WHAT IF Check report

This file was created 2012-01-13 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 pdb1seb.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and F

All-atom RMS fit for the two chains : 0.406
CA-only RMS fit for the two chains : 0.399

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: H

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

Warning: Missing atoms

The atoms listed in the table below are missing from the entry. If many atoms are missing, the other checks can become less sensitive. Be aware that it often happens that groups at the termini of DNA or RNA are really missing, so that the absence of these atoms normally is neither an error nor the result of poor electron density. Some of the atoms listed here might also be listed by other checks, most noticeably by the options in the previous section that list missing atoms in several categories. The plausible atoms with zero occupancy are not listed here, as they already got assigned a non-zero occupancy, and thus are no longer 'missing'.

   1 ILE   (   1-)  A      CG1
   1 ILE   (   1-)  A      CG2
   1 ILE   (   1-)  A      CD1
   2 LYS   (   2-)  A      CG
   2 LYS   (   2-)  A      CD
   2 LYS   (   2-)  A      CE
   2 LYS   (   2-)  A      NZ
 204 ARG   (  23-)  B      CG
 204 ARG   (  23-)  B      CD
 204 ARG   (  23-)  B      NE
 204 ARG   (  23-)  B      CZ
 204 ARG   (  23-)  B      NH1
 204 ARG   (  23-)  B      NH2
 236 ARG   (  55-)  B      CG
 236 ARG   (  55-)  B      CD
 236 ARG   (  55-)  B      NE
 236 ARG   (  55-)  B      CZ
 236 ARG   (  55-)  B      NH1
 236 ARG   (  55-)  B      NH2
 291 GLN   ( 110-)  B      CG
 291 GLN   ( 110-)  B      CD
 291 GLN   ( 110-)  B      OE1
 291 GLN   ( 110-)  B      NE2
 373 SER   ( 192-)  B      OG
 379 LYS   (   7-)  D      CG
And so on for a total of 318 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.

 551 LYS   ( 207-)  D    High
1130 LYS   ( 207-)  H    High

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.

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: H

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.

  69 ASN   (  69-)  A      CG   ND2   1.22   -5.1
 117 VAL   ( 117-)  A      CA   CB    1.63    5.2
 648 ASN   (  69-)  E      CG   ND2   1.22   -5.1
 664 VAL   (  85-)  E      N   -C     1.20   -6.3
 696 VAL   ( 117-)  E      CA   CB    1.63    5.2
 854 ARG   (  94-)  F      N   -C     1.53   10.1
 971 LEU   (  20-)  H      N   -C     1.67   16.9

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

 |  1.001660 -0.000084  0.000151|
 | -0.000084  1.001587  0.000017|
 |  0.000151  0.000017  1.002858|
Proposed new scale matrix

 |  0.010509  0.000000 -0.000002|
 |  0.000000  0.008704  0.000000|
 | -0.000001  0.000000  0.006657|
With corresponding cell

    A    =  95.161  B   = 114.887  C    = 150.218
    Alpha=  90.002  Beta=  89.983  Gamma=  90.001

The CRYST1 cell dimensions

    A    =  95.000  B   = 114.700  C    = 149.800
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 163.256
(Under-)estimated Z-score: 9.417

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.

   5 HIS   (   5-)  A      CG   ND1  CE1 109.82    4.2
  23 MET   (  23-)  A      N    CA   CB  102.51   -4.7
  23 MET   (  23-)  A      CA   CB   CG  122.26    4.1
  76 ARG   (  76-)  A      CB   CG   CD  103.85   -5.1
  94 ASN   (  94-)  A      N    CA   CB  102.81   -4.5
 146 ARG   ( 146-)  A      CB   CG   CD  100.82   -6.6
 149 HIS   ( 149-)  A      CG   ND1  CE1 109.62    4.0
 164 ARG   ( 164-)  A      CB   CG   CD  104.38   -4.9
 167 HIS   ( 167-)  A      CG   ND1  CE1 109.65    4.1
 176 LYS   ( 176-)  A      N    CA   C    99.53   -4.2
 219 VAL   (  38-)  B      C    CA   CB   99.61   -5.5
 279 LYS   (  98-)  B      N    CA   CB  117.79    4.3
 290 LEU   ( 109-)  B      N    CA   C   122.87    4.2
 293 HIS   ( 112-)  B      CG   ND1  CE1 109.72    4.1
 345 VAL   ( 164-)  B      N    CA   C    96.93   -5.1
 358 HIS   ( 177-)  B      CG   ND1  CE1 110.23    4.6
 378 PRO   (   6-)  D      N    CA   C   124.82    5.2
 379 LYS   (   7-)  D      N    CA   C    94.91   -5.8
 430 ASP   (  62-)  D     -C    N    CA  129.13    4.1
 430 ASP   (  62-)  D      N    CA   C    99.84   -4.1
 430 ASP   (  62-)  D      N    CA   CB  117.88    4.3
 431 ASN   (  63-)  D      N    CA   C    98.99   -4.4
 472 GLY   ( 116-)  D      N    CA   C   125.43    4.5
 487 VAL   ( 136-)  D     -C    N    CA  129.49    4.3
 487 VAL   ( 136-)  D      N    CA   C   127.11    5.7
And so on for a total of 54 lines.

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.

  63 ILE   (  63-)  A      CB     6.4    40.63    32.31
 113 THR   ( 113-)  A      C     -6.4    -9.32     0.30
 642 ILE   (  63-)  E      CB     6.4    40.64    32.31
 692 THR   ( 113-)  E      C     -6.4    -9.31     0.30
The average deviation= 1.655

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.

1066 VAL   ( 136-)  H    6.61
 487 VAL   ( 136-)  D    6.59
 396 MET   (  24-)  D    6.58
 975 MET   (  24-)  H    6.55
 958 LYS   (   7-)  H    6.31
 379 LYS   (   7-)  D    6.31
 318 GLU   ( 137-)  B    5.40
 897 GLU   ( 137-)  F    5.40
 924 VAL   ( 164-)  F    5.07
 345 VAL   ( 164-)  B    5.06
  56 ALA   (  56-)  A    4.99
 635 ALA   (  56-)  E    4.98
 649 LEU   (  70-)  E    4.85
  70 LEU   (  70-)  A    4.84
 869 LEU   ( 109-)  F    4.72
 290 LEU   ( 109-)  B    4.70
 957 PRO   (   6-)  H    4.69
 378 PRO   (   6-)  D    4.69
 755 LYS   ( 176-)  E    4.55
 176 LYS   ( 176-)  A    4.54
 472 GLY   ( 116-)  D    4.25
1051 GLY   ( 116-)  H    4.25
 723 LEU   ( 144-)  E    4.20
 144 LEU   ( 144-)  A    4.19
1010 ASN   (  63-)  H    4.17
 431 ASN   (  63-)  D    4.17
 418 TYR   (  46-)  D    4.15
 997 TYR   (  46-)  H    4.13
1152 LYS   ( 229-)  H    4.01
 573 LYS   ( 229-)  D    4.01
 111 LYS   ( 111-)  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 : 1.849

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.

 866 THR   ( 106-)  F    -2.7
 287 THR   ( 106-)  B    -2.7
 692 THR   ( 113-)  E    -2.7
 113 THR   ( 113-)  A    -2.7
 308 ILE   ( 127-)  B    -2.6
 887 ILE   ( 127-)  F    -2.6
 781 THR   (  21-)  F    -2.4
 202 THR   (  21-)  B    -2.4
 917 THR   ( 157-)  F    -2.4
 338 THR   ( 157-)  B    -2.4
 495 LEU   ( 144-)  D    -2.4
1074 LEU   ( 144-)  H    -2.4
 488 PHE   ( 137-)  D    -2.3
1067 PHE   ( 137-)  H    -2.3
  92 LEU   (  92-)  A    -2.3
 671 LEU   (  92-)  E    -2.3
 430 ASP   (  62-)  D    -2.3
1009 ASP   (  62-)  H    -2.3
1073 LEU   ( 143-)  H    -2.3
 494 LEU   ( 143-)  D    -2.3
  32 PHE   (  32-)  A    -2.2
 611 PHE   (  32-)  E    -2.2
  63 ILE   (  63-)  A    -2.2
 642 ILE   (  63-)  E    -2.2
1123 MET   ( 200-)  H    -2.2
And so on for a total of 67 lines.

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.

  15 ASN   (  15-)  A  PRO omega poor
  18 GLN   (  18-)  A  Poor phi/psi
  27 ASP   (  27-)  A  Poor phi/psi
  79 TYR   (  79-)  A  Poor phi/psi
 100 ARG   ( 100-)  A  Poor phi/psi
 113 THR   ( 113-)  A  PRO omega poor
 143 HIS   ( 143-)  A  Poor phi/psi
 213 TYR   (  32-)  B  Poor phi/psi
 271 THR   (  90-)  B  Poor phi/psi
 304 TYR   ( 123-)  B  PRO omega poor
 334 TRP   ( 153-)  B  Poor phi/psi
 372 ARG   ( 191-)  B  Poor phi/psi
 414 ASP   (  42-)  D  Poor phi/psi
 430 ASP   (  62-)  D  Poor phi/psi
 460 GLN   (  92-)  D  Poor phi/psi
 476 GLU   ( 120-)  D  Poor phi/psi
 479 LYS   ( 128-)  D  Poor phi/psi
 486 ARG   ( 135-)  D  Poor phi/psi
 487 VAL   ( 136-)  D  Poor phi/psi
 488 PHE   ( 137-)  D  Poor phi/psi
 489 GLU   ( 138-)  D  Poor phi/psi
 490 ASP   ( 139-)  D  Poor phi/psi
 501 THR   ( 150-)  D  Poor phi/psi
 504 LYS   ( 153-)  D  Poor phi/psi
 505 LYS   ( 154-)  D  Poor phi/psi
And so on for a total of 54 lines.

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

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

chi-1/chi-2 correlation Z-score : -3.624

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!

  11 GLU   (  11-)  A      0
  15 ASN   (  15-)  A      0
  19 SER   (  19-)  A      0
  22 PHE   (  22-)  A      0
  26 PHE   (  26-)  A      0
  31 ILE   (  31-)  A      0
  32 PHE   (  32-)  A      0
  44 ARG   (  44-)  A      0
  51 PHE   (  51-)  A      0
  79 TYR   (  79-)  A      0
  94 ASN   (  94-)  A      0
  99 LEU   (  99-)  A      0
 100 ARG   ( 100-)  A      0
 103 ASN   ( 103-)  A      0
 110 ASP   ( 110-)  A      0
 111 LYS   ( 111-)  A      0
 112 PHE   ( 112-)  A      0
 113 THR   ( 113-)  A      0
 114 PRO   ( 114-)  A      0
 115 PRO   ( 115-)  A      0
 116 VAL   ( 116-)  A      0
 123 ARG   ( 123-)  A      0
 129 THR   ( 129-)  A      0
 130 THR   ( 130-)  A      0
 134 GLU   ( 134-)  A      0
And so on for a total of 505 lines.

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 : 2.264

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!

 970 GLY   (  19-)  H   3.14   14
 391 GLY   (  19-)  D   3.05   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]

  86 PRO   (  86-)  A    0.48 HIGH
  87 PRO   (  87-)  A    0.48 HIGH
 115 PRO   ( 115-)  A    0.46 HIGH
 152 PRO   ( 152-)  A    0.46 HIGH
 155 PRO   ( 155-)  A    0.47 HIGH
 284 PRO   ( 103-)  B    0.46 HIGH
 364 PRO   ( 183-)  B    0.46 HIGH
 380 PRO   (   8-)  D    0.46 HIGH
 548 PRO   ( 204-)  D    0.46 HIGH
 665 PRO   (  86-)  E    0.48 HIGH
 666 PRO   (  87-)  E    0.48 HIGH
 694 PRO   ( 115-)  E    0.46 HIGH
 731 PRO   ( 152-)  E    0.46 HIGH
 734 PRO   ( 155-)  E    0.47 HIGH
 863 PRO   ( 103-)  F    0.46 HIGH
 943 PRO   ( 183-)  F    0.46 HIGH
 959 PRO   (   8-)  H    0.46 HIGH
1127 PRO   ( 204-)  H    0.46 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].

  96 PRO   (  96-)  A  -118.7 half-chair C-delta/C-gamma (-126 degrees)
 546 PRO   ( 202-)  D  -124.5 half-chair C-delta/C-gamma (-126 degrees)
 675 PRO   (  96-)  E  -118.7 half-chair C-delta/C-gamma (-126 degrees)
1125 PRO   ( 202-)  H  -124.5 half-chair C-delta/C-gamma (-126 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.

 232 THR   (  51-)  B      C   <->  812 GLU   (  52-)  F      OE2    0.77    2.03  INTRA BF
 232 THR   (  51-)  B      CA  <->  812 GLU   (  52-)  F      OE2    0.69    2.11  INTRA BF
 157 THR   ( 157-)  A      O   <->  872 HIS   ( 112-)  F      CE1    0.56    2.24  INTRA
 762 ASP   (   2-)  F      CG  <->  766 ARG   (   6-)  F      NH2    0.41    2.69  INTRA BF
 183 ASP   (   2-)  B      CG  <->  187 ARG   (   6-)  B      NH2    0.41    2.69  INTRA BF
 295 LEU   ( 114-)  B      CD1 <->  341 MET   ( 160-)  B      SD     0.36    3.04  INTRA BL
 874 LEU   ( 114-)  F      CD1 <->  920 MET   ( 160-)  F      SD     0.36    3.04  INTRA BL
 655 ARG   (  76-)  E      NH2 <->  817 ASP   (  57-)  F      OD1    0.35    2.35  INTRA BL
 232 THR   (  51-)  B      N   <->  812 GLU   (  52-)  F      OE2    0.35    2.35  INTRA BF
1060 ARG   ( 130-)  H      NH2 <-> 1149 LYS   ( 226-)  H      CA     0.34    2.76  INTRA BF
 481 ARG   ( 130-)  D      NH2 <->  570 LYS   ( 226-)  D      CA     0.34    2.76  INTRA BF
 624 LEU   (  45-)  E      CD1 <->  853 ARG   (  93-)  F      NH2    0.32    2.78  INTRA
  28 GLY   (  28-)  A      O   <->  146 ARG   ( 146-)  A      NH2    0.31    2.39  INTRA BL
1147 ASP   ( 224-)  H      O   <-> 1151 VAL   ( 228-)  H      CG1    0.29    2.51  INTRA BF
 568 ASP   ( 224-)  D      O   <->  572 VAL   ( 228-)  D      CG1    0.29    2.51  INTRA BF
 567 VAL   ( 223-)  D      CG1 <->  572 VAL   ( 228-)  D      CG1    0.28    2.92  INTRA BF
1146 VAL   ( 223-)  H      CG1 <-> 1151 VAL   ( 228-)  H      CG1    0.28    2.92  INTRA BF
 450 VAL   (  82-)  D      CG1 <->  451 ASP   (  83-)  D      N      0.27    2.73  INTRA BF
1029 VAL   (  82-)  H      CG1 <-> 1030 ASP   (  83-)  H      N      0.27    2.73  INTRA BF
 314 ARG   ( 133-)  B      N   <->  317 GLN   ( 136-)  B      O      0.26    2.44  INTRA BF
 893 ARG   ( 133-)  F      N   <->  896 GLN   ( 136-)  F      O      0.26    2.44  INTRA BF
 415 GLN   (  43-)  D      NE2 <->  446 LYS   (  78-)  D      NZ     0.26    2.59  INTRA BF
 994 GLN   (  43-)  H      NE2 <-> 1025 LYS   (  78-)  H      NZ     0.26    2.59  INTRA BF
 476 GLU   ( 120-)  D      CG  <->  477 HIS   ( 121-)  D      N      0.25    2.75  INTRA BF
1055 GLU   ( 120-)  H      CG  <-> 1056 HIS   ( 121-)  H      N      0.25    2.75  INTRA BF
And so on for a total of 249 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

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.

 372 ARG   ( 191-)  B      -7.70
 951 ARG   ( 191-)  F      -7.70
 459 TYR   (  91-)  D      -7.24
1038 TYR   (  91-)  H      -7.21
 679 ARG   ( 100-)  E      -6.54
 100 ARG   ( 100-)  A      -6.50
1081 ASN   ( 151-)  H      -6.08
 502 ASN   ( 151-)  D      -6.08
 961 GLU   (  10-)  H      -5.99
 382 GLU   (  10-)  D      -5.99
 867 GLN   ( 107-)  F      -5.78
 288 GLN   ( 107-)  B      -5.78
 320 LYS   ( 139-)  B      -5.61
 899 LYS   ( 139-)  F      -5.59
1101 ASN   ( 171-)  H      -5.50
 522 ASN   ( 171-)  D      -5.50
 493 ASN   ( 142-)  D      -5.46
1072 ASN   ( 142-)  H      -5.46
1074 LEU   ( 144-)  H      -5.43
 495 LEU   ( 144-)  D      -5.43
 926 ARG   ( 166-)  F      -5.43
 347 ARG   ( 166-)  B      -5.43
 494 LEU   ( 143-)  D      -5.38
1073 LEU   ( 143-)  H      -5.38
 577 TYR   ( 233-)  D      -5.37
1156 TYR   ( 233-)  H      -5.37
 869 LEU   ( 109-)  F      -5.31
 290 LEU   ( 109-)  B      -5.31
 545 MET   ( 201-)  D      -5.29
1124 MET   ( 201-)  H      -5.29
1041 TYR   (  94-)  H      -5.09

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.

 286 LYS   ( 105-)  B       288 - GLN    107- ( B)         -4.76
 488 PHE   ( 137-)  D       490 - ASP    139- ( D)         -4.65
 493 ASN   ( 142-)  D       496 - SER    145- ( D)         -5.11
 865 LYS   ( 105-)  F       867 - GLN    107- ( F)         -4.79
1067 PHE   ( 137-)  H      1069 - ASP    139- ( H)         -4.65
1072 ASN   ( 142-)  H      1075 - SER    145- ( H)         -5.11

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: D

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: E

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: F

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: H

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.

1084 LYS   ( 154-)  H   -3.14
 505 LYS   ( 154-)  D   -3.11
 865 LYS   ( 105-)  F   -2.97
 963 HIS   (  12-)  H   -2.94
 286 LYS   ( 105-)  B   -2.94
 384 HIS   (  12-)  D   -2.94
1071 LYS   ( 141-)  H   -2.85
 492 LYS   ( 141-)  D   -2.83
 967 LYS   (  16-)  H   -2.79
 388 LYS   (  16-)  D   -2.79
 525 LEU   ( 174-)  D   -2.76
1082 LYS   ( 152-)  H   -2.75
1104 LEU   ( 174-)  H   -2.75
 503 LYS   ( 152-)  D   -2.75
1065 ARG   ( 135-)  H   -2.75
 486 ARG   ( 135-)  D   -2.75
 962 LEU   (  11-)  H   -2.71
 383 LEU   (  11-)  D   -2.71
1083 LYS   ( 153-)  H   -2.71
 504 LYS   ( 153-)  D   -2.70
 523 LYS   ( 172-)  D   -2.67
1102 LYS   ( 172-)  H   -2.67
 465 LYS   (  97-)  D   -2.52
1044 LYS   (  97-)  H   -2.52
 479 LYS   ( 128-)  D   -2.52

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.

 382 GLU   (  10-)  D     -  385 LYS   (  13-)  D        -2.27
 478 ASP   ( 127-)  D     -  481 ARG   ( 130-)  D        -1.82
 502 ASN   ( 151-)  D     -  506 VAL   ( 155-)  D        -2.29
 522 ASN   ( 171-)  D     -  525 LEU   ( 174-)  D        -2.10
 869 LEU   ( 109-)  F     -  872 HIS   ( 112-)  F        -1.89
 961 GLU   (  10-)  H     -  964 LYS   (  13-)  H        -2.27
1081 ASN   ( 151-)  H     - 1085 VAL   ( 155-)  H        -2.29
1101 ASN   ( 171-)  H     - 1104 LEU   ( 174-)  H        -2.10

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: H

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.

 118 ASN   ( 118-)  A
 143 HIS   ( 143-)  A
 149 HIS   ( 149-)  A
 245 GLN   (  64-)  B
 273 GLN   (  92-)  B
 294 ASN   ( 113-)  B
 517 HIS   ( 166-)  D
 697 ASN   ( 118-)  E
 722 HIS   ( 143-)  E
 728 HIS   ( 149-)  E
 756 HIS   ( 177-)  E
 824 GLN   (  64-)  F
 852 GLN   (  92-)  F
 873 ASN   ( 113-)  F
1096 HIS   ( 166-)  H

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.

  22 PHE   (  22-)  A      N
  45 LEU   (  45-)  A      N
  47 GLU   (  47-)  A      N
  59 ALA   (  59-)  A      N
 113 THR   ( 113-)  A      OG1
 121 TRP   ( 121-)  A      NE1
 202 THR   (  21-)  B      OG1
 210 ARG   (  29-)  B      NE
 214 ASN   (  33-)  B      N
 216 GLU   (  35-)  B      N
 218 SER   (  37-)  B      OG
 227 GLU   (  46-)  B      N
 236 ARG   (  55-)  B      N
 256 VAL   (  75-)  B      N
 280 VAL   (  99-)  B      N
 292 HIS   ( 111-)  B      N
 320 LYS   ( 139-)  B      N
 321 ALA   ( 140-)  B      N
 323 VAL   ( 142-)  B      N
 331 ASN   ( 150-)  B      ND2
 332 GLY   ( 151-)  B      N
 334 TRP   ( 153-)  B      N
 339 LEU   ( 158-)  B      N
 383 LEU   (  11-)  D      N
 406 SER   (  34-)  D      N
And so on for a total of 98 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

  29 ASP   (  29-)  A      OD1
 143 HIS   ( 143-)  A      ND1
 162 ASP   ( 162-)  A      OD1
 181 ASP   ( 181-)  A      OD1
 191 GLN   (  10-)  B      OE1
 233 GLU   (  52-)  B      OE2
 414 ASP   (  42-)  D      OD1
 722 HIS   ( 143-)  E      ND1
 770 GLN   (  10-)  F      OE1
 812 GLU   (  52-)  F      OE2
 993 ASP   (  42-)  H      OD1

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: 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.

  21 GLU   (  21-)  A   H-bonding suggests Gln
  66 ASP   (  66-)  A   H-bonding suggests Asn
  71 GLU   (  71-)  A   H-bonding suggests Gln; but Alt-Rotamer
 181 ASP   ( 181-)  A   H-bonding suggests Asn
 233 GLU   (  52-)  B   H-bonding suggests Gln; but Alt-Rotamer
 350 GLU   ( 169-)  B   H-bonding suggests Gln
 414 ASP   (  42-)  D   H-bonding suggests Asn
 430 ASP   (  62-)  D   H-bonding suggests Asn
 451 ASP   (  83-)  D   H-bonding suggests Asn; but Alt-Rotamer
 563 ASP   ( 219-)  D   H-bonding suggests Asn; but Alt-Rotamer
 600 GLU   (  21-)  E   H-bonding suggests Gln
 645 ASP   (  66-)  E   H-bonding suggests Asn
 650 GLU   (  71-)  E   H-bonding suggests Gln; but Alt-Rotamer
 760 ASP   ( 181-)  E   H-bonding suggests Asn
 812 GLU   (  52-)  F   H-bonding suggests Gln; but Alt-Rotamer
 929 GLU   ( 169-)  F   H-bonding suggests Gln
 993 ASP   (  42-)  H   H-bonding suggests Asn
1009 ASP   (  62-)  H   H-bonding suggests Asn
1030 ASP   (  83-)  H   H-bonding suggests Asn; but Alt-Rotamer
1142 ASP   ( 219-)  H   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.870
  2nd generation packing quality :  -2.163
  Ramachandran plot appearance   :  -2.800
  chi-1/chi-2 rotamer normality  :  -3.624 (poor)
  Backbone conformation          :  -0.570

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.746
  Bond angles                    :   1.014
  Omega angle restraints         :   0.412 (tight)
  Side chain planarity           :   0.757
  Improper dihedral distribution :   1.372
  B-factor distribution          :   0.894
  Inside/Outside distribution    :   1.056

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 : 2.70


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.2
  2nd generation packing quality :  -0.5
  Ramachandran plot appearance   :  -0.1
  chi-1/chi-2 rotamer normality  :  -1.2
  Backbone conformation          :   0.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.746
  Bond angles                    :   1.014
  Omega angle restraints         :   0.412 (tight)
  Side chain planarity           :   0.757
  Improper dihedral distribution :   1.372
  B-factor distribution          :   0.894
  Inside/Outside distribution    :   1.056
==============

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.