WHAT IF Check report

This file was created 2011-12-18 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 pdb1sbt.ent

Checks that need to be done early-on in validation

Error: Inconsistent SCALE and CRYST1 cards

The SCALE matrix and CRYST1 cards from the PDB file are inconsistent.

Possible cause: A simple element by element comparison of the matrices can not locate an obvious cause.

The CRYST1 cell dimensions

    A    =  66.700  B   =  54.400  C    =  62.900
    Alpha=  90.000  Beta=  91.900  Gamma=  90.000

Cell as derived from the SCALE matrix

    A    =  66.700  B   =  54.348  C    =  62.893
    Alpha=  90.000  Beta=  91.801  Gamma=  90.000

SCALE matrices (as given and from CRYST1)

  0.015000  0.000000  0.000000     0.014993  0.000000  0.000497
  0.000000  0.018400  0.000000     0.000000  0.018382  0.000000
  0.000500  0.000000  0.015900     0.000000  0.000000  0.015907
 

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: Rounded coordinates detected

At least two atoms were detected with all three coordinates rounded to 1 decimal place. Since this is highly unlikely to occur accidentally, the atoms listed in the table below were probably not refined. It could also be that ALL atomic coordinates were rounded to 1 or 2 decimal places (resulting in considerable loss of accuracy).

   1 ALA   (   1-)  A      N    35.700     6.800    12.900
   1 ALA   (   1-)  A      CA    36.300     6.700    14.100
   1 ALA   (   1-)  A      C    36.000     8.100    14.900
   1 ALA   (   1-)  A      O    34.900     8.300    15.300
   1 ALA   (   1-)  A      CB    37.900     6.800    13.800
   2 GLN   (   2-)  A      N    37.100     8.900    14.900
   2 GLN   (   2-)  A      CA    37.000    10.100    15.700
   2 GLN   (   2-)  A      C    37.200    11.300    14.600
   2 GLN   (   2-)  A      O    38.000    11.200    13.700
   2 GLN   (   2-)  A      CB    38.100    10.400    16.800
   2 GLN   (   2-)  A      CG    38.200    11.900    17.000
   2 GLN   (   2-)  A      CD    39.000    12.400    18.100
   2 GLN   (   2-)  A      OE1    40.300    12.000    18.100
   2 GLN   (   2-)  A      NE2    38.500    13.100    19.000
   3 SER   (   3-)  A      N    36.300    12.300    14.800
   3 SER   (   3-)  A      CA    36.300    13.400    13.900
   3 SER   (   3-)  A      C    36.300    14.900    14.400
   3 SER   (   3-)  A      O    35.700    15.200    15.300
   3 SER   (   3-)  A      CB    35.000    13.400    13.100
   3 SER   (   3-)  A      OG    35.000    12.100    12.400
   4 VAL   (   4-)  A      N    37.200    15.700    13.900
   4 VAL   (   4-)  A      CA    37.300    17.100    14.100
   4 VAL   (   4-)  A      C    36.300    17.900    13.300
   4 VAL   (   4-)  A      O    36.400    18.000    12.000
   4 VAL   (   4-)  A      CB    38.900    17.500    13.900
And so on for a total of 1953 lines.

Warning: B-factors outside the range 0.0 - 100.0

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

   1 ALA   (   1-)  A    Zero
   2 GLN   (   2-)  A    Zero
   3 SER   (   3-)  A    Zero
   4 VAL   (   4-)  A    Zero
   5 PRO   (   5-)  A    Zero
   6 TYR   (   6-)  A    Zero
   7 GLY   (   7-)  A    Zero
   8 VAL   (   8-)  A    Zero
   9 SER   (   9-)  A    Zero
  10 GLN   (  10-)  A    Zero
  11 ILE   (  11-)  A    Zero
  12 LYS   (  12-)  A    Zero
  13 ALA   (  13-)  A    Zero
  14 PRO   (  14-)  A    Zero
  15 ALA   (  15-)  A    Zero
  16 LEU   (  16-)  A    Zero
  17 HIS   (  17-)  A    Zero
  18 SER   (  18-)  A    Zero
  19 GLN   (  19-)  A    Zero
  20 GLY   (  20-)  A    Zero
  21 TYR   (  21-)  A    Zero
  22 THR   (  22-)  A    Zero
  23 GLY   (  23-)  A    Zero
  24 SER   (  24-)  A    Zero
  25 ASN   (  25-)  A    Zero
And so on for a total of 275 lines.

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 : 100.00

Warning: B-factor plot impossible

All average B-factors are zero. Plot suppressed.

Chain identifier: A

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

 247 ARG   ( 247-)  A

Warning: Tyrosine convention problem

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

 214 TYR   ( 214-)  A

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.

 120 ASP   ( 120-)  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.

   1 ALA   (   1-)  A      N    CA    1.35   -5.9
   1 ALA   (   1-)  A      CA   C     1.64    5.5
   2 GLN   (   2-)  A      CA   C     1.64    5.5
   2 GLN   (   2-)  A      CD   OE1   1.36    6.5
   3 SER   (   3-)  A      C    O     1.12   -5.4
   4 VAL   (   4-)  A      CA   CB    1.66    6.6
   5 PRO   (   5-)  A      C    O     1.32    4.4
   5 PRO   (   5-)  A      N   -C     1.17   -7.7
   6 TYR   (   6-)  A      CA   CB    1.42   -5.3
   6 TYR   (   6-)  A      CG   CD2   1.56    7.9
   6 TYR   (   6-)  A      CE1  CZ    1.50    5.1
   7 GLY   (   7-)  A      CA   C     1.71   12.7
   8 VAL   (   8-)  A      C    O     1.14   -4.3
   9 SER   (   9-)  A      CA   C     1.65    6.1
  10 GLN   (  10-)  A      CB   CG    1.66    4.6
  10 GLN   (  10-)  A      CD   NE2   1.43    4.9
  10 GLN   (  10-)  A      N   -C     1.42    4.8
  11 ILE   (  11-)  A      CA   C     1.61    4.0
  12 LYS   (  12-)  A      N    CA    1.54    4.3
  12 LYS   (  12-)  A      C    O     1.36    6.5
  14 PRO   (  14-)  A      CA   C     1.62    4.5
  14 PRO   (  14-)  A      CA   CB    1.45   -4.0
  15 ALA   (  15-)  A      N   -C     1.41    4.3
  16 LEU   (  16-)  A      C    O     1.32    4.2
  17 HIS   (  17-)  A      C    O     1.36    6.5
And so on for a total of 547 lines.

Warning: High bond length deviations

Bond lengths were found to deviate more than normal from the mean standard bond lengths (standard values for protein residues were taken from Engh and Huber [REF], for DNA/RNA these values were taken from Parkinson et al [REF]). The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is higher than 1.5 in this structure might indicate that the restraints used in the refinement were not strong enough. This will also occur if a different bond length dictionary is used.

RMS Z-score for bond lengths: 3.566
RMS-deviation in bond distances: 0.075

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

 |  0.993633 -0.000290 -0.000166|
 | -0.000290  0.993625  0.001823|
 | -0.000166  0.001823  0.999321|
Proposed new scale matrix

 |  0.015089  0.000003  0.000500|
 |  0.000005  0.018500 -0.000034|
 |  0.000003 -0.000029  0.015918|
With corresponding cell

    A    =  66.275  B   =  54.053  C    =  62.858
    Alpha=  89.789  Beta=  91.908  Gamma=  90.034

The CRYST1 cell dimensions

    A    =  66.700  B   =  54.400  C    =  62.900
    Alpha=  90.000  Beta=  91.900  Gamma=  90.000

Variance: 132.056
(Under-)estimated Z-score: 8.469

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

   1 ALA   (   1-)  A      C    CA   CB  102.52   -5.3
   2 GLN   (   2-)  A     -O   -C    N   130.55    4.7
   2 GLN   (   2-)  A      N    CA   CB  119.56    5.3
   3 SER   (   3-)  A      C    CA   CB   99.54   -5.6
   5 PRO   (   5-)  A     -O   -C    N   127.73    4.1
   5 PRO   (   5-)  A      CG   CD   N   112.14    6.0
   5 PRO   (   5-)  A      CD   N    CA  105.21   -4.9
   7 GLY   (   7-)  A      CA   C    O   108.12   -6.0
   8 VAL   (   8-)  A     -O   -C    N   136.51    8.4
   8 VAL   (   8-)  A     -C    N    CA  112.38   -5.2
   8 VAL   (   8-)  A      CG1  CB   CG2  99.99   -4.9
  10 GLN   (  10-)  A     -O   -C    N   129.99    4.4
  10 GLN   (  10-)  A      N    CA   C   123.18    4.3
  10 GLN   (  10-)  A      N    CA   CB  100.82   -5.7
  10 GLN   (  10-)  A      CB   CG   CD  105.35   -4.3
  10 GLN   (  10-)  A      CG   CD   NE2 106.29   -6.7
  10 GLN   (  10-)  A      NE2  CD   OE1 129.34    6.7
  11 ILE   (  11-)  A     -O   -C    N   133.66    6.7
  11 ILE   (  11-)  A     -CA  -C    N   106.47   -4.9
  11 ILE   (  11-)  A     -C    N    CA  111.32   -5.8
  11 ILE   (  11-)  A      CA   CB   CG2  98.13   -7.3
  14 PRO   (  14-)  A     -CA  -C    N   110.04   -4.6
  14 PRO   (  14-)  A      C    CA   CB  118.52    4.4
  15 ALA   (  15-)  A      N    CA   CB  104.25   -4.1
  17 HIS   (  17-)  A      CG   ND1  CE1 110.53    4.9
And so on for a total of 520 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: 3.057
RMS-deviation in bond angles: 5.609

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.

 120 ASP   ( 120-)  A
 247 ARG   ( 247-)  A

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.

   1 ALA   (   1-)  A      CA     7.7    43.93    34.09
   6 TYR   (   6-)  A      C      6.5    10.54     0.33
   8 VAL   (   8-)  A      C      6.0     8.43     0.15
   8 VAL   (   8-)  A      CB    -7.2   -42.36   -32.96
  10 GLN   (  10-)  A      C      8.8    13.87     0.15
  26 VAL   (  26-)  A      CB     6.5   -24.45   -32.96
  29 ALA   (  29-)  A      C      6.5     9.98     0.08
  37 SER   (  37-)  A      CA     6.2    45.88    34.32
  44 VAL   (  44-)  A      C     -9.2   -12.48     0.15
  51 VAL   (  51-)  A      C      8.0    11.10     0.15
  54 GLU   (  54-)  A      CA    -6.1    23.88    33.96
  56 PRO   (  56-)  A      C     12.5    20.18     0.42
  58 PHE   (  58-)  A      CA     9.9    49.81    33.98
  58 PHE   (  58-)  A      C     -6.3    -9.98     0.23
  62 ASN   (  62-)  A      C      9.5    15.25     0.27
  65 GLY   (  65-)  A      C    -10.4   -13.68     0.06
  74 ALA   (  74-)  A      CA    11.2    48.33    34.09
  74 ALA   (  74-)  A      C      6.7    10.30     0.08
  75 LEU   (  75-)  A      CA     6.9    44.77    34.19
  79 ILE   (  79-)  A      CA   -10.1    18.00    33.24
  79 ILE   (  79-)  A      C     -7.1    -9.30     0.03
  79 ILE   (  79-)  A      CB     7.6    42.24    32.31
  80 GLY   (  80-)  A      C     -9.6   -12.64     0.06
  84 VAL   (  84-)  A      CA    10.5    48.52    33.23
  84 VAL   (  84-)  A      C     10.2    14.17     0.15
And so on for a total of 57 lines.

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 : 3.619

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.

 246 VAL   ( 246-)  A   12.73
 247 ARG   ( 247-)  A   12.08
  65 GLY   (  65-)  A   10.89
  73 ALA   (  73-)  A   10.17
 234 ILE   ( 234-)  A   10.04
 232 ALA   ( 232-)  A    9.12
  71 THR   (  71-)  A    8.52
  10 GLN   (  10-)  A    7.80
  81 VAL   (  81-)  A    7.11
 112 GLU   ( 112-)  A    6.99
  89 ALA   (  89-)  A    6.52
 243 ASN   ( 243-)  A    6.34
 273 ALA   ( 273-)  A    6.19
 162 SER   ( 162-)  A    6.12
 216 ALA   ( 216-)  A    5.92
 174 VAL   ( 174-)  A    5.83
 159 THR   ( 159-)  A    5.77
 111 ILE   ( 111-)  A    5.66
  38 SER   (  38-)  A    5.52
 261 PHE   ( 261-)  A    5.51
 245 GLN   ( 245-)  A    5.51
 231 ALA   ( 231-)  A    5.47
 105 SER   ( 105-)  A    5.46
 115 ILE   ( 115-)  A    5.36
 145 SER   ( 145-)  A    5.33
 252 ASN   ( 252-)  A    5.26
  85 ALA   (  85-)  A    5.24
 205 ILE   ( 205-)  A    5.11
 222 MET   ( 222-)  A    5.03
 230 ALA   ( 230-)  A    5.01
  62 ASN   (  62-)  A    4.95
 113 TRP   ( 113-)  A    4.93
 248 SER   ( 248-)  A    4.92
  19 GLN   (  19-)  A    4.92
 275 GLN   ( 275-)  A    4.80
 239 PRO   ( 239-)  A    4.66
  79 ILE   (  79-)  A    4.55
  11 ILE   (  11-)  A    4.47
  66 THR   (  66-)  A    4.37
 110 GLY   ( 110-)  A    4.35
 182 SER   ( 182-)  A    4.30
  80 GLY   (  80-)  A    4.28
 214 TYR   ( 214-)  A    4.27
 185 GLN   ( 185-)  A    4.27
 134 ALA   ( 134-)  A    4.17
 209 LEU   ( 209-)  A    4.14
 190 SER   ( 190-)  A    4.12
   3 SER   (   3-)  A    4.07

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 : 3.208

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.

  76 ASN   (  76-)  A   30.99
  64 HIS   (  64-)  A   13.76
  62 ASN   (  62-)  A   12.78
  57 ASN   (  57-)  A   10.60
 226 HIS   ( 226-)  A   10.53
 120 ASP   ( 120-)  A    9.98
  54 GLU   (  54-)  A    9.58
  67 HIS   (  67-)  A    8.79
 117 ASN   ( 117-)  A    8.60
   6 TYR   (   6-)  A    8.11
 217 TYR   ( 217-)  A    8.00
  77 ASN   (  77-)  A    7.85
 189 PHE   ( 189-)  A    7.62
 212 ASN   ( 212-)  A    7.15
 109 ASN   ( 109-)  A    6.84
 261 PHE   ( 261-)  A    6.73
 112 GLU   ( 112-)  A    6.70
  39 HIS   (  39-)  A    6.60
  32 ASP   (  32-)  A    5.66
 171 TYR   ( 171-)  A    5.66
 262 TYR   ( 262-)  A    5.60
 195 GLU   ( 195-)  A    5.40
 263 TYR   ( 263-)  A    5.18
  17 HIS   (  17-)  A    5.11
  58 PHE   (  58-)  A    5.08
  25 ASN   (  25-)  A    5.00
 243 ASN   ( 243-)  A    4.63
 271 GLN   ( 271-)  A    4.60
 156 GLU   ( 156-)  A    4.53
 118 ASN   ( 118-)  A    4.21

Error: Connections to aromatic rings out of plane

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

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

 167 TYR   ( 167-)  A      OH   4.67
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -5.269

Torsion-related checks

Error: Ramachandran Z-score very low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is very low.

Ramachandran Z-score : -5.269

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.

 159 THR   ( 159-)  A    -3.4
  55 THR   (  55-)  A    -3.3
  77 ASN   (  77-)  A    -2.8
 126 LEU   ( 126-)  A    -2.7
  76 ASN   (  76-)  A    -2.6
 104 TYR   ( 104-)  A    -2.5
  75 LEU   (  75-)  A    -2.5
 253 THR   ( 253-)  A    -2.4
 160 GLY   ( 160-)  A    -2.4
 135 LEU   ( 135-)  A    -2.3
  52 PRO   (  52-)  A    -2.3
 156 GLU   ( 156-)  A    -2.2
 168 PRO   ( 168-)  A    -2.2
  80 GLY   (  80-)  A    -2.2
  32 ASP   (  32-)  A    -2.1
 157 GLY   ( 157-)  A    -2.1
  65 GLY   (  65-)  A    -2.1

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.

  12 LYS   (  12-)  A  Poor phi/psi, omega poor
  32 ASP   (  32-)  A  Poor phi/psi
  35 ILE   (  35-)  A  Poor phi/psi
  48 ALA   (  48-)  A  Poor phi/psi
  49 SER   (  49-)  A  omega poor
  52 PRO   (  52-)  A  omega poor
  55 THR   (  55-)  A  Poor phi/psi
  62 ASN   (  62-)  A  omega poor
  63 SER   (  63-)  A  Poor phi/psi
  69 ALA   (  69-)  A  Poor phi/psi
  70 GLY   (  70-)  A  Poor phi/psi
  75 LEU   (  75-)  A  Poor phi/psi
  76 ASN   (  76-)  A  Poor phi/psi
  77 ASN   (  77-)  A  Poor phi/psi
  80 GLY   (  80-)  A  Poor phi/psi
  81 VAL   (  81-)  A  Poor phi/psi
  84 VAL   (  84-)  A  omega poor
  86 PRO   (  86-)  A  Poor phi/psi
  99 ALA   (  99-)  A  Poor phi/psi
 100 GLY   ( 100-)  A  Poor phi/psi
 112 GLU   ( 112-)  A  Poor phi/psi
 132 SER   ( 132-)  A  Poor phi/psi
 136 LYS   ( 136-)  A  omega poor
 146 GLY   ( 146-)  A  Poor phi/psi
 156 GLU   ( 156-)  A  Poor phi/psi
 157 GLY   ( 157-)  A  omega poor
 159 THR   ( 159-)  A  Poor phi/psi, omega poor
 160 GLY   ( 160-)  A  Poor phi/psi
 162 SER   ( 162-)  A  Poor phi/psi
 167 TYR   ( 167-)  A  PRO omega poor
 181 ASP   ( 181-)  A  Poor phi/psi
 194 PRO   ( 194-)  A  omega poor
 239 PRO   ( 239-)  A  Poor phi/psi
 259 ASP   ( 259-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -4.728

Error: chi-1/chi-2 angle correlation Z-score very low

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

chi-1/chi-2 correlation Z-score : -4.728

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.

 248 SER   ( 248-)  A    0.35

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!

  12 LYS   (  12-)  A      0
  19 GLN   (  19-)  A      0
  22 THR   (  22-)  A      0
  24 SER   (  24-)  A      0
  31 ILE   (  31-)  A      0
  32 ASP   (  32-)  A      0
  33 SER   (  33-)  A      0
  42 LEU   (  42-)  A      0
  45 ALA   (  45-)  A      0
  48 ALA   (  48-)  A      0
  50 MET   (  50-)  A      0
  55 THR   (  55-)  A      0
  56 PRO   (  56-)  A      0
  61 ASP   (  61-)  A      0
  62 ASN   (  62-)  A      0
  63 SER   (  63-)  A      0
  72 VAL   (  72-)  A      0
  74 ALA   (  74-)  A      0
  75 LEU   (  75-)  A      0
  76 ASN   (  76-)  A      0
  77 ASN   (  77-)  A      0
  78 SER   (  78-)  A      0
  79 ILE   (  79-)  A      0
  81 VAL   (  81-)  A      0
  87 SER   (  87-)  A      0
And so on for a total of 116 lines.

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

  47 GLY   (  47-)  A   2.35   24
 131 GLY   ( 131-)  A   2.10   80
 157 GLY   ( 157-)  A   1.74   19
 266 GLY   ( 266-)  A   1.64   14
 166 GLY   ( 166-)  A   1.52   10

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]

   5 PRO   (   5-)  A    0.19 LOW
  56 PRO   (  56-)  A    0.11 LOW
  86 PRO   (  86-)  A    0.08 LOW
 129 PRO   ( 129-)  A    0.17 LOW
 168 PRO   ( 168-)  A    0.17 LOW
 172 PRO   ( 172-)  A    0.18 LOW
 194 PRO   ( 194-)  A    0.19 LOW
 210 PRO   ( 210-)  A    0.15 LOW
 225 PRO   ( 225-)  A    0.10 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].

  52 PRO   (  52-)  A   153.4 half-chair C-alpha/N (162 degrees)
 201 PRO   ( 201-)  A  -177.9 envelop N (180 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.

  76 ASN   (  76-)  A      OD1 <->  270 VAL   ( 270-)  A      CG1    1.78    1.02  INTRA BL
  76 ASN   (  76-)  A      OD1 <->  270 VAL   ( 270-)  A      CB     1.26    1.54  INTRA BL
  22 THR   (  22-)  A      CB  <->   87 SER   (  87-)  A      OG     0.99    1.81  INTRA BL
  41 ASP   (  41-)  A      CG  <->   75 LEU   (  75-)  A      CG     0.91    2.29  INTRA BL
  41 ASP   (  41-)  A      CB  <->   75 LEU   (  75-)  A      CD1    0.85    2.35  INTRA BL
  41 ASP   (  41-)  A      CG  <->   75 LEU   (  75-)  A      CD1    0.83    2.37  INTRA BL
  75 LEU   (  75-)  A      CD2 <->   79 ILE   (  79-)  A      O      0.81    1.99  INTRA BL
  22 THR   (  22-)  A      OG1 <->   87 SER   (  87-)  A      OG     0.78    1.62  INTRA BL
  57 ASN   (  57-)  A      ND2 <->   92 ALA   (  92-)  A      O      0.78    1.92  INTRA BL
 204 SER   ( 204-)  A      N   <->  218 ASN   ( 218-)  A      OD1    0.70    2.00  INTRA BL
 104 TYR   ( 104-)  A      CE1 <->  277 HOH   ( 281 )  A      O      0.68    2.12  INTRA BL
  19 GLN   (  19-)  A      NE2 <->  237 LYS   ( 237-)  A      NZ     0.63    2.22  INTRA BL
 253 THR   ( 253-)  A      CG2 <->  272 ALA   ( 272-)  A      CB     0.62    2.58  INTRA BL
 233 LEU   ( 233-)  A      CA  <->  236 SER   ( 236-)  A      OG     0.59    2.21  INTRA BL
  41 ASP   (  41-)  A      OD1 <->   75 LEU   (  75-)  A      CG     0.58    2.22  INTRA BL
 255 THR   ( 255-)  A      N   <->  267 LEU   ( 267-)  A      O      0.54    2.16  INTRA BL
 174 VAL   ( 174-)  A      O   <->  247 ARG   ( 247-)  A      NH2    0.53    2.17  INTRA BL
  84 VAL   (  84-)  A      C   <->   86 PRO   (  86-)  A      CD     0.53    2.67  INTRA BL
  33 SER   (  33-)  A      O   <->   94 LYS   (  94-)  A      CE     0.52    2.28  INTRA BL
  97 GLY   (  97-)  A      CA  <->  101 SER   ( 101-)  A      CB     0.51    2.69  INTRA BL
  12 LYS   (  12-)  A      NZ  <->  269 ASN   ( 269-)  A      CG     0.50    2.60  INTRA BL
  56 PRO   (  56-)  A      CB  <->   59 GLN   (  59-)  A      CG     0.50    2.70  INTRA BL
  60 ASP   (  60-)  A      OD1 <->   63 SER   (  63-)  A      N      0.50    2.20  INTRA BL
  22 THR   (  22-)  A      C   <->   87 SER   (  87-)  A      OG     0.50    2.30  INTRA BL
 199 MET   ( 199-)  A      CG  <->  263 TYR   ( 263-)  A      O      0.48    2.32  INTRA BL
And so on for a total of 264 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

Warning: Abnormal packing environment for some residues

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

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

 256 LYS   ( 256-)  A      -5.74
 167 TYR   ( 167-)  A      -5.36
 217 TYR   ( 217-)  A      -5.34
  76 ASN   (  76-)  A      -5.20
 212 ASN   ( 212-)  A      -5.16

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: 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

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.

  19 GLN   (  19-)  A
  57 ASN   (  57-)  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.

   2 GLN   (   2-)  A      N
   7 GLY   (   7-)  A      N
  13 ALA   (  13-)  A      N
  19 GLN   (  19-)  A      N
  23 GLY   (  23-)  A      N
  33 SER   (  33-)  A      N
  35 ILE   (  35-)  A      N
  57 ASN   (  57-)  A      ND2
  58 PHE   (  58-)  A      N
  59 GLN   (  59-)  A      N
  78 SER   (  78-)  A      N
  79 ILE   (  79-)  A      N
  82 LEU   (  82-)  A      N
  87 SER   (  87-)  A      OG
 126 LEU   ( 126-)  A      N
 135 LEU   ( 135-)  A      N
 161 SER   ( 161-)  A      OG
 165 VAL   ( 165-)  A      N
 189 PHE   ( 189-)  A      N
 191 SER   ( 191-)  A      OG
 195 GLU   ( 195-)  A      N
 196 LEU   ( 196-)  A      N
 204 SER   ( 204-)  A      N
 236 SER   ( 236-)  A      OG
 240 ASN   ( 240-)  A      N
 244 THR   ( 244-)  A      N
 245 GLN   ( 245-)  A      NE2
 255 THR   ( 255-)  A      N
 270 VAL   ( 270-)  A      N
   1.00000   0.00000  -0.00000   33.69053 ROT=    0.0000
   0.00000   1.00000  -0.00000   27.17913 DET=    1.0000
   0.00000   0.00000   1.00000   -0.27257
  -1.00000  -0.00000   0.00000   15.20067 ROT=  180.0000
   0.00000   1.00000   0.00000   -0.06260 DET=    1.0000
   0.00000   0.00000  -1.00000   83.38873
  -1.00000  -0.00000   0.00000   83.98614 ROT=  180.0000
   0.00000   1.00000   0.00000   -0.06260 DET=    1.0000
   0.00000   0.00000  -1.00000   20.52331
  -1.00000  -0.00000   0.00000   81.90067 ROT=  180.0000
   0.00000   1.00000   0.00000   -0.06260 DET=    1.0000
   0.00000   0.00000  -1.00000   83.38873
   1.00000   0.00000  -0.00000  -32.32840 ROT=    0.0198
   0.00000   1.00000  -0.00000  -27.26260 DET=    1.0000
   0.00000   0.00000   1.00000   -0.81772
   1.00000   0.00000  -0.00000  -32.32840 ROT=    0.0198
   0.00000   1.00000  -0.00000   27.13740 DET=    1.0000
   0.00000   0.00000   1.00000   -0.81772
   1.00000   0.00000  -0.00000   34.37160 ROT=    0.0198
   0.00000   1.00000  -0.00000  -27.26260 DET=    1.0000
   0.00000   0.00000   1.00000   -0.81772
  -1.00000  -0.00000   0.00000   48.55067 ROT=  180.0000
   0.00000   1.00000   0.00000  -27.26261 DET=    1.0000
   0.00000   0.00000  -1.00000   83.38873
  -1.00000  -0.00000   0.00000   48.55067 ROT=  180.0000
   0.00000   1.00000   0.00000   27.13740 DET=    1.0000
   0.00000   0.00000  -1.00000   83.38873

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.

  76 ASN   (  76-)  A      OD1
 206 GLN   ( 206-)  A      OE1
 238 HIS   ( 238-)  A      ND1

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.

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.703
  2nd generation packing quality :  -2.413
  Ramachandran plot appearance   :  -5.269 (bad)
  chi-1/chi-2 rotamer normality  :  -4.728 (bad)
  Backbone conformation          :  -1.024

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   3.566 (loose)
  Bond angles                    :   3.057 (loose)
  Omega angle restraints         :   1.255
  Side chain planarity           :   6.519 (loose)
  Improper dihedral distribution :   3.619 (loose)
  Inside/Outside distribution    :   0.953

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.8
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :  -2.6
  chi-1/chi-2 rotamer normality  :  -2.7
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   3.566 (loose)
  Bond angles                    :   3.057 (loose)
  Omega angle restraints         :   1.255
  Side chain planarity           :   6.519 (loose)
  Improper dihedral distribution :   3.619 (loose)
  Inside/Outside distribution    :   0.953
==============

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.