WHAT IF Check report

This file was created 2012-01-13 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 pdb1stf.ent

Administrative problems that can generate validation failures

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.

   9 GLN   (   9-)  E  -   CD
   9 GLN   (   9-)  E  -   OE1
   9 GLN   (   9-)  E  -   NE2
  58 ARG   (  58-)  E  -   CD
  58 ARG   (  58-)  E  -   NE
  58 ARG   (  58-)  E  -   CZ
  58 ARG   (  58-)  E  -   NH1
  58 ARG   (  58-)  E  -   NH2
  59 ARG   (  59-)  E  -   CZ
  59 ARG   (  59-)  E  -   NH1
  59 ARG   (  59-)  E  -   NH2
  84 ASN   (  84-)  E  -   OD1
  84 ASN   (  84-)  E  -   ND2
 139 LYS   ( 139-)  E  -   CG
 139 LYS   ( 139-)  E  -   CD
 139 LYS   ( 139-)  E  -   CE
 139 LYS   ( 139-)  E  -   NZ
 213 MET   (   6-)  I  -   CB
 213 MET   (   6-)  I  -   CG
 213 MET   (   6-)  I  -   SD
 213 MET   (   6-)  I  -   CE
 214 MET   (   7-)  I  -   CE
 227 GLU   (  20-)  I  -   CD
 227 GLU   (  20-)  I  -   OE1
 227 GLU   (  20-)  I  -   OE2
 241 GLU   (  34-)  I  -   CD
 241 GLU   (  34-)  I  -   OE1
 241 GLU   (  34-)  I  -   OE2
 251 LYS   (  46-)  I  -   CE
 251 LYS   (  46-)  I  -   NZ
 273 ASP   (  68-)  I  -   CG
 273 ASP   (  68-)  I  -   OD1
 273 ASP   (  68-)  I  -   OD2
 274 GLU   (  92-)  I  -   CG
 274 GLU   (  92-)  I  -   CD
 274 GLU   (  92-)  I  -   OE1
 274 GLU   (  92-)  I  -   OE2
 290 LYS   ( 106-)  I  -   NZ
 303 LYS   ( 118-)  I  -   CD
 303 LYS   ( 118-)  I  -   CE
 303 LYS   ( 118-)  I  -   NZ
 306 GLU   ( 121-)  I  -   CG
 306 GLU   ( 121-)  I  -   CD
 306 GLU   ( 121-)  I  -   OE1
 306 GLU   ( 121-)  I  -   OE2

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone 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. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT IF will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.

 311 ASN   ( 212-)  E  -   O''

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: E

Note: Ramachandran plot

Chain identifier: I

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

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. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and 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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 1.830 over 2193 bonds
Average difference in B over a bond : 2.78
RMS difference in B over a bond : 6.04

Note: B-factor plot

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

Chain identifier: E

Note: B-factor plot

Chain identifier: I

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.

   7 TRP   (   7-)  E      NE1  CE2   1.28   -8.2
  26 TRP   (  26-)  E      NE1  CE2   1.26   -9.9
  69 TRP   (  69-)  E      NE1  CE2   1.28   -8.2
  81 HIS   (  81-)  E      ND1  CE1   1.39    5.2
 177 TRP   ( 177-)  E      NE1  CE2   1.27   -9.2
 181 TRP   ( 181-)  E      NE1  CE2   1.27   -9.2
 230 HIS   (  23-)  I      ND1  CE1   1.43    8.2
 230 HIS   (  23-)  I      CE1  NE2   1.43    4.2
 270 HIS   (  65-)  I      ND1  CE1   1.41    7.0
 278 HIS   (  96-)  I      ND1  CE1   1.38    5.1
 287 HIS   ( 104-)  I      ND1  CE1   1.41    7.0
 304 HIS   ( 119-)  I      ND1  CE1   1.41    7.3

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

 |  0.996464  0.000344 -0.000422|
 |  0.000344  0.997663  0.000523|
 | -0.000422  0.000523  0.995052|
Proposed new scale matrix

 |  0.014975  0.008632  0.000002|
 | -0.000006  0.017274 -0.000009|
 |  0.000003 -0.000003  0.005936|
With corresponding cell

    A    =  66.765  B   =  66.805  C    = 168.453
    Alpha=  89.924  Beta=  90.049  Gamma= 119.941

The CRYST1 cell dimensions

    A    =  67.000  B   =  67.000  C    = 169.300
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 140.436
(Under-)estimated Z-score: 8.734

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.

  16 VAL   (  16-)  E     -O   -C    N   129.41    4.0
  34 ILE   (  34-)  E      CA   CB   CG1 119.53    5.4
  44 ASN   (  44-)  E      CA   CB   CG  105.63   -7.0
  46 ASN   (  46-)  E      CA   CB   CG  107.54   -5.1
  55 ASP   (  55-)  E      CA   CB   CG  107.98   -4.6
  81 HIS   (  81-)  E      CA   CB   CG  109.33   -4.5
  89 GLU   (  89-)  E      CB   CG   CD  102.11   -6.2
  96 ARG   (  96-)  E      CA   CB   CG  106.01   -4.0
 100 LYS   ( 100-)  E      CA   CB   CG  105.94   -4.1
 106 LYS   ( 106-)  E      N    CA   CB  103.48   -4.1
 112 GLN   ( 112-)  E      NE2  CD   OE1 128.05    5.5
 127 ASN   ( 127-)  E      CA   CB   CG  107.73   -4.9
 128 GLN   ( 128-)  E      NE2  CD   OE1 126.62    4.0
 140 ASP   ( 140-)  E      CA   CB   CG  108.20   -4.4
 141 PHE   ( 141-)  E      CA   CB   CG  109.57   -4.2
 155 ASN   ( 155-)  E      CA   CB   CG  107.66   -4.9
 166 TYR   ( 166-)  E      N    CA   CB  117.37    4.0
 173 ILE   ( 173-)  E      CA   CB   CG2 117.51    4.1
 184 ASN   ( 184-)  E      CA   CB   CG  106.64   -6.0
 191 ARG   ( 191-)  E      CB   CG   CD  105.17   -4.5
 203 TYR   ( 203-)  E      N    CA   CB  117.33    4.0
 207 PHE   ( 207-)  E      CA   CB   CG  108.59   -5.2
 212 ASN   ( 212-)  E      CA   CB   CG  105.61   -7.0
 222 GLN   (  15-)  I      CB   CG   CD  105.78   -4.0
 229 GLN   (  22-)  I      NE2  CD   OE1 126.85    4.3
 230 HIS   (  23-)  I     -C    N    CA  113.86   -4.4
 235 VAL   (  28-)  I      N    CA   CB  102.12   -4.9
 236 ARG   (  29-)  I      CA   CB   CG  104.48   -4.8
 253 VAL   (  48-)  I      N    CA   CB  102.35   -4.8
 254 SER   (  49-)  I      CA   CB   OG   98.38   -6.4
 255 PHE   (  50-)  I      N    CA   CB  117.70    4.2
 257 SER   (  52-)  I      CA   CB   OG  101.96   -4.6
 258 GLN   (  53-)  I      N    CA   CB  117.84    4.3
 258 GLN   (  53-)  I      CG   CD   NE2 122.44    4.0
 270 HIS   (  65-)  I      CA   CB   CG  109.02   -4.8
 272 GLY   (  67-)  I     -C    N    CA  111.68   -5.2
 277 VAL   (  95-)  I      N    CA   CB  102.49   -4.7
 278 HIS   (  96-)  I      ND1  CE1  NE2 105.57   -4.7
 282 PHE   ( 100-)  I      CA   CB   CG  109.64   -4.2
 286 PRO   ( 103-)  I     -O   -C    N   127.96    4.3
 288 GLU   ( 105-)  I      CA   CB   CG  104.63   -4.7
 288 GLU   ( 105-)  I      CB   CG   CD  103.44   -5.4
 289 ASN   ( 105-)  I     -O   -C    N   129.69    4.2
 301 LYS   ( 116-)  I      N    CA   CB  103.54   -4.1
 304 HIS   ( 119-)  I      CA   CB   CG  109.01   -4.8
 305 ASP   ( 120-)  I      CA   CB   CG  108.33   -4.3

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

  48 TYR   (  48-)  E      C     -6.1    -9.18     0.33
  66 GLY   (  66-)  E      C     -6.6    -8.70     0.06
  86 TYR   (  86-)  E      C     -6.1    -9.13     0.33
 110 VAL   ( 110-)  E      C      6.9     9.54     0.15
 163 ALA   ( 163-)  E      C     -6.3    -9.49     0.08
 173 ILE   ( 173-)  E      C      6.5     8.51     0.03
 188 ARG   ( 188-)  E      C     -8.5   -12.80     0.13
 200 CYS   ( 200-)  E      C      6.8    10.23     0.22
 211 LYS   ( 211-)  E      C     -6.2    -9.21     0.11
 223 PRO   (  16-)  I      C     -7.3   -11.04     0.42
 234 GLN   (  27-)  I      C     -9.0   -13.87     0.15
 257 SER   (  52-)  I      C      6.1    10.46     0.37
 270 HIS   (  65-)  I      C     -9.6   -14.24     0.15
 271 VAL   (  66-)  I      C    -10.1   -13.67     0.15
 271 VAL   (  66-)  I      CB     7.1   -23.60   -32.96
 272 GLY   (  67-)  I      C    -10.6   -13.92     0.06
 273 ASP   (  68-)  I      C      6.9    10.58    -0.01
The average deviation= 2.496

Warning: High improper dihedral angle deviations

The RMS Z-score for the improper dihedrals in the structure is high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 2.0 worries us a bit. However, we determined the improper normal distribution from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Improper dihedral RMS Z-score : 2.252

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

  69 TRP   (  69-)  E      CB   4.13
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -1.805

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.

 250 PHE   (  45-)  I    -2.6
  58 ARG   (  58-)  E    -2.6
 134 LEU   ( 134-)  E    -2.6
  86 TYR   (  86-)  E    -2.5
 243 TYR   (  36-)  I    -2.5
 200 CYS   ( 200-)  E    -2.2
 280 ARG   (  98-)  I    -2.1
 116 TYR   ( 116-)  E    -2.1
  80 ILE   (  80-)  E    -2.1
 272 GLY   (  67-)  I    -2.1
 274 GLU   (  92-)  I    -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.

  55 ASP   (  55-)  E  omega poor
  66 GLY   (  66-)  E  omega poor
  78 TYR   (  78-)  E  Poor phi/psi
  93 ARG   (  93-)  E  Poor phi/psi
 110 VAL   ( 110-)  E  omega poor
 116 TYR   ( 116-)  E  Poor phi/psi
 151 GLY   ( 151-)  E  PRO omega poor
 158 ASP   ( 158-)  E  Poor phi/psi
 169 ASN   ( 169-)  E  omega poor
 170 TYR   ( 170-)  E  omega poor
 184 ASN   ( 184-)  E  Poor phi/psi
 195 ASN   ( 195-)  E  omega poor
 200 CYS   ( 200-)  E  Poor phi/psi
 204 THR   ( 204-)  E  omega poor
 223 PRO   (  16-)  I  omega poor
 225 THR   (  18-)  I  Poor phi/psi
 234 GLN   (  27-)  I  omega poor
 244 ASN   (  37-)  I  Poor phi/psi
 255 PHE   (  50-)  I  omega poor
 257 SER   (  52-)  I  omega poor
 260 VAL   (  55-)  I  Poor phi/psi
 261 ALA   (  56-)  I  Poor phi/psi, omega poor
 266 PHE   (  61-)  I  omega poor
 270 HIS   (  65-)  I  omega poor
 271 VAL   (  66-)  I  omega poor
 273 ASP   (  68-)  I  omega poor
 300 ASN   ( 115-)  I  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.663

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.

 124 SER   ( 124-)  E    0.38

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 GLU   (   3-)  E      0
   7 TRP   (   7-)  E      0
  10 LYS   (  10-)  E      0
  21 SER   (  21-)  E      0
  24 SER   (  24-)  E      0
  25 CCS   (  25-)  E      0
  41 ARG   (  41-)  E      0
  46 ASN   (  46-)  E      0
  56 CYS   (  56-)  E      0
  58 ARG   (  58-)  E      0
  60 SER   (  60-)  E      0
  61 TYR   (  61-)  E      0
  63 CYS   (  63-)  E      0
  64 ASN   (  64-)  E      0
  78 TYR   (  78-)  E      0
  85 THR   (  85-)  E      0
  87 PRO   (  87-)  E      0
  89 GLU   (  89-)  E      0
  91 VAL   (  91-)  E      0
  93 ARG   (  93-)  E      0
  94 TYR   (  94-)  E      0
  95 CYS   (  95-)  E      0
  96 ARG   (  96-)  E      0
 100 LYS   ( 100-)  E      0
 102 PRO   ( 102-)  E      0
And so on for a total of 138 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 : 7.744

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]

 102 PRO   ( 102-)  E    0.12 LOW
 291 PRO   ( 107-)  I    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].

  15 PRO   (  15-)  E   100.9 envelop C-beta (108 degrees)
 152 PRO   ( 152-)  E   -61.0 half-chair C-beta/C-alpha (-54 degrees)
 223 PRO   (  16-)  I    42.3 envelop C-delta (36 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.

 150 VAL   ( 150-)  E      N   <->  151 GLY   ( 151-)  E      N      0.19    2.41  INTRA BL
 216 GLY   (   9-)  I      O   <->  258 GLN   (  53-)  I      NE2    0.18    2.52  INTRA BL
  55 ASP   (  55-)  E      OD2 <->   96 ARG   (  96-)  E      NH2    0.12    2.58  INTRA BL
 251 LYS   (  46-)  I      O   <->  270 HIS   (  65-)  I      N      0.11    2.59  INTRA BL
 285 LEU   ( 102-)  I      CA  <->  286 PRO   ( 103-)  I      CD     0.10    2.70  INTRA B3
  51 GLN   (  51-)  E      OE1 <->   89 GLU   (  89-)  E      N      0.09    2.61  INTRA BL
 219 SER   (  12-)  I      N   <->  257 SER   (  52-)  I      O      0.09    2.61  INTRA BL
 263 THR   (  58-)  I      N   <->  283 GLN   ( 101-)  I      O      0.08    2.62  INTRA BL
 235 VAL   (  28-)  I      N   <->  236 ARG   (  29-)  I      N      0.07    2.53  INTRA BL
 271 VAL   (  66-)  I      C   <->  272 GLY   (  67-)  I      CA     0.06    2.24  INTRA BL
 239 LEU   (  32-)  I      O   <->  243 TYR   (  36-)  I      N      0.06    2.64  INTRA BL
 274 GLU   (  92-)  I      N   <->  275 ASP   (  93-)  I      N      0.06    2.54  INTRA B3
 226 ALA   (  19-)  I      N   <->  227 GLU   (  20-)  I      N      0.06    2.54  INTRA B3
 268 LYS   (  63-)  I      NZ  <->  302 ALA   ( 117-)  I      O      0.05    2.65  INTRA BL
 290 LYS   ( 106-)  I      CA  <->  291 PRO   ( 107-)  I      CD     0.04    2.76  INTRA B3
 201 GLY   ( 201-)  E      N   <->  202 LEU   ( 202-)  E      N      0.04    2.56  INTRA BL
 222 GLN   (  15-)  I      N   <->  255 PHE   (  50-)  I      O      0.04    2.66  INTRA BL
 135 GLN   ( 135-)  E      NE2 <->  154 GLY   ( 154-)  E      C      0.04    3.06  INTRA
 271 VAL   (  66-)  I      N   <->  272 GLY   (  67-)  I      N      0.04    2.56  INTRA BL
 151 GLY   ( 151-)  E      CA  <->  152 PRO   ( 152-)  E      CA     0.04    2.76  INTRA B3
  50 GLU   (  50-)  E      OE1 <->   83 ARG   (  83-)  E      NE     0.04    2.66  INTRA BL
 286 PRO   ( 103-)  I      C   <->  288 GLU   ( 105-)  I      N      0.03    2.87  INTRA
 277 VAL   (  95-)  I      CG1 <->  279 LEU   (  97-)  I      CD1    0.03    3.17  INTRA BL
 167 GLY   ( 167-)  E      CA  <->  168 PRO   ( 168-)  E      CD     0.03    2.77  INTRA BL
 128 GLN   ( 128-)  E      CA  <->  129 PRO   ( 129-)  E      CD     0.03    2.77  INTRA BL
 299 THR   ( 115-)  I      CG2 <->  300 ASN   ( 115-)  I      N      0.03    2.97  INTRA
 113 VAL   ( 113-)  E      N   <->  206 SER   ( 206-)  E      O      0.03    2.67  INTRA BL
 222 GLN   (  15-)  I      O   <->  255 PHE   (  50-)  I      N      0.03    2.67  INTRA BL
 273 ASP   (  68-)  I      CB  <->  274 GLU   (  92-)  I      N      0.03    2.67  INTRA B3
 118 GLN   ( 118-)  E      NE2 <->  203 TYR   ( 203-)  E      OH     0.02    2.68  INTRA BL
  17 LYS   (  17-)  E      NZ  <->  313 HOH   ( 354 )  E      O      0.01    2.69  INTRA BL
 247 PHE   (  40-)  I      CA  <->  248 PRO   (  43-)  I      CD     0.01    2.79  INTRA B3
 143 LEU   ( 143-)  E      N   <->  144 TYR   ( 144-)  E      N      0.01    2.59  INTRA BL
 135 GLN   ( 135-)  E      N   <->  200 CYS   ( 200-)  E      O      0.01    2.69  INTRA BL
   3 GLU   (   3-)  E      N   <->    4 TYR   (   4-)  E      N      0.01    2.59  INTRA B3

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: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

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.

 145 ARG   ( 145-)  E      -8.08
  58 ARG   (  58-)  E      -6.24
 309 TYR   ( 124-)  I      -6.09
  94 TYR   (  94-)  E      -5.91
  77 GLN   (  77-)  E      -5.44
 127 ASN   ( 127-)  E      -5.38
 214 MET   (   7-)  I      -5.36
  61 TYR   (  61-)  E      -5.35
  41 ARG   (  41-)  E      -5.20
  78 TYR   (  78-)  E      -5.12
 287 HIS   ( 104-)  I      -5.10
 288 GLU   ( 105-)  I      -5.05

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.

 287 HIS   ( 104-)  I       290 - LYS    106- ( I)         -4.80

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: E

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: I

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: E

Note: Second generation quality Z-score plot

Chain identifier: I

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.

 314 HOH   ( 341 )  I      O    -10.49   55.17   17.43
 314 HOH   ( 611 )  I      O     -6.42   62.05   23.20

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.

 313 HOH   ( 578 )  E      O

Error: HIS, ASN, GLN side chain flips

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

  92 GLN   (  92-)  E
 135 GLN   ( 135-)  E
 278 HIS   (  96-)  I
 287 HIS   ( 104-)  I

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.

  19 GLN   (  19-)  E      NE2
  25 CCS   (  25-)  E      N
  26 TRP   (  26-)  E      N
  91 VAL   (  91-)  E      N
  97 SER   (  97-)  E      N
 151 GLY   ( 151-)  E      N
 160 ALA   ( 160-)  E      N
 170 TYR   ( 170-)  E      N
 175 ASN   ( 175-)  E      ND2
 177 TRP   ( 177-)  E      NE1
 198 GLY   ( 198-)  E      N
 249 VAL   (  44-)  I      N
 272 GLY   (  67-)  I      N
 273 ASP   (  68-)  I      N
 275 ASP   (  93-)  I      N
 310 PHE   ( 125-)  I      N

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.

  81 HIS   (  81-)  E      NE2
 159 HIS   ( 159-)  E      ND1

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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.

  55 ASP   (  55-)  E   H-bonding suggests Asn
 233 ASP   (  26-)  I   H-bonding suggests Asn; but Alt-Rotamer
 240 GLU   (  33-)  I   H-bonding suggests Gln; but Alt-Rotamer
 306 GLU   ( 121-)  I   H-bonding suggests Gln

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 :  -0.759
  2nd generation packing quality :  -0.054
  Ramachandran plot appearance   :  -1.805
  chi-1/chi-2 rotamer normality  :  -2.663
  Backbone conformation          :  -0.607

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.957
  Bond angles                    :   1.378
  Omega angle restraints         :   1.408 (loose)
  Side chain planarity           :   0.794
  Improper dihedral distribution :   2.252 (loose)
  B-factor distribution          :   1.830 (loose)
  Inside/Outside distribution    :   1.017

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 : 2.37


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.0
  2nd generation packing quality :   0.8
  Ramachandran plot appearance   :  -0.1
  chi-1/chi-2 rotamer normality  :  -0.9
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.957
  Bond angles                    :   1.378
  Omega angle restraints         :   1.408 (loose)
  Side chain planarity           :   0.794
  Improper dihedral distribution :   2.252 (loose)
  B-factor distribution          :   1.830 (loose)
  Inside/Outside distribution    :   1.017
==============

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.