WHAT IF Check report

This file was created 2012-01-19 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 pdb2cjw.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.

 358 GDP   ( 999-)  A  -
 361 GDP   ( 999-)  B  -

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.

  28 ASP   ( 100-)  A  -   CG
  28 ASP   ( 100-)  A  -   OD1
  28 ASP   ( 100-)  A  -   OD2
  29 SER   ( 101-)  A  -   OG
  31 GLU   ( 107-)  A  -   CB
  31 GLU   ( 107-)  A  -   CG
  31 GLU   ( 107-)  A  -   CD
  31 GLU   ( 107-)  A  -   OE1
  31 GLU   ( 107-)  A  -   OE2
  59 ASN   ( 135-)  A  -   CG
  59 ASN   ( 135-)  A  -   OD1
  59 ASN   ( 135-)  A  -   ND2
 100 GLN   ( 180-)  A  -   CG
 100 GLN   ( 180-)  A  -   CD
 100 GLN   ( 180-)  A  -   OE1
 100 GLN   ( 180-)  A  -   NE2
 117 ARG   ( 197-)  A  -   CG
 117 ARG   ( 197-)  A  -   CD
 117 ARG   ( 197-)  A  -   NE
 117 ARG   ( 197-)  A  -   CZ
 117 ARG   ( 197-)  A  -   NH1
 117 ARG   ( 197-)  A  -   NH2
 166 LYS   ( 246-)  A  -   CG
 166 LYS   ( 246-)  A  -   CD
 166 LYS   ( 246-)  A  -   CE
And so on for a total of 88 lines.

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: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

  30 CAS   ( 106-)  A
 118 CAS   ( 198-)  A
 129 CAS   ( 209-)  A
 135 CAS   ( 215-)  A
 236 CAS   ( 146-)  B
 288 CAS   ( 198-)  B
 299 CAS   ( 209-)  B

Warning: Unexpected atoms encountered

While reading the PDB file, at least one atom was encountered that was not expected in the residue. This might be caused by a naming convention problem. It can also mean that a residue was found protonated that normally is not (e.g. aspartic acid). The unexpected atoms have been discarded; in case protons were deleted that actually might be needed, they will later be put back by the hydrogen bond validation software. This normally is not a warning you should worry too much about.

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'.

  28 ASP   ( 100-)  A      CB
  29 SER   ( 101-)  A      CB
  59 ASN   ( 135-)  A      CB
 100 GLN   ( 180-)  A      CB
 166 LYS   ( 246-)  A      CB
 167 GLU   ( 247-)  A      CB
 170 GLU   ( 250-)  A      CB
 177 LYS   ( 257-)  A      CB
 178 ARG   ( 258-)  A      CB
 233 HIS   ( 143-)  B      CB
 287 ARG   ( 197-)  B      CG
 338 LYS   ( 248-)  B      CG

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.

  30 CAS   ( 106-)  A    0.25
  58 GLU   ( 134-)  A    0.50
 118 CAS   ( 198-)  A    0.75
 129 CAS   ( 209-)  A    0.90
 135 CAS   ( 215-)  A    0.75
 236 CAS   ( 146-)  B    0.70
 288 CAS   ( 198-)  B    0.25
 299 CAS   ( 209-)  B    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: 0

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.

  40 ARG   ( 116-)  A
 117 ARG   ( 197-)  A
 127 ARG   ( 207-)  A
 157 ARG   ( 237-)  A
 162 ARG   ( 242-)  A
 172 ARG   ( 252-)  A
 213 ARG   ( 116-)  B
 252 ARG   ( 162-)  B
 262 ARG   ( 172-)  B
 266 ARG   ( 176-)  B
 327 ARG   ( 237-)  B
 342 ARG   ( 252-)  B
 348 ARG   ( 258-)  B

Warning: Tyrosine convention problem

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

   3 TYR   (  75-)  A
  38 TYR   ( 114-)  A
 175 TYR   ( 255-)  A
 184 TYR   (  75-)  B
 247 TYR   ( 157-)  B
 345 TYR   ( 255-)  B

Warning: Phenylalanine convention problem

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

  85 PHE   ( 165-)  A
 133 PHE   ( 213-)  A
 180 PHE   (  71-)  B
 255 PHE   ( 165-)  B
 307 PHE   ( 217-)  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.

  45 ASP   ( 121-)  A
 103 ASP   ( 183-)  A
 134 ASP   ( 214-)  A
 209 ASP   ( 112-)  B
 251 ASP   ( 161-)  B
 273 ASP   ( 183-)  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.

  35 GLU   ( 111-)  A
  39 GLU   ( 115-)  A
  60 GLU   ( 140-)  A
  86 GLU   ( 166-)  A
 102 GLU   ( 182-)  A
 153 GLU   ( 233-)  A
 192 GLU   (  83-)  B
 212 GLU   ( 115-)  B
 220 GLU   ( 123-)  B
 295 GLU   ( 205-)  B
 320 GLU   ( 230-)  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

 |  0.997009  0.000789  0.000169|
 |  0.000789  0.997105  0.000142|
 |  0.000169  0.000142  0.994599|
Proposed new scale matrix

 |  0.008597  0.004959 -0.000002|
 | -0.000008  0.009931 -0.000001|
 | -0.000002 -0.000002  0.012351|
With corresponding cell

    A    = 116.269  B   = 116.194  C    =  80.967
    Alpha=  89.996  Beta=  89.981  Gamma= 119.931

The CRYST1 cell dimensions

    A    = 116.617  B   = 116.617  C    =  81.409
    Alpha=  90.000  Beta=  90.000  Gamma= 120.000

Variance: 165.483
(Under-)estimated Z-score: 9.481

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.

  31 GLU   ( 107-)  A      N    CA   CB   97.54   -7.6
 232 ASN   ( 135-)  B      N    CA   CB  120.57    5.9
 232 ASN   ( 135-)  B      CA   CB   CG  102.18  -10.4
 267 ARG   ( 177-)  B      CA   CB   CG  125.96    5.9
 350 GLU   ( 260-)  B      C    CA   CB   92.38   -9.3
 350 GLU   ( 260-)  B      CA   CB   CG  100.71   -6.7

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.

  35 GLU   ( 111-)  A
  39 GLU   ( 115-)  A
  40 ARG   ( 116-)  A
  45 ASP   ( 121-)  A
  60 GLU   ( 140-)  A
  86 GLU   ( 166-)  A
 102 GLU   ( 182-)  A
 103 ASP   ( 183-)  A
 117 ARG   ( 197-)  A
 127 ARG   ( 207-)  A
 134 ASP   ( 214-)  A
 153 GLU   ( 233-)  A
 157 ARG   ( 237-)  A
 162 ARG   ( 242-)  A
 172 ARG   ( 252-)  A
 192 GLU   (  83-)  B
 209 ASP   ( 112-)  B
 212 GLU   ( 115-)  B
 213 ARG   ( 116-)  B
 220 GLU   ( 123-)  B
 251 ASP   ( 161-)  B
 252 ARG   ( 162-)  B
 262 ARG   ( 172-)  B
 266 ARG   ( 176-)  B
 273 ASP   ( 183-)  B
 295 GLU   ( 205-)  B
 320 GLU   ( 230-)  B
 327 ARG   ( 237-)  B
 342 ARG   ( 252-)  B
 348 ARG   ( 258-)  B

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.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

  31 GLU   ( 107-)  A      CA     6.7    44.97    33.96
 232 ASN   ( 135-)  B      CA    -6.3    21.68    33.59
 350 GLU   ( 260-)  B      CA     8.8    48.46    33.96
The average deviation= 0.689

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.

 215 LEU   ( 118-)  B    -2.4
 271 THR   ( 181-)  B    -2.1
 186 ARG   (  77-)  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.

  15 GLY   (  87-)  A  Poor phi/psi
 112 LYS   ( 192-)  A  Poor phi/psi
 134 ASP   ( 214-)  A  Poor phi/psi
 147 ASN   ( 227-)  A  Poor phi/psi
 163 ARG   ( 243-)  A  omega poor
 196 GLY   (  87-)  B  Poor phi/psi
 282 LYS   ( 192-)  B  Poor phi/psi
 304 ASP   ( 214-)  B  Poor phi/psi
 310 THR   ( 220-)  B  omega poor
 317 ASN   ( 227-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -1.196

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.

  17 SER   (  89-)  A    0.36
 259 SER   ( 169-)  B    0.39

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!

   9 ILE   (  81-)  A      0
  11 GLU   (  83-)  A      0
  12 GLN   (  84-)  A      0
  14 VAL   (  86-)  A      0
  26 VAL   (  98-)  A      0
  28 ASP   ( 100-)  A      0
  29 SER   ( 101-)  A      0
  30 CAS   ( 106-)  A      0
  31 GLU   ( 107-)  A      0
  33 LEU   ( 109-)  A      0
  37 THR   ( 113-)  A      0
  44 VAL   ( 120-)  A      0
  55 ASP   ( 131-)  A      0
  56 MET   ( 132-)  A      0
  57 TRP   ( 133-)  A      0
  58 GLU   ( 134-)  A      0
  59 ASN   ( 135-)  A      0
  60 GLU   ( 140-)  A      0
  61 TRP   ( 141-)  A      0
  68 GLN   ( 148-)  A      0
  99 ARG   ( 179-)  A      0
 111 ASN   ( 191-)  A      0
 112 LYS   ( 192-)  A      0
 115 LEU   ( 195-)  A      0
 116 VAL   ( 196-)  A      0
And so on for a total of 120 lines.

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.

 118 CAS   ( 198-)  A     AS   <->  353 CAS   ( 198-)  A      CE2    1.22    1.98  INTRA
 236 CAS   ( 146-)  B     AS   <->  357 CAS   ( 146-)  B      CE2    1.21    1.99  INTRA BF
 129 CAS   ( 209-)  A     AS   <->  355 CAS   ( 209-)  A      CE2    1.21    1.99  INTRA BL
 118 CAS   ( 198-)  A     AS   <->  352 CAS   ( 198-)  A      CE1    1.21    1.99  INTRA
 236 CAS   ( 146-)  B     AS   <->  356 CAS   ( 146-)  B      CE1    1.21    1.99  INTRA BF
 129 CAS   ( 209-)  A     AS   <->  354 CAS   ( 209-)  A      CE1    1.21    1.99  INTRA BL
  96 ARG   ( 176-)  A      NH2 <->  133 PHE   ( 213-)  A      O      0.37    2.33  INTRA
 117 ARG   ( 197-)  A      CD  <->  207 VAL   (  98-)  B      CG2    0.21    2.99  INTRA
 167 GLU   ( 247-)  A      CG  <->  171 ARG   ( 251-)  A      CZ     0.16    3.04  INTRA BF
 164 ASP   ( 244-)  A      OD2 <->  172 ARG   ( 252-)  A      NH1    0.12    2.58  INTRA BF
 312 ALA   ( 222-)  B      N   <->  361 GDP   ( 999-)  B      O6     0.09    2.61  INTRA
   5 ARG   (  77-)  A    A NH2 <->  362 HOH   (2005 )  A      O      0.09    2.61  INTRA
 262 ARG   ( 172-)  B      NH1 <->  276 ILE   ( 186-)  B      CD1    0.09    3.01  INTRA
 129 CAS   ( 209-)  A      SG  <->  355 CAS   ( 209-)  A      CE2    0.09    3.31  INTRA BL
 217 VAL   ( 120-)  B      CG2 <->  330 ARG   ( 240-)  B      NH1    0.08    3.02  INTRA BL
 167 GLU   ( 247-)  A      CG  <->  171 ARG   ( 251-)  A      NH1    0.07    3.03  INTRA BF
 167 GLU   ( 247-)  A      OE2 <->  171 ARG   ( 251-)  A      NH2    0.07    2.63  INTRA BF
 284 ASP   ( 194-)  B      OD1 <->  361 GDP   ( 999-)  B      N1     0.07    2.63  INTRA
 252 ARG   ( 162-)  B      NH1 <->  295 GLU   ( 205-)  B      OE2    0.06    2.64  INTRA BF
 334 ASP   ( 244-)  B      OD2 <->  342 ARG   ( 252-)  B      NH1    0.06    2.64  INTRA BF
  38 TYR   ( 114-)  A      O   <->   53 LEU   ( 129-)  A      N      0.06    2.64  INTRA BL
 197 LYS   (  88-)  B      NZ  <->  361 GDP   ( 999-)  B      O3B    0.06    2.64  INTRA BL
 284 ASP   ( 194-)  B      OD2 <->  361 GDP   ( 999-)  B      N2     0.04    2.66  INTRA
  42 LEU   ( 118-)  A      O   <->   49 ALA   ( 125-)  A      N      0.02    2.68  INTRA
  79 ILE   ( 159-)  A      O   <->  120 GLU   ( 200-)  A      N      0.02    2.68  INTRA BL
 198 SER   (  89-)  B      O   <->  202 ASN   (  93-)  B      ND2    0.02    2.68  INTRA
 144 VAL   ( 224-)  A      N   <->  145 GLN   ( 225-)  A      N      0.02    2.58  INTRA BL
 299 CAS   ( 209-)  B      O   <->  303 PHE   ( 213-)  B      N      0.02    2.68  INTRA BL
 111 ASN   ( 191-)  A      CG  <->  112 LYS   ( 192-)  A      N      0.01    2.99  INTRA BL

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.

  12 GLN   (  84-)  A      -5.99
 193 GLN   (  84-)  B      -5.88
 176 GLN   ( 256-)  A      -5.70
 333 ARG   ( 243-)  B      -5.57
 163 ARG   ( 243-)  A      -5.52
  58 GLU   ( 134-)  A      -5.49
 133 PHE   ( 213-)  A      -5.46
  68 GLN   ( 148-)  A      -5.44
 238 GLN   ( 148-)  B      -5.41
 231 GLU   ( 134-)  B      -5.36
 350 GLU   ( 260-)  B      -5.09

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.

 133 PHE   ( 213-)  A   -2.70

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

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.

 363 HOH   (2033 )  B      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.

  65 HIS   ( 145-)  A
 346 GLN   ( 256-)  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.

  10 GLY   (  82-)  A      N
  13 GLY   (  85-)  A      N
  15 GLY   (  87-)  A      N
  16 LYS   (  88-)  A      N
  17 SER   (  89-)  A      N
  63 HIS   ( 143-)  A      N
  69 VAL   ( 149-)  A      N
  78 SER   ( 158-)  A      OG
 101 THR   ( 181-)  A      N
 111 ASN   ( 191-)  A      ND2
 191 GLY   (  82-)  B      N
 196 GLY   (  87-)  B      N
 197 LYS   (  88-)  B      N
 198 SER   (  89-)  B      N
 211 TYR   ( 114-)  B      OH
 236 CAS   ( 146-)  B      N
 248 SER   ( 158-)  B      OG
 281 ASN   ( 191-)  B      ND2
 313 ALA   ( 223-)  B      N
 339 ASN   ( 249-)  B      ND2
 348 ARG   ( 258-)  B      NE

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

 362 HOH   (2034 )  A      O  0.85  K  4
 363 HOH   (2015 )  B      O  0.91  K  5

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.

  64 ASP   ( 144-)  A   H-bonding suggests Asn
 120 GLU   ( 200-)  A   H-bonding suggests Gln
 284 ASP   ( 194-)  B   H-bonding suggests Asn; 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 :   0.531
  2nd generation packing quality :   0.041
  Ramachandran plot appearance   :  -0.282
  chi-1/chi-2 rotamer normality  :  -1.196
  Backbone conformation          :   0.595

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.463 (tight)
  Bond angles                    :   0.671
  Omega angle restraints         :   0.997
  Side chain planarity           :   0.350 (tight)
  Improper dihedral distribution :   0.739
  B-factor distribution          :   0.670
  Inside/Outside distribution    :   1.022

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 : 2.10


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.0
  2nd generation packing quality :   0.2
  Ramachandran plot appearance   :   0.5
  chi-1/chi-2 rotamer normality  :  -0.2
  Backbone conformation          :   0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.463 (tight)
  Bond angles                    :   0.671
  Omega angle restraints         :   0.997
  Side chain planarity           :   0.350 (tight)
  Improper dihedral distribution :   0.739
  B-factor distribution          :   0.670
  Inside/Outside distribution    :   1.022
==============

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DSSP
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Hydrogen bond networks
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Matthews' Coefficient
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Protein side chain planarity
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Puckering parameters
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Quality Control
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    J. Appl. Cryst. 26, 47--60 (1993).

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

Ion Checks
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      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

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

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

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