WHAT IF Check report

This file was created 2012-01-04 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 pdb1mbn.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    =  64.500  B   =  30.900  C    =  34.700
    Alpha=  90.000  Beta= 106.000  Gamma=  90.000

Dimensions of a reduced cell

    A    =  30.900  B   =  34.700  C    =  64.269
    Alpha= 105.265  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    =  34.700  B   = 124.006  C    =  30.900
    Alpha=  90.000  Beta=  90.000  Gamma=  89.604

Transformation to conventional cell

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

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.

 155 HEM   ( 155-)  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: 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).

   2 LEU   (   2-)  A      CB     0.600    14.200    16.500
   2 LEU   (   2-)  A      CG     1.100    14.300    15.100
   2 LEU   (   2-)  A      CD1     0.400    15.500    14.400
   2 LEU   (   2-)  A      CD2     2.600    14.400    15.000
   3 SER   (   3-)  A      O     1.100    12.800    20.900
   3 SER   (   3-)  A      OG     0.200    10.100    20.300
   4 GLU   (   4-)  A      CA     0.000    12.900    23.600
   4 GLU   (   4-)  A      C     1.300    12.100    23.500
   4 GLU   (   4-)  A      O     2.400    12.600    23.600
   4 GLU   (   4-)  A      CG     0.000    14.000    26.000
   4 GLU   (   4-)  A      CD     0.300    15.400    25.200
   4 GLU   (   4-)  A      OE2     1.200    16.000    25.400
   5 GLY   (   5-)  A      N     1.100    10.800    23.400
   5 GLY   (   5-)  A      CA     2.200     9.800    23.300
   5 GLY   (   5-)  A      C     3.200    10.200    22.200
   5 GLY   (   5-)  A      O     4.400    10.300    22.500
   6 GLU   (   6-)  A      N     2.700    10.400    21.000
   6 GLU   (   6-)  A      CA     3.500    10.700    19.800
   6 GLU   (   6-)  A      C     4.400    11.900    19.900
   6 GLU   (   6-)  A      O     5.500    11.900    19.400
   6 GLU   (   6-)  A      CB     2.600    10.700    18.600
   6 GLU   (   6-)  A      CG     2.000     9.400    18.100
   6 GLU   (   6-)  A      CD     0.900     9.500    17.000
   6 GLU   (   6-)  A      OE1     0.700    10.600    16.700
   6 GLU   (   6-)  A      OE2     0.400     8.500    16.600
And so on for a total of 910 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 VAL   (   1-)  A    Zero
   2 LEU   (   2-)  A    Zero
   3 SER   (   3-)  A    Zero
   4 GLU   (   4-)  A    Zero
   5 GLY   (   5-)  A    Zero
   6 GLU   (   6-)  A    Zero
   7 TRP   (   7-)  A    Zero
   8 GLN   (   8-)  A    Zero
   9 LEU   (   9-)  A    Zero
  10 VAL   (  10-)  A    Zero
  11 LEU   (  11-)  A    Zero
  12 HIS   (  12-)  A    Zero
  13 VAL   (  13-)  A    Zero
  14 TRP   (  14-)  A    Zero
  15 ALA   (  15-)  A    Zero
  16 LYS   (  16-)  A    Zero
  17 VAL   (  17-)  A    Zero
  18 GLU   (  18-)  A    Zero
  19 ALA   (  19-)  A    Zero
  20 ASP   (  20-)  A    Zero
  21 VAL   (  21-)  A    Zero
  22 ALA   (  22-)  A    Zero
  23 GLY   (  23-)  A    Zero
  24 HIS   (  24-)  A    Zero
  25 GLY   (  25-)  A    Zero
And so on for a total of 153 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.

  31 ARG   (  31-)  A
  45 ARG   (  45-)  A
 118 ARG   ( 118-)  A
 139 ARG   ( 139-)  A

Warning: Tyrosine convention problem

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

 103 TYR   ( 103-)  A
 146 TYR   ( 146-)  A
 151 TYR   ( 151-)  A

Warning: Phenylalanine convention problem

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

 106 PHE   ( 106-)  A
 123 PHE   ( 123-)  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.

  20 ASP   (  20-)  A
  60 ASP   (  60-)  A
 126 ASP   ( 126-)  A

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.

  18 GLU   (  18-)  A
  38 GLU   (  38-)  A
  52 GLU   (  52-)  A
  54 GLU   (  54-)  A
  85 GLU   (  85-)  A
 109 GLU   ( 109-)  A
 148 GLU   ( 148-)  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.

   2 LEU   (   2-)  A      CA   C     1.62    4.3
   3 SER   (   3-)  A      CA   C     1.61    4.2
   4 GLU   (   4-)  A      CG   CD    1.64    5.0
   4 GLU   (   4-)  A      CD   OE2   1.10   -7.8
   6 GLU   (   6-)  A      CD   OE1   1.16   -4.8
   7 TRP   (   7-)  A      NE1  CE2   1.32   -5.0
   7 TRP   (   7-)  A      N   -C     1.44    5.3
  14 TRP   (  14-)  A      CA   CB    1.61    4.1
  14 TRP   (  14-)  A      CD1  NE1   1.48    4.9
  14 TRP   (  14-)  A      NE1  CE2   1.21  -14.3
  14 TRP   (  14-)  A      CD2  CE2   1.33   -4.4
  14 TRP   (  14-)  A      CE2  CZ2   1.50    4.9
  15 ALA   (  15-)  A      C    O     1.32    4.2
  16 LYS   (  16-)  A      C    O     1.32    4.2
  18 GLU   (  18-)  A      CD   OE1   1.16   -4.8
  20 ASP   (  20-)  A      CA   C     1.64    5.5
  20 ASP   (  20-)  A      CG   OD1   1.14   -5.5
  24 HIS   (  24-)  A      CB   CG    1.59    6.9
  24 HIS   (  24-)  A      ND1  CE1   1.24   -5.7
  25 GLY   (  25-)  A      N   -C     1.41    4.3
  26 GLN   (  26-)  A      CA   C     1.43   -4.4
  26 GLN   (  26-)  A      C    O     1.33    5.2
  27 ASP   (  27-)  A      CG   OD1   1.13   -6.2
  31 ARG   (  31-)  A      NE   CZ    1.41    5.6
  34 LYS   (  34-)  A      C    O     1.34    5.3
And so on for a total of 105 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: 2.278
RMS-deviation in bond distances: 0.047

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

 |  0.997784  0.000969 -0.000157|
 |  0.000969  0.998276  0.001516|
 | -0.000157  0.001516  0.996986|
Proposed new scale matrix

 |  0.015539 -0.000022  0.004462|
 | -0.000032  0.032418 -0.000049|
 |  0.000005 -0.000046  0.030071|
With corresponding cell

    A    =  64.357  B   =  30.847  C    =  34.600
    Alpha=  89.863  Beta= 106.030  Gamma=  89.889

The CRYST1 cell dimensions

    A    =  64.500  B   =  30.900  C    =  34.700
    Alpha=  90.000  Beta= 106.000  Gamma=  90.000

Variance: 29.180
(Under-)estimated Z-score: 3.981

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.

   2 LEU   (   2-)  A      C    CA   CB  101.54   -4.5
   3 SER   (   3-)  A     -O   -C    N   132.17    5.7
   3 SER   (   3-)  A      N    CA   C   130.35    6.8
   3 SER   (   3-)  A      N    CA   CB  125.60    8.9
   3 SER   (   3-)  A      C    CA   CB   89.04  -11.1
   4 GLU   (   4-)  A     -O   -C    N   129.97    4.4
   4 GLU   (   4-)  A      N    CA   CB  135.73   14.8
   4 GLU   (   4-)  A      C    CA   CB  101.31   -4.6
   4 GLU   (   4-)  A      CG   CD   OE1 106.37   -5.2
   8 GLN   (   8-)  A      N    CA   CB  131.80   12.5
   9 LEU   (   9-)  A      C    CA   CB   94.89   -8.0
  10 VAL   (  10-)  A      N    CA   CB  132.37   12.9
  11 LEU   (  11-)  A      N    CA   C   123.31    4.3
  11 LEU   (  11-)  A      N    CA   CB  119.04    5.0
  12 HIS   (  12-)  A      N    CA   CB  100.86   -5.7
  13 VAL   (  13-)  A      N    CA   CB  137.07   15.6
  13 VAL   (  13-)  A      C    CA   CB  102.11   -4.2
  14 TRP   (  14-)  A      C    CA   CB  126.10    8.4
  14 TRP   (  14-)  A      NE1  CE2  CZ2 121.94   -5.4
  14 TRP   (  14-)  A      CE2  CZ2  CH2 110.65   -5.3
  14 TRP   (  14-)  A      CH2  CZ3  CE3 128.48    5.7
  14 TRP   (  14-)  A      CZ3  CE3  CD2 109.42   -7.1
  14 TRP   (  14-)  A      CE3  CD2  CG  128.12   -5.8
  15 ALA   (  15-)  A      N    CA   CB  119.56    6.1
  15 ALA   (  15-)  A      C    CA   CB   94.56  -10.6
And so on for a total of 221 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: 2.678
RMS-deviation in bond angles: 5.011

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.

  18 GLU   (  18-)  A
  20 ASP   (  20-)  A
  31 ARG   (  31-)  A
  38 GLU   (  38-)  A
  45 ARG   (  45-)  A
  52 GLU   (  52-)  A
  54 GLU   (  54-)  A
  60 ASP   (  60-)  A
  85 GLU   (  85-)  A
 109 GLU   ( 109-)  A
 118 ARG   ( 118-)  A
 126 ASP   ( 126-)  A
 139 ARG   ( 139-)  A
 148 GLU   ( 148-)  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.

   4 GLU   (   4-)  A      CA    -6.5    23.33    33.96
   8 GLN   (   8-)  A      CA   -20.5    -5.56    33.96 Wrong hand
  10 VAL   (  10-)  A      CA    -9.5    19.51    33.23
  11 LEU   (  11-)  A      CA   -10.1    18.76    34.19
  13 VAL   (  13-)  A      CA    -8.6    20.70    33.23
  14 TRP   (  14-)  A      CA    -9.4    18.10    34.04
  17 VAL   (  17-)  A      CA     7.1    43.47    33.23
  20 ASP   (  20-)  A      CA    -7.5    18.73    33.73
  29 LEU   (  29-)  A      CA   -10.1    18.80    34.19
  31 ARG   (  31-)  A      CA    -6.7    22.85    33.91
  37 PRO   (  37-)  A      CA    -9.6    24.68    38.15
  40 LEU   (  40-)  A      CA     9.0    48.01    34.19
  42 LYS   (  42-)  A      CA     7.8    46.85    33.92
  43 PHE   (  43-)  A      CA     9.5    49.18    33.98
  45 ARG   (  45-)  A      CA    -8.6    19.84    33.91
  50 LYS   (  50-)  A      CA    -9.0    19.02    33.92
  52 GLU   (  52-)  A      CA     7.7    46.61    33.96
  56 LYS   (  56-)  A      CA     7.3    46.07    33.92
  58 SER   (  58-)  A      CA     6.2    45.85    34.32
  62 LYS   (  62-)  A      CA   -10.0    17.26    33.92
  64 HIS   (  64-)  A      CA    -9.3    17.03    34.11
  72 LEU   (  72-)  A      CA    -8.9    20.57    34.19
  80 GLY   (  80-)  A      C     -6.2    -8.14     0.06
  84 ALA   (  84-)  A      CA    -6.7    25.57    34.09
  87 LYS   (  87-)  A      CA    -7.7    21.16    33.92
  88 PRO   (  88-)  A      CA    -8.6    26.09    38.15
  93 HIS   (  93-)  A      CA    -6.2    22.77    34.11
  94 ALA   (  94-)  A      CA    -7.5    24.58    34.09
  97 HIS   (  97-)  A      CA    -8.2    19.01    34.11
 100 PRO   ( 100-)  A      CA    -6.7    28.77    38.15
 107 ILE   ( 107-)  A      CA    -8.8    19.88    33.24
 111 ILE   ( 111-)  A      CA    -6.7    23.20    33.24
 114 VAL   ( 114-)  A      CA   -10.3    18.26    33.23
 116 HIS   ( 116-)  A      CA    -7.0    21.22    34.11
 117 SER   ( 117-)  A      CA   -10.6    14.59    34.32
 123 PHE   ( 123-)  A      CA     8.8    48.03    33.98
 126 ASP   ( 126-)  A      CA    -8.1    17.70    33.73
 136 GLU   ( 136-)  A      CA     9.1    48.92    33.96
 137 LEU   ( 137-)  A      CA   -11.1    17.26    34.19
The average deviation= 3.702

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 : 3.343

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.

  95 THR   (  95-)  A   13.46
 125 ALA   ( 125-)  A   12.59
 130 ALA   ( 130-)  A   11.14
 149 LEU   ( 149-)  A   10.40
  86 LEU   (  86-)  A    9.99
 118 ARG   ( 118-)  A    8.31
  11 LEU   (  11-)  A    7.53
 113 HIS   ( 113-)  A    7.49
  75 ILE   (  75-)  A    7.35
   3 SER   (   3-)  A    7.15
  46 PHE   (  46-)  A    7.04
 123 PHE   ( 123-)  A    6.89
  21 VAL   (  21-)  A    6.67
 135 LEU   ( 135-)  A    6.47
  62 LYS   (  62-)  A    6.41
  60 ASP   (  60-)  A    6.19
  59 GLU   (  59-)  A    6.17
  85 GLU   (  85-)  A    6.15
   7 TRP   (   7-)  A    5.88
  26 GLN   (  26-)  A    5.84
 136 GLU   ( 136-)  A    5.74
  68 VAL   (  68-)  A    5.61
  23 GLY   (  23-)  A    5.56
 146 TYR   ( 146-)  A    5.19
 148 GLU   ( 148-)  A    5.10
 133 LYS   ( 133-)  A    4.83
 106 PHE   ( 106-)  A    4.83
  35 SER   (  35-)  A    4.81
  82 HIS   (  82-)  A    4.80
  42 LYS   (  42-)  A    4.78
   4 GLU   (   4-)  A    4.60
 127 ALA   ( 127-)  A    4.59
  39 THR   (  39-)  A    4.56
 142 ILE   ( 142-)  A    4.32
  67 THR   (  67-)  A    4.31
  83 GLU   (  83-)  A    4.31
 151 TYR   ( 151-)  A    4.31
   2 LEU   (   2-)  A    4.24
  61 LEU   (  61-)  A    4.20
 104 LEU   ( 104-)  A    4.15
  65 GLY   (  65-)  A    4.14
  50 LYS   (  50-)  A    4.08
 105 GLU   ( 105-)  A    4.01

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 : 3.865

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.

  64 HIS   (  64-)  A    7.17
  36 HIS   (  36-)  A    6.43
  44 ASP   (  44-)  A    5.68
  24 HIS   (  24-)  A    5.21
 146 TYR   ( 146-)  A    4.91
  27 ASP   (  27-)  A    4.81
 138 PHE   ( 138-)  A    4.50
  12 HIS   (  12-)  A    4.32
  81 HIS   (  81-)  A    4.04

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 : -5.304

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.

 106 PHE   ( 106-)  A    -3.1
 146 TYR   ( 146-)  A    -2.7
 140 LYS   ( 140-)  A    -2.4
 107 ILE   ( 107-)  A    -2.3
   4 GLU   (   4-)  A    -2.3
 117 SER   ( 117-)  A    -2.2
 101 ILE   ( 101-)  A    -2.2
  61 LEU   (  61-)  A    -2.2
  20 ASP   (  20-)  A    -2.2
  82 HIS   (  82-)  A    -2.2
 123 PHE   ( 123-)  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.

  27 ASP   (  27-)  A  Poor phi/psi
  62 LYS   (  62-)  A  Poor phi/psi
  98 LYS   (  98-)  A  Poor phi/psi
 152 GLN   ( 152-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -5.714

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 : -5.714

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.

 117 SER   ( 117-)  A    0.36
  92 SER   (  92-)  A    0.39

Warning: Unusual backbone conformations

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

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

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

   8 GLN   (   8-)  A      0
  20 ASP   (  20-)  A      0
  35 SER   (  35-)  A      0
  43 PHE   (  43-)  A      0
  44 ASP   (  44-)  A      0
  78 LYS   (  78-)  A      0
  79 LYS   (  79-)  A      0
  81 HIS   (  81-)  A      0
  83 GLU   (  83-)  A      0
  95 THR   (  95-)  A      0
  96 LYS   (  96-)  A      0
  97 HIS   (  97-)  A      0
  98 LYS   (  98-)  A      0
 118 ARG   ( 118-)  A      0
 123 PHE   ( 123-)  A      0
 151 TYR   ( 151-)  A      0
  36 HIS   (  36-)  A      1
  42 LYS   (  42-)  A      1
  46 PHE   (  46-)  A      1
  50 LYS   (  50-)  A      1
  51 THR   (  51-)  A      1
  82 HIS   (  82-)  A      1
 100 PRO   ( 100-)  A      1
 119 HIS   ( 119-)  A      1
 125 ALA   ( 125-)  A      1
 149 LEU   ( 149-)  A      1
   3 SER   (   3-)  A      2
  21 VAL   (  21-)  A      2
  58 SER   (  58-)  A      2
  59 GLU   (  59-)  A      2
 120 PRO   ( 120-)  A      2

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 2.612

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]

  37 PRO   (  37-)  A    0.10 LOW
  88 PRO   (  88-)  A    0.11 LOW
 100 PRO   ( 100-)  A    0.13 LOW
 120 PRO   ( 120-)  A    0.14 LOW

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.

  78 LYS   (  78-)  A      NZ  <->   85 GLU   (  85-)  A      OE2    0.89    1.81  INTRA BL
 145 LYS   ( 145-)  A      NZ  <->  148 GLU   ( 148-)  A      CD     0.86    2.24  INTRA BL
  12 HIS   (  12-)  A      NE2 <->   16 LYS   (  16-)  A      NZ     0.68    2.32  INTRA BL
 145 LYS   ( 145-)  A      NZ  <->  148 GLU   ( 148-)  A      OE2    0.62    2.08  INTRA BL
  49 LEU   (  49-)  A      CD2 <->   61 LEU   (  61-)  A      CD1    0.54    2.66  INTRA BL
 145 LYS   ( 145-)  A      NZ  <->  148 GLU   ( 148-)  A      OE1    0.50    2.20  INTRA BL
  42 LYS   (  42-)  A      NZ  <->   98 LYS   (  98-)  A      O      0.48    2.22  INTRA BL
 100 PRO   ( 100-)  A      O   <->  103 TYR   ( 103-)  A      N      0.46    2.24  INTRA BL
   1 VAL   (   1-)  A      CG1 <->    2 LEU   (   2-)  A      CD1    0.46    2.74  INTRA BL
  47 LYS   (  47-)  A      O   <->   50 LYS   (  50-)  A      NZ     0.45    2.25  INTRA BL
 143 ALA   ( 143-)  A      CB  <->  152 GLN   ( 152-)  A      OE1    0.44    2.36  INTRA BL
  42 LYS   (  42-)  A      NZ  <->   98 LYS   (  98-)  A      CB     0.41    2.69  INTRA BL
  78 LYS   (  78-)  A      NZ  <->   85 GLU   (  85-)  A      CD     0.40    2.70  INTRA BL
  43 PHE   (  43-)  A      CE2 <->  155 HEM   ( 155-)  A      CHD    0.40    2.80  INTRA BL
 145 LYS   ( 145-)  A      O   <->  149 LEU   ( 149-)  A      CG     0.36    2.44  INTRA BL
 104 LEU   ( 104-)  A      CD1 <->  142 ILE   ( 142-)  A      CD1    0.36    2.84  INTRA BL
  44 ASP   (  44-)  A      OD1 <->   47 LYS   (  47-)  A      CE     0.33    2.47  INTRA BL
  82 HIS   (  82-)  A      CE1 <->  137 LEU   ( 137-)  A      CD2    0.31    2.89  INTRA BL
   4 GLU   (   4-)  A      OE2 <->   79 LYS   (  79-)  A      NZ     0.31    2.39  INTRA BL
  12 HIS   (  12-)  A      NE2 <->   16 LYS   (  16-)  A      CE     0.29    2.81  INTRA BL
 102 LYS   ( 102-)  A      NZ  <->  105 GLU   ( 105-)  A      OE2    0.28    2.42  INTRA BL
  14 TRP   (  14-)  A      CZ2 <->   73 GLY   (  73-)  A      CA     0.28    2.92  INTRA BL
 154  OH   ( 154-)  A      O   <->  155 HEM   ( 155-)  A      NC     0.27    2.33  INTRA BL
 103 TYR   ( 103-)  A      O   <->  107 ILE   ( 107-)  A      N      0.26    2.44  INTRA BL
  76 LEU   (  76-)  A      O   <->   79 LYS   (  79-)  A      N      0.26    2.44  INTRA BL
And so on for a total of 106 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.

 152 GLN   ( 152-)  A      -5.60
 118 ARG   ( 118-)  A      -5.45

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.

 151 TYR   ( 151-)  A       153 - GLY    153- ( A)         -4.74

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.

  48 HIS   (  48-)  A   -2.77

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.

  91 GLN   (  91-)  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 LEU   (   2-)  A      N
  64 HIS   (  64-)  A      NE2
  80 GLY   (  80-)  A      N
  82 HIS   (  82-)  A      N
  97 HIS   (  97-)  A      NE2
 122 ASP   ( 122-)  A      N
 139 ARG   ( 139-)  A      NH1
 139 ARG   ( 139-)  A      NH2
Only metal coordination for   93 HIS  (  93-) A      NE2

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.

  24 HIS   (  24-)  A      NE2
  26 GLN   (  26-)  A      OE1
 105 GLU   ( 105-)  A      OE1
 109 GLU   ( 109-)  A      OE1
 119 HIS   ( 119-)  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 :  -0.513
  2nd generation packing quality :  -1.369
  Ramachandran plot appearance   :  -5.304 (bad)
  chi-1/chi-2 rotamer normality  :  -5.714 (bad)
  Backbone conformation          :   0.588

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   2.278 (loose)
  Bond angles                    :   2.678 (loose)
  Omega angle restraints         :   0.475 (tight)
  Side chain planarity           :   2.893 (loose)
  Improper dihedral distribution :   3.343 (loose)
  Inside/Outside distribution    :   0.896

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 : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.2
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :  -4.4 (bad)
  chi-1/chi-2 rotamer normality  :  -4.2 (bad)
  Backbone conformation          :   0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   2.278 (loose)
  Bond angles                    :   2.678 (loose)
  Omega angle restraints         :   0.475 (tight)
  Side chain planarity           :   2.893 (loose)
  Improper dihedral distribution :   3.343 (loose)
  Inside/Outside distribution    :   0.896
==============

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.