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 pdb2nt1.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    = 110.185  B   =  91.792  C    = 153.036
    Alpha=  90.000  Beta= 110.910  Gamma=  90.000

Dimensions of a reduced cell

    A    =  91.792  B   = 110.185  C    = 153.036
    Alpha= 110.910  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    = 110.185  B   = 285.916  C    =  91.792
    Alpha=  90.000  Beta=  90.000  Gamma=  89.810

Transformation to conventional cell

 |  1.000000  0.000000  0.000000|
 |  1.000000  0.000000  2.000000|
 |  0.000000 -1.000000  0.000000|

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: C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 1.305
CA-only RMS fit for the two chains : 0.862

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.420
CA-only RMS fit for the two chains : 0.166

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 1.285
CA-only RMS fit for the two chains : 0.861

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and C

All-atom RMS fit for the two chains : 1.315
CA-only RMS fit for the two chains : 0.883

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: B and C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and D

All-atom RMS fit for the two chains : 0.532
CA-only RMS fit for the two chains : 0.166

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: B and D

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: Chain identifier inconsistency

WHAT IF believes that certain residue(s) have the wrong chain identifier. It has corrected these chain identifiers as indicated in the table. In this table the residues (ligands, drugs, lipids, ions, sugars, etc) that got their chain identifier corrected are listed with the new chain identifier that is used throughout this validation report. WHAT IF does not care about the chain identifiers of water molecules.

2007 PO4   ( 509-)  D  A
2047 PO4   ( 510-)  B  C

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

1997 PO4   ( 499-)  A  -
1998 PO4   ( 500-)  A  -
1999 PO4   ( 501-)  A  -
2000 PO4   ( 502-)  A  -
2001 PO4   ( 503-)  A  -
2002 PO4   ( 504-)  A  -
2003 PO4   ( 505-)  A  -
2004 PO4   ( 506-)  A  -
2005 PO4   ( 507-)  A  -
2006 PO4   ( 508-)  A  -
2007 PO4   ( 509-)  D  A
2008 PO4   ( 510-)  A  -
2009 PO4   ( 511-)  A  -
2010 PO4   ( 512-)  A  -
2011 PO4   ( 513-)  A  -
2012 PO4   ( 514-)  A  -
2013 PO4   ( 515-)  A  -
2014 PO4   ( 516-)  A  -
2015 PO4   ( 517-)  A  -
2016 PO4   ( 518-)  A  -
2017 PO4   ( 519-)  A  -
2018 PO4   ( 499-)  B  -
2019 PO4   ( 500-)  B  -
2020 PO4   ( 501-)  B  -
2021 PO4   ( 502-)  B  -
And so on for a total of 78 lines.

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

  57 GLN   (  57-)  A    0.50
  73 GLN   (  73-)  A    0.50
 151 GLU   ( 151-)  A    0.50
 358 ASP   ( 358-)  A    0.50
 388 GLU   ( 388-)  A    0.50
 554 GLN   (  57-)  B    0.50
 570 GLN   (  73-)  B    0.50
 648 GLU   ( 151-)  B    0.50
 855 ASP   ( 358-)  B    0.50
 885 GLU   ( 388-)  B    0.50
1051 GLN   (  57-)  C    0.50
1067 GLN   (  73-)  C    0.50
1145 GLU   ( 151-)  C    0.50
1352 ASP   ( 358-)  C    0.50
1382 GLU   ( 388-)  C    0.50
1548 GLN   (  57-)  D    0.50
1564 GLN   (  73-)  D    0.50
1642 GLU   ( 151-)  D    0.50
1849 ASP   ( 358-)  D    0.50
1879 GLU   ( 388-)  D    0.50

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: 0

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

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

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

  11 TYR   (  11-)  A
  22 TYR   (  22-)  A
 108 TYR   ( 108-)  A
 116 TYR   ( 116-)  A
 135 TYR   ( 135-)  A
 205 TYR   ( 205-)  A
 212 TYR   ( 212-)  A
 304 TYR   ( 304-)  A
 313 TYR   ( 313-)  A
 373 TYR   ( 373-)  A
 412 TYR   ( 412-)  A
 418 TYR   ( 418-)  A
 487 TYR   ( 487-)  A
 492 TYR   ( 492-)  A
 508 TYR   (  11-)  B
 519 TYR   (  22-)  B
 605 TYR   ( 108-)  B
 613 TYR   ( 116-)  B
 632 TYR   ( 135-)  B
 709 TYR   ( 212-)  B
 801 TYR   ( 304-)  B
 870 TYR   ( 373-)  B
 909 TYR   ( 412-)  B
 984 TYR   ( 487-)  B
 989 TYR   ( 492-)  B
1005 TYR   (  11-)  C
1016 TYR   (  22-)  C
1102 TYR   ( 108-)  C
1110 TYR   ( 116-)  C
1129 TYR   ( 135-)  C
1199 TYR   ( 205-)  C
1206 TYR   ( 212-)  C
1298 TYR   ( 304-)  C
1367 TYR   ( 373-)  C
1406 TYR   ( 412-)  C
1481 TYR   ( 487-)  C
1502 TYR   (  11-)  D
1513 TYR   (  22-)  D
1599 TYR   ( 108-)  D
1607 TYR   ( 116-)  D
1626 TYR   ( 135-)  D
1696 TYR   ( 205-)  D
1703 TYR   ( 212-)  D
1795 TYR   ( 304-)  D
1864 TYR   ( 373-)  D
1903 TYR   ( 412-)  D
1909 TYR   ( 418-)  D
1978 TYR   ( 487-)  D

Warning: Phenylalanine convention problem

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

  26 PHE   (  26-)  A
  75 PHE   (  75-)  A
 109 PHE   ( 109-)  A
 142 PHE   ( 142-)  A
 147 PHE   ( 147-)  A
 246 PHE   ( 246-)  A
 331 PHE   ( 331-)  A
 417 PHE   ( 417-)  A
 426 PHE   ( 426-)  A
 523 PHE   (  26-)  B
 528 PHE   (  31-)  B
 572 PHE   (  75-)  B
 578 PHE   (  81-)  B
 606 PHE   ( 109-)  B
 639 PHE   ( 142-)  B
 644 PHE   ( 147-)  B
 828 PHE   ( 331-)  B
 844 PHE   ( 347-)  B
 908 PHE   ( 411-)  B
 914 PHE   ( 417-)  B
 923 PHE   ( 426-)  B
1020 PHE   (  26-)  C
1069 PHE   (  75-)  C
1103 PHE   ( 109-)  C
1136 PHE   ( 142-)  C
1141 PHE   ( 147-)  C
1240 PHE   ( 246-)  C
1310 PHE   ( 316-)  C
1405 PHE   ( 411-)  C
1411 PHE   ( 417-)  C
1420 PHE   ( 426-)  C
1517 PHE   (  26-)  D
1522 PHE   (  31-)  D
1566 PHE   (  75-)  D
1572 PHE   (  81-)  D
1600 PHE   ( 109-)  D
1619 PHE   ( 128-)  D
1633 PHE   ( 142-)  D
1638 PHE   ( 147-)  D
1737 PHE   ( 246-)  D
1822 PHE   ( 331-)  D
1838 PHE   ( 347-)  D
1888 PHE   ( 397-)  D
1902 PHE   ( 411-)  D
1908 PHE   ( 417-)  D
1914 PHE   ( 423-)  D
1917 PHE   ( 426-)  D

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.

 153 ASP   ( 153-)  A
 650 ASP   ( 153-)  B
1644 ASP   ( 153-)  D

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.

 111 GLU   ( 111-)  A
 609 GLU   ( 112-)  B
 648 GLU   ( 151-)  B
 846 GLU   ( 349-)  B
1066 GLU   (  72-)  C
1105 GLU   ( 111-)  C
1106 GLU   ( 112-)  C
1541 GLU   (  50-)  D
1563 GLU   (  72-)  D
1602 GLU   ( 111-)  D
1603 GLU   ( 112-)  D
1642 GLU   ( 151-)  D

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.

 111 GLU   ( 111-)  A      CG   CD    1.62    4.3
 169 GLN   ( 169-)  A      CB   CG    1.69    5.5
 352 VAL   ( 352-)  A      CA   CB    1.62    4.3
 375 VAL   ( 375-)  A      CA   CB    1.63    4.9
 379 THR   ( 379-)  A      CB   CG2   1.38   -4.4
 907 THR   ( 410-)  B      CA   CB    1.61    4.2
1055 THR   (  61-)  C      CA   CB    1.62    4.5
1160 GLN   ( 166-)  C      CG   CD    1.64    4.9
1163 GLN   ( 169-)  C      CB   CG    1.67    5.1
1363 THR   ( 369-)  C      CA   CB    1.62    4.3
1901 THR   ( 410-)  D      CA   CB    1.65    6.0
1509 CYS   (  18-)  D      SG  -SG*   2.21    4.2
1514 CYS   (  23-)  D      SG  -SG*   2.21    4.2

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

 |  0.995044  0.000214  0.000101|
 |  0.000214  0.996018 -0.000160|
 |  0.000101 -0.000160  0.995298|
Proposed new scale matrix

 |  0.009121 -0.000001  0.003482|
 | -0.000002  0.010938  0.000002|
 |  0.000000  0.000001  0.007028|
With corresponding cell

    A    = 109.640  B   =  91.428  C    = 152.307
    Alpha=  90.026  Beta= 110.898  Gamma=  89.975

The CRYST1 cell dimensions

    A    = 110.185  B   =  91.792  C    = 153.036
    Alpha=  90.000  Beta= 110.910  Gamma=  90.000

Variance: 1411.473
(Under-)estimated Z-score: 27.689

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.

  39 ARG   (  39-)  A      CG   CD   NE  120.53    5.9
  44 ARG   (  44-)  A      CB   CG   CD  101.63   -6.2
 169 GLN   ( 169-)  A     -C    N    CA  128.94    4.0
 206 HIS   ( 206-)  A      CG   ND1  CE1 109.67    4.1
 344 GLY   ( 344-)  A      N    CA   C   129.42    5.8
 379 THR   ( 379-)  A      C    CA   CB  119.84    5.1
 422 HIS   ( 422-)  A      CG   ND1  CE1 109.61    4.0
 541 ARG   (  44-)  B      CB   CG   CD  104.71   -4.7
 560 THR   (  63-)  B     -CA  -C    N   125.67    4.4
 560 THR   (  63-)  B     -C    N    CA  135.82    7.8
 560 THR   (  63-)  B      N    CA   CB  118.81    4.9
 770 HIS   ( 273-)  B      CG   ND1  CE1 109.97    4.4
 787 HIS   ( 290-)  B      CG   ND1  CE1 109.83    4.2
 803 HIS   ( 306-)  B      CG   ND1  CE1 109.84    4.2
 814 LEU   ( 317-)  B      CA   CB   CG  131.07    4.2
 843 LYS   ( 346-)  B      N    CA   C    99.26   -4.3
 862 HIS   ( 365-)  B      CG   ND1  CE1 109.61    4.0
 892 ARG   ( 395-)  B      CG   CD   NE  117.34    4.0
1033 ARG   (  39-)  C      CG   CD   NE  117.58    4.2
1033 ARG   (  39-)  C      CD   NE   CZ  130.87    5.1
1038 ARG   (  44-)  C      CB   CG   CD   99.74   -7.2
1086 ASN   (  92-)  C      N    CA   C    97.08   -5.0
1156 HIS   ( 162-)  C      CG   ND1  CE1 109.71    4.1
1198 ILE   ( 204-)  C      C    CA   CB  100.92   -4.8
1279 ARG   ( 285-)  C      CB   CG   CD  105.80   -4.1
1280 LEU   ( 286-)  C      CA   CB   CG  132.88    4.7
1300 HIS   ( 306-)  C      CG   ND1  CE1 109.84    4.2
1306 TRP   ( 312-)  C      CA   CB   CG  121.96    4.4
1307 TYR   ( 313-)  C     -C    N    CA  110.62   -6.2
1308 LEU   ( 314-)  C     -CA  -C    N   125.17    4.5
1308 LEU   ( 314-)  C     -C    N    CA  137.66    8.9
1308 LEU   ( 314-)  C      C    CA   CB  118.83    4.6
1359 HIS   ( 365-)  C      CG   ND1  CE1 109.60    4.0
1360 SER   ( 366-)  C      C    CA   CB  119.02    4.7
1373 THR   ( 379-)  C      C    CA   CB  121.01    5.7
1390 ASN   ( 396-)  C     -C    N    CA  128.99    4.0
1427 ARG   ( 433-)  C      CB   CG   CD  105.95   -4.1
1445 HIS   ( 451-)  C      CG   ND1  CE1 109.60    4.0
1484 HIS   ( 490-)  C      CG   ND1  CE1 109.74    4.1
1491 GLN   ( 497-)  C      C    CA   CB  102.38   -4.1
1535 ARG   (  44-)  D      CB   CG   CD  103.79   -5.2
1551 HIS   (  60-)  D      CG   ND1  CE1 109.70    4.1
1584 ILE   (  93-)  D      N    CA   CB  118.40    4.6
1622 ARG   ( 131-)  D      CB   CG   CD  104.80   -4.6
1764 HIS   ( 273-)  D      CG   ND1  CE1 109.70    4.1
1781 HIS   ( 290-)  D      CG   ND1  CE1 109.96    4.4
1797 HIS   ( 306-)  D      CG   ND1  CE1 109.65    4.0
1819 HIS   ( 328-)  D      CG   ND1  CE1 109.71    4.1
1971 LEU   ( 480-)  D      CA   CB   CG  131.72    4.4

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.

 111 GLU   ( 111-)  A
 153 ASP   ( 153-)  A
 609 GLU   ( 112-)  B
 648 GLU   ( 151-)  B
 650 ASP   ( 153-)  B
 846 GLU   ( 349-)  B
1066 GLU   (  72-)  C
1105 GLU   ( 111-)  C
1106 GLU   ( 112-)  C
1541 GLU   (  50-)  D
1563 GLU   (  72-)  D
1602 GLU   ( 111-)  D
1603 GLU   ( 112-)  D
1642 GLU   ( 151-)  D
1644 ASP   ( 153-)  D

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.

 560 THR   (  63-)  B      CA    -6.3    23.31    33.84
1198 ILE   ( 204-)  C      CB    -8.5    21.32    32.31
1307 TYR   ( 313-)  C      CA    -7.1    22.88    34.03
1308 LEU   ( 314-)  C      CA   -13.2    13.94    34.19
The average deviation= 1.280

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.

1086 ASN   (  92-)  C    8.49
 344 GLY   ( 344-)  A    5.68
1793 ALA   ( 302-)  D    5.32
1151 LYS   ( 157-)  C    4.89
1867 VAL   ( 376-)  D    4.85
 157 LYS   ( 157-)  A    4.83
 843 LYS   ( 346-)  B    4.64
1307 TYR   ( 313-)  C    4.09

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.

 482 THR   ( 482-)  A    -3.0
 979 THR   ( 482-)  B    -2.9
1476 THR   ( 482-)  C    -2.7
1973 THR   ( 482-)  D    -2.7
1961 LEU   ( 470-)  D    -2.6
 595 PRO   (  98-)  B    -2.5
1124 ILE   ( 130-)  C    -2.5
 406 ILE   ( 406-)  A    -2.4
 130 ILE   ( 130-)  A    -2.4
 286 LEU   ( 286-)  A    -2.4
1589 PRO   (  98-)  D    -2.4
 379 THR   ( 379-)  A    -2.3
1837 LYS   ( 346-)  D    -2.3
 224 LYS   ( 224-)  A    -2.3
1373 THR   ( 379-)  C    -2.3
1218 LYS   ( 224-)  C    -2.3
 905 LYS   ( 408-)  B    -2.3
1307 TYR   ( 313-)  C    -2.3
1554 THR   (  63-)  D    -2.3
 346 LYS   ( 346-)  A    -2.2
 946 LEU   ( 449-)  B    -2.2
1835 GLY   ( 344-)  D    -2.2
1621 ILE   ( 130-)  D    -2.2
1525 LEU   (  34-)  D    -2.2
1780 PRO   ( 289-)  D    -2.2
1938 VAL   ( 447-)  D    -2.1
1150 LEU   ( 156-)  C    -2.1
 842 SER   ( 345-)  B    -2.1
1007 SER   (  13-)  C    -2.1
 344 GLY   ( 344-)  A    -2.1
 996 ARG   (   2-)  C    -2.1
  39 ARG   (  39-)  A    -2.1
1889 VAL   ( 398-)  D    -2.1
1609 ILE   ( 118-)  D    -2.1
  13 SER   (  13-)  A    -2.1
 846 GLU   ( 349-)  B    -2.1
 347 PHE   ( 347-)  A    -2.1
 944 VAL   ( 447-)  B    -2.0
 627 ILE   ( 130-)  B    -2.0
 891 VAL   ( 394-)  B    -2.0
1885 VAL   ( 394-)  D    -2.0
1280 LEU   ( 286-)  C    -2.0
1940 LEU   ( 449-)  D    -2.0
 743 PHE   ( 246-)  B    -2.0
 345 SER   ( 345-)  A    -2.0
1768 ARG   ( 277-)  D    -2.0
 977 LEU   ( 480-)  B    -2.0
1055 THR   (  61-)  C    -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.

  14 VAL   (  14-)  A  omega poor
  19 ASN   (  19-)  A  Poor phi/psi
  22 TYR   (  22-)  A  omega poor
  46 GLY   (  46-)  A  Poor phi/psi
  51 LEU   (  51-)  A  omega poor
  53 MET   (  53-)  A  omega poor
  55 PRO   (  55-)  A  omega poor
  75 PHE   (  75-)  A  Poor phi/psi
  80 GLY   (  80-)  A  omega poor
  83 GLY   (  83-)  A  omega poor
 108 TYR   ( 108-)  A  omega poor
 124 ALA   ( 124-)  A  Poor phi/psi
 128 PHE   ( 128-)  A  Poor phi/psi
 144 LEU   ( 144-)  A  Poor phi/psi
 170 ARG   ( 170-)  A  PRO omega poor
 192 ASN   ( 192-)  A  Poor phi/psi
 196 SER   ( 196-)  A  omega poor
 221 ALA   ( 221-)  A  omega poor
 224 LYS   ( 224-)  A  Poor phi/psi
 233 GLU   ( 233-)  A  Poor phi/psi
 262 ARG   ( 262-)  A  omega poor
 281 LEU   ( 281-)  A  Poor phi/psi
 288 LEU   ( 288-)  A  PRO omega poor
 323 THR   ( 323-)  A  Poor phi/psi
 344 GLY   ( 344-)  A  omega poor
And so on for a total of 163 lines.

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.109

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.

1857 SER   ( 366-)  D    0.37
1855 SER   ( 364-)  D    0.39
 863 SER   ( 366-)  B    0.39

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!

   6 PRO   (   6-)  A      0
   9 PHE   (   9-)  A      0
  11 TYR   (  11-)  A      0
  12 SER   (  12-)  A      0
  18 CYS   (  18-)  A      0
  19 ASN   (  19-)  A      0
  22 TYR   (  22-)  A      0
  24 ASP   (  24-)  A      0
  26 PHE   (  26-)  A      0
  28 PRO   (  28-)  A      0
  29 PRO   (  29-)  A      0
  33 ALA   (  33-)  A      0
  34 LEU   (  34-)  A      0
  45 SER   (  45-)  A      0
  48 ARG   (  48-)  A      0
  49 MET   (  49-)  A      0
  53 MET   (  53-)  A      0
  57 GLN   (  57-)  A      0
  59 ASN   (  59-)  A      0
  60 HIS   (  60-)  A      0
  61 THR   (  61-)  A      0
  65 LEU   (  65-)  A      0
  70 GLN   (  70-)  A      0
  73 GLN   (  73-)  A      0
  75 PHE   (  75-)  A      0
And so on for a total of 855 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 : 7.271

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!

 692 GLY   ( 195-)  B   1.52   12

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]

 253 PRO   ( 253-)  A    0.19 LOW
 289 PRO   ( 289-)  A    0.20 LOW
 475 PRO   ( 475-)  A    0.18 LOW
 619 PRO   ( 122-)  B    0.46 HIGH
 750 PRO   ( 253-)  B    0.12 LOW
 925 PRO   ( 428-)  B    0.11 LOW
1247 PRO   ( 253-)  C    0.17 LOW
1892 PRO   ( 401-)  D    0.49 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].

  55 PRO   (  55-)  A   -60.8 half-chair C-beta/C-alpha (-54 degrees)
 171 PRO   ( 171-)  A  -128.4 half-chair C-delta/C-gamma (-126 degrees)
 178 PRO   ( 178-)  A   -57.3 half-chair C-beta/C-alpha (-54 degrees)
 182 PRO   ( 182-)  A   107.6 envelop C-beta (108 degrees)
 299 PRO   ( 299-)  A    27.8 envelop C-delta (36 degrees)
 503 PRO   (   6-)  B     7.2 envelop N (0 degrees)
 568 PRO   (  71-)  B  -112.6 envelop C-gamma (-108 degrees)
 595 PRO   (  98-)  B   115.4 envelop C-beta (108 degrees)
 675 PRO   ( 178-)  B   -60.5 half-chair C-beta/C-alpha (-54 degrees)
 679 PRO   ( 182-)  B   109.3 envelop C-beta (108 degrees)
 698 PRO   ( 201-)  B   100.2 envelop C-beta (108 degrees)
 733 PRO   ( 236-)  B  -113.9 envelop C-gamma (-108 degrees)
 786 PRO   ( 289-)  B   -59.8 half-chair C-beta/C-alpha (-54 degrees)
1023 PRO   (  29-)  C   134.5 half-chair C-beta/C-alpha (126 degrees)
1133 PRO   ( 139-)  C  -113.0 envelop C-gamma (-108 degrees)
1172 PRO   ( 178-)  C   -59.0 half-chair C-beta/C-alpha (-54 degrees)
1176 PRO   ( 182-)  C   111.0 envelop C-beta (108 degrees)
1230 PRO   ( 236-)  C  -117.6 half-chair C-delta/C-gamma (-126 degrees)
1283 PRO   ( 289-)  C    47.3 half-chair C-delta/C-gamma (54 degrees)
1589 PRO   (  98-)  D   102.6 envelop C-beta (108 degrees)
1673 PRO   ( 182-)  D   100.1 envelop C-beta (108 degrees)
1736 PRO   ( 245-)  D    46.7 half-chair C-delta/C-gamma (54 degrees)
1780 PRO   ( 289-)  D   -61.6 half-chair C-beta/C-alpha (-54 degrees)
1919 PRO   ( 428-)  D    43.7 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.

 358 ASP   ( 358-)  A      CB  <-> 2075 HOH   ( 878 )  A      O      0.61    2.19  INTRA
1698 GLN   ( 207-)  D      NE2 <-> 1754 ASP   ( 263-)  D      OD1    0.58    2.12  INTRA BL
1803 TRP   ( 312-)  D      CB  <-> 2078 HOH   ( 761 )  D      O      0.57    2.23  INTRA
  73 GLN   (  73-)  A      OE1 <-> 2075 HOH   ( 800 )  A      O      0.57    1.83  INTRA
 207 GLN   ( 207-)  A      NE2 <->  263 ASP   ( 263-)  A      OD1    0.56    2.14  INTRA
 704 GLN   ( 207-)  B      NE2 <->  760 ASP   ( 263-)  B      OD1    0.56    2.14  INTRA
 502 ILE   (   5-)  B      CD1 <->  519 TYR   (  22-)  B      CE1    0.54    2.66  INTRA
 844 PHE   ( 347-)  B      N   <-> 2076 HOH   ( 800 )  B      O      0.51    2.19  INTRA BF
  84 ALA   (  84-)  A      CB  <-> 2016 PO4   ( 518-)  A      O4     0.50    2.30  INTRA BF
1067 GLN   (  73-)  C      CG  <-> 2077 HOH   (1142 )  C      O      0.48    2.32  INTRA
1992 NAG   ( 498-)  D      O4  <-> 2078 HOH   ( 769 )  D      O      0.47    1.93  INTRA
 120 ARG   ( 120-)  A      CD  <-> 2016 PO4   ( 518-)  A      O2     0.47    2.33  INTRA BF
1038 ARG   (  44-)  C      CD  <-> 2038 PO4   ( 501-)  C      O1     0.46    2.34  INTRA
 541 ARG   (  44-)  B      CD  <-> 2021 PO4   ( 502-)  B      O4     0.46    2.34  INTRA
1337 VAL   ( 343-)  C      CG1 <-> 2077 HOH   ( 963 )  C      O      0.46    2.34  INTRA BF
 120 ARG   ( 120-)  A      NH1 <-> 2016 PO4   ( 518-)  A      O3     0.44    2.26  INTRA BF
1879 GLU   ( 388-)  D      CB  <-> 2078 HOH   ( 606 )  D      O      0.43    2.37  INTRA
1333 SER   ( 339-)  C      O   <-> 2054 PO4   ( 517-)  C      O3     0.42    1.98  INTRA BF
1198 ILE   ( 204-)  C      CD1 <-> 2077 HOH   (1138 )  C      O      0.42    2.38  INTRA
 703 HIS   ( 206-)  B      NE2 <->  752 HIS   ( 255-)  B      NE2    0.42    2.58  INTRA BL
1201 GLN   ( 207-)  C      NE2 <-> 1257 ASP   ( 263-)  C      OD1    0.41    2.29  INTRA
1932 LYS   ( 441-)  D      NZ  <-> 2078 HOH   ( 628 )  D      O      0.41    2.29  INTRA BF
 169 GLN   ( 169-)  A      CG  <->  170 ARG   ( 170-)  A      N      0.41    2.59  INTRA BF
 186 LYS   ( 186-)  A      NZ  <-> 2075 HOH   ( 685 )  A      O      0.41    2.29  INTRA BL
1753 ARG   ( 262-)  D      NH2 <-> 2078 HOH   ( 754 )  D      O      0.39    2.31  INTRA
And so on for a total of 406 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

 938 LYS   ( 441-)  B      -6.75
1163 GLN   ( 169-)  C      -6.64
 441 LYS   ( 441-)  A      -6.63
 666 GLN   ( 169-)  B      -6.63
1932 LYS   ( 441-)  D      -6.60
1435 LYS   ( 441-)  C      -6.45
1660 GLN   ( 169-)  D      -6.13
 814 LEU   ( 317-)  B      -6.02
1194 GLN   ( 200-)  C      -5.95
 200 GLN   ( 200-)  A      -5.80
 697 GLN   ( 200-)  B      -5.76
 531 LEU   (  34-)  B      -5.67
 262 ARG   ( 262-)  A      -5.57
1987 ARG   ( 496-)  D      -5.56
1256 ARG   ( 262-)  C      -5.53
1525 LEU   (  34-)  D      -5.50
1691 GLN   ( 200-)  D      -5.48
1753 ARG   ( 262-)  D      -5.47
 993 ARG   ( 496-)  B      -5.46
 759 ARG   ( 262-)  B      -5.40
1535 ARG   (  44-)  D      -5.35
 496 ARG   ( 496-)  A      -5.32
1551 HIS   (  60-)  D      -5.31
1522 PHE   (  31-)  D      -5.27
 557 HIS   (  60-)  B      -5.24
 528 PHE   (  31-)  B      -5.21
 169 GLN   ( 169-)  A      -5.21
1341 PHE   ( 347-)  C      -5.19
 541 ARG   (  44-)  B      -5.17
1025 PHE   (  31-)  C      -5.15
1490 ARG   ( 496-)  C      -5.13
  44 ARG   (  44-)  A      -5.13
1038 ARG   (  44-)  C      -5.12
1344 GLN   ( 350-)  C      -5.12
1188 LYS   ( 194-)  C      -5.11
  31 PHE   (  31-)  A      -5.11
 123 MET   ( 123-)  A      -5.10
 170 ARG   ( 170-)  A      -5.10
 194 LYS   ( 194-)  A      -5.09
 111 GLU   ( 111-)  A      -5.08
 667 ARG   ( 170-)  B      -5.07
 353 ARG   ( 353-)  A      -5.05
1347 ARG   ( 353-)  C      -5.03

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.

 557 HIS   (  60-)  B       560 - THR     63- ( B)         -4.56
1550 ASN   (  59-)  D      1552 - THR     61- ( D)         -4.73

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: A

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: B

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: C

Note: Quality value plot

The quality value smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -2.0) indicate unusual packing.

Chain identifier: D

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

  62 GLY   (  62-)  A   -2.75
1164 ARG   ( 170-)  C   -2.67
1056 GLY   (  62-)  C   -2.67
1120 CYS   ( 126-)  C   -2.62
 170 ARG   ( 170-)  A   -2.58
1470 ALA   ( 476-)  C   -2.56
 973 ALA   ( 476-)  B   -2.55

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

Error: Water clusters without contacts with non-water atoms

The water molecules listed in the table below are part of water molecule clusters that do not make contacts with non-waters. These water molecules are part of clusters that have a distance at least 1 Angstrom larger than the sum of the Van der Waals radii to the nearest non-solvent atom. Because these kinds of water clusters usually are not observed with X-ray diffraction their presence could indicate a refinement artifact. The number in brackets is the identifier of the water molecule in the input file.

2077 HOH   (1165 )  C      O
2077 HOH   (1166 )  C      O
ERROR. No atoms within 50 A?
ERROR. No atoms within 50 A?

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.

2078 HOH   ( 856 )  D      O    -11.51   10.80   84.26

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.

2075 HOH   ( 663 )  A      O
2075 HOH   ( 734 )  A      O
2075 HOH   ( 770 )  A      O
2075 HOH   ( 788 )  A      O
2075 HOH   ( 818 )  A      O
2075 HOH   ( 868 )  A      O
2075 HOH   ( 877 )  A      O
2076 HOH   ( 671 )  B      O
2076 HOH   ( 774 )  B      O
2076 HOH   ( 783 )  B      O
2076 HOH   ( 798 )  B      O
2077 HOH   ( 865 )  C      O
2077 HOH   ( 960 )  C      O
2077 HOH   ( 963 )  C      O
2077 HOH   (1050 )  C      O
2077 HOH   (1104 )  C      O
2077 HOH   (1133 )  C      O
2077 HOH   (1135 )  C      O
2077 HOH   (1142 )  C      O
2077 HOH   (1165 )  C      O
2077 HOH   (1166 )  C      O
2078 HOH   ( 582 )  D      O
2078 HOH   ( 629 )  D      O
2078 HOH   ( 723 )  D      O
2078 HOH   ( 737 )  D      O
2078 HOH   ( 761 )  D      O
2078 HOH   ( 811 )  D      O
2078 HOH   ( 813 )  D      O
Bound group on Asn; dont flip   19 ASN  (  19-) A
Bound to: 1989 NAG  ( 498-) A
Bound group on Asn; dont flip  516 ASN  (  19-) B
Bound to: 1990 NAG  ( 498-) B
Bound group on Asn; dont flip 1013 ASN  (  19-) C
Bound to: 1991 NAG  ( 498-) C
Bound group on Asn; dont flip 1510 ASN  (  19-) D
Bound to: 1992 NAG  ( 498-) D
ERROR. No convergence in HB2STD
Old,New value: 2537.903 2537.914
ERROR. No convergence in HB2STD
Old,New value: 2538.074 2538.084

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.

  57 GLN   (  57-)  A
 145 HIS   ( 145-)  A
 207 GLN   ( 207-)  A
 328 HIS   ( 328-)  A
 557 HIS   (  60-)  B
 659 HIS   ( 162-)  B
 771 HIS   ( 274-)  B
 825 HIS   ( 328-)  B
 893 ASN   ( 396-)  B
1551 HIS   (  60-)  D
1698 GLN   ( 207-)  D
1765 HIS   ( 274-)  D
1797 HIS   ( 306-)  D
1819 HIS   ( 328-)  D
1931 GLN   ( 440-)  D
1986 HIS   ( 495-)  D

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

  48 ARG   (  48-)  A      N
 120 ARG   ( 120-)  A      NH1
 129 SER   ( 129-)  A      N
 131 ARG   ( 131-)  A      N
 140 ASP   ( 140-)  A      N
 141 ASP   ( 141-)  A      N
 147 PHE   ( 147-)  A      N
 169 GLN   ( 169-)  A      NE2
 172 VAL   ( 172-)  A      N
 177 SER   ( 177-)  A      OG
 184 TRP   ( 184-)  A      N
 194 LYS   ( 194-)  A      N
 199 GLY   ( 199-)  A      N
 228 TRP   ( 228-)  A      NE1
 243 GLY   ( 243-)  A      N
 246 PHE   ( 246-)  A      N
 306 HIS   ( 306-)  A      NE2
 343 VAL   ( 343-)  A      N
 348 TRP   ( 348-)  A      N
 353 ARG   ( 353-)  A      NE
 356 SER   ( 356-)  A      OG
 358 ASP   ( 358-)  A      N
 377 GLY   ( 377-)  A      N
 379 THR   ( 379-)  A      OG1
 382 ASN   ( 382-)  A      ND2
And so on for a total of 123 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.

 112 GLU   ( 112-)  A      OE2
 169 GLN   ( 169-)  A      OE1
 263 ASP   ( 263-)  A      OD1
 273 HIS   ( 273-)  A      ND1
 290 HIS   ( 290-)  A      ND1
 419 HIS   ( 419-)  A      NE2
 584 ASP   (  87-)  B      OD1
 770 HIS   ( 273-)  B      ND1
 808 HIS   ( 311-)  B      ND1
1054 HIS   (  60-)  C      ND1
1147 ASP   ( 153-)  C      OD2
1413 HIS   ( 419-)  C      NE2
1754 ASP   ( 263-)  D      OD1
1797 HIS   ( 306-)  D      ND1
1802 HIS   ( 311-)  D      ND1
1910 HIS   ( 419-)  D      NE2

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and 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 nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple 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 method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

2075 HOH   ( 613 )  A      O  1.01  K  4 Ion-B
2075 HOH   ( 649 )  A      O  0.94  K  4
2075 HOH   ( 733 )  A      O  1.01  K  4 H2O-B
2077 HOH   ( 864 )  C      O  1.02  K  4
2077 HOH   ( 943 )  C      O  0.93  K  5

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.

 112 GLU   ( 112-)  A   H-bonding suggests Gln
 137 ASP   ( 137-)  A   H-bonding suggests Asn
 153 ASP   ( 153-)  A   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
 203 ASP   ( 203-)  A   H-bonding suggests Asn; but Alt-Rotamer
 218 ASP   ( 218-)  A   H-bonding suggests Asn; but Alt-Rotamer
 233 GLU   ( 233-)  A   H-bonding suggests Gln
 380 ASP   ( 380-)  A   H-bonding suggests Asn; but Alt-Rotamer
 399 ASP   ( 399-)  A   H-bonding suggests Asn
 634 ASP   ( 137-)  B   H-bonding suggests Asn
 700 ASP   ( 203-)  B   H-bonding suggests Asn; but Alt-Rotamer
 730 GLU   ( 233-)  B   H-bonding suggests Gln
 812 ASP   ( 315-)  B   H-bonding suggests Asn
1081 ASP   (  87-)  C   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
1147 ASP   ( 153-)  C   H-bonding suggests Asn; Ligand-contact
1197 ASP   ( 203-)  C   H-bonding suggests Asn
1227 GLU   ( 233-)  C   H-bonding suggests Gln
1374 ASP   ( 380-)  C   H-bonding suggests Asn; but Alt-Rotamer
1461 ASP   ( 467-)  C   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
1628 ASP   ( 137-)  D   H-bonding suggests Asn
1694 ASP   ( 203-)  D   H-bonding suggests Asn; but Alt-Rotamer
1709 ASP   ( 218-)  D   H-bonding suggests Asn; but Alt-Rotamer
1724 GLU   ( 233-)  D   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 :  -0.417
  2nd generation packing quality :  -1.672
  Ramachandran plot appearance   :  -1.443
  chi-1/chi-2 rotamer normality  :  -3.109 (poor)
  Backbone conformation          :  -0.409

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.952
  Bond angles                    :   0.961
  Omega angle restraints         :   1.322 (loose)
  Side chain planarity           :   0.957
  Improper dihedral distribution :   1.078
  B-factor distribution          :   0.574
  Inside/Outside distribution    :   1.020

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 :   0.2
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :   0.0
  chi-1/chi-2 rotamer normality  :  -1.5
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.952
  Bond angles                    :   0.961
  Omega angle restraints         :   1.322 (loose)
  Side chain planarity           :   0.957
  Improper dihedral distribution :   1.078
  B-factor distribution          :   0.574
  Inside/Outside distribution    :   1.020
==============

WHAT IF
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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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      protein structures
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Matthews' Coefficient
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      Solvent content of Protein Crystals
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Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
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    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
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Quality Control
    G.Vriend and C.Sander,
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      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.