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 pdb3rau.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 : 0.994
CA-only RMS fit for the two chains : 0.685

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

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.

 716 ACT   ( 362-)  A  -
 717 ACT   ( 363-)  A  -
 718 ACT   ( 364-)  A  -
 719 ACT   ( 365-)  A  -
 722 ACT   ( 363-)  B  -
 723 ACT   ( 364-)  B  -
 724 ACT   ( 365-)  B  -
 726 ACT   ( 366-)  B  -

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

  66 ARG   (  69-)  A  -
 218 LEU   ( 221-)  A  -
 225 SER   ( 228-)  A  -
 299 MET   ( 302-)  A  -
 420 SER   (  66-)  B  -
 423 ARG   (  69-)  B  -
 434 SER   (  80-)  B  -
 457 LYS   ( 103-)  B  -
 582 SER   ( 228-)  B  -

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

  66 ARG   (  69-)  A  -
 218 LEU   ( 221-)  A  -
 225 SER   ( 228-)  A  -
 299 MET   ( 302-)  A  -
 420 SER   (  66-)  B  -
 423 ARG   (  69-)  B  -
 434 SER   (  80-)  B  -
 457 LYS   ( 103-)  B  -
 582 SER   ( 228-)  B  -
 705 VAL   ( 351-)  B  -

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

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.

 160 GLN   ( 163-)  A    High
 229 ARG   ( 232-)  A    High
 325 ASP   ( 328-)  A    High
 681 LEU   ( 327-)  B    High
 682 ASP   ( 328-)  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.

   8 TRP   (  11-)  A    0.29
  86 GLU   (  89-)  A    0.15
 105 GLU   ( 108-)  A    0.41
 169 GLN   ( 172-)  A    0.91
 213 GLU   ( 216-)  A    0.32
 259 GLU   ( 262-)  A    0.17
 275 ASP   ( 278-)  A    0.48
 370 GLU   (  16-)  B    0.46
 397 GLU   (  43-)  B    0.25
 440 SER   (  86-)  B    0.68
 462 GLU   ( 108-)  B    0.13

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

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.

   3 ARG   (   6-)  A
 360 ARG   (   6-)  B

Warning: Tyrosine convention problem

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

  38 TYR   (  41-)  A
 153 TYR   ( 156-)  A
 162 TYR   ( 165-)  A
 317 TYR   ( 320-)  A
 395 TYR   (  41-)  B
 510 TYR   ( 156-)  B
 519 TYR   ( 165-)  B
 674 TYR   ( 320-)  B

Warning: Phenylalanine convention problem

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

 198 PHE   ( 201-)  A
 297 PHE   ( 300-)  A
 654 PHE   ( 300-)  B
 711 PHE   ( 357-)  B

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.

 415 ASP   (  61-)  B
 463 ASP   ( 109-)  B
 646 ASP   ( 292-)  B
 682 ASP   ( 328-)  B
 709 ASP   ( 355-)  B

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.

  33 GLU   (  36-)  A
  60 GLU   (  63-)  A
 135 GLU   ( 138-)  A
 258 GLU   ( 261-)  A
 390 GLU   (  36-)  B
 462 GLU   ( 108-)  B
 492 GLU   ( 138-)  B
 615 GLU   ( 261-)  B

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.

 225 SER   ( 228-)  A      CB   OG    1.27   -7.1

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.324
RMS-deviation in bond distances: 0.008

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

 |  0.999106  0.000047  0.000044|
 |  0.000047  0.998515 -0.000447|
 |  0.000044 -0.000447  0.997751|
Proposed new scale matrix

 |  0.026674 -0.000940 -0.004050|
 |  0.000000  0.016338 -0.001098|
 |  0.000000  0.000006  0.012612|
With corresponding cell

    A    =  37.490  B   =  61.244  C    =  80.399
    Alpha=  85.920  Beta=  81.254  Gamma=  87.985

The CRYST1 cell dimensions

    A    =  37.523  B   =  61.333  C    =  80.582
    Alpha=  85.870  Beta=  81.270  Gamma=  87.990

Variance: 61.949
(Under-)estimated Z-score: 5.801

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.

 225 SER   ( 228-)  A      CA   CB   OG  119.28    4.1
 623 ARG   ( 269-)  B      CB   CG   CD  105.26   -4.4

Warning: Low bond angle variability

Bond angles were found to deviate less than normal from the standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond angles: 0.529
RMS-deviation in bond angles: 1.025

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.

   3 ARG   (   6-)  A
  33 GLU   (  36-)  A
  60 GLU   (  63-)  A
 135 GLU   ( 138-)  A
 258 GLU   ( 261-)  A
 360 ARG   (   6-)  B
 390 GLU   (  36-)  B
 415 ASP   (  61-)  B
 462 GLU   ( 108-)  B
 463 ASP   ( 109-)  B
 492 GLU   ( 138-)  B
 615 GLU   ( 261-)  B
 646 ASP   ( 292-)  B
 682 ASP   ( 328-)  B
 709 ASP   ( 355-)  B

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.

 374 PHE   (  20-)  B    -2.3
  17 PHE   (  20-)  A    -2.2
 230 ILE   ( 233-)  A    -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.

 131 ARG   ( 134-)  A  Poor phi/psi
 194 ASN   ( 197-)  A  Poor phi/psi
 261 GLN   ( 264-)  A  Poor phi/psi
 488 ARG   ( 134-)  B  Poor phi/psi
 618 GLN   ( 264-)  B  Poor phi/psi
 698 VAL   ( 344-)  B  omega poor
 chi-1/chi-2 correlation Z-score : -0.596

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.

 272 SER   ( 275-)  A    0.34
 582 SER   ( 228-)  B    0.35
 308 SER   ( 311-)  A    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!

   4 MET   (   7-)  A      0
  16 ASP   (  19-)  A      0
  18 HIS   (  21-)  A      0
  19 PHE   (  22-)  A      0
  31 TYR   (  34-)  A      0
  34 ASN   (  37-)  A      0
  38 TYR   (  41-)  A      0
  39 ASN   (  42-)  A      0
  54 ARG   (  57-)  A      0
  57 ARG   (  60-)  A      0
  58 ASP   (  61-)  A      0
  78 ARG   (  81-)  A      0
  80 PRO   (  83-)  A      0
  81 MET   (  84-)  A      0
  83 SER   (  86-)  A      0
  87 ALA   (  90-)  A      0
  88 ALA   (  91-)  A      0
  96 ILE   (  99-)  A      0
  97 PHE   ( 100-)  A      0
  98 SER   ( 101-)  A      0
 105 GLU   ( 108-)  A      0
 158 PHE   ( 161-)  A      0
 159 PRO   ( 162-)  A      0
 160 GLN   ( 163-)  A      0
 162 TYR   ( 165-)  A      0
And so on for a total of 137 lines.

Warning: Unusual PRO puckering amplitudes

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

 362 PRO   (   8-)  B    0.20 LOW

Warning: Unusual PRO puckering phases

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

 437 PRO   (  83-)  B    18.7 half-chair N/C-delta (18 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

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

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

 479 HIS   ( 125-)  B      CD2 <->  500 HIS   ( 146-)  B      CD2    0.38    2.82  INTRA BL
  57 ARG   (  60-)  A      NE  <->  727 HOH   ( 408 )  A      O      0.26    2.44  INTRA BL
 607 HIS   ( 253-)  B      ND1 <->  629 SER   ( 275-)  B      OG     0.26    2.44  INTRA
 250 HIS   ( 253-)  A      ND1 <->  272 SER   ( 275-)  A      OG     0.18    2.52  INTRA BL
 173 LEU   ( 176-)  A      CD1 <->  218 LEU   ( 221-)  A    A CD2    0.17    3.03  INTRA BL
 435 ARG   (  81-)  B      NE  <->  728 HOH   ( 443 )  B      O      0.16    2.54  INTRA
 433 GLN   (  79-)  B      CG  <->  465 LYS   ( 111-)  B      NZ     0.16    2.94  INTRA
 369 LYS   (  15-)  B      NZ  <->  728 HOH   ( 404 )  B      O      0.14    2.56  INTRA
 713 LYS   ( 359-)  B      NZ  <->  728 HOH   ( 403 )  B      O      0.13    2.57  INTRA BF
 214 ALA   ( 217-)  A      O   <->  218 LEU   ( 221-)  A    A CD2    0.10    2.70  INTRA BL
 372 GLY   (  18-)  B      N   <->  449 THR   (  95-)  B      O      0.10    2.60  INTRA
 122 HIS   ( 125-)  A      ND1 <->  143 HIS   ( 146-)  A      ND1    0.10    2.90  INTRA BL
 453 ILE   (  99-)  B      CG2 <->  454 PHE   ( 100-)  B      N      0.09    2.91  INTRA
  84 GLY   (  87-)  A      N   <->  727 HOH   ( 391 )  A      O      0.09    2.61  INTRA BL
 457 LYS   ( 103-)  B    A NZ  <->  728 HOH   ( 453 )  B      O      0.08    2.62  INTRA
 220 ASN   ( 223-)  A      O   <->  224 ALA   ( 227-)  A      N      0.08    2.62  INTRA
 195 ARG   ( 198-)  A      NH2 <->  713 LYS   ( 359-)  B      O      0.08    2.62  INTRA
  66 ARG   (  69-)  A    A NH2 <->  342 ASN   ( 345-)  A      O      0.07    2.63  INTRA
 586 ARG   ( 232-)  B      NH1 <->  728 HOH   ( 447 )  B      O      0.07    2.63  INTRA BF
 441 GLY   (  87-)  B      N   <->  728 HOH   ( 429 )  B      O      0.07    2.63  INTRA
 100 LYS   ( 103-)  A      NZ  <->  727 HOH   ( 472 )  A      O      0.06    2.64  INTRA BF
 104 HIS   ( 107-)  A      ND1 <->  727 HOH   ( 535 )  A      O      0.05    2.65  INTRA
 239 GLN   ( 242-)  A      OE1 <->  727 HOH   ( 437 )  A      O      0.05    2.35  INTRA
 337 LYS   ( 340-)  A      NZ  <->  727 HOH   ( 516 )  A      O      0.05    2.65  INTRA BF
 381 LYS   (  27-)  B      NZ  <->  396 ASN   (  42-)  B      OD1    0.04    2.66  INTRA BF
 369 LYS   (  15-)  B      N   <->  474 ASN   ( 120-)  B      OD1    0.04    2.66  INTRA BL
 517 GLN   ( 163-)  B      N   <->  728 HOH   ( 445 )  B      O      0.04    2.66  INTRA BF
 358 VAL   ( 361-)  A      C   <->  559 ARG   ( 205-)  B      NH1    0.04    3.06  INTRA
 235 LYS   ( 238-)  A      NZ  <->  727 HOH   ( 523 )  A      O      0.03    2.67  INTRA BF
 716 ACT   ( 362-)  A      CH3 <->  727 HOH   ( 531 )  A      O      0.03    2.77  INTRA
 383 PHE   (  29-)  B      CD1 <->  387 ASN   (  33-)  B      ND2    0.03    3.07  INTRA
   8 TRP   (  11-)  A      CE3 <->  124 MET   ( 127-)  A      CG     0.03    3.17  INTRA BL
 694 LYS   ( 340-)  B      NZ  <->  728 HOH   ( 377 )  B      O      0.03    2.67  INTRA
 360 ARG   (   6-)  B      NH2 <->  494 MET   ( 140-)  B      CE     0.02    3.08  INTRA BF
 369 LYS   (  15-)  B      NZ  <->  522 ASP   ( 168-)  B      OD2    0.02    2.68  INTRA
 546 LYS   ( 192-)  B      NZ  <->  550 ASP   ( 196-)  B      OD2    0.02    2.68  INTRA BF
 406 ARG   (  52-)  B      NE  <->  467 GLU   ( 113-)  B      OE2    0.02    2.68  INTRA BL
 141 CYS   ( 144-)  A      SG  <->  145 GLN   ( 148-)  A      NE2    0.02    3.28  INTRA BL
 498 CYS   ( 144-)  B      SG  <->  543 LEU   ( 189-)  B      CG     0.02    3.38  INTRA
 586 ARG   ( 232-)  B      NH1 <->  589 LYS   ( 235-)  B      CD     0.02    3.08  INTRA BF
  49 ARG   (  52-)  A      NE  <->  110 GLU   ( 113-)  A      OE2    0.01    2.69  INTRA BL
 656 MET   ( 302-)  B      O   <->  660 GLY   ( 306-)  B      N      0.01    2.69  INTRA
 129 ASP   ( 132-)  A      CG  <->  130 LYS   ( 133-)  A      N      0.01    2.99  INTRA
  12 LYS   (  15-)  A      NZ  <->  165 ASP   ( 168-)  A      OD2    0.01    2.69  INTRA BL

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

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.

 414 ARG   (  60-)  B      -7.19
  57 ARG   (  60-)  A      -6.85
   3 ARG   (   6-)  A      -6.75
 360 ARG   (   6-)  B      -6.39
 157 HIS   ( 160-)  A      -6.13
 514 HIS   ( 160-)  B      -5.99
 411 ARG   (  57-)  B      -5.88
  54 ARG   (  57-)  A      -5.79
 517 GLN   ( 163-)  B      -5.66
 685 GLN   ( 331-)  B      -5.27
 387 ASN   (  33-)  B      -5.19
 315 PHE   ( 318-)  A      -5.14
 672 PHE   ( 318-)  B      -5.09
  78 ARG   (  81-)  A      -5.05

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: 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

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.

 727 HOH   ( 475 )  A      O    -16.59   43.69   65.05
 727 HOH   ( 476 )  A      O     14.74    2.44   26.12
 727 HOH   ( 480 )  A      O     11.19    2.93  -38.47
 727 HOH   ( 521 )  A      O    -26.59   51.71   30.58

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.

 728 HOH   ( 454 )  B      O

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

 256 GLN   ( 259-)  A
 342 ASN   ( 345-)  A
 664 ASN   ( 310-)  B

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.

  10 ASP   (  13-)  A      N
  38 TYR   (  41-)  A      N
 133 SER   ( 136-)  A      N
 163 SER   ( 166-)  A      N
 181 GLN   ( 184-)  A      NE2
 206 GLN   ( 209-)  A      NE2
 233 ASP   ( 236-)  A      N
 325 ASP   ( 328-)  A      N
 341 VAL   ( 344-)  A      N
 367 ASP   (  13-)  B      N
 486 ASP   ( 132-)  B      N
 518 ALA   ( 164-)  B      N
 520 SER   ( 166-)  B      N
 526 GLN   ( 172-)  B      N
 538 GLN   ( 184-)  B      NE2
 563 GLN   ( 209-)  B      NE2
 623 ARG   ( 269-)  B      NE
 682 ASP   ( 328-)  B      N
 693 VAL   ( 339-)  B      N
 698 VAL   ( 344-)  B      N
 725 GOL   ( 362-)  B      O1
 725 GOL   ( 362-)  B      O3

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.

  39 ASN   (  42-)  A      OD1
 278 ASN   ( 281-)  A      OD1
 430 HIS   (  76-)  B      NE2
 468 GLN   ( 114-)  B      OE1
 635 ASN   ( 281-)  B      OD1

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.

 727 HOH   ( 403 )  A      O  1.04  K  4
 727 HOH   ( 447 )  A      O  0.93  K  5

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

 106 ASP   ( 109-)  A   H-bonding suggests Asn; but Alt-Rotamer
 293 ASP   ( 296-)  A   H-bonding suggests Asn; but Alt-Rotamer
 616 GLU   ( 262-)  B   H-bonding suggests Gln
 632 ASP   ( 278-)  B   H-bonding suggests Asn
 650 ASP   ( 296-)  B   H-bonding suggests Asn
 669 ASP   ( 315-)  B   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 :   0.462
  2nd generation packing quality :  -0.326
  Ramachandran plot appearance   :   1.120
  chi-1/chi-2 rotamer normality  :  -0.596
  Backbone conformation          :   1.032

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.324 (tight)
  Bond angles                    :   0.529 (tight)
  Omega angle restraints         :   0.791
  Side chain planarity           :   0.335 (tight)
  Improper dihedral distribution :   0.533
  B-factor distribution          :   1.443
  Inside/Outside distribution    :   1.027

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 : 1.95


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.8
  2nd generation packing quality :  -0.7
  Ramachandran plot appearance   :   1.2
  chi-1/chi-2 rotamer normality  :  -0.1
  Backbone conformation          :   0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.324 (tight)
  Bond angles                    :   0.529 (tight)
  Omega angle restraints         :   0.791
  Side chain planarity           :   0.335 (tight)
  Improper dihedral distribution :   0.533
  B-factor distribution          :   1.443
  Inside/Outside distribution    :   1.027
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    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
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      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,
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      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
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      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.