WHAT IF Check report

This file was created 2012-01-05 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 pdb1ppn.ent

Checks that need to be done early-on in validation

Warning: Unconventional cell on CRYST1

The derived `conventional cell' is different from the cell given on the CRYST1 card.

The CRYST1 cell dimensions

    A    =  65.700  B   =  50.700  C    =  31.500
    Alpha=  90.000  Beta=  98.400  Gamma=  90.000

Dimensions of a reduced cell

    A    =  31.500  B   =  50.700  C    =  65.700
    Alpha=  90.000  Beta=  98.400  Gamma=  90.000

Dimensions of the conventional cell

    A    =  31.500  B   =  50.700  C    =  65.700
    Alpha=  90.000  Beta=  98.400  Gamma=  90.000

Transformation to conventional cell

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

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.

 215 MOH   ( 456-)  A  -

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

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

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

 169 ASN   ( 169-)  A  -

Warning: Alternate atom problems quasi solved

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

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

 169 ASN   ( 169-)  A  -

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

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

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

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

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 8.44

Note: B-factor plot

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

Chain identifier: A

Geometric checks

Warning: Unusual bond lengths

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

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

   7 TRP   (   7-)  A      NE1  CE2   1.31   -5.6
   9 GLN   (   9-)  A      CD   OE1   1.32    4.4
  26 TRP   (  26-)  A      NE1  CE2   1.32   -4.2
  35 GLU   (  35-)  A      N    CA    1.56    5.2
  44 ASN   (  44-)  A      CG   OD1   1.34    5.2
  46 ASN   (  46-)  A      CG   OD1   1.33    4.8
  64 ASN   (  64-)  A      CG   OD1   1.32    4.4
  73 GLN   (  73-)  A      CD   OE1   1.33    4.9
  77 GLN   (  77-)  A      CD   OE1   1.33    4.7
  81 HIS   (  81-)  A      ND1  CE1   1.39    5.5
  84 ASN   (  84-)  A      CG   OD1   1.32    4.6
 112 GLN   ( 112-)  A      CD   OE1   1.32    4.3
 114 GLN   ( 114-)  A      CD   OE1   1.33    4.9
 128 GLN   ( 128-)  A      CD   OE1   1.33    4.9
 142 GLN   ( 142-)  A      CD   OE1   1.32    4.4
 145 ARG   ( 145-)  A      NE   CZ    1.39    4.0
 155 ASN   ( 155-)  A      CG   OD1   1.32    4.3
 159 HIS   ( 159-)  A      ND1  CE1   1.40    6.4
 169 ASN   ( 169-)  A      CG   OD1   1.39    8.0
 177 TRP   ( 177-)  A      CD1  NE1   1.46    4.1
 177 TRP   ( 177-)  A      NE1  CE2   1.31   -5.2
 181 TRP   ( 181-)  A      NE1  CE2   1.31   -5.1
 184 ASN   ( 184-)  A      CG   OD1   1.32    4.3
 189 ILE   ( 189-)  A      N    CA    1.54    4.4
 195 ASN   ( 195-)  A      CG   OD1   1.32    4.2
 199 VAL   ( 199-)  A      C    O     1.31    4.0
 212 ASN   ( 212-)  A      CG   OD1   1.33    5.0

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  0.996381  0.000443 -0.000700|
 |  0.000443  0.994819  0.000140|
 | -0.000700  0.000140  0.991724|
Proposed new scale matrix

 |  0.015278 -0.000007  0.002278|
 | -0.000009  0.019827 -0.000003|
 |  0.000023 -0.000005  0.032358|
With corresponding cell

    A    =  65.461  B   =  50.437  C    =  31.249
    Alpha=  89.992  Beta=  98.519  Gamma=  89.949

The CRYST1 cell dimensions

    A    =  65.700  B   =  50.700  C    =  31.500
    Alpha=  90.000  Beta=  98.400  Gamma=  90.000

Variance: 235.764
(Under-)estimated Z-score: 11.316

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.

   3 GLU   (   3-)  A      CA   C    O   114.00   -4.0
   3 GLU   (   3-)  A      CA   CB   CG  100.66   -6.7
   4 TYR   (   4-)  A      CG   CD1  CE1 114.35   -4.6
   4 TYR   (   4-)  A      CD1  CG   CD2 124.36    4.2
   5 VAL   (   5-)  A     -C    N    CA  131.07    5.2
   5 VAL   (   5-)  A      N    CA   CB  118.96    5.0
   6 ASP   (   6-)  A     -C    N    CA  111.89   -5.5
   7 TRP   (   7-)  A      CA   CB   CG  105.86   -4.1
   7 TRP   (   7-)  A      CG   CD1  NE1 103.91   -4.8
   7 TRP   (   7-)  A      CZ3  CE3  CD2 123.94    4.1
   8 ARG   (   8-)  A      NE   CZ   NH2 110.84   -4.8
   9 GLN   (   9-)  A      CA   CB   CG  102.69   -5.7
   9 GLN   (   9-)  A      CB   CG   CD   98.91   -8.1
   9 GLN   (   9-)  A      CG   CD   NE2 128.95    8.4
   9 GLN   (   9-)  A      NE2  CD   OE1 114.47   -8.1
  13 VAL   (  13-)  A      CA   CB   CG1 121.94    6.7
  14 THR   (  14-)  A     -C    N    CA  129.63    4.4
  19 GLN   (  19-)  A     -O   -C    N   116.49   -4.1
  19 GLN   (  19-)  A      N    CA   CB  103.58   -4.1
  19 GLN   (  19-)  A      CB   CG   CD  105.58   -4.1
  19 GLN   (  19-)  A      NE2  CD   OE1 118.37   -4.2
  21 SER   (  21-)  A     -C    N    CA  130.08    4.7
  21 SER   (  21-)  A      C    CA   CB  102.13   -4.2
  22 CYS   (  22-)  A      N    CA   CB  102.48   -4.7
  23 GLY   (  23-)  A      CA   C    O   111.60   -4.4
And so on for a total of 188 lines.

Warning: High bond angle deviations

Bond angles were found to deviate more than normal from the mean standard bond angles (normal values for protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set, and this is indeed observed for very high resolution X-ray structures. The fact that it is higher than 2.0 in this structure might indicate that the restraints used in the refinement were not strong enough. This will also occur if a different bond angle dictionary is used.

RMS Z-score for bond angles: 2.251
RMS-deviation in bond angles: 4.021

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.

  13 VAL   (  13-)  A      CB    10.6   -19.02   -32.96
  17 LYS   (  17-)  A      C      7.7    11.75     0.11
  19 GLN   (  19-)  A      C     -6.2    -9.58     0.15
  43 GLY   (  43-)  A      C      6.7     8.86     0.06
  54 LEU   (  54-)  A      CA    -8.9    20.62    34.19
  58 ARG   (  58-)  A      CA   -36.4   -25.80    33.91 Wrong hand
  59 ARG   (  59-)  A      CA    -6.6    23.02    33.91
  75 VAL   (  75-)  A      CB     7.0   -23.77   -32.96
  81 HIS   (  81-)  A      C     10.4    15.72     0.15
  85 THR   (  85-)  A      CB    -6.3    20.09    34.09
  96 ARG   (  96-)  A      CA   -18.6     3.32    33.91
 110 VAL   ( 110-)  A      CB     6.4   -24.51   -32.96
 155 ASN   ( 155-)  A      CA    -8.2    17.99    33.59
 188 ARG   ( 188-)  A      C     -7.6   -11.41     0.13
 198 GLY   ( 198-)  A      C     -6.7    -8.85     0.06
The average deviation= 2.830

Error: High improper dihedral angle deviations

The RMS Z-score for the improper dihedrals in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 2.5 worries us. However, we determined the improper normal distribution from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Improper dihedral RMS Z-score : 2.561

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.

 120 ALA   ( 120-)  A    5.15
  99 GLU   (  99-)  A    5.00
  22 CYS   (  22-)  A    4.25
 140 ASP   ( 140-)  A    4.19
 124 SER   ( 124-)  A    4.05

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.733

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

  41 ARG   (  41-)  A    6.67
  58 ARG   (  58-)  A    6.67
  98 ARG   (  98-)  A    5.85
 175 ASN   ( 175-)  A    4.27
 169 ASN   ( 169-)  A    4.25
 111 ARG   ( 111-)  A    4.21

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.

 116 TYR   ( 116-)  A    -2.7
  93 ARG   (  93-)  A    -2.7
  86 TYR   (  86-)  A    -2.6
  96 ARG   (  96-)  A    -2.6
 203 TYR   ( 203-)  A    -2.4
 134 LEU   ( 134-)  A    -2.3
  80 ILE   (  80-)  A    -2.2
 156 LYS   ( 156-)  A    -2.2
 128 GLN   ( 128-)  A    -2.1
 161 VAL   ( 161-)  A    -2.1
 200 CYS   ( 200-)  A    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

   9 GLN   (   9-)  A  omega poor
  23 GLY   (  23-)  A  Poor phi/psi
  55 ASP   (  55-)  A  omega poor
  57 ASP   (  57-)  A  omega poor
  58 ARG   (  58-)  A  Poor phi/psi
  93 ARG   (  93-)  A  Poor phi/psi
  99 GLU   (  99-)  A  omega poor
 112 GLN   ( 112-)  A  omega poor
 116 TYR   ( 116-)  A  Poor phi/psi, omega poor
 128 GLN   ( 128-)  A  Poor phi/psi
 151 GLY   ( 151-)  A  PRO omega poor
 158 ASP   ( 158-)  A  Poor phi/psi, omega poor
 170 TYR   ( 170-)  A  omega poor
 200 CYS   ( 200-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.334

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 : -3.334

Warning: Unusual backbone conformations

For the residues listed in the table below, the backbone formed by itself and two neighbouring residues on either side is in a conformation that is not seen very often in the database of solved protein structures. The number given in the table is the number of similar backbone conformations in the database with the same amino acid in the centre.

For this check, backbone conformations are compared with database structures using C-alpha superpositions with some restraints on the backbone oxygen positions.

A residue mentioned in the table can be part of a strange loop, or there might be something wrong with it or its directly surrounding residues. There are a few of these in every protein, but in any case it is worth looking at!

   3 GLU   (   3-)  A      0
   7 TRP   (   7-)  A      0
  10 LYS   (  10-)  A      0
  12 ALA   (  12-)  A      0
  21 SER   (  21-)  A      0
  24 SER   (  24-)  A      0
  25 CYS   (  25-)  A      0
  41 ARG   (  41-)  A      0
  48 TYR   (  48-)  A      0
  56 CYS   (  56-)  A      0
  58 ARG   (  58-)  A      0
  60 SER   (  60-)  A      0
  61 TYR   (  61-)  A      0
  63 CYS   (  63-)  A      0
  64 ASN   (  64-)  A      0
  67 TYR   (  67-)  A      0
  78 TYR   (  78-)  A      0
  80 ILE   (  80-)  A      0
  81 HIS   (  81-)  A      0
  86 TYR   (  86-)  A      0
  89 GLU   (  89-)  A      0
  91 VAL   (  91-)  A      0
  93 ARG   (  93-)  A      0
  94 TYR   (  94-)  A      0
  95 CYS   (  95-)  A      0
And so on for a total of 97 lines.

Warning: Omega angle restraints not strong enough

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

Standard deviation of omega values : 8.070

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]

   2 PRO   (   2-)  A    0.16 LOW
  87 PRO   (  87-)  A    0.51 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].

  87 PRO   (  87-)  A  -125.9 half-chair C-delta/C-gamma (-126 degrees)
 102 PRO   ( 102-)  A    28.6 envelop C-delta (36 degrees)
 115 PRO   ( 115-)  A  -132.7 half-chair C-delta/C-gamma (-126 degrees)
 152 PRO   ( 152-)  A   110.5 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.

  61 TYR   (  61-)  A      CE2 <->  216 HOH   ( 416 )  A      O      0.98    1.82  INTRA BF
  85 THR   (  85-)  A      CG2 <->  216 HOH   ( 376 )  A      O      0.89    1.91  INTRA
 148 ILE   ( 148-)  A      CD1 <->  169 ASN   ( 169-)  A    A ND2    0.67    2.43  INTRA BF
 216 HOH   ( 359 )  A      O   <->  216 HOH   ( 440 )  A      O      0.65    1.55  INTRA BF
  61 TYR   (  61-)  A      CD2 <->  216 HOH   ( 416 )  A      O      0.39    2.41  INTRA BF
 169 ASN   ( 169-)  A    A OD1 <->  216 HOH   ( 387 )  A      O      0.37    2.03  INTRA
  69 TRP   (  69-)  A      O   <->   73 GLN   (  73-)  A      CG     0.26    2.54  INTRA
  59 ARG   (  59-)  A      NH1 <->   61 TYR   (  61-)  A      OH     0.23    2.47  INTRA BF
  52 GLU   (  52-)  A      OE2 <->   97 SER   (  97-)  A      OG     0.21    2.19  INTRA
  86 TYR   (  86-)  A      N   <->   87 PRO   (  87-)  A      CD     0.21    2.79  INTRA BL
 159 HIS   ( 159-)  A      NE2 <->  175 ASN   ( 175-)  A      OD1    0.15    2.55  INTRA BL
  85 THR   (  85-)  A      CB  <->  216 HOH   ( 376 )  A      O      0.14    2.66  INTRA
  61 TYR   (  61-)  A      CZ  <->  216 HOH   ( 416 )  A      O      0.12    2.68  INTRA BF
  86 TYR   (  86-)  A      CA  <->   87 PRO   (  87-)  A      CD     0.10    2.70  INTRA BL
  83 ARG   (  83-)  A      NH1 <->  216 HOH   ( 291 )  A      O      0.10    2.60  INTRA
 216 HOH   ( 346 )  A      O   <->  216 HOH   ( 403 )  A      O      0.10    2.10  INTRA
  52 GLU   (  52-)  A      CG  <->   86 TYR   (  86-)  A      CE2    0.08    3.12  INTRA BL
 138 GLY   ( 138-)  A      O   <->  142 GLN   ( 142-)  A      CG     0.08    2.72  INTRA
 190 LYS   ( 190-)  A      NZ  <->  216 HOH   ( 443 )  A      O      0.05    2.65  INTRA BF
 153 CYS   ( 153-)  A      SG  <->  200 CYS   ( 200-)  A      N      0.05    3.25  INTRA BL
  92 GLN   (  92-)  A      NE2 <->  216 HOH   ( 289 )  A      O      0.04    2.66  INTRA
   6 ASP   (   6-)  A      OD2 <->    8 ARG   (   8-)  A      NH2    0.03    2.67  INTRA BL
 100 LYS   ( 100-)  A      N   <->  101 GLY   ( 101-)  A      N      0.03    2.57  INTRA B3
  17 LYS   (  17-)  A      NZ  <->   47 GLU   (  47-)  A      OE2    0.03    2.67  INTRA BL
  60 SER   (  60-)  A      OG  <->   67 TYR   (  67-)  A      N      0.03    2.67  INTRA BL
  43 GLY   (  43-)  A      N   <->   44 ASN   (  44-)  A      N      0.02    2.58  INTRA BL
 151 GLY   ( 151-)  A      CA  <->  152 PRO   ( 152-)  A      C      0.02    2.98  INTRA BL
  51 GLN   (  51-)  A      OE1 <->   89 GLU   (  89-)  A      N      0.01    2.69  INTRA BL
   6 ASP   (   6-)  A      N   <->  216 HOH   ( 271 )  A      O      0.01    2.69  INTRA
 206 SER   ( 206-)  A      N   <->  216 HOH   ( 248 )  A      O      0.01    2.69  INTRA BL
 200 CYS   ( 200-)  A      N   <->  216 HOH   ( 256 )  A      O      0.01    2.69  INTRA BL
 135 GLU   ( 135-)  A      OE2 <->  154 GLY   ( 154-)  A      N      0.01    2.69  INTRA BL

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

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.

 145 ARG   ( 145-)  A      -7.94
  94 TYR   (  94-)  A      -6.58
  78 TYR   (  78-)  A      -5.48
  77 GLN   (  77-)  A      -5.45
 127 ASN   ( 127-)  A      -5.39
  41 ARG   (  41-)  A      -5.11
  64 ASN   (  64-)  A      -5.08
  61 TYR   (  61-)  A      -5.06

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

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.

 192 GLY   ( 192-)  A   -2.91

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

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

  43 GLY   (  43-)  A     -   46 ASN   (  46-)  A        -1.22

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

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

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

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

 216 HOH   ( 257 )  A      O      3.25   16.18    5.22
 216 HOH   ( 290 )  A      O     30.25  -17.04    7.51
 216 HOH   ( 295 )  A      O     -0.28   12.21    3.04
 216 HOH   ( 312 )  A      O     23.30  -11.92   22.84
 216 HOH   ( 338 )  A      O     32.39   -6.98   -3.12
 216 HOH   ( 347 )  A      O     -5.41    5.13   -6.50
 216 HOH   ( 356 )  A      O     20.19    1.00   -8.61
 216 HOH   ( 357 )  A      O     26.74   10.53   -7.90
 216 HOH   ( 372 )  A      O     43.19   -8.58    3.73
 216 HOH   ( 399 )  A      O      7.56  -15.29  -11.01
 216 HOH   ( 405 )  A      O     -1.71    6.11   -8.36
 216 HOH   ( 438 )  A      O      4.68  -11.57  -13.00

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.

 216 HOH   ( 223 )  A      O
 216 HOH   ( 300 )  A      O
 216 HOH   ( 320 )  A      O
 216 HOH   ( 343 )  A      O
 216 HOH   ( 381 )  A      O
 216 HOH   ( 384 )  A      O
 216 HOH   ( 385 )  A      O
 216 HOH   ( 399 )  A      O
 216 HOH   ( 402 )  A      O
 216 HOH   ( 412 )  A      O
 216 HOH   ( 435 )  A      O
 216 HOH   ( 441 )  A      O

Error: HIS, ASN, GLN side chain flips

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

  44 ASN   (  44-)  A
  46 ASN   (  46-)  A
  77 GLN   (  77-)  A
  81 HIS   (  81-)  A

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.

  25 CYS   (  25-)  A      N
  26 TRP   (  26-)  A      N
  69 TRP   (  69-)  A      N
  91 VAL   (  91-)  A      N
  97 SER   (  97-)  A      N
  99 GLU   (  99-)  A      N
 109 GLY   ( 109-)  A      N
 151 GLY   ( 151-)  A      N
 169 ASN   ( 169-)  A      N
 175 ASN   ( 175-)  A      ND2

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

Warning: 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.

 216 HOH   ( 218 )  A      O  0.87  K  4
 216 HOH   ( 297 )  A      O  0.91  K  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.

  35 GLU   (  35-)  A   H-bonding suggests Gln; but Alt-Rotamer
 158 ASP   ( 158-)  A   H-bonding suggests Asn

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 :  -0.829
  2nd generation packing quality :  -1.944
  Ramachandran plot appearance   :  -1.838
  chi-1/chi-2 rotamer normality  :  -3.334 (poor)
  Backbone conformation          :  -0.362

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.292
  Bond angles                    :   2.251 (loose)
  Omega angle restraints         :   1.467 (loose)
  Side chain planarity           :   1.936
  Improper dihedral distribution :   2.561 (loose)
  Inside/Outside distribution    :   1.044

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 : 1.60


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.6
  2nd generation packing quality :  -1.6
  Ramachandran plot appearance   :  -2.3
  chi-1/chi-2 rotamer normality  :  -3.7 (poor)
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.292
  Bond angles                    :   2.251 (loose)
  Omega angle restraints         :   1.467 (loose)
  Side chain planarity           :   1.936
  Improper dihedral distribution :   2.561 (loose)
  Inside/Outside distribution    :   1.044
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
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      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
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      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
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    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
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      protein structures
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Matthews' Coefficient
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      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,
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    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.