WHAT IF Check report

This file was created 2013-12-10 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 pdb4b04.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    =  82.600  B   =  82.780  C    =  91.720
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    =  82.600  B   =  82.780  C    =  91.720
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    =  82.780  B   =  82.600  C    =  91.720
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

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

Crystal class of the cell: ORTHORHOMBIC

Crystal class of the conventional CELL: TETRAGONAL

Space group name: P 21 21 21

Bravais type of conventional cell is: P

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 1.820
CA-only RMS fit for the two chains : 1.295

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: C and D

All-atom RMS fit for the two chains : 4.914
CA-only RMS fit for the two chains : 2.770

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: C and D

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: 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.

 192 ARG   ( 100-)  B    High
 324 ARG   (  81-)  C    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. The header of the PDB file states that TLS groups were used. So, if WHAT IF complains about your B-factors, while you think that they are OK, then check for TLS related B-factor problems first.

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) : 93.000

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 1.786 over 4250 bonds
Average difference in B over a bond : 5.20
RMS difference in B over a bond : 6.70

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

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.

 402 VAL   ( 163-)  C      CA   CB    1.61    4.2

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

 |  0.995932 -0.000123  0.001094|
 | -0.000123  1.000099  0.000400|
 |  0.001094  0.000400  0.995550|
Proposed new scale matrix

 |  0.012156  0.000001 -0.000013|
 |  0.000001  0.012079 -0.000005|
 | -0.000012 -0.000004  0.010952|
With corresponding cell

    A    =  82.261  B   =  82.790  C    =  91.310
    Alpha=  89.954  Beta=  89.874  Gamma=  90.014

The CRYST1 cell dimensions

    A    =  82.600  B   =  82.780  C    =  91.720
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 209.136
(Under-)estimated Z-score: 10.658

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.

  59 ALA   ( 118-)  A     -C    N    CA  113.81   -4.4
  68 SER   ( 127-)  A      C    CA   CB  101.27   -4.6
  92 HIS   ( 151-)  A      CG   ND1  CE1 109.94    4.3
 248 VAL   ( 156-)  B      C    CA   CB  101.93   -4.3
 277 HIS   ( 185-)  B      CG   ND1  CE1 109.74    4.1
 303 MET   (  60-)  C      CB   CG   SD   95.81   -5.6
 304 HIS   (  61-)  C      CG   ND1  CE1 109.73    4.1
 368 HIS   ( 129-)  C      CG   ND1  CE1 110.01    4.4
 390 HIS   ( 151-)  C      CG   ND1  CE1 109.80    4.2
 393 VAL   ( 154-)  C      C    CA   CB  102.30   -4.1
 410 HIS   ( 171-)  C      CG   ND1  CE1 109.61    4.0
 424 HIS   ( 185-)  C      CG   ND1  CE1 109.74    4.1
 544 VAL   ( 156-)  D      C    CA   CB   98.31   -6.2
 559 HIS   ( 171-)  D     -C    N    CA  113.71   -4.4

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.

 135 PHE   ( 194-)  A    4.26

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.

 516 ILE   ( 128-)  D    -2.6
 427 ILE   ( 188-)  C    -2.5
 560 HIS   ( 172-)  D    -2.4
 577 ILE   ( 189-)  D    -2.4
 130 ILE   ( 189-)  A    -2.3
 301 LEU   ( 209-)  B    -2.3
 395 VAL   ( 156-)  C    -2.2
 190 ARG   (  98-)  B    -2.2
  69 ILE   ( 128-)  A    -2.2
 264 HIS   ( 172-)  B    -2.1
 428 ILE   ( 189-)  C    -2.1
 510 PRO   ( 122-)  D    -2.1
 248 VAL   ( 156-)  B    -2.1
 503 GLY   ( 115-)  D    -2.0
  95 VAL   ( 154-)  A    -2.0
 207 GLY   ( 115-)  B    -2.0
 502 LEU   ( 114-)  D    -2.0
 393 VAL   ( 154-)  C    -2.0

Warning: Backbone evaluation reveals unusual conformations

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

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

   2 HIS   (  61-)  A  omega poor
  59 ALA   ( 118-)  A  omega poor
  92 HIS   ( 151-)  A  omega poor
 113 HIS   ( 172-)  A  Poor phi/psi
 151 GLU   ( 210-)  A  omega poor
 174 GLU   (  82-)  B  omega poor
 191 TRP   (  99-)  B  Poor phi/psi
 201 LEU   ( 109-)  B  Poor phi/psi
 243 HIS   ( 151-)  B  omega poor
 265 LEU   ( 173-)  B  omega poor
 411 HIS   ( 172-)  C  Poor phi/psi
 426 GLY   ( 187-)  C  omega poor
 449 GLU   ( 210-)  C  omega poor
 465 ASP   (  73-)  D  omega poor
 485 ALA   (  94-)  D  omega poor
 539 HIS   ( 151-)  D  omega poor
 544 VAL   ( 156-)  D  omega poor
 561 LEU   ( 173-)  D  omega poor
 598 GLU   ( 210-)  D  omega poor
 chi-1/chi-2 correlation Z-score : -3.156

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 : -3.156

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!

   5 GLU   (  64-)  A      0
   6 VAL   (  65-)  A      0
   7 TRP   (  66-)  A      0
   8 PRO   (  67-)  A      0
  21 ARG   (  80-)  A      0
  36 SER   (  95-)  A      0
  41 ARG   ( 100-)  A      0
  43 THR   ( 102-)  A      0
  47 TYR   ( 106-)  A      0
  65 PHE   ( 124-)  A      0
  67 MET   ( 126-)  A      0
  71 PHE   ( 130-)  A      0
  84 GLN   ( 143-)  A      0
  85 PRO   ( 144-)  A      0
  94 ALA   ( 153-)  A      0
  95 VAL   ( 154-)  A      0
  97 VAL   ( 156-)  A      0
 111 TYR   ( 170-)  A      0
 112 HIS   ( 171-)  A      0
 133 ARG   ( 192-)  A      0
 151 GLU   ( 210-)  A      0
 152 ALA   ( 211-)  A      0
 153 HIS   (  61-)  B      0
 154 ALA   (  62-)  B      0
 156 GLU   (  64-)  B      0
And so on for a total of 187 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!

 200 GLY   ( 108-)  B   2.40   80

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

 236 PRO   ( 144-)  B    0.15 LOW
 578 PRO   ( 190-)  D    0.16 LOW

Warning: Unusual PRO puckering phases

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

  44 PRO   ( 103-)  A   118.9 half-chair C-beta/C-alpha (126 degrees)
 131 PRO   ( 190-)  A  -119.5 half-chair C-delta/C-gamma (-126 degrees)
 214 PRO   ( 122-)  B   117.7 half-chair C-beta/C-alpha (126 degrees)
 342 PRO   ( 103-)  C   103.8 envelop C-beta (108 degrees)
 510 PRO   ( 122-)  D   117.5 half-chair C-beta/C-alpha (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.

  80 ARG   ( 139-)  A      NH2 <->  602 HOH   (2025 )  A      O      0.44    2.26  INTRA BL
 220 ILE   ( 128-)  B      CG2 <->  221 HIS   ( 129-)  B      CD2    0.39    2.81  INTRA BF
  67 MET   ( 126-)  A      CE  <->   70 HIS   ( 129-)  A      CD2    0.36    2.84  INTRA BF
 230 HIS   ( 138-)  B      ND1 <->  603 HOH   (2014 )  B      O      0.32    2.38  INTRA BL
 317 GLN   (  74-)  C      NE2 <->  604 HOH   (2002 )  C      O      0.31    2.39  INTRA BF
 168 MET   (  76-)  B      CE  <->  178 LEU   (  86-)  B      CD1    0.31    2.89  INTRA BF
 441 ASP   ( 202-)  C      OD2 <->  445 ARG   ( 206-)  C      NH2    0.30    2.40  INTRA BF
 217 ASP   ( 125-)  B      OD1 <->  219 SER   ( 127-)  B      CB     0.27    2.53  INTRA BF
 480 THR   (  89-)  D      OG1 <->  481 HIS   (  90-)  D      CD2    0.26    2.54  INTRA BF
 105 LEU   ( 164-)  A      CD1 <->  281 ILE   ( 189-)  B      CD1    0.26    2.94  INTRA
 303 MET   (  60-)  C      SD  <->  322 ASN   (  79-)  C      ND2    0.25    3.05  INTRA BF
 458 TRP   (  66-)  D      O   <->  461 LEU   (  69-)  D      N      0.23    2.47  INTRA BL
  79 HIS   ( 138-)  A      ND1 <->  602 HOH   (2026 )  A      O      0.20    2.50  INTRA BL
 155 ASP   (  63-)  B      N   <->  163 LEU   (  71-)  B      O      0.20    2.50  INTRA BL
 559 HIS   ( 171-)  D      C   <->  560 HIS   ( 172-)  D      CG     0.20    2.90  INTRA BL
 181 THR   (  89-)  B      C   <->  182 HIS   (  90-)  B      CD2    0.19    2.91  INTRA
 544 VAL   ( 156-)  D      CG1 <->  574 ARG   ( 186-)  D      NH2    0.19    2.91  INTRA
 273 LYS   ( 181-)  B      NZ  <->  277 HIS   ( 185-)  B      CE1    0.18    2.92  INTRA BF
  17 MET   (  76-)  A      SD  <->   23 GLU   (  82-)  A      CG     0.18    3.22  INTRA BF
 338 SER   (  95-)  C      OG  <->  392 ALA   ( 153-)  C      N      0.17    2.53  INTRA BF
 263 HIS   ( 171-)  B      C   <->  264 HIS   ( 172-)  B      CG     0.17    2.93  INTRA
 323 ARG   (  80-)  C      NH1 <->  344 ALA   ( 105-)  C      CB     0.16    2.94  INTRA BF
 332 THR   (  89-)  C      OG1 <->  333 HIS   (  90-)  C      CD2    0.15    2.65  INTRA BL
 185 ASN   (  93-)  B      ND2 <->  243 HIS   ( 151-)  B      CE1    0.15    2.95  INTRA BF
  48 GLU   ( 107-)  A      OE2 <->  602 HOH   (2013 )  A      O      0.14    2.26  INTRA
And so on for a total of 92 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Warning: Abnormal packing environment for some residues

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

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

  41 ARG   ( 100-)  A      -6.18
 192 ARG   ( 100-)  B      -6.17
 112 HIS   ( 171-)  A      -6.12
 531 GLN   ( 143-)  D      -6.10
 410 HIS   ( 171-)  C      -6.09
 424 HIS   ( 185-)  C      -5.78
 235 GLN   ( 143-)  B      -5.77
 594 ARG   ( 206-)  D      -5.71
 299 GLN   ( 207-)  B      -5.69
 177 ARG   (  85-)  B      -5.56
 298 ARG   ( 206-)  B      -5.55
 476 ARG   (  85-)  D      -5.52
 382 GLN   ( 143-)  C      -5.47
  84 GLN   ( 143-)  A      -5.45
  95 VAL   ( 154-)  A      -5.40
 328 ARG   (  85-)  C      -5.39
 542 VAL   ( 154-)  D      -5.38
  26 ARG   (  85-)  A      -5.35
 598 GLU   ( 210-)  D      -5.33
 393 VAL   ( 154-)  C      -5.21
 301 LEU   ( 209-)  B      -5.05

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.

 190 ARG   (  98-)  B       192 - ARG    100- ( B)         -5.14
 234 SER   ( 142-)  B       236 - PRO    144- ( B)         -4.79
 530 SER   ( 142-)  D       532 - PRO    144- ( D)         -4.92

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

Error: 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.

  31 HIS   (  90-)  A
  37 HIS   (  96-)  A
  72 GLN   ( 131-)  A
 132 ASN   ( 191-)  A
 182 HIS   (  90-)  B
 185 ASN   (  93-)  B
 235 GLN   ( 143-)  B
 283 ASN   ( 191-)  B
 430 ASN   ( 191-)  C
 585 GLN   ( 197-)  D

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

   2 HIS   (  61-)  A      N
  46 ALA   ( 105-)  A      N
  60 HIS   ( 119-)  A      N
  69 ILE   ( 128-)  A      N
  95 VAL   ( 154-)  A      N
  99 ARG   ( 158-)  A      NH1
 100 SER   ( 159-)  A      N
 167 ASP   (  75-)  B      N
 176 ARG   (  84-)  B      NE
 181 THR   (  89-)  B      OG1
 191 TRP   (  99-)  B      N
 205 TYR   ( 113-)  B      N
 211 HIS   ( 119-)  B      N
 246 VAL   ( 154-)  B      N
 264 HIS   ( 172-)  B      N
 264 HIS   ( 172-)  B      ND1
 279 GLY   ( 187-)  B      N
 296 ARG   ( 204-)  B      NE
 304 HIS   (  61-)  C      N
 333 HIS   (  90-)  C      ND1
 358 HIS   ( 119-)  C      N
 367 ILE   ( 128-)  C      N
 393 VAL   ( 154-)  C      N
 426 GLY   ( 187-)  C      N
 427 ILE   ( 188-)  C      N
 430 ASN   ( 191-)  C      ND2
 481 HIS   (  90-)  D      ND1
 507 HIS   ( 119-)  D      N
 542 VAL   ( 154-)  D      N
 560 HIS   ( 172-)  D      N
 569 LYS   ( 181-)  D      NZ
 579 ASN   ( 191-)  D      ND2
 599 ALA   ( 211-)  D      N

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.

  70 HIS   ( 129-)  A      NE2
  92 HIS   ( 151-)  A      ND1
 243 HIS   ( 151-)  B      ND1
 390 HIS   ( 151-)  C      ND1
 517 HIS   ( 129-)  D      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.

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.

  14 ASP   (  73-)  A   H-bonding suggests Asn; but Alt-Rotamer
  76 ASP   ( 135-)  A   H-bonding suggests Asn; but Alt-Rotamer
 165 ASP   (  73-)  B   H-bonding suggests Asn; but Alt-Rotamer
 276 ASP   ( 184-)  B   H-bonding suggests Asn; but Alt-Rotamer
 316 ASP   (  73-)  C   H-bonding suggests Asn
 374 ASP   ( 135-)  C   H-bonding suggests Asn; but Alt-Rotamer
 465 ASP   (  73-)  D   H-bonding suggests Asn
 523 ASP   ( 135-)  D   H-bonding suggests Asn; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.276
  2nd generation packing quality :  -0.133
  Ramachandran plot appearance   :  -1.445
  chi-1/chi-2 rotamer normality  :  -3.156 (poor)
  Backbone conformation          :   0.597

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.921
  Bond angles                    :   1.006
  Omega angle restraints         :   1.185
  Side chain planarity           :   0.895
  Improper dihedral distribution :   0.991
  B-factor distribution          :   1.786 (loose)
  Inside/Outside distribution    :   0.962

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.20


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.8
  2nd generation packing quality :   0.2
  Ramachandran plot appearance   :  -0.2
  chi-1/chi-2 rotamer normality  :  -1.7
  Backbone conformation          :   0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.921
  Bond angles                    :   1.006
  Omega angle restraints         :   1.185
  Side chain planarity           :   0.895
  Improper dihedral distribution :   0.991
  B-factor distribution          :   1.786 (loose)
  Inside/Outside distribution    :   0.962
==============

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.