6567 )  A      O     76.94  -36.95   16.16
1738 HOH   (6573 )  A      O     68.54  -26.25   26.94
1738 HOH   (6590 )  A      O     76.58  -32.72   24.22
1738 HOH   (6599 )  A      O     67.13  -29.18   26.49
1738 HOH   (6609 )  A      O     42.44    0.52   79.67
1738 HOH   (6610 )  A      O     77.58  -32.13   26.22
1738 HOH   (6613 )  A      O     79.55  -32.08   28.18
1738 HOH   (6616 )  A      O     79.68  -34.33   29.98
1738 HOH   (6621 )  A      O     79.82  -35.22   32.94
1738 HOH   (6753 )  A      O     73.36  -21.11   31.03
1739 HOH   (6465 )  B      O     72.29   -4.65   34.00
1739 HOH   (6524 )  B      O     74.93   -4.15   36.29
1739 HOH   (6531 )  B      O     71.15   -3.55   36.10
1739 HOH   (6534 )  B      O     21.09  -33.19   -5.68
1739 HOH   (6548 )  B      O     70.71   -5.46   31.55
And so on for a total of 71 lines.

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.

1738 HOH   (6469 )  A      O
1738 HOH   (6622 )  A      O
1738 HOH   (6679 )  A      O
1740 HOH   (6445 )  C      O
1741 HOH   (6365 )  D      O
Bound group on Asn; dont flip  146 ASN  ( 146-) A
Bound to: 1705 NAG  ( 500-) A
Bound group on Asn; dont flip  191 ASN  ( 191-) A
Bound to: 1710 NAG  (4500-) A
Bound group on Asn; dont flip  328 ASN  ( 328-) A
Bound to: 1708 NAG  ( 506-) A
Bound group on Asn; dont flip  571 ASN  ( 146-) B
Bound to: 1711 NAG  ( 500-) B
Bound group on Asn; dont flip  616 ASN  ( 191-) B
Bound to: 1715 NAG  (3500-) B
Bound group on Asn; dont flip  998 ASN  ( 146-) C
Bound to: 1716 NAG  ( 500-) C
Bound group on Asn; dont flip 1180 ASN  ( 328-) C
Bound to: 1719 NAG  ( 504-) C
Bound group on Asn; dont flip 1423 ASN  ( 146-) D
Bound to: 1721 NAG  ( 500-) D
Bound group on Asn; dont flip 1605 ASN  ( 328-) D
Bound to: 1724 NAG  ( 503-) D
Marked this atom as acceptor 1728  CL  (5001-) A     CL
Marked this atom as acceptor 1730  CL  (5002-) B     CL
Marked this atom as acceptor 1732  CL  (5003-) C     CL
Marked this atom as acceptor 1734  CL  (5004-) D     CL

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.

  19 ASN   (  19-)  A
 214 HIS   ( 214-)  A
 307 GLN   ( 307-)  A
 388 GLN   ( 388-)  A
 524 ASN   (  99-)  B
 562 HIS   ( 137-)  B
 639 HIS   ( 214-)  B
 833 GLN   ( 408-)  B
 927 GLN   (  75-)  C
1040 ASN   ( 188-)  C
1066 HIS   ( 214-)  C
1332 GLN   (  55-)  D
1376 ASN   (  99-)  D
1491 HIS   ( 214-)  D
1584 GLN   ( 307-)  D
1655 GLN   ( 378-)  D
1685 GLN   ( 408-)  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.

  19 ASN   (  19-)  A      N
  64 GLY   (  64-)  A      N
  89 ARG   (  89-)  A      N
  92 TYR   (  92-)  A      OH
 118 ASN   ( 118-)  A      ND2
 119 ALA   ( 119-)  A      N
 132 VAL   ( 132-)  A      N
 167 VAL   ( 167-)  A      N
 184 GLY   ( 184-)  A      N
 207 ASN   ( 207-)  A      N
 207 ASN   ( 207-)  A      ND2
 232 HIS   ( 232-)  A      N
 250 SER   ( 250-)  A      OG
 251 LYS   ( 251-)  A      N
 256 SER   ( 256-)  A      OG
 259 ARG   ( 259-)  A      NH1
 259 ARG   ( 259-)  A      NH2
 285 THR   ( 285-)  A      OG1
 315 ASN   ( 315-)  A      ND2
 362 SER   ( 362-)  A      OG
 363 TYR   ( 363-)  A      OH
 387 THR   ( 387-)  A      OG1
 401 ARG   ( 401-)  A      NH1
 401 ARG   ( 401-)  A      NH2
 489 GLY   (  64-)  B      N
And so on for a total of 100 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.

 225 ASP   ( 225-)  A      OD2
 232 HIS   ( 232-)  A      ND1
 315 ASN   ( 315-)  A      OD1
 650 ASP   ( 225-)  B      OD2
 740 ASN   ( 315-)  B      OD1
1077 ASP   ( 225-)  C      OD2
1084 HIS   ( 232-)  C      ND1
1311 GLU   (  34-)  D      OE1
1502 ASP   ( 225-)  D      OD2
1509 HIS   ( 232-)  D      ND1

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.

1738 HOH   (6186 )  A      O  0.85  K  4
1738 HOH   (6212 )  A      O  0.90  K  4
1738 HOH   (6281 )  A      O  1.08  K  5 Ion-B
1738 HOH   (6408 )  A      O  0.96 NA  4 Ion-B
1738 HOH   (6494 )  A      O  1.09  K  4 Ion-B
1738 HOH   (6543 )  A      O  0.98  K  4
1738 HOH   (6714 )  A      O  0.92  K  5 Ion-B
1738 HOH   (6735 )  A      O  0.89 NA  4 ION-B
1739 HOH   (6003 )  B      O  0.88  K  5
1739 HOH   (6010 )  B      O  1.11  K  4
1739 HOH   (6090 )  B      O  0.90  K  4
1739 HOH   (6119 )  B      O  1.10  K  4
1739 HOH   (6295 )  B      O  0.95  K  5
1739 HOH   (6321 )  B      O  1.09  K  7 Ion-B
1739 HOH   (6369 )  B      O  1.14  K  4 Ion-B
1739 HOH   (6580 )  B      O  0.86 NA  7
1739 HOH   (6585 )  B      O  0.90  K  4
1739 HOH   (6614 )  B      O  0.88  K  8
1739 HOH   (6652 )  B      O  1.10  K  4 Ion-B
1739 HOH   (6662 )  B      O  0.88 NA  7 Ion-B
1740 HOH   (6029 )  C      O  1.02  K  4
1740 HOH   (6192 )  C      O  1.02  K  4
1740 HOH   (6209 )  C      O  0.95  K  4
1740 HOH   (6243 )  C      O  0.93  K  4
1740 HOH   (6317 )  C      O  0.88  K  4 Ion-B
1740 HOH   (6436 )  C      O  1.01  K  4
1740 HOH   (6469 )  C      O  1.14  K  6 Ion-B
1740 HOH   (6528 )  C      O  1.07  K  4
1740 HOH   (6667 )  C      O  1.05  K  4
1740 HOH   (6679 )  C      O  0.95  K  4
1740 HOH   (6722 )  C      O  1.07  K  4 Ion-B
1740 HOH   (6751 )  C      O  0.95  K  4 Ion-B
1741 HOH   (6227 )  D      O  1.11  K  4 ION-B
1741 HOH   (6280 )  D      O  0.88  K  4 Ion-B
1741 HOH   (6413 )  D      O  0.95 NA  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.

 176 ASP   ( 176-)  A   H-bonding suggests Asn
 324 GLU   ( 324-)  A   H-bonding suggests Gln
 334 ASP   ( 334-)  A   H-bonding suggests Asn
 759 ASP   ( 334-)  B   H-bonding suggests Asn; but Alt-Rotamer
1186 ASP   ( 334-)  C   H-bonding suggests Asn; but Alt-Rotamer
1311 GLU   (  34-)  D   H-bonding suggests Gln; but Alt-Rotamer
1519 GLU   ( 242-)  D   H-bonding suggests Gln
1611 ASP   ( 334-)  D   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 :  -0.183
  2nd generation packing quality :  -1.776
  Ramachandran plot appearance   :  -0.160
  chi-1/chi-2 rotamer normality  :   0.101
  Backbone conformation          :  -0.977

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.768
  Bond angles                    :   0.836
  Omega angle restraints         :   1.093
  Side chain planarity           :   1.214
  Improper dihedral distribution :   1.016
  B-factor distribution          :   0.840
  Inside/Outside distribution    :   1.014

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 1.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.1
  2nd generation packing quality :  -1.6
  Ramachandran plot appearance   :  -0.7
  chi-1/chi-2 rotamer normality  :  -0.5
  Backbone conformation          :  -1.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.768
  Bond angles                    :   0.836
  Omega angle restraints         :   1.093
  Side chain planarity           :   1.214
  Improper dihedral distribution :   1.016
  B-factor distribution          :   0.840
  Inside/Outside distribution    :   1.014
==============

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.