WHAT IF Check report

This file was created 2013-12-10 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 pdb4i9q.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    =  73.781  B   = 119.412  C    = 146.016
    Alpha=  90.000  Beta=  90.260  Gamma=  90.000

Dimensions of a reduced cell

    A    =  73.781  B   = 119.412  C    = 146.016
    Alpha=  90.000  Beta=  90.260  Gamma=  90.000

Dimensions of the conventional cell

    A    =  73.781  B   = 119.412  C    = 146.016
    Alpha=  90.000  Beta=  89.740  Gamma=  90.000

Transformation to conventional cell

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

Crystal class of the cell: MONOCLINIC

Crystal class of the conventional CELL: ORTHORHOMBIC

Space group name: P 1 21 1

Bravais type of conventional cell is: P

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

Warning: Ligands for which topology could not be determined

The ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms, or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

1781 XG4   (1001-)  A  -
1782 XG4   (1002-)  A  -
1785 XG4   (1001-)  B  -
1786 XG4   (1002-)  B  -

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

 127 SER   ( 127-)  A  -
 196 GLU   ( 196-)  A  -
 299 ASN   ( 299-)  A  -
 531 LEU   ( 580-)  A  -
 623 GLU   ( 672-)  A  -
 832 GLU   ( 881-)  A  -
 836 SER   ( 885-)  A  -
 849 DADE  (   3-)  T  -
 991 SER   ( 127-)  B  -
1070 GLN   ( 206-)  B  -
1158 SER   ( 294-)  B  -
1159 GLU   ( 295-)  B  -
1194 ARG   ( 330-)  B  -
1722 SER   ( 885-)  B  -

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

 127 SER   ( 127-)  A  -
 196 GLU   ( 196-)  A  -
 299 ASN   ( 299-)  A  -
 414 SER   ( 414-)  A  -
 531 LEU   ( 580-)  A  -
 623 GLU   ( 672-)  A  -
 832 GLU   ( 881-)  A  -
 836 SER   ( 885-)  A  -
 849 DADE  (   3-)  T  -
 991 SER   ( 127-)  B  -
1070 GLN   ( 206-)  B  -
1158 SER   ( 294-)  B  -
1159 GLU   ( 295-)  B  -
1194 ARG   ( 330-)  B  -
1278 SER   ( 414-)  B  -
1722 SER   ( 885-)  B  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

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

Warning: Artificial side chains detected

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

  71 TRP   (  71-)  A
 439 LEU   ( 439-)  A
1249 SER   ( 385-)  B
1594 GLU   ( 757-)  B

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'.

1365 GLU   ( 501-)  B      CG
1365 GLU   ( 501-)  B      CD
1365 GLU   ( 501-)  B      OE1
1365 GLU   ( 501-)  B      OE2
1368 LYS   ( 531-)  B      CG
1368 LYS   ( 531-)  B      CD
1368 LYS   ( 531-)  B      CE
1368 LYS   ( 531-)  B      NZ
1369 LYS   ( 532-)  B      CG
1369 LYS   ( 532-)  B      CD
1369 LYS   ( 532-)  B      CE
1369 LYS   ( 532-)  B      NZ
1377 GLU   ( 540-)  B      CG
1377 GLU   ( 540-)  B      CD
1377 GLU   ( 540-)  B      OE1
1377 GLU   ( 540-)  B      OE2

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.

1063 MET   ( 199-)  B    High
1739 DCYT  ( 104-)  P    High
1751 DTHY  (   1-)  D    High
1752 DCYT  (   2-)  D    High
1767 DCYT  (  17-)  D    High
1768 DGUA  ( 103-)  C    High
1769 DCYT  ( 104-)  C    High
1770 DGUA  ( 105-)  C    High
1771 DGUA  ( 106-)  C    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. 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: 14

Crystal temperature (K) :100.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Nomenclature related problems

Warning: Tyrosine convention problem

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

 277 TYR   ( 277-)  A
1169 TYR   ( 305-)  B

Warning: Phenylalanine convention problem

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

 567 PHE   ( 616-)  A
 652 PHE   ( 701-)  A
1491 PHE   ( 654-)  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.

  17 GLU   (  17-)  A
  32 GLU   (  32-)  A
  76 GLU   (  76-)  A
 160 GLU   ( 160-)  A
 172 GLU   ( 172-)  A
 194 GLU   ( 194-)  A
 219 GLU   ( 219-)  A
 254 GLU   ( 254-)  A
 295 GLU   ( 295-)  A
 314 GLU   ( 314-)  A
 375 GLU   ( 375-)  A
 448 GLU   ( 448-)  A
 474 GLU   ( 474-)  A
 500 GLU   ( 549-)  A
 563 GLU   ( 612-)  A
 589 GLU   ( 638-)  A
 623 GLU   ( 672-)  A
 698 GLU   ( 747-)  A
 706 GLU   ( 755-)  A
 713 GLU   ( 762-)  A
 721 GLU   ( 770-)  A
 777 GLU   ( 826-)  A
 779 GLU   ( 828-)  A
 832 GLU   ( 881-)  A
 843 GLU   ( 892-)  A
 881 GLU   (  17-)  B
 896 GLU   (  32-)  B
 964 GLU   ( 100-)  B
 989 GLU   ( 125-)  B
1024 GLU   ( 160-)  B
1036 GLU   ( 172-)  B
1058 GLU   ( 194-)  B
1083 GLU   ( 219-)  B
1178 GLU   ( 314-)  B
1338 GLU   ( 474-)  B
1444 GLU   ( 607-)  B
1449 GLU   ( 612-)  B
1451 GLU   ( 614-)  B
1509 GLU   ( 672-)  B
1584 GLU   ( 747-)  B
1592 GLU   ( 755-)  B
1607 GLU   ( 770-)  B
1663 GLU   ( 826-)  B
1665 GLU   ( 828-)  B
1674 GLU   ( 837-)  B
1710 GLU   ( 873-)  B
1718 GLU   ( 881-)  B

Geometric checks

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.999265  0.000015  0.000374|
 |  0.000015  0.999403  0.000007|
 |  0.000374  0.000007  0.999721|
Proposed new scale matrix

 |  0.013564  0.000000  0.000057|
 |  0.000000  0.008379  0.000000|
 | -0.000003  0.000000  0.006851|
With corresponding cell

    A    =  73.725  B   = 119.346  C    = 145.967
    Alpha=  90.002  Beta=  90.219  Gamma=  90.001

The CRYST1 cell dimensions

    A    =  73.781  B   = 119.412  C    = 146.016
    Alpha=  90.000  Beta=  90.260  Gamma=  90.000

Variance: 34.953
(Under-)estimated Z-score: 4.357

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.

 847 DTHY  (   1-)  T      O4   C4   N3  122.33    4.0
 850 DCYT  (   4-)  T      OP2  P   -O3*  95.02   -4.2
 850 DCYT  (   4-)  T      OP1  P    OP2 138.87   12.8
 851 DGUA  (   5-)  T      N9   C8   N7  113.39    4.6
 855 DGUA  (   9-)  T      N9   C8   N7  113.56    4.9
 858 DGUA  (  12-)  T      N9   C8   N7  113.46    4.7
 862 DGUA  (  16-)  T      N9   C8   N7  113.52    4.8
 863 DCYT  (  17-)  T      C3'  C2'  C1'  96.90   -4.1
 863 DCYT  (  17-)  T      O4'  C1'  N1  111.08    4.1
 864 DGUA  (  18-)  T      N9   C8   N7  113.42    4.6
1738 DGUA  ( 103-)  P      N9   C8   N7  113.48    4.8
1740 DGUA  ( 105-)  P      N9   C8   N7  113.55    4.9
1741 DGUA  ( 106-)  P      N9   C8   N7  113.51    4.8
1744 DTHY  ( 109-)  P      O4   C4   N3  122.30    4.0
1745 DGUA  ( 110-)  P      N9   C8   N7  113.46    4.7
1755 DGUA  (   5-)  D      N9   C8   N7  113.47    4.7
1759 DGUA  (   9-)  D      N9   C8   N7  113.53    4.9
1762 DGUA  (  12-)  D      N9   C8   N7  113.40    4.6
1763 DTHY  (  13-)  D      O4   C4   N3  122.30    4.0
1766 DGUA  (  16-)  D      N9   C8   N7  113.49    4.8
1768 DGUA  ( 103-)  C      N9   C8   N7  113.27    4.3
1770 DGUA  ( 105-)  C      N9   C8   N7  113.39    4.6
1771 DGUA  ( 106-)  C      N9   C8   N7  113.51    4.8
1774 DTHY  ( 109-)  C      O4   C4   N3  122.35    4.1
1775 DGUA  ( 110-)  C      N9   C8   N7  113.46    4.7
1776 DCYT  ( 111-)  C      O4'  C1'  N1  111.36    4.5
1777 DTHY  ( 112-)  C      O4   C4   N3  122.35    4.1
1778 DTHY  ( 113-)  C      O4   C4   N3  122.33    4.1

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.

  17 GLU   (  17-)  A
  32 GLU   (  32-)  A
  76 GLU   (  76-)  A
 160 GLU   ( 160-)  A
 172 GLU   ( 172-)  A
 194 GLU   ( 194-)  A
 219 GLU   ( 219-)  A
 254 GLU   ( 254-)  A
 295 GLU   ( 295-)  A
 314 GLU   ( 314-)  A
 375 GLU   ( 375-)  A
 448 GLU   ( 448-)  A
 474 GLU   ( 474-)  A
 500 GLU   ( 549-)  A
 563 GLU   ( 612-)  A
 589 GLU   ( 638-)  A
 623 GLU   ( 672-)  A
 698 GLU   ( 747-)  A
 706 GLU   ( 755-)  A
 713 GLU   ( 762-)  A
 721 GLU   ( 770-)  A
 777 GLU   ( 826-)  A
 779 GLU   ( 828-)  A
 832 GLU   ( 881-)  A
 843 GLU   ( 892-)  A
 881 GLU   (  17-)  B
 896 GLU   (  32-)  B
 964 GLU   ( 100-)  B
 989 GLU   ( 125-)  B
1024 GLU   ( 160-)  B
1036 GLU   ( 172-)  B
1058 GLU   ( 194-)  B
1083 GLU   ( 219-)  B
1178 GLU   ( 314-)  B
1338 GLU   ( 474-)  B
1444 GLU   ( 607-)  B
1449 GLU   ( 612-)  B
1451 GLU   ( 614-)  B
1509 GLU   ( 672-)  B
1584 GLU   ( 747-)  B
1592 GLU   ( 755-)  B
1607 GLU   ( 770-)  B
1663 GLU   ( 826-)  B
1665 GLU   ( 828-)  B
1674 GLU   ( 837-)  B
1710 GLU   ( 873-)  B
1718 GLU   ( 881-)  B

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.

 573 THR   ( 622-)  A    -2.8
1146 PHE   ( 282-)  B    -2.7
1459 THR   ( 622-)  B    -2.7
 499 THR   ( 548-)  A    -2.7
  47 THR   (  47-)  A    -2.5
1078 THR   ( 214-)  B    -2.3
 548 ILE   ( 597-)  A    -2.3
 911 THR   (  47-)  B    -2.1
 214 THR   ( 214-)  A    -2.1
1434 ILE   ( 597-)  B    -2.1
 446 VAL   ( 446-)  A    -2.0
1455 LEU   ( 618-)  B    -2.0
 635 ASP   ( 684-)  A    -2.0
 569 LEU   ( 618-)  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.

  51 ASP   (  51-)  A  Poor phi/psi
  98 ASN   (  98-)  A  Poor phi/psi
 217 ASN   ( 217-)  A  Poor phi/psi
 257 TYR   ( 257-)  A  Poor phi/psi
 282 PHE   ( 282-)  A  Poor phi/psi
 299 ASN   ( 299-)  A  Poor phi/psi
 339 GLN   ( 339-)  A  Poor phi/psi
 352 LYS   ( 352-)  A  Poor phi/psi
 377 ASN   ( 377-)  A  Poor phi/psi
 424 ASN   ( 424-)  A  Poor phi/psi
 445 ALA   ( 445-)  A  Poor phi/psi
 453 VAL   ( 453-)  A  Poor phi/psi
 498 ARG   ( 547-)  A  Poor phi/psi
 499 THR   ( 548-)  A  Poor phi/psi
 563 GLU   ( 612-)  A  Poor phi/psi
 573 THR   ( 622-)  A  Poor phi/psi
 637 GLU   ( 686-)  A  Poor phi/psi
 657 LYS   ( 706-)  A  Poor phi/psi
 667 GLU   ( 716-)  A  Poor phi/psi
 680 GLY   ( 729-)  A  Poor phi/psi
 706 GLU   ( 755-)  A  Poor phi/psi
 738 ASN   ( 787-)  A  Poor phi/psi
 751 LYS   ( 800-)  A  Poor phi/psi
 839 LYS   ( 888-)  A  Poor phi/psi
 845 LYS   ( 894-)  A  Poor phi/psi
And so on for a total of 51 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.

 372 SER   ( 372-)  A    0.36
1236 SER   ( 372-)  B    0.36

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!

   7 THR   (   7-)  A      0
   9 GLU   (   9-)  A      0
  11 ILE   (  11-)  A      0
  13 ASP   (  13-)  A      0
  32 GLU   (  32-)  A      0
  33 TYR   (  33-)  A      0
  45 GLN   (  45-)  A      0
  46 ALA   (  46-)  A      0
  49 TYR   (  49-)  A      0
  52 ILE   (  52-)  A      0
  53 TYR   (  53-)  A      0
  63 ALA   (  63-)  A      0
  64 ASN   (  64-)  A      0
  65 MET   (  65-)  A      0
  83 LEU   (  83-)  A      0
  85 MET   (  85-)  A      0
  86 ASP   (  86-)  A      0
  97 TYR   (  97-)  A      0
  98 ASN   (  98-)  A      0
  99 TYR   (  99-)  A      0
 105 HIS   ( 105-)  A      0
 121 ASP   ( 121-)  A      0
 123 PHE   ( 123-)  A      0
 125 GLU   ( 125-)  A      0
 128 GLN   ( 128-)  A      0
And so on for a total of 648 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 : 3.713

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].

 155 PRO   ( 155-)  A  -113.1 envelop C-gamma (-108 degrees)
 179 PRO   ( 179-)  A   102.7 envelop C-beta (108 degrees)
 800 PRO   ( 849-)  A   101.3 envelop C-beta (108 degrees)
1302 PRO   ( 438-)  B   101.2 envelop C-beta (108 degrees)
1686 PRO   ( 849-)  B   101.9 envelop C-beta (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.

 498 ARG   ( 547-)  A      O   <->  500 GLU   ( 549-)  A      N      0.48    2.22  INTRA BF
 959 ASP   (  95-)  B      OD1 <-> 1238 LYS   ( 374-)  B      NZ     0.43    2.27  INTRA BF
 719 GLU   ( 768-)  A      O   <->  723 ARG   ( 772-)  A      NH2    0.41    2.29  INTRA
 500 GLU   ( 549-)  A      O   <->  504 MET   ( 553-)  A      N      0.39    2.31  INTRA BF
 284 ASN   ( 284-)  A      ND2 <-> 1748 DTHY  ( 113-)  P      OP2    0.39    2.31  INTRA BL
1380 PHE   ( 543-)  B      O   <-> 1384 ARG   ( 547-)  B      NH2    0.38    2.32  INTRA BF
1746 DCYT  ( 111-)  P      N4  <-> 1791 HOH   ( 204 )  P      O      0.37    2.33  INTRA BL
 553 ASN   ( 602-)  A      O   <->  557 ASN   ( 606-)  A      ND2    0.37    2.33  INTRA BL
1505 ARG   ( 668-)  B      NH1 <-> 1792 HOH   (1164 )  B      O      0.37    2.33  INTRA BF
1149 GLN   ( 285-)  B      NE2 <-> 1792 HOH   (1202 )  B      O      0.37    2.33  INTRA
1439 ASN   ( 602-)  B      O   <-> 1443 ASN   ( 606-)  B      ND2    0.36    2.34  INTRA BL
 126 PRO   ( 126-)  A      O   <->  228 ASN   ( 228-)  A      ND2    0.34    2.36  INTRA BF
1360 GLY   ( 496-)  B      O   <-> 1364 LYS   ( 500-)  B      N      0.34    2.36  INTRA BF
 609 ARG   ( 658-)  A      NH1 <-> 1789 HOH   (1174 )  A      O      0.34    2.36  INTRA BF
 789 GLY   ( 838-)  A      N   <-> 1789 HOH   (1169 )  A      O      0.33    2.37  INTRA BL
 243 SER   ( 243-)  A      O   <->  246 ARG   ( 246-)  A      NH1    0.32    2.38  INTRA BF
1763 DTHY  (  13-)  D      N3  <-> 1772 DADE  ( 107-)  C      N1     0.32    2.68  INTRA BF
1203 GLN   ( 339-)  B      OE1 <-> 1206 ASN   ( 342-)  B      ND2    0.32    2.38  INTRA
 854 DADE  (   8-)  T      N1  <-> 1747 DTHY  ( 112-)  P      N3     0.32    2.68  INTRA BL
 685 LYS   ( 734-)  A      NZ  <-> 1789 HOH   (1305 )  A      O      0.32    2.38  INTRA BL
 861 DCYT  (  15-)  T      O2  <-> 1740 DGUA  ( 105-)  P      N2     0.31    2.39  INTRA BF
1124 ARG   ( 260-)  B      NH2 <-> 1752 DCYT  (   2-)  D      OP2    0.30    2.40  INTRA BF
 849 DADE  (   3-)  T    A N6  <-> 1790 HOH   ( 109 )  T      O      0.30    2.40  INTRA BF
1762 DGUA  (  12-)  D      N2  <-> 1773 DCYT  ( 108-)  C      O2     0.30    2.40  INTRA BF
 339 GLN   ( 339-)  A      OE1 <->  342 ASN   ( 342-)  A      ND2    0.30    2.40  INTRA BL
And so on for a total of 254 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.

 256 MET   ( 256-)  A      -7.62
1120 MET   ( 256-)  B      -7.60
1020 TYR   ( 156-)  B      -7.34
 593 ARG   ( 642-)  A      -7.26
 156 TYR   ( 156-)  A      -7.23
1255 TYR   ( 391-)  B      -7.20
 391 TYR   ( 391-)  A      -7.11
1121 TYR   ( 257-)  B      -6.89
1479 ARG   ( 642-)  B      -6.66
 257 TYR   ( 257-)  A      -6.36
 917 TYR   (  53-)  B      -6.35
 751 LYS   ( 800-)  A      -6.35
 498 ARG   ( 547-)  A      -6.32
 845 LYS   ( 894-)  A      -6.16
1637 LYS   ( 800-)  B      -6.12
 467 ARG   ( 467-)  A      -6.06
1331 ARG   ( 467-)  B      -5.93
 994 LYS   ( 130-)  B      -5.90
1168 LYS   ( 304-)  B      -5.86
 304 LYS   ( 304-)  A      -5.84
 844 LYS   ( 893-)  A      -5.83
 130 LYS   ( 130-)  A      -5.69
 724 GLN   ( 773-)  A      -5.67
 254 GLU   ( 254-)  A      -5.66
1110 ARG   ( 246-)  B      -5.66
1037 GLN   ( 173-)  B      -5.64
 173 GLN   ( 173-)  A      -5.59
1610 GLN   ( 773-)  B      -5.48
1253 GLN   ( 389-)  B      -5.42
1702 TRP   ( 865-)  B      -5.41
 495 ASN   ( 495-)  A      -5.39
 389 GLN   ( 389-)  A      -5.38
 494 ARG   ( 494-)  A      -5.38
 816 TRP   ( 865-)  A      -5.33
1570 GLN   ( 733-)  B      -5.27
  53 TYR   (  53-)  A      -5.24
1591 GLN   ( 754-)  B      -5.16
 388 VAL   ( 388-)  A      -5.15
1146 PHE   ( 282-)  B      -5.12
 448 GLU   ( 448-)  A      -5.09
1556 ARG   ( 719-)  B      -5.07
1252 VAL   ( 388-)  B      -5.06
 305 TYR   ( 305-)  A      -5.03
 705 GLN   ( 754-)  A      -5.02

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.

 304 LYS   ( 304-)  A       306 - ASP    306- ( A)         -5.25
 844 LYS   ( 893-)  A       846 - ALA    895- ( A)         -5.42
1119 ASN   ( 255-)  B      1121 - TYR    257- ( B)         -6.21
1168 LYS   ( 304-)  B      1170 - ASP    306- ( B)         -5.13

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.

1369 LYS   ( 532-)  B   -2.52
1121 TYR   ( 257-)  B   -2.52
 631 LEU   ( 680-)  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

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

1792 HOH   (1105 )  B      O    -13.53  -43.71  -64.38
1792 HOH   (1152 )  B      O    -13.42  -41.92  -62.98

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

1792 HOH   (1125 )  B      O

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

 105 HIS   ( 105-)  A
 203 ASN   ( 203-)  A
 386 HIS   ( 386-)  A
 515 ASN   ( 564-)  A
 774 GLN   ( 823-)  A
1057 ASN   ( 193-)  B
1516 HIS   ( 679-)  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.

   2 LYS   (   2-)  A      NZ
   5 TYR   (   5-)  A      N
   8 VAL   (   8-)  A      N
  23 ASN   (  23-)  A      N
  40 HIS   (  40-)  A      N
  64 ASN   (  64-)  A      N
  74 ARG   (  74-)  A      NE
  85 MET   (  85-)  A      N
 102 LYS   ( 102-)  A      N
 103 TYR   ( 103-)  A      N
 121 ASP   ( 121-)  A      N
 153 ASN   ( 153-)  A      N
 184 ASP   ( 184-)  A      N
 193 ASN   ( 193-)  A      N
 218 VAL   ( 218-)  A      N
 220 SER   ( 220-)  A      N
 241 ARG   ( 241-)  A      NE
 241 ARG   ( 241-)  A      NH2
 248 THR   ( 248-)  A      N
 257 TYR   ( 257-)  A      N
 287 SER   ( 287-)  A      N
 304 LYS   ( 304-)  A      N
 317 HIS   ( 317-)  A      N
 338 ARG   ( 338-)  A      NE
 342 ASN   ( 342-)  A      N
And so on for a total of 113 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.

 255 ASN   ( 255-)  A      OD1
 509 ASN   ( 558-)  A      OD1
 721 GLU   ( 770-)  A      OE1
1109 HIS   ( 245-)  B      ND1
1393 GLN   ( 556-)  B      OE1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

1783  CA   (1003-)  A   -.-  -.-  Part of ionic cluster
1783  CA   (1003-)  A     0.61   0.82 Scores about as good as NA *1
1784  NA   (1004-)  A   -.-  -.-  Part of ionic cluster
1784  NA   (1004-)  A     0.41   0.49 Scores about as good as  K (Few ligands (4) )
1787  CA   (1003-)  B   -.-  -.-  Part of ionic cluster
1787  CA   (1003-)  B     0.54   0.76 Scores about as good as NA (Few ligands (4) ) *1
1788  NA   (1004-)  B   -.-  -.-  Part of ionic cluster
1788  NA   (1004-)  B   -.-  -.-  Too few ligands (3)

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.

  21 ASP   (  21-)  A   H-bonding suggests Asn; but Alt-Rotamer
 116 GLU   ( 116-)  A   H-bonding suggests Gln
 134 ASP   ( 134-)  A   H-bonding suggests Asn; but Alt-Rotamer
 272 ASP   ( 272-)  A   H-bonding suggests Asn; but Alt-Rotamer
 346 ASP   ( 346-)  A   H-bonding suggests Asn
 585 ASP   ( 634-)  A   H-bonding suggests Asn
 600 ASP   ( 649-)  A   H-bonding suggests Asn
 885 ASP   (  21-)  B   H-bonding suggests Asn; but Alt-Rotamer
 915 ASP   (  51-)  B   H-bonding suggests Asn; but Alt-Rotamer
 959 ASP   (  95-)  B   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
 978 ASP   ( 114-)  B   H-bonding suggests Asn
 998 ASP   ( 134-)  B   H-bonding suggests Asn; but Alt-Rotamer
1014 ASP   ( 150-)  B   H-bonding suggests Asn; but Alt-Rotamer
1048 ASP   ( 184-)  B   H-bonding suggests Asn
1136 ASP   ( 272-)  B   H-bonding suggests Asn; but Alt-Rotamer
1210 ASP   ( 346-)  B   H-bonding suggests Asn
1239 GLU   ( 375-)  B   H-bonding suggests Gln
1275 ASP   ( 411-)  B   H-bonding suggests Asn
1471 ASP   ( 634-)  B   H-bonding suggests Asn
1486 ASP   ( 649-)  B   H-bonding suggests Asn
1607 GLU   ( 770-)  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 :  -0.588
  2nd generation packing quality :  -1.439
  Ramachandran plot appearance   :  -1.405
  chi-1/chi-2 rotamer normality  :  -0.804
  Backbone conformation          :  -0.874

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.228 (tight)
  Bond angles                    :   0.453 (tight)
  Omega angle restraints         :   0.675 (tight)
  Side chain planarity           :   0.126 (tight)
  Improper dihedral distribution :   0.345
  B-factor distribution          :   0.893
  Inside/Outside distribution    :   0.993

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 : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.0
  2nd generation packing quality :  -0.6
  Ramachandran plot appearance   :   0.0
  chi-1/chi-2 rotamer normality  :   0.5
  Backbone conformation          :  -0.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.228 (tight)
  Bond angles                    :   0.453 (tight)
  Omega angle restraints         :   0.675 (tight)
  Side chain planarity           :   0.126 (tight)
  Improper dihedral distribution :   0.345
  B-factor distribution          :   0.893
  Inside/Outside distribution    :   0.993
==============

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.