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 pdb3p9q.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 : 0.530
CA-only RMS fit for the two chains : 0.304

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 : 0.556
CA-only RMS fit for the two chains : 0.342

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 : 0.547
CA-only RMS fit for the two chains : 0.348

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and C

All-atom RMS fit for the two chains : 0.455
CA-only RMS fit for the two chains : 0.172

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: B and C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: B and D

All-atom RMS fit for the two chains : 0.476
CA-only RMS fit for the two chains : 0.190

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: B and D

Warning: Ligands for which topology could not be determined

The ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms, or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

2909 HDD   ( 760-)  A  -         Atom types
2911 HDD   ( 760-)  B  -         Atom types
2913 HDD   ( 760-)  C  -         Atom types
2915 HDD   ( 760-)  D  -         Atom types

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.

2027 VAL   ( 602-)  C  -

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.

2027 VAL   ( 602-)  C  -
REMOVED.LIS
BUG. File already open at 77

Non-validating, descriptive output paragraph

Note: Ramachandran plot

In this Ramachandran plot x-signs represent glycines, squares represent prolines, and plus-signs represent the other residues. If too many plus- signs fall outside the contoured areas then the molecule is poorly refined (or worse). Proline can only occur in the narrow region around phi=-60 that also falls within the other contour islands.

In a colour picture, the residues that are part of a helix are shown in blue, strand residues in red. Preferred regions for helical residues are drawn in blue, for strand residues in red, and for all other residues in green. A full explanation of the Ramachandran plot together with a series of examples can be found at the WHAT_CHECK website.

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

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

Warning: Artificial side chains detected

At least two residues (listed in the table below) were detected with chi-1 equal to 0.00 or 180.00. Since this is highly unlikely to occur accidentally, the listed residues have probably not been refined.

1073 VAL   ( 374-)  B
1220 ARG   ( 521-)  B

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.

 247 CYS   ( 274-)  A    0.50
 494 ARG   ( 521-)  A    0.50
 973 CYS   ( 274-)  B    0.50
1068 ARG   ( 369-)  B    0.50
1699 CYS   ( 274-)  C    0.50
1946 ARG   ( 521-)  C    0.50
2425 CYS   ( 274-)  D    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: 4

Crystal temperature (K) :100.000

Warning: More than 2 percent of buried atoms has low B-factor

For protein structures determined at room temperature, no more than about 1 percent of the B factors of buried atoms is below 5.0.

Percentage of buried atoms with B less than 5 : 4.16

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Nomenclature related problems

Warning: Arginine nomenclature problem

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

 251 ARG   ( 278-)  A
 286 ARG   ( 313-)  A
 342 ARG   ( 369-)  A
 395 ARG   ( 422-)  A
 509 ARG   ( 536-)  A
 585 ARG   ( 612-)  A
 609 ARG   ( 636-)  A
 810 ARG   ( 111-)  B
 864 ARG   ( 165-)  B
 882 ARG   ( 183-)  B
 959 ARG   ( 260-)  B
1076 ARG   ( 377-)  B
1170 ARG   ( 471-)  B
1208 ARG   ( 509-)  B
1220 ARG   ( 521-)  B
1486 ARG   (  61-)  C
1536 ARG   ( 111-)  C
1608 ARG   ( 183-)  C
1703 ARG   ( 278-)  C
1847 ARG   ( 422-)  C
1896 ARG   ( 471-)  C
1934 ARG   ( 509-)  C
1961 ARG   ( 536-)  C
1967 ARG   ( 542-)  C
2212 ARG   (  61-)  D
2262 ARG   ( 111-)  D
2334 ARG   ( 183-)  D
2418 ARG   ( 267-)  D
2429 ARG   ( 278-)  D
2622 ARG   ( 471-)  D
2687 ARG   ( 536-)  D
2763 ARG   ( 612-)  D
2853 ARG   ( 702-)  D

Warning: Tyrosine convention problem

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

 110 TYR   ( 137-)  A
 114 TYR   ( 141-)  A
 163 TYR   ( 190-)  A
 388 TYR   ( 415-)  A
 413 TYR   ( 440-)  A
 433 TYR   ( 460-)  A
 511 TYR   ( 538-)  A
 656 TYR   ( 683-)  A
 836 TYR   ( 137-)  B
 840 TYR   ( 141-)  B
 889 TYR   ( 190-)  B
1033 TYR   ( 334-)  B
1114 TYR   ( 415-)  B
1139 TYR   ( 440-)  B
1159 TYR   ( 460-)  B
1237 TYR   ( 538-)  B
1382 TYR   ( 683-)  B
1562 TYR   ( 137-)  C
1566 TYR   ( 141-)  C
1759 TYR   ( 334-)  C
1840 TYR   ( 415-)  C
1865 TYR   ( 440-)  C
1885 TYR   ( 460-)  C
2108 TYR   ( 683-)  C
2288 TYR   ( 137-)  D
2292 TYR   ( 141-)  D
2566 TYR   ( 415-)  D
2591 TYR   ( 440-)  D
2611 TYR   ( 460-)  D
2834 TYR   ( 683-)  D

Warning: Phenylalanine convention problem

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

 125 PHE   ( 152-)  A
 139 PHE   ( 166-)  A
 179 PHE   ( 206-)  A
 180 PHE   ( 207-)  A
 187 PHE   ( 214-)  A
 190 PHE   ( 217-)  A
 250 PHE   ( 277-)  A
 290 PHE   ( 317-)  A
 304 PHE   ( 331-)  A
 311 PHE   ( 338-)  A
 320 PHE   ( 347-)  A
 324 PHE   ( 351-)  A
 355 PHE   ( 382-)  A
 364 PHE   ( 391-)  A
 375 PHE   ( 402-)  A
 416 PHE   ( 443-)  A
 484 PHE   ( 511-)  A
 627 PHE   ( 654-)  A
 677 PHE   ( 704-)  A
 851 PHE   ( 152-)  B
 865 PHE   ( 166-)  B
 905 PHE   ( 206-)  B
 906 PHE   ( 207-)  B
 913 PHE   ( 214-)  B
 916 PHE   ( 217-)  B
And so on for a total of 85 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.

  43 ASP   (  70-)  A
  63 ASP   (  90-)  A
  64 ASP   (  91-)  A
  80 ASP   ( 107-)  A
  91 ASP   ( 118-)  A
 119 ASP   ( 146-)  A
 128 ASP   ( 155-)  A
 150 ASP   ( 177-)  A
 154 ASP   ( 181-)  A
 170 ASP   ( 197-)  A
 189 ASP   ( 216-)  A
 232 ASP   ( 259-)  A
 278 ASP   ( 305-)  A
 303 ASP   ( 330-)  A
 325 ASP   ( 352-)  A
 328 ASP   ( 355-)  A
 353 ASP   ( 380-)  A
 374 ASP   ( 401-)  A
 427 ASP   ( 454-)  A
 498 ASP   ( 525-)  A
 518 ASP   ( 545-)  A
 524 ASP   ( 551-)  A
 542 ASP   ( 569-)  A
 551 ASP   ( 578-)  A
 558 ASP   ( 585-)  A
And so on for a total of 138 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.

  14 GLU   (  41-)  A
  36 GLU   (  63-)  A
  42 GLU   (  69-)  A
  79 GLU   ( 106-)  A
 166 GLU   ( 193-)  A
 221 GLU   ( 248-)  A
 256 GLU   ( 283-)  A
 279 GLU   ( 306-)  A
 300 GLU   ( 327-)  A
 306 GLU   ( 333-)  A
 319 GLU   ( 346-)  A
 335 GLU   ( 362-)  A
 360 GLU   ( 387-)  A
 403 GLU   ( 430-)  A
 434 GLU   ( 461-)  A
 445 GLU   ( 472-)  A
 456 GLU   ( 483-)  A
 476 GLU   ( 503-)  A
 492 GLU   ( 519-)  A
 514 GLU   ( 541-)  A
 538 GLU   ( 565-)  A
 583 GLU   ( 610-)  A
 612 GLU   ( 639-)  A
 693 GLU   ( 720-)  A
 740 GLU   (  41-)  B
And so on for a total of 98 lines.

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.

1584 ILE   ( 159-)  C      CG1    CG2
1584 ILE   ( 159-)  C      CG2    CG1

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

   2 LEU   (  29-)  A      N    CA    1.33   -6.9
  44 VAL   (  71-)  A      CA   CB    1.63    4.8
  45 ARG   (  72-)  A      C    O     1.32    4.3
  80 ASP   ( 107-)  A      CG   OD1   1.33    4.3
 157 GLY   ( 184-)  A      N    CA    1.52    4.3
 164 THR   ( 191-)  A      CA   CB    1.61    4.0
 248 HIS   ( 275-)  A      N    CA    1.54    4.5
 294 GLU   ( 321-)  A      CD   OE1   1.36    5.8
 302 GLY   ( 329-)  A      N    CA    1.52    4.0
 323 ASP   ( 350-)  A      CB   CG    1.40   -4.8
 573 GLY   ( 600-)  A      N    CA    1.52    4.2
 736 ARG   (  37-)  B      CG   CD    1.66    4.6
 736 ARG   (  37-)  B      CZ   NH2   1.42    5.3
 797 GLY   (  98-)  B      N    CA    1.54    5.5
 835 GLY   ( 136-)  B      N    CA    1.52    4.1
 904 ILE   ( 205-)  B      CA   CB    1.62    4.3
1076 ARG   ( 377-)  B      CG   CD    1.38   -4.6
1158 ASN   ( 459-)  B      CG   OD1   1.32    4.2
1175 GLY   ( 476-)  B      N    CA    1.52    4.1
1191 ASN   ( 492-)  B      CG   ND2   1.22   -5.4
1220 ARG   ( 521-)  B      CG   CD    1.69    5.6
1326 GLY   ( 627-)  B      N    CA    1.52    4.3
1484 ASP   (  59-)  C      CB   CG    1.69    7.2
1484 ASP   (  59-)  C      CG   OD1   1.40    7.8
1584 ILE   ( 159-)  C      CG1  CD1   3.03   38.9
And so on for a total of 52 lines.

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

 |  0.990131  0.000215  0.001108|
 |  0.000215  0.991388  0.000098|
 |  0.001108  0.000098  0.992861|
Proposed new scale matrix

 |  0.010779 -0.000003  0.003815|
 | -0.000002  0.007583  0.000000|
 | -0.000010  0.000000  0.008720|
With corresponding cell

    A    =  92.735  B   = 131.869  C    = 121.599
    Alpha=  90.010  Beta= 109.427  Gamma=  89.973

The CRYST1 cell dimensions

    A    =  93.660  B   = 133.020  C    = 122.590
    Alpha=  90.000  Beta= 109.590  Gamma=  90.000

Variance: 7242.412
(Under-)estimated Z-score: 62.720

Warning: Unusual bond angles

The bond angles listed in the table below were found to deviate more than 4 sigma from standard bond angles (both standard values and sigma for protein residues have been taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]). In the table below for each strange angle the bond angle and the number of standard deviations it differs from the standard values is given. Please note that disulphide bridges are neglected. Atoms starting with "-" belong to the previous residue in the sequence.

   2 LEU   (  29-)  A     -C    N    CA  103.34  -10.2
   2 LEU   (  29-)  A      C    CA   CB  120.71    5.6
  45 ARG   (  72-)  A      CG   CD   NE  100.18   -6.1
  89 HIS   ( 116-)  A      CA   CB   CG  109.09   -4.7
  98 ARG   ( 125-)  A      CB   CG   CD  104.97   -4.6
 108 HIS   ( 135-)  A      CG   ND1  CE1 110.24    4.6
 131 LYS   ( 158-)  A      C    CA   CB  119.99    5.2
 166 GLU   ( 193-)  A      CA   CB   CG  105.55   -4.3
 168 ILE   ( 195-)  A      CA   CB   CG1 118.09    4.5
 190 PHE   ( 217-)  A      CA   CB   CG  108.97   -4.8
 248 HIS   ( 275-)  A      C    CA   CB  101.47   -4.5
 267 LYS   ( 294-)  A      CD   CE   NZ   98.37   -4.2
 350 ARG   ( 377-)  A      CG   CD   NE   99.31   -6.6
 358 GLU   ( 385-)  A      CA   CB   CG  106.00   -4.1
 389 THR   ( 416-)  A     -CA  -C    N   124.56    4.2
 422 HIS   ( 449-)  A      CG   ND1  CE1 109.83    4.2
 471 SER   ( 498-)  A      CA   CB   OG  102.86   -4.1
 495 HIS   ( 522-)  A      CG   ND1  CE1 109.82    4.2
 513 ARG   ( 540-)  A      CB   CG   CD  103.04   -5.5
 583 GLU   ( 610-)  A      CA   CB   CG  105.94   -4.1
 659 MET   ( 686-)  A      CA   CB   CG  105.85   -4.1
 736 ARG   (  37-)  B      CG   CD   NE  121.68    6.6
 761 ASN   (  62-)  B      C    CA   CB  117.98    4.1
 772 LYS   (  73-)  B      CA   CB   CG  103.07   -5.5
 786 ARG   (  87-)  B      CG   CD   NE  103.21   -4.3
And so on for a total of 94 lines.

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.

  14 GLU   (  41-)  A
  36 GLU   (  63-)  A
  42 GLU   (  69-)  A
  43 ASP   (  70-)  A
  63 ASP   (  90-)  A
  64 ASP   (  91-)  A
  79 GLU   ( 106-)  A
  80 ASP   ( 107-)  A
  91 ASP   ( 118-)  A
 119 ASP   ( 146-)  A
 128 ASP   ( 155-)  A
 150 ASP   ( 177-)  A
 154 ASP   ( 181-)  A
 166 GLU   ( 193-)  A
 170 ASP   ( 197-)  A
 189 ASP   ( 216-)  A
 221 GLU   ( 248-)  A
 232 ASP   ( 259-)  A
 251 ARG   ( 278-)  A
 256 GLU   ( 283-)  A
 278 ASP   ( 305-)  A
 279 GLU   ( 306-)  A
 286 ARG   ( 313-)  A
 300 GLU   ( 327-)  A
 303 ASP   ( 330-)  A
And so on for a total of 270 lines.

Warning: Chirality deviations detected

The atoms listed in the table below have an improper dihedral value that is deviating from expected values. As the improper dihedral values are all getting very close to ideal values in recent X-ray structures, and as we actually do not know how big the spread around these values should be, this check only warns for 6 sigma deviations.

Improper dihedrals are a measure of the chirality/planarity of the structure at a specific atom. Values around -35 or +35 are expected for chiral atoms, and values around 0 for planar atoms. Planar side chains are left out of the calculations, these are better handled by the planarity checks.

Three numbers are given for each atom in the table. The first is the Z-score for the improper dihedral. The second number is the measured improper dihedral. The third number is the expected value for this atom type. A final column contains an extra warning if the chirality for an atom is opposite to the expected value.

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

   2 LEU   (  29-)  A      CA    -6.5    24.32    34.19
 131 LYS   ( 158-)  A      C     -6.6    -9.83     0.11
1261 LEU   ( 562-)  B      CG    13.2    -9.78   -33.01
1332 LEU   ( 633-)  B      CG     8.4   -18.18   -33.01
1584 ILE   ( 159-)  C      CB   -16.5    10.84    32.31
2031 LEU   ( 606-)  C      CG    10.7   -14.12   -33.01
2058 LEU   ( 633-)  C      CG     6.6   -21.39   -33.01
2150 ASP   ( 725-)  C      CA    -9.8    14.29    33.73
2158 LEU   ( 733-)  C      CG     7.1   -20.46   -33.01
2733 LEU   ( 582-)  D      CG    14.8    -6.88   -33.01
2756 ILE   ( 605-)  D      CB     6.1    40.20    32.31
2767 LEU   ( 616-)  D      CG     8.2   -18.58   -33.01
2799 LEU   ( 648-)  D      CG     9.5   -16.22   -33.01
The average deviation= 1.839

Error: Tau angle problems

The side chains of the residues listed in the table below contain a tau angle (N-Calpha-C) that was found to deviate from te expected value by more than 4.0 times the expected standard deviation. The number in the table is the number of standard deviations this RMS value deviates from the expected value.

2150 ASP   ( 725-)  C    5.11
2173 ILE   ( 748-)  C    4.89
 721 ILE   ( 748-)  A    4.58
1453 SER   (  28-)  C    4.52
 646 ALA   ( 673-)  A    4.29
2179 SER   (  28-)  D    4.25
2766 ASP   ( 615-)  D    4.17
   1 SER   (  28-)  A    4.14

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

 900 ASN   ( 201-)  B   10.88
1085 ASN   ( 386-)  B    8.47
1191 ASN   ( 492-)  B    7.56
1129 GLU   ( 430-)  B    7.15
 818 HIS   ( 119-)  B    6.72
 776 ASN   (  77-)  B    6.41
 991 HIS   ( 292-)  B    6.27
2352 ASN   ( 201-)  D    6.18
2403 ASN   ( 252-)  D    6.10
1381 ASN   ( 682-)  B    6.02
 124 ASP   ( 151-)  A    5.50
 368 HIS   ( 395-)  A    5.46
1128 HIS   ( 429-)  B    5.36
 185 HIS   ( 212-)  A    5.34
 130 ASN   ( 157-)  A    5.33
 434 GLU   ( 461-)  A    5.32
1820 HIS   ( 395-)  C    5.30
1140 HIS   ( 441-)  B    5.19
 297 GLU   ( 324-)  A    5.18
 815 HIS   ( 116-)  B    5.16
1100 ASP   ( 401-)  B    5.06
1495 ASP   (  70-)  C    5.02
 174 ASN   ( 201-)  A    4.96
1032 GLU   ( 333-)  B    4.86
1186 GLU   ( 487-)  B    4.84
 433 TYR   ( 460-)  A    4.71
  35 ASN   (  62-)  A    4.67
1866 HIS   ( 441-)  C    4.63
2257 GLU   ( 106-)  D    4.58
2842 HIS   ( 691-)  D    4.47
1532 ASP   ( 107-)  C    4.46
1206 HIS   ( 507-)  B    4.39
 460 GLU   ( 487-)  A    4.38
   9 HIS   (  36-)  A    4.36
1649 GLU   ( 224-)  C    4.34
2531 ASP   ( 380-)  D    4.31
1104 ASP   ( 405-)  B    4.25
2833 ASN   ( 682-)  D    4.25
  50 ASN   (  77-)  A    4.21
 232 ASP   ( 259-)  A    4.18
2107 ASN   ( 682-)  C    4.12
1515 ASP   (  90-)  C    4.12
2673 HIS   ( 522-)  D    4.12
1017 HIS   ( 318-)  B    4.09

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.

 904 ILE   ( 205-)  B    -2.7
2903 PRO   ( 752-)  D    -2.7
 422 HIS   ( 449-)  A    -2.7
2577 PRO   ( 426-)  D    -2.7
2785 TYR   ( 634-)  D    -2.6
 399 PRO   ( 426-)  A    -2.6
1630 ILE   ( 205-)  C    -2.5
2356 ILE   ( 205-)  D    -2.5
1125 PRO   ( 426-)  B    -2.5
1802 ARG   ( 377-)  C    -2.5
 178 ILE   ( 205-)  A    -2.5
 607 TYR   ( 634-)  A    -2.5
1148 HIS   ( 449-)  B    -2.5
1282 LYS   ( 583-)  B    -2.4
2355 PRO   ( 204-)  D    -2.4
2860 LYS   ( 709-)  D    -2.4
 903 PRO   ( 204-)  B    -2.4
1333 TYR   ( 634-)  B    -2.4
 857 LYS   ( 158-)  B    -2.4
2299 THR   ( 148-)  D    -2.4
1451 PRO   ( 752-)  B    -2.4
   2 LEU   (  29-)  A    -2.4
2151 GLY   ( 726-)  C    -2.4
2061 ARG   ( 636-)  C    -2.3
1573 THR   ( 148-)  C    -2.3
And so on for a total of 61 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.

   9 HIS   (  36-)  A  omega poor
  34 ARG   (  61-)  A  omega poor
  50 ASN   (  77-)  A  Poor phi/psi
  54 THR   (  81-)  A  omega poor
  66 ASN   (  93-)  A  omega poor
  70 ALA   (  97-)  A  omega poor
 101 HIS   ( 128-)  A  Poor phi/psi
 111 PHE   ( 138-)  A  omega poor
 140 SER   ( 167-)  A  omega poor
 142 VAL   ( 169-)  A  omega poor
 143 GLN   ( 170-)  A  omega poor
 154 ASP   ( 181-)  A  omega poor
 197 GLU   ( 224-)  A  PRO omega poor
 201 ALA   ( 228-)  A  Poor phi/psi
 202 ILE   ( 229-)  A  PRO omega poor
 209 HIS   ( 236-)  A  omega poor
 247 CYS   ( 274-)  A  Poor phi/psi
 251 ARG   ( 278-)  A  omega poor
 262 VAL   ( 289-)  A  omega poor
 275 LEU   ( 302-)  A  omega poor
 311 PHE   ( 338-)  A  omega poor
 387 SER   ( 414-)  A  omega poor
 419 ASP   ( 446-)  A  Poor phi/psi
 434 GLU   ( 461-)  A  PRO omega poor
 441 ASN   ( 468-)  A  Poor phi/psi
And so on for a total of 144 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.

2395 SER   ( 244-)  D    0.35
 943 SER   ( 244-)  B    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!

   3 ALA   (  30-)  A      0
   8 SER   (  35-)  A      0
   9 HIS   (  36-)  A      0
  13 ALA   (  40-)  A      0
  15 PRO   (  42-)  A      0
  18 PRO   (  45-)  A      0
  21 GLN   (  48-)  A      0
  23 THR   (  50-)  A      0
  24 ALA   (  51-)  A      0
  33 THR   (  60-)  A      0
  34 ARG   (  61-)  A      0
  48 SER   (  75-)  A      0
  49 GLU   (  76-)  A      0
  50 ASN   (  77-)  A      0
  57 GLN   (  84-)  A      0
  62 ALA   (  89-)  A      0
  64 ASP   (  91-)  A      0
  65 GLN   (  92-)  A      0
  69 ARG   (  96-)  A      0
  73 ARG   ( 100-)  A      0
  79 GLU   ( 106-)  A      0
  93 GLU   ( 120-)  A      0
  99 ILE   ( 126-)  A      0
 100 VAL   ( 127-)  A      0
 101 HIS   ( 128-)  A      0
And so on for a total of 1128 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!

2225 GLY   (  74-)  D   2.11   54
1499 GLY   (  74-)  C   2.09   59
  47 GLY   (  74-)  A   2.05   56
 773 GLY   (  74-)  B   2.04   61

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]

  15 PRO   (  42-)  A    0.17 LOW
  22 PRO   (  49-)  A    0.17 LOW
  25 PRO   (  52-)  A    0.07 LOW
 236 PRO   ( 263-)  A    0.20 LOW
 315 PRO   ( 342-)  A    0.20 LOW
 366 PRO   ( 393-)  A    0.47 HIGH
 412 PRO   ( 439-)  A    0.05 LOW
 430 PRO   ( 457-)  A    0.12 LOW
 548 PRO   ( 575-)  A    0.06 LOW
 631 PRO   ( 658-)  A    0.18 LOW
 719 PRO   ( 746-)  A    0.11 LOW
 737 PRO   (  38-)  B    0.07 LOW
 839 PRO   ( 140-)  B    0.11 LOW
 962 PRO   ( 263-)  B    0.08 LOW
1055 PRO   ( 356-)  B    0.47 HIGH
1078 PRO   ( 379-)  B    0.16 LOW
1176 PRO   ( 477-)  B    0.48 HIGH
1274 PRO   ( 575-)  B    0.09 LOW
1276 PRO   ( 577-)  B    0.13 LOW
1293 PRO   ( 594-)  B    0.46 HIGH
1477 PRO   (  52-)  C    0.09 LOW
1688 PRO   ( 263-)  C    0.07 LOW
1767 PRO   ( 342-)  C    0.10 LOW
1818 PRO   ( 393-)  C    0.48 HIGH
1861 PRO   ( 436-)  C    0.17 LOW
2000 PRO   ( 575-)  C    0.19 LOW
2002 PRO   ( 577-)  C    0.10 LOW
2171 PRO   ( 746-)  C    0.16 LOW
2200 PRO   (  49-)  D    0.17 LOW
2414 PRO   ( 263-)  D    0.09 LOW
2517 PRO   ( 366-)  D    0.47 HIGH
2530 PRO   ( 379-)  D    0.18 LOW
2590 PRO   ( 439-)  D    0.16 LOW
2897 PRO   ( 746-)  D    0.15 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].

 113 PRO   ( 140-)  A   -62.1 half-chair C-beta/C-alpha (-54 degrees)
 220 PRO   ( 247-)  A  -116.4 envelop C-gamma (-108 degrees)
 405 PRO   ( 432-)  A    99.7 envelop C-beta (108 degrees)
 481 PRO   ( 508-)  A   106.7 envelop C-beta (108 degrees)
 622 PRO   ( 649-)  A   -38.1 envelop C-alpha (-36 degrees)
 725 PRO   ( 752-)  A   -64.2 envelop C-beta (-72 degrees)
 748 PRO   (  49-)  B    52.9 half-chair C-delta/C-gamma (54 degrees)
 757 PRO   (  58-)  B  -112.4 envelop C-gamma (-108 degrees)
 929 PRO   ( 230-)  B   -53.2 half-chair C-beta/C-alpha (-54 degrees)
 946 PRO   ( 247-)  B  -113.6 envelop C-gamma (-108 degrees)
1131 PRO   ( 432-)  B   101.7 envelop C-beta (108 degrees)
1207 PRO   ( 508-)  B   100.4 envelop C-beta (108 degrees)
1451 PRO   ( 752-)  B   -56.1 half-chair C-beta/C-alpha (-54 degrees)
1483 PRO   (  58-)  C  -113.2 envelop C-gamma (-108 degrees)
1655 PRO   ( 230-)  C   -59.3 half-chair C-beta/C-alpha (-54 degrees)
1672 PRO   ( 247-)  C  -122.6 half-chair C-delta/C-gamma (-126 degrees)
1791 PRO   ( 366-)  C  -112.1 envelop C-gamma (-108 degrees)
1933 PRO   ( 508-)  C    99.8 envelop C-beta (108 degrees)
2093 PRO   ( 668-)  C   -41.8 envelop C-alpha (-36 degrees)
2381 PRO   ( 230-)  D   -61.8 half-chair C-beta/C-alpha (-54 degrees)
2398 PRO   ( 247-)  D  -117.1 half-chair C-delta/C-gamma (-126 degrees)
2659 PRO   ( 508-)  D    99.5 envelop C-beta (108 degrees)
2726 PRO   ( 575-)  D  -115.0 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.

2543 HIS   ( 392-)  D      ND1 <-> 2566 TYR   ( 415-)  D      CB     1.56    1.54  INTRA BL
1817 HIS   ( 392-)  C      ND1 <-> 1840 TYR   ( 415-)  C      CB     1.56    1.54  INTRA BL
 365 HIS   ( 392-)  A      ND1 <->  388 TYR   ( 415-)  A      CB     1.53    1.57  INTRA BL
1091 HIS   ( 392-)  B      ND1 <-> 1114 TYR   ( 415-)  B      CB     1.52    1.58  INTRA BL
2602 MET   ( 451-)  D      SD  <-> 2920 HOH   (3617 )  D      O      1.13    1.87  INTRA BL
1150 MET   ( 451-)  B      SD  <-> 2918 HOH   (3614 )  B      O      0.95    2.05  INTRA
1876 MET   ( 451-)  C      SD  <-> 2919 HOH   (3612 )  C      O      0.90    2.10  INTRA BL
  46 LYS   (  73-)  A      CD  <-> 2919 HOH   (3442 )  C      O      0.86    1.94  INTRA
 424 MET   ( 451-)  A      SD  <-> 2917 HOH   (3609 )  A      O      0.80    2.20  INTRA
2567 THR   ( 416-)  D    A CG2 <-> 2920 HOH   (3576 )  D      O      0.77    2.03  INTRA
2003 ASP   ( 578-)  C      CB  <-> 2919 HOH   (2919 )  C      O      0.73    2.07  INTRA
2543 HIS   ( 392-)  D      CE1 <-> 2566 TYR   ( 415-)  D      CB     0.67    2.53  INTRA BL
 174 ASN   ( 201-)  A      CG  <-> 2909 HDD   ( 760-)  A    A CMB    0.67    2.53  INTRA BL
1817 HIS   ( 392-)  C      CE1 <-> 1840 TYR   ( 415-)  C      CB     0.66    2.54  INTRA BL
 900 ASN   ( 201-)  B      CG  <-> 2911 HDD   ( 760-)  B    A CMB    0.62    2.58  INTRA BL
2917 HOH   (2305 )  A      O   <-> 2917 HOH   (3509 )  A      O      0.61    1.59  INTRA
2224 LYS   (  73-)  D      CD  <-> 2918 HOH   (2705 )  B      O      0.60    2.20  INTRA
 365 HIS   ( 392-)  A      CE1 <->  388 TYR   ( 415-)  A      CB     0.60    2.60  INTRA BL
1817 HIS   ( 392-)  C      CG  <-> 1840 TYR   ( 415-)  C      CB     0.59    2.61  INTRA BL
1091 HIS   ( 392-)  B      CE1 <-> 1114 TYR   ( 415-)  B      CB     0.59    2.61  INTRA BL
1817 HIS   ( 392-)  C      ND1 <-> 1840 TYR   ( 415-)  C      CG     0.57    2.53  INTRA BL
 365 HIS   ( 392-)  A      ND1 <->  388 TYR   ( 415-)  A      CG     0.57    2.53  INTRA BL
2543 HIS   ( 392-)  D      CG  <-> 2566 TYR   ( 415-)  D      CB     0.57    2.63  INTRA BL
 174 ASN   ( 201-)  A      ND2 <-> 2909 HDD   ( 760-)  A    A CMB    0.57    2.53  INTRA BL
1091 HIS   ( 392-)  B      CG  <-> 1114 TYR   ( 415-)  B      CB     0.56    2.64  INTRA BL
And so on for a total of 277 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

The Inside/Outside distribution normality RMS Z-score over a 15 residue window is plotted as function of the residue number. High areas in the plot (above 1.5) indicate unusual inside/outside patterns.

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Warning: Abnormal packing environment for some residues

The residues listed in the table below have an unusual packing environment.

The packing environment of the residues is compared with the average packing environment for all residues of the same type in good PDB files. A low packing score can indicate one of several things: Poor packing, misthreading of the sequence through the density, crystal contacts, contacts with a co-factor, or the residue is part of the active site. It is not uncommon to see a few of these, but in any case this requires further inspection of the residue.

  34 ARG   (  61-)  A      -6.91
 452 ARG   ( 479-)  A      -6.85
1904 ARG   ( 479-)  C      -6.84
1178 ARG   ( 479-)  B      -6.82
2630 ARG   ( 479-)  D      -6.81
 451 LYS   ( 478-)  A      -6.74
1903 LYS   ( 478-)  C      -6.68
2629 LYS   ( 478-)  D      -6.49
 760 ARG   (  61-)  B      -6.44
  94 ARG   ( 121-)  A      -6.41
 686 GLN   ( 713-)  A      -6.41
2864 GLN   ( 713-)  D      -6.41
2272 ARG   ( 121-)  D      -6.40
1546 ARG   ( 121-)  C      -6.39
 820 ARG   ( 121-)  B      -6.36
2138 GLN   ( 713-)  C      -6.31
1486 ARG   (  61-)  C      -6.27
1177 LYS   ( 478-)  B      -6.25
1412 GLN   ( 713-)  B      -6.21
1196 ARG   ( 497-)  B      -6.10
 470 ARG   ( 497-)  A      -6.10
1922 ARG   ( 497-)  C      -6.07
2648 ARG   ( 497-)  D      -6.01
2212 ARG   (  61-)  D      -5.88
2183 GLU   (  32-)  D      -5.79
And so on for a total of 71 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

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.

 411 ALA   ( 438-)  A   -2.81
1137 ALA   ( 438-)  B   -2.73
2589 ALA   ( 438-)  D   -2.72
1863 ALA   ( 438-)  C   -2.69
1458 ASP   (  33-)  C   -2.67
 553 ASN   ( 580-)  A   -2.62
1903 LYS   ( 478-)  C   -2.59
2731 ASN   ( 580-)  D   -2.59
 320 PHE   ( 347-)  A   -2.59
1652 TRP   ( 227-)  C   -2.58
 200 TRP   ( 227-)  A   -2.57
 681 ILE   ( 708-)  A   -2.52
1926 PHE   ( 501-)  C   -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.

 564 TYR   ( 591-)  A     -  567 PRO   ( 594-)  A        -1.58
1469 PRO   (  44-)  C     - 1472 ALA   (  47-)  C        -1.37

Note: Second generation quality Z-score plot

The second generation quality Z-score smoothed over a 10 residue window is plotted as function of the residue number. Low areas in the plot (below -1.3) indicate unusual packing.

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

2917 HOH   (1624 )  A      O     45.30   -9.58  -36.95
2917 HOH   (2153 )  A      O     43.79   -7.20  -39.14
2920 HOH   (2356 )  D      O    -11.58  -30.69  -24.96

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.

 341 GLN   ( 368-)  A
 432 ASN   ( 459-)  A
 488 GLN   ( 515-)  A
1067 GLN   ( 368-)  B
1158 ASN   ( 459-)  B
1328 HIS   ( 629-)  B
1793 GLN   ( 368-)  C
1874 HIS   ( 449-)  C
1971 GLN   ( 546-)  C
1997 ASN   ( 572-)  C
2054 HIS   ( 629-)  C
2096 ASN   ( 671-)  C
2199 GLN   (  48-)  D
2543 HIS   ( 392-)  D
2600 HIS   ( 449-)  D
2700 HIS   ( 549-)  D
2780 HIS   ( 629-)  D

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

   1 SER   (  28-)  A      OG
   9 HIS   (  36-)  A      N
  35 ASN   (  62-)  A      N
  50 ASN   (  77-)  A      N
  66 ASN   (  93-)  A      N
  98 ARG   ( 125-)  A      NE
 100 VAL   ( 127-)  A      N
 103 ARG   ( 130-)  A      NH2
 138 ARG   ( 165-)  A      NH1
 140 SER   ( 167-)  A      OG
 152 VAL   ( 179-)  A      N
 176 THR   ( 203-)  A      N
 176 THR   ( 203-)  A      OG1
 180 PHE   ( 207-)  A      N
 181 ILE   ( 208-)  A      N
 202 ILE   ( 229-)  A      N
 208 ALA   ( 235-)  A      N
 225 ASN   ( 252-)  A      ND2
 240 ARG   ( 267-)  A      NE
 242 MET   ( 269-)  A      N
 324 PHE   ( 351-)  A      N
 359 ASN   ( 386-)  A      ND2
 367 GLY   ( 394-)  A      N
 370 VAL   ( 397-)  A      N
 376 THR   ( 403-)  A      N
And so on for a total of 177 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.

  91 ASP   ( 118-)  A      OD2
 174 ASN   ( 201-)  A      OD1
 185 HIS   ( 212-)  A      ND1
 365 HIS   ( 392-)  A      ND1
 390 ASP   ( 417-)  A      OD2
 422 HIS   ( 449-)  A    A NE2
 817 ASP   ( 118-)  B      OD2
 900 ASN   ( 201-)  B      OD1
 911 HIS   ( 212-)  B      ND1
1091 HIS   ( 392-)  B      ND1
1116 ASP   ( 417-)  B      OD2
1148 HIS   ( 449-)  B    A NE2
1160 GLU   ( 461-)  B      OE2
1543 ASP   ( 118-)  C      OD2
1626 ASN   ( 201-)  C      OD1
1637 HIS   ( 212-)  C      ND1
1842 ASP   ( 417-)  C      OD2
1886 GLU   ( 461-)  C      OE2
2269 ASP   ( 118-)  D      OD2
2352 ASN   ( 201-)  D      OD1
2363 HIS   ( 212-)  D      ND1
2568 ASP   ( 417-)  D      OD2
2612 GLU   ( 461-)  D      OE2

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.

2917 HOH   ( 848 )  A      O  0.92  K  4

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.

  63 ASP   (  90-)  A   H-bonding suggests Asn; but Alt-Rotamer
  91 ASP   ( 118-)  A   H-bonding suggests Asn; but Alt-Rotamer
 300 GLU   ( 327-)  A   H-bonding suggests Gln
 789 ASP   (  90-)  B   H-bonding suggests Asn; but Alt-Rotamer
 817 ASP   ( 118-)  B   H-bonding suggests Asn; but Alt-Rotamer
1026 GLU   ( 327-)  B   H-bonding suggests Gln
1224 ASP   ( 525-)  B   H-bonding suggests Asn
1342 ASP   ( 643-)  B   H-bonding suggests Asn
1424 ASP   ( 725-)  B   H-bonding suggests Asn
1515 ASP   (  90-)  C   H-bonding suggests Asn; but Alt-Rotamer
1543 ASP   ( 118-)  C   H-bonding suggests Asn; but Alt-Rotamer
1752 GLU   ( 327-)  C   H-bonding suggests Gln
1950 ASP   ( 525-)  C   H-bonding suggests Asn
2150 ASP   ( 725-)  C   H-bonding suggests Asn; but Alt-Rotamer
2241 ASP   (  90-)  D   H-bonding suggests Asn; but Alt-Rotamer
2269 ASP   ( 118-)  D   H-bonding suggests Asn; but Alt-Rotamer
2478 GLU   ( 327-)  D   H-bonding suggests Gln
2851 ASP   ( 700-)  D   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.793
  2nd generation packing quality :  -2.020
  Ramachandran plot appearance   :  -0.810
  chi-1/chi-2 rotamer normality  :  -0.567
  Backbone conformation          :  -0.496

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.231
  Bond angles                    :   1.121
  Omega angle restraints         :   1.163
  Side chain planarity           :   1.903
  Improper dihedral distribution :   1.526 (loose)
  B-factor distribution          :   0.799
  Inside/Outside distribution    :   1.066

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 : 1.48


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.4
  2nd generation packing quality :  -1.7
  Ramachandran plot appearance   :  -1.3
  chi-1/chi-2 rotamer normality  :  -1.1
  Backbone conformation          :  -1.0

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.231
  Bond angles                    :   1.121
  Omega angle restraints         :   1.163
  Side chain planarity           :   1.903
  Improper dihedral distribution :   1.526 (loose)
  B-factor distribution          :   0.799
  Inside/Outside distribution    :   1.066
==============

WHAT IF
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Bond lengths and angles, DNA/RNA
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DSSP
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      Dictionary of protein secondary structure: pattern
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    Biopolymers 22, 2577--2637 (1983).

Hydrogen bond networks
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      protein structures
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Matthews' Coefficient
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      Solvent content of Protein Crystals
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Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
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Puckering parameters
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    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.