WHAT IF Check report

This file was created 2012-01-30 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 pdb3n8v.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 : 0.527
CA-only RMS fit for the two chains : 0.268

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.

1114 BOG   ( 751-)  A  -
1116 NDG   ( 662-)  A  -
1117 NDG   ( 672-)  A  -
1118 BMA   ( 673-)  A  -
1119 MAN   ( 674-)  A  -
1121 BOG   (1750-)  B  -
1122 BOG   (1751-)  B  -
1124 NDG   (1662-)  B  -
1125 NDG   (1681-)  B  -
1126 BMA   (1673-)  B  -
1127 BMA   (1674-)  B  -
1128 NDG   (1672-)  B  -
1129 BOG   (1752-)  B  -
1130 MAN   ( 675-)  A  -
1131 A10   ( 755-)  A  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

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

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

1107 NAG   ( 661-)  A  -   O4  bound to 1116 NDG   ( 662-)  A  -   C1
1108 NAG   ( 681-)  A  -   O4  bound to 1109 NAG   ( 682-)  A  -   C1
1110 NAG   ( 671-)  A  -   O4  bound to 1117 NDG   ( 672-)  A  -   C1
1111 NAG   (1661-)  B  -   O4  bound to 1124 NDG   (1662-)  B  -   C1
1113 NAG   (1671-)  B  -   O4  bound to 1128 NDG   (1672-)  B  -   C1

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

 144 GLU   ( 175-)  A  -   CB
 144 GLU   ( 175-)  A  -   CG
 144 GLU   ( 175-)  A  -   CD
 144 GLU   ( 175-)  A  -   OE1
 144 GLU   ( 175-)  A  -   OE2

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: 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'.

  59 HIS   (  90-)  A      CG
  59 HIS   (  90-)  A      ND1
  59 HIS   (  90-)  A      CD2
  59 HIS   (  90-)  A      CE1
  59 HIS   (  90-)  A      NE2
 137 LYS   ( 168-)  A      CG
 137 LYS   ( 168-)  A      CD
 137 LYS   ( 168-)  A      CE
 137 LYS   ( 168-)  A      NZ
 138 LYS   ( 169-)  A      CG
 138 LYS   ( 169-)  A      CD
 138 LYS   ( 169-)  A      CE
 138 LYS   ( 169-)  A      NZ
 155 LYS   ( 186-)  A      CG
 155 LYS   ( 186-)  A      CD
 155 LYS   ( 186-)  A      CE
 155 LYS   ( 186-)  A      NZ
 184 LYS   ( 215-)  A      CG
 184 LYS   ( 215-)  A      CD
 184 LYS   ( 215-)  A      CE
 184 LYS   ( 215-)  A      NZ
 246 ARG   ( 277-)  A      CG
 246 ARG   ( 277-)  A      CD
 246 ARG   ( 277-)  A      NE
 246 ARG   ( 277-)  A      CZ
And so on for a total of 115 lines.

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: 2

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.

 149 ARG   ( 180-)  A
 601 ARG   (  79-)  B

Warning: Tyrosine convention problem

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

  24 TYR   (  55-)  A
  33 TYR   (  64-)  A
 223 TYR   ( 254-)  A
 324 TYR   ( 355-)  A
 373 TYR   ( 404-)  A
 386 TYR   ( 417-)  A
 435 TYR   ( 466-)  A
 560 TYR   (  38-)  B
 577 TYR   (  55-)  B
 776 TYR   ( 254-)  B
 870 TYR   ( 348-)  B
 877 TYR   ( 355-)  B
 926 TYR   ( 404-)  B
 939 TYR   ( 417-)  B

Warning: Phenylalanine convention problem

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

  19 PHE   (  50-)  A
 156 PHE   ( 187-)  A
 167 PHE   ( 198-)  A
 170 PHE   ( 201-)  A
 216 PHE   ( 247-)  A
 325 PHE   ( 356-)  A
 378 PHE   ( 409-)  A
 572 PHE   (  50-)  B
 720 PHE   ( 198-)  B
 723 PHE   ( 201-)  B
 917 PHE   ( 395-)  B
 992 PHE   ( 470-)  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.

  79 ASP   ( 110-)  A
 142 ASP   ( 173-)  A
 370 ASP   ( 401-)  A
 410 ASP   ( 441-)  A
 553 ASP   ( 584-)  A
 632 ASP   ( 110-)  B
 695 ASP   ( 173-)  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.

  42 GLU   (  73-)  A
 109 GLU   ( 140-)  A
 259 GLU   ( 290-)  A
 349 GLU   ( 380-)  A
 389 GLU   ( 420-)  A
 462 GLU   ( 493-)  A
 471 GLU   ( 502-)  A
 493 GLU   ( 524-)  A
 697 GLU   ( 175-)  B
 841 GLU   ( 319-)  B
 848 GLU   ( 326-)  B
 868 GLU   ( 346-)  B
 886 GLU   ( 364-)  B
 902 GLU   ( 380-)  B
 942 GLU   ( 420-)  B
1024 GLU   ( 502-)  B
1046 GLU   ( 524-)  B
1075 GLU   ( 553-)  B

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

 |  0.997424  0.000160  0.000023|
 |  0.000160  0.997261  0.000038|
 |  0.000023  0.000038  0.997636|
Proposed new scale matrix

 |  0.005511  0.003182  0.000000|
 | -0.000001  0.006365  0.000000|
 |  0.000000  0.000000  0.009772|
With corresponding cell

    A    = 181.449  B   = 181.388  C    = 102.332
    Alpha=  90.001  Beta=  90.001  Gamma= 119.993

The CRYST1 cell dimensions

    A    = 181.907  B   = 181.907  C    = 102.579
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 249.339
(Under-)estimated Z-score: 11.638

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.

  67 TRP   (  98-)  A     -C    N    CA  129.96    4.6

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.

  42 GLU   (  73-)  A
  79 ASP   ( 110-)  A
 109 GLU   ( 140-)  A
 142 ASP   ( 173-)  A
 149 ARG   ( 180-)  A
 259 GLU   ( 290-)  A
 349 GLU   ( 380-)  A
 370 ASP   ( 401-)  A
 389 GLU   ( 420-)  A
 410 ASP   ( 441-)  A
 462 GLU   ( 493-)  A
 471 GLU   ( 502-)  A
 493 GLU   ( 524-)  A
 553 ASP   ( 584-)  A
 601 ARG   (  79-)  B
 632 ASP   ( 110-)  B
 695 ASP   ( 173-)  B
 697 GLU   ( 175-)  B
 841 GLU   ( 319-)  B
 848 GLU   ( 326-)  B
 868 GLU   ( 346-)  B
 886 GLU   ( 364-)  B
 902 GLU   ( 380-)  B
 942 GLU   ( 420-)  B
1024 GLU   ( 502-)  B
1046 GLU   ( 524-)  B
1075 GLU   ( 553-)  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.

 483 PRO   ( 514-)  A    -3.0
 487 PHE   ( 518-)  A    -2.9
 545 PRO   ( 576-)  A    -2.9
1098 PRO   ( 576-)  B    -2.8
   8 TYR   (  39-)  A    -2.6
 354 TYR   ( 385-)  A    -2.5
1083 THR   ( 561-)  B    -2.4
1040 PHE   ( 518-)  B    -2.4
 413 ILE   ( 444-)  A    -2.4
  12 HIS   (  43-)  A    -2.3
 651 THR   ( 129-)  B    -2.3
 378 PHE   ( 409-)  A    -2.3
 561 TYR   (  39-)  B    -2.2
 842 HIS   ( 320-)  B    -2.2
  30 ARG   (  61-)  A    -2.2
 931 PHE   ( 409-)  B    -2.2
 809 VAL   ( 287-)  B    -2.2
 966 ILE   ( 444-)  B    -2.2
 774 LEU   ( 252-)  B    -2.2
 530 THR   ( 561-)  A    -2.2
 658 TYR   ( 136-)  B    -2.2
  98 THR   ( 129-)  A    -2.2
 256 VAL   ( 287-)  A    -2.1
 547 VAL   ( 578-)  A    -2.1
 118 THR   ( 149-)  A    -2.1
 343 ARG   ( 374-)  A    -2.1
 591 CYS   (  69-)  B    -2.1
 914 PRO   ( 392-)  B    -2.1
 667 VAL   ( 145-)  B    -2.1
1039 ILE   ( 517-)  B    -2.0
 414 LEU   ( 445-)  A    -2.0
 114 VAL   ( 145-)  A    -2.0
 225 MET   ( 256-)  A    -2.0
1061 ILE   ( 539-)  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.

  12 HIS   (  43-)  A  Poor phi/psi
  13 GLN   (  44-)  A  Poor phi/psi
  30 ARG   (  61-)  A  Poor phi/psi
  38 CYS   (  69-)  A  Poor phi/psi
  66 ARG   (  97-)  A  omega poor
  67 TRP   (  98-)  A  Poor phi/psi
  68 LEU   (  99-)  A  Poor phi/psi
  95 SER   ( 126-)  A  PRO omega poor
 116 TYR   ( 147-)  A  omega poor
 195 HIS   ( 226-)  A  Poor phi/psi
 199 LEU   ( 230-)  A  Poor phi/psi
 216 PHE   ( 247-)  A  Poor phi/psi
 218 ASP   ( 249-)  A  Poor phi/psi
 227 ASN   ( 258-)  A  Poor phi/psi
 342 TYR   ( 373-)  A  Poor phi/psi
 378 PHE   ( 409-)  A  Poor phi/psi
 428 ARG   ( 459-)  A  Poor phi/psi
 483 PRO   ( 514-)  A  Poor phi/psi
 565 HIS   (  43-)  B  Poor phi/psi
 583 ARG   (  61-)  B  Poor phi/psi
 591 CYS   (  69-)  B  Poor phi/psi
 648 SER   ( 126-)  B  PRO omega poor
 651 THR   ( 129-)  B  Poor phi/psi
 669 TYR   ( 147-)  B  omega poor
 752 LEU   ( 230-)  B  Poor phi/psi
 769 PHE   ( 247-)  B  Poor phi/psi
 771 ASP   ( 249-)  B  Poor phi/psi
 780 ASN   ( 258-)  B  Poor phi/psi
 908 HIS   ( 386-)  B  Poor phi/psi
 931 PHE   ( 409-)  B  Poor phi/psi
 961 ASN   ( 439-)  B  Poor phi/psi
 981 ARG   ( 459-)  B  Poor phi/psi
1037 ASN   ( 515-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.029

Warning: chi-1/chi-2 angle correlation Z-score low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is a bit low.

chi-1/chi-2 correlation Z-score : -3.029

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.

 700 SER   ( 178-)  B    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!

   5 CYS   (  36-)  A      0
   6 CYS   (  37-)  A      0
   8 TYR   (  39-)  A      0
   9 PRO   (  40-)  A      0
  10 CYS   (  41-)  A      0
  11 GLN   (  42-)  A      0
  12 HIS   (  43-)  A      0
  13 GLN   (  44-)  A      0
  21 LEU   (  52-)  A      0
  22 ASP   (  53-)  A      0
  28 CYS   (  59-)  A      0
  29 THR   (  60-)  A      0
  30 ARG   (  61-)  A      0
  31 THR   (  62-)  A      0
  33 TYR   (  64-)  A      0
  34 SER   (  65-)  A      0
  36 PRO   (  67-)  A      0
  38 CYS   (  69-)  A      0
  39 THR   (  70-)  A      0
  43 ILE   (  74-)  A      0
  63 THR   (  94-)  A      0
  64 HIS   (  95-)  A      0
  66 ARG   (  97-)  A      0
  67 TRP   (  98-)  A      0
  74 ALA   ( 105-)  A      0
And so on for a total of 432 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!

 684 PRO   ( 162-)  B   1.59   11

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].

   9 PRO   (  40-)  A    32.4 envelop C-delta (36 degrees)
 141 PRO   ( 172-)  A   104.0 envelop C-beta (108 degrees)
 158 PRO   ( 189-)  A    40.7 envelop C-delta (36 degrees)
 290 PRO   ( 321-)  A    51.8 half-chair C-delta/C-gamma (54 degrees)
 431 PRO   ( 462-)  A  -115.3 envelop C-gamma (-108 degrees)
 483 PRO   ( 514-)  A   156.7 half-chair C-alpha/N (162 degrees)
 497 PRO   ( 528-)  A   100.4 envelop C-beta (108 degrees)
 507 PRO   ( 538-)  A  -116.8 envelop C-gamma (-108 degrees)
 545 PRO   ( 576-)  A   -39.0 envelop C-alpha (-36 degrees)
 594 PRO   (  72-)  B   -61.1 half-chair C-beta/C-alpha (-54 degrees)
 649 PRO   ( 127-)  B   104.2 envelop C-beta (108 degrees)
 798 PRO   ( 276-)  B  -114.5 envelop C-gamma (-108 degrees)
 802 PRO   ( 280-)  B  -141.3 envelop C-delta (-144 degrees)
 914 PRO   ( 392-)  B   -55.6 half-chair C-beta/C-alpha (-54 degrees)
 952 PRO   ( 430-)  B    52.6 half-chair C-delta/C-gamma (54 degrees)
 984 PRO   ( 462-)  B  -126.3 half-chair C-delta/C-gamma (-126 degrees)
1036 PRO   ( 514-)  B  -112.6 envelop C-gamma (-108 degrees)
1060 PRO   ( 538-)  B  -113.1 envelop C-gamma (-108 degrees)
1064 PRO   ( 542-)  B   102.3 envelop C-beta (108 degrees)
1098 PRO   ( 576-)  B   -61.0 half-chair C-beta/C-alpha (-54 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.

1119 MAN   ( 674-)  A      O6  <-> 1130 MAN   ( 675-)  A      C1     0.95    1.45  INTRA BL
1126 BMA   (1673-)  B      O6  <-> 1127 BMA   (1674-)  B      C1     0.95    1.45  INTRA BL
1113 NAG   (1671-)  B      O4  <-> 1128 NDG   (1672-)  B      C1     0.95    1.45  INTRA BL
1126 BMA   (1673-)  B      C6  <-> 1127 BMA   (1674-)  B      C1     0.84    2.36  INTRA BL
1119 MAN   ( 674-)  A      C6  <-> 1130 MAN   ( 675-)  A      C1     0.81    2.39  INTRA BL
1113 NAG   (1671-)  B      C4  <-> 1128 NDG   (1672-)  B      C1     0.76    2.44  INTRA BL
 357 HIS   ( 388-)  A      N   <->  358 PRO   ( 389-)  A      CD     0.29    2.71  INTRA BF
 719 MET   ( 197-)  B      SD  <->  823 TYR   ( 301-)  B      OH     0.27    2.73  INTRA BL
 581 CYS   (  59-)  B      CB  <->  591 CYS   (  69-)  B      SG     0.27    3.13  INTRA BL
 512 GLU   ( 543-)  A      CB  <-> 1133 HOH   ( 655 )  B      O      0.26    2.54  INTRA BF
 910 HIS   ( 388-)  B      CE1 <-> 1123 HEM   (1801-)  B     FE      0.26    2.84  INTRA BF
 910 HIS   ( 388-)  B      N   <->  911 PRO   ( 389-)  B      CD     0.22    2.78  INTRA BL
 932 ASN   ( 410-)  B      OD1 <->  934 SER   ( 412-)  B      N      0.22    2.48  INTRA BF
 511 PRO   ( 542-)  A      O   <->  583 ARG   (  61-)  B      NH1    0.19    2.51  INTRA BL
 357 HIS   ( 388-)  A      CE1 <-> 1115 HEM   ( 801-)  A     FE      0.18    2.92  INTRA BF
1119 MAN   ( 674-)  A      C6  <-> 1130 MAN   ( 675-)  A      O5     0.17    2.63  INTRA BL
 209 ARG   ( 240-)  A      NH2 <->  242 MET   ( 273-)  A      SD     0.16    3.14  INTRA BF
 694 PRO   ( 172-)  B      O   <->  978 ARG   ( 456-)  B      NH2    0.15    2.55  INTRA BF
 153 ARG   ( 184-)  A      NH2 <->  360 MET   ( 391-)  A      O      0.15    2.55  INTRA BF
 958 GLY   ( 436-)  B      N   <-> 1034 CYS   ( 512-)  B      SG     0.15    3.15  INTRA BF
 218 ASP   ( 249-)  A      OD1 <->  286 LYS   ( 317-)  A      NZ     0.14    2.56  INTRA BF
1066 TYR   ( 544-)  B      O   <-> 1068 LYS   ( 546-)  B      N      0.13    2.57  INTRA BL
  66 ARG   (  97-)  A      N   <->   67 TRP   (  98-)  A      CB     0.13    2.77  INTRA BF
 141 PRO   ( 172-)  A      O   <->  425 ARG   ( 456-)  A      NH2    0.12    2.58  INTRA BF
 289 HIS   ( 320-)  A      ND1 <->  571 ARG   (  49-)  B      O      0.12    2.58  INTRA BF
And so on for a total of 73 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.

 139 GLN   ( 170-)  A      -7.53
 583 ARG   (  61-)  B      -6.99
  30 ARG   (  61-)  A      -6.72
 244 TYR   ( 275-)  A      -6.44
 709 PHE   ( 187-)  B      -6.29
 156 PHE   ( 187-)  A      -6.22
 154 ARG   ( 185-)  A      -6.13
 797 TYR   ( 275-)  B      -6.12
 707 ARG   ( 185-)  B      -6.11
  21 LEU   (  52-)  A      -6.03
 560 TYR   (  38-)  B      -5.95
   7 TYR   (  38-)  A      -5.94
 737 LYS   ( 215-)  B      -5.84
 402 ARG   ( 433-)  A      -5.79
 185 MET   ( 216-)  A      -5.68
1033 LYS   ( 511-)  B      -5.58
 343 ARG   ( 374-)  A      -5.58
 397 ARG   ( 428-)  A      -5.50
 950 ARG   ( 428-)  B      -5.47
 702 ARG   ( 180-)  B      -5.44
 574 LEU   (  52-)  B      -5.39
  67 TRP   (  98-)  A      -5.37
 955 ARG   ( 433-)  B      -5.29
 149 ARG   ( 180-)  A      -5.27
   2 VAL   (  33-)  A      -5.26
 555 VAL   (  33-)  B      -5.25
 892 GLN   ( 370-)  B      -5.23
 769 PHE   ( 247-)  B      -5.19
 794 LEU   ( 272-)  B      -5.18
 738 MET   ( 216-)  B      -5.15
 126 ARG   ( 157-)  A      -5.13
 706 ARG   ( 184-)  B      -5.10
 438 ARG   ( 469-)  A      -5.08
 153 ARG   ( 184-)  A      -5.05
 991 ARG   ( 469-)  B      -5.04
 564 GLN   (  42-)  B      -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.

  21 LEU   (  52-)  A        23 - ARG     54- ( A)         -4.94
 574 LEU   (  52-)  B       576 - ARG     54- ( B)         -4.56

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.

 770 LYS   ( 248-)  B   -3.36
 246 ARG   ( 277-)  A   -3.00
 137 LYS   ( 168-)  A   -2.93
 428 ARG   ( 459-)  A   -2.87
 690 LYS   ( 168-)  B   -2.87
 708 LYS   ( 186-)  B   -2.67
 155 LYS   ( 186-)  A   -2.64
 334 LEU   ( 365-)  A   -2.61
 912 LEU   ( 390-)  B   -2.56
 692 GLN   ( 170-)  B   -2.55
 887 LEU   ( 365-)  B   -2.53
 184 LYS   ( 215-)  A   -2.52

Warning: Abnormal packing Z-score for sequential residues

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

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

 333 GLU   ( 364-)  A     -  336 PHE   ( 367-)  A        -1.99
 689 GLY   ( 167-)  B     -  692 GLN   ( 170-)  B        -1.95
 886 GLU   ( 364-)  B     -  889 PHE   ( 367-)  B        -1.98

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.

1133 HOH   ( 597 )  B      O     18.67  -88.56   39.45

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.

1132 HOH   (  17 )  A      O
1132 HOH   ( 612 )  A      O
1132 HOH   ( 633 )  A      O
1132 HOH   ( 635 )  A      O
1132 HOH   ( 645 )  A      O
1132 HOH   ( 652 )  A      O
1132 HOH   ( 680 )  A      O
1132 HOH   ( 691 )  A      O
1133 HOH   (  13 )  B      O
1133 HOH   (  27 )  B      O
1133 HOH   ( 587 )  B      O
1133 HOH   ( 598 )  B      O
1133 HOH   ( 603 )  B      O
1133 HOH   ( 606 )  B      O
1133 HOH   ( 609 )  B      O
1133 HOH   ( 620 )  B      O
1133 HOH   ( 622 )  B      O
1133 HOH   ( 628 )  B      O
1133 HOH   ( 638 )  B      O
1133 HOH   ( 641 )  B      O
1133 HOH   ( 644 )  B      O
1133 HOH   ( 653 )  B      O
Bound group on Asn; dont flip   37 ASN  (  68-) A
Bound to: 1107 NAG  ( 661-) A
Bound group on Asn; dont flip  113 ASN  ( 144-) A
Bound to: 1110 NAG  ( 671-) A
Bound group on Asn; dont flip  379 ASN  ( 410-) A
Bound to: 1108 NAG  ( 681-) A
Bound group on Asn; dont flip  590 ASN  (  68-) B
Bound to: 1111 NAG  (1661-) B
Bound group on Asn; dont flip  666 ASN  ( 144-) B
Bound to: 1113 NAG  (1671-) B
Bound group on Asn; dont flip  932 ASN  ( 410-) B
Bound to: 1125 NDG  (1681-) B
Metal-coordinating Histidine residue 357 fixed to   2
Metal-coordinating Histidine residue 910 fixed to   2

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.

  64 HIS   (  95-)  A
 173 HIS   ( 204-)  A
 251 GLN   ( 282-)  A
 578 GLN   (  56-)  B
 726 HIS   ( 204-)  B
 759 ASN   ( 237-)  B
 804 GLN   ( 282-)  B
 842 HIS   ( 320-)  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.

   5 CYS   (  36-)  A      N
   8 TYR   (  39-)  A      N
  14 GLY   (  45-)  A      N
  18 ARG   (  49-)  A      NE
  43 ILE   (  74-)  A      N
  52 ARG   (  83-)  A      N
  52 ARG   (  83-)  A      NH2
  69 TRP   ( 100-)  A      N
  70 ASP   ( 101-)  A      N
  89 ARG   ( 120-)  A      NH1
 100 ASN   ( 131-)  A      ND2
 101 ILE   ( 132-)  A      N
 105 TYR   ( 136-)  A      N
 107 SER   ( 138-)  A      N
 107 SER   ( 138-)  A      OG
 109 GLU   ( 140-)  A      N
 118 THR   ( 149-)  A      OG1
 144 GLU   ( 175-)  A      N
 153 ARG   ( 184-)  A      NE
 153 ARG   ( 184-)  A      NH1
 154 ARG   ( 185-)  A      N
 161 GLN   ( 192-)  A      N
 175 THR   ( 206-)  A      N
 175 THR   ( 206-)  A      OG1
 177 GLN   ( 208-)  A      NE2
And so on for a total of 119 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.

 159 ASP   ( 190-)  A      OD1
 172 GLN   ( 203-)  A      OE1
 173 HIS   ( 204-)  A      NE2
 243 HIS   ( 274-)  A      ND1
 258 GLN   ( 289-)  A      OE1
 351 ASN   ( 382-)  A      OD1
 352 GLN   ( 383-)  A      OE1
 712 ASP   ( 190-)  B      OD1
 725 GLN   ( 203-)  B      OE1
 861 GLU   ( 339-)  B      OE1
 910 HIS   ( 388-)  B      NE2
1046 GLU   ( 524-)  B      OE1

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.

 198 ASP   ( 229-)  A   H-bonding suggests Asn; but Alt-Rotamer
 385 ASP   ( 416-)  A   H-bonding suggests Asn
 419 ASP   ( 450-)  A   H-bonding suggests Asn; but Alt-Rotamer
 623 ASP   ( 101-)  B   H-bonding suggests Asn
 751 ASP   ( 229-)  B   H-bonding suggests Asn; but Alt-Rotamer
 902 GLU   ( 380-)  B   H-bonding suggests Gln
 938 ASP   ( 416-)  B   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact

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 :  -2.062
  2nd generation packing quality :  -2.478
  Ramachandran plot appearance   :  -1.724
  chi-1/chi-2 rotamer normality  :  -3.029 (poor)
  Backbone conformation          :  -1.207

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.320 (tight)
  Bond angles                    :   0.509 (tight)
  Omega angle restraints         :   0.734
  Side chain planarity           :   0.220 (tight)
  Improper dihedral distribution :   0.418
  B-factor distribution          :   0.404
  Inside/Outside distribution    :   1.102

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 : 3.05


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.0
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :   0.9
  chi-1/chi-2 rotamer normality  :  -0.7
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.320 (tight)
  Bond angles                    :   0.509 (tight)
  Omega angle restraints         :   0.734
  Side chain planarity           :   0.220 (tight)
  Improper dihedral distribution :   0.418
  B-factor distribution          :   0.404
  Inside/Outside distribution    :   1.102
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.