WHAT IF Check report

This file was created 2011-12-16 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 pdb1ir1.ent

Checks that need to be done early-on in validation

Warning: Class of space group could be incorrect

The space group symbol indicates a different class than the unit cell given on the CRYST1 card of the PDB file.

Possible cause: The unit cell may have pseudo-symmetry, or one of the cell dimensions or the space group might be given incorrectly.

Crystal class of the cell: TETRAGONAL

Crystal class of the space group: ORTHORHOMBIC

Space group name: C 2 2 21

Warning: Unconventional cell on CRYST1

The derived `conventional cell' is different from the cell given on the CRYST1 card.

The CRYST1 cell dimensions

    A    = 157.800  B   = 157.800  C    = 200.900
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    = 111.581  B   = 111.581  C    = 200.900
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    = 111.581  B   = 111.581  C    = 200.900
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

 |  0.500000 -0.500000  0.000000|
 |  0.500000  0.500000  0.000000|
 |  0.000000  0.000000  1.000000|

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 : 0.406
CA-only RMS fit for the two chains : 0.128

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 : 0.358
CA-only RMS fit for the two chains : 0.104

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 : 0.393
CA-only RMS fit for the two chains : 0.073

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: S and T

All-atom RMS fit for the two chains : 0.500
CA-only RMS fit for the two chains : 0.106

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: S and U

All-atom RMS fit for the two chains : 0.572
CA-only RMS fit for the two chains : 0.121

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.

2346 MME   (   1-)  S  -
2349 MME   (   1-)  T  -
2352 MME   (   1-)  U  -
2357 CAP   ( 501-)  A  -
2359 CAP   ( 501-)  B  -
2361 CAP   ( 501-)  C  -
2363 CAP   ( 501-)  D  -
2364 MME   (   1-)  V  -

Administrative problems that can generate validation failures

Warning: Groups attached to potentially hydrogenbonding atoms

Residues were observed with groups attached to (or very near to) atoms that potentially can form hydrogen bonds. WHAT IF is not very good at dealing with such exceptional cases (Mainly because it's author is not...). So be warned that the hydrogenbonding-related analyses of these residues might be in error.

For example, an aspartic acid can be protonated on one of its delta oxygens. This is possible because the one delta oxygen 'helps' the other one holding that proton. However, if a delta oxygen has a group bound to it, then it can no longer 'help' the other delta oxygen bind the proton. However, both delta oxygens, in principle, can still be hydrogen bond acceptors. Such problems can occur in the amino acids Asp, Glu, and His. I have opted, for now to simply allow no hydrogen bonds at all for any atom in any side chain that somewhere has a 'funny' group attached to it. I know this is wrong, but there are only 12 hours in a day.

 465 LYS   (   2-)  S  -   N   bound to 2346 MME   (   1-)  S  -   C
1051 LYS   (   2-)  T  -   N   bound to 2349 MME   (   1-)  T  -   C
1637 LYS   (   2-)  U  -   N   bound to 2352 MME   (   1-)  U  -   C
2223 LYS   (   2-)  V  -   N   bound to 2364 MME   (   1-)  V  -   C

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: S

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: T

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: U

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: V

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

Warning: What type of B-factor?

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

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

Crystal temperature (K) :298.000

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: S

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: T

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: U

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: V

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.

2249 ARG   (  28-)  V

Warning: Phenylalanine convention problem

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

1787 PHE   (  40-)  D

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.

  17 GLU   (  28-)  A
 552 GLU   (  89-)  S
1249 GLU   (  88-)  C
1724 GLU   (  89-)  U

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.

 190 KCX   ( 201-)  A      CH     CX
 190 KCX   ( 201-)  A      OX1    OQ1
 190 KCX   ( 201-)  A      OX2    OQ2
 776 KCX   ( 201-)  B      CH     CX
 776 KCX   ( 201-)  B      OX1    OQ1
 776 KCX   ( 201-)  B      OX2    OQ2
1362 KCX   ( 201-)  C      CH     CX
1362 KCX   ( 201-)  C      OX1    OQ1
1362 KCX   ( 201-)  C      OX2    OQ2
1948 KCX   ( 201-)  D      CH     CX
1948 KCX   ( 201-)  D      OX1    OQ1
1948 KCX   ( 201-)  D      OX2    OQ2

Geometric checks

Warning: Low bond length variability

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

RMS Z-score for bond lengths: 0.273
RMS-deviation in bond distances: 0.007

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

 |  0.998070 -0.000031 -0.000018|
 | -0.000031  0.998492  0.000054|
 | -0.000018  0.000054  0.998592|
Proposed new scale matrix

 |  0.006349  0.000000  0.000000|
 |  0.000000  0.006347  0.000000|
 |  0.000000  0.000000  0.004985|
With corresponding cell

    A    = 157.499  B   = 157.565  C    = 200.601
    Alpha=  90.002  Beta=  90.002  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 157.800  B   = 157.800  C    = 200.900
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 210.206
(Under-)estimated Z-score: 10.685

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.

 189 THR   ( 200-)  A      N    CA   C    99.92   -4.0
 252 PRO   ( 263-)  A      N    CA   C   122.65    4.3
 568 ASP   ( 105-)  S      N    CA   C    99.22   -4.3
 588 PHE   (  13-)  B      N    CA   C    97.18   -5.0
 654 ARG   (  79-)  B      CB   CG   CD  103.71   -5.2
 775 THR   ( 200-)  B      N    CA   C    98.64   -4.5
 838 PRO   ( 263-)  B      N    CA   C   122.66    4.3
 900 HIS   ( 325-)  B      C    CA   CB  102.32   -4.1
1154 ASP   ( 105-)  T      N    CA   C    98.74   -4.5
1244 ARG   (  83-)  C      CB   CG   CD  105.76   -4.2
1361 THR   ( 200-)  C      N    CA   C    99.98   -4.0
1424 PRO   ( 263-)  C      N    CA   C   122.89    4.4
1486 HIS   ( 325-)  C      C    CA   CB  102.36   -4.1
1663 ARG   (  28-)  U      CB   CG   CD  104.87   -4.6
1740 ASP   ( 105-)  U      N    CA   C    99.33   -4.2
1827 TYR   (  80-)  D      N    CA   C   122.53    4.0
1829 GLY   (  82-)  D      N    CA   C   100.80   -4.0
2010 PRO   ( 263-)  D      N    CA   C   121.98    4.1
2072 HIS   ( 325-)  D      C    CA   CB  102.40   -4.1
2276 HIS   (  55-)  V      CG   ND1  CE1 109.62    4.0
2326 ASP   ( 105-)  V      N    CA   C    99.28   -4.3

Warning: Low bond angle variability

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

RMS Z-score for bond angles: 0.656
RMS-deviation in bond angles: 1.446

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.

  17 GLU   (  28-)  A
 552 GLU   (  89-)  S
1249 GLU   (  88-)  C
1724 GLU   (  89-)  U
2249 ARG   (  28-)  V

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.

 291 ASP   ( 302-)  A    6.68
2049 ASP   ( 302-)  D    6.56
 877 ASP   ( 302-)  B    6.36
1463 ASP   ( 302-)  C    6.30
1827 TYR   (  80-)  D    6.15
1285 VAL   ( 124-)  C    5.86
1871 VAL   ( 124-)  D    5.59
 588 PHE   (  13-)  B    5.42
 113 VAL   ( 124-)  A    5.28
 699 VAL   ( 124-)  B    5.26
 599 TYR   (  24-)  B    5.10
2016 TYR   ( 269-)  D    4.94
 959 VAL   ( 384-)  B    4.81
 844 TYR   ( 269-)  B    4.78
1281 ILE   ( 120-)  C    4.77
  13 TYR   (  24-)  A    4.76
1771 TYR   (  24-)  D    4.75
1545 VAL   ( 384-)  C    4.68
 695 ILE   ( 120-)  B    4.67
1185 TYR   (  24-)  C    4.63
 258 TYR   ( 269-)  A    4.61
1829 GLY   (  82-)  D    4.58
 775 THR   ( 200-)  B    4.56
 925 ARG   ( 350-)  B    4.46
1316 ILE   ( 155-)  C    4.41
 373 VAL   ( 384-)  A    4.41
 109 ILE   ( 120-)  A    4.39
2131 VAL   ( 384-)  D    4.36
 876 ILE   ( 301-)  B    4.34
  71 GLY   (  82-)  A    4.30
1430 TYR   ( 269-)  C    4.28
1243 GLY   (  82-)  C    4.22
 730 ILE   ( 155-)  B    4.22
2011 ILE   ( 264-)  D    4.21
1867 ILE   ( 120-)  D    4.20
1902 ILE   ( 155-)  D    4.20
 339 ARG   ( 350-)  A    4.18
 839 ILE   ( 264-)  B    4.16
2097 ARG   ( 350-)  D    4.15
 657 GLY   (  82-)  B    4.13
 144 ILE   ( 155-)  A    4.11
1511 ARG   ( 350-)  C    4.07
 789 TRP   ( 214-)  B    4.06
 383 PHE   ( 394-)  A    4.06
 969 PHE   ( 394-)  B    4.03
1425 ILE   ( 264-)  C    4.03
 189 THR   ( 200-)  A    4.02
2134 MET   ( 387-)  D    4.02
1462 ILE   ( 301-)  C    4.01

Warning: High tau angle deviations

The RMS Z-score for the tau angles (N-Calpha-C) in the structure is too high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 1.5 worries us. However, we determined the tau normal distributions from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Tau angle RMS Z-score : 1.515

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.

2116 VAL   ( 369-)  D    -2.6
 358 VAL   ( 369-)  A    -2.5
1530 VAL   ( 369-)  C    -2.5
 944 VAL   ( 369-)  B    -2.4
 286 MET   ( 297-)  A    -2.4
 588 PHE   (  13-)  B    -2.3
1458 MET   ( 297-)  C    -2.3
1687 TYR   (  52-)  U    -2.3
2277 HIS   (  56-)  V    -2.3
 127 LEU   ( 138-)  A    -2.3
1101 TYR   (  52-)  T    -2.3
1691 HIS   (  56-)  U    -2.3
1226 THR   (  65-)  C    -2.3
 640 THR   (  65-)  B    -2.2
   3 LYS   (  14-)  A    -2.2
1812 THR   (  65-)  D    -2.2
2273 TYR   (  52-)  V    -2.2
2044 MET   ( 297-)  D    -2.2
  54 THR   (  65-)  A    -2.2
 519 HIS   (  56-)  S    -2.1
1625 GLU   ( 464-)  C    -2.1
1299 LEU   ( 138-)  C    -2.1
1105 HIS   (  56-)  T    -2.1
 658 ARG   (  83-)  B    -2.1
1498 GLY   ( 337-)  C    -2.1
 912 GLY   ( 337-)  B    -2.1
1016 GLY   ( 441-)  B    -2.1
1602 GLY   ( 441-)  C    -2.1
 326 GLY   ( 337-)  A    -2.1
2084 GLY   ( 337-)  D    -2.1
1175 LYS   (  14-)  C    -2.0
 471 ASN   (   8-)  S    -2.0
1152 GLY   ( 103-)  T    -2.0
1235 LEU   (  74-)  C    -2.0
 897 GLY   ( 322-)  B    -2.0
 515 TYR   (  52-)  S    -2.0
1629 GLU   ( 468-)  C    -2.0

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  51 SER   (  62-)  A  Poor phi/psi
  52 THR   (  63-)  A  Poor phi/psi
 152 ASN   ( 163-)  A  Poor phi/psi
 164 LYS   ( 175-)  A  PRO omega poor
 196 ASN   ( 207-)  A  Poor phi/psi
 286 MET   ( 297-)  A  Poor phi/psi
 320 VAL   ( 331-)  A  Poor phi/psi
 359 SER   ( 370-)  A  Poor phi/psi
 476 GLU   (  13-)  S  Poor phi/psi
 478 LEU   (  15-)  S  Poor phi/psi
 500 LYS   (  37-)  S  Poor phi/psi
 534 LYS   (  71-)  S  Poor phi/psi
 572 GLN   ( 109-)  S  Poor phi/psi
 637 SER   (  62-)  B  Poor phi/psi
 638 THR   (  63-)  B  Poor phi/psi
 738 ASN   ( 163-)  B  Poor phi/psi
 750 LYS   ( 175-)  B  PRO omega poor
 782 ASN   ( 207-)  B  Poor phi/psi
 872 MET   ( 297-)  B  Poor phi/psi
 906 VAL   ( 331-)  B  Poor phi/psi
 945 SER   ( 370-)  B  Poor phi/psi
1016 GLY   ( 441-)  B  Poor phi/psi
1062 GLU   (  13-)  T  Poor phi/psi
1064 LEU   (  15-)  T  Poor phi/psi
1086 LYS   (  37-)  T  Poor phi/psi
And so on for a total of 54 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.

1442 SER   ( 281-)  C    0.38
2028 SER   ( 281-)  D    0.38

Warning: Unusual backbone conformations

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

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

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

   4 ALA   (  15-)  A      0
  12 THR   (  23-)  A      0
  14 TYR   (  25-)  A      0
  15 THR   (  26-)  A      0
  35 PRO   (  46-)  A      0
  50 SER   (  61-)  A      0
  51 SER   (  62-)  A      0
  52 THR   (  63-)  A      0
  55 TRP   (  66-)  A      0
  59 TRP   (  70-)  A      0
  63 LEU   (  74-)  A      0
  65 ASN   (  76-)  A      0
  74 TYR   (  85-)  A      0
  77 GLU   (  88-)  A      0
  80 ALA   (  91-)  A      0
  83 GLU   (  94-)  A      0
  96 LEU   ( 107-)  A      0
  99 GLU   ( 110-)  A      0
 109 ILE   ( 120-)  A      0
 110 VAL   ( 121-)  A      0
 112 ASN   ( 123-)  A      0
 113 VAL   ( 124-)  A      0
 116 PHE   ( 127-)  A      0
 120 ARG   ( 131-)  A      0
 121 ALA   ( 132-)  A      0
And so on for a total of 873 lines.

Warning: Omega angles too tightly restrained

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

Standard deviation of omega values : 1.460

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!

1498 GLY   ( 337-)  C   1.95   22
2084 GLY   ( 337-)  D   1.95   30
 912 GLY   ( 337-)  B   1.94   23
 326 GLY   ( 337-)  A   1.89   20

Warning: Unusual peptide bond conformations

For the residues listed in the table below, the backbone formed by the residue mentioned and the one C-terminal of it show systematic angular deviations from normality that are consistent with a cis-peptide that accidentally got refine in a trans conformation. This check follows the recommendations by Jabs, Weiss, and Hilgenfeld [REF]. This check has not yet fully matured...

1063 THR   (  14-)  T   1.60

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]

2200 PRO   ( 453-)  D    0.18 LOW

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.

2223 LYS   (   2-)  V      N   <-> 2364 MME   (   1-)  V      C      1.37    1.33  INTRA B3
2223 LYS   (   2-)  V      CA  <-> 2364 MME   (   1-)  V      C      0.77    2.43  INTRA
 587 GLU   (  12-)  B      N   <-> 2367 HOH   ( 659 )  B      O      0.42    2.28  INTRA BF
1145 ASN   (  96-)  T      ND2 <-> 1642 GLN   (   7-)  U      NE2    0.39    2.46  INTRA
 559 ASN   (  96-)  S      ND2 <-> 1056 GLN   (   7-)  T      NE2    0.39    2.46  INTRA
1172 TYR   ( 123-)  T      CD2 <-> 2368 HOH   ( 266 )  T      O      0.37    2.43  INTRA BF
1169 PRO   ( 120-)  T      C   <-> 2368 HOH   ( 266 )  T      O      0.34    2.46  INTRA BF
 797 ALA   ( 222-)  B      CB  <-> 2367 HOH   ( 867 )  B      O      0.32    2.48  INTRA
1156 ASN   ( 107-)  T      ND2 <-> 2368 HOH   ( 198 )  T      O      0.31    2.39  INTRA
1930 LYS   ( 183-)  D      NZ  <-> 2371 HOH   ( 821 )  D      O      0.31    2.39  INTRA
1517 LYS   ( 356-)  C      NZ  <-> 2369 HOH   ( 897 )  C      O      0.30    2.40  INTRA
 470 GLN   (   7-)  S      CG  <-> 2372 HOH   ( 269 )  V      O      0.29    2.51  INTRA BF
 465 LYS   (   2-)  S      NZ  <-> 2366 HOH   ( 308 )  S      O      0.28    2.42  INTRA
 520 ASN   (  57-)  S      ND2 <-> 2366 HOH   ( 282 )  S      O      0.28    2.42  INTRA BF
2267 THR   (  46-)  V      OG1 <-> 2372 HOH   ( 269 )  V      O      0.27    2.13  INTRA
  77 GLU   (  88-)  A      CD  <-> 2365 HOH   ( 930 )  A      O      0.25    2.55  INTRA
1839 GLY   (  92-)  D      N   <-> 2371 HOH   ( 868 )  D      O      0.25    2.45  INTRA
1292 ARG   ( 131-)  C      NH2 <-> 2369 HOH   ( 898 )  C      O      0.24    2.46  INTRA
 524 TYR   (  61-)  S      CE2 <-> 2367 HOH   ( 867 )  B      O      0.24    2.56  INTRA
 328 ARG   ( 339-)  A      NH2 <->  381 GLU   ( 392-)  A      OE1    0.24    2.46  INTRA
 593 LYS   (  18-)  B      NZ  <-> 2367 HOH   ( 835 )  B      O      0.24    2.46  INTRA
 147 GLU   ( 158-)  A      OE2 <->  314 HIS   ( 325-)  A      NE2    0.23    2.47  INTRA BL
1627 LYS   ( 466-)  C      NZ  <-> 2369 HOH   ( 836 )  C      O      0.23    2.47  INTRA BF
 470 GLN   (   7-)  S      NE2 <-> 2317 ASN   (  96-)  V      ND2    0.22    2.63  INTRA
1106 ASN   (  57-)  T      ND2 <-> 2368 HOH   ( 194 )  T      O      0.22    2.48  INTRA
And so on for a total of 228 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: S

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: T

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: U

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: V

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.

1496 LEU   ( 335-)  C      -6.98
2082 LEU   ( 335-)  D      -6.93
 324 LEU   ( 335-)  A      -6.91
 910 LEU   ( 335-)  B      -6.89
1292 ARG   ( 131-)  C      -6.66
 706 ARG   ( 131-)  B      -6.55
1878 ARG   ( 131-)  D      -6.39
1710 PHE   (  75-)  U      -6.10
 724 GLN   ( 149-)  B      -6.06
 120 ARG   ( 131-)  A      -6.04
 138 GLN   ( 149-)  A      -6.03
1124 PHE   (  75-)  T      -6.03
2296 PHE   (  75-)  V      -6.02
1310 GLN   ( 149-)  C      -6.00
 538 PHE   (  75-)  S      -5.99
 470 GLN   (   7-)  S      -5.97
1896 GLN   ( 149-)  D      -5.96
1642 GLN   (   7-)  U      -5.91
2228 GLN   (   7-)  V      -5.90
1600 ARG   ( 439-)  C      -5.78
1056 GLN   (   7-)  T      -5.77
 428 ARG   ( 439-)  A      -5.76
2186 ARG   ( 439-)  D      -5.73
1014 ARG   ( 439-)  B      -5.66
   3 LYS   (  14-)  A      -5.57
And so on for a total of 62 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.

 323 LYS   ( 334-)  A       325 - GLU    336- ( A)         -5.46
 456 PHE   ( 467-)  A       458 - PHE    469- ( A)         -4.70
 909 LYS   ( 334-)  B       911 - GLU    336- ( B)         -5.46
1042 PHE   ( 467-)  B      1044 - PHE    469- ( B)         -4.52
1495 LYS   ( 334-)  C      1497 - GLU    336- ( C)         -5.52
1628 PHE   ( 467-)  C      1630 - PHE    469- ( C)         -4.67
2081 LYS   ( 334-)  D      2083 - GLU    336- ( D)         -5.47
2214 PHE   ( 467-)  D      2216 - PHE    469- ( D)         -4.58

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: S

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: T

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: U

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: V

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.

 288 ALA   ( 299-)  A   -2.76
1159 VAL   ( 110-)  T   -2.76
 573 VAL   ( 110-)  S   -2.73
2331 VAL   ( 110-)  V   -2.72
 874 ALA   ( 299-)  B   -2.70
1627 LYS   ( 466-)  C   -2.67
1460 ALA   ( 299-)  C   -2.65
2046 ALA   ( 299-)  D   -2.65
1266 LEU   ( 105-)  C   -2.64
1852 LEU   ( 105-)  D   -2.63
1745 VAL   ( 110-)  U   -2.62
1012 LEU   ( 437-)  B   -2.54
 426 LEU   ( 437-)  A   -2.54

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: S

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: T

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: U

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: V

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.

2365 HOH   ( 519 )  A      O     40.76   35.19   60.08
2365 HOH   ( 720 )  A      O     27.89   67.82   39.09
2365 HOH   ( 782 )  A      O    -29.10   -3.18   43.04
2365 HOH   ( 811 )  A      O     33.21   67.33   22.49
2365 HOH   ( 812 )  A      O    -12.28  -23.99   55.33
2365 HOH   ( 817 )  A      O     11.89   27.55   48.85
2365 HOH   ( 821 )  A      O     14.53   41.43   49.90
2365 HOH   ( 840 )  A      O     48.28   39.50    0.59
2365 HOH   ( 865 )  A      O     34.28   70.45   22.54
2365 HOH   ( 868 )  A      O     44.55   51.87   12.52
2365 HOH   ( 869 )  A      O     46.85   50.62   12.93
2365 HOH   ( 871 )  A      O     51.71   46.97   30.84
2365 HOH   ( 876 )  A      O    -23.31  -11.61   45.55
2365 HOH   ( 881 )  A      O    -13.96  -22.86   56.70
2365 HOH   ( 889 )  A      O     30.71   71.68   57.80
2365 HOH   ( 918 )  A      O    -28.79   -5.60   42.19
2365 HOH   ( 922 )  A      O     36.06   51.38    1.82
2365 HOH   ( 927 )  A      O    -20.65  -19.65   61.03
2365 HOH   ( 928 )  A      O    -15.44  -22.36   62.50
2366 HOH   ( 170 )  S      O     40.05   23.70    0.07
2366 HOH   ( 260 )  S      O     38.93   14.57    4.99
2366 HOH   ( 265 )  S      O     24.88   79.63   81.70
2366 HOH   ( 270 )  S      O     50.68   26.15    7.26
2366 HOH   ( 272 )  S      O     40.15   11.96    3.20
2366 HOH   ( 287 )  S      O     23.03   81.04   80.39
And so on for a total of 63 lines.

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.

2365 HOH   ( 779 )  A      O
2365 HOH   ( 817 )  A      O
2365 HOH   ( 825 )  A      O
2365 HOH   ( 843 )  A      O
2365 HOH   ( 863 )  A      O
2365 HOH   ( 864 )  A      O
2365 HOH   ( 867 )  A      O
2365 HOH   ( 870 )  A      O
2365 HOH   ( 915 )  A      O
2365 HOH   ( 920 )  A      O
2365 HOH   ( 928 )  A      O
2366 HOH   ( 199 )  S      O
2366 HOH   ( 200 )  S      O
2366 HOH   ( 210 )  S      O
2366 HOH   ( 234 )  S      O
2366 HOH   ( 241 )  S      O
2366 HOH   ( 246 )  S      O
2366 HOH   ( 252 )  S      O
2366 HOH   ( 264 )  S      O
2366 HOH   ( 288 )  S      O
2366 HOH   ( 296 )  S      O
2367 HOH   ( 767 )  B      O
2367 HOH   ( 775 )  B      O
2367 HOH   ( 821 )  B      O
2367 HOH   ( 822 )  B      O
And so on for a total of 87 lines.

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.

 492 GLN   (  29-)  S
 519 HIS   (  56-)  S
 782 ASN   ( 207-)  B
 857 HIS   ( 282-)  B
 879 GLN   ( 304-)  B
1056 GLN   (   7-)  T
1097 HIS   (  48-)  T
1104 HIS   (  55-)  T
1247 HIS   (  86-)  C
1465 GLN   ( 304-)  C
1562 GLN   ( 401-)  C
1664 GLN   (  29-)  U
1690 HIS   (  55-)  U
1691 HIS   (  56-)  U
1842 ASN   (  95-)  D
2051 GLN   ( 304-)  D
2133 HIS   ( 386-)  D
2148 GLN   ( 401-)  D
2228 GLN   (   7-)  V
2250 GLN   (  29-)  V

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.

  54 THR   (  65-)  A      OG1
  56 THR   (  67-)  A      N
 164 LYS   ( 175-)  A      N
 164 LYS   ( 175-)  A      NZ
 167 LEU   ( 178-)  A      N
 168 GLY   ( 179-)  A      N
 186 LEU   ( 197-)  A      N
 190 KCX   ( 201-)  A      OX1
 196 ASN   ( 207-)  A      ND2
 200 PHE   ( 211-)  A      N
 206 ARG   ( 217-)  A      NH1
 228 TYR   ( 239-)  A      OH
 235 THR   ( 246-)  A      N
 284 ARG   ( 295-)  A      NE
 292 ARG   ( 303-)  A      NE
 312 GLY   ( 323-)  A      N
 323 LYS   ( 334-)  A      NZ
 368 SER   ( 379-)  A      OG
 370 GLY   ( 381-)  A      N
 390 GLN   ( 401-)  A      NE2
 393 GLY   ( 404-)  A      N
 402 ASN   ( 413-)  A      ND2
 443 GLU   ( 454-)  A      N
 463 THR   ( 474-)  A      N
 492 GLN   (  29-)  S      NE2
And so on for a total of 123 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.

 257 ASP   ( 268-)  A      OD1
 257 ASP   ( 268-)  A      OD2
 316 HIS   ( 327-)  A      ND1
 390 GLN   ( 401-)  A      OE1
 782 ASN   ( 207-)  B      OD1
 843 ASP   ( 268-)  B      OD1
 843 ASP   ( 268-)  B      OD2
 902 HIS   ( 327-)  B      ND1
 976 GLN   ( 401-)  B      OE1
1429 ASP   ( 268-)  C      OD1
1488 HIS   ( 327-)  C      ND1
2015 ASP   ( 268-)  D      OD1
2015 ASP   ( 268-)  D      OD2
2074 HIS   ( 327-)  D      ND1

Warning: Unusual water packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF] and Mueller, Koepke and Sheldrick [REF]. It must be stated that the validation of ions in PDB files is very difficult. Ideal ion-ligand distances often differ no more than 0.1 Angstrom, and in a 2.0 Angstrom resolution structure 0.1 Angstrom is not very much. Nayal and Di Cera showed that this method nevertheless has great potential for detecting water molecules that actually should be metal ions. The method has not been extensively validated, though. Part of our implementation (comparing waters with multiple ion types) is even fully new and despite that we see it work well in the few cases that are trivial, we must emphasize that this method is untested.

The score listed is the valency score. This number should be close to (preferably a bit above) 1.0 for the suggested ion to be a likely alternative for the water molecule. Ions listed in brackets are good alternate choices. *1 indicates that the suggested ion-type has been observed elsewhere in the PDB file too. *2 indicates that the suggested ion-type has been observed in the REMARK 280 cards of the PDB file. Ion-B and ION-B indicate that the B-factor of this water is high, or very high, respectively. H2O-B indicates that the B-factors of atoms that surround this water/ion are suspicious. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

2365 HOH   ( 517 )  A      O  0.88  K  4 NCS 3/3
2365 HOH   ( 597 )  A      O  0.87  K  4 NCS 3/3
2365 HOH   ( 693 )  A      O  1.10  K  4 NCS 3/3
2365 HOH   ( 703 )  A      O  0.92  K  6
2365 HOH   ( 736 )  A      O  1.01  K  5
2365 HOH   ( 917 )  A      O  1.02  K  5 ION-B
2365 HOH   ( 925 )  A      O  0.91  K  5 ION-B
2366 HOH   ( 167 )  S      O  1.12  K  4 NCS 3/3
2366 HOH   ( 276 )  S      O  0.93 NA  4 *2 Ion-B
2366 HOH   ( 284 )  S      O  0.82 NA  5 *2 ION-B
2367 HOH   ( 554 )  B      O  1.10  K  4 NCS 3/3
2367 HOH   ( 621 )  B      O  0.92  K  4 NCS 2/2
2367 HOH   ( 778 )  B      O  0.93  K  4 ION-B
2367 HOH   ( 871 )  B      O  0.88 NA  4 *2 ION-B
2368 HOH   ( 125 )  T      O  0.98  K  4 NCS 3/3
2368 HOH   ( 127 )  T      O  0.86  K  4 NCS 3/3
2368 HOH   ( 235 )  T      O  0.90  K  4 ION-B
2369 HOH   ( 521 )  C      O  1.10  K  4 NCS 3/3
2369 HOH   ( 533 )  C      O  0.91  K  4 NCS 3/3
2369 HOH   ( 596 )  C      O  1.12  K  4 NCS 3/3
2369 HOH   ( 717 )  C      O  1.03  K  5 NCS 3/3
2370 HOH   ( 143 )  U      O  0.93  K  4 Ion-B
2370 HOH   ( 241 )  U      O  1.04  K  4 ION-B
2371 HOH   ( 530 )  D      O  1.00  K  4 NCS 3/3
2371 HOH   ( 609 )  D      O  0.86  K  4 NCS 3/3
2371 HOH   ( 652 )  D      O  1.08  K  4 NCS 3/3
2372 HOH   ( 128 )  V      O  0.88  K  4 NCS 3/3
2372 HOH   ( 167 )  V      O  0.96  K  4 NCS 1/1
2372 HOH   ( 276 )  V      O  0.99  K  4 Ion-B

Warning: Possible wrong residue type

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

 257 ASP   ( 268-)  A   H-bonding suggests Asn; but Alt-Rotamer
 291 ASP   ( 302-)  A   H-bonding suggests Asn
 494 ASP   (  31-)  S   H-bonding suggests Asn
 843 ASP   ( 268-)  B   H-bonding suggests Asn; but Alt-Rotamer
1080 ASP   (  31-)  T   H-bonding suggests Asn
1321 ASP   ( 160-)  C   H-bonding suggests Asn; but Alt-Rotamer
1429 ASP   ( 268-)  C   H-bonding suggests Asn; but Alt-Rotamer
1907 ASP   ( 160-)  D   H-bonding suggests Asn; but Alt-Rotamer
2015 ASP   ( 268-)  D   H-bonding suggests Asn; but Alt-Rotamer
2049 ASP   ( 302-)  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 :  -1.276
  2nd generation packing quality :  -0.455
  Ramachandran plot appearance   :  -0.722
  chi-1/chi-2 rotamer normality  :  -0.987
  Backbone conformation          :  -0.665

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.273 (tight)
  Bond angles                    :   0.656 (tight)
  Omega angle restraints         :   0.266 (tight)
  Side chain planarity           :   0.275 (tight)
  Improper dihedral distribution :   0.564
  B-factor distribution          :   0.628
  Inside/Outside distribution    :   1.070

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 : 1.80


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.9
  2nd generation packing quality :  -0.7
  Ramachandran plot appearance   :  -0.7
  chi-1/chi-2 rotamer normality  :  -0.7
  Backbone conformation          :  -0.9

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.273 (tight)
  Bond angles                    :   0.656 (tight)
  Omega angle restraints         :   0.266 (tight)
  Side chain planarity           :   0.275 (tight)
  Improper dihedral distribution :   0.564
  B-factor distribution          :   0.628
  Inside/Outside distribution    :   1.070
==============

WHAT IF
    G.Vriend,
      WHAT IF: a molecular modelling and drug design program,
    J. Mol. Graph. 8, 52--56 (1990).

WHAT_CHECK (verification routines from WHAT IF)
    R.W.W.Hooft, G.Vriend, C.Sander and E.E.Abola,
      Errors in protein structures
    Nature 381, 272 (1996).
    (see also http://swift.cmbi.ru.nl/gv/whatcheck for a course and extra inform

Bond lengths and angles, protein residues
    R.Engh and R.Huber,
      Accurate bond and angle parameters for X-ray protein structure
      refinement,
    Acta Crystallogr. A47, 392--400 (1991).

Bond lengths and angles, DNA/RNA
    G.Parkinson, J.Voitechovsky, L.Clowney, A.T.Bruenger and H.Berman,
      New parameters for the refinement of nucleic acid-containing structures
    Acta Crystallogr. D52, 57--64 (1996).

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

Hydrogen bond networks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Positioning hydrogen atoms by optimizing hydrogen bond networks in
      protein structures
    PROTEINS, 26, 363--376 (1996).

Matthews' Coefficient
    B.W.Matthews
      Solvent content of Protein Crystals
    J. Mol. Biol. 33, 491--497 (1968).

Protein side chain planarity
    R.W.W. Hooft, C. Sander and G. Vriend,
      Verification of protein structures: side-chain planarity
    J. Appl. Cryst. 29, 714--716 (1996).

Puckering parameters
    D.Cremer and J.A.Pople,
      A general definition of ring puckering coordinates
    J. Am. Chem. Soc. 97, 1354--1358 (1975).

Quality Control
    G.Vriend and C.Sander,
      Quality control of protein models: directional atomic
      contact analysis,
    J. Appl. Cryst. 26, 47--60 (1993).

Ramachandran plot
    G.N.Ramachandran, C.Ramakrishnan and V.Sasisekharan,
      Stereochemistry of Polypeptide Chain Conformations
    J. Mol. Biol. 7, 95--99 (1963).

Symmetry Checks
    R.W.W.Hooft, C.Sander and G.Vriend,
      Reconstruction of symmetry related molecules from protein
      data bank (PDB) files
    J. Appl. Cryst. 27, 1006--1009 (1994).

Ion Checks
    I.D.Brown and K.K.Wu,
      Empirical Parameters for Calculating Cation-Oxygen Bond Valences
    Acta Cryst. B32, 1957--1959 (1975).

    M.Nayal and E.Di Cera,
      Valence Screening of Water in Protein Crystals Reveals Potential Na+
      Binding Sites
    J.Mol.Biol. 256 228--234 (1996).

    P.Mueller, S.Koepke and G.M.Sheldrick,
      Is the bond-valence method able to identify metal atoms in protein
      structures?
    Acta Cryst. D 59 32--37 (2003).

Checking checks
    K.Wilson, C.Sander, R.W.W.Hooft, G.Vriend, et al.
      Who checks the checkers
    J.Mol.Biol. (1998) 276,417-436.