WHAT IF Check report

This file was created 2011-12-22 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 pdb1eoo.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: A and B

All-atom RMS fit for the two chains : 0.736
CA-only RMS fit for the two chains : 0.369

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

Administrative problems that can generate validation failures

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

 268 LYS   ( 245-)  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

Note: Ramachandran plot

Chain identifier: B

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'.

  39 GLN   (  16-)  A      CB
  39 GLN   (  16-)  A      CG
  39 GLN   (  16-)  A      CD
  39 GLN   (  16-)  A      OE1
  39 GLN   (  16-)  A      NE2
  40 LYS   (  17-)  A      CB
  40 LYS   (  17-)  A      CG
  40 LYS   (  17-)  A      CD
  40 LYS   (  17-)  A      CE
  40 LYS   (  17-)  A      NZ
  58 SER   (  35-)  A      OG
  77 LYS   (  54-)  A      CG
  77 LYS   (  54-)  A      CD
  77 LYS   (  54-)  A      CE
  77 LYS   (  54-)  A      NZ
  90 LYS   (  67-)  A      CG
  90 LYS   (  67-)  A      CD
  90 LYS   (  67-)  A      CE
  90 LYS   (  67-)  A      NZ
 121 LYS   (  98-)  A      CG
 121 LYS   (  98-)  A      CD
 121 LYS   (  98-)  A      CE
 121 LYS   (  98-)  A      NZ
 122 GLU   (  99-)  A      CG
 122 GLU   (  99-)  A      CD
And so on for a total of 156 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:

Crystal temperature (K) :100.000

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

Nomenclature related problems

Warning: Tyrosine convention problem

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

  41 TYR   (  18-)  A
  95 TYR   (  72-)  A
 151 TYR   ( 128-)  A
 253 TYR   ( 230-)  A
 264 TYR   ( 241-)  A
 339 TYR   (  72-)  B
 395 TYR   ( 128-)  B
 430 TYR   ( 163-)  B
 482 TYR   ( 215-)  B
 508 TYR   ( 241-)  B

Warning: Phenylalanine convention problem

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

  98 PHE   (  75-)  A
 222 PHE   ( 199-)  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.

 195 ASP   ( 172-)  A
 221 ASP   ( 198-)  A
 439 ASP   ( 172-)  B
 465 ASP   ( 198-)  B
 477 ASP   ( 210-)  B

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.

 312 GLU   (  45-)  B
 324 GLU   (  57-)  B
 468 GLU   ( 201-)  B

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.

  14 DADE  (   2-)  D      C5   C6    1.36   -4.6

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

 |  0.999565 -0.000375  0.000118|
 | -0.000375  0.997470  0.000107|
 |  0.000118  0.000107  1.002831|
Proposed new scale matrix

 |  0.013780  0.000005 -0.000002|
 |  0.000003  0.008327  0.000000|
 |  0.000000  0.000000  0.005458|
With corresponding cell

    A    =  72.569  B   = 120.090  C    = 183.232
    Alpha=  90.002  Beta=  89.994  Gamma=  90.043

The CRYST1 cell dimensions

    A    =  72.600  B   = 120.400  C    = 182.700
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 61.963
(Under-)estimated Z-score: 5.801

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 DADE  (   5-)  C      C2'  C1'  N9  105.15   -5.7
   6 DTHY  (   6-)  C      C2'  C1'  N1  104.08   -6.3
  16 DGUA  (   4-)  D      O4'  C1'  N9  112.51    5.9
  22 DTHY  (  10-)  D      O4'  C1'  C2' 110.86    4.3
  23 DTHY  (  11-)  D      C2'  C1'  N1  121.26    4.4
  94 HIS   (  71-)  A      CG   ND1  CE1 109.87    4.3
 129 THR   ( 106-)  A      N    CA   C    96.54   -5.2
 336 GLN   (  69-)  B      N    CA   C   123.93    4.5
 338 HIS   (  71-)  B      CG   ND1  CE1 109.92    4.3
 373 THR   ( 106-)  B      N    CA   C    97.49   -4.9

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.

 195 ASP   ( 172-)  A
 221 ASP   ( 198-)  A
 312 GLU   (  45-)  B
 324 GLU   (  57-)  B
 439 ASP   ( 172-)  B
 465 ASP   ( 198-)  B
 468 GLU   ( 201-)  B
 477 ASP   ( 210-)  B

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.

  26 LEU   (   3-)  A    5.99
 129 THR   ( 106-)  A    5.45
 432 GLY   ( 165-)  B    5.27
 373 THR   ( 106-)  B    5.05
 336 GLN   (  69-)  B    4.93
 181 GLU   ( 158-)  A    4.92
 483 TRP   ( 216-)  B    4.89
 188 GLY   ( 165-)  A    4.78
 234 GLU   ( 211-)  A    4.69
 271 ARG   (   4-)  B    4.69
 297 ILE   (  30-)  B    4.61
 263 ILE   ( 240-)  A    4.51
  53 ILE   (  30-)  A    4.45
 491 GLN   ( 224-)  B    4.35
 507 ILE   ( 240-)  B    4.08
 478 GLU   ( 211-)  B    4.05

Warning: High tau angle deviations

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

Tau angle RMS Z-score : 1.832

Warning: Uncalibrated side chain planarity problems

The residues listed in the table below contain a planar group that was found to deviate from planarity by more than 0.10 Angstrom RMS. Please be aware that this check cannot be callibrated and that the cutoff of 0.10 Angstrom thus is a wild guess.

  23 DTHY  (  11-)  D    0.13
 Ramachandran Z-score : -2.590

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.

 410 THR   ( 143-)  B    -3.2
 340 PRO   (  73-)  B    -2.8
  96 PRO   (  73-)  A    -2.7
 361 THR   (  94-)  B    -2.6
 117 THR   (  94-)  A    -2.5
  80 GLU   (  57-)  A    -2.4
 432 GLY   ( 165-)  B    -2.4
 115 LYS   (  92-)  A    -2.3
 370 ILE   ( 103-)  B    -2.3
 235 PHE   ( 212-)  A    -2.3
 228 ILE   ( 205-)  A    -2.2
 396 ILE   ( 129-)  B    -2.2
 256 ILE   ( 233-)  A    -2.2
 291 ILE   (  24-)  B    -2.1
 500 ILE   ( 233-)  B    -2.1
 386 LYS   ( 119-)  B    -2.1
 472 ILE   ( 205-)  B    -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.

  93 ASN   (  70-)  A  Poor phi/psi
  95 TYR   (  72-)  A  PRO omega poor
 123 ASN   ( 100-)  A  Poor phi/psi
 135 SER   ( 112-)  A  Poor phi/psi
 143 ASN   ( 120-)  A  Poor phi/psi
 210 THR   ( 187-)  A  Poor phi/psi
 252 LYS   ( 229-)  A  Poor phi/psi
 265 ARG   ( 242-)  A  Poor phi/psi
 267 ARG   ( 244-)  A  Poor phi/psi
 339 TYR   (  72-)  B  PRO omega poor
 379 SER   ( 112-)  B  Poor phi/psi
 387 ASN   ( 120-)  B  Poor phi/psi
 411 ARG   ( 144-)  B  Poor phi/psi
 412 LYS   ( 145-)  B  Poor phi/psi
 413 SER   ( 146-)  B  Poor phi/psi
 429 PRO   ( 162-)  B  Poor phi/psi
 432 GLY   ( 165-)  B  Poor phi/psi
 454 THR   ( 187-)  B  Poor phi/psi
 472 ILE   ( 205-)  B  Poor phi/psi
 496 LYS   ( 229-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.138

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 : -3.138

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.

 501 SER   ( 234-)  B    0.36
 308 SER   (  41-)  B    0.38

Warning: Unusual backbone conformations

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

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

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

   3 DADE  (   3-)  C      0
   4 DGUA  (   4-)  C      0
   5 DADE  (   5-)  C      0
   6 DTHY  (   6-)  C      0
   7 DADE  (   7-)  C      0
   8 DTHY  (   8-)  C      0
   9 DCYT  (   9-)  C      0
  10 DTHY  (  10-)  C      0
  11 DTHY  (  11-)  C      0
  12 DCYT  (  12-)  C      0
  13 DGUA  (   1-)  D      0
  14 DADE  (   2-)  D      0
  15 DADE  (   3-)  D      0
  16 DGUA  (   4-)  D      0
  17 DADE  (   5-)  D      0
  18 DTHY  (   6-)  D      0
  19 DADE  (   7-)  D      0
  20 DTHY  (   8-)  D      0
  21 DCYT  (   9-)  D      0
  22 DTHY  (  10-)  D      0
  23 DTHY  (  11-)  D      0
  24 DCYT  (  12-)  D      0
  25 SER   (   2-)  A      0
  26 LEU   (   3-)  A      0
  39 GLN   (  16-)  A      0
And so on for a total of 212 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 : 1.782

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]

 183 PRO   ( 160-)  A    0.00 LOW
 185 PRO   ( 162-)  A    0.00 LOW
 427 PRO   ( 160-)  B    0.00 LOW
 429 PRO   ( 162-)  B    0.00 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].

 106 PRO   (  83-)  A  -115.5 envelop C-gamma (-108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

  11 DTHY  (  11-)  C      N3  <->   14 DADE  (   2-)  D      N1     0.40    2.60  INTRA BL
 498 ASN   ( 231-)  B      ND2 <->  516 HOH   ( 279 )  B      O      0.39    2.31  INTRA
  10 DTHY  (  10-)  C      N3  <->   15 DADE  (   3-)  D      N1     0.38    2.62  INTRA BL
   2 DADE  (   2-)  C      N1  <->   23 DTHY  (  11-)  D      N3     0.36    2.64  INTRA BL
 109 LYS   (  86-)  A      NZ  <->  150 GLN   ( 127-)  A      OE1    0.36    2.34  INTRA BL
   9 DCYT  (   9-)  C      N3  <->   16 DGUA  (   4-)  D      N1     0.33    2.67  INTRA BL
 125 LYS   ( 102-)  A      NZ  <->  515 HOH   ( 324 )  A      O      0.31    2.39  INTRA BF
  82 HIS   (  59-)  A      O   <->  102 LYS   (  79-)  A      NZ     0.28    2.42  INTRA BF
  27 ARG   (   4-)  A      NH1 <->  195 ASP   ( 172-)  A      OD1    0.26    2.44  INTRA BL
   7 DADE  (   7-)  C      N1  <->   18 DTHY  (   6-)  D      N3     0.26    2.74  INTRA BL
  27 ARG   (   4-)  A      NH2 <->  515 HOH   ( 282 )  A      O      0.24    2.46  INTRA BF
  16 DGUA  (   4-)  D      C2' <->   17 DADE  (   5-)  D      C8     0.24    2.96  INTRA BL
 224 GLU   ( 201-)  A      CB  <->  226 LYS   ( 203-)  A      NZ     0.23    2.87  INTRA BF
  18 DTHY  (   6-)  D      C4  <->   19 DADE  (   7-)  D      N7     0.23    2.87  INTRA BL
 114 ILE   (  91-)  A      O   <->  115 LYS   (  92-)  A      NZ     0.23    2.37  INTRA BL
 288 CYS   (  21-)  B      SG  <->  423 LEU   ( 156-)  B      CD2    0.22    3.18  INTRA BF
 143 ASN   ( 120-)  A      ND2 <->  515 HOH   ( 258 )  A      O      0.22    2.48  INTRA
 216 HIS   ( 193-)  A      CE1 <->  515 HOH   ( 295 )  A      O      0.22    2.58  INTRA
 485 ASN   ( 218-)  B      O   <->  496 LYS   ( 229-)  B      NZ     0.21    2.49  INTRA
  92 GLN   (  69-)  A      NE2 <->  515 HOH   ( 306 )  A      O      0.20    2.50  INTRA BF
 335 GLN   (  68-)  B      CB  <->  338 HIS   (  71-)  B      CD2    0.20    3.00  INTRA
 282 ASN   (  15-)  B      ND2 <->  516 HOH   ( 310 )  B      O      0.19    2.51  INTRA BF
  29 ASP   (   6-)  A      OD2 <->   82 HIS   (  59-)  A      NE2    0.19    2.51  INTRA
   3 DADE  (   3-)  C      N1  <->   22 DTHY  (  10-)  D      N3     0.19    2.81  INTRA BL
   1 DGUA  (   1-)  C      N1  <->   24 DCYT  (  12-)  D      N3     0.18    2.82  INTRA BL
And so on for a total of 135 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

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.

 447 LEU   ( 180-)  B      -6.42
 267 ARG   ( 244-)  A      -6.34
 203 LEU   ( 180-)  A      -6.20
 488 ARG   ( 221-)  B      -6.02
 244 ARG   ( 221-)  A      -5.96
 415 LEU   ( 148-)  B      -5.92
  92 GLN   (  69-)  A      -5.86
 509 ARG   ( 242-)  B      -5.72
  91 GLN   (  68-)  A      -5.59
 511 ARG   ( 244-)  B      -5.45
 265 ARG   ( 242-)  A      -5.40
 123 ASN   ( 100-)  A      -5.39
 282 ASN   (  15-)  B      -5.29
 164 VAL   ( 141-)  A      -5.27
 367 ASN   ( 100-)  B      -5.25
 364 ASN   (  97-)  B      -5.09
 334 LYS   (  67-)  B      -5.05
 468 GLU   ( 201-)  B      -5.02

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.

 163 ARG   ( 140-)  A       165 - ALA    142- ( A)         -4.88

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

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.

 184 LYS   ( 161-)  A   -4.01
 411 ARG   ( 144-)  B   -3.45
 428 LYS   ( 161-)  B   -3.42
 337 ASN   (  70-)  B   -3.04
  92 GLN   (  69-)  A   -2.93
 416 LYS   ( 149-)  B   -2.81
 427 PRO   ( 160-)  B   -2.80
 172 LYS   ( 149-)  A   -2.79
 268 LYS   ( 245-)  A   -2.77
 121 LYS   (  98-)  A   -2.69
  40 LYS   (  17-)  A   -2.61

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.

 182 ILE   ( 159-)  A     -  185 PRO   ( 162-)  A        -2.01
 282 ASN   (  15-)  B     -  285 TYR   (  18-)  B        -1.68
 426 ILE   ( 159-)  B     -  429 PRO   ( 162-)  B        -2.11

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

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

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

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

 513 HOH   ( 268 )  C      O     30.46   61.03   37.82
 514 HOH   ( 163 )  D      O     38.33   59.96   54.22
 514 HOH   ( 267 )  D      O     32.38   62.63   38.18

Error: Water molecules without hydrogen bonds

The water molecules listed in the table below do not form any hydrogen bonds, neither with the protein or DNA/RNA, nor with other water molecules. This is a strong indication of a refinement problem. The last number on each line is the identifier of the water molecule in the input file.

 516 HOH   ( 334 )  B      O

Error: HIS, ASN, GLN side chain flips

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

  92 GLN   (  69-)  A
  94 HIS   (  71-)  A
 120 ASN   (  97-)  A
 216 HIS   ( 193-)  A
 218 HIS   ( 195-)  A
 250 ASN   ( 227-)  A
 254 ASN   ( 231-)  A
 462 HIS   ( 195-)  B
 498 ASN   ( 231-)  B

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.

  54 TYR   (  31-)  A      OH
  57 GLY   (  34-)  A      N
  92 GLN   (  69-)  A      N
 102 LYS   (  79-)  A      N
 129 THR   ( 106-)  A      OG1
 144 ILE   ( 121-)  A      N
 186 TYR   ( 163-)  A      N
 218 HIS   ( 195-)  A      N
 231 SER   ( 208-)  A      N
 245 THR   ( 222-)  A      N
 247 GLN   ( 224-)  A      N
 249 ARG   ( 226-)  A      NE
 255 ASN   ( 232-)  A      N
 301 GLY   (  34-)  B      N
 316 ARG   (  49-)  B      NH1
 336 GLN   (  69-)  B      NE2
 337 ASN   (  70-)  B      N
 346 LYS   (  79-)  B      N
 368 GLU   ( 101-)  B      N
 369 LYS   ( 102-)  B      N
 390 TYR   ( 123-)  B      N
 414 SER   ( 147-)  B      N
 424 ASN   ( 157-)  B      N
 424 ASN   ( 157-)  B      ND2
 430 TYR   ( 163-)  B      N
 475 SER   ( 208-)  B      N
 489 THR   ( 222-)  B      N
 495 ASP   ( 228-)  B      N
 499 ASN   ( 232-)  B      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.

 143 ASN   ( 120-)  A      OD1
 177 ASN   ( 154-)  A      OD1
 387 ASN   ( 120-)  B      OD1
 398 HIS   ( 131-)  B      NE2

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

 515 HOH   ( 317 )  A      O  0.86  K  4

Warning: Possible wrong residue type

The residues listed in the table below have a weird environment that cannot be improved by rotamer flips. This can mean one of three things, non of which WHAT CHECK really can do much about. 1) The side chain has actually another rotamer than is present in the PDB file; 2) A counter ion is present in the structure but is not given in the PDB file; 3) The residue actually is another amino acid type. The annotation 'Alt-rotamer' indicates that WHAT CHECK thinks you might want to find an alternate rotamer for this residue. The annotation 'Sym-induced' indicates that WHAT CHECK believes that symmetry contacts might have something to do with the difficulties of this residue's side chain. Determination of these two annotations is difficult, so their absence is less meaningful than their presence. The annotation Ligand-bound indicates that a ligand seems involved with this residue. In nine of ten of these cases this indicates that the ligand is causing the weird situation rather than the residue.

  36 ASP   (  13-)  A   H-bonding suggests Asn
  80 GLU   (  57-)  A   H-bonding suggests Gln; but Alt-Rotamer
 324 GLU   (  57-)  B   H-bonding suggests Gln; but Alt-Rotamer
 495 ASP   ( 228-)  B   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 :  -0.740
  2nd generation packing quality :  -2.182
  Ramachandran plot appearance   :  -2.590
  chi-1/chi-2 rotamer normality  :  -3.138 (poor)
  Backbone conformation          :  -0.669

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.642 (tight)
  Bond angles                    :   0.874
  Omega angle restraints         :   0.324 (tight)
  Side chain planarity           :   0.690
  Improper dihedral distribution :   1.245
  B-factor distribution          :   0.599
  Inside/Outside distribution    :   0.977

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 : 2.16


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.1
  2nd generation packing quality :  -1.2
  Ramachandran plot appearance   :  -1.2
  chi-1/chi-2 rotamer normality  :  -1.7
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.642 (tight)
  Bond angles                    :   0.874
  Omega angle restraints         :   0.324 (tight)
  Side chain planarity           :   0.690
  Improper dihedral distribution :   1.245
  B-factor distribution          :   0.599
  Inside/Outside distribution    :   0.977
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    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
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      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
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      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

DSSP
    W.Kabsch and C.Sander,
      Dictionary of protein secondary structure: pattern
      recognition of hydrogen bond and geometrical features
    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
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      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
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      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      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.