WHAT IF Check report

This file was created 2012-01-19 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 pdb2b0e.ent

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'.

  38 LYS   (  17-)  A      CG
  38 LYS   (  17-)  A      CD
  38 LYS   (  17-)  A      CE
  38 LYS   (  17-)  A      NZ
  56 SER   (  35-)  A      OG
  59 LYS   (  38-)  A      CG
  59 LYS   (  38-)  A      CD
  59 LYS   (  38-)  A      CE
  59 LYS   (  38-)  A      NZ
  75 LYS   (  54-)  A      CG
  75 LYS   (  54-)  A      CD
  75 LYS   (  54-)  A      CE
  75 LYS   (  54-)  A      NZ
  78 GLU   (  57-)  A      CG
  78 GLU   (  57-)  A      CD
  78 GLU   (  57-)  A      OE1
  78 GLU   (  57-)  A      OE2
  88 LYS   (  67-)  A      CG
  88 LYS   (  67-)  A      CD
  88 LYS   (  67-)  A      CE
  88 LYS   (  67-)  A      NZ
  90 GLN   (  69-)  A      CG
  90 GLN   (  69-)  A      CD
  90 GLN   (  69-)  A      OE1
  90 GLN   (  69-)  A      NE2
And so on for a total of 163 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

  33 TYR   (  12-)  A
  82 TYR   (  61-)  A
  93 TYR   (  72-)  A
 116 TYR   (  95-)  A
 144 TYR   ( 128-)  A
 152 TYR   ( 136-)  A
 154 TYR   ( 138-)  A
 251 TYR   ( 241-)  A
 266 TYR   (  12-)  B
 349 TYR   (  95-)  B
 389 TYR   ( 138-)  B

Warning: Phenylalanine convention problem

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

 329 PHE   (  75-)  B
 445 PHE   ( 199-)  B

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.

  27 ASP   (   6-)  A
  57 ASP   (  36-)  A
  95 ASP   (  74-)  A
 182 ASP   ( 172-)  A
 220 ASP   ( 210-)  A
 267 ASP   (  13-)  B
 273 ASP   (  19-)  B
 328 ASP   (  74-)  B
 344 ASP   (  90-)  B
 377 ASP   ( 126-)  B
 418 ASP   ( 172-)  B
 425 ASP   ( 179-)  B
 453 ASP   ( 207-)  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.

  48 GLU   (  27-)  A
  85 GLU   (  64-)  A
 103 GLU   (  82-)  A
 165 GLU   ( 155-)  A
 230 GLU   ( 220-)  A
 245 GLU   ( 235-)  A
 268 GLU   (  14-)  B
 401 GLU   ( 155-)  B
 466 GLU   ( 220-)  B

Geometric checks

Warning: Low bond length variability

Bond lengths were found to deviate less than normal from the mean Engh and Huber [REF] and/or Parkinson et al [REF] standard bond lengths. The RMS Z-score given below is expected to be near 1.0 for a normally restrained data set. The fact that it is lower than 0.667 in this structure might indicate that too-strong restraints have been used in the refinement. This can only be a problem for high resolution X-ray structures.

RMS Z-score for bond lengths: 0.466
RMS-deviation in bond distances: 0.010

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

 |  0.998998 -0.000504  0.000216|
 | -0.000504  1.000241 -0.000647|
 |  0.000216 -0.000647  0.997848|
Proposed new scale matrix

 |  0.020812  0.006252  0.008917|
 |  0.000010  0.021524  0.005297|
 | -0.000004  0.000011  0.017077|
With corresponding cell

    A    =  48.052  B   =  48.521  C    =  63.784
    Alpha=  97.085  Beta= 108.980  Gamma= 106.733

The CRYST1 cell dimensions

    A    =  48.100  B   =  48.500  C    =  63.900
    Alpha=  97.000  Beta= 109.000  Gamma= 106.700

Variance: 37.823
(Under-)estimated Z-score: 4.533

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  105.10   -5.7
   6 DADE  (   6-)  C      C2'  C1'  N9  103.10   -6.9
  15 DGUA  (   4-)  D      O3'  C3'  C4' 100.31   -4.5
  19 DTHY  (   8-)  D      C2'  C1'  N1  121.85    4.8
 313 HIS   (  59-)  B      CG   ND1  CE1 109.64    4.0
 357 THR   ( 106-)  B      N    CA   C    98.90   -4.4
 382 HIS   ( 131-)  B      CG   ND1  CE1 109.61    4.0
 439 HIS   ( 193-)  B      CG   ND1  CE1 109.61    4.0

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.

  27 ASP   (   6-)  A
  48 GLU   (  27-)  A
  57 ASP   (  36-)  A
  85 GLU   (  64-)  A
  95 ASP   (  74-)  A
 103 GLU   (  82-)  A
 165 GLU   ( 155-)  A
 182 ASP   ( 172-)  A
 220 ASP   ( 210-)  A
 230 GLU   ( 220-)  A
 245 GLU   ( 235-)  A
 267 ASP   (  13-)  B
 268 GLU   (  14-)  B
 273 ASP   (  19-)  B
 328 ASP   (  74-)  B
 344 ASP   (  90-)  B
 377 ASP   ( 126-)  B
 401 GLU   ( 155-)  B
 418 ASP   ( 172-)  B
 425 ASP   ( 179-)  B
 453 ASP   ( 207-)  B
 466 GLU   ( 220-)  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.

 143 GLN   ( 127-)  A    6.11
  38 LYS   (  17-)  A    5.62
 271 LYS   (  17-)  B    4.45
 237 ASN   ( 227-)  A    4.38
  70 ARG   (  49-)  A    4.34
 416 LEU   ( 170-)  B    4.21
 357 THR   ( 106-)  B    4.11

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 : 1.534

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.

 327 PRO   (  73-)  B    -2.9
  94 PRO   (  73-)  A    -2.9
 348 THR   (  94-)  B    -2.7
 115 THR   (  94-)  A    -2.5
 196 THR   ( 186-)  A    -2.3
 145 ILE   ( 129-)  A    -2.3
 227 ARG   ( 217-)  A    -2.2
 175 GLY   ( 165-)  A    -2.2
  85 GLU   (  64-)  A    -2.1
 128 SER   ( 112-)  A    -2.1
 408 PRO   ( 162-)  B    -2.1
 370 LYS   ( 119-)  B    -2.1
 116 TYR   (  95-)  A    -2.1
 354 ILE   ( 103-)  B    -2.1
 451 ILE   ( 205-)  B    -2.0
 215 ILE   ( 205-)  A    -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.

  91 ASN   (  70-)  A  Poor phi/psi
  93 TYR   (  72-)  A  PRO omega poor
 128 SER   ( 112-)  A  Poor phi/psi
 136 ASN   ( 120-)  A  Poor phi/psi
 197 THR   ( 187-)  A  Poor phi/psi
 239 LYS   ( 229-)  A  Poor phi/psi
 253 GLY   ( 243-)  A  Poor phi/psi
 254 ARG   ( 244-)  A  Poor phi/psi
 324 ASN   (  70-)  B  Poor phi/psi
 326 TYR   (  72-)  B  PRO omega poor
 363 SER   ( 112-)  B  Poor phi/psi
 371 ASN   ( 120-)  B  Poor phi/psi
 433 THR   ( 187-)  B  Poor phi/psi
 475 LYS   ( 229-)  B  Poor phi/psi
 490 ARG   ( 244-)  B  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -2.703

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.

  26 SER   (   5-)  A    0.36
 244 SER   ( 234-)  A    0.38
 480 SER   ( 234-)  B    0.39

Warning: Unusual backbone conformations

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

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

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

   3 DADE  (   3-)  C      0
   4 DGUA  (   4-)  C      0
   5 DADE  (   5-)  C      0
   6 DADE  (   6-)  C      0
   7  DU   (   7-)  C      0
   8 DTHY  (   8-)  C      0
   9 DCYT  (   9-)  C      0
  10 DTHY  (  10-)  C      0
  11 DTHY  (  11-)  C      0
  12 DADE  (   1-)  D      0
  13 DADE  (   2-)  D      0
  14 DADE  (   3-)  D      0
  15 DGUA  (   4-)  D      0
  16 DADE  (   5-)  D      0
  17 DADE  (   6-)  D      0
  18  DU   (   7-)  D      0
  19 DTHY  (   8-)  D      0
  20 DCYT  (   9-)  D      0
  21 DTHY  (  10-)  D      0
  22 DTHY  (  11-)  D      0
  23 SER   (   2-)  A      0
  24 LEU   (   3-)  A      0
  38 LYS   (  17-)  A      0
  42 CYS   (  21-)  A      0
  48 GLU   (  27-)  A      0
And so on for a total of 194 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 : 1.518

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].

  87 PRO   (  66-)  A  -118.0 half-chair C-delta/C-gamma (-126 degrees)
 101 PRO   (  80-)  A  -115.4 envelop C-gamma (-108 degrees)
 327 PRO   (  73-)  B   -63.0 half-chair C-beta/C-alpha (-54 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  <->   13 DADE  (   2-)  D      N1     0.58    2.42  INTRA BF
 419 LYS   ( 173-)  B      NZ  <->  499 HOH   ( 330 )  B      O      0.40    2.30  INTRA
 419 LYS   ( 173-)  B      NZ  <->  499 HOH   ( 259 )  B      O      0.38    2.32  INTRA
  12 DADE  (   1-)  D      O5' <->   13 DADE  (   2-)  D      C8     0.36    2.44  INTRA BF
  16 DADE  (   5-)  D      OP1 <->  370 LYS   ( 119-)  B      NZ     0.32    2.38  INTRA
  10 DTHY  (  10-)  C      N3  <->   14 DADE  (   3-)  D      N1     0.29    2.71  INTRA
  21 DTHY  (  10-)  D      C2' <->   22 DTHY  (  11-)  D      C6     0.29    2.91  INTRA BF
   3 DADE  (   3-)  C      N1  <->   21 DTHY  (  10-)  D      N3     0.28    2.72  INTRA
   2 DADE  (   2-)  C      N1  <->   22 DTHY  (  11-)  D      N3     0.28    2.72  INTRA BF
   6 DADE  (   6-)  C      N1  <->   18  DU   (   7-)  D      N3     0.28    2.72  INTRA BL
 239 LYS   ( 229-)  A      NZ  <->  498 HOH   ( 429 )  A      O      0.25    2.45  INTRA
 346 LYS   (  92-)  B      NZ  <->  497 HOH   ( 408 )  D      O      0.24    2.46  INTRA
   4 DGUA  (   4-)  C      N1  <->   20 DCYT  (   9-)  D      N3     0.21    2.79  INTRA BL
 464 ASN   ( 218-)  B      ND2 <->  490 ARG   ( 244-)  B      NH2    0.20    2.65  INTRA
   7  DU   (   7-)  C      N3  <->   17 DADE  (   6-)  D      N1     0.20    2.80  INTRA BL
  17 DADE  (   6-)  D      C5' <->  499 HOH   ( 320 )  B      O      0.20    2.60  INTRA BF
   2 DADE  (   2-)  C      OP1 <->  477 ASN   ( 231-)  B      ND2    0.18    2.52  INTRA BF
 355 LYS   ( 104-)  B      NZ  <->  499 HOH   ( 302 )  B      O      0.17    2.53  INTRA
  16 DADE  (   5-)  D      P   <->  370 LYS   ( 119-)  B      NZ     0.16    3.14  INTRA
  12 DADE  (   1-)  D      C6  <->   13 DADE  (   2-)  D      C2     0.16    3.04  INTRA
 467 ARG   ( 221-)  B      C   <->  472 ARG   ( 226-)  B      NH1    0.16    2.94  INTRA
 460 ASP   ( 214-)  B      OD1 <->  490 ARG   ( 244-)  B      NH2    0.15    2.55  INTRA
 333 LYS   (  79-)  B      NZ  <->  336 GLU   (  82-)  B      CD     0.15    2.95  INTRA BF
   8 DTHY  (   8-)  C      N3  <->   16 DADE  (   5-)  D      N1     0.15    2.85  INTRA BL
  35 GLU   (  14-)  A      OE2 <->  283 LYS   (  29-)  B      NZ     0.14    2.56  INTRA
And so on for a total of 100 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.

 467 ARG   ( 221-)  B      -6.62
 190 LEU   ( 180-)  A      -6.52
 254 ARG   ( 244-)  A      -6.17
 426 LEU   ( 180-)  B      -6.13
 490 ARG   ( 244-)  B      -6.13
 313 HIS   (  59-)  B      -5.87
 252 ARG   ( 242-)  A      -5.71
 116 TYR   (  95-)  A      -5.50
 231 ARG   ( 221-)  A      -5.27
 349 TYR   (  95-)  B      -5.12
 447 GLU   ( 201-)  B      -5.08
  89 GLN   (  68-)  A      -5.03

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.

 171 LYS   ( 161-)  A   -3.53
  90 GLN   (  69-)  A   -3.48
 323 GLN   (  69-)  B   -3.37
  91 ASN   (  70-)  A   -3.25
 395 LYS   ( 149-)  B   -3.07
 322 GLN   (  68-)  B   -3.01
 407 LYS   ( 161-)  B   -2.97
 491 LYS   ( 245-)  B   -2.94
 159 LYS   ( 149-)  A   -2.92
 338 ASN   (  84-)  B   -2.91
 391 ARG   ( 140-)  B   -2.78
 404 GLU   ( 158-)  B   -2.72
 324 ASN   (  70-)  B   -2.67
 156 ARG   ( 140-)  A   -2.60
 213 LYS   ( 203-)  A   -2.60
  59 LYS   (  38-)  A   -2.59
 449 LYS   ( 203-)  B   -2.58
  88 LYS   (  67-)  A   -2.50

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.

 233 SER   ( 223-)  A     -  236 ARG   ( 226-)  A        -1.72
 320 PRO   (  66-)  B     -  324 ASN   (  70-)  B        -2.55

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.

 498 HOH   ( 364 )  A      O     -7.17   19.31  -23.27
 498 HOH   ( 366 )  A      O     -6.09   22.87  -24.39
 498 HOH   ( 371 )  A      O      5.83   -4.94   33.03
 499 HOH   ( 253 )  B      O      6.73   -5.39   35.65

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.

 499 HOH   ( 281 )  B      O
ERROR. Strange cone in HB2INI
Affected atom    7  DU  (   7-) C      P
ERROR. Strange cone in HB2INI
Affected atom   18  DU  (   7-) D      P
Expected ambiguity-2 in FILL1HARR 0 60 552
Expected ambiguity-2 in FILL1HARR 0 60 552

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.

  36 ASN   (  15-)  A
  91 ASN   (  70-)  A
 269 ASN   (  15-)  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.

   6 DADE  (   6-)  C      N6
  48 GLU   (  27-)  A      N
  55 GLY   (  34-)  A      N
  72 ILE   (  51-)  A      N
  89 GLN   (  68-)  A      N
 127 THR   ( 111-)  A      OG1
 137 ILE   ( 121-)  A      N
 155 THR   ( 139-)  A      N
 157 VAL   ( 141-)  A      N
 163 ILE   ( 153-)  A      N
 173 TYR   ( 163-)  A      N
 193 SER   ( 183-)  A      OG
 198 ASN   ( 188-)  A      ND2
 218 SER   ( 208-)  A      N
 232 THR   ( 222-)  A      N
 239 LYS   ( 229-)  A      N
 240 TYR   ( 230-)  A      N
 242 ASN   ( 232-)  A      N
 279 SER   (  25-)  B      OG
 281 GLU   (  27-)  B      N
 288 GLY   (  34-)  B      N
 324 ASN   (  70-)  B      N
 372 ILE   ( 121-)  B      N
 381 ALA   ( 130-)  B      N
 402 LEU   ( 156-)  B      N
 407 LYS   ( 161-)  B      N
 409 TYR   ( 163-)  B      N
 421 VAL   ( 175-)  B      N
 454 SER   ( 208-)  B      N
 468 THR   ( 222-)  B      N
 471 LEU   ( 225-)  B      N
 478 ASN   ( 232-)  B      N
 490 ARG   ( 244-)  B      NE

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.

  92 HIS   (  71-)  A      ND1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

 494  CA   ( 307-)  A     0.92   1.15 Scores about as good as NA *2
 495  CA   ( 322-)  A     0.86   1.06 Scores about as good as NA *2

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.

 499 HOH   ( 299 )  B      O  1.03  K  4 NCS 1/1
 499 HOH   ( 300 )  B      O  1.01  K  4 Ion-B
 499 HOH   ( 344 )  B      O  1.09  K  5 Ion-B

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.

  27 ASP   (   6-)  A   H-bonding suggests Asn; but Alt-Rotamer
  40 ASP   (  19-)  A   H-bonding suggests Asn; but Alt-Rotamer
 208 ASP   ( 198-)  A   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 :  -0.721
  2nd generation packing quality :  -2.037
  Ramachandran plot appearance   :  -1.697
  chi-1/chi-2 rotamer normality  :  -2.703
  Backbone conformation          :  -0.306

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.466 (tight)
  Bond angles                    :   0.735
  Omega angle restraints         :   0.276 (tight)
  Side chain planarity           :   0.510 (tight)
  Improper dihedral distribution :   0.940
  B-factor distribution          :   0.826
  Inside/Outside distribution    :   1.005

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 : 1.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.3
  2nd generation packing quality :  -1.5
  Ramachandran plot appearance   :  -1.5
  chi-1/chi-2 rotamer normality  :  -1.9
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.466 (tight)
  Bond angles                    :   0.735
  Omega angle restraints         :   0.276 (tight)
  Side chain planarity           :   0.510 (tight)
  Improper dihedral distribution :   0.940
  B-factor distribution          :   0.826
  Inside/Outside distribution    :   1.005
==============

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.