WHAT IF Check report

This file was created 2011-12-16 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 pdb2ixn.ent

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: 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 PRO   (   3-)  A      CG
   1 PRO   (   3-)  A      CD

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: 2

Crystal temperature (K) :100.000

Warning: More than 2 percent of buried atoms has low B-factor

For protein structures determined at room temperature, no more than about 1 percent of the B factors of buried atoms is below 5.0.

Percentage of buried atoms with B less than 5 : 2.51

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: Tyrosine convention problem

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

  42 TYR   (  44-)  A
  82 TYR   (  89-)  A
 111 TYR   ( 118-)  A
 173 TYR   ( 180-)  A
 189 TYR   ( 196-)  A
 225 TYR   ( 232-)  A
 227 TYR   ( 234-)  A
 334 TYR   (  44-)  B
 375 TYR   (  89-)  B
 404 TYR   ( 118-)  B
 417 TYR   ( 131-)  B
 466 TYR   ( 180-)  B
 478 TYR   ( 196-)  B
 514 TYR   ( 232-)  B
 516 TYR   ( 234-)  B
 571 TYR   ( 292-)  B

Warning: Phenylalanine convention problem

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

  73 PHE   (  80-)  A
 145 PHE   ( 152-)  A
 191 PHE   ( 198-)  A
 194 PHE   ( 201-)  A
 221 PHE   ( 228-)  A
 228 PHE   ( 235-)  A
 284 PHE   ( 291-)  A
 286 PHE   ( 293-)  A
 315 PHE   (  25-)  B
 390 PHE   ( 104-)  B
 438 PHE   ( 152-)  B
 480 PHE   ( 198-)  B
 483 PHE   ( 201-)  B
 510 PHE   ( 228-)  B
 570 PHE   ( 291-)  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.

  83 ASP   (  90-)  A
 123 ASP   ( 130-)  A
 373 ASP   (  87-)  B
 416 ASP   ( 130-)  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.

   2 GLU   (   4-)  A
  15 GLU   (  17-)  A
  16 GLU   (  18-)  A
  44 GLU   (  46-)  A
 114 GLU   ( 121-)  A
 161 GLU   ( 168-)  A
 176 GLU   ( 183-)  A
 216 GLU   ( 223-)  A
 264 GLU   ( 271-)  A
 273 GLU   ( 280-)  A
 288 GLU   ( 295-)  A
 308 GLU   (  18-)  B
 389 GLU   ( 103-)  B
 407 GLU   ( 121-)  B
 454 GLU   ( 168-)  B
 508 GLU   ( 226-)  B

Geometric checks

Warning: Unusual bond lengths

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

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

   7 THR   (   9-)  A      CA   C     1.63    5.1
  70 ILE   (  72-)  A      CA   CB    1.63    5.0
 210 ILE   ( 217-)  A      CG1  CD1   1.75    6.1
 216 GLU   ( 223-)  A      CG   CD    1.62    4.2
 227 TYR   ( 234-)  A      CA   CB    1.43   -4.9
 298 LEU   (   8-)  B      CA   C     1.63    5.0
 299 THR   (   9-)  B      N    CA    1.60    7.3
 299 THR   (   9-)  B      CA   C     1.61    4.1
 403 ILE   ( 117-)  B      CG1  CD1   1.68    4.2
 445 THR   ( 159-)  B      CA   CB    1.45   -4.0

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

 |  0.999581 -0.000313  0.000017|
 | -0.000313  0.998699 -0.000569|
 |  0.000017 -0.000569  0.998308|
Proposed new scale matrix

 |  0.006335  0.000002  0.000000|
 |  0.000002  0.005855  0.000003|
 |  0.000000  0.000011  0.018642|
With corresponding cell

    A    = 157.862  B   = 170.805  C    =  53.644
    Alpha=  90.065  Beta=  90.001  Gamma=  90.036

The CRYST1 cell dimensions

    A    = 157.930  B   = 171.042  C    =  53.735
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 29.606
(Under-)estimated Z-score: 4.010

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.

   1 PRO   (   3-)  A      N    CA   CB  111.07    7.3
   5 LEU   (   7-)  A      CA   CB   CG  132.03    4.5
   6 LEU   (   8-)  A      N    CA   C   122.95    4.2
  22 HIS   (  24-)  A      CG   ND1  CE1 109.80    4.2
  37 HIS   (  39-)  A      CG   ND1  CE1 109.69    4.1
  44 GLU   (  46-)  A      N    CA   CB  117.62    4.2
  44 GLU   (  46-)  A      CA   CB   CG  104.52   -4.8
  55 ASN   (  57-)  A     -C    N    CA  114.35   -4.1
  67 HIS   (  69-)  A      CG   ND1  CE1 109.64    4.0
  70 ILE   (  72-)  A      C    CA   CB  118.13    4.2
 121 ARG   ( 128-)  A      CG   CD   NE  120.07    5.6
 147 LEU   ( 154-)  A      CA   CB   CG  131.21    4.3
 154 LEU   ( 161-)  A      CA   CB   CG  130.78    4.1
 210 ILE   ( 217-)  A      CB   CG1  CD1 123.97    4.8
 240 SER   ( 247-)  A     -C    N    CA  129.07    4.1
 244 ARG   ( 251-)  A      CG   CD   NE  120.91    6.1
 249 MET   ( 256-)  A      N    CA   CB  117.71    4.2
 298 LEU   (   8-)  B      N    CA   C   123.99    4.6
 298 LEU   (   8-)  B      N    CA   CB  102.44   -4.7
 299 THR   (   9-)  B     -C    N    CA  129.95    4.6
 299 THR   (   9-)  B      N    CA   C   124.84    4.9
 299 THR   (   9-)  B      C    CA   CB   97.88   -6.4
 300 PRO   (  10-)  B     -C    N    CA  150.40    5.6
 300 PRO   (  10-)  B     -C    N    CD  100.18   -6.1
 314 HIS   (  24-)  B      CG   ND1  CE1 109.92    4.3
 338 ILE   (  48-)  B     -C    N    CA  128.93    4.0
 347 ASN   (  57-)  B     -C    N    CA  110.22   -6.4
 354 ASP   (  64-)  B     -C    N    CA  112.12   -5.3
 354 ASP   (  64-)  B      C    CA   CB  117.73    4.0
 359 HIS   (  69-)  B      CG   ND1  CE1 109.87    4.3
 403 ILE   ( 117-)  B      CB   CG1  CD1 122.65    4.2
 456 LEU   ( 170-)  B     -C    N    CA  113.97   -4.3
 492 THR   ( 210-)  B      C    CA   CB  101.65   -4.4
 513 ARG   ( 231-)  B      CG   CD   NE  118.45    4.7
 530 ARG   ( 251-)  B      CG   CD   NE  118.64    4.8
 542 VAL   ( 263-)  B      N    CA   C    99.16   -4.3
 544 THR   ( 265-)  B      C    CA   CB  102.18   -4.2

Error: Nomenclature error(s)

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

   2 GLU   (   4-)  A
  15 GLU   (  17-)  A
  16 GLU   (  18-)  A
  44 GLU   (  46-)  A
  83 ASP   (  90-)  A
 114 GLU   ( 121-)  A
 123 ASP   ( 130-)  A
 161 GLU   ( 168-)  A
 176 GLU   ( 183-)  A
 216 GLU   ( 223-)  A
 264 GLU   ( 271-)  A
 273 GLU   ( 280-)  A
 288 GLU   ( 295-)  A
 308 GLU   (  18-)  B
 373 ASP   (  87-)  B
 389 GLU   ( 103-)  B
 407 GLU   ( 121-)  B
 416 ASP   ( 130-)  B
 454 GLU   ( 168-)  B
 508 GLU   ( 226-)  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.

   7 THR   (   9-)  A      CA    -6.5    23.06    33.84
  44 GLU   (  46-)  A      CA   -12.3    13.81    33.96
 297 LEU   (   7-)  B      CA    -6.4    24.45    34.19
The average deviation= 1.336

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.

 348 LEU   (  58-)  B    6.54
 237 VAL   ( 244-)  A    5.98
 481 LEU   ( 199-)  B    5.47
 192 LEU   ( 199-)  A    5.27
 298 LEU   (   8-)  B    5.16
   6 LEU   (   8-)  A    4.73
 299 THR   (   9-)  B    4.65
 386 LEU   ( 100-)  B    4.63
 455 TYR   ( 169-)  B    4.47
 249 MET   ( 256-)  A    4.44
 542 VAL   ( 263-)  B    4.20
 136 LEU   ( 143-)  A    4.01

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 : 1.702

Torsion-related checks

Error: Ramachandran Z-score very low

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

Ramachandran Z-score : -4.063

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.

   7 THR   (   9-)  A    -3.4
 356 THR   (  66-)  B    -3.1
 300 PRO   (  10-)  B    -3.0
  45 PRO   (  47-)  A    -3.0
 151 SER   ( 158-)  A    -2.7
 299 THR   (   9-)  B    -2.7
 278 LEU   ( 285-)  A    -2.7
 279 PRO   ( 286-)  A    -2.7
   3 LYS   (   5-)  A    -2.6
   5 LEU   (   7-)  A    -2.6
 193 PRO   ( 200-)  A    -2.6
  70 ILE   (  72-)  A    -2.6
 140 TYR   ( 147-)  A    -2.5
 210 ILE   ( 217-)  A    -2.5
   4 ARG   (   6-)  A    -2.5
 407 GLU   ( 121-)  B    -2.5
 492 THR   ( 210-)  B    -2.5
 195 LEU   ( 202-)  A    -2.4
 121 ARG   ( 128-)  A    -2.4
 144 ILE   ( 151-)  A    -2.4
 295 LYS   (   5-)  B    -2.4
  66 LYS   (  68-)  A    -2.4
 333 GLN   (  43-)  B    -2.4
 338 ILE   (  48-)  B    -2.3
  46 ILE   (  48-)  A    -2.3
 205 LYS   ( 212-)  A    -2.3
 240 SER   ( 247-)  A    -2.3
 114 GLU   ( 121-)  A    -2.3
 238 LYS   ( 245-)  A    -2.3
 316 THR   (  26-)  B    -2.2
 440 LEU   ( 154-)  B    -2.2
 366 PHE   (  80-)  B    -2.1
 499 ILE   ( 217-)  B    -2.1
 110 ILE   ( 117-)  A    -2.1
 539 ILE   ( 260-)  B    -2.1
 297 LEU   (   7-)  B    -2.1
 326 VAL   (  36-)  B    -2.1
 294 GLU   (   4-)  B    -2.1
 562 SER   ( 283-)  B    -2.1
 565 PRO   ( 286-)  B    -2.1
 560 VAL   ( 281-)  B    -2.1
 226 LEU   ( 233-)  A    -2.1
 139 LEU   ( 146-)  A    -2.0
 191 PHE   ( 198-)  A    -2.0
 412 LYS   ( 126-)  B    -2.0
  20 ARG   (  22-)  A    -2.0
  41 GLN   (  43-)  A    -2.0
 327 LYS   (  37-)  B    -2.0
  34 VAL   (  36-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

   2 GLU   (   4-)  A  omega poor
   6 LEU   (   8-)  A  omega poor
   7 THR   (   9-)  A  Poor phi/psi, PRO omega poor
   9 ASP   (  11-)  A  omega poor
  19 THR   (  21-)  A  omega poor
  20 ARG   (  22-)  A  Poor phi/psi
  34 VAL   (  36-)  A  omega poor
  36 GLY   (  38-)  A  omega poor
  40 SER   (  42-)  A  omega poor
  41 GLN   (  43-)  A  Poor phi/psi
  43 LYS   (  45-)  A  omega poor
  44 GLU   (  46-)  A  Poor phi/psi
  70 ILE   (  72-)  A  omega poor
 115 SER   ( 122-)  A  omega poor
 151 SER   ( 158-)  A  Poor phi/psi
 174 TRP   ( 181-)  A  Poor phi/psi
 180 SER   ( 187-)  A  omega poor
 186 LEU   ( 193-)  A  omega poor
 189 TYR   ( 196-)  A  omega poor
 197 GLY   ( 204-)  A  Poor phi/psi
 202 THR   ( 209-)  A  omega poor
 236 LYS   ( 243-)  A  omega poor
 240 SER   ( 247-)  A  Poor phi/psi
 286 PHE   ( 293-)  A  omega poor
 291 PRO   ( 298-)  A  omega poor
 295 LYS   (   5-)  B  omega poor
 298 LEU   (   8-)  B  omega poor
 299 THR   (   9-)  B  Poor phi/psi, PRO omega poor
 300 PRO   (  10-)  B  omega poor
 328 GLY   (  38-)  B  omega poor
 336 GLU   (  46-)  B  PRO omega poor
 339 SER   (  49-)  B  omega poor
 347 ASN   (  57-)  B  omega poor
 355 ILE   (  65-)  B  omega poor
 357 GLN   (  67-)  B  Poor phi/psi, omega poor
 362 ILE   (  72-)  B  omega poor
 381 ASN   (  95-)  B  Poor phi/psi
 438 PHE   ( 152-)  B  omega poor
 463 GLU   ( 177-)  B  omega poor
 465 LYS   ( 179-)  B  omega poor
 466 TYR   ( 180-)  B  Poor phi/psi
 467 TRP   ( 181-)  B  Poor phi/psi
 472 GLY   ( 186-)  B  omega poor
 494 LYS   ( 212-)  B  omega poor
 526 VAL   ( 244-)  B  omega poor
 558 ALA   ( 279-)  B  omega poor
 575 PHE   ( 296-)  B  omega poor
 577 PRO   ( 298-)  B  omega poor
 chi-1/chi-2 correlation Z-score : -5.249

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 : -5.249

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.

  86 SER   (  93-)  A    0.38
  95 SER   ( 102-)  A    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 LYS   (   5-)  A      0
   5 LEU   (   7-)  A      0
   6 LEU   (   8-)  A      0
   7 THR   (   9-)  A      0
   8 PRO   (  10-)  A      0
   9 ASP   (  11-)  A      0
  10 ASP   (  12-)  A      0
  34 VAL   (  36-)  A      0
  35 LYS   (  37-)  A      0
  40 SER   (  42-)  A      0
  41 GLN   (  43-)  A      0
  42 TYR   (  44-)  A      0
  44 GLU   (  46-)  A      0
  45 PRO   (  47-)  A      0
  46 ILE   (  48-)  A      0
  55 ASN   (  57-)  A      0
  66 LYS   (  68-)  A      0
  67 HIS   (  69-)  A      0
  70 ILE   (  72-)  A      0
  71 LYS   (  73-)  A      0
  72 ARG   (  79-)  A      0
  73 PHE   (  80-)  A      0
  76 VAL   (  83-)  A      0
  97 PHE   ( 104-)  A      0
 114 GLU   ( 121-)  A      0
And so on for a total of 187 lines.

Warning: Omega angle restraints not strong enough

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

Standard deviation of omega values : 8.608

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!

 541 GLY   ( 262-)  B   1.71   20

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]

   1 PRO   (   3-)  A    0.00 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].

  45 PRO   (  47-)  A   132.1 half-chair C-beta/C-alpha (126 degrees)
  68 PRO   (  70-)  A    -5.5 envelop N (0 degrees)
 193 PRO   ( 200-)  A   108.4 envelop C-beta (108 degrees)
 248 PRO   ( 255-)  A    51.7 half-chair C-delta/C-gamma (54 degrees)
 279 PRO   ( 286-)  A   107.3 envelop C-beta (108 degrees)
 300 PRO   (  10-)  B   -34.3 envelop C-alpha (-36 degrees)
 482 PRO   ( 200-)  B   102.9 envelop C-beta (108 degrees)
 565 PRO   ( 286-)  B   160.0 half-chair C-alpha/N (162 degrees)
 577 PRO   ( 298-)  B    40.7 envelop C-delta (36 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

 409 TRP   ( 123-)  B      CE3 <->  459 MET   ( 173-)  B      CE     0.82    2.38  INTRA BL
 116 TRP   ( 123-)  A      CE3 <->  166 MET   ( 173-)  A      CE     0.59    2.61  INTRA BL
 356 THR   (  66-)  B      O   <->  358 LYS   (  68-)  B      N      0.52    2.18  INTRA
  72 ARG   (  79-)  A      CD  <->   73 PHE   (  80-)  A      N      0.47    2.53  INTRA
  38 GLU   (  40-)  A      CB  <->   41 GLN   (  43-)  A      NE2    0.35    2.75  INTRA BL
  44 GLU   (  46-)  A      O   <->   45 PRO   (  47-)  A      C      0.33    2.27  INTRA BL
 555 MET   ( 276-)  B      O   <->  559 GLU   ( 280-)  B      N      0.28    2.42  INTRA BL
 409 TRP   ( 123-)  B      CZ3 <->  459 MET   ( 173-)  B      CE     0.27    2.93  INTRA BL
 278 LEU   ( 285-)  A      CB  <->  279 PRO   ( 286-)  A      CD     0.27    2.83  INTRA BL
  14 TRP   (  16-)  A      O   <->   17 SER   (  19-)  A      OG     0.27    2.13  INTRA BL
 356 THR   (  66-)  B      C   <->  358 LYS   (  68-)  B      N      0.26    2.64  INTRA
  44 GLU   (  46-)  A      O   <->   46 ILE   (  48-)  A      N      0.26    2.44  INTRA BL
 515 LEU   ( 233-)  B      O   <->  518 GLY   ( 236-)  B      N      0.23    2.47  INTRA BL
 417 TYR   ( 131-)  B      CE2 <->  459 MET   ( 173-)  B      SD     0.21    3.19  INTRA BL
 566 ILE   ( 287-)  B      C   <->  568 GLN   ( 289-)  B      N      0.20    2.70  INTRA BL
 301 ASP   (  11-)  B      N   <->  302 ASP   (  12-)  B      N      0.20    2.40  INTRA BL
 114 GLU   ( 121-)  A      CB  <->  131 ASN   ( 138-)  A      ND2    0.20    2.90  INTRA BL
 325 SER   (  35-)  B      CB  <->  444 SER   ( 158-)  B      OG     0.20    2.60  INTRA BL
 418 GLY   ( 132-)  B      N   <->  421 HIS   ( 135-)  B      CD2    0.19    2.91  INTRA BL
 294 GLU   (   4-)  B      CB  <->  572 PHE   ( 293-)  B      O      0.19    2.61  INTRA
 476 ASP   ( 194-)  B      CG  <->  477 ASP   ( 195-)  B      N      0.19    2.81  INTRA
 269 MET   ( 276-)  A      O   <->  273 GLU   ( 280-)  A      N      0.18    2.52  INTRA BL
  44 GLU   (  46-)  A      CB  <->   45 PRO   (  47-)  A      CD     0.18    2.92  INTRA BL
 296 ARG   (   6-)  B      NH2 <->  569 HIS   ( 290-)  B      ND1    0.18    2.82  INTRA
 497 LYS   ( 215-)  B      N   <->  500 SER   ( 218-)  B      OG     0.17    2.53  INTRA BL
And so on for a total of 147 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

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.

 365 ARG   (  79-)  B      -7.24
  73 PHE   (  80-)  A      -6.96
 205 LYS   ( 212-)  A      -6.15
 257 LYS   ( 264-)  A      -6.08
 362 ILE   (  72-)  B      -5.99
   5 LEU   (   7-)  A      -5.80
 246 HIS   ( 253-)  A      -5.77
 245 TRP   ( 252-)  A      -5.75
 494 LYS   ( 212-)  B      -5.74
  70 ILE   (  72-)  A      -5.73
 532 HIS   ( 253-)  B      -5.65
 543 LYS   ( 264-)  B      -5.59
 502 HIS   ( 220-)  B      -5.44
 366 PHE   (  80-)  B      -5.39
   4 ARG   (   6-)  A      -5.30
 297 LEU   (   7-)  B      -5.27
 380 ARG   (  94-)  B      -5.20
 531 TRP   ( 252-)  B      -5.19
  43 LYS   (  45-)  A      -5.14
 183 VAL   ( 190-)  A      -5.02

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.

 243 LEU   ( 250-)  A   -2.60
 280 ILE   ( 287-)  A   -2.52

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: 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.

  55 ASN   (  57-)  A
 118 ASN   ( 125-)  A
 357 GLN   (  67-)  B
 397 GLN   ( 111-)  B
 411 ASN   ( 125-)  B
 421 HIS   ( 135-)  B
 493 HIS   ( 211-)  B
 532 HIS   ( 253-)  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.

  14 TRP   (  16-)  A      N
  20 ARG   (  22-)  A      N
  20 ARG   (  22-)  A      NH1
  47 SER   (  49-)  A      N
  66 LYS   (  68-)  A      N
  73 PHE   (  80-)  A      N
 116 TRP   ( 123-)  A      N
 117 GLY   ( 124-)  A      N
 123 ASP   ( 130-)  A      N
 125 GLY   ( 132-)  A      N
 145 PHE   ( 152-)  A      N
 152 THR   ( 159-)  A      N
 184 TRP   ( 191-)  A      NE1
 203 THR   ( 210-)  A      N
 205 LYS   ( 212-)  A      N
 210 ILE   ( 217-)  A      N
 227 TYR   ( 234-)  A      N
 227 TYR   ( 234-)  A      OH
 245 TRP   ( 252-)  A      N
 245 TRP   ( 252-)  A      NE1
 249 MET   ( 256-)  A      N
 258 THR   ( 265-)  A      N
 259 TRP   ( 266-)  A      NE1
 270 TYR   ( 277-)  A      OH
 276 SER   ( 283-)  A      N
And so on for a total of 58 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.

   2 GLU   (   4-)  A      OE2
  88 ASN   (  95-)  A      OD1
 129 GLU   ( 136-)  A      OE1
 170 GLU   ( 177-)  A      OE1
 190 HIS   ( 197-)  A      ND1
 294 GLU   (   4-)  B      OE1
 406 ASP   ( 120-)  B      OD1
 416 ASP   ( 130-)  B      OD1
 422 GLU   ( 136-)  B      OE1

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.

   2 GLU   (   4-)  A   H-bonding suggests Gln
  15 GLU   (  17-)  A   H-bonding suggests Gln
  29 ASP   (  31-)  A   H-bonding suggests Asn
  44 GLU   (  46-)  A   H-bonding suggests Gln
  62 ASP   (  64-)  A   H-bonding suggests Asn; but Alt-Rotamer
  77 GLU   (  84-)  A   H-bonding suggests Gln
  96 GLU   ( 103-)  A   H-bonding suggests Gln
 113 ASP   ( 120-)  A   H-bonding suggests Asn
 150 ASP   ( 157-)  A   H-bonding suggests Asn; but Alt-Rotamer
 302 ASP   (  12-)  B   H-bonding suggests Asn
 354 ASP   (  64-)  B   H-bonding suggests Asn; but Alt-Rotamer
 406 ASP   ( 120-)  B   H-bonding suggests Asn; but Alt-Rotamer
 443 ASP   ( 157-)  B   H-bonding suggests Asn; but Alt-Rotamer
 463 GLU   ( 177-)  B   H-bonding suggests Gln; but Alt-Rotamer
 550 GLU   ( 271-)  B   H-bonding suggests Gln

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.141
  2nd generation packing quality :  -1.961
  Ramachandran plot appearance   :  -4.063 (bad)
  chi-1/chi-2 rotamer normality  :  -5.249 (bad)
  Backbone conformation          :  -1.016

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.924
  Bond angles                    :   1.084
  Omega angle restraints         :   1.565 (loose)
  Side chain planarity           :   0.752
  Improper dihedral distribution :   1.188
  B-factor distribution          :   0.650
  Inside/Outside distribution    :   1.011

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 : 2.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -0.4
  Ramachandran plot appearance   :  -1.6
  chi-1/chi-2 rotamer normality  :  -2.8
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.924
  Bond angles                    :   1.084
  Omega angle restraints         :   1.565 (loose)
  Side chain planarity           :   0.752
  Improper dihedral distribution :   1.188
  B-factor distribution          :   0.650
  Inside/Outside distribution    :   1.011
==============

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Bond lengths and angles, DNA/RNA
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DSSP
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Hydrogen bond networks
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Matthews' Coefficient
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Protein side chain planarity
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Puckering parameters
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Quality Control
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    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
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Symmetry Checks
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Ion Checks
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    M.Nayal and E.Di Cera,
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    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
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Checking checks
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