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 pdb3cvs.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.769
CA-only RMS fit for the two chains : 0.412

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and B

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 : 0.822
CA-only RMS fit for the two chains : 0.455

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: A and D

All-atom RMS fit for the two chains : 0.817
CA-only RMS fit for the two chains : 0.467

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 D

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 : 0.792
CA-only RMS fit for the two chains : 0.391

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: B and D

All-atom RMS fit for the two chains : 0.758
CA-only RMS fit for the two chains : 0.370

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: 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.

  43 GLU   (  43-)  A    High
  56 ARG   (  56-)  A    High
  57 HIS   (  57-)  A    High
  97 ARG   (  97-)  A    High
 140 GLN   ( 140-)  A    High
 148 ASP   ( 148-)  A    High
 203 GLU   ( 203-)  A    High
 207 LYS   ( 207-)  A    High
 243 GLN   ( 243-)  A    High
 255 ARG   ( 255-)  A    High
 258 GLU   ( 258-)  A    High
 278 GLN   ( 278-)  A    High
 379 ARG   (  97-)  B    High
 412 MET   ( 130-)  B    High
 415 LYS   ( 133-)  B    High
 459 LYS   ( 177-)  B    High
 473 GLU   ( 191-)  B    High
 557 GLU   ( 275-)  B    High
 562 ASP   ( 280-)  B    High
 563 GLU   ( 281-)  B    High
 564 ALA   ( 282-)  B    High
 565 MET   (   1-)  C    High
 596 ASP   (  32-)  C    High
 620 ARG   (  56-)  C    High
 624 HIS   (  60-)  C    High
And so on for a total of 62 lines.

Warning: What type of B-factor?

WHAT IF does not yet know well how to cope with B-factors in case TLS has been used. It simply assumes that the B-factor listed on the ATOM and HETATM cards are the total B-factors. When TLS refinement is used that assumption sometimes is not correct. TLS seems not mentioned in the header of the PDB file. But anyway, if WHAT IF complains about your B-factors, and you think that they are OK, then check for TLS related B-factor problems first.

Obviously, the temperature at which the X-ray data was collected has some importance too:

Crystal temperature (K) :100.000

Note: B-factor plot

The average atomic B-factor per residue is plotted as function of the residue number.

Chain identifier: A

Note: B-factor plot

Chain identifier: B

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.

  56 ARG   (  56-)  A
  97 ARG   (  97-)  A
 379 ARG   (  97-)  B

Warning: Tyrosine convention problem

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

 988 TYR   ( 142-)  D

Warning: Phenylalanine convention problem

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

 719 PHE   ( 155-)  C
 995 PHE   ( 149-)  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.

  32 ASP   (  32-)  A
  53 ASP   (  53-)  A
 314 ASP   (  32-)  B
 335 ASP   (  53-)  B
 596 ASP   (  32-)  C

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.

  43 GLU   (  43-)  A
 485 GLU   ( 203-)  B
 744 GLU   ( 180-)  C
 755 GLU   ( 191-)  C
 767 GLU   ( 203-)  C
 822 GLU   ( 258-)  C
 839 GLU   ( 275-)  C
1121 GLU   ( 275-)  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.

1142 DGUA  (  15-)  F      N9   C4    1.41    4.2

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

 |  0.999325  0.000082 -0.000078|
 |  0.000082  0.999456  0.000339|
 | -0.000078  0.000339  0.999132|
Proposed new scale matrix

 |  0.013311 -0.000001  0.000977|
 |  0.000000  0.009882 -0.000003|
 |  0.000000 -0.000003  0.009751|
With corresponding cell

    A    =  75.126  B   = 101.190  C    = 102.825
    Alpha=  89.962  Beta=  94.198  Gamma=  89.996

The CRYST1 cell dimensions

    A    =  75.174  B   = 101.247  C    = 102.917
    Alpha=  90.000  Beta=  94.190  Gamma=  90.000

Variance: 32.703
(Under-)estimated Z-score: 4.215

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.

 621 HIS   (  57-)  C      CG   ND1  CE1 109.77    4.2
1129 DGUA  (   1-)  E      N9   C8   N7  113.33    4.5
1138 DGUA  (  10-)  E      N9   C8   N7  113.20    4.2
1141 DGUA  (  14-)  F      C2'  C1'  N9  121.46    4.5
1142 DGUA  (  15-)  F      N9   C8   N7  113.70    5.2
1150 DGUA  (  23-)  F      N9   C8   N7  113.40    4.6
1165 DGUA  (  14-)  H      N9   C8   N7  113.23    4.3
1166 DGUA  (  15-)  H      N9   C8   N7  113.18    4.2
1174 DGUA  (  23-)  H      N9   C8   N7  113.22    4.2

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.

  32 ASP   (  32-)  A
  43 GLU   (  43-)  A
  53 ASP   (  53-)  A
  56 ARG   (  56-)  A
  97 ARG   (  97-)  A
 314 ASP   (  32-)  B
 335 ASP   (  53-)  B
 379 ARG   (  97-)  B
 485 GLU   ( 203-)  B
 596 ASP   (  32-)  C
 744 GLU   ( 180-)  C
 755 GLU   ( 191-)  C
 767 GLU   ( 203-)  C
 822 GLU   ( 258-)  C
 839 GLU   ( 275-)  C
1121 GLU   ( 275-)  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.

 347 ALA   (  65-)  B    5.14

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.

 544 PRO   ( 262-)  B    -3.0
 262 PRO   ( 262-)  A    -3.0
 826 PRO   ( 262-)  C    -3.0
 528 PRO   ( 246-)  B    -3.0
1108 PRO   ( 262-)  D    -2.9
 903 HIS   (  57-)  D    -2.9
 814 PRO   ( 250-)  C    -2.8
 246 PRO   ( 246-)  A    -2.6
 621 HIS   (  57-)  C    -2.6
 902 ARG   (  56-)  D    -2.4
1092 PRO   ( 246-)  D    -2.3
 235 LEU   ( 235-)  A    -2.3
  56 ARG   (  56-)  A    -2.3
 730 PRO   ( 166-)  C    -2.2
 426 GLU   ( 144-)  B    -2.2
  57 HIS   (  57-)  A    -2.2
 757 THR   ( 193-)  C    -2.2
 971 LEU   ( 125-)  D    -2.1
 799 LEU   ( 235-)  C    -2.1
 291 PRO   (   9-)  B    -2.1
1012 PRO   ( 166-)  D    -2.1
 393 VAL   ( 111-)  B    -2.1
 990 GLU   ( 144-)  D    -2.1
 689 LEU   ( 125-)  C    -2.1
 675 VAL   ( 111-)  C    -2.1
 761 THR   ( 197-)  C    -2.0
 105 LEU   ( 105-)  A    -2.0
 125 LEU   ( 125-)  A    -2.0
 669 LEU   ( 105-)  C    -2.0
 849 THR   (   3-)  D    -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.

   8 PRO   (   8-)  A  PRO omega poor
  26 SER   (  26-)  A  Poor phi/psi
  83 ASP   (  83-)  A  Poor phi/psi
 125 LEU   ( 125-)  A  Poor phi/psi
 173 GLY   ( 173-)  A  Poor phi/psi
 229 GLN   ( 229-)  A  Poor phi/psi
 261 LYS   ( 261-)  A  PRO omega poor
 290 PRO   (   8-)  B  PRO omega poor
 308 SER   (  26-)  B  Poor phi/psi
 339 HIS   (  57-)  B  Poor phi/psi
 455 GLY   ( 173-)  B  Poor phi/psi
 511 GLN   ( 229-)  B  Poor phi/psi
 528 PRO   ( 246-)  B  Poor phi/psi
 530 MET   ( 248-)  B  Poor phi/psi
 543 LYS   ( 261-)  B  PRO omega poor
 557 GLU   ( 275-)  B  Poor phi/psi
 558 GLY   ( 276-)  B  Poor phi/psi
 572 PRO   (   8-)  C  PRO omega poor
 590 SER   (  26-)  C  Poor phi/psi
 689 LEU   ( 125-)  C  Poor phi/psi
 793 GLN   ( 229-)  C  Poor phi/psi
 811 GLY   ( 247-)  C  Poor phi/psi
 825 LYS   ( 261-)  C  PRO omega poor
 841 TRP   ( 277-)  C  Poor phi/psi
 854 PRO   (   8-)  D  PRO omega poor
 872 SER   (  26-)  D  Poor phi/psi
 971 LEU   ( 125-)  D  Poor phi/psi
1075 GLN   ( 229-)  D  Poor phi/psi
1107 LYS   ( 261-)  D  PRO omega poor
 chi-1/chi-2 correlation Z-score : -2.653

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.

 577 SER   (  13-)  C    0.39

Warning: Unusual backbone conformations

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

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

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

   7 GLN   (   7-)  A      0
   8 PRO   (   8-)  A      0
  12 TRP   (  12-)  A      0
  25 SER   (  25-)  A      0
  26 SER   (  26-)  A      0
  27 VAL   (  27-)  A      0
  31 ALA   (  31-)  A      0
  33 SER   (  33-)  A      0
  34 TYR   (  34-)  A      0
  41 VAL   (  41-)  A      0
  44 TYR   (  44-)  A      0
  45 ARG   (  45-)  A      0
  56 ARG   (  56-)  A      0
  57 HIS   (  57-)  A      0
  95 LEU   (  95-)  A      0
  97 ARG   (  97-)  A      0
 100 ALA   ( 100-)  A      0
 102 ARG   ( 102-)  A      0
 110 CYS   ( 110-)  A      0
 111 VAL   ( 111-)  A      0
 124 GLN   ( 124-)  A      0
 125 LEU   ( 125-)  A      0
 142 TYR   ( 142-)  A      0
 149 PHE   ( 149-)  A      0
 155 PHE   ( 155-)  A      0
And so on for a total of 369 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.164

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!

 663 GLY   (  99-)  C   2.10   15
 955 GLY   ( 109-)  D   2.06   11
 529 GLY   ( 247-)  B   2.02   80
 109 GLY   ( 109-)  A   1.92   13
 391 GLY   ( 109-)  B   1.92   12
 840 GLY   ( 276-)  C   1.67   24
 673 GLY   ( 109-)  C   1.62   15
 158 PRO   ( 158-)  A   1.53   11

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.

 902 ARG   (  56-)  D      NH2 <->  903 HIS   (  57-)  D      CE1    0.44    2.66  INTRA BF
 406 GLN   ( 124-)  B      NE2 <->  460 ARG   ( 178-)  B      NH1    0.41    2.44  INTRA BF
 565 MET   (   1-)  C      N   <->  624 HIS   (  60-)  C      CE1    0.40    2.70  INTRA BF
1157 DTHY  (   5-)  G      C2' <-> 1158 DGUA  (   6-)  G      C5'    0.39    2.81  INTRA BF
 124 GLN   ( 124-)  A      NE2 <->  178 ARG   ( 178-)  A      NH1    0.37    2.48  INTRA BF
 231 LYS   ( 231-)  A      NZ  <-> 1181 HOH   ( 301 )  A      O      0.36    2.34  INTRA BL
 902 ARG   (  56-)  D      NH2 <->  903 HIS   (  57-)  D      NE2    0.32    2.68  INTRA BF
1154 DADE  (   2-)  G      N1  <-> 1175 DTHY  (  24-)  H      N3     0.31    2.69  INTRA BF
 952 ARG   ( 106-)  D      NE  <-> 1184 HOH   ( 315 )  D      O      0.30    2.40  INTRA BL
1139 DCYT  (  11-)  E      C2  <-> 1140 DCYT  (  12-)  E      C5     0.29    2.91  INTRA BF
1159 DADE  (   7-)  G      N1  <-> 1170 DTHY  (  19-)  H      N3     0.28    2.72  INTRA BF
 781 ARG   ( 217-)  C      NE  <->  801 ASP   ( 237-)  C      OD2    0.23    2.47  INTRA BF
1172 DADE  (  21-)  H      C2' <-> 1173 DTHY  (  22-)  H      C5'    0.23    2.97  INTRA BF
1136 8OG   (   8-)  E      N7  <-> 1145 DADE  (  18-)  F      N1     0.22    2.78  INTRA BF
 722 PRO   ( 158-)  C      CD  <->  723 GLN   ( 159-)  C      NE2    0.22    2.88  INTRA BL
1135 DADE  (   7-)  E      N1  <-> 1146 DTHY  (  19-)  F      N3     0.22    2.78  INTRA BF
 310 GLU   (  28-)  B      OE2 <->  401 ARG   ( 119-)  B      NH2    0.22    2.48  INTRA BL
 531 THR   ( 249-)  B      O   <->  534 GLN   ( 252-)  B      N      0.21    2.49  INTRA BF
1136 8OG   (   8-)  E      O6  <-> 1145 DADE  (  18-)  F      N6     0.20    2.50  INTRA BF
1156 DADE  (   4-)  G      C2' <-> 1157 DTHY  (   5-)  G      C5'    0.20    3.00  INTRA BF
 926 ARG   (  80-)  D      NH2 <-> 1184 HOH   ( 323 )  D      O      0.20    2.50  INTRA BF
 847 MET   (   1-)  D      N   <-> 1184 HOH   ( 326 )  D      O      0.20    2.50  INTRA BF
 661 ARG   (  97-)  C      CD  <->  662 LEU   (  98-)  C      N      0.20    2.80  INTRA BF
 574 TYR   (  10-)  C      CD2 <->  670 ARG   ( 106-)  C      NH1    0.20    2.90  INTRA BF
 311 THR   (  29-)  B      N   <->  318 ALA   (  36-)  B      O      0.18    2.52  INTRA BL
And so on for a total of 251 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.

 571 GLN   (   7-)  C      -6.74
   7 GLN   (   7-)  A      -6.67
 407 LEU   ( 125-)  B      -6.42
 853 GLN   (   7-)  D      -6.29
 289 GLN   (   7-)  B      -6.07
 563 GLU   ( 281-)  B      -6.01
 845 GLU   ( 281-)  C      -5.92
 281 GLU   ( 281-)  A      -5.92
 902 ARG   (  56-)  D      -5.66
 125 LEU   ( 125-)  A      -5.63
1127 GLU   ( 281-)  D      -5.56
 666 ARG   ( 102-)  C      -5.54
 689 LEU   ( 125-)  C      -5.50
 971 LEU   ( 125-)  D      -5.41
 586 ARG   (  22-)  C      -5.02
 868 ARG   (  22-)  D      -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.

 901 ALA   (  55-)  D   -2.67

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: 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.

1182 HOH   ( 312 )  B      O
1183 HOH   ( 320 )  C      O
1183 HOH   ( 321 )  C      O
1184 HOH   ( 290 )  D      O
ERROR. Strange cone in HB2INI
Affected atom 1136 8OG  (   8-) E      P
ERROR. Strange cone in HB2INI
Affected atom 1160 8OG  (   8-) G      P
Expected ambiguity-2 in FILL1HARR 0 97 675
Expected ambiguity-2 in FILL1HARR 0 97 675

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.

  60 HIS   (  60-)  A
  89 GLN   (  89-)  A
 124 GLN   ( 124-)  A
 342 HIS   (  60-)  B
 406 GLN   ( 124-)  B
 466 HIS   ( 184-)  B
 552 HIS   ( 270-)  B
 688 GLN   ( 124-)  C
 748 HIS   ( 184-)  C
 970 GLN   ( 124-)  D
1030 HIS   ( 184-)  D
1116 HIS   ( 270-)  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.

  12 TRP   (  12-)  A      NE1
  14 TRP   (  14-)  A      NE1
  34 TYR   (  34-)  A      N
 102 ARG   ( 102-)  A      N
 106 ARG   ( 106-)  A      NE
 110 CYS   ( 110-)  A      N
 112 ASP   ( 112-)  A      N
 114 PHE   ( 114-)  A      N
 159 GLN   ( 159-)  A      N
 196 MET   ( 196-)  A      N
 197 THR   ( 197-)  A      N
 234 PHE   ( 234-)  A      N
 235 LEU   ( 235-)  A      N
 288 TRP   (   6-)  B      NE1
 294 TRP   (  12-)  B      NE1
 296 TRP   (  14-)  B      NE1
 316 TYR   (  34-)  B      N
 383 ALA   ( 101-)  B      N
 388 ARG   ( 106-)  B      NE
 392 CYS   ( 110-)  B      N
 396 PHE   ( 114-)  B      N
 433 GLU   ( 151-)  B      N
 441 GLN   ( 159-)  B      N
 479 THR   ( 197-)  B      N
 498 GLY   ( 216-)  B      N
And so on for a total of 52 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.

 116 GLN   ( 116-)  A      OE1
 270 HIS   ( 270-)  A      ND1
 552 HIS   ( 270-)  B      ND1
 834 HIS   ( 270-)  C      ND1

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.

1181 HOH   ( 296 )  A      O  0.91 NA  4 *2 ION-B H2O-B
1184 HOH   ( 317 )  D      O  1.08  K  5 ION-B

Warning: Possible wrong residue type

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

  32 ASP   (  32-)  A   H-bonding suggests Asn
 258 GLU   ( 258-)  A   H-bonding suggests Gln
 607 GLU   (  43-)  C   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 :  -0.510
  2nd generation packing quality :  -1.216
  Ramachandran plot appearance   :  -1.784
  chi-1/chi-2 rotamer normality  :  -2.653
  Backbone conformation          :   0.549

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.356 (tight)
  Bond angles                    :   0.627 (tight)
  Omega angle restraints         :   0.212 (tight)
  Side chain planarity           :   0.229 (tight)
  Improper dihedral distribution :   0.601
  B-factor distribution          :   1.118
  Inside/Outside distribution    :   0.961

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 : 2.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :  -0.1
  Ramachandran plot appearance   :  -0.0
  chi-1/chi-2 rotamer normality  :  -0.9
  Backbone conformation          :   0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.356 (tight)
  Bond angles                    :   0.627 (tight)
  Omega angle restraints         :   0.212 (tight)
  Side chain planarity           :   0.229 (tight)
  Improper dihedral distribution :   0.601
  B-factor distribution          :   1.118
  Inside/Outside distribution    :   0.961
==============

WHAT IF
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WHAT_CHECK (verification routines from WHAT IF)
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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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    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
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      protein structures
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Matthews' Coefficient
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      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

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