WHAT IF Check report

This file was created 2011-12-17 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb3s2o.ent

Checks that need to be done early-on in validation

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.

 381 EV6   ( 393-)  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.

 108 ASP   ( 106-)  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.

 108 ASP   ( 106-)  A  -

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.

   3 GLU   (   1-)  A  -   CG
   3 GLU   (   1-)  A  -   CD
   3 GLU   (   1-)  A  -   OE1
   3 GLU   (   1-)  A  -   OE2
   9 ARG   (   7-)  A  -   CZ
   9 ARG   (   7-)  A  -   NH1
   9 ARG   (   7-)  A  -   NH2
  66 ARG   (  64-)  A  -   NE
  66 ARG   (  64-)  A  -   CZ
  66 ARG   (  64-)  A  -   NH1
  66 ARG   (  64-)  A  -   NH2
 108 ASP   ( 106-)  A  - A CG
 108 ASP   ( 106-)  A  - A OD1
 108 ASP   ( 106-)  A  - A OD2
 109 LYS   ( 107-)  A  -   NZ
 258 GLN   ( 266-)  A  -   CD
 258 GLN   ( 266-)  A  -   OE1
 258 GLN   ( 266-)  A  -   NE2
 263 GLN   ( 271-)  A  -   CG
 263 GLN   ( 271-)  A  -   CD
 263 GLN   ( 271-)  A  -   OE1
 263 GLN   ( 271-)  A  -   NE2
 373 ASP   ( 381-)  A  -   CG
 373 ASP   ( 381-)  A  -   OD1
 373 ASP   ( 381-)  A  -   OD2

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

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'.

   9 ARG   (   7-)  A      NE
 109 LYS   ( 107-)  A      CE
 144 LYS   ( 142-)  A      NZ
 258 GLN   ( 266-)  A      CG

Warning: C-terminal nitrogen atoms detected.

It is becoming habit to indicate that a residue is not the true C-terminus by including only the backbone N of the next residue. This has been observed in this PDB file.

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. In many cases the N- or C-terminal residues are too disordered to see. In case of the N-terminus, you can see from the residue numbers if there are missing residues, but at the C-terminus this is impossible. Therefore, often the position of the backbone nitrogen of the first residue missing at the C-terminal end is calculated and added to indicate that there are missing residues. As a single N causes validation trouble, we remove these single-N-residues before doing the validation. But, if you get weird errors at, or near, the left-over incomplete C-terminal residue, please check by hand if a missing Oxt or removed N is the cause.

 378 ILE   ( 386-)  A

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

  79 GLU   (  77-)  A    0.50
 108 ASP   ( 106-)  A    1.50
 173 HIS   ( 181-)  A    0.50

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: 1

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

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.

 130 ARG   ( 128-)  A
 339 ARG   ( 347-)  A

Warning: Tyrosine convention problem

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

  70 TYR   (  68-)  A
 176 TYR   ( 184-)  A
 182 TYR   ( 190-)  A
 212 TYR   ( 220-)  A

Warning: Phenylalanine convention problem

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

   1 PHE   (  -1-)  A
 249 PHE   ( 257-)  A
 272 PHE   ( 280-)  A
 314 PHE   ( 322-)  A
 366 PHE   ( 374-)  A

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.

   6 ASP   (   4-)  A
 132 ASP   ( 130-)  A
 140 ASP   ( 138-)  A
 215 ASP   ( 223-)  A
 303 ASP   ( 311-)  A
 309 ASP   ( 317-)  A
 355 ASP   ( 363-)  A

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.

   3 GLU   (   1-)  A
  19 GLU   (  17-)  A
  79 GLU   (  77-)  A
  81 GLU   (  79-)  A
 136 GLU   ( 134-)  A
 211 GLU   ( 219-)  A
 234 GLU   ( 242-)  A

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 157 CYS   ( 155-)  A      SG  -SG*   2.41    9.2
 351 CYS   ( 359-)  A      SG  -SG*   2.41    9.2

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

 |  0.998378 -0.000505  0.000758|
 | -0.000505  0.998276 -0.000512|
 |  0.000758 -0.000512  0.996671|
Proposed new scale matrix

 |  0.009834  0.005682 -0.000005|
 |  0.000006  0.011354  0.000006|
 | -0.000004  0.000003  0.005896|
With corresponding cell

    A    = 101.720  B   = 101.752  C    = 169.617
    Alpha=  90.094  Beta=  89.913  Gamma= 120.047

The CRYST1 cell dimensions

    A    = 101.880  B   = 101.880  C    = 170.181
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 69.392
(Under-)estimated Z-score: 6.139

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.

   3 GLU   (   1-)  A      CB   CG   CD  103.77   -5.2

Error: Nomenclature error(s)

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

   3 GLU   (   1-)  A
   6 ASP   (   4-)  A
  19 GLU   (  17-)  A
  79 GLU   (  77-)  A
  81 GLU   (  79-)  A
 130 ARG   ( 128-)  A
 132 ASP   ( 130-)  A
 136 GLU   ( 134-)  A
 140 ASP   ( 138-)  A
 211 GLU   ( 219-)  A
 215 ASP   ( 223-)  A
 234 GLU   ( 242-)  A
 303 ASP   ( 311-)  A
 309 ASP   ( 317-)  A
 339 ARG   ( 347-)  A
 355 ASP   ( 363-)  A

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.

 268 PRO   ( 276-)  A    -2.9
 151 LEU   ( 149-)  A    -2.4
 306 THR   ( 314-)  A    -2.4
  77 LYS   (  75-)  A    -2.4
 359 THR   ( 367-)  A    -2.3
 259 LEU   ( 267-)  A    -2.2
 304 VAL   ( 312-)  A    -2.2
 292 ILE   ( 300-)  A    -2.1
 189 TRP   ( 197-)  A    -2.1
  61 THR   (  59-)  A    -2.1
  66 ARG   (  64-)  A    -2.1
 130 ARG   ( 128-)  A    -2.1
 187 ARG   ( 195-)  A    -2.1
 298 LEU   ( 306-)  A    -2.1
  40 PHE   (  38-)  A    -2.0
 135 LEU   ( 133-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

   6 ASP   (   4-)  A  Poor phi/psi
  24 SER   (  22-)  A  PRO omega poor
  39 ASN   (  37-)  A  omega poor
  46 PRO   (  44-)  A  Poor phi/psi
  77 LYS   (  75-)  A  omega poor
 117 TRP   ( 115-)  A  omega poor
 119 GLY   ( 117-)  A  omega poor
 124 ALA   ( 122-)  A  omega poor
 130 ARG   ( 128-)  A  PRO omega poor
 154 LEU   ( 152-)  A  omega poor
 165 SER   ( 173-)  A  omega poor
 189 TRP   ( 197-)  A  Poor phi/psi, omega poor
 201 ASN   ( 209-)  A  Poor phi/psi
 204 ASP   ( 212-)  A  omega poor
 206 LYS   ( 214-)  A  Poor phi/psi
 214 TYR   ( 222-)  A  omega poor
 225 ASN   ( 233-)  A  omega poor
 285 ASN   ( 293-)  A  Poor phi/psi
 303 ASP   ( 311-)  A  Poor phi/psi, omega poor
 304 VAL   ( 312-)  A  Poor phi/psi
 305 ALA   ( 313-)  A  omega poor
 308 GLN   ( 316-)  A  omega poor
 309 ASP   ( 317-)  A  Poor phi/psi
 332 GLY   ( 340-)  A  omega poor
 355 ASP   ( 363-)  A  Poor phi/psi
 364 GLY   ( 372-)  A  PRO omega poor
 370 ASP   ( 378-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.612

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.

 211 GLU   ( 219-)  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!

   5 VAL   (   3-)  A      0
   6 ASP   (   4-)  A      0
   7 ASN   (   5-)  A      0
   9 ARG   (   7-)  A      0
  11 LYS   (   9-)  A      0
  12 SER   (  10-)  A      0
  14 GLN   (  12-)  A      0
  16 TYR   (  14-)  A      0
  22 VAL   (  20-)  A      0
  24 SER   (  22-)  A      0
  25 PRO   (  23-)  A      0
  26 PRO   (  24-)  A      0
  35 THR   (  33-)  A      0
  44 ALA   (  42-)  A      0
  50 LEU   (  48-)  A      0
  51 HIS   (  49-)  A      0
  56 ARG   (  54-)  A      0
  66 ARG   (  64-)  A      0
  74 THR   (  72-)  A      0
  75 GLN   (  73-)  A      0
  85 ASP   (  83-)  A      0
  91 HIS   (  89-)  A      0
  94 ASN   (  92-)  A      0
  98 ARG   (  96-)  A      0
 104 ILE   ( 102-)  A      0
And so on for a total of 183 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 7.125

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]

  26 PRO   (  24-)  A    0.19 LOW
 184 PRO   ( 192-)  A    0.45 HIGH

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].

 268 PRO   ( 276-)  A   -18.9 half-chair C-alpha/N (-18 degrees)
 294 PRO   ( 302-)  A   123.6 half-chair C-beta/C-alpha (126 degrees)
 365 PRO   ( 373-)  A   -60.7 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.

 259 LEU   ( 267-)  A      CD1 <->  311 CYS   ( 319-)  A      CB     0.51    2.69  INTRA BF
  77 LYS   (  75-)  A      NZ  <->   79 GLU   (  77-)  A      OE2    0.35    2.35  INTRA
 198 VAL   ( 206-)  A      CG1 <->  205 LEU   ( 213-)  A      CD1    0.31    2.89  INTRA BF
 302 GLU   ( 310-)  A      CG  <->  303 ASP   ( 311-)  A      N      0.30    2.70  INTRA BF
 127 GLU   ( 125-)  A      OE2 <->  187 ARG   ( 195-)  A      NH1    0.27    2.43  INTRA BF
   1 PHE   (  -1-)  A      N   <->  381 HOH   ( 414 )  A      O      0.23    2.47  INTRA BF
  56 ARG   (  54-)  A      NH1 <->   81 GLU   (  79-)  A      OE1    0.19    2.51  INTRA BL
 381 HOH   ( 404 )  A      O   <->  381 HOH   ( 457 )  A      O      0.19    2.01  INTRA BF
 158 GLY   ( 156-)  A      CA  <->  162 VAL   ( 170-)  A      CG1    0.19    3.01  INTRA BF
 140 ASP   ( 138-)  A      OD1 <->  339 ARG   ( 347-)  A      NH2    0.18    2.52  INTRA
  22 VAL   (  20-)  A      CG1 <->  101 ILE   (  99-)  A      CD1    0.18    3.02  INTRA BL
 147 HIS   ( 145-)  A      NE2 <->  381 HOH   ( 445 )  A      O      0.18    2.52  INTRA BF
 203 GLN   ( 211-)  A      C   <->  204 ASP   ( 212-)  A      O      0.18    2.42  INTRA BF
 259 LEU   ( 267-)  A      CD1 <->  311 CYS   ( 319-)  A      SG     0.18    3.22  INTRA BF
 204 ASP   ( 212-)  A      CG  <->  205 LEU   ( 213-)  A      N      0.17    2.83  INTRA BF
 302 GLU   ( 310-)  A      CG  <->  303 ASP   ( 311-)  A      OD1    0.17    2.63  INTRA BF
 237 VAL   ( 245-)  A      O   <->  241 LYS   ( 249-)  A      N      0.17    2.53  INTRA BF
  12 SER   (  10-)  A      N   <->  160 ALA   ( 168-)  A      O      0.17    2.53  INTRA BF
 198 VAL   ( 206-)  A      CB  <->  205 LEU   ( 213-)  A      CD1    0.16    3.04  INTRA BF
  69 VAL   (  67-)  A      CG1 <->   78 TRP   (  76-)  A      CZ3    0.14    3.06  INTRA BL
  42 VAL   (  40-)  A      O   <->  104 ILE   ( 102-)  A      N      0.13    2.57  INTRA BL
 302 GLU   ( 310-)  A      O   <->  304 VAL   ( 312-)  A      N      0.12    2.58  INTRA BF
 158 GLY   ( 156-)  A      CA  <->  162 VAL   ( 170-)  A      CB     0.11    3.09  INTRA BF
  32 LEU   (  30-)  A      O   <->  121 LEU   ( 119-)  A      N      0.11    2.59  INTRA BL
 132 ASP   ( 130-)  A      OD1 <->  134 SER   ( 132-)  A      N      0.10    2.60  INTRA BF
And so on for a total of 58 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

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.

 376 TYR   ( 384-)  A      -7.79
  66 ARG   (  64-)  A      -7.46
  75 GLN   (  73-)  A      -6.74
 357 PHE   ( 365-)  A      -6.32
 147 HIS   ( 145-)  A      -6.31
 248 LYS   ( 256-)  A      -6.20
 214 TYR   ( 222-)  A      -5.80
 308 GLN   ( 316-)  A      -5.72
 341 ARG   ( 349-)  A      -5.65
 130 ARG   ( 128-)  A      -5.58
 257 GLU   ( 265-)  A      -5.54
  94 ASN   (  92-)  A      -5.54
 145 GLN   ( 143-)  A      -5.41
 263 GLN   ( 271-)  A      -5.27
  70 TYR   (  68-)  A      -5.23
 369 LEU   ( 377-)  A      -5.22
 358 ARG   ( 366-)  A      -5.18
  52 ARG   (  50-)  A      -5.12
  51 HIS   (  49-)  A      -5.11
 254 TRP   ( 262-)  A      -5.10
 186 ARG   ( 194-)  A      -5.04

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.

  51 HIS   (  49-)  A        53 - TYR     51- ( A)         -4.81

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

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.

 109 LYS   ( 107-)  A   -2.93

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.

  55 GLN   (  53-)  A     -   58 LEU   (  56-)  A        -1.82

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

Water, ion, and hydrogenbond related checks

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.

 381 HOH   ( 425 )  A      O
Marked this atom as acceptor  380 EV6  ( 393-) A     CL11

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.

  75 GLN   (  73-)  A
 296 GLN   ( 304-)  A

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.

  27 GLN   (  25-)  A      NE2
  45 ALA   (  43-)  A      N
  47 HIS   (  45-)  A      NE2
  52 ARG   (  50-)  A      N
 107 SER   ( 105-)  A      OG
 109 LYS   ( 107-)  A      N
 112 ILE   ( 110-)  A      N
 113 ASN   ( 111-)  A      N
 119 GLY   ( 117-)  A      N
 125 TYR   ( 123-)  A      OH
 130 ARG   ( 128-)  A      NE
 132 ASP   ( 130-)  A      N
 139 PHE   ( 137-)  A      N
 170 GLY   ( 178-)  A      N
 187 ARG   ( 195-)  A      N
 190 TYR   ( 198-)  A      N
 197 ARG   ( 205-)  A      N
 216 LYS   ( 224-)  A      N
 217 SER   ( 225-)  A      N
 231 LYS   ( 239-)  A      N
 246 THR   ( 254-)  A      N
 254 TRP   ( 262-)  A      N
 287 SER   ( 295-)  A      OG
 309 ASP   ( 317-)  A      N
 316 ILE   ( 324-)  A      N
 343 ARG   ( 351-)  A      NH2
 376 TYR   ( 384-)  A      N

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.

 118 GLU   ( 116-)  A   H-bonding suggests Gln
 215 ASP   ( 223-)  A   H-bonding suggests Asn
 355 ASP   ( 363-)  A   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 :  -1.278
  2nd generation packing quality :  -2.596
  Ramachandran plot appearance   :  -2.261
  chi-1/chi-2 rotamer normality  :  -2.612
  Backbone conformation          :  -1.252

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.722
  Bond angles                    :   0.780
  Omega angle restraints         :   1.295 (loose)
  Side chain planarity           :   0.528 (tight)
  Improper dihedral distribution :   0.839
  B-factor distribution          :   0.588
  Inside/Outside distribution    :   1.004

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 : 2.60


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.6
  2nd generation packing quality :  -1.2
  Ramachandran plot appearance   :   0.1
  chi-1/chi-2 rotamer normality  :  -0.4
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.722
  Bond angles                    :   0.780
  Omega angle restraints         :   1.295 (loose)
  Side chain planarity           :   0.528 (tight)
  Improper dihedral distribution :   0.839
  B-factor distribution          :   0.588
  Inside/Outside distribution    :   1.004
==============

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
    G.Vriend and C.Sander,
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      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.