WHAT IF Check report

This file was created 2011-12-17 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 pdb3n80.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 : 0.272
CA-only RMS fit for the two chains : 0.098

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 : 0.339
CA-only RMS fit for the two chains : 0.122

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 : 0.295
CA-only RMS fit for the two chains : 0.133

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: A and E

All-atom RMS fit for the two chains : 0.318
CA-only RMS fit for the two chains : 0.149

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 E

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 F

All-atom RMS fit for the two chains : 0.316
CA-only RMS fit for the two chains : 0.143

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 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.

3962 GAI   ( 801-)  A  -
3963 GAI   ( 811-)  A  -
3964 GAI   ( 812-)  A  -
3970 GAI   ( 802-)  B  -
3977 GAI   ( 803-)  C  -
3978 GAI   ( 813-)  C  -
3979 GAI   ( 823-)  C  -
3986 GAI   ( 804-)  D  -
3987 GAI   ( 814-)  D  -
3988 GAI   ( 833-)  D  -
3993 GAI   ( 805-)  E  -
3994 GAI   ( 815-)  E  -
4000 GAI   ( 806-)  F  -
4001 GAI   ( 816-)  F  -
4002 GAI   ( 826-)  F  -
4003 GAI   ( 839-)  F  -
4012 GAI   ( 807-)  G  -
4013 GAI   ( 817-)  G  -
4014 GAI   ( 838-)  G  -
4020 GAI   ( 808-)  H  -
4026 GAI   ( 818-)  H  -

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

2767 CSO   ( 302-)  F  -

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

2767 CSO   ( 302-)  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

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

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

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

1977 GLN   (   6-)  E    0.50

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

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

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.

  80 ARG   (  86-)  A
  84 ARG   (  90-)  A
  91 ARG   (  97-)  A
  93 ARG   (  99-)  A
 124 ARG   ( 130-)  A
 413 ARG   ( 419-)  A
 574 ARG   (  86-)  B
 578 ARG   (  90-)  B
 585 ARG   (  97-)  B
 587 ARG   (  99-)  B
 618 ARG   ( 130-)  B
 907 ARG   ( 419-)  B
1016 ARG   (  34-)  C
1068 ARG   (  86-)  C
1072 ARG   (  90-)  C
1079 ARG   (  97-)  C
1081 ARG   (  99-)  C
1112 ARG   ( 130-)  C
1401 ARG   ( 419-)  C
1562 ARG   (  86-)  D
1566 ARG   (  90-)  D
1573 ARG   (  97-)  D
1575 ARG   (  99-)  D
1606 ARG   ( 130-)  D
1895 ARG   ( 419-)  D
And so on for a total of 51 lines.

Warning: Tyrosine convention problem

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

 112 TYR   ( 118-)  A
 126 TYR   ( 132-)  A
 350 TYR   ( 356-)  A
 373 TYR   ( 379-)  A
 419 TYR   ( 425-)  A
 435 TYR   ( 441-)  A
 450 TYR   ( 456-)  A
 479 TYR   ( 485-)  A
 620 TYR   ( 132-)  B
 641 TYR   ( 153-)  B
 844 TYR   ( 356-)  B
 867 TYR   ( 379-)  B
 913 TYR   ( 425-)  B
 929 TYR   ( 441-)  B
 944 TYR   ( 456-)  B
 973 TYR   ( 485-)  B
1100 TYR   ( 118-)  C
1114 TYR   ( 132-)  C
1338 TYR   ( 356-)  C
1361 TYR   ( 379-)  C
1407 TYR   ( 425-)  C
1423 TYR   ( 441-)  C
1438 TYR   ( 456-)  C
1462 TYR   ( 480-)  C
1467 TYR   ( 485-)  C
And so on for a total of 61 lines.

Warning: Phenylalanine convention problem

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

  12 PHE   (  18-)  A
  31 PHE   (  37-)  A
 144 PHE   ( 150-)  A
 218 PHE   ( 224-)  A
 286 PHE   ( 292-)  A
 289 PHE   ( 295-)  A
 290 PHE   ( 296-)  A
 303 PHE   ( 309-)  A
 312 PHE   ( 318-)  A
 329 PHE   ( 335-)  A
 374 PHE   ( 380-)  A
 380 PHE   ( 386-)  A
 404 PHE   ( 410-)  A
 506 PHE   (  18-)  B
 525 PHE   (  37-)  B
 638 PHE   ( 150-)  B
 658 PHE   ( 170-)  B
 780 PHE   ( 292-)  B
 783 PHE   ( 295-)  B
 784 PHE   ( 296-)  B
 797 PHE   ( 309-)  B
 806 PHE   ( 318-)  B
 823 PHE   ( 335-)  B
 868 PHE   ( 380-)  B
 874 PHE   ( 386-)  B
And so on for a total of 101 lines.

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.

  24 ASP   (  30-)  A
 115 ASP   ( 121-)  A
 131 ASP   ( 137-)  A
 276 ASP   ( 282-)  A
 330 ASP   ( 336-)  A
 429 ASP   ( 435-)  A
 431 ASP   ( 437-)  A
 518 ASP   (  30-)  B
 609 ASP   ( 121-)  B
 625 ASP   ( 137-)  B
 824 ASP   ( 336-)  B
 923 ASP   ( 435-)  B
 925 ASP   ( 437-)  B
1012 ASP   (  30-)  C
1103 ASP   ( 121-)  C
1119 ASP   ( 137-)  C
1264 ASP   ( 282-)  C
1318 ASP   ( 336-)  C
1417 ASP   ( 435-)  C
1419 ASP   ( 437-)  C
1506 ASP   (  30-)  D
1597 ASP   ( 121-)  D
1613 ASP   ( 137-)  D
1758 ASP   ( 282-)  D
1812 ASP   ( 336-)  D
And so on for a total of 51 lines.

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.

  10 GLU   (  16-)  A
  40 GLU   (  46-)  A
  90 GLU   (  96-)  A
 100 GLU   ( 106-)  A
 204 GLU   ( 210-)  A
 282 GLU   ( 288-)  A
 306 GLU   ( 312-)  A
 311 GLU   ( 317-)  A
 341 GLU   ( 347-)  A
 392 GLU   ( 398-)  A
 473 GLU   ( 479-)  A
 481 GLU   ( 487-)  A
 545 GLU   (  57-)  B
 584 GLU   (  96-)  B
 594 GLU   ( 106-)  B
 698 GLU   ( 210-)  B
 736 GLU   ( 248-)  B
 776 GLU   ( 288-)  B
 800 GLU   ( 312-)  B
 805 GLU   ( 317-)  B
 835 GLU   ( 347-)  B
 886 GLU   ( 398-)  B
 967 GLU   ( 479-)  B
 975 GLU   ( 487-)  B
 998 GLU   (  16-)  C
And so on for a total of 96 lines.

Geometric checks

Warning: Low bond length variability

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

RMS Z-score for bond lengths: 0.559
RMS-deviation in bond distances: 0.014

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

 |  0.997247  0.000575  0.000011|
 |  0.000575  0.997906  0.000141|
 |  0.000011  0.000141  0.997524|
Proposed new scale matrix

 |  0.007078 -0.000004  0.000000|
 | -0.000004  0.006580  0.000000|
 |  0.000000  0.000000  0.005655|
With corresponding cell

    A    = 141.273  B   = 151.981  C    = 176.835
    Alpha=  90.002  Beta=  90.002  Gamma=  89.934

The CRYST1 cell dimensions

    A    = 141.662  B   = 152.291  C    = 177.282
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 765.300
(Under-)estimated Z-score: 20.388

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.

1217 HIS   ( 235-)  C      CG   ND1  CE1 109.65    4.0
1632 HIS   ( 156-)  D      CG   ND1  CE1 109.65    4.1
2130 VAL   ( 159-)  E      C    CA   CB  118.40    4.4
2222 ARG   ( 251-)  E      CB   CG   CD  105.41   -4.3
2447 GLU   ( 476-)  E      CB   CG   CD  119.99    4.3
2624 VAL   ( 159-)  F      C    CA   CB  118.22    4.3
2700 HIS   ( 235-)  F      CG   ND1  CE1 109.61    4.0

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  10 GLU   (  16-)  A
  24 ASP   (  30-)  A
  40 GLU   (  46-)  A
  80 ARG   (  86-)  A
  84 ARG   (  90-)  A
  90 GLU   (  96-)  A
  91 ARG   (  97-)  A
  93 ARG   (  99-)  A
 100 GLU   ( 106-)  A
 115 ASP   ( 121-)  A
 124 ARG   ( 130-)  A
 131 ASP   ( 137-)  A
 204 GLU   ( 210-)  A
 276 ASP   ( 282-)  A
 282 GLU   ( 288-)  A
 306 GLU   ( 312-)  A
 311 GLU   ( 317-)  A
 330 ASP   ( 336-)  A
 341 GLU   ( 347-)  A
 392 GLU   ( 398-)  A
 413 ARG   ( 419-)  A
 429 ASP   ( 435-)  A
 431 ASP   ( 437-)  A
 473 GLU   ( 479-)  A
 481 GLU   ( 487-)  A
And so on for a total of 198 lines.

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

1877 PHE   ( 401-)  D    -3.3
 889 PHE   ( 401-)  B    -3.3
2866 PHE   ( 401-)  F    -3.3
2372 PHE   ( 401-)  E    -3.2
 395 PHE   ( 401-)  A    -3.2
1383 PHE   ( 401-)  C    -3.2
3854 PHE   ( 401-)  H    -3.2
3360 PHE   ( 401-)  G    -3.1
3126 PRO   ( 167-)  G    -2.8
 655 PRO   ( 167-)  B    -2.8
2632 PRO   ( 167-)  F    -2.8
2138 PRO   ( 167-)  E    -2.7
1149 PRO   ( 167-)  C    -2.7
 161 PRO   ( 167-)  A    -2.6
1643 PRO   ( 167-)  D    -2.6
3620 PRO   ( 167-)  H    -2.5
1615 TYR   ( 139-)  D    -2.4
3098 TYR   ( 139-)  G    -2.4
1121 TYR   ( 139-)  C    -2.3
 921 THR   ( 433-)  B    -2.3
3392 THR   ( 433-)  G    -2.3
3592 TYR   ( 139-)  H    -2.3
2404 THR   ( 433-)  E    -2.3
2898 THR   ( 433-)  F    -2.3
3886 THR   ( 433-)  H    -2.3
2868 PRO   ( 403-)  F    -2.3
 133 TYR   ( 139-)  A    -2.3
 427 THR   ( 433-)  A    -2.3
1909 THR   ( 433-)  D    -2.2
 627 TYR   ( 139-)  B    -2.2
2110 TYR   ( 139-)  E    -2.2
2604 TYR   ( 139-)  F    -2.2
1415 THR   ( 433-)  C    -2.2
 139 PRO   ( 145-)  A    -2.2
3598 PRO   ( 145-)  H    -2.2
 633 PRO   ( 145-)  B    -2.2
3856 PRO   ( 403-)  H    -2.2
2993 ARG   (  34-)  G    -2.2
2692 THR   ( 227-)  F    -2.1
  28 ARG   (  34-)  A    -2.1
 371 ARG   ( 377-)  A    -2.1
3104 PRO   ( 145-)  G    -2.1
1385 PRO   ( 403-)  C    -2.1
 891 PRO   ( 403-)  B    -2.1
1127 PRO   ( 145-)  C    -2.1
 397 PRO   ( 403-)  A    -2.1
1902 GLY   ( 426-)  D    -2.0
1016 ARG   (  34-)  C    -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.

   5 PRO   (  11-)  A  omega poor
  20 ASN   (  26-)  A  Poor phi/psi
  23 HIS   (  29-)  A  omega poor
  28 ARG   (  34-)  A  Poor phi/psi
  32 PRO   (  38-)  A  omega poor
 129 TRP   ( 135-)  A  omega poor
 134 HIS   ( 140-)  A  omega poor
 136 LYS   ( 142-)  A  omega poor
 137 THR   ( 143-)  A  omega poor
 144 PHE   ( 150-)  A  omega poor
 148 THR   ( 154-)  A  omega poor
 192 PRO   ( 198-)  A  omega poor
 221 THR   ( 227-)  A  Poor phi/psi
 254 SER   ( 260-)  A  Poor phi/psi
 256 LEU   ( 262-)  A  Poor phi/psi
 259 VAL   ( 265-)  A  omega poor
 263 LEU   ( 269-)  A  Poor phi/psi
 265 GLY   ( 271-)  A  omega poor
 266 LYS   ( 272-)  A  omega poor
 291 ASN   ( 297-)  A  Poor phi/psi
 292 GLN   ( 298-)  A  Poor phi/psi
 300 SER   ( 306-)  A  omega poor
 338 GLN   ( 344-)  A  omega poor
 395 PHE   ( 401-)  A  Poor phi/psi
 397 PRO   ( 403-)  A  Poor phi/psi
And so on for a total of 240 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.

 605 SER   ( 117-)  B    0.35
1099 SER   ( 117-)  C    0.36
 487 VAL   ( 493-)  A    0.36
 111 SER   ( 117-)  A    0.37
3076 SER   ( 117-)  G    0.37
3570 SER   ( 117-)  H    0.37
2582 SER   ( 117-)  F    0.37
1593 SER   ( 117-)  D    0.38
2088 SER   ( 117-)  E    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!

   7 GLN   (  13-)  A      0
   8 GLN   (  14-)  A      0
  12 PHE   (  18-)  A      0
  13 CYS   (  19-)  A      0
  14 ASN   (  20-)  A      0
  17 PHE   (  23-)  A      0
  20 ASN   (  26-)  A      0
  29 LYS   (  35-)  A      0
  31 PHE   (  37-)  A      0
  37 SER   (  43-)  A      0
  42 ILE   (  48-)  A      0
  43 CYS   (  49-)  A      0
  66 LEU   (  72-)  A      0
  92 ASP   (  98-)  A      0
 103 ASP   ( 109-)  A      0
 104 ASN   ( 110-)  A      0
 129 TRP   ( 135-)  A      0
 132 LYS   ( 138-)  A      0
 133 TYR   ( 139-)  A      0
 141 ASP   ( 147-)  A      0
 143 ASP   ( 149-)  A      0
 144 PHE   ( 150-)  A      0
 153 VAL   ( 159-)  A      0
 155 VAL   ( 161-)  A      0
 162 TRP   ( 168-)  A      0
And so on for a total of 1301 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!

2046 PRO   (  75-)  E   1.57   10

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]

 216 PRO   ( 222-)  A    0.20 LOW
 710 PRO   ( 222-)  B    0.19 LOW
2186 PRO   ( 215-)  E    0.18 LOW
3174 PRO   ( 215-)  G    0.20 LOW
3675 PRO   ( 222-)  H    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].

 209 PRO   ( 215-)  A  -113.1 envelop C-gamma (-108 degrees)
3611 PRO   ( 158-)  H    52.0 half-chair C-delta/C-gamma (54 degrees)
3668 PRO   ( 215-)  H  -112.6 envelop C-gamma (-108 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.

2334 GLU   ( 363-)  E    A CG  <-> 4031 HOH   (4639 )  E      O      0.56    2.24  INTRA
3460 ALA   (   7-)  H      N   <-> 4034 HOH   (4869 )  H      O      0.47    2.23  INTRA
 502 GLN   (  14-)  B      NE2 <-> 4028 HOH   (1439 )  B      O      0.44    2.26  INTRA
1016 ARG   (  34-)  C      NE  <-> 4029 HOH   ( 936 )  C      O      0.35    2.35  INTRA
 989 ALA   (   7-)  C      N   <-> 4029 HOH   (4614 )  C      O      0.34    2.36  INTRA
 840 LYS   ( 352-)  B      NZ  <-> 4028 HOH   (4796 )  B      O      0.34    2.36  INTRA
 777 GLN   ( 289-)  B      NE2 <-> 4028 HOH   (4702 )  B      O      0.32    2.38  INTRA
 544 LYS   (  56-)  B      NZ  <-> 4028 HOH   (1647 )  B      O      0.32    2.38  INTRA
 254 SER   ( 260-)  A      O   <->  739 ARG   ( 251-)  B    A NH1    0.30    2.40  INTRA
1266 ASP   ( 284-)  C      OD1 <-> 1303 ARG   ( 321-)  C      NH1    0.30    2.40  INTRA
3991 EDO   ( 914-)  D      C1  <-> 4030 HOH   ( 508 )  D      O      0.28    2.52  INTRA
3499 GLU   (  46-)  H      CB  <-> 4023 EDO   ( 918-)  H      C2     0.27    2.93  INTRA
4023 EDO   ( 918-)  H      C1  <-> 4034 HOH   (3294 )  H      O      0.27    2.53  INTRA
3991 EDO   ( 914-)  D      C2  <-> 4030 HOH   ( 508 )  D      O      0.27    2.53  INTRA
2792 LYS   ( 327-)  F      NZ  <-> 4032 HOH   (2202 )  F      O      0.26    2.44  INTRA
1284 CSO   ( 302-)  C    A SG  <-> 1285 CYS   ( 303-)  C      N      0.24    2.96  INTRA
1299 GLU   ( 317-)  C      CG  <-> 4029 HOH   (4736 )  C      O      0.24    2.56  INTRA
 815 LYS   ( 327-)  B      NZ  <-> 4028 HOH   (1420 )  B      O      0.23    2.47  INTRA
2959 LYS   ( 494-)  F      NZ  <-> 4032 HOH   (2357 )  F      O      0.22    2.48  INTRA
1309 LYS   ( 327-)  C      NZ  <-> 4029 HOH   ( 773 )  C      O      0.20    2.50  INTRA
3780 LYS   ( 327-)  H      NZ  <-> 4034 HOH   (1954 )  H      O      0.20    2.50  INTRA
1540 LYS   (  64-)  D      NZ  <-> 4030 HOH   ( 713 )  D      O      0.19    2.51  INTRA
3213 GLN   ( 254-)  G    A NE2 <-> 3715 LEU   ( 262-)  H      CD2    0.19    2.91  INTRA
3244 TRP   ( 285-)  G      CE2 <-> 3947 LYS   ( 494-)  H      NZ     0.19    2.91  INTRA
1343 LYS   ( 361-)  C      NZ  <-> 4029 HOH   ( 601 )  C      O      0.19    2.51  INTRA
And so on for a total of 198 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

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.

3336 ARG   ( 377-)  G      -6.40
 865 ARG   ( 377-)  B      -6.06
1984 GLN   (  13-)  E      -5.99
 501 GLN   (  13-)  B      -5.88
 995 GLN   (  13-)  C      -5.87
2478 GLN   (  13-)  F      -5.85
3466 GLN   (  13-)  H      -5.85
1853 ARG   ( 377-)  D      -5.84
   7 GLN   (  13-)  A      -5.83
 371 ARG   ( 377-)  A      -5.83
1489 GLN   (  13-)  D      -5.69
2972 GLN   (  13-)  G      -5.69
2348 ARG   ( 377-)  E      -5.67
2827 GLN   ( 362-)  F      -5.63
2333 GLN   ( 362-)  E      -5.62
3815 GLN   ( 362-)  H      -5.62
3321 GLN   ( 362-)  G      -5.62
 356 GLN   ( 362-)  A      -5.61
1838 GLN   ( 362-)  D      -5.59
1344 GLN   ( 362-)  C      -5.57
3900 GLN   ( 447-)  H      -5.55
 850 GLN   ( 362-)  B      -5.53
3830 ARG   ( 377-)  H      -5.51
 441 GLN   ( 447-)  A      -5.49
1923 GLN   ( 447-)  D      -5.46
And so on for a total of 61 lines.

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

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

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: G

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: H

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.

1737 ASN   ( 261-)  D   -2.81
1814 LYS   ( 338-)  D   -2.58
2107 ALA   ( 136-)  E   -2.50

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

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

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.

4028 HOH   (3212 )  B      O     67.38  118.77   80.80
4028 HOH   (3485 )  B      O     22.95  135.48  107.39
4029 HOH   ( 643 )  C      O     83.69  160.38  103.21
4029 HOH   ( 650 )  C      O     62.69  101.23  164.16
4029 HOH   (1159 )  C      O     76.91  113.12  169.12
4029 HOH   (1749 )  C      O     37.52   43.26   99.00
4030 HOH   ( 643 )  D      O     46.63  130.12  147.60
4031 HOH   (4380 )  E      O     98.29   99.70   95.65
4033 HOH   (3950 )  G      O     75.54   32.50   96.35
4033 HOH   (4035 )  G      O     81.06   24.60  101.34
4034 HOH   (2028 )  H      O     29.48   -3.22   75.01
4034 HOH   (2051 )  H      O     24.51  126.90   82.99

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.

4027 HOH   ( 605 )  A      O
4027 HOH   (1221 )  A      O
4029 HOH   ( 817 )  C      O
4030 HOH   ( 517 )  D      O
4031 HOH   (2360 )  E      O
4032 HOH   (4664 )  F      O
4034 HOH   (3890 )  H      O
ERROR. No convergence in HB2STD
Old,New value: 8194.737 8194.804
ERROR. No convergence in HB2STD
Old,New value: 8190.004 8190.043
ERROR. No convergence in HB2STD
Old,New value: 8509.531 8509.549

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.

   7 GLN   (  13-)  A
  65 GLN   (  71-)  A
 434 ASN   ( 440-)  A
 501 GLN   (  13-)  B
 910 ASN   ( 422-)  B
1032 GLN   (  50-)  C
1340 ASN   ( 358-)  C
1526 GLN   (  50-)  D
1616 HIS   ( 140-)  D
1866 GLN   ( 390-)  D
1920 GLN   ( 444-)  D
2361 GLN   ( 390-)  E
2823 ASN   ( 358-)  F
3321 GLN   ( 362-)  G
3349 GLN   ( 390-)  G
3466 GLN   (  13-)  H
3467 GLN   (  14-)  H
3473 ASN   (  20-)  H
3744 HIS   ( 291-)  H

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.

  13 CYS   (  19-)  A      N
  15 GLN   (  21-)  A      N
 117 ASP   ( 123-)  A      N
 125 TYR   ( 131-)  A      OH
 136 LYS   ( 142-)  A      N
 150 HIS   ( 156-)  A      NE2
 169 GLN   ( 175-)  A      NE2
 187 VAL   ( 193-)  A      N
 340 ASP   ( 346-)  A      N
 371 ARG   ( 377-)  A      N
 396 GLY   ( 402-)  A      N
 408 GLU   ( 414-)  A      N
 427 THR   ( 433-)  A      OG1
 449 CYS   ( 455-)  A      N
 451 ASP   ( 457-)  A      N
 452 VAL   ( 458-)  A      N
 457 SER   ( 463-)  A      OG
 462 TYR   ( 468-)  A      OH
 509 GLN   (  21-)  B      N
 611 ASP   ( 123-)  B      N
 652 GLN   ( 164-)  B      NE2
 663 GLN   ( 175-)  B      NE2
 681 VAL   ( 193-)  B      N
 786 GLN   ( 298-)  B      NE2
 834 ASP   ( 346-)  B      N
And so on for a total of 141 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.

 150 HIS   ( 156-)  A      ND1
 158 GLN   ( 164-)  A      OE1
 269 ASN   ( 275-)  A      OD1
 400 GLN   ( 406-)  A      OE1
 451 ASP   ( 457-)  A      OD1
 652 GLN   ( 164-)  B      OE1
 763 ASN   ( 275-)  B      OD1
 894 GLN   ( 406-)  B      OE1
 945 ASP   ( 457-)  B      OD1
1146 GLN   ( 164-)  C      OE1
1257 ASN   ( 275-)  C      OD1
1388 GLN   ( 406-)  C      OE1
1439 ASP   ( 457-)  C      OD1
1640 GLN   ( 164-)  D      OE1
1751 ASN   ( 275-)  D      OD1
1882 GLN   ( 406-)  D      OE1
1933 ASP   ( 457-)  D      OD1
2135 GLN   ( 164-)  E      OE1
2246 ASN   ( 275-)  E      OD1
2377 GLN   ( 406-)  E      OE1
2428 ASP   ( 457-)  E      OD1
2621 HIS   ( 156-)  F      ND1
2629 GLN   ( 164-)  F      OE1
2740 ASN   ( 275-)  F      OD1
2871 GLN   ( 406-)  F      OE1
2922 ASP   ( 457-)  F      OD1
3123 GLN   ( 164-)  G      OE1
3234 ASN   ( 275-)  G      OD1
3365 GLN   ( 406-)  G      OE1
3416 ASP   ( 457-)  G      OD1
3609 HIS   ( 156-)  H      ND1
3617 GLN   ( 164-)  H      OE1
3728 ASN   ( 275-)  H      OD1
3859 GLN   ( 406-)  H      OE1
3910 ASP   ( 457-)  H      OD1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method has great potential, but the method has not been validated. Part of our implementation (comparing ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

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

4019  MG   ( 609-)  H     0.74   1.24 Scores about as good as CA

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.

4027 HOH   ( 554 )  A      O  1.11  K  4 Ion-B NCS 2/2
4027 HOH   ( 720 )  A      O  0.87  K  4 NCS 3/3
4027 HOH   (1097 )  A      O  0.92  K  4 NCS 3/3
4027 HOH   (1130 )  A      O  1.02  K  4 NCS 3/3
4027 HOH   (1189 )  A      O  1.12  K  4 NCS 3/3
4027 HOH   (1670 )  A      O  0.91 NA  4 *1 NCS 3/3
4027 HOH   (1671 )  A      O  0.88  K  6 NCS 3/3
4027 HOH   (1843 )  A      O  0.98  K  4 NCS 3/3
4027 HOH   (1941 )  A      O  0.95  K  4
4028 HOH   ( 553 )  B      O  0.86  K  5 NCS 3/3
4028 HOH   ( 581 )  B      O  1.05  K  4 NCS 3/3
4028 HOH   ( 582 )  B      O  0.96  K  4 ION-B H2O-B NCS 2/2
4028 HOH   (1086 )  B      O  0.94 NA  4 *1 NCS 3/3
4028 HOH   (1480 )  B      O  0.99  K  4 NCS 3/3
4028 HOH   (1608 )  B      O  0.99  K  4 NCS 2/2
4028 HOH   (3181 )  B      O  1.03  K  4 NCS 3/3
4028 HOH   (3223 )  B      O  0.97  K  4
4028 HOH   (4646 )  B      O  0.88  K  4 Ion-B NCS 2/2
4029 HOH   ( 831 )  C      O  0.99  K  5 Ion-B
4029 HOH   ( 922 )  C      O  1.03  K  4 NCS 3/3
4029 HOH   (1183 )  C      O  1.09  K  4 NCS 3/3
4029 HOH   (1791 )  C      O  1.11  K  4 NCS 3/3
4029 HOH   (4579 )  C      O  0.86 NA  4 *1 Ion-B
4030 HOH   ( 615 )  D      O  1.12  K  4 H2O-B NCS 3/3
4030 HOH   ( 687 )  D      O  0.86  K  4 NCS 3/3
And so on for a total of 69 lines.

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.

 103 ASP   ( 109-)  A   H-bonding suggests Asn
 262 GLU   ( 268-)  A   H-bonding suggests Gln; but Alt-Rotamer
 541 GLU   (  53-)  B   H-bonding suggests Gln
 756 GLU   ( 268-)  B   H-bonding suggests Gln; but Alt-Rotamer
1250 GLU   ( 268-)  C   H-bonding suggests Gln; but Alt-Rotamer
1744 GLU   ( 268-)  D   H-bonding suggests Gln; but Alt-Rotamer
2024 GLU   (  53-)  E   H-bonding suggests Gln
2239 GLU   ( 268-)  E   H-bonding suggests Gln; but Alt-Rotamer
2733 GLU   ( 268-)  F   H-bonding suggests Gln; but Alt-Rotamer
2812 GLU   ( 347-)  F   H-bonding suggests Gln; Ligand-contact
3227 GLU   ( 268-)  G   H-bonding suggests Gln; but Alt-Rotamer
3499 GLU   (  46-)  H   H-bonding suggests Gln; but Alt-Rotamer; Ligand-contact
3506 GLU   (  53-)  H   H-bonding suggests Gln; but Alt-Rotamer
3721 GLU   ( 268-)  H   H-bonding suggests Gln; but Alt-Rotamer

Final summary

Note: Summary report for users of a structure

This is an overall summary of the quality of the structure as compared with current reliable structures. This summary is most useful for biologists seeking a good structure to use for modelling calculations.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators.


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.190
  2nd generation packing quality :  -1.075
  Ramachandran plot appearance   :   0.171
  chi-1/chi-2 rotamer normality  :   0.186
  Backbone conformation          :   0.060

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.559 (tight)
  Bond angles                    :   0.756
  Omega angle restraints         :   1.142
  Side chain planarity           :   0.873
  Improper dihedral distribution :   0.854
  B-factor distribution          :   0.616
  Inside/Outside distribution    :   1.046

Note: Summary report for depositors of a structure

This is an overall summary of the quality of the X-ray structure as compared with structures solved at similar resolutions. This summary can be useful for a crystallographer to see if the structure makes the best possible use of the data. Warning. This table works well for structures solved in the resolution range of the structures in the WHAT IF database, which is presently (summer 2008) mainly 1.1 - 1.3 Angstrom. The further the resolution of your file deviates from this range the more meaningless this table becomes.

The second part of the table mostly gives an impression of how well the model conforms to common refinement restraint values. The first part of the table shows a number of global quality indicators, which have been calibrated against structures of similar resolution.

Resolution found in PDB file : 1.50


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.5
  2nd generation packing quality :  -1.2
  Ramachandran plot appearance   :  -0.4
  chi-1/chi-2 rotamer normality  :  -0.3
  Backbone conformation          :  -0.4

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.559 (tight)
  Bond angles                    :   0.756
  Omega angle restraints         :   1.142
  Side chain planarity           :   0.873
  Improper dihedral distribution :   0.854
  B-factor distribution          :   0.616
  Inside/Outside distribution    :   1.046
==============

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.