WHAT IF Check report

This file was created 2012-01-30 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 pdb3dhu.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 C

All-atom RMS fit for the two chains : 0.405
CA-only RMS fit for the two chains : 0.355

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 C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and D

All-atom RMS fit for the two chains : 0.398
CA-only RMS fit for the two chains : 0.341

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: B and 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: 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 GLN   (   6-)  A      CG
   1 GLN   (   6-)  A      CD
   1 GLN   (   6-)  A      OE1
   1 GLN   (   6-)  A      NE2
  89 GLU   (  94-)  A      CG
  89 GLU   (  94-)  A      CD
  89 GLU   (  94-)  A      OE1
  89 GLU   (  94-)  A      OE2
 122 ASP   ( 127-)  A      CG
 122 ASP   ( 127-)  A      OD1
 122 ASP   ( 127-)  A      OD2
 128 LYS   ( 133-)  A      CG
 128 LYS   ( 133-)  A      CD
 128 LYS   ( 133-)  A      CE
 128 LYS   ( 133-)  A      NZ
 144 GLU   ( 149-)  A      CG
 144 GLU   ( 149-)  A      CD
 144 GLU   ( 149-)  A      OE1
 144 GLU   ( 149-)  A      OE2
 186 LYS   ( 191-)  A      CG
 186 LYS   ( 191-)  A      CD
 186 LYS   ( 191-)  A      CE
 186 LYS   ( 191-)  A      NZ
 189 GLU   ( 194-)  A      CG
 189 GLU   ( 194-)  A      CD
And so on for a total of 115 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: 0

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

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

  86 ARG   (  91-)  A
 241 ARG   ( 246-)  A
 266 ARG   ( 271-)  A
 508 ARG   (  91-)  B
 659 ARG   ( 246-)  B
 684 ARG   ( 271-)  B
 926 ARG   (  91-)  C
1081 ARG   ( 246-)  C
1106 ARG   ( 271-)  C
1348 ARG   (  91-)  D
1499 ARG   ( 246-)  D
1524 ARG   ( 271-)  D

Warning: Tyrosine convention problem

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

 140 TYR   ( 145-)  A
 148 TYR   ( 153-)  A
 262 TYR   ( 267-)  A
 365 TYR   ( 370-)  A
 394 TYR   ( 399-)  A
 439 TYR   (  22-)  B
 558 TYR   ( 145-)  B
 566 TYR   ( 153-)  B
 680 TYR   ( 267-)  B
 812 TYR   ( 399-)  B
 980 TYR   ( 145-)  C
 988 TYR   ( 153-)  C
1102 TYR   ( 267-)  C
1205 TYR   ( 370-)  C
1234 TYR   ( 399-)  C
1398 TYR   ( 145-)  D
1406 TYR   ( 153-)  D
1520 TYR   ( 267-)  D
1623 TYR   ( 370-)  D
1652 TYR   ( 399-)  D

Warning: Phenylalanine convention problem

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

 117 PHE   ( 122-)  A
 222 PHE   ( 227-)  A
 294 PHE   ( 299-)  A
 539 PHE   ( 122-)  B
 640 PHE   ( 227-)  B
 685 PHE   ( 272-)  B
 712 PHE   ( 299-)  B
 957 PHE   ( 122-)  C
1062 PHE   ( 227-)  C
1134 PHE   ( 299-)  C
1379 PHE   ( 122-)  D
1480 PHE   ( 227-)  D
1525 PHE   ( 272-)  D
1552 PHE   ( 299-)  D

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.

 131 ASP   ( 136-)  A
 329 ASP   ( 334-)  A
 549 ASP   ( 136-)  B
 747 ASP   ( 334-)  B
 971 ASP   ( 136-)  C
1169 ASP   ( 334-)  C
1389 ASP   ( 136-)  D
1432 ASP   ( 179-)  D
1587 ASP   ( 334-)  D

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.

 203 GLU   ( 208-)  A
 859 GLU   (  24-)  C
1043 GLU   ( 208-)  C
1210 GLU   ( 375-)  C
1281 GLU   (  24-)  D

Geometric checks

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

 |  0.996799  0.000241  0.000227|
 |  0.000241  0.996842 -0.000067|
 |  0.000227 -0.000067  0.996438|
Proposed new scale matrix

 |  0.004960 -0.000001  0.001138|
 | -0.000004  0.015731  0.000001|
 | -0.000002  0.000000  0.006615|
With corresponding cell

    A    = 201.618  B   =  63.570  C    = 155.102
    Alpha=  90.011  Beta= 102.909  Gamma=  89.973

The CRYST1 cell dimensions

    A    = 202.279  B   =  63.773  C    = 155.677
    Alpha=  90.000  Beta= 102.930  Gamma=  90.000

Variance: 621.150
(Under-)estimated Z-score: 18.368

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.

   8 MET   (  13-)  A      CG   SD   CE   91.61   -4.2
 410 LEU   ( 415-)  A      CA   CB   CG  135.03    5.4
 430 MET   (  13-)  B      CG   SD   CE   90.17   -4.9
 715 ARG   ( 302-)  B      CG   CD   NE  118.49    4.7
 828 LEU   ( 415-)  B      CA   CB   CG  130.59    4.1
1137 ARG   ( 302-)  C      CG   CD   NE  118.77    4.9
1167 HIS   ( 332-)  C      CG   ND1  CE1 109.61    4.0
1250 LEU   ( 415-)  C      CA   CB   CG  131.60    4.4
1668 LEU   ( 415-)  D      CA   CB   CG  133.31    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.

  86 ARG   (  91-)  A
 131 ASP   ( 136-)  A
 203 GLU   ( 208-)  A
 241 ARG   ( 246-)  A
 266 ARG   ( 271-)  A
 329 ASP   ( 334-)  A
 508 ARG   (  91-)  B
 549 ASP   ( 136-)  B
 659 ARG   ( 246-)  B
 684 ARG   ( 271-)  B
 747 ASP   ( 334-)  B
 859 GLU   (  24-)  C
 926 ARG   (  91-)  C
 971 ASP   ( 136-)  C
1043 GLU   ( 208-)  C
1081 ARG   ( 246-)  C
1106 ARG   ( 271-)  C
1169 ASP   ( 334-)  C
1210 GLU   ( 375-)  C
1281 GLU   (  24-)  D
1348 ARG   (  91-)  D
1389 ASP   ( 136-)  D
1432 ASP   ( 179-)  D
1499 ARG   ( 246-)  D
1524 ARG   ( 271-)  D
1587 ASP   ( 334-)  D

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.

 293 ILE   ( 298-)  A    4.01

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.

 377 PRO   ( 382-)  A    -2.7
 795 PRO   ( 382-)  B    -2.5
1217 PRO   ( 382-)  C    -2.4
1384 THR   ( 131-)  D    -2.4
1007 VAL   ( 172-)  C    -2.4
1635 PRO   ( 382-)  D    -2.4
 522 TYR   ( 105-)  B    -2.4
1362 TYR   ( 105-)  D    -2.3
 940 TYR   ( 105-)  C    -2.3
1641 THR   ( 388-)  D    -2.3
1068 TYR   ( 233-)  C    -2.3
 966 THR   ( 131-)  C    -2.3
 383 THR   ( 388-)  A    -2.2
 801 THR   ( 388-)  B    -2.2
1275 PHE   (  18-)  D    -2.2
1223 THR   ( 388-)  C    -2.2
 100 TYR   ( 105-)  A    -2.2
 435 PHE   (  18-)  B    -2.2
1052 GLY   ( 217-)  C    -2.2
 853 PHE   (  18-)  C    -2.2
1470 GLY   ( 217-)  D    -2.2
 585 VAL   ( 172-)  B    -2.2
 167 VAL   ( 172-)  A    -2.2
1425 VAL   ( 172-)  D    -2.2
 212 GLY   ( 217-)  A    -2.2
 630 GLY   ( 217-)  B    -2.2
 805 THR   ( 392-)  B    -2.1
 524 HIS   ( 107-)  B    -2.1
  13 PHE   (  18-)  A    -2.1
 387 THR   ( 392-)  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.

  92 MET   (  97-)  A  omega poor
  99 VAL   ( 104-)  A  omega poor
 101 ASN   ( 106-)  A  omega poor
 103 THR   ( 108-)  A  omega poor
 120 ASP   ( 125-)  A  Poor phi/psi
 132 TRP   ( 137-)  A  Poor phi/psi
 140 TYR   ( 145-)  A  omega poor
 163 TYR   ( 168-)  A  omega poor
 167 VAL   ( 172-)  A  Poor phi/psi
 194 ALA   ( 199-)  A  omega poor
 227 ASP   ( 232-)  A  Poor phi/psi
 230 VAL   ( 235-)  A  Poor phi/psi
 277 MET   ( 282-)  A  omega poor
 280 MET   ( 285-)  A  omega poor
 309 LEU   ( 314-)  A  Poor phi/psi
 316 LEU   ( 321-)  A  omega poor
 356 VAL   ( 361-)  A  Poor phi/psi
 400 ASP   ( 405-)  A  Poor phi/psi
 437 ARG   (  20-)  B  omega poor
 475 ASN   (  58-)  B  Poor phi/psi
 485 ALA   (  68-)  B  omega poor
 521 VAL   ( 104-)  B  omega poor
 550 TRP   ( 137-)  B  Poor phi/psi
 558 TYR   ( 145-)  B  omega poor
 585 VAL   ( 172-)  B  Poor phi/psi
And so on for a total of 64 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.

1402 GLU   ( 149-)  D    0.36

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!

   6 ASN   (  11-)  A      0
   7 GLU   (  12-)  A      0
  17 TYR   (  22-)  A      0
  20 ALA   (  25-)  A      0
  22 ASN   (  27-)  A      0
  38 THR   (  43-)  A      0
  45 PRO   (  50-)  A      0
  51 GLU   (  56-)  A      0
  52 VAL   (  57-)  A      0
  55 LYS   (  60-)  A      0
  57 THR   (  62-)  A      0
  58 LEU   (  63-)  A      0
  63 ALA   (  68-)  A      0
  65 LYS   (  70-)  A      0
  71 ASN   (  76-)  A      0
  74 TYR   (  79-)  A      0
  76 THR   (  81-)  A      0
  90 LEU   (  95-)  A      0
  99 VAL   ( 104-)  A      0
 100 TYR   ( 105-)  A      0
 101 ASN   ( 106-)  A      0
 113 HIS   ( 118-)  A      0
 116 TRP   ( 121-)  A      0
 118 TYR   ( 123-)  A      0
 124 GLN   ( 129-)  A      0
And so on for a total of 625 lines.

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

 212 GLY   ( 217-)  A   1.97   13
 630 GLY   ( 217-)  B   1.87   12
1052 GLY   ( 217-)  C   1.86   10
1470 GLY   ( 217-)  D   1.62   11

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]

  61 PRO   (  66-)  A    0.06 LOW
 587 PRO   ( 174-)  B    0.14 LOW
 762 PRO   ( 349-)  B    0.10 LOW
1376 PRO   ( 119-)  D    0.19 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].

 377 PRO   ( 382-)  A   -58.0 half-chair C-beta/C-alpha (-54 degrees)
 795 PRO   ( 382-)  B   -56.4 half-chair C-beta/C-alpha (-54 degrees)
1217 PRO   ( 382-)  C   -55.2 half-chair C-beta/C-alpha (-54 degrees)
1635 PRO   ( 382-)  D   -65.8 envelop C-beta (-72 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.

1497 GLN   ( 244-)  D      NE2 <-> 1684 HOH   ( 552 )  D      O      0.66    2.04  INTRA
1079 GLN   ( 244-)  C      NE2 <-> 1683 HOH   ( 567 )  C      O      0.65    2.05  INTRA
1163 VAL   ( 328-)  C      O   <-> 1166 ARG   ( 331-)  C      NH1    0.47    2.23  INTRA
 336 LYS   ( 341-)  A      NZ  <->  400 ASP   ( 405-)  A      OD2    0.34    2.36  INTRA
 960 ASP   ( 125-)  C      OD1 <->  962 ASP   ( 127-)  C      OD1    0.32    2.08  INTRA
  55 LYS   (  60-)  A      NZ  <-> 1681 HOH   ( 721 )  A      O      0.31    2.39  INTRA
 379 LYS   ( 384-)  A      NZ  <-> 1681 HOH   ( 782 )  A      O      0.29    2.41  INTRA
 967 ASN   ( 132-)  C      C   <-> 1683 HOH   ( 778 )  C      O      0.28    2.52  INTRA
1304 TRP   (  47-)  D      CZ2 <-> 1422 ARG   ( 169-)  D      CD     0.25    2.95  INTRA
 928 HIS   (  93-)  C      NE2 <-> 1001 ASP   ( 166-)  C      OD2    0.23    2.47  INTRA BL
 168 ALA   ( 173-)  A      N   <->  169 PRO   ( 174-)  A      CD     0.23    2.77  INTRA BL
 366 ARG   ( 371-)  A      NH1 <-> 1681 HOH   ( 724 )  A      O      0.23    2.47  INTRA
 586 ALA   ( 173-)  B      N   <->  587 PRO   ( 174-)  B      CD     0.23    2.77  INTRA BL
 561 HIS   ( 148-)  B      O   <-> 1682 HOH   ( 609 )  B      O      0.22    2.18  INTRA
1234 TYR   ( 399-)  C      O   <-> 1243 THR   ( 408-)  C      N      0.20    2.50  INTRA
  42 TRP   (  47-)  A      CZ2 <->  164 ARG   ( 169-)  A      CD     0.20    3.00  INTRA BL
  57 THR   (  62-)  A      N   <->  318 ASP   ( 323-)  A      OD1    0.19    2.51  INTRA
1570 HIS   ( 317-)  D      NE2 <-> 1578 ASP   ( 325-)  D      OD2    0.19    2.51  INTRA BL
  34 LYS   (  39-)  A      NZ  <-> 1681 HOH   ( 693 )  A      O      0.18    2.52  INTRA
 699 HIS   ( 286-)  B      NE2 <-> 1220 GLY   ( 385-)  C      O      0.18    2.52  INTRA BL
 585 VAL   ( 172-)  B      C   <->  587 PRO   ( 174-)  B      CD     0.17    3.03  INTRA BL
1426 ALA   ( 173-)  D      N   <-> 1427 PRO   ( 174-)  D      CD     0.15    2.85  INTRA BL
 784 ARG   ( 371-)  B      NH1 <-> 1682 HOH   ( 626 )  B      O      0.15    2.55  INTRA
 523 ASN   ( 106-)  B      ND2 <->  524 HIS   ( 107-)  B      ND1    0.15    2.85  INTRA BL
1206 ARG   ( 371-)  C      NH1 <-> 1683 HOH   ( 683 )  C      O      0.15    2.55  INTRA
And so on for a total of 141 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.

 319 ARG   ( 324-)  A      -6.09
1159 ARG   ( 324-)  C      -6.08
1577 ARG   ( 324-)  D      -6.05
 628 TYR   ( 215-)  B      -6.03
 737 ARG   ( 324-)  B      -5.96
 210 TYR   ( 215-)  A      -5.87
1468 TYR   ( 215-)  D      -5.74
1050 TYR   ( 215-)  C      -5.74
  54 ARG   (  59-)  A      -5.63
 894 ARG   (  59-)  C      -5.53
1605 ARG   ( 352-)  D      -5.50
1187 ARG   ( 352-)  C      -5.48
 347 ARG   ( 352-)  A      -5.45
 765 ARG   ( 352-)  B      -5.44
1316 ARG   (  59-)  D      -5.44
 476 ARG   (  59-)  B      -5.42
1496 TRP   ( 243-)  D      -5.37
1078 TRP   ( 243-)  C      -5.31
 656 TRP   ( 243-)  B      -5.27
 238 TRP   ( 243-)  A      -5.25
 326 ARG   ( 331-)  A      -5.25
 744 ARG   ( 331-)  B      -5.25
1137 ARG   ( 302-)  C      -5.24
 281 HIS   ( 286-)  A      -5.17
1121 HIS   ( 286-)  C      -5.15
 715 ARG   ( 302-)  B      -5.14
 297 ARG   ( 302-)  A      -5.14
 699 HIS   ( 286-)  B      -5.11
 638 GLN   ( 225-)  B      -5.10
 952 GLU   ( 117-)  C      -5.05
1374 GLU   ( 117-)  D      -5.04
 534 GLU   ( 117-)  B      -5.04
1539 HIS   ( 286-)  D      -5.01
1555 ARG   ( 302-)  D      -5.01
 112 GLU   ( 117-)  A      -5.00

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.

1386 LYS   ( 133-)  D   -3.16
 128 LYS   ( 133-)  A   -2.99
 546 LYS   ( 133-)  B   -2.97
1580 MET   ( 327-)  D   -2.90
1162 MET   ( 327-)  C   -2.89
 322 MET   ( 327-)  A   -2.77
 740 MET   ( 327-)  B   -2.73
1402 GLU   ( 149-)  D   -2.65
1444 LYS   ( 191-)  D   -2.60
 186 LYS   ( 191-)  A   -2.57
1282 ALA   (  25-)  D   -2.53
1263 GLN   (   6-)  D   -2.52

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

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.

1681 HOH   ( 609 )  A      O    -47.71   34.89   70.34
1681 HOH   ( 746 )  A      O    -50.28   29.80   67.28
1681 HOH   ( 756 )  A      O      6.83   66.02   67.26
1682 HOH   ( 618 )  B      O    -21.03   68.14   -1.09
1683 HOH   ( 664 )  C      O     25.99   74.60    1.26
1683 HOH   ( 775 )  C      O     14.40   53.19    8.10
1684 HOH   ( 677 )  D      O      7.69   49.21   71.90

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.

1681 HOH   ( 521 )  A      O
1681 HOH   ( 698 )  A      O
1682 HOH   ( 713 )  B      O
1682 HOH   ( 745 )  B      O
1683 HOH   ( 551 )  C      O
1683 HOH   ( 682 )  C      O
1684 HOH   ( 722 )  D      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.

 113 HIS   ( 118-)  A
 239 GLN   ( 244-)  A
 657 GLN   ( 244-)  B
 953 HIS   ( 118-)  C
1079 GLN   ( 244-)  C
1136 GLN   ( 301-)  C
1153 GLN   ( 318-)  C
1375 HIS   ( 118-)  D
1381 HIS   ( 124-)  D
1497 GLN   ( 244-)  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.

   3 GLN   (   8-)  A      N
  16 ASN   (  21-)  A      ND2
  18 SER   (  23-)  A      N
  66 ASP   (  71-)  A      N
 102 HIS   ( 107-)  A      N
 126 THR   ( 131-)  A      N
 146 TRP   ( 151-)  A      N
 149 GLN   ( 154-)  A      NE2
 226 TYR   ( 231-)  A      OH
 228 TYR   ( 233-)  A      N
 258 PHE   ( 263-)  A      N
 263 VAL   ( 268-)  A      N
 270 ASN   ( 275-)  A      N
 270 ASN   ( 275-)  A      ND2
 275 ARG   ( 280-)  A      NH2
 289 ASN   ( 294-)  A      ND2
 296 GLN   ( 301-)  A      NE2
 304 ASN   ( 309-)  A      ND2
 319 ARG   ( 324-)  A      NH1
 415 GLN   ( 420-)  A      N
 433 SER   (  16-)  B      OG
 438 ASN   (  21-)  B      ND2
 440 SER   (  23-)  B      N
 488 ASP   (  71-)  B      N
 524 HIS   ( 107-)  B      N
And so on for a total of 74 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.

 288 ASN   ( 293-)  A      OD1
 289 ASN   ( 294-)  A      OD1
 555 ASP   ( 142-)  B      OD1
 706 ASN   ( 293-)  B      OD1
 707 ASN   ( 294-)  B      OD1
1128 ASN   ( 293-)  C      OD1
1129 ASN   ( 294-)  C      OD1
1546 ASN   ( 293-)  D      OD1
1547 ASN   ( 294-)  D      OD1

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.

1681 HOH   ( 591 )  A      O  0.92  K  4
1681 HOH   ( 659 )  A      O  0.94  K  5 Ion-B
1682 HOH   ( 529 )  B      O  0.89  K  4
1682 HOH   ( 601 )  B      O  0.86  K  4 Ion-B
1683 HOH   ( 508 )  C      O  1.00  K  4
1684 HOH   ( 596 )  D      O  1.06  K  4
1684 HOH   ( 716 )  D      O  1.14  K  4 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.

  35 ASP   (  40-)  A   H-bonding suggests Asn; but Alt-Rotamer
 151 ASP   ( 156-)  A   H-bonding suggests Asn
 329 ASP   ( 334-)  A   H-bonding suggests Asn
 457 ASP   (  40-)  B   H-bonding suggests Asn; but Alt-Rotamer
 651 ASP   ( 238-)  B   H-bonding suggests Asn
 747 ASP   ( 334-)  B   H-bonding suggests Asn
 875 ASP   (  40-)  C   H-bonding suggests Asn
 960 ASP   ( 125-)  C   H-bonding suggests Asn
 991 ASP   ( 156-)  C   H-bonding suggests Asn
1297 ASP   (  40-)  D   H-bonding suggests Asn
1491 ASP   ( 238-)  D   H-bonding suggests Asn
1494 ASP   ( 241-)  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 :  -0.163
  2nd generation packing quality :  -1.341
  Ramachandran plot appearance   :  -0.691
  chi-1/chi-2 rotamer normality  :  -1.398
  Backbone conformation          :  -0.098

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.602 (tight)
  Bond angles                    :   0.712
  Omega angle restraints         :   1.125
  Side chain planarity           :   0.643 (tight)
  Improper dihedral distribution :   0.754
  B-factor distribution          :   0.568
  Inside/Outside distribution    :   0.988

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 : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.2
  2nd generation packing quality :  -0.9
  Ramachandran plot appearance   :  -0.1
  chi-1/chi-2 rotamer normality  :  -0.5
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.602 (tight)
  Bond angles                    :   0.712
  Omega angle restraints         :   1.125
  Side chain planarity           :   0.643 (tight)
  Improper dihedral distribution :   0.754
  B-factor distribution          :   0.568
  Inside/Outside distribution    :   0.988
==============

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.