WHAT IF Check report

This file was created 2011-12-18 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 pdb2yid.ent

Checks that need to be done early-on in validation

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

3377 TD7   (2001-)  A  -
3380 TD7   (2001-)  B  -
3383 TD7   (2001-)  C  -
3388 TD7   (2001-)  D  -

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: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

 952 PHE   ( 495-)  B
1130 VAL   ( 676-)  B
1853 LYS   ( 552-)  C

Warning: Missing atoms

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

   1 ASP   ( 361-)  A      CG
   1 ASP   ( 361-)  A      OD1
   1 ASP   ( 361-)  A      OD2
   2 SER   ( 362-)  A      OG
   3 ILE   ( 363-)  A      CG1
   3 ILE   ( 363-)  A      CG2
   3 ILE   ( 363-)  A      CD1
   4 GLU   ( 364-)  A      CG
   4 GLU   ( 364-)  A      CD
   4 GLU   ( 364-)  A      OE1
   4 GLU   ( 364-)  A      OE2
   6 LYS   ( 366-)  A      CG
   6 LYS   ( 366-)  A      CD
   6 LYS   ( 366-)  A      CE
   6 LYS   ( 366-)  A      NZ
  35 THR   ( 395-)  A      OG1
  35 THR   ( 395-)  A      CG2
  38 THR   ( 411-)  A      OG1
  38 THR   ( 411-)  A      CG2
  39 LEU   ( 412-)  A      CG
  39 LEU   ( 412-)  A      CD1
  39 LEU   ( 412-)  A      CD2
  40 TRP   ( 413-)  A      CG
  40 TRP   ( 413-)  A      CD1
  40 TRP   ( 413-)  A      CD2
And so on for a total of 528 lines.

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

   9 ARG   ( 369-)  A    High
  36 ARG   ( 396-)  A    High
  45 GLU   ( 418-)  A    High
  49 ASP   ( 422-)  A    High
  53 LYS   ( 430-)  A    High
  54 LYS   ( 431-)  A    High
  68 ARG   ( 445-)  A    High
  84 ARG   ( 461-)  A    High
 404 ARG   ( 781-)  A    High
 447 ILE   ( 827-)  A    High
 704 GLU   (1087-)  A    High
 774 ARG   (1157-)  A    High
 879 GLU   ( 418-)  B    High
 882 VAL   ( 421-)  B    High
 887 LYS   ( 430-)  B    High
 918 ARG   ( 461-)  B    High
 927 LYS   ( 470-)  B    High
1235 ARG   ( 781-)  B    High
1244 GLU   ( 790-)  B    High
1248 ARG   ( 794-)  B    High
1262 ARG   ( 808-)  B    High
1322 ARG   ( 868-)  B    High
1604 ARG   (1150-)  B    High
1687 ARG   ( 369-)  C    High
1716 ARG   ( 398-)  C    High
And so on for a total of 53 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. 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: 4

Crystal temperature (K) :110.000

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

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.

 329 ILE   ( 706-)  A      CG1  CD1   1.35   -4.1
2284 ILE   ( 987-)  C      CG1  CD1   1.72    5.3

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

 |  0.996450  0.000118 -0.000113|
 |  0.000118  0.996328  0.000142|
 | -0.000113  0.000142  0.996843|
Proposed new scale matrix

 |  0.012570  0.002358  0.002506|
 | -0.000001  0.012410  0.002465|
 |  0.000000  0.000000  0.006335|
With corresponding cell

    A    =  79.556  B   =  81.983  C    = 162.960
    Alpha=  99.218  Beta=  99.036  Gamma= 100.618

The CRYST1 cell dimensions

    A    =  79.843  B   =  82.287  C    = 163.478
    Alpha=  99.230  Beta=  99.030  Gamma= 100.630

Variance: 1324.040
(Under-)estimated Z-score: 26.817

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 ASP   ( 365-)  A      CA   CB   CG  116.95    4.4
   7 ASN   ( 367-)  A      CA   CB   CG  116.66    4.1
  11 ILE   ( 371-)  A      CB   CG1  CD1 123.22    4.5
  28 ASP   ( 388-)  A      CA   CB   CG  118.43    5.8
 139 PRO   ( 516-)  A     -CA  -C    N   123.30    4.3
 230 GLU   ( 607-)  A      CB   CG   CD  119.79    4.2
 361 ASP   ( 738-)  A      CA   CB   CG  118.06    5.5
 399 GLU   ( 776-)  A      CB   CG   CD  119.49    4.1
 429 GLU   ( 806-)  A      CB   CG   CD  119.62    4.1
 442 GLU   ( 822-)  A      CB   CG   CD  119.78    4.2
 479 PRO   ( 862-)  A     -CA  -C    N   122.99    4.1
 494 ASP   ( 877-)  A      CA   CB   CG  118.53    5.9
 552 ASP   ( 935-)  A      CA   CB   CG  117.03    4.4
 570 PHE   ( 953-)  A      CA   CB   CG  119.17    5.4
 641 ARG   (1024-)  A     -C    N    CA  129.06    4.1
 675 ASP   (1058-)  A      CA   CB   CG  117.63    5.0
 684 PHE   (1067-)  A      CA   CB   CG  108.92   -4.9
 722 ASP   (1105-)  A      CA   CB   CG  117.15    4.6
 780 GLU   (1163-)  A      CB   CG   CD  120.04    4.4
 868 ASP   ( 388-)  B      CA   CB   CG  118.25    5.7
 950 GLU   ( 493-)  B      CB   CG   CD  119.83    4.3
 973 PRO   ( 516-)  B     -CA  -C    N   123.36    4.3
1023 ASN   ( 566-)  B      CA   CB   CG  117.59    5.0
1090 SER   ( 636-)  B     -C    N    CA  129.55    4.4
1192 ASP   ( 738-)  B      CA   CB   CG  118.84    6.2
And so on for a total of 65 lines.

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.

3058 THR   ( 909-)  D    -3.5
2206 THR   ( 909-)  C    -3.5
1363 THR   ( 909-)  B    -3.5
 526 THR   ( 909-)  A    -3.4
1136 PHE   ( 682-)  B    -3.3
 305 PHE   ( 682-)  A    -3.3
2833 PHE   ( 682-)  D    -3.3
1981 PHE   ( 682-)  C    -3.3
2412 THR   (1115-)  C    -2.9
3264 THR   (1115-)  D    -2.9
1569 THR   (1115-)  B    -2.9
 732 THR   (1115-)  A    -2.8
1134 ILE   ( 680-)  B    -2.6
1979 ILE   ( 680-)  C    -2.6
2831 ILE   ( 680-)  D    -2.6
 303 ILE   ( 680-)  A    -2.6
1904 PRO   ( 603-)  C    -2.6
1057 PRO   ( 603-)  B    -2.6
1839 PRO   ( 538-)  C    -2.5
 995 PRO   ( 538-)  B    -2.5
2689 PRO   ( 538-)  D    -2.4
 161 PRO   ( 538-)  A    -2.4
2083 ILE   ( 784-)  C    -2.4
1238 ILE   ( 784-)  B    -2.4
  74 TYR   ( 451-)  A    -2.3
2561 PHE   ( 397-)  D    -2.3
3306 ARG   (1157-)  D    -2.3
1715 PHE   ( 397-)  C    -2.2
2580 ARG   ( 429-)  D    -2.2
 407 ILE   ( 784-)  A    -2.2
2754 PRO   ( 603-)  D    -2.2
 708 ARG   (1091-)  A    -2.2
1135 GLY   ( 681-)  B    -2.2
2935 ILE   ( 784-)  D    -2.2
2832 GLY   ( 681-)  D    -2.2
 304 GLY   ( 681-)  A    -2.2
1980 GLY   ( 681-)  C    -2.2
2388 ARG   (1091-)  C    -2.2
3240 ARG   (1091-)  D    -2.1
2967 GLU   ( 816-)  D    -2.0
2750 LEU   ( 599-)  D    -2.0
 222 LEU   ( 599-)  A    -2.0
1900 LEU   ( 599-)  C    -2.0
1053 LEU   ( 599-)  B    -2.0
1270 GLU   ( 816-)  B    -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.

  31 ARG   ( 391-)  A  Poor phi/psi
  68 ARG   ( 445-)  A  Poor phi/psi
  74 TYR   ( 451-)  A  Poor phi/psi
 161 PRO   ( 538-)  A  Poor phi/psi
 230 GLU   ( 607-)  A  Poor phi/psi
 248 ASP   ( 625-)  A  Poor phi/psi
 289 TYR   ( 666-)  A  Poor phi/psi
 305 PHE   ( 682-)  A  Poor phi/psi
 355 LYS   ( 732-)  A  Poor phi/psi
 364 CYS   ( 741-)  A  Poor phi/psi
 470 GLY   ( 853-)  A  Poor phi/psi
 519 ASP   ( 902-)  A  Poor phi/psi
 687 LYS   (1070-)  A  Poor phi/psi
 761 ALA   (1144-)  A  PRO omega poor
 871 ARG   ( 391-)  B  Poor phi/psi
 902 ARG   ( 445-)  B  Poor phi/psi
 908 TYR   ( 451-)  B  Poor phi/psi
 995 PRO   ( 538-)  B  Poor phi/psi
1061 GLU   ( 607-)  B  Poor phi/psi
1079 ASP   ( 625-)  B  Poor phi/psi
1120 TYR   ( 666-)  B  Poor phi/psi
1136 PHE   ( 682-)  B  Poor phi/psi
1195 CYS   ( 741-)  B  Poor phi/psi
1356 ASP   ( 902-)  B  Poor phi/psi
1524 LYS   (1070-)  B  Poor phi/psi
And so on for a total of 53 lines.

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.

2323 GLU   (1026-)  C    0.36
3175 GLU   (1026-)  D    0.36
 941 SER   ( 484-)  B    0.40

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 ILE   ( 363-)  A      0
  19 ASN   ( 379-)  A      0
  27 ILE   ( 387-)  A      0
  32 LEU   ( 392-)  A      0
  35 THR   ( 395-)  A      0
  36 ARG   ( 396-)  A      0
  37 LEU   ( 410-)  A      0
  38 THR   ( 411-)  A      0
  48 VAL   ( 421-)  A      0
  49 ASP   ( 422-)  A      0
  50 VAL   ( 427-)  A      0
  51 GLN   ( 428-)  A      0
  66 TYR   ( 443-)  A      0
  67 CYS   ( 444-)  A      0
  68 ARG   ( 445-)  A      0
  69 HIS   ( 446-)  A      0
  73 GLU   ( 450-)  A      0
  74 TYR   ( 451-)  A      0
  75 THR   ( 452-)  A      0
  76 HIS   ( 453-)  A      0
  78 LEU   ( 455-)  A      0
  91 GLU   ( 468-)  A      0
  92 THR   ( 469-)  A      0
  94 HIS   ( 471-)  A      0
 123 TYR   ( 500-)  A      0
And so on for a total of 1157 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 : 3.214

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].

 139 PRO   ( 516-)  A  -113.7 envelop C-gamma (-108 degrees)
 161 PRO   ( 538-)  A   -34.2 envelop C-alpha (-36 degrees)
 262 PRO   ( 639-)  A    10.2 half-chair N/C-delta (18 degrees)
 555 PRO   ( 938-)  A    46.6 half-chair C-delta/C-gamma (54 degrees)
 764 PRO   (1147-)  A   -48.9 half-chair C-beta/C-alpha (-54 degrees)
 995 PRO   ( 538-)  B   -35.2 envelop C-alpha (-36 degrees)
1093 PRO   ( 639-)  B    35.1 envelop C-delta (36 degrees)
1392 PRO   ( 938-)  B    50.9 half-chair C-delta/C-gamma (54 degrees)
1601 PRO   (1147-)  B   -48.0 half-chair C-beta/C-alpha (-54 degrees)
1839 PRO   ( 538-)  C   -37.1 envelop C-alpha (-36 degrees)
1904 PRO   ( 603-)  C   -46.8 half-chair C-beta/C-alpha (-54 degrees)
1938 PRO   ( 639-)  C    32.8 envelop C-delta (36 degrees)
2116 PRO   ( 817-)  C  -112.5 envelop C-gamma (-108 degrees)
2235 PRO   ( 938-)  C    48.0 half-chair C-delta/C-gamma (54 degrees)
2444 PRO   (1147-)  C   -50.9 half-chair C-beta/C-alpha (-54 degrees)
2689 PRO   ( 538-)  D   -30.6 envelop C-alpha (-36 degrees)
2754 PRO   ( 603-)  D   -39.1 envelop C-alpha (-36 degrees)
2790 PRO   ( 639-)  D    33.2 envelop C-delta (36 degrees)
3087 PRO   ( 938-)  D    49.2 half-chair C-delta/C-gamma (54 degrees)
3296 PRO   (1147-)  D   -50.0 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.

 960 GLN   ( 503-)  B      NE2 <-> 1018 PHE   ( 561-)  B      O      0.36    2.34  INTRA
 227 SER   ( 604-)  A      O   <-> 3377 TD7   (2001-)  A      N4'    0.31    2.39  INTRA BL
 735 LYS   (1118-)  A      NZ  <->  786 GLU   (1169-)  A      OE2    0.27    2.43  INTRA BF
1814 THR   ( 513-)  C      CG2 <-> 2016 CYS   ( 717-)  C      SG     0.26    3.14  INTRA BL
1058 SER   ( 604-)  B      O   <-> 3380 TD7   (2001-)  B      N4'    0.25    2.45  INTRA BL
2415 LYS   (1118-)  C      NZ  <-> 2466 GLU   (1169-)  C      OE2    0.25    2.45  INTRA BF
1572 LYS   (1118-)  B      NZ  <-> 1623 GLU   (1169-)  B      OE2    0.25    2.45  INTRA BF
3267 LYS   (1118-)  D      NZ  <-> 3318 GLU   (1169-)  D      OE2    0.25    2.45  INTRA BF
1465 HIS   (1011-)  B      ND1 <-> 1477 GLY   (1023-)  B      N      0.25    2.75  INTRA BL
3160 HIS   (1011-)  D      ND1 <-> 3172 GLY   (1023-)  D      N      0.24    2.76  INTRA BL
 628 HIS   (1011-)  A      ND1 <->  640 GLY   (1023-)  A      N      0.23    2.77  INTRA BL
2308 HIS   (1011-)  C      ND1 <-> 2320 GLY   (1023-)  C      N      0.23    2.77  INTRA BL
2139 ARG   ( 842-)  C      NH2 <-> 2229 THR   ( 932-)  C      O      0.21    2.49  INTRA BL
1166 ASP   ( 712-)  B      OD2 <-> 1221 LYS   ( 767-)  B      NZ     0.21    2.49  INTRA BF
1009 LYS   ( 552-)  B      NZ  <-> 3390 HOH   (3031 )  B      O      0.21    2.49  INTRA BL
1942 HIS   ( 643-)  C      NE2 <-> 1972 HIS   ( 673-)  C      ND1    0.21    2.79  INTRA BL
3169 HIS   (1020-)  D      NE2 <-> 3383 TD7   (2001-)  C      OL2    0.20    2.50  INTRA
1804 GLN   ( 503-)  C      NE2 <-> 1862 PHE   ( 561-)  C      O      0.20    2.50  INTRA BF
2898 HIS   ( 747-)  D      ND1 <-> 3392 HOH   (3021 )  D      O      0.20    2.50  INTRA BL
2794 HIS   ( 643-)  D      NE2 <-> 2824 HIS   ( 673-)  D      ND1    0.20    2.80  INTRA BL
2660 GLU   ( 509-)  D      OE1 <-> 2896 ARG   ( 745-)  D      NE     0.20    2.50  INTRA
 266 HIS   ( 643-)  A      NE2 <->  296 HIS   ( 673-)  A      ND1    0.20    2.80  INTRA BL
1296 ARG   ( 842-)  B      NH2 <-> 1386 THR   ( 932-)  B      O      0.20    2.50  INTRA
3389 HOH   (3028 )  A      O   <-> 3390 HOH   (3137 )  B      O      0.19    2.21  INTRA
1097 HIS   ( 643-)  B      NE2 <-> 1127 HIS   ( 673-)  B      ND1    0.19    2.81  INTRA BL
And so on for a total of 242 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.

2125 GLN   ( 826-)  C      -7.29
 927 LYS   ( 470-)  B      -6.73
2977 GLN   ( 826-)  D      -6.57
1222 ARG   ( 768-)  B      -6.44
2067 ARG   ( 768-)  C      -6.43
2580 ARG   ( 429-)  D      -6.42
1043 MET   ( 589-)  B      -6.00
1470 GLN   (1016-)  B      -5.99
1025 HIS   ( 571-)  B      -5.97
 367 ARG   ( 744-)  A      -5.96
2043 ARG   ( 744-)  C      -5.94
1890 MET   ( 589-)  C      -5.94
2740 MET   ( 589-)  D      -5.93
3165 GLN   (1016-)  D      -5.92
1866 LEU   ( 565-)  C      -5.91
 391 ARG   ( 768-)  A      -5.89
1872 HIS   ( 571-)  C      -5.89
 212 MET   ( 589-)  A      -5.87
2963 LYS   ( 812-)  D      -5.86
1022 LEU   ( 565-)  B      -5.86
 446 GLN   ( 826-)  A      -5.85
 633 GLN   (1016-)  A      -5.79
2313 GLN   (1016-)  C      -5.78
2895 ARG   ( 744-)  D      -5.73
2622 HIS   ( 471-)  D      -5.69
And so on for a total of 59 lines.

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

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.

 902 ARG   ( 445-)  B   -3.27
1543 LYS   (1089-)  B   -3.21
2386 LYS   (1089-)  C   -3.21
 690 LEU   (1073-)  A   -3.20
2370 LEU   (1073-)  C   -3.19
1527 LEU   (1073-)  B   -3.19
3222 LEU   (1073-)  D   -3.18
1545 ARG   (1091-)  B   -2.97
 194 HIS   ( 571-)  A   -2.94
2722 HIS   ( 571-)  D   -2.91
 390 LYS   ( 767-)  A   -2.79
 441 VAL   ( 821-)  A   -2.75
3221 MET   (1072-)  D   -2.75
1526 MET   (1072-)  B   -2.74
 689 MET   (1072-)  A   -2.74
2369 MET   (1072-)  C   -2.74
2972 VAL   ( 821-)  D   -2.73
2120 VAL   ( 821-)  C   -2.72
1275 VAL   ( 821-)  B   -2.70
2919 ARG   ( 768-)  D   -2.68
2570 ARG   ( 417-)  D   -2.67
 878 ARG   ( 417-)  B   -2.67
2001 ILE   ( 702-)  C   -2.66
 325 ILE   ( 702-)  A   -2.63
  44 ARG   ( 417-)  A   -2.61
1156 ILE   ( 702-)  B   -2.60
2853 ILE   ( 702-)  D   -2.60
2124 GLN   ( 825-)  C   -2.60
2659 LEU   ( 508-)  D   -2.57
 131 LEU   ( 508-)  A   -2.57
 284 ALA   ( 661-)  A   -2.57
 965 LEU   ( 508-)  B   -2.56
1728 LYS   ( 420-)  C   -2.54
2573 LYS   ( 420-)  D   -2.54
1774 LYS   ( 473-)  C   -2.52
 930 LYS   ( 473-)  B   -2.52
  96 LYS   ( 473-)  A   -2.52
2624 LYS   ( 473-)  D   -2.51

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.

 202 HIS   ( 579-)  A
 678 GLN   (1061-)  A
1023 ASN   ( 566-)  B
1033 HIS   ( 579-)  B
1455 GLN   (1001-)  B
1474 HIS   (1020-)  B
1515 GLN   (1061-)  B
1880 HIS   ( 579-)  C
2358 GLN   (1061-)  C
2543 ASN   ( 379-)  D
2730 HIS   ( 579-)  D
3210 GLN   (1061-)  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.

  36 ARG   ( 396-)  A      N
  42 LEU   ( 415-)  A      N
  92 THR   ( 469-)  A      N
 131 LEU   ( 508-)  A      N
 162 HIS   ( 539-)  A      NE2
 163 ARG   ( 540-)  A      N
 163 ARG   ( 540-)  A      NE
 163 ARG   ( 540-)  A      NH2
 166 LEU   ( 543-)  A      N
 171 ASN   ( 548-)  A      ND2
 201 TYR   ( 578-)  A      N
 229 LEU   ( 606-)  A      N
 235 VAL   ( 612-)  A      N
 252 GLU   ( 629-)  A      N
 260 VAL   ( 637-)  A      N
 269 ALA   ( 646-)  A      N
 270 ALA   ( 647-)  A      N
 319 THR   ( 696-)  A      OG1
 356 LYS   ( 733-)  A      N
 357 ASP   ( 734-)  A      N
 371 ASN   ( 748-)  A      N
 395 LYS   ( 772-)  A      N
 472 THR   ( 855-)  A      N
 535 ARG   ( 918-)  A      NH1
 552 ASP   ( 935-)  A      N
And so on for a total of 166 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

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

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

Waters are not listed by this option.

   7 ASN   ( 367-)  A      OD1
 102 GLN   ( 479-)  A      OE1
 183 GLU   ( 560-)  A      OE1
 244 GLN   ( 621-)  A      OE1
 406 ASP   ( 783-)  A      OD2
 462 ASP   ( 845-)  A      OD1
 637 HIS   (1020-)  A      ND1
 996 HIS   ( 539-)  B      NE2
1064 ASP   ( 610-)  B      OD2
1237 ASP   ( 783-)  B      OD2
1299 ASP   ( 845-)  B      OD1
1861 GLU   ( 560-)  C      OE1
1922 GLN   ( 621-)  C      OE1
2082 ASP   ( 783-)  C      OD2
2198 GLN   ( 901-)  C    A OE1
2317 HIS   (1020-)  C      ND1
2690 HIS   ( 539-)  D      NE2
2711 GLU   ( 560-)  D      OE1
2772 GLN   ( 621-)  D      OE1
2934 ASP   ( 783-)  D      OD2
2994 ASP   ( 845-)  D      OD1
3050 GLN   ( 901-)  D      OE1
3169 HIS   (1020-)  D      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+.

3379  CA   (2003-)  A     0.80   1.04 Scores about as good as NA *2
3382  CA   (2003-)  B     0.88   1.12 Scores about as good as NA *2
3385  CA   (2003-)  C     0.84   1.08 Scores about as good as NA *2
3387  CA   (2003-)  D     0.74   0.96 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.

3389 HOH   (3050 )  A      O  1.09  K  4 Ion-B
3389 HOH   (3116 )  A      O  0.94  K  5
3390 HOH   (3124 )  B      O  0.85  K  5
3391 HOH   (3015 )  C      O  1.11  K  5 Ion-B H2O-B NCS 1/1
3391 HOH   (3055 )  C      O  0.86  K  6 Ion-B NCS 1/1
3391 HOH   (3175 )  C      O  1.15  K  4 NCS 2/2

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.

 233 ASP   ( 610-)  A   H-bonding suggests Asn; but Alt-Rotamer
 255 ASP   ( 632-)  A   H-bonding suggests Asn; but Alt-Rotamer
 320 ASP   ( 697-)  A   H-bonding suggests Asn
 388 ASP   ( 765-)  A   H-bonding suggests Asn; but Alt-Rotamer
 418 ASP   ( 795-)  A   H-bonding suggests Asn
 429 GLU   ( 806-)  A   H-bonding suggests Gln
 462 ASP   ( 845-)  A   H-bonding suggests Asn; but Alt-Rotamer
 596 ASP   ( 979-)  A   H-bonding suggests Asn
 704 GLU   (1087-)  A   H-bonding suggests Gln
 773 ASP   (1156-)  A   H-bonding suggests Asn; but Alt-Rotamer
 852 GLU   ( 372-)  B   H-bonding suggests Gln
1064 ASP   ( 610-)  B   H-bonding suggests Asn; but Alt-Rotamer
1086 ASP   ( 632-)  B   H-bonding suggests Asn; but Alt-Rotamer
1151 ASP   ( 697-)  B   H-bonding suggests Asn
1219 ASP   ( 765-)  B   H-bonding suggests Asn; but Alt-Rotamer
1249 ASP   ( 795-)  B   H-bonding suggests Asn
1260 GLU   ( 806-)  B   H-bonding suggests Gln
1299 ASP   ( 845-)  B   H-bonding suggests Asn; but Alt-Rotamer
1433 ASP   ( 979-)  B   H-bonding suggests Asn; but Alt-Rotamer
1541 GLU   (1087-)  B   H-bonding suggests Gln
1555 ASP   (1101-)  B   H-bonding suggests Asn
1610 ASP   (1156-)  B   H-bonding suggests Asn; but Alt-Rotamer
1726 GLU   ( 418-)  C   H-bonding suggests Gln
1911 ASP   ( 610-)  C   H-bonding suggests Asn; but Alt-Rotamer
1996 ASP   ( 697-)  C   H-bonding suggests Asn
2064 ASP   ( 765-)  C   H-bonding suggests Asn; but Alt-Rotamer
2094 ASP   ( 795-)  C   H-bonding suggests Asn
2142 ASP   ( 845-)  C   H-bonding suggests Asn; but Alt-Rotamer
2276 ASP   ( 979-)  C   H-bonding suggests Asn; but Alt-Rotamer
2384 GLU   (1087-)  C   H-bonding suggests Gln
2398 ASP   (1101-)  C   H-bonding suggests Asn
2453 ASP   (1156-)  C   H-bonding suggests Asn; but Alt-Rotamer
2536 GLU   ( 372-)  D   H-bonding suggests Gln
2571 GLU   ( 418-)  D   H-bonding suggests Gln
2783 ASP   ( 632-)  D   H-bonding suggests Asn; but Alt-Rotamer
2848 ASP   ( 697-)  D   H-bonding suggests Asn
2916 ASP   ( 765-)  D   H-bonding suggests Asn; but Alt-Rotamer
2946 ASP   ( 795-)  D   H-bonding suggests Asn
2957 GLU   ( 806-)  D   H-bonding suggests Gln
2994 ASP   ( 845-)  D   H-bonding suggests Asn; but Alt-Rotamer
3128 ASP   ( 979-)  D   H-bonding suggests Asn
3305 ASP   (1156-)  D   H-bonding suggests Asn

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 :  -0.344
  2nd generation packing quality :  -1.396
  Ramachandran plot appearance   :  -0.527
  chi-1/chi-2 rotamer normality  :  -1.889
  Backbone conformation          :  -0.253

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.633 (tight)
  Bond angles                    :   0.879
  Omega angle restraints         :   0.584 (tight)
  Side chain planarity           :   1.069
  Improper dihedral distribution :   0.903
  B-factor distribution          :   1.192
  Inside/Outside distribution    :   1.039

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 : 2.25


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.4
  2nd generation packing quality :  -1.5
  Ramachandran plot appearance   :   0.4
  chi-1/chi-2 rotamer normality  :  -0.5
  Backbone conformation          :  -0.6

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.633 (tight)
  Bond angles                    :   0.879
  Omega angle restraints         :   0.584 (tight)
  Side chain planarity           :   1.069
  Improper dihedral distribution :   0.903
  B-factor distribution          :   1.192
  Inside/Outside distribution    :   1.039
==============

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.