WHAT IF Check report

This file was created 2011-12-15 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 pdb3gxm.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    = 110.505  B   =  91.779  C    = 152.751
    Alpha=  90.000  Beta= 111.240  Gamma=  90.000

Dimensions of a reduced cell

    A    =  91.779  B   = 110.505  C    = 152.689
    Alpha= 111.180  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    = 110.505  B   = 284.750  C    =  91.779
    Alpha=  90.000  Beta=  90.000  Gamma=  89.966

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 : 1.258
CA-only RMS fit for the two chains : 0.835

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 : 0.445
CA-only RMS fit for the two chains : 0.179

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 : 1.249
CA-only RMS fit for the two chains : 0.815

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 : 1.299
CA-only RMS fit for the two chains : 0.839

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 : 0.545
CA-only RMS fit for the two chains : 0.200

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: 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 SO4   ( 499-)  A  -
1998 SO4   ( 500-)  A  -
1999 SO4   ( 501-)  A  -
2000 SO4   ( 502-)  A  -
2001 SO4   ( 503-)  A  -
2002 SO4   ( 504-)  A  -
2003 SO4   ( 505-)  A  -
2004 SO4   ( 506-)  A  -
2005 SO4   ( 499-)  B  -
2006 SO4   ( 500-)  B  -
2007 SO4   ( 501-)  B  -
2008 SO4   ( 502-)  B  -
2009 SO4   ( 503-)  B  -
2010 SO4   ( 504-)  B  -
2011 SO4   ( 505-)  B  -
2012 SO4   ( 499-)  C  -
2013 SO4   ( 500-)  C  -
2014 SO4   ( 501-)  C  -
2015 SO4   ( 502-)  C  -
2016 SO4   ( 503-)  C  -
2017 SO4   ( 504-)  C  -
2018 SO4   ( 505-)  C  -
2019 SO4   ( 499-)  D  -
2020 SO4   ( 500-)  D  -
2021 SO4   ( 501-)  D  -
2022 SO4   ( 502-)  D  -
2023 SO4   ( 503-)  D  -
2024 SO4   ( 504-)  D  -

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.

 151 GLU   ( 151-)  A    0.50
 648 GLU   ( 151-)  B    0.50
1145 GLU   ( 151-)  C    0.50
1642 GLU   ( 151-)  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

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: 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
 487 TYR   ( 487-)  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
 915 TYR   ( 418-)  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
1307 TYR   ( 313-)  C
1367 TYR   ( 373-)  C
1406 TYR   ( 412-)  C
1481 TYR   ( 487-)  C
1513 TYR   (  22-)  D
1599 TYR   ( 108-)  D
1607 TYR   ( 116-)  D
1624 TYR   ( 133-)  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
1983 TYR   ( 492-)  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
 128 PHE   ( 128-)  A
 142 PHE   ( 142-)  A
 147 PHE   ( 147-)  A
 246 PHE   ( 246-)  A
 316 PHE   ( 316-)  A
 331 PHE   ( 331-)  A
 337 PHE   ( 337-)  A
 417 PHE   ( 417-)  A
 426 PHE   ( 426-)  A
 523 PHE   (  26-)  B
 572 PHE   (  75-)  B
 606 PHE   ( 109-)  B
 625 PHE   ( 128-)  B
 639 PHE   ( 142-)  B
 644 PHE   ( 147-)  B
 813 PHE   ( 316-)  B
 828 PHE   ( 331-)  B
 844 PHE   ( 347-)  B
 908 PHE   ( 411-)  B
 914 PHE   ( 417-)  B
 920 PHE   ( 423-)  B
 923 PHE   ( 426-)  B
And so on for a total of 52 lines.

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
1147 ASP   ( 153-)  C
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.

 112 GLU   ( 112-)  A
 235 GLU   ( 235-)  A
 609 GLU   ( 112-)  B
 648 GLU   ( 151-)  B
 846 GLU   ( 349-)  B
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: 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

 |  0.996828 -0.000075  0.000273|
 | -0.000075  0.997148  0.000053|
 |  0.000273  0.000053  0.996234|
Proposed new scale matrix

 |  0.009077  0.000000  0.003528|
 |  0.000000  0.010927  0.000000|
 | -0.000002  0.000000  0.007051|
With corresponding cell

    A    = 110.159  B   =  91.515  C    = 152.153
    Alpha=  90.001  Beta= 111.223  Gamma=  90.001

The CRYST1 cell dimensions

    A    = 110.505  B   =  91.779  C    = 152.751
    Alpha=  90.000  Beta= 111.240  Gamma=  90.000

Variance: 727.842
(Under-)estimated Z-score: 19.883

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.

  44 ARG   (  44-)  A      CB   CG   CD  103.12   -5.5
 162 HIS   ( 162-)  A      CG   ND1  CE1 109.72    4.1
 165 LEU   ( 165-)  A      CA   CB   CG  130.43    4.0
 206 HIS   ( 206-)  A      CG   ND1  CE1 109.65    4.0
 311 HIS   ( 311-)  A      CG   ND1  CE1 109.85    4.3
 560 THR   (  63-)  B     -C    N    CA  133.40    6.5
 560 THR   (  63-)  B      N    CA   CB  117.55    4.1
 703 HIS   ( 206-)  B      CG   ND1  CE1 109.78    4.2
 752 HIS   ( 255-)  B      CG   ND1  CE1 109.82    4.2
 770 HIS   ( 273-)  B      CG   ND1  CE1 109.64    4.0
 783 LEU   ( 286-)  B      CA   CB   CG  135.11    5.4
 803 HIS   ( 306-)  B      CG   ND1  CE1 109.64    4.0
 817 ALA   ( 320-)  B     -C    N    CA  131.32    5.3
 850 ARG   ( 353-)  B      CB   CG   CD  104.54   -4.8
 850 ARG   ( 353-)  B      CG   CD   NE  117.99    4.4
 992 HIS   ( 495-)  B      CG   ND1  CE1 109.64    4.0
1033 ARG   (  39-)  C      CG   CD   NE  118.94    5.0
1038 ARG   (  44-)  C      CB   CG   CD   99.43   -7.3
1085 LEU   (  91-)  C      C    CA   CB  118.55    4.4
1086 ASN   (  92-)  C      N    CA   C    88.36   -8.2
1308 LEU   ( 314-)  C     -CA  -C    N   124.72    4.3
1308 LEU   ( 314-)  C     -C    N    CA  134.60    7.2
1337 VAL   ( 343-)  C     -C    N    CA  129.35    4.2
1337 VAL   ( 343-)  C      C    CA   CB  117.99    4.2
1338 GLY   ( 344-)  C     -CA  -C    N   124.23    4.0
1338 GLY   ( 344-)  C     -C    N    CA  129.52    5.2
1369 VAL   ( 375-)  C      C    CA   CB  118.07    4.2
1413 HIS   ( 419-)  C      CG   ND1  CE1 109.76    4.2
1416 HIS   ( 422-)  C      CG   ND1  CE1 109.79    4.2
1535 ARG   (  44-)  D      CB   CG   CD  105.64   -4.2
1703 TYR   ( 212-)  D      CA   CB   CG  121.62    4.2
1803 TRP   ( 312-)  D      CA   CB   CG  105.22   -4.4
1971 LEU   ( 480-)  D      CA   CB   CG  132.53    4.6
1986 HIS   ( 495-)  D      CG   ND1  CE1 109.62    4.0

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.

 112 GLU   ( 112-)  A
 153 ASP   ( 153-)  A
 235 GLU   ( 235-)  A
 609 GLU   ( 112-)  B
 648 GLU   ( 151-)  B
 650 ASP   ( 153-)  B
 846 GLU   ( 349-)  B
1105 GLU   ( 111-)  C
1106 GLU   ( 112-)  C
1147 ASP   ( 153-)  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.

1085 LEU   (  91-)  C      CA    -7.9    22.06    34.19
1307 TYR   ( 313-)  C      CA    -8.1    21.21    34.03
1308 LEU   ( 314-)  C      CA    -8.9    20.53    34.19
1337 VAL   ( 343-)  C      CA    -8.8    20.46    33.23
The average deviation= 1.057

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   13.40
1296 ALA   ( 302-)  C    5.20
1589 PRO   (  98-)  D    4.83
1803 TRP   ( 312-)  D    4.80
 343 VAL   ( 343-)  A    4.77
1103 PHE   ( 109-)  C    4.24

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.

 313 TYR   ( 313-)  A    -3.3
1476 THR   ( 482-)  C    -2.8
  30 THR   (  30-)  A    -2.8
 482 THR   ( 482-)  A    -2.8
1337 VAL   ( 343-)  C    -2.7
 967 LEU   ( 470-)  B    -2.6
1961 LEU   ( 470-)  D    -2.6
 843 LYS   ( 346-)  B    -2.5
1218 LYS   ( 224-)  C    -2.5
 979 THR   ( 482-)  B    -2.5
1973 THR   ( 482-)  D    -2.5
  98 PRO   (  98-)  A    -2.4
 595 PRO   (  98-)  B    -2.4
1389 ARG   ( 395-)  C    -2.4
 984 TYR   ( 487-)  B    -2.4
 130 ILE   ( 130-)  A    -2.4
1024 THR   (  30-)  C    -2.3
 814 LEU   ( 317-)  B    -2.3
 224 LYS   ( 224-)  A    -2.3
1889 VAL   ( 398-)  D    -2.3
 379 THR   ( 379-)  A    -2.3
1391 PHE   ( 397-)  C    -2.2
1340 LYS   ( 346-)  C    -2.2
1780 PRO   ( 289-)  D    -2.2
1978 TYR   ( 487-)  D    -2.2
1317 THR   ( 323-)  C    -2.2
 344 GLY   ( 344-)  A    -2.2
 970 LYS   ( 473-)  B    -2.2
 466 LYS   ( 466-)  A    -2.2
 343 VAL   ( 343-)  A    -2.1
 652 LYS   ( 155-)  B    -2.1
 502 ILE   (   5-)  B    -2.1
 905 LYS   ( 408-)  B    -2.1
 447 VAL   ( 447-)  A    -2.1
1980 ILE   ( 489-)  D    -2.1
   2 ARG   (   2-)  A    -2.1
 487 TYR   ( 487-)  A    -2.1
1622 ARG   ( 131-)  D    -2.1
 449 LEU   ( 449-)  A    -2.1
 556 ASN   (  59-)  B    -2.1
1192 LYS   ( 198-)  C    -2.1
 323 THR   ( 323-)  A    -2.0
 196 SER   ( 196-)  A    -2.0
1055 THR   (  61-)  C    -2.0
1972 GLU   ( 481-)  D    -2.0
1441 VAL   ( 447-)  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.

   4 CYS   (   4-)  A  omega poor
  11 TYR   (  11-)  A  omega poor
  13 SER   (  13-)  A  Poor phi/psi
  14 VAL   (  14-)  A  omega poor
  19 ASN   (  19-)  A  Poor phi/psi
  56 ILE   (  56-)  A  omega poor
  73 GLN   (  73-)  A  omega poor
  75 PHE   (  75-)  A  Poor phi/psi
 108 TYR   ( 108-)  A  omega poor
 124 ALA   ( 124-)  A  Poor phi/psi
 133 TYR   ( 133-)  A  Poor phi/psi
 147 PHE   ( 147-)  A  omega poor
 156 LEU   ( 156-)  A  Poor phi/psi
 181 SER   ( 181-)  A  PRO omega poor
 192 ASN   ( 192-)  A  Poor phi/psi
 199 GLY   ( 199-)  A  omega poor
 224 LYS   ( 224-)  A  Poor phi/psi
 230 VAL   ( 230-)  A  omega poor
 233 GLU   ( 233-)  A  Poor phi/psi
 239 GLY   ( 239-)  A  Poor phi/psi
 241 LEU   ( 241-)  A  omega poor
 281 LEU   ( 281-)  A  Poor phi/psi
 282 ASP   ( 282-)  A  Poor phi/psi
 288 LEU   ( 288-)  A  PRO omega poor
 342 CYS   ( 342-)  A  omega poor
And so on for a total of 151 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 : -3.073

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.

1598 SER   ( 107-)  D    0.36
 107 SER   ( 107-)  A    0.38
1721 VAL   ( 230-)  D    0.38
1857 SER   ( 366-)  D    0.40

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
  23 CYS   (  23-)  A      0
  24 ASP   (  24-)  A      0
  26 PHE   (  26-)  A      0
  29 PRO   (  29-)  A      0
  32 PRO   (  32-)  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
  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 865 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 : 7.175

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]

 236 PRO   ( 236-)  A    0.07 LOW
 253 PRO   ( 253-)  A    0.15 LOW
 475 PRO   ( 475-)  A    0.20 LOW
 526 PRO   (  29-)  B    0.20 LOW
 596 PRO   (  99-)  B    0.45 HIGH
 750 PRO   ( 253-)  B    0.19 LOW
1092 PRO   (  98-)  C    0.46 HIGH
1116 PRO   ( 122-)  C    0.08 LOW
1247 PRO   ( 253-)  C    0.07 LOW
1613 PRO   ( 122-)  D    0.48 HIGH
1744 PRO   ( 253-)  D    0.18 LOW
1966 PRO   ( 475-)  D    0.16 LOW

Warning: Unusual PRO puckering phases

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

   6 PRO   (   6-)  A   -61.0 half-chair C-beta/C-alpha (-54 degrees)
  55 PRO   (  55-)  A   -51.5 half-chair C-beta/C-alpha (-54 degrees)
  98 PRO   (  98-)  A   103.8 envelop C-beta (108 degrees)
 171 PRO   ( 171-)  A  -155.6 half-chair N/C-delta (-162 degrees)
 178 PRO   ( 178-)  A   -56.6 half-chair C-beta/C-alpha (-54 degrees)
 182 PRO   ( 182-)  A   113.3 envelop C-beta (108 degrees)
 201 PRO   ( 201-)  A   108.1 envelop C-beta (108 degrees)
 452 PRO   ( 452-)  A   107.1 envelop C-beta (108 degrees)
 568 PRO   (  71-)  B  -129.4 half-chair C-delta/C-gamma (-126 degrees)
 595 PRO   (  98-)  B  -144.4 envelop C-delta (-144 degrees)
 647 PRO   ( 150-)  B   -57.4 half-chair C-beta/C-alpha (-54 degrees)
 668 PRO   ( 171-)  B   101.5 envelop C-beta (108 degrees)
 675 PRO   ( 178-)  B   -54.0 half-chair C-beta/C-alpha (-54 degrees)
 679 PRO   ( 182-)  B   105.5 envelop C-beta (108 degrees)
 733 PRO   ( 236-)  B  -121.8 half-chair C-delta/C-gamma (-126 degrees)
 742 PRO   ( 245-)  B   -34.2 envelop C-alpha (-36 degrees)
 816 PRO   ( 319-)  B   -45.0 half-chair C-beta/C-alpha (-54 degrees)
 982 PRO   ( 485-)  B    50.7 half-chair C-delta/C-gamma (54 degrees)
1000 PRO   (   6-)  C   -61.3 half-chair C-beta/C-alpha (-54 degrees)
1023 PRO   (  29-)  C   133.9 half-chair C-beta/C-alpha (126 degrees)
1049 PRO   (  55-)  C   -51.3 half-chair C-beta/C-alpha (-54 degrees)
1165 PRO   ( 171-)  C   114.7 envelop C-beta (108 degrees)
1176 PRO   ( 182-)  C   110.9 envelop C-beta (108 degrees)
1239 PRO   ( 245-)  C   -46.1 half-chair C-beta/C-alpha (-54 degrees)
1313 PRO   ( 319-)  C    -2.2 envelop N (0 degrees)
1469 PRO   ( 475-)  C   100.6 envelop C-beta (108 degrees)
1546 PRO   (  55-)  D   -54.5 half-chair C-beta/C-alpha (-54 degrees)
1669 PRO   ( 178-)  D   -25.6 half-chair C-alpha/N (-18 degrees)
1736 PRO   ( 245-)  D   -57.1 half-chair C-beta/C-alpha (-54 degrees)
1780 PRO   ( 289-)  D   -55.5 half-chair C-beta/C-alpha (-54 degrees)
1790 PRO   ( 299-)  D  -115.8 envelop C-gamma (-108 degrees)
1823 PRO   ( 332-)  D  -112.3 envelop C-gamma (-108 degrees)
1943 PRO   ( 452-)  D   107.0 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.

1336 CYS   ( 342-)  C      SG  <-> 1337 VAL   ( 343-)  C      N      0.72    2.48  INTRA
1336 CYS   ( 342-)  C      SG  <-> 2027 HOH   (1068 )  C      O      0.57    2.43  INTRA
1803 TRP   ( 312-)  D      CH2 <-> 1807 PHE   ( 316-)  D      C      0.54    2.66  INTRA BF
 703 HIS   ( 206-)  B      NE2 <->  752 HIS   ( 255-)  B      NE2    0.53    2.47  INTRA BL
 342 CYS   ( 342-)  A      SG  <->  343 VAL   ( 343-)  A      N      0.51    2.69  INTRA BF
1761 ASN   ( 270-)  D      ND2 <-> 2028 HOH   ( 614 )  D      O      0.49    2.21  INTRA
 207 GLN   ( 207-)  A      NE2 <->  263 ASP   ( 263-)  A      OD1    0.48    2.22  INTRA
1163 GLN   ( 169-)  C      NE2 <-> 2027 HOH   ( 817 )  C      O      0.47    2.23  INTRA
 567 GLN   (  70-)  B      NE2 <->  934 VAL   ( 437-)  B      CG2    0.47    2.63  INTRA
1502 TYR   (  11-)  D      CE2 <-> 1844 ARG   ( 353-)  D      NE     0.46    2.64  INTRA
1237 GLY   ( 243-)  C      O   <-> 1839 TRP   ( 348-)  D      CD1    0.44    2.36  INTRA BF
 938 LYS   ( 441-)  B      NZ  <-> 2002 SO4   ( 504-)  A      O1     0.40    2.30  INTRA BF
 770 HIS   ( 273-)  B      ND1 <-> 2008 SO4   ( 502-)  B      O3     0.40    2.30  INTRA
 704 GLN   ( 207-)  B      NE2 <->  760 ASP   ( 263-)  B      OD1    0.40    2.30  INTRA BL
1201 GLN   ( 207-)  C      NE2 <-> 1257 ASP   ( 263-)  C      OD1    0.40    2.30  INTRA
1698 GLN   ( 207-)  D      NE2 <-> 1754 ASP   ( 263-)  D      OD1    0.38    2.32  INTRA
1038 ARG   (  44-)  C      CD  <-> 2017 SO4   ( 504-)  C      O1     0.36    2.44  INTRA
 186 LYS   ( 186-)  A      NZ  <-> 2025 HOH   ( 665 )  A      O      0.35    2.35  INTRA BL
 243 GLY   ( 243-)  A      O   <->  845 TRP   ( 348-)  B      CD1    0.35    2.45  INTRA BF
 120 ARG   ( 120-)  A      NH2 <->  234 ASN   ( 234-)  A      OD1    0.35    2.35  INTRA BL
1697 HIS   ( 206-)  D      NE2 <-> 1746 HIS   ( 255-)  D      NE2    0.33    2.67  INTRA BL
1954 ARG   ( 463-)  D      NH2 <-> 2028 HOH   ( 948 )  D      O      0.32    2.38  INTRA
 142 PHE   ( 142-)  A      O   <->  211 ARG   ( 211-)  A      NH2    0.32    2.38  INTRA BF
1640 LEU   ( 149-)  D      O   <-> 2028 HOH   ( 665 )  D      O      0.32    2.08  INTRA BL
 262 ARG   ( 262-)  A      NE  <-> 2025 HOH   ( 752 )  A      O      0.32    2.38  INTRA
And so on for a total of 339 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.

1435 LYS   ( 441-)  C      -6.78
1163 GLN   ( 169-)  C      -6.68
 666 GLN   ( 169-)  B      -6.66
 938 LYS   ( 441-)  B      -6.65
 169 GLN   ( 169-)  A      -6.65
 441 LYS   ( 441-)  A      -6.61
1932 LYS   ( 441-)  D      -6.55
1691 GLN   ( 200-)  D      -6.27
1194 GLN   ( 200-)  C      -6.11
 697 GLN   ( 200-)  B      -6.08
1660 GLN   ( 169-)  D      -6.02
 200 GLN   ( 200-)  A      -5.94
 814 LEU   ( 317-)  B      -5.67
 262 ARG   ( 262-)  A      -5.59
1256 ARG   ( 262-)  C      -5.56
 528 PHE   (  31-)  B      -5.50
1753 ARG   ( 262-)  D      -5.47
 759 ARG   ( 262-)  B      -5.43
 993 ARG   ( 496-)  B      -5.40
1808 LEU   ( 317-)  D      -5.38
1522 PHE   (  31-)  D      -5.38
 847 GLN   ( 350-)  B      -5.36
 767 ASN   ( 270-)  B      -5.31
1535 ARG   (  44-)  D      -5.29
1987 ARG   ( 496-)  D      -5.26
1038 ARG   (  44-)  C      -5.25
1025 PHE   (  31-)  C      -5.24
 541 ARG   (  44-)  B      -5.19
1188 LYS   ( 194-)  C      -5.19
1602 GLU   ( 111-)  D      -5.15
1551 HIS   (  60-)  D      -5.13
  31 PHE   (  31-)  A      -5.13
 531 LEU   (  34-)  B      -5.13
1525 LEU   (  34-)  D      -5.13
 557 HIS   (  60-)  B      -5.11
 496 ARG   ( 496-)  A      -5.06
 123 MET   ( 123-)  A      -5.01
1490 ARG   ( 496-)  C      -5.00

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.

 556 ASN   (  59-)  B       560 - THR     63- ( B)         -4.53

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.

1056 GLY   (  62-)  C   -2.86
  62 GLY   (  62-)  A   -2.84
 476 ALA   ( 476-)  A   -2.55
1164 ARG   ( 170-)  C   -2.55
1470 ALA   ( 476-)  C   -2.54
 667 ARG   ( 170-)  B   -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

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 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.

2025 HOH   (1051 )  A      O
2026 HOH   ( 602 )  B      O
2027 HOH   ( 788 )  C      O
2027 HOH   (1001 )  C      O
2027 HOH   (1068 )  C      O
2028 HOH   ( 630 )  D      O
2028 HOH   ( 744 )  D      O
2028 HOH   ( 962 )  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: 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.

 223 HIS   ( 223-)  A
 274 HIS   ( 274-)  A
 306 HIS   ( 306-)  A
 328 HIS   ( 328-)  A
 557 HIS   (  60-)  B
 771 HIS   ( 274-)  B
 893 ASN   ( 396-)  B
 937 GLN   ( 440-)  B
 992 HIS   ( 495-)  B
1051 GLN   (  57-)  C
1322 HIS   ( 328-)  C
1344 GLN   ( 350-)  C
1489 HIS   ( 495-)  C
1551 HIS   (  60-)  D
1561 GLN   (  70-)  D
1564 GLN   (  73-)  D
1714 HIS   ( 223-)  D
1761 ASN   ( 270-)  D
1853 GLN   ( 362-)  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.

  43 THR   (  43-)  A      OG1
  62 GLY   (  62-)  A      N
 131 ARG   ( 131-)  A      N
 140 ASP   ( 140-)  A      N
 141 ASP   ( 141-)  A      N
 147 PHE   ( 147-)  A      N
 202 GLY   ( 202-)  A      N
 209 TRP   ( 209-)  A      NE1
 227 PHE   ( 227-)  A      N
 228 TRP   ( 228-)  A      NE1
 240 LEU   ( 240-)  A      N
 246 PHE   ( 246-)  A      N
 286 LEU   ( 286-)  A      N
 329 ARG   ( 329-)  A      NE
 344 GLY   ( 344-)  A      N
 348 TRP   ( 348-)  A      N
 353 ARG   ( 353-)  A      NE
 356 SER   ( 356-)  A      OG
 357 TRP   ( 357-)  A      NE1
 358 ASP   ( 358-)  A      N
 377 GLY   ( 377-)  A      N
 379 THR   ( 379-)  A      OG1
 382 ASN   ( 382-)  A      ND2
 384 ALA   ( 384-)  A      N
 399 ASP   ( 399-)  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.

  87 ASP   (  87-)  A      OD1
 233 GLU   ( 233-)  A      OE1
 263 ASP   ( 263-)  A      OD2
 290 HIS   ( 290-)  A      ND1
 306 HIS   ( 306-)  A      ND1
 419 HIS   ( 419-)  A      NE2
 648 GLU   ( 151-)  B      OE1
 770 HIS   ( 273-)  B      ND1
 803 HIS   ( 306-)  B      ND1
 812 ASP   ( 315-)  B      OD1
 916 HIS   ( 419-)  B      NE2
1413 HIS   ( 419-)  C      NE2
1802 HIS   ( 311-)  D      ND1
1910 HIS   ( 419-)  D      NE2
1972 GLU   ( 481-)  D      OE1

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.

2027 HOH   (1184 )  C      O  0.86  K  4 ION-B
2028 HOH   (1151 )  D      O  0.85 NA  4

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
 203 ASP   ( 203-)  A   H-bonding suggests Asn
 218 ASP   ( 218-)  A   H-bonding suggests Asn
 233 GLU   ( 233-)  A   H-bonding suggests Gln
 380 ASP   ( 380-)  A   H-bonding suggests Asn; but Alt-Rotamer
 634 ASP   ( 137-)  B   H-bonding suggests Asn
 700 ASP   ( 203-)  B   H-bonding suggests Asn
 715 ASP   ( 218-)  B   H-bonding suggests Asn
 730 GLU   ( 233-)  B   H-bonding suggests Gln
1197 ASP   ( 203-)  C   H-bonding suggests Asn
1212 ASP   ( 218-)  C   H-bonding suggests Asn
1227 GLU   ( 233-)  C   H-bonding suggests Gln
1309 ASP   ( 315-)  C   H-bonding suggests Asn; but Alt-Rotamer
1374 ASP   ( 380-)  C   H-bonding suggests Asn; but Alt-Rotamer
1694 ASP   ( 203-)  D   H-bonding suggests Asn
1724 GLU   ( 233-)  D   H-bonding suggests Gln; but Alt-Rotamer
1871 ASP   ( 380-)  D   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.406
  2nd generation packing quality :  -1.592
  Ramachandran plot appearance   :  -1.607
  chi-1/chi-2 rotamer normality  :  -3.073 (poor)
  Backbone conformation          :  -0.527

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.697
  Bond angles                    :   0.837
  Omega angle restraints         :   1.305 (loose)
  Side chain planarity           :   0.661 (tight)
  Improper dihedral distribution :   0.903
  B-factor distribution          :   0.513
  Inside/Outside distribution    :   1.024

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 : 2.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.2
  2nd generation packing quality :  -0.7
  Ramachandran plot appearance   :  -0.3
  chi-1/chi-2 rotamer normality  :  -1.6
  Backbone conformation          :  -0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.697
  Bond angles                    :   0.837
  Omega angle restraints         :   1.305 (loose)
  Side chain planarity           :   0.661 (tight)
  Improper dihedral distribution :   0.903
  B-factor distribution          :   0.513
  Inside/Outside distribution    :   1.024
==============

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.