WHAT IF Check report

This file was created 2013-12-10 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 pdb4mze.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 : 0.855
CA-only RMS fit for the two chains : 0.567

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.

 876 BMA   ( 604-)  A  -
 877 MAN   ( 605-)  A  -
 878 MAN   ( 606-)  A  -
 879 MAN   ( 607-)  A  -
 880 MAN   ( 608-)  A  -
 881 MAN   ( 609-)  A  -
 891 PEG   ( 622-)  A  -
 892 PEG   ( 623-)  A  -
 895 BMA   ( 603-)  B  -
 896 MAN   ( 604-)  B  -
 906 PEG   ( 620-)  B  -
 908 PEG   ( 621-)  B  -
 909 BMA   ( 608-)  B  -
 910 MAN   ( 605-)  B  -
 911 FUL   ( 611-)  A  -

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.

 170 SER   ( 310-)  A  -
 328 SER   ( 468-)  A  -

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.

 170 SER   ( 310-)  A  -
 328 SER   ( 468-)  A  -

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.

 866 NAG   ( 602-)  A  -   O4  bound to  867 NAG   ( 603-)  A  -   C1
 867 NAG   ( 603-)  A  -   O4  bound to  876 BMA   ( 604-)  A  -   C1
 869 NAG   ( 601-)  B  -   O4  bound to  870 NAG   ( 602-)  B  -   C1
 870 NAG   ( 602-)  B  -   O4  bound to  895 BMA   ( 603-)  B  -   C1
 871 NAG   ( 606-)  B  -   O4  bound to  872 NAG   ( 607-)  B  -   C1
 872 NAG   ( 607-)  B  -   O4  bound to  909 BMA   ( 608-)  B  -   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

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.

 248 LEU   ( 388-)  A    High
 249 ASN   ( 389-)  A    High

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. 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) :110.000

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.

 113 ARG   ( 253-)  A
 317 ARG   ( 457-)  A
 545 ARG   ( 253-)  B
 749 ARG   ( 457-)  B

Warning: Tyrosine convention problem

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

 801 TYR   ( 509-)  B

Warning: Phenylalanine convention problem

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

 164 PHE   ( 304-)  A
 171 PHE   ( 311-)  A
 539 PHE   ( 247-)  B
 596 PHE   ( 304-)  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.

 378 GLU   ( 518-)  A
 409 GLU   ( 549-)  A
 426 GLU   ( 566-)  A
 633 GLU   ( 341-)  B
 638 GLU   ( 346-)  B
 806 GLU   ( 514-)  B
 810 GLU   ( 518-)  B

Geometric checks

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: 0.617
RMS-deviation in bond distances: 0.016

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

 |  0.996338  0.000373 -0.000714|
 |  0.000373  0.997099 -0.000450|
 | -0.000714 -0.000450  0.995866|
Proposed new scale matrix

 |  0.011945 -0.000004  0.000009|
 | -0.000004  0.010377  0.000005|
 |  0.000007  0.000004  0.009532|
With corresponding cell

    A    =  83.719  B   =  96.366  C    = 104.905
    Alpha=  90.052  Beta=  90.082  Gamma=  89.957

The CRYST1 cell dimensions

    A    =  84.029  B   =  96.643  C    = 105.339
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 377.128
(Under-)estimated Z-score: 14.312

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.

 284 ARG   ( 424-)  A      CB   CG   CD  105.47   -4.3
 436 HIS   ( 144-)  B      CG   ND1  CE1 109.61    4.0
 703 ARG   ( 411-)  B      CG   CD   NE  117.94    4.4
 853 MET   ( 561-)  B      CG   SD   CE   91.19   -4.4

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.

 113 ARG   ( 253-)  A
 317 ARG   ( 457-)  A
 378 GLU   ( 518-)  A
 409 GLU   ( 549-)  A
 426 GLU   ( 566-)  A
 545 ARG   ( 253-)  B
 633 GLU   ( 341-)  B
 638 GLU   ( 346-)  B
 749 ARG   ( 457-)  B
 806 GLU   ( 514-)  B
 810 GLU   ( 518-)  B

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.

 553 LEU   ( 261-)  B    4.00

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.

 767 THR   ( 475-)  B    -3.4
 335 THR   ( 475-)  A    -3.2
  36 PRO   ( 176-)  A    -2.6
 547 SER   ( 255-)  B    -2.5
 399 TYR   ( 539-)  A    -2.4
 103 ILE   ( 243-)  A    -2.4
 115 SER   ( 255-)  A    -2.4
 428 PRO   ( 568-)  A    -2.3
 535 ILE   ( 243-)  B    -2.3
 337 VAL   ( 477-)  A    -2.2
 824 THR   ( 532-)  B    -2.2
 511 LYS   ( 219-)  B    -2.2
 382 ARG   ( 522-)  A    -2.2
 769 VAL   ( 477-)  B    -2.1
 416 ASP   ( 556-)  A    -2.1
 509 ILE   ( 217-)  B    -2.1
 287 SER   ( 427-)  A    -2.1
 250 SER   ( 390-)  A    -2.0
 392 THR   ( 532-)  A    -2.0
 719 SER   ( 427-)  B    -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.

  20 THR   ( 160-)  A  omega poor
  29 THR   ( 169-)  A  PRO omega poor
  59 ASN   ( 199-)  A  Poor phi/psi
  95 LEU   ( 235-)  A  Poor phi/psi
 115 SER   ( 255-)  A  Poor phi/psi
 122 ASN   ( 262-)  A  Poor phi/psi
 129 CYS   ( 269-)  A  omega poor
 172 ASP   ( 312-)  A  omega poor
 182 VAL   ( 322-)  A  Poor phi/psi
 187 TYR   ( 327-)  A  omega poor
 203 PRO   ( 343-)  A  Poor phi/psi
 209 ILE   ( 349-)  A  omega poor
 233 SER   ( 373-)  A  Poor phi/psi
 238 VAL   ( 378-)  A  omega poor
 240 SER   ( 380-)  A  omega poor
 263 GLN   ( 403-)  A  omega poor
 287 SER   ( 427-)  A  Poor phi/psi
 289 HIS   ( 429-)  A  omega poor
 316 SER   ( 456-)  A  Poor phi/psi
 320 ASN   ( 460-)  A  Poor phi/psi
 335 THR   ( 475-)  A  Poor phi/psi
 353 SER   ( 493-)  A  omega poor
 360 LYS   ( 500-)  A  Poor phi/psi
 364 ASN   ( 504-)  A  Poor phi/psi
 369 TYR   ( 509-)  A  omega poor
And so on for a total of 63 lines.

Warning: Unusual backbone conformations

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

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

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

   6 VAL   ( 146-)  A      0
   9 LYS   ( 149-)  A      0
  11 LEU   ( 151-)  A      0
  17 TRP   ( 157-)  A      0
  18 ARG   ( 158-)  A      0
  20 THR   ( 160-)  A      0
  21 SER   ( 161-)  A      0
  27 MET   ( 167-)  A      0
  28 LYS   ( 168-)  A      0
  29 THR   ( 169-)  A      0
  30 PRO   ( 170-)  A      0
  44 PRO   ( 184-)  A      0
  52 ARG   ( 192-)  A      0
  53 THR   ( 193-)  A      0
  54 PRO   ( 194-)  A      0
  61 LEU   ( 201-)  A      0
  72 ARG   ( 212-)  A      0
  74 CYS   ( 214-)  A      0
  75 GLN   ( 215-)  A      0
  77 ILE   ( 217-)  A      0
  79 LYS   ( 219-)  A      0
  86 ILE   ( 226-)  A      0
  95 LEU   ( 235-)  A      0
  97 PRO   ( 237-)  A      0
 101 PRO   ( 241-)  A      0
And so on for a total of 411 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!

 778 PRO   ( 486-)  B   1.90   10
 319 GLY   ( 459-)  A   1.51   15

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]

 101 PRO   ( 241-)  A    0.12 LOW
 762 PRO   ( 470-)  B    0.18 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].

  36 PRO   ( 176-)  A   -64.3 envelop C-beta (-72 degrees)
  38 PRO   ( 178-)  A  -124.9 half-chair C-delta/C-gamma (-126 degrees)
 174 PRO   ( 314-)  A  -112.3 envelop C-gamma (-108 degrees)
 230 PRO   ( 370-)  A  -121.8 half-chair C-delta/C-gamma (-126 degrees)
 533 PRO   ( 241-)  B    23.9 half-chair N/C-delta (18 degrees)
 860 PRO   ( 568-)  B   -64.5 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 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.

 868 NAG   ( 610-)  A      O6  <->  911 FUL   ( 611-)  A      C1     0.96    1.44  INTRA BF
 895 BMA   ( 603-)  B      O6  <->  910 MAN   ( 605-)  B      C1     0.94    1.46  INTRA B3
 872 NAG   ( 607-)  B      O4  <->  909 BMA   ( 608-)  B      C1     0.93    1.47  INTRA BF
 895 BMA   ( 603-)  B      C6  <->  910 MAN   ( 605-)  B      C1     0.84    2.36  INTRA
 868 NAG   ( 610-)  A      C6  <->  911 FUL   ( 611-)  A      C1     0.77    2.43  INTRA BF
 872 NAG   ( 607-)  B      C4  <->  909 BMA   ( 608-)  B      C1     0.62    2.58  INTRA
 530 ASP   ( 238-)  B      OD1 <->  856 LYS   ( 564-)  B      NZ     0.59    2.11  INTRA BF
 833 LYS   ( 541-)  B      NZ  <->  858 GLU   ( 566-)  B      OE2    0.51    2.19  INTRA BF
 685 LYS   ( 393-)  B      NZ  <->  913 HOH   ( 920 )  B      O      0.45    2.25  INTRA BF
 446 ASP   ( 154-)  B      OD2 <->  710 LYS   ( 418-)  B      NZ     0.43    2.27  INTRA BF
 807 ARG   ( 515-)  B      NE  <->  810 GLU   ( 518-)  B      OE2    0.35    2.35  INTRA
 817 THR   ( 525-)  B      O   <->  845 LYS   ( 553-)  B      NZ     0.28    2.42  INTRA BF
 289 HIS   ( 429-)  A      ND1 <->  293 GLN   ( 433-)  A      NE2    0.26    2.74  INTRA BL
 721 HIS   ( 429-)  B      ND1 <->  725 GLN   ( 433-)  B      NE2    0.26    2.74  INTRA BL
 306 ARG   ( 446-)  A      NH2 <->  886 EDO   ( 616-)  A      O1     0.23    2.47  INTRA BF
 511 LYS   ( 219-)  B      NZ  <->  913 HOH   ( 999 )  B      O      0.20    2.50  INTRA BF
 398 HIS   ( 538-)  A      ND1 <->  912 HOH   ( 959 )  A      O      0.19    2.51  INTRA BF
 633 GLU   ( 341-)  B      OE1 <->  913 HOH   ( 974 )  B      O      0.19    2.21  INTRA BF
 830 HIS   ( 538-)  B      ND1 <->  913 HOH   ( 889 )  B      O      0.19    2.51  INTRA
 205 ASN   ( 345-)  A      N   <->  912 HOH   (1028 )  A      O      0.19    2.51  INTRA BF
 375 ARG   ( 515-)  A      NE  <->  378 GLU   ( 518-)  A      OE2    0.18    2.52  INTRA BL
 419 ARG   ( 559-)  A      NE  <->  912 HOH   ( 955 )  A      O      0.14    2.56  INTRA BF
 439 GLY   ( 147-)  B      N   <->  913 HOH   ( 912 )  B      O      0.14    2.56  INTRA
 413 LYS   ( 553-)  A      O   <->  415 LEU   ( 555-)  A      N      0.13    2.57  INTRA BF
 846 SER   ( 554-)  B      OG  <->  899 PO4   ( 611-)  B      O2     0.12    2.28  INTRA BF
And so on for a total of 87 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

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.

 450 ARG   ( 158-)  B      -6.37
 680 LEU   ( 388-)  B      -6.21
  72 ARG   ( 212-)  A      -6.15
 248 LEU   ( 388-)  A      -6.13
 504 ARG   ( 212-)  B      -6.12
 382 ARG   ( 522-)  A      -6.10
 814 ARG   ( 522-)  B      -6.10
 133 LYS   ( 273-)  A      -5.66
 265 TYR   ( 405-)  A      -5.64
 697 TYR   ( 405-)  B      -5.64
 565 LYS   ( 273-)  B      -5.60
 249 ASN   ( 389-)  A      -5.48
 399 TYR   ( 539-)  A      -5.45
 168 ASN   ( 308-)  A      -5.36
 434 ILE   ( 142-)  B      -5.33
 600 ASN   ( 308-)  B      -5.33
 359 GLN   ( 499-)  A      -5.31
 475 MET   ( 183-)  B      -5.23
 791 GLN   ( 499-)  B      -5.16
  43 MET   ( 183-)  A      -5.14
   2 ILE   ( 142-)  A      -5.06

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.

  27 MET   ( 167-)  A        29 - THR    169- ( A)         -4.22

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

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.

 634 HIS   ( 342-)  B   -2.93
 643 ASN   ( 351-)  B   -2.79
 211 ASN   ( 351-)  A   -2.72
 658 ALA   ( 366-)  B   -2.68
 226 ALA   ( 366-)  A   -2.57

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.

 912 HOH   ( 878 )  A      O     26.18   13.94  -16.76
 912 HOH   ( 937 )  A      O     11.80   -6.54   33.14
 912 HOH   (1035 )  A      O     -0.79   43.09   42.06
 913 HOH   ( 833 )  B      O     34.24   40.75   12.94
 913 HOH   ( 934 )  B      O     21.79  -10.64   -9.86

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.

 912 HOH   (1033 )  A      O
Bound group on Asn; dont flip  168 ASN  ( 308-) A
Bound to:  865 NAG  ( 601-) A
Bound group on Asn; dont flip  211 ASN  ( 351-) A
Bound to:  866 NAG  ( 602-) A
Bound group on Asn; dont flip  383 ASN  ( 523-) A
Bound to:  868 NAG  ( 610-) A
Bound group on Asn; dont flip  600 ASN  ( 308-) B
Bound to:  869 NAG  ( 601-) B
Bound group on Asn; dont flip  643 ASN  ( 351-) B
Bound to:  871 NAG  ( 606-) B
Bound group on Asn; dont flip  815 ASN  ( 523-) B
Bound to:  873 NAG  ( 609-) B

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.

 105 HIS   ( 245-)  A
 293 GLN   ( 433-)  A
 725 GLN   ( 433-)  B
 843 ASN   ( 551-)  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.

   1 ARG   ( 141-)  A      NH1
   2 ILE   ( 142-)  A      N
  18 ARG   ( 158-)  A      NH1
  46 THR   ( 186-)  A      N
  55 SER   ( 195-)  A      OG
  76 ASP   ( 216-)  A      N
  79 LYS   ( 219-)  A      N
 104 SER   ( 244-)  A      N
 112 ASN   ( 252-)  A      N
 127 GLN   ( 267-)  A      NE2
 134 VAL   ( 274-)  A      N
 140 TYR   ( 280-)  A      OH
 206 GLU   ( 346-)  A      N
 211 ASN   ( 351-)  A      N
 306 ARG   ( 446-)  A      NH1
 316 SER   ( 456-)  A      N
 331 ASP   ( 471-)  A      N
 337 VAL   ( 477-)  A      N
 341 ALA   ( 481-)  A      N
 359 GLN   ( 499-)  A      N
 369 TYR   ( 509-)  A      OH
 383 ASN   ( 523-)  A      N
 390 TYR   ( 530-)  A      N
 395 CYS   ( 535-)  A      N
 417 THR   ( 557-)  A      N
And so on for a total of 53 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.

 322 GLU   ( 462-)  A      OE1
 322 GLU   ( 462-)  A      OE2
 409 GLU   ( 549-)  A      OE1
 532 ASN   ( 240-)  B      OD1
 754 GLU   ( 462-)  B      OE1
 754 GLU   ( 462-)  B      OE2
 841 GLU   ( 549-)  B      OE2

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

 898  CA   ( 612-)  B     0.90   1.14 Scores about as good as NA

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.

 269 GLU   ( 409-)  A   H-bonding suggests Gln; Ligand-contact
 331 ASP   ( 471-)  A   H-bonding suggests Asn
 409 GLU   ( 549-)  A   H-bonding suggests Gln
 437 ASP   ( 145-)  B   H-bonding suggests Asn
 556 ASP   ( 264-)  B   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
 568 GLU   ( 276-)  B   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
 763 ASP   ( 471-)  B   H-bonding suggests Asn
 789 ASP   ( 497-)  B   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
 841 GLU   ( 549-)  B   H-bonding suggests Gln; but Alt-Rotamer

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 :  -0.449
  2nd generation packing quality :  -1.913
  Ramachandran plot appearance   :  -0.264
  chi-1/chi-2 rotamer normality  :  -1.066
  Backbone conformation          :  -0.406

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.617 (tight)
  Bond angles                    :   0.771
  Omega angle restraints         :   1.215
  Side chain planarity           :   0.732
  Improper dihedral distribution :   0.940
  B-factor distribution          :   1.395
  Inside/Outside distribution    :   1.030

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 : 1.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -1.5
  Ramachandran plot appearance   :  -0.2
  chi-1/chi-2 rotamer normality  :  -0.7
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.617 (tight)
  Bond angles                    :   0.771
  Omega angle restraints         :   1.215
  Side chain planarity           :   0.732
  Improper dihedral distribution :   0.940
  B-factor distribution          :   1.395
  Inside/Outside distribution    :   1.030
==============

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

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Bond lengths and angles, DNA/RNA
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DSSP
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Hydrogen bond networks
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      protein structures
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Matthews' Coefficient
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      Solvent content of Protein Crystals
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Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
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    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.