WHAT IF Check report

This file was created 2011-12-15 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 pdb3e28.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: B and C

All-atom RMS fit for the two chains : 0.825
CA-only RMS fit for the two chains : 0.343

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 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: D and F

All-atom RMS fit for the two chains : 1.021
CA-only RMS fit for the two chains : 0.558

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: D and F

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.

1234 SO4   ( 231-)  A  -
1235 SO4   ( 232-)  A  -
1236 SO4   ( 233-)  A  -
1238 SO4   ( 234-)  A  -
1239 SO4   ( 231-)  B  -
1241 SO4   ( 232-)  B  -
1242 SO4   ( 231-)  C  -
1243 SO4   ( 232-)  C  -
1245 SO4   ( 233-)  C  -
1246 SO4   ( 231-)  D  -
1248 SO4   ( 232-)  D  -
1249 SO4   ( 231-)  E  -
1250 SO4   ( 232-)  E  -
1252 SO4   ( 233-)  E  -
1253 SO4   ( 231-)  F  -
1254 SO4   ( 232-)  F  -

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

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

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

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: 6

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

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

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

  31 TYR   (  37-)  A
 649 TYR   (  37-)  D
1052 TYR   (  37-)  F

Warning: Phenylalanine convention problem

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

  69 PHE   (  75-)  A
 175 PHE   ( 181-)  A
 181 PHE   ( 187-)  A
 275 PHE   (  75-)  B
 328 PHE   ( 128-)  B
 381 PHE   ( 181-)  B
 387 PHE   ( 187-)  B
 429 PHE   (   8-)  C
 481 PHE   (  75-)  C
 587 PHE   ( 181-)  C
 593 PHE   ( 187-)  C
 633 PHE   (   8-)  D
 687 PHE   (  75-)  D
 740 PHE   ( 128-)  D
 793 PHE   ( 181-)  D
 883 PHE   (  75-)  E
 989 PHE   ( 181-)  E
 995 PHE   ( 187-)  E
1090 PHE   (  75-)  F
1143 PHE   ( 128-)  F
1196 PHE   ( 181-)  F
1202 PHE   ( 187-)  F

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.

   2 ASP   (   2-)  A
 104 ASP   ( 110-)  A
 138 ASP   ( 144-)  A
 179 ASP   ( 185-)  A
 184 ASP   ( 190-)  A
 217 ASP   (   2-)  B
 310 ASP   ( 110-)  B
 344 ASP   ( 144-)  B
 382 ASP   ( 182-)  B
 385 ASP   ( 185-)  B
 416 ASP   ( 216-)  B
 588 ASP   ( 182-)  C
 591 ASP   ( 185-)  C
 627 ASP   (   2-)  D
 656 ASP   (  44-)  D
 756 ASP   ( 144-)  D
 797 ASP   ( 185-)  D
 852 ASP   (  44-)  E
 993 ASP   ( 185-)  E
1059 ASP   (  44-)  F
1125 ASP   ( 110-)  F

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.

  20 GLU   (  20-)  A
  21 GLU   (  21-)  A
  85 GLU   (  91-)  A
 163 GLU   ( 169-)  A
 196 GLU   ( 202-)  A
 211 GLU   ( 217-)  A
 250 GLU   (  50-)  B
 259 GLU   (  59-)  B
 291 GLU   (  91-)  B
 399 GLU   ( 199-)  B
 402 GLU   ( 202-)  B
 417 GLU   ( 217-)  B
 456 GLU   (  50-)  C
 465 GLU   (  59-)  C
 605 GLU   ( 199-)  C
 623 GLU   ( 217-)  C
 781 GLU   ( 169-)  D
 811 GLU   ( 199-)  D
 867 GLU   (  59-)  E
 899 GLU   (  91-)  E
 948 GLU   ( 140-)  E
1025 GLU   ( 217-)  E
1026 GLU   ( 218-)  E
1065 GLU   (  50-)  F
1074 GLU   (  59-)  F
1106 GLU   (  91-)  F
1155 GLU   ( 140-)  F
1168 GLU   ( 153-)  F
1184 GLU   ( 169-)  F
1217 GLU   ( 202-)  F

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

 |  0.998147  0.000206 -0.000025|
 |  0.000206  0.998141 -0.000102|
 | -0.000025 -0.000102  0.998427|
Proposed new scale matrix

 |  0.004352  0.000000  0.000288|
 | -0.000001  0.006912  0.000000|
 |  0.000000  0.000002  0.019042|
With corresponding cell

    A    = 229.776  B   = 144.679  C    =  52.630
    Alpha=  90.007  Beta=  93.781  Gamma=  89.989

The CRYST1 cell dimensions

    A    = 230.193  B   = 144.943  C    =  52.714
    Alpha=  90.000  Beta=  93.780  Gamma=  90.000

Variance: 131.420
(Under-)estimated Z-score: 8.449

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.

   2 ASP   (   2-)  A      C    CA   CB  117.88    4.1
 244 ASP   (  44-)  B      C    CA   CB   97.99   -6.4
 322 HIS   ( 122-)  B      CG   ND1  CE1 109.76    4.2
 450 ASP   (  44-)  C      C    CA   CB   99.09   -5.8
 528 HIS   ( 122-)  C      CG   ND1  CE1 109.64    4.0
 906 HIS   (  98-)  E      CG   ND1  CE1 109.80    4.2
 913 HIS   ( 105-)  E      CG   ND1  CE1 109.60    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.

   2 ASP   (   2-)  A
  20 GLU   (  20-)  A
  21 GLU   (  21-)  A
  85 GLU   (  91-)  A
 104 ASP   ( 110-)  A
 138 ASP   ( 144-)  A
 163 GLU   ( 169-)  A
 179 ASP   ( 185-)  A
 184 ASP   ( 190-)  A
 196 GLU   ( 202-)  A
 211 GLU   ( 217-)  A
 217 ASP   (   2-)  B
 250 GLU   (  50-)  B
 259 GLU   (  59-)  B
 291 GLU   (  91-)  B
 310 ASP   ( 110-)  B
 344 ASP   ( 144-)  B
 382 ASP   ( 182-)  B
 385 ASP   ( 185-)  B
 399 GLU   ( 199-)  B
 402 GLU   ( 202-)  B
 416 ASP   ( 216-)  B
 417 GLU   ( 217-)  B
 456 GLU   (  50-)  C
 465 GLU   (  59-)  C
And so on for a total of 51 lines.

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.

 217 ASP   (   2-)  B    4.23

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.

1061 ARG   (  46-)  F    -2.5
1138 ILE   ( 123-)  F    -2.4
 919 LYS   ( 111-)  E    -2.3
 838 TYR   (  12-)  E    -2.3
1083 ASN   (  68-)  F    -2.3
 667 LEU   (  55-)  D    -2.3
 105 LYS   ( 111-)  A    -2.3
 273 THR   (  73-)  B    -2.2
1079 ARG   (  64-)  F    -2.2
  62 ASN   (  68-)  A    -2.2
 685 THR   (  73-)  D    -2.2
  40 ARG   (  46-)  A    -2.2
 547 LYS   ( 141-)  C    -2.2
 986 GLY   ( 178-)  E    -2.2
1048 GLN   (  33-)  F    -2.1
 522 ILE   ( 116-)  C    -2.1
 172 GLY   ( 178-)  A    -2.1
 495 LYS   (  89-)  C    -2.1
 378 GLY   ( 178-)  B    -2.1
 881 THR   (  73-)  E    -2.1
 208 ILE   ( 214-)  A    -2.1
 584 GLY   ( 178-)  C    -2.1
 474 ASN   (  68-)  C    -2.1
 255 LEU   (  55-)  B    -2.1
1189 LEU   ( 174-)  F    -2.1
1230 LEU   ( 215-)  F    -2.1
 268 ASN   (  68-)  B    -2.1
1193 GLY   ( 178-)  F    -2.1
 316 ILE   ( 116-)  B    -2.1
 790 GLY   ( 178-)  D    -2.1
 418 GLU   ( 218-)  B    -2.1
   2 ASP   (   2-)  A    -2.1
 944 LYS   ( 136-)  E    -2.1
 728 ILE   ( 116-)  D    -2.0
1033 LYS   (   5-)  F    -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.

  22 ASN   (  22-)  A  Poor phi/psi
  31 TYR   (  37-)  A  omega poor
  55 PHE   (  61-)  A  omega poor
  61 ALA   (  67-)  A  Poor phi/psi
  83 LYS   (  89-)  A  Poor phi/psi
 214 ILE   ( 220-)  A  omega poor
 232 ARG   (  17-)  B  Poor phi/psi
 237 TYR   (  37-)  B  omega poor
 244 ASP   (  44-)  B  omega poor
 254 ASN   (  54-)  B  Poor phi/psi
 261 PHE   (  61-)  B  omega poor
 267 ALA   (  67-)  B  Poor phi/psi
 289 LYS   (  89-)  B  Poor phi/psi
 418 GLU   ( 218-)  B  omega poor
 467 PHE   (  61-)  C  omega poor
 473 ALA   (  67-)  C  Poor phi/psi
 475 GLN   (  69-)  C  omega poor
 495 LYS   (  89-)  C  Poor phi/psi
 591 ASP   ( 185-)  C  Poor phi/psi
 593 PHE   ( 187-)  C  omega poor
 624 GLU   ( 218-)  C  Poor phi/psi
 641 GLN   (  16-)  D  omega poor
 645 GLN   (  33-)  D  Poor phi/psi
 649 TYR   (  37-)  D  omega poor
 666 ASN   (  54-)  D  Poor phi/psi
 672 LEU   (  60-)  D  omega poor
 673 PHE   (  61-)  D  omega poor
 679 ALA   (  67-)  D  Poor phi/psi
 701 LYS   (  89-)  D  Poor phi/psi
 722 ASP   ( 110-)  D  omega poor
 797 ASP   ( 185-)  D  omega poor
 828 ASP   (   2-)  E  omega poor
 844 HIS   (  36-)  E  Poor phi/psi
 869 PHE   (  61-)  E  omega poor
 875 ALA   (  67-)  E  Poor phi/psi
 877 GLN   (  69-)  E  omega poor
 897 LYS   (  89-)  E  Poor phi/psi
 919 LYS   ( 111-)  E  Poor phi/psi
 944 LYS   ( 136-)  E  Poor phi/psi, omega poor
 947 PRO   ( 139-)  E  omega poor
 995 PHE   ( 187-)  E  omega poor
1030 ASP   (   2-)  F  omega poor
1061 ARG   (  46-)  F  omega poor
1076 PHE   (  61-)  F  omega poor
1082 ALA   (  67-)  F  Poor phi/psi
1084 GLN   (  69-)  F  omega poor
1104 LYS   (  89-)  F  Poor phi/psi
1109 ILE   (  94-)  F  omega poor
1207 GLY   ( 192-)  F  omega poor
1212 SER   ( 197-)  F  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -3.703

Warning: chi-1/chi-2 angle correlation Z-score low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is a bit low.

chi-1/chi-2 correlation Z-score : -3.703

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.

 198 SER   ( 204-)  A    0.35
1012 SER   ( 204-)  E    0.37
 816 SER   ( 204-)  D    0.38

Warning: Unusual backbone conformations

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

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

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

  21 GLU   (  21-)  A      0
  22 ASN   (  22-)  A      0
  23 SER   (  23-)  A      0
  24 THR   (  24-)  A      0
  25 TYR   (  25-)  A      0
  26 HIS   (  32-)  A      0
  27 GLN   (  33-)  A      0
  40 ARG   (  46-)  A      0
  41 VAL   (  47-)  A      0
  51 PRO   (  57-)  A      0
  53 GLU   (  59-)  A      0
  59 ASN   (  65-)  A      0
  60 VAL   (  66-)  A      0
  61 ALA   (  67-)  A      0
  62 ASN   (  68-)  A      0
  65 ILE   (  71-)  A      0
  67 THR   (  73-)  A      0
  80 ASP   (  86-)  A      0
  82 LEU   (  88-)  A      0
  85 GLU   (  91-)  A      0
  86 HIS   (  92-)  A      0
  93 THR   (  99-)  A      0
  95 CYS   ( 101-)  A      0
 102 MET   ( 108-)  A      0
 107 LEU   ( 113-)  A      0
And so on for a total of 378 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!

 943 GLY   ( 135-)  E   2.87   25

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]

 660 PRO   (  48-)  D    0.11 LOW
 947 PRO   ( 139-)  E    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].

 441 PRO   (  35-)  C   -55.5 half-chair C-beta/C-alpha (-54 degrees)
 463 PRO   (  57-)  C    52.9 half-chair C-delta/C-gamma (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.

 498 HIS   (  92-)  C      NE2 <->  827 MET   (   1-)  E      CE     0.77    2.33  INTRA BF
1113 HIS   (  98-)  F      ND1 <-> 1254 SO4   ( 232-)  F      O3     0.66    2.04  INTRA BF
 486 VAL   (  80-)  C      CG2 <-> 1257 HOH   ( 246 )  C      O      0.55    2.25  INTRA BL
 246 ARG   (  46-)  B      N   <-> 1241 SO4   ( 232-)  B      O3     0.45    2.25  INTRA BF
 383 VAL   ( 183-)  B      CG1 <-> 1241 SO4   ( 232-)  B      O4     0.45    2.35  INTRA BF
 450 ASP   (  44-)  C      CB  <-> 1240  ZN   ( 230-)  C     ZN      0.36    2.84  INTRA BF
 854 ARG   (  46-)  E      N   <-> 1252 SO4   ( 233-)  E      O4     0.36    2.34  INTRA BF
 492 ASP   (  86-)  C      O   <->  495 LYS   (  89-)  C      NZ     0.34    2.36  INTRA BF
 626 MET   (   1-)  D      O   <->  630 LYS   (   5-)  D      NZ     0.33    2.37  INTRA BF
 244 ASP   (  44-)  B      CB  <-> 1237  ZN   ( 230-)  B     ZN      0.33    2.87  INTRA BF
 991 VAL   ( 183-)  E      CG1 <-> 1252 SO4   ( 233-)  E      S      0.29    3.11  INTRA BF
1093 LEU   (  78-)  F      CD1 <-> 1178 ILE   ( 163-)  F      CD1    0.27    2.93  INTRA BL
 214 ILE   ( 220-)  A      CG2 <->  215 LEU   ( 221-)  A      N      0.26    2.74  INTRA BF
 192 ARG   ( 198-)  A      NH2 <-> 1235 SO4   ( 232-)  A      O1     0.24    2.46  INTRA BF
 663 LYS   (  51-)  D      NZ  <-> 1258 HOH   ( 252 )  D      O      0.24    2.46  INTRA BF
 124 HIS   ( 130-)  A      NE2 <->  147 GLU   ( 153-)  A      OE2    0.23    2.47  INTRA BL
 417 GLU   ( 217-)  B      O   <->  420 ILE   ( 220-)  B      CG2    0.20    2.60  INTRA BF
 945 LEU   ( 137-)  E      CD1 <-> 1027 ASN   ( 219-)  E      ND2    0.20    2.90  INTRA BF
 495 LYS   (  89-)  C      NZ  <-> 1257 HOH   ( 250 )  C      O      0.20    2.50  INTRA BF
  57 HIS   (  63-)  A      NE2 <->   59 ASN   (  65-)  A      ND2    0.19    2.81  INTRA BL
  66 HIS   (  72-)  A      NE2 <->  325 ASP   ( 125-)  B      OD2    0.18    2.52  INTRA BL
 648 HIS   (  36-)  D      CD2 <->  671 GLU   (  59-)  D      OE1    0.18    2.62  INTRA BF
 192 ARG   ( 198-)  A      NH2 <-> 1235 SO4   ( 232-)  A      S      0.18    3.12  INTRA BF
 298 HIS   (  98-)  B      ND1 <-> 1241 SO4   ( 232-)  B      O1     0.18    2.52  INTRA BF
1197 ASP   ( 182-)  F      OD1 <-> 1199 ASN   ( 184-)  F      ND2    0.18    2.52  INTRA BF
And so on for a total of 147 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

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.

  40 ARG   (  46-)  A      -7.77
1061 ARG   (  46-)  F      -7.56
 658 ARG   (  46-)  D      -7.56
 854 ARG   (  46-)  E      -7.55
 246 ARG   (  46-)  B      -7.39
 452 ARG   (  46-)  C      -7.08
  27 GLN   (  33-)  A      -6.80
1048 GLN   (  33-)  F      -6.59
 645 GLN   (  33-)  D      -6.53
 264 ARG   (  64-)  B      -6.16
 232 ARG   (  17-)  B      -6.05
  58 ARG   (  64-)  A      -5.93
 438 ARG   (  17-)  C      -5.88
 840 TRP   (  14-)  E      -5.81
1045 ARG   (  17-)  F      -5.75
  94 ASN   ( 100-)  A      -5.69
 642 ARG   (  17-)  D      -5.63
 712 ASN   ( 100-)  D      -5.56
 908 ASN   ( 100-)  E      -5.41
1115 ASN   ( 100-)  F      -5.37
 506 ASN   ( 100-)  C      -5.33
 300 ASN   ( 100-)  B      -5.30
 624 GLU   ( 218-)  C      -5.16
  21 GLU   (  21-)  A      -5.05

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: 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: E

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: F

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.

 711 THR   (  99-)  D   -2.65

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

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Water, ion, and hydrogenbond related checks

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.

1259 HOH   ( 252 )  E      O
Metal-coordinating Histidine residue  92 fixed to   1
Metal-coordinating Histidine residue 298 fixed to   1
Metal-coordinating Histidine residue 504 fixed to   1
Metal-coordinating Histidine residue 710 fixed to   1
Metal-coordinating Histidine residue 906 fixed to   1
Metal-coordinating Histidine residue1113 fixed to   1

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.

  26 HIS   (  32-)  A
  30 HIS   (  36-)  A
 384 ASN   ( 184-)  B
 419 ASN   ( 219-)  B
 590 ASN   ( 184-)  C
 844 HIS   (  36-)  E
 913 HIS   ( 105-)  E
1107 HIS   (  92-)  F

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.

  40 ARG   (  46-)  A      N
  41 VAL   (  47-)  A      N
  54 LEU   (  60-)  A      N
  86 HIS   (  92-)  A      N
 107 LEU   ( 113-)  A      N
 118 ARG   ( 124-)  A      NE
 131 LEU   ( 137-)  A      N
 154 ARG   ( 160-)  A      NE
 157 ILE   ( 163-)  A      N
 201 ASN   ( 207-)  A      ND2
 219 ILE   (   4-)  B      N
 246 ARG   (  46-)  B      N
 247 VAL   (  47-)  B      N
 264 ARG   (  64-)  B      NH2
 272 HIS   (  72-)  B      N
 273 THR   (  73-)  B      N
 277 CYS   (  77-)  B      N
 292 HIS   (  92-)  B      N
 311 LYS   ( 111-)  B      N
 313 LEU   ( 113-)  B      N
 354 GLN   ( 154-)  B      NE2
 360 ARG   ( 160-)  B      NE
 418 GLU   ( 218-)  B      N
 452 ARG   (  46-)  C      N
 453 VAL   (  47-)  C      N
And so on for a total of 69 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.

 231 GLN   (  16-)  B      OE1
 292 HIS   (  92-)  B      NE2
 641 GLN   (  16-)  D      OE1
 684 HIS   (  72-)  D      ND1
1127 ASP   ( 112-)  F      OD2

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.

 179 ASP   ( 185-)  A   H-bonding suggests Asn; but Alt-Rotamer
 369 GLU   ( 169-)  B   H-bonding suggests Gln
 390 ASP   ( 190-)  B   H-bonding suggests Asn; but Alt-Rotamer
 575 GLU   ( 169-)  C   H-bonding suggests Gln
 756 ASP   ( 144-)  D   H-bonding suggests Asn
 858 GLU   (  50-)  E   H-bonding suggests Gln; but Alt-Rotamer
 933 ASP   ( 125-)  E   H-bonding suggests Asn
1155 GLU   ( 140-)  F   H-bonding suggests Gln
1205 ASP   ( 190-)  F   H-bonding suggests Asn; but Alt-Rotamer
1232 GLU   ( 217-)  F   H-bonding suggests Gln

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 :   0.193
  2nd generation packing quality :  -1.389
  Ramachandran plot appearance   :  -0.863
  chi-1/chi-2 rotamer normality  :  -3.703 (poor)
  Backbone conformation          :   0.533

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.531 (tight)
  Bond angles                    :   0.727
  Omega angle restraints         :   1.207
  Side chain planarity           :   0.571 (tight)
  Improper dihedral distribution :   0.654
  B-factor distribution          :   0.354
  Inside/Outside distribution    :   1.033

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 : 2.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.2
  2nd generation packing quality :  -0.2
  Ramachandran plot appearance   :   0.9
  chi-1/chi-2 rotamer normality  :  -1.8
  Backbone conformation          :   0.8

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.531 (tight)
  Bond angles                    :   0.727
  Omega angle restraints         :   1.207
  Side chain planarity           :   0.571 (tight)
  Improper dihedral distribution :   0.654
  B-factor distribution          :   0.354
  Inside/Outside distribution    :   1.033
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
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    Acta Crystallogr. A47, 392--400 (1991).

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

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

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

Matthews' Coefficient
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      Solvent content of Protein Crystals
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Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
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    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.