WHAT IF Check report

This file was created 2012-08-12 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 pdb1ctp.ent

Checks that need to be done early-on in validation

Warning: Matthews Coefficient (Vm) high

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 40711.258
Volume of the Unit Cell V= 5043952.0
Space group multiplicity: 24
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 5.162
Vm by authors and this calculated Vm agree reasonably well
Matthews coefficient read from REMARK 280 Vm= 4.910

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.

 352 MYR   (   0-)  E  -

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: 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.

 191 TPO   ( 197-)  E
 336 TYI   (   7-)  I

Warning: Missing atoms

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

   1 LYS   (   7-)  E      CG
   1 LYS   (   7-)  E      CD
   1 LYS   (   7-)  E      CE
   1 LYS   (   7-)  E      NZ
   2 LYS   (   8-)  E      CG
   2 LYS   (   8-)  E      CD
   2 LYS   (   8-)  E      CE
   2 LYS   (   8-)  E      NZ
   5 GLU   (  11-)  E      CG
   5 GLU   (  11-)  E      CD
   5 GLU   (  11-)  E      OE1
   5 GLU   (  11-)  E      OE2
   6 GLN   (  12-)  E      CG
   6 GLN   (  12-)  E      CD
   6 GLN   (  12-)  E      OE1
   6 GLN   (  12-)  E      NE2
   7 GLU   (  13-)  E      CG
   7 GLU   (  13-)  E      CD
   7 GLU   (  13-)  E      OE1
   7 GLU   (  13-)  E      OE2
  10 LYS   (  16-)  E      CG
  10 LYS   (  16-)  E      CD
  10 LYS   (  16-)  E      CE
  10 LYS   (  16-)  E      NZ
  11 GLU   (  17-)  E      CG
And so on for a total of 177 lines.

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. 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 : 2.207 over 2417 bonds
Average difference in B over a bond : 4.35
RMS difference in B over a bond : 6.64

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.

  27 PRO   (  33-)  E      C    O     1.33    4.8
  69 ASP   (  75-)  E      CG   OD2   1.17   -4.1
  80 GLU   (  86-)  E      CD   OE2   1.40    8.1
  81 HIS   (  87-)  E      CG   CD2   1.40    4.4
  85 GLU   (  91-)  E      CD   OE2   1.34    4.7
 106 ASP   ( 112-)  E      CG   OD1   1.36    6.0
 115 GLU   ( 121-)  E      CD   OE1   1.36    5.8
 121 GLU   ( 127-)  E      CD   OE2   1.36    5.9
 134 GLU   ( 140-)  E      CD   OE1   1.33    4.2
 178 ASP   ( 184-)  E      CG   OD1   1.34    4.8
 239 GLN   ( 245-)  E      CD   OE1   1.31    4.1
 254 HIS   ( 260-)  E      CG   CD2   1.31   -4.3
 258 ASP   ( 264-)  E      CG   OD1   1.33    4.2
 270 ASP   ( 276-)  E      CG   OD1   1.35    5.4
 305 GLU   ( 311-)  E      CD   OE1   1.35    5.4
 313 ASP   ( 328-)  E      CG   OD1   1.33    4.1
 317 GLU   ( 332-)  E      CD   OE2   1.33    4.2
 323 SER   ( 338-)  E      C    O     1.32    4.4
 324 GLU   ( 341-)  E      N    CA    1.56    5.4
 332 GLU   ( 349-)  E      CD   OE2   1.39    7.4
 338 ASP   (   9-)  I      CG   OD1   1.36    5.9
 345 THR   (  16-)  I      CB   OG1   1.36   -4.3

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

 |  1.003918  0.000139 -0.000130|
 |  0.000139  1.004619  0.000738|
 | -0.000130  0.000738  1.002203|
Proposed new scale matrix

 |  0.005808  0.000000  0.000000|
 |  0.000000  0.005804 -0.000004|
 |  0.000000 -0.000004  0.005818|
With corresponding cell

    A    = 172.169  B   = 172.289  C    = 171.875
    Alpha=  89.916  Beta=  90.002  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 171.500  B   = 171.500  C    = 171.500
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 148.389
(Under-)estimated Z-score: 8.978

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.

   4 SER   (  10-)  E      N    CA   CB  101.76   -5.1
   5 GLU   (  11-)  E      CA   C    O   127.68    4.0
   6 GLN   (  12-)  E      N    CA   CB  102.66   -4.6
   9 VAL   (  15-)  E     -C    N    CA  109.47   -6.8
   9 VAL   (  15-)  E      CA   CB   CG2  92.68  -10.5
  10 LYS   (  16-)  E      CA   C    O   131.40    6.2
  12 PHE   (  18-)  E      CA   C    O   128.09    4.3
  13 LEU   (  19-)  E      N    CA   CB  102.82   -4.5
  15 LYS   (  21-)  E      C    CA   CB  100.32   -5.1
  17 LYS   (  23-)  E      CA   CB   CG  104.38   -4.9
  19 ASP   (  25-)  E      N    CA   CB  117.64    4.2
  22 LYS   (  28-)  E      N    CA   CB  118.82    4.9
  23 LYS   (  29-)  E      N    CA   CB  100.75   -5.7
  26 ASN   (  32-)  E     -C    N    CA  113.56   -4.5
  26 ASN   (  32-)  E      CA   C    O   129.30    5.0
  26 ASN   (  32-)  E      C    CA   CB  126.12    8.4
  27 PRO   (  33-)  E      N    CA   C   123.74    4.8
  27 PRO   (  33-)  E      N    CA   CB  109.15    5.6
  28 ALA   (  34-)  E     -CA  -C    N   107.49   -4.4
  28 ALA   (  34-)  E      C    CA   CB  122.85    8.2
  29 GLN   (  35-)  E      CB   CG   CD  105.71   -4.1
  29 GLN   (  35-)  E      CG   CD   NE2 108.34   -5.4
  30 ASN   (  36-)  E     -C    N    CA  113.95   -4.3
  30 ASN   (  36-)  E      N    CA   CB  117.81    4.3
  31 THR   (  37-)  E      C    CA   CB  102.09   -4.2
And so on for a total of 296 lines.

Warning: High bond angle deviations

Bond angles were found to deviate more than normal from the mean standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set, and this is indeed observed for very high resolution X-ray structures. The fact that it is higher than 2.0 in this structure might indicate that the restraints used in the refinement were not strong enough. This will also occur if a different bond angle dictionary is used.

RMS Z-score for bond angles: 2.254
RMS-deviation in bond angles: 4.191

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.

   9 VAL   (  15-)  E      CB    -7.8   -43.12   -32.96
  19 ASP   (  25-)  E      CA    -6.2    21.32    33.73
  22 LYS   (  28-)  E      CA    -8.5    19.84    33.92
  27 PRO   (  33-)  E      CA    -8.8    25.72    38.15
  28 ALA   (  34-)  E      CA    -9.7    21.76    34.09
  32 ALA   (  38-)  E      CA     7.9    44.15    34.09
  40 ILE   (  46-)  E      CB     6.2    40.42    32.31
  45 THR   (  51-)  E      CA     6.9    45.40    33.84
  70 LYS   (  76-)  E      CA    -6.1    23.84    33.92
  72 LYS   (  78-)  E      CA    -6.1    23.81    33.92
  73 VAL   (  79-)  E      CA    -9.1    20.01    33.23
  80 GLU   (  86-)  E      CA    -6.7    22.94    33.96
  92 VAL   (  98-)  E      CB    -8.2   -43.65   -32.96
 107 ASN   ( 113-)  E      CA    -7.2    19.87    33.59
 128 ARG   ( 134-)  E      CA    -6.0    24.03    33.91
 135 PRO   ( 141-)  E      N     -6.4   -23.55    -2.48
 135 PRO   ( 141-)  E      CA    -6.9    28.46    38.15
 174 ILE   ( 180-)  E      CA    -7.8    21.50    33.24
 201 PRO   ( 207-)  E      N      7.6    22.57    -2.48
 201 PRO   ( 207-)  E      CA    -6.3    29.22    38.15
 207 LYS   ( 213-)  E      CA     7.7    46.68    33.92
 212 ALA   ( 218-)  E      CA    -8.6    23.18    34.09
 213 VAL   ( 219-)  E      CB     9.1   -21.02   -32.96
 237 PRO   ( 243-)  E      N      6.1    17.42    -2.48
 256 SER   ( 262-)  E      CA     8.2    49.64    34.32
 264 ARG   ( 270-)  E      CA    -9.4    18.48    33.91
 271 LEU   ( 277-)  E      CA     8.3    46.82    34.19
 282 VAL   ( 288-)  E      CB   -10.8   -47.17   -32.96
 293 THR   ( 299-)  E      CA     6.7    45.07    33.84
 297 ILE   ( 303-)  E      CB     8.2    42.91    32.31
 304 VAL   ( 310-)  E      CA     6.4    42.57    33.23
 312 PHE   ( 327-)  E      CA    -8.1    21.05    33.98
 316 GLU   ( 331-)  E      CA     6.6    44.76    33.96
 325 LYS   ( 342-)  E      CA   -11.5    14.80    33.92
 334 THR   (   5-)  I      CA     7.4    46.16    33.84
 335 THR   (   6-)  I      CA    12.4    54.51    33.84
 344 ARG   (  15-)  I      CA    -6.8    22.83    33.91
 351 ILE   (  22-)  I      CB     8.6    43.50    32.31
The average deviation= 3.149

Error: High improper dihedral angle deviations

The RMS Z-score for the improper dihedrals in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 2.5 worries us. 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 : 2.670

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

 257 SER   ( 263-)  E   11.83
 256 SER   ( 262-)  E    6.87
 312 PHE   ( 327-)  E    4.44
 206 SER   ( 212-)  E    4.44
 108 SER   ( 114-)  E    4.44
  87 ARG   (  93-)  E    4.41
  52 MET   (  58-)  E    4.38
 186 LYS   ( 192-)  E    4.35
 235 ASP   ( 241-)  E    4.33
 239 GLN   ( 245-)  E    4.32
  27 PRO   (  33-)  E    4.26
 197 GLU   ( 203-)  E    4.15
   8 SER   (  14-)  E    4.10
 320 ILE   ( 335-)  E    4.05
 317 GLU   ( 332-)  E    4.02
 344 ARG   (  15-)  I    4.02

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 2.025

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

  61 ASN   (  67-)  E    5.87
 349 ASN   (  20-)  I    5.19
  56 HIS   (  62-)  E    4.82
 107 ASN   ( 113-)  E    4.39
 329 GLU   ( 346-)  E    4.35
 155 ASP   ( 161-)  E    4.33
 209 TYR   ( 215-)  E    4.16

Torsion-related checks

Warning: Ramachandran Z-score low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is a bit low.

Ramachandran Z-score : -3.892

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.

  59 THR   (  65-)  E    -2.9
  57 LYS   (  63-)  E    -2.9
 159 ARG   ( 165-)  E    -2.8
  34 LEU   (  40-)  E    -2.8
 340 ILE   (  11-)  I    -2.6
 196 PRO   ( 202-)  E    -2.6
 206 SER   ( 212-)  E    -2.6
 237 PRO   ( 243-)  E    -2.5
 174 ILE   ( 180-)  E    -2.5
 204 ILE   ( 210-)  E    -2.4
 344 ARG   (  15-)  I    -2.3
 154 LEU   ( 160-)  E    -2.3
 201 PRO   ( 207-)  E    -2.3
 281 GLY   ( 287-)  E    -2.3
  70 LYS   (  76-)  E    -2.3
 105 LYS   ( 111-)  E    -2.3
 205 LEU   ( 211-)  E    -2.2
  76 LEU   (  82-)  E    -2.2
 293 THR   ( 299-)  E    -2.2
 256 SER   ( 262-)  E    -2.1
  66 LYS   (  72-)  E    -2.1
 171 GLN   ( 177-)  E    -2.0
  92 VAL   (  98-)  E    -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.

   2 LYS   (   8-)  E  Poor phi/psi
  27 PRO   (  33-)  E  Poor phi/psi
  29 GLN   (  35-)  E  Poor phi/psi
  32 ALA   (  38-)  E  Poor phi/psi
  34 LEU   (  40-)  E  Poor phi/psi
  35 ASP   (  41-)  E  Poor phi/psi
  45 THR   (  51-)  E  Poor phi/psi
  48 PHE   (  54-)  E  Poor phi/psi
  59 THR   (  65-)  E  Poor phi/psi
 178 ASP   ( 184-)  E  Poor phi/psi
 181 PHE   ( 187-)  E  Poor phi/psi
 234 ALA   ( 240-)  E  Poor phi/psi
 236 GLN   ( 242-)  E  Poor phi/psi
 280 ASN   ( 286-)  E  Poor phi/psi
 281 GLY   ( 287-)  E  Poor phi/psi
 314 ASP   ( 329-)  E  Poor phi/psi
 317 GLU   ( 332-)  E  Poor phi/psi
 318 GLU   ( 333-)  E  Poor phi/psi
 322 VAL   ( 337-)  E  Poor phi/psi
 325 LYS   ( 342-)  E  Poor phi/psi
 326 CYS   ( 343-)  E  Poor phi/psi
 335 THR   (   6-)  I  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -5.704

Error: chi-1/chi-2 angle correlation Z-score very low

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

chi-1/chi-2 correlation Z-score : -5.704

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!

  26 ASN   (  32-)  E      0
  27 PRO   (  33-)  E      0
  29 GLN   (  35-)  E      0
  30 ASN   (  36-)  E      0
  31 THR   (  37-)  E      0
  33 HIS   (  39-)  E      0
  36 GLN   (  42-)  E      0
  39 ARG   (  45-)  E      0
  40 ILE   (  46-)  E      0
  42 THR   (  48-)  E      0
  45 THR   (  51-)  E      0
  47 SER   (  53-)  E      0
  48 PHE   (  54-)  E      0
  50 ARG   (  56-)  E      0
  56 HIS   (  62-)  E      0
  58 GLU   (  64-)  E      0
  59 THR   (  65-)  E      0
  77 LYS   (  83-)  E      0
  78 GLN   (  84-)  E      0
  92 VAL   (  98-)  E      0
  93 ASN   (  99-)  E      0
 101 GLU   ( 107-)  E      0
 103 SER   ( 109-)  E      0
 108 SER   ( 114-)  E      0
 109 ASN   ( 115-)  E      0
And so on for a total of 142 lines.

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 180 GLY   ( 186-)  E   1.77   16
 340 ILE   (  11-)  I   1.56   13

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]

  95 PRO   ( 101-)  E    0.03 LOW
 135 PRO   ( 141-)  E    0.08 LOW
 310 PRO   ( 316-)  E    0.12 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].

 118 PRO   ( 124-)  E    18.9 half-chair N/C-delta (18 degrees)
 196 PRO   ( 202-)  E   113.0 envelop C-beta (108 degrees)
 201 PRO   ( 207-)  E    -5.2 envelop N (0 degrees)
 231 PRO   ( 237-)  E    -2.8 envelop N (0 degrees)
 252 PRO   ( 258-)  E    52.6 half-chair C-delta/C-gamma (54 degrees)
 307 PRO   ( 313-)  E  -118.3 half-chair C-delta/C-gamma (-126 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.

   9 VAL   (  15-)  E      CG2 <->   10 LYS   (  16-)  E      N      0.70    2.30  INTRA
 216 TRP   ( 222-)  E      NE1 <->  353 HOH   ( 402 )  E      O      0.70    2.00  INTRA
 188 ARG   ( 194-)  E      NH2 <->  207 LYS   ( 213-)  E      O      0.54    2.16  INTRA
 197 GLU   ( 203-)  E      OE2 <->  344 ARG   (  15-)  I      NH2    0.50    2.20  INTRA BL
 134 GLU   ( 140-)  E      OE2 <->  256 SER   ( 262-)  E      OG     0.45    1.95  INTRA
  34 LEU   (  40-)  E      O   <->   36 GLN   (  42-)  E      N      0.42    2.28  INTRA
 270 ASP   ( 276-)  E      O   <->  273 LYS   ( 279-)  E      N      0.40    2.30  INTRA
 335 THR   (   6-)  I      CG2 <->  336 TYI   (   7-)  I      N      0.38    2.62  INTRA
  78 GLN   (  84-)  E      NE2 <->   81 HIS   (  87-)  E      CD2    0.37    2.73  INTRA BF
 191 TPO   ( 197-)  E      CG2 <->  192 LEU   ( 198-)  E      N      0.37    2.63  INTRA BL
  87 ARG   (  93-)  E      O   <->   90 GLN   (  96-)  E      NE2    0.36    2.34  INTRA
 106 ASP   ( 112-)  E      OD1 <->  108 SER   ( 114-)  E      N      0.36    2.34  INTRA
  59 THR   (  65-)  E      CG2 <->   61 ASN   (  67-)  E      N      0.35    2.75  INTRA
   1 LYS   (   7-)  E      O   <->    4 SER   (  10-)  E      N      0.34    2.36  INTRA
   1 LYS   (   7-)  E      O   <->    2 LYS   (   8-)  E      C      0.33    2.27  INTRA
 224 GLU   ( 230-)  E      CD  <->  348 ARG   (  19-)  I      NH2    0.32    2.78  INTRA BL
  29 GLN   (  35-)  E      NE2 <->  333 PHE   ( 350-)  E      C      0.32    2.78  INTRA
  97 LEU   ( 103-)  E      O   <->   98 VAL   ( 104-)  E      C      0.30    2.30  INTRA BL
 136 HIS   ( 142-)  E      NE2 <->  140 TYR   ( 146-)  E      CE2    0.30    2.80  INTRA
  24 TRP   (  30-)  E      O   <->   87 ARG   (  93-)  E      NH2    0.29    2.41  INTRA
 158 TYR   ( 164-)  E      O   <->  159 ARG   ( 165-)  E      CA     0.29    2.11  INTRA B3
  94 PHE   ( 100-)  E      CG  <->   95 PRO   ( 101-)  E      CD     0.29    2.91  INTRA
 224 GLU   ( 230-)  E      OE1 <->  348 ARG   (  19-)  I      NH2    0.28    2.42  INTRA BL
 270 ASP   ( 276-)  E      O   <->  272 THR   ( 278-)  E      N      0.27    2.43  INTRA
  95 PRO   ( 101-)  E      CG  <->  300 TYR   ( 306-)  E      CE1    0.27    2.93  INTRA BL
And so on for a total of 209 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: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

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

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.

 250 ARG   ( 256-)  E   -3.62
 186 LYS   ( 192-)  E   -3.38
 207 LYS   ( 213-)  E   -3.19
 325 LYS   ( 342-)  E   -3.12
 248 LYS   ( 254-)  E   -2.53
 211 LYS   ( 217-)  E   -2.52
 279 LYS   ( 285-)  E   -2.50

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.

 317 GLU   ( 332-)  E     -  321 ARG   ( 336-)  E        -1.89

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

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.

  62 HIS   (  68-)  E
 265 ASN   ( 271-)  E
 277 ASN   ( 283-)  E

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.

  28 ALA   (  34-)  E      N
  32 ALA   (  38-)  E      N
  33 HIS   (  39-)  E      N
  61 ASN   (  67-)  E      N
  90 GLN   (  96-)  E      NE2
  96 PHE   ( 102-)  E      N
 103 SER   ( 109-)  E      N
 103 SER   ( 109-)  E      OG
 123 PHE   ( 129-)  E      N
 124 SER   ( 130-)  E      N
 127 ARG   ( 133-)  E      NE
 127 ARG   ( 133-)  E      NH1
 127 ARG   ( 133-)  E      NH2
 128 ARG   ( 134-)  E      NH1
 143 GLN   ( 149-)  E      NE2
 159 ARG   ( 165-)  E      NH1
 160 ASP   ( 166-)  E      N
 188 ARG   ( 194-)  E      NH2
 193 CYS   ( 199-)  E      N
 194 GLY   ( 200-)  E      N
 197 GLU   ( 203-)  E      N
 216 TRP   ( 222-)  E      NE1
 229 TYR   ( 235-)  E      N
 232 PHE   ( 238-)  E      N
 248 LYS   ( 254-)  E      N
 256 SER   ( 262-)  E      N
 259 LEU   ( 265-)  E      N
 268 GLN   ( 274-)  E      N
 276 GLY   ( 282-)  E      N
 278 LEU   ( 284-)  E      N
 302 ARG   ( 308-)  E      NH1
 335 THR   (   6-)  I      N
 341 ALA   (  12-)  I      N
 348 ARG   (  19-)  I      NE

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.

 152 HIS   ( 158-)  E      NE2
 197 GLU   ( 203-)  E      OE2
 284 ASP   ( 290-)  E      OD2

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.

 214 ASP   ( 220-)  E   H-bonding suggests Asn

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:

  2nd generation packing quality :  -2.903
  Ramachandran plot appearance   :  -3.892 (poor)
  chi-1/chi-2 rotamer normality  :  -5.704 (bad)
  Backbone conformation          :  -0.193

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.191
  Bond angles                    :   2.254 (loose)
  Omega angle restraints         :   0.738
  Side chain planarity           :   1.868
  Improper dihedral distribution :   2.670 (loose)
  B-factor distribution          :   2.207 (loose)
  Inside/Outside distribution    :   1.034

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 : 2.90


Structure Z-scores, positive is better than average:

  2nd generation packing quality :  -1.0
  Ramachandran plot appearance   :  -1.4
  chi-1/chi-2 rotamer normality  :  -3.2 (poor)
  Backbone conformation          :   0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.191
  Bond angles                    :   2.254 (loose)
  Omega angle restraints         :   0.738
  Side chain planarity           :   1.868
  Improper dihedral distribution :   2.670 (loose)
  B-factor distribution          :   2.207 (loose)
  Inside/Outside distribution    :   1.034
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    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.