WHAT IF Check report

This file was created 2011-12-17 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 pdb1rld.ent

Administrative problems that can generate validation failures

Warning: Strange inter-chain connections detected

The pairs of residues listed in the table below seem covalently bound while belonging to different chains in the PDB file.

Sometimes this is unavoidable (e.g. if two protein chains are covalently connected via a Cys-Cys or other bond). But if it can be avoided (e.g. often we observe sugars with one chain identifier connected to protein chains with another chain identifier), it should be avoided. WHAT IF and WHAT-CHECK try to deal with all exceptions thrown at it, but if you want these programs to work optimally (i.e. make as few false error messages as is possible) you should help them by getting as much of the administration correct as is humanly possible.

 221 CYS   ( 247-)  A  -   SG   785 CYS   ( 247-)  B  -   SG

Warning: Strange inter-chain connections could NOT be corrected

Often inter-chain connections are simple administrative problems. In this case not. The observed inter-chain connection(s) either are real, or they are too strange for WHAT IF to correct. Human inspection seems required.

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: S

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: T

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

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

  53 ARG   (  79-)  A    High
  63 ARG   (  89-)  A    High
  67 GLU   (  93-)  A    High
  68 LYS   (  94-)  A    High
  69 ASP   (  95-)  A    High
 102 LYS   ( 128-)  A    High
 105 ARG   ( 131-)  A    High
 310 GLU   ( 336-)  A    High
 562 GLU   ( 621-)  S    High
 617 ARG   (  79-)  B    High
 627 ARG   (  89-)  B    High
 631 GLU   (  93-)  B    High
 632 LYS   (  94-)  B    High
 633 ASP   (  95-)  B    High
 666 LYS   ( 128-)  B    High
 669 ARG   ( 131-)  B    High
 874 GLU   ( 336-)  B    High
1126 GLU   ( 621-)  T    High

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.

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: S

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: T

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.

  43 VAL   (  69-)  A      CA   C     1.61    4.2
  43 VAL   (  69-)  A      CA   CB    1.63    5.2
  44 TRP   (  70-)  A      CA   CB    1.65    6.1
  44 TRP   (  70-)  A      NE1  CE2   1.33   -4.0
  89 ASN   ( 115-)  A      CA   CB    1.45   -4.1
 186 MET   ( 212-)  A      CA   CB    1.44   -4.7
 191 ARG   ( 217-)  A      CA   CB    1.45   -4.2
 212 HIS   ( 238-)  A      CD2  NE2   1.28   -4.4
 261 ASN   ( 287-)  A      CA   CB    1.45   -4.2
 272 HIS   ( 298-)  A      CD2  NE2   1.29   -4.1
 301 HIS   ( 327-)  A      CG   ND1   1.30   -4.1
 323 LEU   ( 349-)  A      CB   CG    1.44   -4.4
 359 TRP   ( 385-)  A      CA   CB    1.62    4.6
 359 TRP   ( 385-)  A      N   -C     1.41    4.2
 425 TRP   ( 451-)  A      CG   CD2   1.36   -4.1
 436 TRP   ( 462-)  A      CA   CB    1.63    4.8
 479 TRP   ( 538-)  S      CG   CD2   1.35   -4.7
 508 TRP   ( 567-)  S      NE1  CE2   1.30   -6.2
 557 ILE   ( 616-)  S      CA   CB    1.64    5.5
 606 THR   (  63-)  B      CA   C     1.62    4.3
 606 THR   (  63-)  B      CA   CB    1.61    4.1
 607 VAL   (  69-)  B      CA   C     1.62    4.6
 607 VAL   (  69-)  B      CA   CB    1.64    5.4
 608 TRP   (  70-)  B      CA   CB    1.64    5.6
 651 VAL   ( 113-)  B      CA   CB    1.62    4.7
 744 VAL   ( 206-)  B      CA   CB    1.61    4.0
 776 HIS   ( 238-)  B      CD2  NE2   1.27   -4.9
 825 ASN   ( 287-)  B      CA   CB    1.42   -5.3
 906 TRP   ( 368-)  B      CD1  NE1   1.28   -4.4
1000 TRP   ( 462-)  B      CA   CB    1.62    4.6
1043 TRP   ( 538-)  T      CG   CD2   1.34   -5.3
1072 TRP   ( 567-)  T      NE1  CE2   1.32   -4.9
1121 ILE   ( 616-)  T      CA   CB    1.63    5.1

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

 |  1.003302  0.000683 -0.000075|
 |  0.000683  1.003543 -0.000221|
 | -0.000075 -0.000221  1.001103|
Proposed new scale matrix

 |  0.006514 -0.000004  0.000000|
 | -0.000004  0.006513  0.000001|
 |  0.000000  0.000002  0.008804|
With corresponding cell

    A    = 153.504  B   = 153.541  C    = 113.581
    Alpha=  90.025  Beta=  90.002  Gamma=  89.922

The CRYST1 cell dimensions

    A    = 153.010  B   = 153.010  C    = 113.450
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 287.235
(Under-)estimated Z-score: 12.491

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 LEU   (  22-)  A      N    CA   C    96.74   -5.2
   4 TYR   (  25-)  A      N    CA   C    98.55   -4.5
   9 GLN   (  30-)  A      CG   CD   NE2 123.45    4.7
   9 GLN   (  30-)  A      NE2  CD   OE1 114.70   -7.9
  11 LYS   (  32-)  A      CA   CB   CG  126.70    6.3
  11 LYS   (  32-)  A      CB   CG   CD  121.55    4.5
  14 ASP   (  35-)  A      N    CA   CB  117.58    4.2
  14 ASP   (  35-)  A      C    CA   CB  102.06   -4.2
  14 ASP   (  35-)  A      CA   CB   CG  122.28    9.7
  15 ILE   (  36-)  A      N    CA   C    96.39   -5.3
  19 PHE   (  40-)  A      CA   CB   CG  117.87    4.1
  20 ARG   (  41-)  A      CB   CG   CD  104.89   -4.6
  22 THR   (  43-)  A      N    CA   C    99.98   -4.0
  24 GLN   (  45-)  A      CA   C    O   113.98   -4.0
  25 PRO   (  46-)  A     -CA  -C    N   128.36    7.6
  27 VAL   (  48-)  A     -CA  -C    N   126.06    4.6
  30 GLU   (  51-)  A      CB   CG   CD  119.69    4.2
  40 SER   (  61-)  A     -CA  -C    N   106.52   -4.8
  40 SER   (  61-)  A     -C    N    CA  132.21    5.8
  42 THR   (  63-)  A     -C    N    CA  131.59    5.5
  43 VAL   (  69-)  A     -O   -C    N   115.26   -4.8
  43 VAL   (  69-)  A     -CA  -C    N   127.95    5.9
  43 VAL   (  69-)  A      N    CA   C   134.41    8.3
  43 VAL   (  69-)  A      N    CA   CB  103.44   -4.2
  44 TRP   (  70-)  A     -C    N    CA  136.56    8.3
And so on for a total of 610 lines.

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.

  15 ILE   (  36-)  A      CB     6.9    41.32    32.31
 283 ILE   ( 309-)  A      CB     6.9    41.30    32.31
 315 ILE   ( 341-)  A      CB     6.3    40.55    32.31
 356 ILE   ( 382-)  A      CB     8.4    43.18    32.31
 373 VAL   ( 399-)  A      CB    -6.5   -41.41   -32.96
 440 VAL   ( 466-)  A      CB    -7.3   -42.56   -32.96
 455 THR   ( 514-)  S      C     -6.2    -9.02     0.30
 579 ILE   (  36-)  B      CB     6.1    40.21    32.31
 744 VAL   ( 206-)  B      CB    -6.1   -40.97   -32.96
 847 ILE   ( 309-)  B      CB     6.8    41.21    32.31
 879 ILE   ( 341-)  B      CB     6.5    40.74    32.31
 920 ILE   ( 382-)  B      CB     8.3    43.15    32.31
1004 VAL   ( 466-)  B      CB    -6.8   -41.92   -32.96
1019 THR   ( 514-)  T      C     -6.7    -9.74     0.30
The average deviation= 1.762

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.

 922 VAL   ( 384-)  B   12.45
 358 VAL   ( 384-)  A   12.01
  43 VAL   (  69-)  A    9.41
 607 VAL   (  69-)  B    9.28
 840 ASP   ( 302-)  B    7.26
 276 ASP   ( 302-)  A    7.17
 129 ILE   ( 155-)  A    6.81
 432 ALA   ( 458-)  A    6.67
 387 ASN   ( 413-)  A    6.46
1058 ARG   ( 553-)  T    6.30
 996 ALA   ( 458-)  B    6.27
 494 ARG   ( 553-)  S    6.07
 693 ILE   ( 155-)  B    6.06
 565 LEU   (  22-)  B    6.04
 951 ASN   ( 413-)  B    5.91
 855 ALA   ( 317-)  B    5.89
   1 LEU   (  22-)  A    5.89
 644 ASP   ( 106-)  B    5.78
1052 GLU   ( 547-)  T    5.69
  80 ASP   ( 106-)  A    5.63
 309 LEU   ( 335-)  A    5.63
 488 GLU   ( 547-)  S    5.63
 579 ILE   (  36-)  B    5.51
 257 TYR   ( 283-)  A    5.47
  15 ILE   (  36-)  A    5.46
And so on for a total of 73 lines.

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 : 2.230

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.

 342 TRP   ( 368-)  A    8.59
 906 TRP   ( 368-)  B    8.41
1000 TRP   ( 462-)  B    6.92
 436 TRP   ( 462-)  A    6.23
  44 TRP   (  70-)  A    6.14
 608 TRP   (  70-)  B    6.08
 188 TRP   ( 214-)  A    6.01
 752 TRP   ( 214-)  B    5.72

Error: Connections to aromatic rings out of plane

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

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

 213 TYR   ( 239-)  A      OH   4.48
1053 HIS   ( 548-)  T      CB   4.08
 489 HIS   ( 548-)  S      CB   4.03
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -3.371

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 : -3.371

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.

  49 THR   (  75-)  A    -3.0
  44 TRP   (  70-)  A    -3.0
 608 TRP   (  70-)  B    -3.0
 613 THR   (  75-)  B    -3.0
 948 PRO   ( 410-)  B    -3.0
 489 HIS   ( 548-)  S    -3.0
1053 HIS   ( 548-)  T    -2.9
 384 PRO   ( 410-)  A    -2.9
1057 TYR   ( 552-)  T    -2.7
 632 LYS   (  94-)  B    -2.7
  68 LYS   (  94-)  A    -2.7
 493 TYR   ( 552-)  S    -2.6
1064 PRO   ( 559-)  T    -2.6
 907 VAL   ( 369-)  B    -2.6
 343 VAL   ( 369-)  A    -2.6
  42 THR   (  63-)  A    -2.6
 606 THR   (  63-)  B    -2.6
1123 TYR   ( 618-)  T    -2.5
 559 TYR   ( 618-)  S    -2.5
1119 SER   ( 614-)  T    -2.5
 555 SER   ( 614-)  S    -2.5
 500 PRO   ( 559-)  S    -2.5
 213 TYR   ( 239-)  A    -2.4
 415 GLY   ( 441-)  A    -2.4
 777 TYR   ( 239-)  B    -2.4
And so on for a total of 67 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.

  40 SER   (  61-)  A  Poor phi/psi
  42 THR   (  63-)  A  omega poor
  44 TRP   (  70-)  A  Poor phi/psi
  46 ASP   (  72-)  A  Poor phi/psi
  66 GLY   (  92-)  A  Poor phi/psi
  68 LYS   (  94-)  A  Poor phi/psi
  99 PHE   ( 125-)  A  Poor phi/psi
 141 ARG   ( 167-)  A  PRO omega poor
 149 LYS   ( 175-)  A  PRO omega poor
 181 ASN   ( 207-)  A  Poor phi/psi
 271 MET   ( 297-)  A  Poor phi/psi
 308 LYS   ( 334-)  A  omega poor
 343 VAL   ( 369-)  A  Poor phi/psi
 344 SER   ( 370-)  A  Poor phi/psi
 383 HIS   ( 409-)  A  PRO omega poor
 384 PRO   ( 410-)  A  Poor phi/psi
 408 GLY   ( 434-)  A  Poor phi/psi
 415 GLY   ( 441-)  A  Poor phi/psi
 435 VAL   ( 461-)  A  omega poor
 437 LYS   ( 463-)  A  omega poor
 440 VAL   ( 466-)  A  Poor phi/psi
 449 ASN   ( 508-)  S  Poor phi/psi
 454 GLU   ( 513-)  S  Poor phi/psi
 456 LEU   ( 515-)  S  Poor phi/psi
 478 GLY   ( 537-)  S  Poor phi/psi
And so on for a total of 58 lines.

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 : -4.698

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.

 253 SER   ( 279-)  A    0.37
 817 SER   ( 279-)  B    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!

   4 TYR   (  25-)  A      0
  13 THR   (  34-)  A      0
  25 PRO   (  46-)  A      0
  27 VAL   (  48-)  A      0
  39 GLU   (  60-)  A      0
  40 SER   (  61-)  A      0
  41 SER   (  62-)  A      0
  42 THR   (  63-)  A      0
  43 VAL   (  69-)  A      0
  44 TRP   (  70-)  A      0
  46 ASP   (  72-)  A      0
  48 LEU   (  74-)  A      0
  49 THR   (  75-)  A      0
  51 LEU   (  77-)  A      0
  58 CYS   (  84-)  A      0
  59 TYR   (  85-)  A      0
  65 VAL   (  91-)  A      0
  67 GLU   (  93-)  A      0
  68 LYS   (  94-)  A      0
  69 ASP   (  95-)  A      0
  70 GLN   (  96-)  A      0
  81 LEU   ( 107-)  A      0
  84 GLU   ( 110-)  A      0
  94 ILE   ( 120-)  A      0
  95 VAL   ( 121-)  A      0
And so on for a total of 446 lines.

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...

  79 LEU   ( 105-)  A   1.53
 309 LEU   ( 335-)  A   1.63
 343 VAL   ( 369-)  A   3.12
 873 LEU   ( 335-)  B   1.60
 907 VAL   ( 369-)  B   3.06

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]

   6 PRO   (  27-)  A    0.46 HIGH
 116 PRO   ( 142-)  A    0.50 HIGH
 237 PRO   ( 263-)  A    0.53 HIGH
 362 PRO   ( 388-)  A    0.46 HIGH
 384 PRO   ( 410-)  A    0.49 HIGH
 389 PRO   ( 415-)  A    0.55 HIGH
 570 PRO   (  27-)  B    0.47 HIGH
 680 PRO   ( 142-)  B    0.48 HIGH
 689 PRO   ( 151-)  B    0.46 HIGH
 801 PRO   ( 263-)  B    0.53 HIGH
 914 PRO   ( 376-)  B    0.46 HIGH
 926 PRO   ( 388-)  B    0.45 HIGH
 948 PRO   ( 410-)  B    0.49 HIGH
 953 PRO   ( 415-)  B    0.55 HIGH
1011 PRO   ( 506-)  T    0.47 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].

  78 PRO   ( 104-)  A  -115.1 envelop C-gamma (-108 degrees)
 126 PRO   ( 152-)  A  -116.3 envelop C-gamma (-108 degrees)
 184 PRO   ( 210-)  A  -139.4 envelop C-delta (-144 degrees)
 346 PRO   ( 372-)  A  -135.9 envelop C-delta (-144 degrees)
 350 PRO   ( 376-)  A  -121.3 half-chair C-delta/C-gamma (-126 degrees)
 384 PRO   ( 410-)  A   137.6 envelop C-alpha (144 degrees)
 389 PRO   ( 415-)  A   104.2 envelop C-beta (108 degrees)
 427 PRO   ( 453-)  A  -113.7 envelop C-gamma (-108 degrees)
 481 PRO   ( 540-)  S   -54.8 half-chair C-beta/C-alpha (-54 degrees)
 561 PRO   ( 620-)  S  -112.5 envelop C-gamma (-108 degrees)
 642 PRO   ( 104-)  B  -120.4 half-chair C-delta/C-gamma (-126 degrees)
 690 PRO   ( 152-)  B  -119.5 half-chair C-delta/C-gamma (-126 degrees)
 748 PRO   ( 210-)  B  -136.8 envelop C-delta (-144 degrees)
 910 PRO   ( 372-)  B  -135.5 envelop C-delta (-144 degrees)
 914 PRO   ( 376-)  B  -120.9 half-chair C-delta/C-gamma (-126 degrees)
 948 PRO   ( 410-)  B   138.7 envelop C-alpha (144 degrees)
 953 PRO   ( 415-)  B   102.9 envelop C-beta (108 degrees)
 991 PRO   ( 453-)  B  -114.1 envelop C-gamma (-108 degrees)
1045 PRO   ( 540-)  T   -56.7 half-chair C-beta/C-alpha (-54 degrees)
1125 PRO   ( 620-)  T  -112.8 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 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.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

 146 CYS   ( 172-)  A      SG   <->   381 LEU   ( 407-)  A      CD1  0.29    3.11  INTRA BF
 710 CYS   ( 172-)  B      SG   <->   945 LEU   ( 407-)  B      CD1  0.27    3.13  INTRA BF
 112 LEU   ( 138-)  A      O    <->   290 LYS   ( 316-)  A      NZ   0.26    2.44  INTRA BL
 923 TRP   ( 385-)  B      N    <->  1000 TRP   ( 462-)  B      NE1  0.26    2.59  INTRA BL
 676 LEU   ( 138-)  B      O    <->   854 LYS   ( 316-)  B      NZ   0.25    2.45  INTRA BL
 359 TRP   ( 385-)  A      N    <->   436 TRP   ( 462-)  A      NE1  0.21    2.64  INTRA BL
 104 LEU   ( 130-)  A      O    <->   841 ARG   ( 303-)  B      NH2  0.20    2.50  INTRA BF
 277 ARG   ( 303-)  A      NH2  <->   668 LEU   ( 130-)  B      O    0.17    2.53  INTRA BF
  45 THR   (  71-)  A      O    <->    48 LEU   (  74-)  A      N    0.15    2.55  INTRA BF
 609 THR   (  71-)  B      O    <->   612 LEU   (  74-)  B      N    0.15    2.55  INTRA BF
 269 ARG   ( 295-)  A      CD   <->   285 PHE   ( 311-)  A      CE1  0.15    3.05  INTRA BL
 608 TRP   (  70-)  B      CG   <->   609 THR   (  71-)  B      N    0.15    2.85  INTRA BF
 738 THR   ( 200-)  B      OG1  <->   776 HIS   ( 238-)  B      ND1  0.14    2.56  INTRA BL
 697 ARG   ( 159-)  B      NH2  <->   934 ASP   ( 396-)  B      O    0.14    2.56  INTRA BL
 293 ARG   ( 319-)  A      NH2  <->   325 ASP   ( 351-)  A      O    0.14    2.56  INTRA BL
 892 VAL   ( 354-)  B      N    <->   904 GLN   ( 366-)  B      O    0.14    2.56  INTRA BL
 836 HIS   ( 298-)  B      ND1  <->   840 ASP   ( 302-)  B      OD2  0.14    2.56  INTRA BL
 359 TRP   ( 385-)  A      CB   <->   436 TRP   ( 462-)  A      NE1  0.14    2.96  INTRA BL
 133 ARG   ( 159-)  A      NH2  <->   370 ASP   ( 396-)  A      O    0.14    2.56  INTRA BL
 833 ARG   ( 295-)  B      CD   <->   849 PHE   ( 311-)  B      CE1  0.13    3.07  INTRA BL
 328 VAL   ( 354-)  A      N    <->   340 GLN   ( 366-)  A      O    0.13    2.57  INTRA BL
1095 ALA   ( 590-)  T      O    <->  1099 TYR   ( 594-)  T      N    0.13    2.57  INTRA
 484 GLU   ( 543-)  S      OE1  <->   541 ARG   ( 600-)  S      NH1  0.13    2.57  INTRA
  44 TRP   (  70-)  A      CG   <->    45 THR   (  71-)  A      N    0.13    2.87  INTRA BF
 923 TRP   ( 385-)  B      CB   <->  1000 TRP   ( 462-)  B      NE1  0.12    2.98  INTRA BL
And so on for a total of 148 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: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

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.

1071 TYR   ( 566-)  T      -7.88
 507 TYR   ( 566-)  S      -7.88
1080 PHE   ( 575-)  T      -6.13
 516 PHE   ( 575-)  S      -6.08
 448 ILE   ( 507-)  S      -5.76
1012 ILE   ( 507-)  T      -5.76
1076 LYS   ( 571-)  T      -5.75
 512 LYS   ( 571-)  S      -5.72
 687 GLN   ( 149-)  B      -5.67
 425 TRP   ( 451-)  A      -5.65
 989 TRP   ( 451-)  B      -5.61
 123 GLN   ( 149-)  A      -5.61
 977 GLN   ( 439-)  B      -5.56
 413 GLN   ( 439-)  A      -5.55
 105 ARG   ( 131-)  A      -5.49
1062 LYS   ( 557-)  T      -5.43
 444 VAL   ( 503-)  S      -5.42
1008 VAL   ( 503-)  T      -5.40
 498 LYS   ( 557-)  S      -5.40
 477 ASN   ( 536-)  S      -5.34
 669 ARG   ( 131-)  B      -5.33
1041 ASN   ( 536-)  T      -5.33
 888 ARG   ( 350-)  B      -5.20
 324 ARG   ( 350-)  A      -5.19
 825 ASN   ( 287-)  B      -5.18
 261 ASN   ( 287-)  A      -5.17
 168 ARG   ( 194-)  A      -5.16
1126 GLU   ( 621-)  T      -5.15
 732 ARG   ( 194-)  B      -5.15
 562 GLU   ( 621-)  S      -5.13
 488 GLU   ( 547-)  S      -5.07
1052 GLU   ( 547-)  T      -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: S

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: T

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.

 837 ALA   ( 299-)  B   -2.84
 273 ALA   ( 299-)  A   -2.84
1115 VAL   ( 610-)  T   -2.81
 551 VAL   ( 610-)  S   -2.80
 381 LEU   ( 407-)  A   -2.75
 945 LEU   ( 407-)  B   -2.73

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.

 437 LYS   ( 463-)  A     -  440 VAL   ( 466-)  A        -1.77
1001 LYS   ( 463-)  B     - 1004 VAL   ( 466-)  B        -1.83

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: S

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: T

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.

 179 ASN   ( 205-)  A
 360 HIS   ( 386-)  A
 477 ASN   ( 536-)  S
 496 ASN   ( 555-)  S
 550 GLN   ( 609-)  S
 743 ASN   ( 205-)  B
 924 HIS   ( 386-)  B
1041 ASN   ( 536-)  T
1060 ASN   ( 555-)  T
1114 GLN   ( 609-)  T

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.

   2 THR   (  23-)  A      N
   3 TYR   (  24-)  A      N
   4 TYR   (  25-)  A      N
   7 GLU   (  28-)  A      N
  13 THR   (  34-)  A      N
  14 ASP   (  35-)  A      N
  20 ARG   (  41-)  A      NE
  30 GLU   (  51-)  A      N
  55 LYS   (  81-)  A      N
  67 GLU   (  93-)  A      N
  68 LYS   (  94-)  A      N
  70 GLN   (  96-)  A      N
  84 GLU   ( 110-)  A      N
  86 SER   ( 112-)  A      OG
  93 SER   ( 119-)  A      OG
  98 VAL   ( 124-)  A      N
 114 ILE   ( 140-)  A      N
 130 GLN   ( 156-)  A      N
 141 ARG   ( 167-)  A      N
 149 LYS   ( 175-)  A      N
 152 LEU   ( 178-)  A      N
 153 GLY   ( 179-)  A      N
 154 LEU   ( 180-)  A      N
 158 ASN   ( 184-)  A      ND2
 178 GLU   ( 204-)  A      N
And so on for a total of 151 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.

  39 GLU   (  60-)  A      OE2
  46 ASP   (  72-)  A      OD2
 132 GLU   ( 158-)  A      OE1
 241 HIS   ( 267-)  A      NE2
 242 ASP   ( 268-)  A      OD1
 340 GLN   ( 366-)  A      OE1
 357 HIS   ( 383-)  A      NE2
 394 ASN   ( 420-)  A      OD1
 470 GLU   ( 529-)  S      OE2
 529 GLU   ( 588-)  S      OE1
 603 GLU   (  60-)  B      OE2
 610 ASP   (  72-)  B      OD2
 696 GLU   ( 158-)  B      OE1
 805 HIS   ( 267-)  B      NE2
 806 ASP   ( 268-)  B      OD1
 904 GLN   ( 366-)  B      OE1
 921 HIS   ( 383-)  B      NE2
 958 ASN   ( 420-)  B      OD1
1034 GLU   ( 529-)  T      OE2
1093 GLU   ( 588-)  T      OE1

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.

  14 ASP   (  35-)  A   H-bonding suggests Asn
  39 GLU   (  60-)  A   H-bonding suggests Gln
  46 ASP   (  72-)  A   H-bonding suggests Asn; but Alt-Rotamer
  67 GLU   (  93-)  A   H-bonding suggests Gln
 242 ASP   ( 268-)  A   H-bonding suggests Asn; but Alt-Rotamer
 260 ASP   ( 286-)  A   H-bonding suggests Asn
 276 ASP   ( 302-)  A   H-bonding suggests Asn
 312 GLU   ( 338-)  A   H-bonding suggests Gln
 321 ASP   ( 347-)  A   H-bonding suggests Asn
 438 GLU   ( 464-)  A   H-bonding suggests Gln
 486 GLU   ( 545-)  S   H-bonding suggests Gln
 529 GLU   ( 588-)  S   H-bonding suggests Gln; but Alt-Rotamer
 578 ASP   (  35-)  B   H-bonding suggests Asn
 603 GLU   (  60-)  B   H-bonding suggests Gln
 610 ASP   (  72-)  B   H-bonding suggests Asn; but Alt-Rotamer
 631 GLU   (  93-)  B   H-bonding suggests Gln
 806 ASP   ( 268-)  B   H-bonding suggests Asn; but Alt-Rotamer
 824 ASP   ( 286-)  B   H-bonding suggests Asn
 840 ASP   ( 302-)  B   H-bonding suggests Asn
 876 GLU   ( 338-)  B   H-bonding suggests Gln
 885 ASP   ( 347-)  B   H-bonding suggests Asn
1002 GLU   ( 464-)  B   H-bonding suggests Gln
1050 GLU   ( 545-)  T   H-bonding suggests Gln
1093 GLU   ( 588-)  T   H-bonding suggests Gln; 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 :  -1.164
  2nd generation packing quality :  -1.275
  Ramachandran plot appearance   :  -3.371 (poor)
  chi-1/chi-2 rotamer normality  :  -4.698 (bad)
  Backbone conformation          :  -0.561

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.041
  Bond angles                    :   1.936
  Omega angle restraints         :   1.049
  Side chain planarity           :   1.189
  Improper dihedral distribution :   1.684 (loose)
  B-factor distribution          :   0.760
  Inside/Outside distribution    :   1.056

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 : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :  -0.1
  Ramachandran plot appearance   :  -1.1
  chi-1/chi-2 rotamer normality  :  -2.6
  Backbone conformation          :  -0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.041
  Bond angles                    :   1.936
  Omega angle restraints         :   1.049
  Side chain planarity           :   1.189
  Improper dihedral distribution :   1.684 (loose)
  B-factor distribution          :   0.760
  Inside/Outside distribution    :   1.056
==============

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.