WHAT IF Check report

This file was created 2012-01-29 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 pdb3a13.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 : 0.474
CA-only RMS fit for the two chains : 0.221

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 : 5.463
CA-only RMS fit for the two chains : 5.280

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 E

All-atom RMS fit for the two chains : 15.480
CA-only RMS fit for the two chains : 15.388

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 : 0.300
CA-only RMS fit for the two chains : 0.113

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

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 G

All-atom RMS fit for the two chains : 0.471
CA-only RMS fit for the two chains : 0.226

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 G

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.

4364 CAP   ( 446-)  A  -
4366 CAP   ( 446-)  B  -
4368 CAP   ( 446-)  C  -
4370 CAP   ( 446-)  D  -
4372 CAP   ( 446-)  E  -
4374 CAP   ( 446-)  F  -
4376 CAP   ( 446-)  G  -
4378 CAP   ( 446-)  H  -
4380 CAP   ( 446-)  I  -
4382 CAP   ( 446-)  J  -

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

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

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

Warning: Missing atoms

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

   2 ASP   (  10-)  A      CG
   2 ASP   (  10-)  A      OD1
   2 ASP   (  10-)  A      OD2
  10 GLU   (  18-)  A      CG
  10 GLU   (  18-)  A      CD
  10 GLU   (  18-)  A      OE1
  10 GLU   (  18-)  A      OE2
  46 THR   (  54-)  A      OG1
  46 THR   (  54-)  A      CG2
  48 THR   (  56-)  A      OG1
  48 THR   (  56-)  A      CG2
  49 THR   (  57-)  A      OG1
  49 THR   (  57-)  A      CG2
  50 LEU   (  58-)  A      CG
  50 LEU   (  58-)  A      CD1
  50 LEU   (  58-)  A      CD2
  51 TYR   (  59-)  A      CG
  51 TYR   (  59-)  A      CD1
  51 TYR   (  59-)  A      CD2
  51 TYR   (  59-)  A      CE1
  51 TYR   (  59-)  A      CE2
  51 TYR   (  59-)  A      CZ
  51 TYR   (  59-)  A      OH
 145 LYS   ( 153-)  A      CG
 145 LYS   ( 153-)  A      CD
And so on for a total of 530 lines.

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) : 95.000

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

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

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.

  58 ARG   (  66-)  A
 109 ARG   ( 117-)  A
 114 ARG   ( 122-)  A
 401 ARG   ( 409-)  A
 546 ARG   ( 117-)  B
 694 ARG   ( 265-)  B
 933 ARG   (  66-)  C
 984 ARG   ( 117-)  C
1275 ARG   ( 409-)  C
1369 ARG   (  66-)  D
1420 ARG   ( 117-)  D
1425 ARG   ( 122-)  D
1712 ARG   ( 409-)  D
1736 ARG   ( 433-)  D
1857 ARG   ( 117-)  E
1862 ARG   ( 122-)  E
2005 ARG   ( 265-)  E
2073 ARG   ( 338-)  E
2144 ARG   ( 409-)  E
2294 ARG   ( 122-)  F
2510 ARG   ( 338-)  F
2605 ARG   ( 433-)  F
2675 ARG   (  66-)  G
3113 ARG   (  66-)  H
3169 ARG   ( 122-)  H
3550 ARG   (  66-)  I
3749 ARG   ( 265-)  I
3819 ARG   ( 335-)  I
3893 ARG   ( 409-)  I
3917 ARG   ( 433-)  I
4043 ARG   ( 122-)  J
4186 ARG   ( 265-)  J
4256 ARG   ( 338-)  J
4327 ARG   ( 409-)  J
4351 ARG   ( 433-)  J

Warning: Tyrosine convention problem

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

   4 TYR   (  12-)  A
  83 TYR   (  91-)  A
 441 TYR   (  12-)  B
 504 TYR   (  75-)  B
 520 TYR   (  91-)  B
 879 TYR   (  12-)  C
 904 TYR   (  37-)  C
 926 TYR   (  59-)  C
 929 TYR   (  62-)  C
 958 TYR   (  91-)  C
1378 TYR   (  75-)  D
1394 TYR   (  91-)  D
1502 TYR   ( 199-)  D
1751 TYR   (  11-)  E
1752 TYR   (  12-)  E
1802 TYR   (  62-)  E
1831 TYR   (  91-)  E
2077 TYR   ( 342-)  E
2159 TYR   ( 424-)  E
2184 TYR   (  12-)  F
2234 TYR   (  62-)  F
2247 TYR   (  75-)  F
2263 TYR   (  91-)  F
2700 TYR   (  91-)  G
3058 TYR   (  11-)  H
3059 TYR   (  12-)  H
3084 TYR   (  37-)  H
3109 TYR   (  62-)  H
3138 TYR   (  91-)  H
3575 TYR   (  91-)  I
3933 TYR   (  12-)  J
3983 TYR   (  62-)  J
4012 TYR   (  91-)  J
4260 TYR   ( 342-)  J
4342 TYR   ( 424-)  J

Warning: Phenylalanine convention problem

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

  69 PHE   (  77-)  A
 128 PHE   ( 136-)  A
 133 PHE   ( 141-)  A
 194 PHE   ( 202-)  A
 291 PHE   ( 299-)  A
 506 PHE   (  77-)  B
 570 PHE   ( 141-)  B
 728 PHE   ( 299-)  B
 944 PHE   (  77-)  C
1008 PHE   ( 141-)  C
1380 PHE   (  77-)  D
1444 PHE   ( 141-)  D
1659 PHE   ( 356-)  D
1817 PHE   (  77-)  E
1881 PHE   ( 141-)  E
1942 PHE   ( 202-)  E
2249 PHE   (  77-)  F
2308 PHE   ( 136-)  F
2313 PHE   ( 141-)  F
2374 PHE   ( 202-)  F
2686 PHE   (  77-)  G
2750 PHE   ( 141-)  G
2908 PHE   ( 299-)  G
2965 PHE   ( 356-)  G
3124 PHE   (  77-)  H
3188 PHE   ( 141-)  H
3249 PHE   ( 202-)  H
3403 PHE   ( 356-)  H
3561 PHE   (  77-)  I
3625 PHE   ( 141-)  I
3783 PHE   ( 299-)  I
3840 PHE   ( 356-)  I
3998 PHE   (  77-)  J
4057 PHE   ( 136-)  J
4062 PHE   ( 141-)  J
4274 PHE   ( 356-)  J

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.

 320 ASP   ( 328-)  A
1058 ASP   ( 191-)  C
1140 ASP   ( 273-)  C
2248 ASP   (  76-)  F
2483 ASP   ( 311-)  F
2500 ASP   ( 328-)  F
2685 ASP   (  76-)  G
3116 ASP   (  69-)  H
3201 ASP   ( 154-)  H
3812 ASP   ( 328-)  I
3931 ASP   (  10-)  J
4112 ASP   ( 191-)  J
4246 ASP   ( 328-)  J

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.

 136 GLU   ( 144-)  A
 316 GLU   ( 324-)  A
 415 GLU   ( 423-)  A
 447 GLU   (  18-)  B
 492 GLU   (  63-)  B
 527 GLU   (  98-)  B
 632 GLU   ( 203-)  B
 633 GLU   ( 204-)  B
1071 GLU   ( 204-)  C
1089 GLU   ( 222-)  C
1191 GLU   ( 324-)  C
1193 GLU   ( 326-)  C
1368 GLU   (  65-)  D
1506 GLU   ( 203-)  D
1507 GLU   ( 204-)  D
1510 GLU   ( 207-)  D
1803 GLU   (  63-)  E
1914 GLU   ( 174-)  E
1944 GLU   ( 204-)  E
1947 GLU   ( 207-)  E
1962 GLU   ( 222-)  E
2081 GLU   ( 346-)  E
2221 GLU   (  49-)  F
2707 GLU   (  98-)  G
2816 GLU   ( 207-)  G
2831 GLU   ( 222-)  G
2845 GLU   ( 236-)  G
3032 GLU   ( 423-)  G
3039 GLU   ( 430-)  G
3065 GLU   (  18-)  H
3082 GLU   (  35-)  H
3112 GLU   (  65-)  H
3145 GLU   (  98-)  H
3254 GLU   ( 207-)  H
3505 GLU   (  18-)  I
3549 GLU   (  65-)  I
3582 GLU   (  98-)  I
3688 GLU   ( 204-)  I
3691 GLU   ( 207-)  I
3939 GLU   (  18-)  J
3956 GLU   (  35-)  J
3984 GLU   (  63-)  J
3986 GLU   (  65-)  J
4095 GLU   ( 174-)  J
4128 GLU   ( 207-)  J
4143 GLU   ( 222-)  J
4157 GLU   ( 236-)  J
4348 GLU   ( 430-)  J
4354 GLU   ( 436-)  J

Warning: Heavy atom naming convention problem

The atoms listed in the table below have nonstandard names in the input file. (Be aware that we sometimes consider an asterix and an apostrophe identical, and thus do not warn for the use of asterixes. Please be aware that the PDB wants us to deliberately make some nomenclature errors; especially in non-canonical amino acids.

 181 KCX   ( 189-)  A      CH     CX
 181 KCX   ( 189-)  A      OX1    OQ1
 181 KCX   ( 189-)  A      OX2    OQ2
 618 KCX   ( 189-)  B      CH     CX
 618 KCX   ( 189-)  B      OX1    OQ1
 618 KCX   ( 189-)  B      OX2    OQ2
1056 KCX   ( 189-)  C      CH     CX
1056 KCX   ( 189-)  C      OX1    OQ1
1056 KCX   ( 189-)  C      OX2    OQ2
1492 KCX   ( 189-)  D      CH     CX
1492 KCX   ( 189-)  D      OX1    OQ1
1492 KCX   ( 189-)  D      OX2    OQ2
1929 KCX   ( 189-)  E      CH     CX
1929 KCX   ( 189-)  E      OX1    OQ1
1929 KCX   ( 189-)  E      OX2    OQ2
2361 KCX   ( 189-)  F      CH     CX
2361 KCX   ( 189-)  F      OX1    OQ1
2361 KCX   ( 189-)  F      OX2    OQ2
2798 KCX   ( 189-)  G      CH     CX
2798 KCX   ( 189-)  G      OX1    OQ1
2798 KCX   ( 189-)  G      OX2    OQ2
3236 KCX   ( 189-)  H      CH     CX
3236 KCX   ( 189-)  H      OX1    OQ1
3236 KCX   ( 189-)  H      OX2    OQ2
3673 KCX   ( 189-)  I      CH     CX
3673 KCX   ( 189-)  I      OX1    OQ1
3673 KCX   ( 189-)  I      OX2    OQ2
4110 KCX   ( 189-)  J      CH     CX
4110 KCX   ( 189-)  J      OX1    OQ1
4110 KCX   ( 189-)  J      OX2    OQ2

Geometric checks

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.999059  0.000179 -0.000064|
 |  0.000179  0.998886  0.000068|
 | -0.000064  0.000068  0.998661|
Proposed new scale matrix

 |  0.005763 -0.000001  0.000000|
 |  0.000000  0.004052  0.000000|
 |  0.000000  0.000000  0.006908|
With corresponding cell

    A    = 173.508  B   = 246.821  C    = 144.755
    Alpha=  90.002  Beta=  90.002  Gamma=  89.991

The CRYST1 cell dimensions

    A    = 173.678  B   = 247.090  C    = 144.940
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 187.330
(Under-)estimated Z-score: 10.087

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.

  58 ARG   (  66-)  A
 109 ARG   ( 117-)  A
 114 ARG   ( 122-)  A
 136 GLU   ( 144-)  A
 316 GLU   ( 324-)  A
 320 ASP   ( 328-)  A
 401 ARG   ( 409-)  A
 415 GLU   ( 423-)  A
 447 GLU   (  18-)  B
 492 GLU   (  63-)  B
 527 GLU   (  98-)  B
 546 ARG   ( 117-)  B
 632 GLU   ( 203-)  B
 633 GLU   ( 204-)  B
 694 ARG   ( 265-)  B
 933 ARG   (  66-)  C
 984 ARG   ( 117-)  C
1058 ASP   ( 191-)  C
1071 GLU   ( 204-)  C
1089 GLU   ( 222-)  C
1140 ASP   ( 273-)  C
1191 GLU   ( 324-)  C
1193 GLU   ( 326-)  C
1275 ARG   ( 409-)  C
1368 GLU   (  65-)  D
And so on for a total of 97 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.

3101 THR   (  54-)  H    -3.1
2573 PRO   ( 401-)  F    -3.1
 921 THR   (  54-)  C    -3.0
1528 THR   ( 225-)  D    -3.0
 393 PRO   ( 401-)  A    -3.0
1965 THR   ( 225-)  E    -3.0
  52 PRO   (  60-)  A    -2.9
3975 THR   (  54-)  J    -2.9
3709 THR   ( 225-)  I    -2.9
1092 THR   ( 225-)  C    -2.9
1794 THR   (  54-)  E    -2.8
4146 THR   ( 225-)  J    -2.8
 654 THR   ( 225-)  B    -2.7
3272 THR   ( 225-)  H    -2.7
2397 THR   ( 225-)  F    -2.7
2834 THR   ( 225-)  G    -2.7
2232 PRO   (  60-)  F    -2.7
 217 THR   ( 225-)  A    -2.7
3718 LEU   ( 234-)  I    -2.6
 355 PHE   ( 363-)  A    -2.6
1537 LEU   ( 234-)  D    -2.5
2535 PHE   ( 363-)  F    -2.5
 792 PHE   ( 363-)  B    -2.5
2098 PHE   ( 363-)  E    -2.5
2298 LEU   ( 126-)  F    -2.5
And so on for a total of 92 lines.

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.

  16 ASP   (  24-)  A  omega poor
  43 SER   (  51-)  A  Poor phi/psi
  44 THR   (  52-)  A  omega poor
  67 TYR   (  75-)  A  Poor phi/psi
 155 LYS   ( 163-)  A  PRO omega poor
 179 TYR   ( 187-)  A  omega poor
 187 THR   ( 195-)  A  Poor phi/psi
 224 ALA   ( 232-)  A  Poor phi/psi
 241 LEU   ( 249-)  A  omega poor
 276 MET   ( 284-)  A  Poor phi/psi
 301 GLY   ( 309-)  A  Poor phi/psi
 349 TYR   ( 357-)  A  Poor phi/psi
 410 GLY   ( 418-)  A  Poor phi/psi
 453 ASP   (  24-)  B  omega poor
 458 PHE   (  29-)  B  omega poor
 480 SER   (  51-)  B  Poor phi/psi
 481 THR   (  52-)  B  omega poor
 514 TRP   (  85-)  B  omega poor
 580 GLU   ( 151-)  B  Poor phi/psi
 581 ILE   ( 152-)  B  omega poor
 592 LYS   ( 163-)  B  PRO omega poor
 616 TYR   ( 187-)  B  omega poor
 624 THR   ( 195-)  B  Poor phi/psi
 661 ALA   ( 232-)  B  Poor phi/psi
 713 MET   ( 284-)  B  Poor phi/psi
And so on for a total of 147 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.

4095 GLU   ( 174-)  J    0.36

Warning: Unusual backbone conformations

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

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

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

   6 ASP   (  14-)  A      0
  15 ARG   (  23-)  A      0
  27 GLU   (  35-)  A      0
  42 SER   (  50-)  A      0
  43 SER   (  51-)  A      0
  44 THR   (  52-)  A      0
  47 TRP   (  55-)  A      0
  51 TYR   (  59-)  A      0
  52 PRO   (  60-)  A      0
  53 TRP   (  61-)  A      0
  54 TYR   (  62-)  A      0
  67 TYR   (  75-)  A      0
  68 ASP   (  76-)  A      0
  72 MET   (  80-)  A      0
  74 ASP   (  82-)  A      0
  76 SER   (  84-)  A      0
  85 PHE   (  93-)  A      0
  86 HIS   (  94-)  A      0
  90 GLU   (  98-)  A      0
  91 ALA   (  99-)  A      0
  92 ASN   ( 100-)  A      0
 100 ILE   ( 108-)  A      0
 101 ALA   ( 109-)  A      0
 103 ASN   ( 111-)  A      0
 107 MET   ( 115-)  A      0
And so on for a total of 1552 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!

2497 GLY   ( 325-)  F   2.64   19
2934 GLY   ( 325-)  G   2.38   10
1628 GLY   ( 325-)  D   2.27   12
1192 GLY   ( 325-)  C   2.26   15
3372 GLY   ( 325-)  H   2.24   14
1696 GLY   ( 393-)  D   1.89   80
3877 GLY   ( 393-)  I   1.81   80
 822 GLY   ( 393-)  B   1.70   80
3001 GLY   ( 392-)  G   1.66   14
1299 ARG   ( 433-)  C   1.64   20
1260 GLY   ( 393-)  C   1.61   80
3440 GLY   ( 393-)  H   1.55   80
1910 PRO   ( 170-)  E   1.55   10
3002 GLY   ( 393-)  G   1.55   80
2128 GLY   ( 393-)  E   1.51   80

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]

1595 PRO   ( 292-)  D    0.15 LOW
3776 PRO   ( 292-)  I    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].

  52 PRO   (  60-)  A   -23.0 half-chair C-alpha/N (-18 degrees)
 154 PRO   ( 162-)  A   107.2 envelop C-beta (108 degrees)
 393 PRO   ( 401-)  A   125.9 half-chair C-beta/C-alpha (126 degrees)
 435 PRO   ( 443-)  A    51.3 half-chair C-delta/C-gamma (54 degrees)
 849 PRO   ( 420-)  B   108.1 envelop C-beta (108 degrees)
 996 PRO   ( 129-)  C  -112.7 envelop C-gamma (-108 degrees)
1244 PRO   ( 377-)  C    44.7 envelop C-delta (36 degrees)
1286 PRO   ( 420-)  C   122.8 half-chair C-beta/C-alpha (126 degrees)
1363 PRO   (  60-)  D   177.9 envelop N (180 degrees)
1704 PRO   ( 401-)  D   107.0 envelop C-beta (108 degrees)
1723 PRO   ( 420-)  D   101.8 envelop C-beta (108 degrees)
1800 PRO   (  60-)  E    48.6 half-chair C-delta/C-gamma (54 degrees)
1842 PRO   ( 102-)  E   103.7 envelop C-beta (108 degrees)
2112 PRO   ( 377-)  E  -113.2 envelop C-gamma (-108 degrees)
2155 PRO   ( 420-)  E   102.9 envelop C-beta (108 degrees)
2232 PRO   (  60-)  F   -42.7 envelop C-alpha (-36 degrees)
2464 PRO   ( 292-)  F    47.1 half-chair C-delta/C-gamma (54 degrees)
2570 PRO   ( 398-)  F  -126.3 half-chair C-delta/C-gamma (-126 degrees)
2573 PRO   ( 401-)  F   137.5 envelop C-alpha (144 degrees)
2986 PRO   ( 377-)  G  -114.3 envelop C-gamma (-108 degrees)
3029 PRO   ( 420-)  G   121.4 half-chair C-beta/C-alpha (126 degrees)
3203 PRO   ( 156-)  H  -121.9 half-chair C-delta/C-gamma (-126 degrees)
3445 PRO   ( 398-)  H  -117.9 half-chair C-delta/C-gamma (-126 degrees)
3448 PRO   ( 401-)  H   102.9 envelop C-beta (108 degrees)
3467 PRO   ( 420-)  H   102.0 envelop C-beta (108 degrees)
3544 PRO   (  60-)  I   166.4 half-chair C-alpha/N (162 degrees)
3885 PRO   ( 401-)  I   107.9 envelop C-beta (108 degrees)
3981 PRO   (  60-)  J   -64.9 envelop C-beta (-72 degrees)
4295 PRO   ( 377-)  J   103.5 envelop C-beta (108 degrees)
4338 PRO   ( 420-)  J   105.3 envelop C-beta (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.

1458 ARG   ( 155-)  D      CZ  <-> 1712 ARG   ( 409-)  D      NH1    0.67    2.43  INTRA BF
 800 HIS   ( 371-)  B      ND1 <->  802 GLY   ( 373-)  B      N      0.67    2.33  INTRA BF
 800 HIS   ( 371-)  B      CE1 <->  802 GLY   ( 373-)  B      CA     0.59    2.61  INTRA BF
3026 GLN   ( 417-)  G      C   <-> 4389 HOH   ( 564 )  G      O      0.57    2.23  INTRA BF
1238 HIS   ( 371-)  C      ND1 <-> 1240 GLY   ( 373-)  C      N      0.56    2.44  INTRA BF
4358 HIS   ( 440-)  J      CE1 <-> 4392 HOH   ( 694 )  J      O      0.55    2.25  INTRA BF
3418 HIS   ( 371-)  H      ND1 <-> 3420 GLY   ( 373-)  H      N      0.54    2.46  INTRA BF
3894 GLN   ( 410-)  I      NE2 <-> 3914 GLU   ( 430-)  I      CG     0.54    2.56  INTRA BF
 350 SER   ( 358-)  A      CB  <-> 4383 HOH   ( 678 )  A      O      0.49    2.31  INTRA BF
4324 ARG   ( 406-)  J      NH2 <-> 4392 HOH   ( 693 )  J      O      0.48    2.22  INTRA BF
 848 ILE   ( 419-)  B      CG2 <->  852 GLU   ( 423-)  B      CG     0.48    2.72  INTRA BF
 820 GLY   ( 391-)  B      O   <->  823 THR   ( 394-)  B      N      0.48    2.22  INTRA
2900 ASN   ( 291-)  G      ND2 <-> 4389 HOH   ( 587 )  G      O      0.46    2.24  INTRA BL
1102 LEU   ( 235-)  C      CD1 <-> 4385 HOH   ( 666 )  C      O      0.45    2.35  INTRA
1468 LYS   ( 165-)  D      CB  <-> 1494 ASP   ( 191-)  D      OD2    0.44    2.36  INTRA BL
3006 HIS   ( 397-)  G      ND1 <-> 3007 PRO   ( 398-)  G      CD     0.44    2.66  INTRA BF
3912 HIS   ( 428-)  I      NE2 <-> 4391 HOH   ( 531 )  I      O      0.44    2.26  INTRA BF
2774 LYS   ( 165-)  G      NZ  <-> 2800 ASP   ( 191-)  G      OD2    0.44    2.26  INTRA BL
1731 HIS   ( 428-)  D      CE1 <-> 4386 HOH   ( 583 )  D      O      0.43    2.37  INTRA BF
1450 ARG   ( 147-)  D      NH1 <-> 1458 ARG   ( 155-)  D      O      0.43    2.27  INTRA
4309 GLY   ( 391-)  J      O   <-> 4313 LEU   ( 395-)  J      CD1    0.42    2.38  INTRA BF
2175 HIS   ( 440-)  E      CD2 <-> 4387 HOH   ( 691 )  E      O      0.42    2.38  INTRA BF
 839 GLN   ( 410-)  B      CG  <-> 4384 HOH   ( 628 )  B      O      0.42    2.38  INTRA BF
 848 ILE   ( 419-)  B      CG2 <->  852 GLU   ( 423-)  B      CD     0.42    2.78  INTRA BF
3282 LEU   ( 235-)  H      CD1 <-> 4390 HOH   ( 602 )  H      O      0.42    2.38  INTRA
And so on for a total of 898 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

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

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.

2932 LEU   ( 323-)  G      -7.07
 752 LEU   ( 323-)  B      -7.04
2495 LEU   ( 323-)  F      -7.01
3370 LEU   ( 323-)  H      -7.00
1190 LEU   ( 323-)  C      -7.00
2668 TYR   (  59-)  G      -6.99
 315 LEU   ( 323-)  A      -6.88
1626 LEU   ( 323-)  D      -6.82
3807 LEU   ( 323-)  I      -6.78
 926 TYR   (  59-)  C      -6.74
2030 ARG   ( 290-)  E      -6.70
1157 ARG   ( 290-)  C      -6.70
2462 ARG   ( 290-)  F      -6.69
4211 ARG   ( 290-)  J      -6.59
3337 ARG   ( 290-)  H      -6.54
2899 ARG   ( 290-)  G      -6.46
 282 ARG   ( 290-)  A      -6.46
 719 ARG   ( 290-)  B      -6.45
4358 HIS   ( 440-)  J      -6.43
1593 ARG   ( 290-)  D      -6.39
3774 ARG   ( 290-)  I      -6.37
3105 LEU   (  58-)  H      -6.24
4084 LYS   ( 163-)  J      -6.19
1903 LYS   ( 163-)  E      -6.18
  47 TRP   (  55-)  A      -5.98
And so on for a total of 98 lines.

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.

 314 LYS   ( 322-)  A       316 - GLU    324- ( A)         -5.85
 751 LYS   ( 322-)  B       753 - GLU    324- ( B)         -5.94
 924 THR   (  57-)  C       926 - TYR     59- ( C)         -5.50
1189 LYS   ( 322-)  C      1191 - GLU    324- ( C)         -5.98
1625 LYS   ( 322-)  D      1627 - GLU    324- ( D)         -5.87
2172 LYS   ( 437-)  E      2175 - HIS    440- ( E)         -4.75
2494 LYS   ( 322-)  F      2496 - GLU    324- ( F)         -5.86
2931 LYS   ( 322-)  G      2933 - GLU    324- ( G)         -5.92
3369 LYS   ( 322-)  H      3371 - GLU    324- ( H)         -6.11
3806 LYS   ( 322-)  I      3808 - GLU    324- ( I)         -5.82
3976 TRP   (  55-)  J      3978 - THR     57- ( J)         -4.76
4355 LYS   ( 437-)  J      4358 - HIS    440- ( J)         -5.12

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

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: I

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: J

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.

3106 TYR   (  59-)  H   -3.32
 488 TYR   (  59-)  B   -3.31
  50 LEU   (  58-)  A   -3.14
1799 TYR   (  59-)  E   -3.12
2231 TYR   (  59-)  F   -3.10
  51 TYR   (  59-)  A   -3.06
3980 TYR   (  59-)  J   -3.06
4241 LYS   ( 322-)  J   -2.93
1153 ALA   ( 286-)  C   -2.88
2667 LEU   (  58-)  G   -2.87
 487 LEU   (  58-)  B   -2.84
1798 LEU   (  58-)  E   -2.73
3979 LEU   (  58-)  J   -2.71
3055 ILE   (   8-)  H   -2.56
2058 LYS   ( 322-)  E   -2.56
2161 LYS   ( 426-)  E   -2.55
 875 ILE   (   8-)  C   -2.55
1726 GLU   ( 423-)  D   -2.51

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

2057 THR   ( 317-)  E     - 2060 GLU   ( 324-)  E        -1.71
4240 GLY   ( 321-)  J     - 4243 GLU   ( 324-)  J        -1.81

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

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

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.

4384 HOH   ( 673 )  B      O     80.74  -13.51  -12.32
4384 HOH   ( 674 )  B      O     81.47  -15.44  -14.06
4384 HOH   ( 675 )  B      O     87.65  -16.11  -15.04
4385 HOH   ( 625 )  C      O     91.70   27.11    0.77
4385 HOH   ( 647 )  C      O     85.23   52.56   44.23
4386 HOH   ( 646 )  D      O     84.74    5.01   83.35
4386 HOH   ( 693 )  D      O     87.67   13.59   48.31
4387 HOH   ( 607 )  E      O     99.41  -21.40   76.46
4388 HOH   ( 671 )  F      O     94.26   64.25  -11.55
4389 HOH   ( 676 )  G      O      3.66   -1.54   -5.84
4389 HOH   ( 692 )  G      O      5.98   13.59   20.48
4389 HOH   ( 693 )  G      O      5.44   15.49   18.48
4389 HOH   ( 694 )  G      O      3.35   18.45   18.58
4389 HOH   ( 701 )  G      O      3.03   15.55   18.02
4391 HOH   ( 553 )  I      O     -5.15  -30.43   77.24
4391 HOH   ( 687 )  I      O      2.15   -5.20  116.09
4391 HOH   ( 697 )  I      O     18.45  -19.20  110.61
4392 HOH   ( 600 )  J      O      1.13   25.13   78.19
4392 HOH   ( 624 )  J      O     -0.63   29.11   83.33
4392 HOH   ( 689 )  J      O      1.97   15.36   79.37

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.

4385 HOH   ( 577 )  C      O
4386 HOH   ( 645 )  D      O
4387 HOH   ( 691 )  E      O
4388 HOH   ( 577 )  F      O
4392 HOH   ( 587 )  J      O
4392 HOH   ( 608 )  J      O

Error: HIS, ASN, GLN side chain flips

Listed here are Histidine, Asparagine or Glutamine residues for which the orientation determined from hydrogen bonding analysis are different from the assignment given in the input. Either they could form energetically more favourable hydrogen bonds if the terminal group was rotated by 180 degrees, or there is no assignment in the input file (atom type 'A') but an assignment could be made. Be aware, though, that if the topology could not be determined for one or more ligands, then this option will make errors.

 304 GLN   ( 312-)  A
 306 HIS   ( 314-)  A
 333 HIS   ( 341-)  A
 343 HIS   ( 351-)  A
 346 GLN   ( 354-)  A
 668 GLN   ( 239-)  B
 708 HIS   ( 279-)  B
 743 HIS   ( 314-)  B
 783 GLN   ( 354-)  B
1060 ASN   ( 193-)  C
1181 HIS   ( 314-)  C
1221 GLN   ( 354-)  C
1617 HIS   ( 314-)  D
1654 HIS   ( 351-)  D
1657 GLN   ( 354-)  D
1731 HIS   ( 428-)  D
2089 GLN   ( 354-)  E
2145 GLN   ( 410-)  E
2523 HIS   ( 351-)  F
2526 GLN   ( 354-)  F
2848 GLN   ( 239-)  G
2888 HIS   ( 279-)  G
2923 HIS   ( 314-)  G
2960 HIS   ( 351-)  G
2963 GLN   ( 354-)  G
3361 HIS   ( 314-)  H
3401 GLN   ( 354-)  H
3436 GLN   ( 389-)  H
3457 GLN   ( 410-)  H
3796 GLN   ( 312-)  I
3835 HIS   ( 351-)  I
3838 GLN   ( 354-)  I
4235 HIS   ( 314-)  J
4272 GLN   ( 354-)  J

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.

  47 TRP   (  55-)  A      NE1
  48 THR   (  56-)  A      N
  53 TRP   (  61-)  A      N
  58 ARG   (  66-)  A      NH2
  77 TRP   (  85-)  A      NE1
 103 ASN   ( 111-)  A      ND2
 113 LEU   ( 121-)  A      N
 155 LYS   ( 163-)  A      N
 158 VAL   ( 166-)  A      N
 191 TYR   ( 199-)  A      N
 192 ASN   ( 200-)  A      ND2
 197 ARG   ( 205-)  A      NE
 256 LEU   ( 264-)  A      N
 271 HIS   ( 279-)  A      NE2
 273 HIS   ( 281-)  A      NE2
 274 ARG   ( 282-)  A      NE
 304 GLN   ( 312-)  A      NE2
 314 LYS   ( 322-)  A      NZ
 359 SER   ( 367-)  A      OG
 361 GLY   ( 369-)  A      N
 370 VAL   ( 378-)  A      N
 381 GLN   ( 389-)  A      NE2
 383 GLY   ( 391-)  A      N
 384 GLY   ( 392-)  A      N
 418 LYS   ( 426-)  A      N
And so on for a total of 276 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.

 247 ASP   ( 255-)  A      OD1
 478 GLU   (  49-)  B      OE1
 684 ASP   ( 255-)  B      OD1
 684 ASP   ( 255-)  B      OD2
1122 ASP   ( 255-)  C      OD1
1146 HIS   ( 279-)  C      NE2
1558 ASP   ( 255-)  D      OD1
1582 HIS   ( 279-)  D      NE2
1636 ASN   ( 333-)  D      OD1
1933 ASN   ( 193-)  E      OD1
1995 ASP   ( 255-)  E      OD1
1995 ASP   ( 255-)  E      OD2
2054 HIS   ( 314-)  E      ND1
2221 GLU   (  49-)  F      OE1
2427 ASP   ( 255-)  F      OD1
2427 ASP   ( 255-)  F      OD2
2486 HIS   ( 314-)  F      ND1
2658 GLU   (  49-)  G      OE1
2864 ASP   ( 255-)  G      OD1
2864 ASP   ( 255-)  G      OD2
2888 HIS   ( 279-)  G      NE2
3302 ASP   ( 255-)  H      OD1
3302 ASP   ( 255-)  H      OD2
3326 HIS   ( 279-)  H      NE2
3739 ASP   ( 255-)  I      OD1
4114 ASN   ( 193-)  J      OD1
4176 ASP   ( 255-)  J      OD1
4176 ASP   ( 255-)  J      OD2
4200 HIS   ( 279-)  J      NE2

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+.

4365  MG   ( 445-)  B     0.71   1.32 Scores about as good as CA *1 and *2
4367  MG   ( 445-)  C     0.61   1.03 Is perhaps CA *1 and *2
4371  CA   ( 445-)  E     0.86   1.10 Scores about as good as NA
4377  MG   ( 445-)  H     0.54   1.09 Is perhaps NA
4381  CA   ( 445-)  J     0.86   1.10 Scores about as good as NA

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.

4383 HOH   ( 526 )  A      O  0.99  K  5
4383 HOH   ( 659 )  A      O  1.12  K  4 Ion-B NCS 1/1
4384 HOH   ( 566 )  B      O  0.97  K  4
4385 HOH   ( 570 )  C      O  1.12  K  4 NCS 3/3
4385 HOH   ( 625 )  C      O  0.94  K  5
4386 HOH   ( 548 )  D      O  0.95  K  5 NCS 3/3
4386 HOH   ( 595 )  D      O  1.04 NA  4 (or CA *1 and *2)
4387 HOH   ( 665 )  E      O  1.12  K  5 Ion-B
4387 HOH   ( 673 )  E      O  0.97  K  4
4388 HOH   ( 527 )  F      O  1.00  K  5 NCS 4/4
4389 HOH   ( 539 )  G      O  1.02  K  5 NCS 2/2
4389 HOH   ( 556 )  G      O  0.92  K  4 NCS 4/4
4390 HOH   ( 530 )  H      O  0.97  K  4 NCS 6/6
4391 HOH   ( 677 )  I      O  1.08  K  4 NCS 4/4
4391 HOH   ( 705 )  I      O  0.87  K  4 Ion-B NCS 2/2
4392 HOH   ( 688 )  J      O  0.86  K  4 H2O-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.

 247 ASP   ( 255-)  A   H-bonding suggests Asn; but Alt-Rotamer
 405 ASP   ( 413-)  A   H-bonding suggests Asn
 684 ASP   ( 255-)  B   H-bonding suggests Asn; but Alt-Rotamer
 842 ASP   ( 413-)  B   H-bonding suggests Asn; but Alt-Rotamer
1122 ASP   ( 255-)  C   H-bonding suggests Asn; but Alt-Rotamer
1316 ASP   (  10-)  D   H-bonding suggests Asn; but Alt-Rotamer
1457 ASP   ( 154-)  D   H-bonding suggests Asn; but Alt-Rotamer
1558 ASP   ( 255-)  D   H-bonding suggests Asn; but Alt-Rotamer
1716 ASP   ( 413-)  D   H-bonding suggests Asn; but Alt-Rotamer
1995 ASP   ( 255-)  E   H-bonding suggests Asn; but Alt-Rotamer
2148 ASP   ( 413-)  E   H-bonding suggests Asn
2427 ASP   ( 255-)  F   H-bonding suggests Asn; but Alt-Rotamer
2864 ASP   ( 255-)  G   H-bonding suggests Asn; but Alt-Rotamer
3022 ASP   ( 413-)  G   H-bonding suggests Asn
3302 ASP   ( 255-)  H   H-bonding suggests Asn; but Alt-Rotamer
3460 ASP   ( 413-)  H   H-bonding suggests Asn
3497 ASP   (  10-)  I   H-bonding suggests Asn; but Alt-Rotamer
3739 ASP   ( 255-)  I   H-bonding suggests Asn; but Alt-Rotamer
3897 ASP   ( 413-)  I   H-bonding suggests Asn
4176 ASP   ( 255-)  J   H-bonding suggests Asn; but Alt-Rotamer
4331 ASP   ( 413-)  J   H-bonding suggests Asn; 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 :  -0.556
  2nd generation packing quality :  -1.099
  Ramachandran plot appearance   :  -1.446
  chi-1/chi-2 rotamer normality  :  -1.543
  Backbone conformation          :  -0.184

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.325 (tight)
  Bond angles                    :   0.549 (tight)
  Omega angle restraints         :   0.970
  Side chain planarity           :   0.299 (tight)
  Improper dihedral distribution :   0.527
  B-factor distribution          :   0.360
  Inside/Outside distribution    :   1.032

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 : 2.34


Structure Z-scores, positive is better than average:

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

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.325 (tight)
  Bond angles                    :   0.549 (tight)
  Omega angle restraints         :   0.970
  Side chain planarity           :   0.299 (tight)
  Improper dihedral distribution :   0.527
  B-factor distribution          :   0.360
  Inside/Outside distribution    :   1.032
==============

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

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Bond lengths and angles, DNA/RNA
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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,
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      protein structures
    PROTEINS, 26, 363--376 (1996).

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.