WHAT IF Check report

This file was created 2011-12-13 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 pdb2a5v.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 1.367
CA-only RMS fit for the two chains : 1.031

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 : 0.432
CA-only RMS fit for the two chains : 0.246

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 1.116
CA-only RMS fit for the two chains : 0.748

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 : 0.366
CA-only RMS fit for the two chains : 0.174

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 : 1.372
CA-only RMS fit for the two chains : 1.183

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.

 831 SCN   ( 501-)  A  -
 836 SCN   ( 502-)  B  -
 839 SCN   ( 503-)  C  -
 845 SCN   ( 504-)  D  -

Administrative problems that can generate validation failures

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

   1 HIS   (  -5-)  A  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: Missing atoms

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

   1 HIS   (  -5-)  A      N

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: 4

Crystal temperature (K) :100.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Nomenclature related problems

Warning: Tyrosine convention problem

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

 132 TYR   ( 126-)  A
 303 TYR   (  89-)  B
 340 TYR   ( 126-)  B
 506 TYR   (  89-)  C
 715 TYR   (  89-)  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.

 135 ASP   ( 129-)  A
 343 ASP   ( 129-)  B
 546 ASP   ( 129-)  C
 755 ASP   ( 129-)  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.

  94 GLU   (  88-)  A
 302 GLU   (  88-)  B
 420 GLU   ( 206-)  B
 505 GLU   (  88-)  C
 714 GLU   (  88-)  D

Geometric checks

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.997628  0.000314  0.000048|
 |  0.000314  0.997056 -0.000275|
 |  0.000048 -0.000275  0.995819|
Proposed new scale matrix

 |  0.014766 -0.000004  0.000881|
 | -0.000004  0.014266  0.000004|
 |  0.000000  0.000003  0.011925|
With corresponding cell

    A    =  67.723  B   =  70.097  C    =  84.008
    Alpha=  90.034  Beta=  93.415  Gamma=  89.964

The CRYST1 cell dimensions

    A    =  67.884  B   =  70.302  C    =  84.361
    Alpha=  90.000  Beta=  93.410  Gamma=  90.000

Variance: 275.197
(Under-)estimated Z-score: 12.226

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.

 173 ARG   ( 167-)  A      CG   CD   NE  101.43   -5.3
 372 HIS   ( 158-)  B      CG   ND1  CE1 109.68    4.1
 381 ARG   ( 167-)  B      CG   CD   NE  103.56   -4.1
 494 HIS   (  77-)  C      CG   ND1  CE1 109.72    4.1
 793 ARG   ( 167-)  D      CG   CD   NE   99.45   -6.5

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.

  94 GLU   (  88-)  A
 135 ASP   ( 129-)  A
 302 GLU   (  88-)  B
 343 ASP   ( 129-)  B
 420 GLU   ( 206-)  B
 505 GLU   (  88-)  C
 546 ASP   ( 129-)  C
 714 GLU   (  88-)  D
 755 ASP   ( 129-)  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.

 684 ALA   (  58-)  D    4.18

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.

 650 ARG   (  24-)  D    -2.5
 655 SER   (  29-)  D    -2.3
  35 SER   (  29-)  A    -2.3
 209 ILE   ( 203-)  A    -2.3
 218 THR   (   4-)  B    -2.3
 620 ILE   ( 203-)  C    -2.2
 103 PRO   (  97-)  A    -2.2
 514 PRO   (  97-)  C    -2.2
 244 GLN   (  30-)  B    -2.1
  10 THR   (   4-)  A    -2.1
 291 HIS   (  77-)  B    -2.1
  83 HIS   (  77-)  A    -2.0
 444 HIS   (  27-)  C    -2.0
 703 HIS   (  77-)  D    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  52 ALA   (  46-)  A  omega poor
  85 ILE   (  79-)  A  omega poor
 112 SER   ( 106-)  A  Poor phi/psi
 153 SER   ( 147-)  A  Poor phi/psi
 203 ARG   ( 197-)  A  omega poor
 260 ALA   (  46-)  B  omega poor
 293 ILE   (  79-)  B  omega poor
 294 ASP   (  80-)  B  Poor phi/psi, omega poor
 320 SER   ( 106-)  B  Poor phi/psi
 399 VAL   ( 185-)  B  omega poor
 412 ASP   ( 198-)  B  omega poor
 443 GLN   (  26-)  C  omega poor
 463 ALA   (  46-)  C  omega poor
 496 ILE   (  79-)  C  omega poor
 523 SER   ( 106-)  C  Poor phi/psi
 564 SER   ( 147-)  C  Poor phi/psi
 615 ASP   ( 198-)  C  omega poor
 655 SER   (  29-)  D  Poor phi/psi
 672 ALA   (  46-)  D  omega poor
 732 SER   ( 106-)  D  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.057

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.

 143 SER   ( 137-)  A    0.35
 300 SER   (  86-)  B    0.37
 554 SER   ( 137-)  C    0.37
 351 SER   ( 137-)  B    0.37
  92 SER   (  86-)  A    0.37

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 HIS   (  -3-)  A      0
   4 HIS   (  -2-)  A      0
   5 HIS   (  -1-)  A      0
   6 HIS   (   0-)  A      0
   8 PRO   (   2-)  A      0
  30 ARG   (  24-)  A      0
  32 GLN   (  26-)  A      0
  34 PRO   (  28-)  A      0
  35 SER   (  29-)  A      0
  36 GLN   (  30-)  A      0
  37 SER   (  31-)  A      0
  46 ALA   (  40-)  A      0
  48 GLN   (  42-)  A      0
  50 PRO   (  44-)  A      0
  62 VAL   (  56-)  A      0
  72 LEU   (  66-)  A      0
  74 ASP   (  68-)  A      0
  79 ARG   (  73-)  A      0
  81 ALA   (  75-)  A      0
  83 HIS   (  77-)  A      0
  86 ASP   (  80-)  A      0
  98 THR   (  92-)  A      0
 111 ASP   ( 105-)  A      0
 112 SER   ( 106-)  A      0
 113 CYS   ( 107-)  A      0
And so on for a total of 274 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]

  31 PRO   (  25-)  A    0.18 LOW
 540 PRO   ( 123-)  C    0.19 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].

 129 PRO   ( 123-)  A   -63.6 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 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.

 132 TYR   ( 126-)  A      OH  <->  543 TYR   ( 126-)  C      OH     0.43    1.97  INTRA BF
  86 ASP   (  80-)  A      CG  <->  294 ASP   (  80-)  B      OD1    0.37    2.43  INTRA BF
 325 ASN   ( 111-)  B      CB  <->  847 HOH   ( 594 )  B      O      0.36    2.44  INTRA
 343 ASP   ( 129-)  B      OD1 <->  584 ARG   ( 167-)  C      NH2    0.33    2.37  INTRA BF
 154 ARG   ( 148-)  A      NH1 <->  156 ASP   ( 150-)  A      OD2    0.28    2.42  INTRA
 572 ARG   ( 155-)  C      NH2 <->  576 GLU   ( 159-)  C      OE2    0.27    2.43  INTRA BF
 381 ARG   ( 167-)  B      NH2 <->  546 ASP   ( 129-)  C      OD1    0.26    2.44  INTRA BF
 809 VAL   ( 183-)  D      CG2 <->  822 LEU   ( 196-)  D      CD1    0.25    2.95  INTRA BF
 214 HIS   (   0-)  B      O   <->  847 HOH   ( 599 )  B      O      0.25    2.15  INTRA BF
 431 LYS   (  14-)  C      NZ  <->  848 HOH   ( 551 )  C      O      0.25    2.45  INTRA BF
 497 ASP   (  80-)  C      CB  <->  706 ASP   (  80-)  D      OD2    0.24    2.56  INTRA BF
 154 ARG   ( 148-)  A      NH1 <->  156 ASP   ( 150-)  A      CG     0.24    2.86  INTRA
 460 LYS   (  43-)  C      N   <->  848 HOH   ( 547 )  C      O      0.24    2.46  INTRA BF
 497 ASP   (  80-)  C      CB  <->  706 ASP   (  80-)  D      CG     0.23    2.97  INTRA BF
 257 LYS   (  43-)  B      N   <->  847 HOH   ( 524 )  B      O      0.22    2.48  INTRA BL
  57 CYS   (  51-)  A      SG  <->  831 SCN   ( 501-)  A      C      0.20    3.20  INTRA BF
 135 ASP   ( 129-)  A      OD1 <->  793 ARG   ( 167-)  D      NH2    0.19    2.51  INTRA BF
  86 ASP   (  80-)  A      CG  <->  294 ASP   (  80-)  B      CG     0.17    3.03  INTRA BF
 468 CYS   (  51-)  C      SG  <->  493 GLY   (  76-)  C      N      0.17    3.13  INTRA BF
 459 GLN   (  42-)  C      NE2 <->  680 SER   (  54-)  D      OG     0.17    2.53  INTRA BF
 173 ARG   ( 167-)  A      NH2 <->  755 ASP   ( 129-)  D      OD1    0.17    2.53  INTRA BF
 340 TYR   ( 126-)  B      OH  <->  752 TYR   ( 126-)  D      OH     0.17    2.23  INTRA BF
  57 CYS   (  51-)  A      SG  <->  831 SCN   ( 501-)  A      N      0.15    3.15  INTRA BF
 565 ARG   ( 148-)  C      NH2 <->  568 GLU   ( 151-)  C      OE2    0.14    2.56  INTRA BF
 468 CYS   (  51-)  C      SG  <->  469 ALA   (  52-)  C      N      0.13    3.07  INTRA BF
And so on for a total of 86 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.

 240 GLN   (  26-)  B      -6.59
 443 GLN   (  26-)  C      -6.54
 203 ARG   ( 197-)  A      -6.45
 626 HIS   (   0-)  D      -6.36
 214 HIS   (   0-)  B      -6.29
  32 GLN   (  26-)  A      -6.07
 614 ARG   ( 197-)  C      -5.90
 625 HIS   (  -1-)  D      -5.88
 823 ARG   ( 197-)  D      -5.84
 411 ARG   ( 197-)  B      -5.82
 460 LYS   (  43-)  C      -5.81
 652 GLN   (  26-)  D      -5.81
 769 ARG   ( 143-)  D      -5.63
 149 ARG   ( 143-)  A      -5.56
 560 ARG   ( 143-)  C      -5.55
 238 ARG   (  24-)  B      -5.51
 256 GLN   (  42-)  B      -5.50
 213 HIS   (  -1-)  B      -5.48
 357 ARG   ( 143-)  B      -5.47
   6 HIS   (   0-)  A      -5.47
 217 ASN   (   3-)  B      -5.46
 212 HIS   (  -2-)  B      -5.44
 535 ASN   ( 118-)  C      -5.44
 332 ASN   ( 118-)  B      -5.44
 124 ASN   ( 118-)  A      -5.43
 744 ASN   ( 118-)  D      -5.43
 441 ARG   (  24-)  C      -5.28
 584 ARG   ( 167-)  C      -5.28
 257 LYS   (  43-)  B      -5.22
 173 ARG   ( 167-)  A      -5.21
 459 GLN   (  42-)  C      -5.18
 650 ARG   (  24-)  D      -5.15
  30 ARG   (  24-)  A      -5.13
 793 ARG   ( 167-)  D      -5.06
 381 ARG   ( 167-)  B      -5.03
 668 GLN   (  42-)  D      -5.01

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 HIS   (  -2-)  B       214 - HIS      0- ( B)         -5.74
 624 HIS   (  -2-)  D       626 - HIS      0- ( D)         -5.57

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: 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.

 847 HOH   ( 612 )  B      O     21.71   54.24   28.13

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.

 846 HOH   ( 571 )  A      O
 846 HOH   ( 574 )  A      O
 846 HOH   ( 597 )  A      O
 846 HOH   ( 599 )  A      O
 847 HOH   ( 563 )  B      O
 847 HOH   ( 582 )  B      O
 847 HOH   ( 583 )  B      O
 847 HOH   ( 605 )  B      O
 847 HOH   ( 611 )  B      O
 848 HOH   ( 553 )  C      O
 849 HOH   ( 434 )  D      O
 849 HOH   ( 455 )  D      O
 849 HOH   ( 457 )  D      O
Metal-coordinating Histidine residue 110 fixed to   1
Metal-coordinating Histidine residue   3 fixed to   1
Metal-coordinating Histidine residue   6 fixed to   1
Metal-coordinating Histidine residue 413 fixed to   1
Metal-coordinating Histidine residue 164 fixed to   1
Metal-coordinating Histidine residue 211 fixed to   1
Metal-coordinating Histidine residue   2 fixed to   1
Metal-coordinating Histidine residue   4 fixed to   1
Metal-coordinating Histidine residue 372 fixed to   1
Metal-coordinating Histidine residue 318 fixed to   1
Metal-coordinating Histidine residue 212 fixed to   1
Metal-coordinating Histidine residue 214 fixed to   1
Metal-coordinating Histidine residue 205 fixed to   1
Metal-coordinating Histidine residue 521 fixed to   1
Metal-coordinating Histidine residue 730 fixed to   1
Metal-coordinating Histidine residue 623 fixed to   1
Metal-coordinating Histidine residue 625 fixed to   1
Metal-coordinating Histidine residue 575 fixed to   1
Metal-coordinating Histidine residue 624 fixed to   1
Metal-coordinating Histidine residue 626 fixed to   1
Metal-coordinating Histidine residue 616 fixed to   1
Metal-coordinating Histidine residue 784 fixed to   1

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.

  48 GLN   (  42-)  A
 101 ASN   (  95-)  A
 194 GLN   ( 188-)  A
 256 GLN   (  42-)  B
 402 GLN   ( 188-)  B
 459 GLN   (  42-)  C
 622 HIS   (  -4-)  D
 668 GLN   (  42-)  D
 814 GLN   ( 188-)  D
 825 HIS   ( 199-)  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.

  41 ARG   (  35-)  A      NE
  52 ALA   (  46-)  A      N
  63 ALA   (  57-)  A      N
  86 ASP   (  80-)  A      N
 104 LEU   (  98-)  A      N
 149 ARG   ( 143-)  A      NE
 260 ALA   (  46-)  B      N
 271 ALA   (  57-)  B      N
 294 ASP   (  80-)  B      N
 309 ASN   (  95-)  B      N
 312 LEU   (  98-)  B      N
 322 GLY   ( 108-)  B      N
 323 ALA   ( 109-)  B      N
 341 VAL   ( 127-)  B      N
 347 ARG   ( 133-)  B      NH2
 450 ASP   (  33-)  C      N
 452 ARG   (  35-)  C      NE
 463 ALA   (  46-)  C      N
 472 ARG   (  55-)  C      NH1
 474 ALA   (  57-)  C      N
 497 ASP   (  80-)  C      N
 515 LEU   (  98-)  C      N
 526 ALA   ( 109-)  C      N
 527 VAL   ( 110-)  C      N
 607 ASP   ( 190-)  C      N
 608 ASP   ( 191-)  C      N
 661 ARG   (  35-)  D      NE
 683 ALA   (  57-)  D      N
 684 ALA   (  58-)  D      N
 706 ASP   (  80-)  D      N
 724 LEU   (  98-)  D      N
 816 ASP   ( 190-)  D      N
 829 ILE   ( 203-)  D      N
Only metal coordination for    2 HIS  (  -4-) A      ND1
Only metal coordination for    3 HIS  (  -3-) A      ND1
Only metal coordination for    6 HIS  (   0-) A      NE2
Only metal coordination for  110 HIS  ( 104-) A      NE2
Only metal coordination for  164 HIS  ( 158-) A      ND1
Only metal coordination for  204 ASP  ( 198-) A      OD2
Only metal coordination for  205 HIS  ( 199-) A      NE2
Only metal coordination for  211 HIS  (  -3-) B      ND1
Only metal coordination for  214 HIS  (   0-) B      NE2
Only metal coordination for  318 HIS  ( 104-) B      NE2
Only metal coordination for  372 HIS  ( 158-) B      ND1
Only metal coordination for  412 ASP  ( 198-) B      OD2
Only metal coordination for  413 HIS  ( 199-) B      NE2
Only metal coordination for  521 HIS  ( 104-) C      NE2
Only metal coordination for  575 HIS  ( 158-) C      ND1
Only metal coordination for  615 ASP  ( 198-) C      OD2
Only metal coordination for  616 HIS  ( 199-) C      NE2
Only metal coordination for  623 HIS  (  -3-) D      ND1
Only metal coordination for  624 HIS  (  -2-) D      ND1
Only metal coordination for  625 HIS  (  -1-) D      NE2
Only metal coordination for  626 HIS  (   0-) D      NE2
Only metal coordination for  730 HIS  ( 104-) D      NE2

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.

 204 ASP   ( 198-)  A      OD1
 294 ASP   (  80-)  B      OD1
 824 ASP   ( 198-)  D      OD2

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.

 847 HOH   ( 530 )  B      O  0.94  K  4

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.

 111 ASP   ( 105-)  A   H-bonding suggests Asn; but Alt-Rotamer
 319 ASP   ( 105-)  B   H-bonding suggests Asn; but Alt-Rotamer
 522 ASP   ( 105-)  C   H-bonding suggests Asn; but Alt-Rotamer
 731 ASP   ( 105-)  D   H-bonding suggests Asn; 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 :   0.067
  2nd generation packing quality :  -0.665
  Ramachandran plot appearance   :  -0.880
  chi-1/chi-2 rotamer normality  :  -2.057
  Backbone conformation          :   0.755

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.591 (tight)
  Bond angles                    :   0.764
  Omega angle restraints         :   1.072
  Side chain planarity           :   0.557 (tight)
  Improper dihedral distribution :   0.771
  B-factor distribution          :   0.364
  Inside/Outside distribution    :   0.948

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.6
  2nd generation packing quality :  -0.2
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :  -0.7
  Backbone conformation          :   0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.591 (tight)
  Bond angles                    :   0.764
  Omega angle restraints         :   1.072
  Side chain planarity           :   0.557 (tight)
  Improper dihedral distribution :   0.771
  B-factor distribution          :   0.364
  Inside/Outside distribution    :   0.948
==============

WHAT IF
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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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Matthews' Coefficient
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Protein side chain planarity
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Puckering parameters
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Quality Control
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    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
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      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
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      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
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      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.