WHAT IF Check report

This file was created 2011-12-21 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 pdb1ag8.ent

Checks that need to be done early-on in validation

Warning: Unconventional orthorhombic cell

The primitive P 2 2 2 or P 21 21 21 cell specified does not conform to the convention that the axes should be given in order of increasing length.

The CRYST1 cell dimensions

    A    = 122.600  B   = 198.400  C    =  91.600
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Warning: Conventional cell

The conventional cell as mentioned earlier has been derived.

The CRYST1 cell dimensions

    A    = 122.600  B   = 198.400  C    =  91.600
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    =  91.600  B   = 122.600  C    = 198.400
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    =  91.600  B   = 122.600  C    = 198.400
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

 |  0.000000  0.000000 -1.000000|
 | -1.000000  0.000000  0.000000|
 |  0.000000  1.000000  0.000000|

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.422
CA-only RMS fit for the two chains : 0.065

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.446
CA-only RMS fit for the two chains : 0.104

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.474
CA-only RMS fit for the two chains : 0.086

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and C

All-atom RMS fit for the two chains : 0.431
CA-only RMS fit for the two chains : 0.090

Note: Non crystallographic symmetry RMS plot

The plot shows the RMS differences between two similar chains on a residue- by-residue basis. Individual "spikes" can be indicative of interesting or wrong residues. If all residues show a high RMS value, the structure could be incorrectly refined.

Chain identifiers of the two chains: B and D

All-atom RMS fit for the two chains : 0.473
CA-only RMS fit for the two chains : 0.076

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

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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:

Crystal temperature (K) :113.000

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 16.55

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

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Geometric checks

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.

 136 THR   ( 143-)  A      N    CA   C    99.02   -4.3
 183 VAL   ( 190-)  A      N    CA   C    98.36   -4.6
 244 HIS   ( 251-)  A      CG   ND1  CE1 109.76    4.2
 261 GLU   ( 268-)  A      N    CA   C    99.59   -4.1
 629 THR   ( 143-)  B      N    CA   C    98.89   -4.4
 676 VAL   ( 190-)  B      N    CA   C    99.53   -4.2
 962 GLU   ( 476-)  B      N    CA   C   122.52    4.0
1169 VAL   ( 190-)  C      N    CA   C    99.81   -4.1
1247 GLU   ( 268-)  C      N    CA   C    99.96   -4.0
1455 GLU   ( 476-)  C      N    CA   C   123.08    4.2
1662 VAL   ( 190-)  D      N    CA   C    99.02   -4.4
1723 HIS   ( 251-)  D      CG   ND1  CE1 109.61    4.0
1740 GLU   ( 268-)  D      N    CA   C    99.99   -4.0

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.

 192 LEU   ( 199-)  A    5.49
 685 LEU   ( 199-)  B    5.22
1178 LEU   ( 199-)  C    5.00
1671 LEU   ( 199-)  D    4.94
 183 VAL   ( 190-)  A    4.72
 629 THR   ( 143-)  B    4.45
1662 VAL   ( 190-)  D    4.43
 136 THR   ( 143-)  A    4.40
1168 VAL   ( 189-)  C    4.39
 675 VAL   ( 189-)  B    4.38
1063 ARG   (  84-)  C    4.37
 261 GLU   ( 268-)  A    4.25
1120 GLY   ( 141-)  C    4.20
 676 VAL   ( 190-)  B    4.19
1247 GLU   ( 268-)  C    4.08
1740 GLU   ( 268-)  D    4.07
1169 VAL   ( 190-)  C    4.06
1613 GLY   ( 141-)  D    4.04
1556 ARG   (  84-)  D    4.01

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.

1176 THR   ( 197-)  C    -3.3
1873 PHE   ( 401-)  D    -3.3
1669 THR   ( 197-)  D    -3.2
1380 PHE   ( 401-)  C    -3.2
 190 THR   ( 197-)  A    -3.1
 683 THR   ( 197-)  B    -3.1
 394 PHE   ( 401-)  A    -3.0
 887 PHE   ( 401-)  B    -3.0
 748 LEU   ( 262-)  B    -2.8
1611 TYR   ( 139-)  D    -2.7
1241 LEU   ( 262-)  C    -2.7
 132 TYR   ( 139-)  A    -2.6
1150 PRO   ( 171-)  C    -2.6
 863 ARG   ( 377-)  B    -2.6
 164 PRO   ( 171-)  A    -2.6
1940 TYR   ( 468-)  D    -2.5
1741 ILE   ( 269-)  D    -2.5
 625 TYR   ( 139-)  B    -2.5
 461 TYR   ( 468-)  A    -2.5
1643 PRO   ( 171-)  D    -2.5
 160 PRO   ( 167-)  A    -2.5
1322 PRO   ( 343-)  C    -2.5
 336 PRO   ( 343-)  A    -2.4
 829 PRO   ( 343-)  B    -2.4
1146 PRO   ( 167-)  C    -2.4
And so on for a total of 64 lines.

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.

  17 ILE   (  24-)  A  Poor phi/psi
  18 ASN   (  25-)  A  Poor phi/psi
  19 ASN   (  26-)  A  Poor phi/psi
  27 LYS   (  34-)  A  Poor phi/psi
  42 CYS   (  49-)  A  Poor phi/psi
 138 PRO   ( 145-)  A  Poor phi/psi
 205 GLY   ( 212-)  A  Poor phi/psi
 220 THR   ( 227-)  A  Poor phi/psi
 253 SER   ( 260-)  A  Poor phi/psi
 255 LEU   ( 262-)  A  Poor phi/psi
 262 ILE   ( 269-)  A  Poor phi/psi
 291 GLN   ( 298-)  A  Poor phi/psi
 363 GLY   ( 370-)  A  Poor phi/psi
 381 ASP   ( 388-)  A  Poor phi/psi
 394 PHE   ( 401-)  A  Poor phi/psi
 396 PRO   ( 403-)  A  Poor phi/psi
 415 ASN   ( 422-)  A  Poor phi/psi
 447 ASN   ( 454-)  A  Poor phi/psi
 448 CYS   ( 455-)  A  Poor phi/psi
 450 ASP   ( 457-)  A  Poor phi/psi
 462 LYS   ( 469-)  A  Poor phi/psi
 510 ILE   (  24-)  B  Poor phi/psi
 511 ASN   (  25-)  B  Poor phi/psi
 512 ASN   (  26-)  B  Poor phi/psi
 520 LYS   (  34-)  B  Poor phi/psi
And so on for a total of 73 lines.

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.

1096 SER   ( 117-)  C    0.33
1589 SER   ( 117-)  D    0.36
 110 SER   ( 117-)  A    0.37
 436 SER   ( 443-)  A    0.37
1422 SER   ( 443-)  C    0.38
 929 SER   ( 443-)  B    0.38
1915 SER   ( 443-)  D    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 THR   (  10-)  A      0
   7 GLN   (  14-)  A      0
  11 LEU   (  18-)  A      0
  13 ASN   (  20-)  A      0
  16 PHE   (  23-)  A      0
  17 ILE   (  24-)  A      0
  18 ASN   (  25-)  A      0
  19 ASN   (  26-)  A      0
  21 TRP   (  28-)  A      0
  22 HIS   (  29-)  A      0
  26 SER   (  33-)  A      0
  30 PHE   (  37-)  A      0
  41 ILE   (  48-)  A      0
  42 CYS   (  49-)  A      0
  43 HIS   (  50-)  A      0
  64 GLN   (  71-)  A      0
  65 LEU   (  72-)  A      0
 102 ASP   ( 109-)  A      0
 103 ASN   ( 110-)  A      0
 128 TRP   ( 135-)  A      0
 132 TYR   ( 139-)  A      0
 140 ASP   ( 147-)  A      0
 142 ASP   ( 149-)  A      0
 143 TYR   ( 150-)  A      0
 152 VAL   ( 159-)  A      0
And so on for a total of 670 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.301

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

 253 SER   ( 260-)  A   1.98
 746 SER   ( 260-)  B   1.65

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]

 497 PRO   (  11-)  B    0.45 HIGH

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

 376 PRO   ( 383-)  A  -117.5 half-chair C-delta/C-gamma (-126 degrees)
 489 PRO   ( 496-)  A  -121.2 half-chair C-delta/C-gamma (-126 degrees)
1855 PRO   ( 383-)  D  -115.7 envelop C-gamma (-108 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.

 358 LEU   ( 365-)  A      CD2 <->  386 MET   ( 393-)  A      SD     0.59    2.81  INTRA
1773 CYS   ( 301-)  D      SG  <-> 1775 CYS   ( 303-)  D      SG     0.58    2.87  INTRA
 358 LEU   ( 365-)  A      CD1 <->  386 MET   ( 393-)  A      SD     0.51    2.89  INTRA
 294 CYS   ( 301-)  A      SG  <->  296 CYS   ( 303-)  A      SG     0.47    2.98  INTRA BL
1837 LEU   ( 365-)  D      CD2 <-> 1865 MET   ( 393-)  D      SD     0.45    2.95  INTRA
1837 LEU   ( 365-)  D      CD1 <-> 1865 MET   ( 393-)  D      SD     0.44    2.96  INTRA
1270 HIS   ( 291-)  C      NE2 <-> 1308 ARG   ( 329-)  C      NH1    0.41    2.59  INTRA
1837 LEU   ( 365-)  D      CG  <-> 1865 MET   ( 393-)  D      SD     0.40    3.00  INTRA
1344 LEU   ( 365-)  C      CD2 <-> 1372 MET   ( 393-)  C      SD     0.39    3.01  INTRA
1344 LEU   ( 365-)  C      CG  <-> 1372 MET   ( 393-)  C      SD     0.38    3.02  INTRA
 231 VAL   ( 238-)  A      O   <->  254 ASN   ( 261-)  A      ND2    0.35    2.35  INTRA BL
1861 LEU   ( 389-)  D      CD1 <-> 1879 ILE   ( 407-)  D      N      0.34    2.76  INTRA
 851 LEU   ( 365-)  B      CG  <->  879 MET   ( 393-)  B      SD     0.31    3.09  INTRA
 439 LEU   ( 446-)  A      O   <->  975 LYS   ( 489-)  B      NZ     0.29    2.41  INTRA BL
 304 GLN   ( 311-)  A      NE2 <->  404 LYS   ( 411-)  A      O      0.27    2.43  INTRA
 895 LYS   ( 409-)  B      O   <->  905 ARG   ( 419-)  B      NH2    0.27    2.43  INTRA BL
1078 ARG   (  99-)  C      NH1 <-> 1097 TYR   ( 118-)  C      O      0.26    2.44  INTRA BL
1795 VAL   ( 323-)  D      CG1 <-> 1841 CYS   ( 369-)  D      SG     0.26    3.14  INTRA
1750 MET   ( 278-)  D      CE  <-> 1885 MET   ( 413-)  D      SD     0.25    3.15  INTRA
 460 GLY   ( 467-)  A      O   <->  468 ARG   ( 475-)  A      NH2    0.22    2.48  INTRA BL
 953 GLY   ( 467-)  B      O   <->  961 ARG   ( 475-)  B      NH2    0.21    2.49  INTRA BL
 481 VAL   ( 488-)  A      O   <->  961 ARG   ( 475-)  B      NH1    0.21    2.49  INTRA BL
1344 LEU   ( 365-)  C      CD1 <-> 1372 MET   ( 393-)  C      SD     0.21    3.19  INTRA
 899 MET   ( 413-)  B      SD  <->  927 TYR   ( 441-)  B      CD2    0.21    3.19  INTRA
 875 LEU   ( 389-)  B      CD1 <->  879 MET   ( 393-)  B      SD     0.21    3.19  INTRA
And so on for a total of 155 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

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.

 370 ARG   ( 377-)  A      -6.46
 863 ARG   ( 377-)  B      -6.29
1356 ARG   ( 377-)  C      -6.23
1550 ARG   (  78-)  D      -5.44
 564 ARG   (  78-)  B      -5.39
 499 GLN   (  13-)  B      -5.39
  71 ARG   (  78-)  A      -5.37
 784 GLN   ( 298-)  B      -5.36
1770 GLN   ( 298-)  D      -5.36
1057 ARG   (  78-)  C      -5.36
 291 GLN   ( 298-)  A      -5.34
1277 GLN   ( 298-)  C      -5.33
 504 LEU   (  18-)  B      -5.32
1426 GLN   ( 447-)  C      -5.26
1490 LEU   (  18-)  D      -5.25
 997 LEU   (  18-)  C      -5.23
1849 ARG   ( 377-)  D      -5.22
1276 ASN   ( 297-)  C      -5.19
  11 LEU   (  18-)  A      -5.18
1769 ASN   ( 297-)  D      -5.18
 290 ASN   ( 297-)  A      -5.17
 783 ASN   ( 297-)  B      -5.17
1485 GLN   (  13-)  D      -5.16
   6 GLN   (  13-)  A      -5.15
 948 GLN   ( 462-)  B      -5.07
1441 GLN   ( 462-)  C      -5.07
 992 GLN   (  13-)  C      -5.07
 440 GLN   ( 447-)  A      -5.05

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

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: C

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: D

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.

1868 ALA   ( 396-)  D   -2.58
 389 ALA   ( 396-)  A   -2.57
1608 ALA   ( 136-)  D   -2.51
1766 LEU   ( 294-)  D   -2.50

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

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

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.

  19 ASN   (  26-)  A
 168 GLN   ( 175-)  A
 180 ASN   ( 187-)  A
 293 GLN   ( 300-)  A
 512 ASN   (  26-)  B
 661 GLN   ( 175-)  B
 673 ASN   ( 187-)  B
 786 GLN   ( 300-)  B
 948 GLN   ( 462-)  B
 993 GLN   (  14-)  C
1005 ASN   (  26-)  C
1154 GLN   ( 175-)  C
1166 ASN   ( 187-)  C
1498 ASN   (  26-)  D
1647 GLN   ( 175-)  D
1659 ASN   ( 187-)  D
1772 GLN   ( 300-)  D
1813 GLN   ( 341-)  D
1816 GLN   ( 344-)  D
1934 GLN   ( 462-)  D

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.

  14 GLN   (  21-)  A      N
  18 ASN   (  25-)  A      N
  20 GLU   (  27-)  A      N
  22 HIS   (  29-)  A      NE2
  24 ALA   (  31-)  A      N
  36 SER   (  43-)  A      N
  69 TRP   (  76-)  A      N
 103 ASN   ( 110-)  A      ND2
 108 ILE   ( 115-)  A      N
 124 TYR   ( 131-)  A      OH
 133 HIS   ( 140-)  A      NE2
 145 SER   ( 152-)  A      N
 145 SER   ( 152-)  A      OG
 161 TRP   ( 168-)  A      N
 166 LEU   ( 173-)  A      N
 209 GLY   ( 216-)  A      N
 216 GLY   ( 223-)  A      N
 217 PHE   ( 224-)  A      N
 220 THR   ( 227-)  A      N
 237 THR   ( 244-)  A      OG1
 256 LYS   ( 263-)  A      N
 264 GLY   ( 271-)  A      N
 265 LYS   ( 272-)  A      N
 266 SER   ( 273-)  A      OG
 268 ASN   ( 275-)  A      ND2
And so on for a total of 201 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

 157 GLN   ( 164-)  A      OE1
 212 ASN   ( 219-)  A      OD1
 337 GLN   ( 344-)  A      OE1
 399 GLN   ( 406-)  A      OE1
 450 ASP   ( 457-)  A      OD1
 650 GLN   ( 164-)  B      OE1
 705 ASN   ( 219-)  B      OD1
 754 GLU   ( 268-)  B      OE2
 761 ASN   ( 275-)  B      OD1
 783 ASN   ( 297-)  B      OD1
 830 GLN   ( 344-)  B      OE1
 892 GLN   ( 406-)  B      OE1
 943 ASP   ( 457-)  B      OD1
 962 GLU   ( 476-)  B      OE1
1143 GLN   ( 164-)  C      OE1
1198 ASN   ( 219-)  C      OD1
1233 GLN   ( 254-)  C      OE1
1247 GLU   ( 268-)  C      OE2
1254 ASN   ( 275-)  C      OD1
1323 GLN   ( 344-)  C      OE1
1385 GLN   ( 406-)  C      OE1
1436 ASP   ( 457-)  C      OD1
1498 ASN   (  26-)  D      OD1
1636 GLN   ( 164-)  D      OE1
1691 ASN   ( 219-)  D      OD1
1740 GLU   ( 268-)  D      OE2
1747 ASN   ( 275-)  D      OD1
1816 GLN   ( 344-)  D      OE1
1878 GLN   ( 406-)  D      OE1
1929 ASP   ( 457-)  D      OD1

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.

  51 ASP   (  58-)  A   H-bonding suggests Asn; but Alt-Rotamer
  86 ASP   (  93-)  A   H-bonding suggests Asn
 102 ASP   ( 109-)  A   H-bonding suggests Asn; but Alt-Rotamer
 261 GLU   ( 268-)  A   H-bonding suggests Gln
 392 GLU   ( 399-)  A   H-bonding suggests Gln
 754 GLU   ( 268-)  B   H-bonding suggests Gln; but Alt-Rotamer
 885 GLU   ( 399-)  B   H-bonding suggests Gln
1088 ASP   ( 109-)  C   H-bonding suggests Asn; but Alt-Rotamer
1247 GLU   ( 268-)  C   H-bonding suggests Gln
1414 ASP   ( 435-)  C   H-bonding suggests Asn; but Alt-Rotamer
1518 ASP   (  46-)  D   H-bonding suggests Asn
1532 ASP   (  60-)  D   H-bonding suggests Asn; but Alt-Rotamer
1581 ASP   ( 109-)  D   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.145
  2nd generation packing quality :  -0.784
  Ramachandran plot appearance   :  -1.374
  chi-1/chi-2 rotamer normality  :  -2.385
  Backbone conformation          :   0.255

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.331 (tight)
  Bond angles                    :   0.617 (tight)
  Omega angle restraints         :   0.236 (tight)
  Side chain planarity           :   0.409 (tight)
  Improper dihedral distribution :   0.801
  Inside/Outside distribution    :   1.047

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 : 2.65


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.6
  2nd generation packing quality :   1.4
  Ramachandran plot appearance   :   0.8
  chi-1/chi-2 rotamer normality  :   0.3
  Backbone conformation          :   1.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.331 (tight)
  Bond angles                    :   0.617 (tight)
  Omega angle restraints         :   0.236 (tight)
  Side chain planarity           :   0.409 (tight)
  Improper dihedral distribution :   0.801
  Inside/Outside distribution    :   1.047
==============

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.