WHAT IF Check report

This file was created 2012-01-30 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Verification log for pdb9ick.ent

Checks that need to be done early-on in validation

Note: No crystallographic symmetry between molecules

No extra crystallographic symmetry was observed between the independent molecules.

Note: Counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Z equals the number of matrices of the space group multiplied by the number of NCS relations. These numbers seem to be consistent.

Space group as read from CRYST card: P 21 21 2
Number of matrices in space group: 4
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 1
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 4
Z, spacegroup, and NCS seem to agree administratively

Note: Matthews coefficient OK

The Matthews coefficient [REF] is defined as the density of the protein structure in cubic Angstroms per Dalton. Normal values are between 1.5 (tightly packed, little room for solvent) and 4.0 (loosely packed, much space for solvent). Some very loosely packed structures can get values a bit higher than that.

Molecular weight of all polymer chains: 41306.344
Volume of the Unit Cell V= 499588.125
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z: Vm= 3.024
Vm by authors and this calculated Vm agree remarkably well
Matthews coefficient read from REMARK 280 Vm= 3.000

Note: No atoms with high occupancy detected at special positions

Either there were no atoms at special positions, or all atoms at special positions have adequately reduced occupancies. An atom is considered to be located at a special position if it is within 0.3 Angstrom from one of its own symmetry copies. See also the next check...

Note: All atoms are sufficiently far away from symmetry axes

None of the atoms in the structure is closer than 0.77 Angstrom to a proper symmetry axis.

Note: Chain identifiers OK

WHAT IF has not detected any serious chain identifier problems. But be aware that WHAT IF doesn't care about the chain identifiers of waters.

Administrative problems that can generate validation failures

Note: No strange inter-chain connections detected

No covalent bonds have been detected between molecules with non-identical chain identifiers.

Note: No duplicate atom names in ligands

All atom names in ligands seem adequately unique.

Note: No mixed usage of alternate atom problems detected

Either this structure does not contain alternate atoms, or they have not been mixed up, or the errors have remained unnoticed.

Note: In all cases the primary alternate atom was used

WHAT IF saw no need to make any alternate atom corrections (which means they are all correct, or there are none).

Note: No residues detected inside ligands

Either this structure does not contain ligands with amino acid groups inside it, or their naming is proper (enough).

Note: No attached groups interfere with hydrogen bond calculations

It seems there are no sugars, lipids, etc., bound (very close) to atoms that otherwise could form hydrogen bonds.

Warning: Plausible side chain atoms detected with zero occupancy

Plausible side chain atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. In this case some atoms were found with zero occupancy, but with coordinates that place them at a plausible position. Although WHAT IF knows how to deal with missing side chain atoms, validation will go more reliable if all atoms are presnt. So, please consider manually setting the occupancy of the listed atoms at 1.0.

  14 GLU   (   9-)  A  -   CB
  14 GLU   (   9-)  A  -   CG
  14 GLU   (   9-)  A  -   CD
  14 GLU   (   9-)  A  -   OE1
 251 ASP   ( 246-)  A  -   CB
 251 ASP   ( 246-)  A  -   CG
 251 ASP   ( 246-)  A  -   OD2
 252 GLU   ( 247-)  A  -   CB
 252 GLU   ( 247-)  A  -   CG
 252 GLU   ( 247-)  A  -   CD
 252 GLU   ( 247-)  A  -   OE2

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone atoms were detected with (near) zero occupancy

When crystallographers do not see an atom they either leave it out completely, or give it an occupancy of zero or a very high B-factor. WHAT IF neglects these atoms. However, if a backbone atom is present in the PDB file, and its position seems 'logical' (i.e. normal bond lengths with all atoms it should be bound to, and those atoms exist normally) WHAT IF will set the occupancy to 1.0 if it believes that the full presence of this atom will be beneficial to the rest of the validation process. If you get weird errors at, or near, these atoms, please check by hand what is going on, and repair things intelligently before running this validation again.

  14 GLU   (   9-)  A  -   N
  14 GLU   (   9-)  A  -   CA
  14 GLU   (   9-)  A  -   C
  14 GLU   (   9-)  A  -   O
 251 ASP   ( 246-)  A  -   N
 251 ASP   ( 246-)  A  -   CA
 251 ASP   ( 246-)  A  -   C
 251 ASP   ( 246-)  A  -   O
 252 GLU   ( 247-)  A  -   N
 252 GLU   ( 247-)  A  -   CA
 252 GLU   ( 247-)  A  -   C
 252 GLU   ( 247-)  A  -   O

Note: All residues have a complete backbone.

No residues have missing backbone atoms.

Note: No C-alpha only residues

There are no residues that consist of only an alpha carbon atom.

Note: Non-canonicals

WHAT IF has not detected any non-canonical residue that it does not understand (or there are no non-canonical residues in the PDB file).

Non-validating, descriptive output paragraph

Note: Content of the PDB file as interpreted by WHAT IF

Content of the PDB file as interpreted by WHAT IF. WHAT IF has read your PDB file, and stored it internally in what is called 'the soup'. The content of this soup is listed here. An extensive explanation of all frequently used WHAT IF output formats can be found at swift.cmbi.ru.nl. Look under output formats. A course on reading this 'Molecules' table is part of the WHAT CHECK web pages.

     1     1 (    2)     7 (    8) T DNA/RNA             pdb9ick.ent
     2     8 (    1)    13 (    6) P DNA/RNA             pdb9ick.ent
     3    14 (    9)   340 (  335) A Protein             pdb9ick.ent
     4   341 (  335)   341 (  335) A E O2 <-   340       pdb9ick.ent
     5   342 (  341)   342 (  341) A  NA                 pdb9ick.ent
     6   343 (  342)   343 (  342) A  NA                 pdb9ick.ent
     7   344 ( HOH )   344 ( HOH ) T water   (   12)     pdb9ick.ent
     8   345 ( HOH )   345 ( HOH ) P water   (   21)     pdb9ick.ent
     9   346 ( HOH )   346 ( HOH ) A water   (  120)     pdb9ick.ent

Note: Some notes regarding the PDB file contents

The numbers and remarks listed below have no explicit validation purpose, they are merely meant for the crystallographer or NMR spectroscopists to perhaps pinpoint something unexpected. See the WHAT_CHECK course for an explanation of terms like 'poor', 'missing', etcetera (in case those words pop up in the lines underneath this message).

The total number of amino acids found is 327.
of which 24 have poor or missing atoms.
Number of nucleic acids 13
of which 2 have poor or missing atoms.
Number of water molecules 153
of which 4 are poor.

Note: Chain identifiers seem OK

All ions seem to have a logical chain identifier, or there are no ions present in the input file.

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: Secondary structure

This is the secondary structure according to DSSP. Only helix (H), overwound or 3/10-helix (3), strand (S), turn (T) and coil (blank) are shown [REF]. All DSSP related information can be found at the DSSP page This is not really a structure validation option, but a very scattered secondary structure (i.e. many strands of only a few residues length, many Ts inside helices, etc) tends to indicate a poor structure. A full explanation of the DSSP secondary structure determination program together with a series of examples can be found at the WHAT_CHECK website.
                  20        30        40        50        60        70
                   |         |         |         |         |         |
   14 -   73 ETLNGGITDMLTELANFEKNVSQAIHKYNAYRKAASVIAKYPHKIKSGAEAKKLPGVGTK
(   9)-(  68)  TTHHHHHHHHHHHHHHHHTT  HHHHHHHHHHHHHHHH  T    HHHHHTTTT  HH
                  80        90       100       110       120       130
                   |         |         |         |         |         |
   74 -  133 IAEKIDEFLATGKLRKLEKIRQDDTSSSINFLTRVSGIGPSAARKFVDEGIKTLEDLRKN
(  69)-( 128)HHHHHHHHHHTT  HHHHHHHH HHHHHHHHHTTTTT  HHHHHHHHHTT  THHHHHHT
                 140       150       160       170       180       190
                   |         |         |         |         |         |
  134 -  193 EDKLNHHQRIGLKYFGDFEKRIPREEMLQMQDIVLNEVKKVDSEYIATVCGSFRRGAESS
( 129)-( 188)333T HHHHHHHHTHHHHHT SSHHHHHHHHHHHHHHHHHH TT SSSS T3333  TSS
                 200       210       220       230       240       250
                   |         |         |         |         |         |
  194 -  253 GDMDVLLTHPSFTSESTKQPKLLHQVVEQLQKVHFITDTLSKGETKFMGVCQLPSKNDEK
( 189)-( 248)TTSSSSSSSTT  TTT   THHHHHHHHHHHHTT SSSSSSS TTSSSSSS    TTTT
                 260       270       280       290       300       310
                   |         |         |         |         |         |
  254 -  313 EYPHRRIDIRLIPKDQYYCGVLYFTGSDIFNKNMRAHALEKGFTINEYTIRPLGVTGVAG
( 249)-( 308)    SSSSSSSSS333HHHHHHHHH  HHHHHHHHHHHHHTTSSS TT SSS  TTT
                 320       330       340
                   |         |         |
  314 -  340 EPLPVDSEKDIFDYIQWKYREPKDRSE
( 309)-( 335)     TTHHHHHHHT      T333
 
 
 

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

Note: No rounded coordinates detected

No significant rounding of atom coordinates has been detected.

Note: No artificial side chains detected

No artificial side-chain positions characterized by chi-1=0.0 or chi-1=180.0 have been detected.

Warning: Missing atoms

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

   7 DTHY  (   8-)  T      C3'
   7 DTHY  (   8-)  T      O3'
   7 DTHY  (   8-)  T      C5'
   7 DTHY  (   8-)  T      C4'
   7 DTHY  (   8-)  T      O4'
   7 DTHY  (   8-)  T      C1'
   7 DTHY  (   8-)  T      C2'
   7 DTHY  (   8-)  T      N1
   7 DTHY  (   8-)  T      C6
   7 DTHY  (   8-)  T      C5
   7 DTHY  (   8-)  T      C4
   7 DTHY  (   8-)  T      O4
   7 DTHY  (   8-)  T      N3
   7 DTHY  (   8-)  T      C2
   7 DTHY  (   8-)  T      O2
   7 DTHY  (   8-)  T      C7
  14 GLU   (   9-)  A      OE2
 251 ASP   ( 246-)  A      OD1
 252 GLU   ( 247-)  A      OE1

Note: All B-factors fall in the range 0.0 - 100.0

All B-factors are larger than zero, and none are observed above 100.0.

Note: No C-terminal nitrogen detected

The PDB indicates that a residue is not the true C-terminus by including only the backbone N of the next residue. This has not been observed in this PDB file.

Note: Test capping of (pseudo) C-termini

No extra capping groups were found on pseudo C-termini. This can imply that no pseudo C-termini are present.

Note: No OXT found in the middle of chains

No OXT groups were found in the middle of protein chains.

Note: Weights checked OK

All atomic occupancy factors ('weights') fall in the 0.0-1.0 range.

Note: Normal distribution of occupancy values

The distribution of the occupancy values in this file seems 'normal'.

Be aware that this evaluation is merely the result of comparing this file with about 500 well-refined high-resolution files in the PDB. If this file has much higher or much lower resolution than the PDB files used in WHAT IF's training set, non-normal values might very well be perfectly fine, or normal values might actually be not so normal. So, this check is actually more an indicator and certainly not a check in which I have great confidence.

Note: All occupancies seem to add up to 0.0 - 1.0.

In principle, the occupancy of all alternates of one atom should add up till 0.0 - 1.0. 0.0 is used for the missing atom (i.e. an atom not seen in the electron density). Obviously, there is nothing terribly wrong when a few occupancies add up to a bit more than 1.0, because the mathematics of refinement allow for that. However, if it happens often, it seems worth evaluating this in light of the refinement protocol used.

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: Number of buried atoms with low B-factor is OK

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 : 0.09

Note: B-factor distribution normal

The distribution of B-factors within residues is within expected ranges. A value over 1.5 here would mean that the B-factors show signs of over- refinement.

RMS Z-score : 1.385 over 2280 bonds
Average difference in B over a bond : 4.45
RMS difference in B over a bond : 5.82

Note: B-factor plot

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

Chain identifier: A

Nomenclature related problems

Note: Introduction to the nomenclature section.

Nomenclature problems seem, at first, rather unimportant. After all who cares if we call the delta atoms in leucine delta2 and delta1 rather than the other way around. Chemically speaking that is correct. But structures have not been solved and deposited just for chemists to look at them. Most times a structure is used, it is by software in a bioinformatics lab. And if they compare structures in which the one used C delta1 and delta2 and the other uses C delta2 and delta1, then that comparison will fail. Also, we recalculate all structures every so many years to make sure that everybody always can get access to the best coordinates that can be obtained from the (your?) experimental data. These recalculations will be troublesome if there are nomenclature problems.

Several nomenclature problems actually are worse than that. At the WHAT_CHECK website you can get an overview of the importance of all nomenclature problems that we list.

Note: Valine nomenclature OK

No errors were detected in valine nomenclature.

Note: Threonine nomenclature OK

No errors were detected in threonine nomenclature.

Note: Isoleucine nomenclature OK

No errors were detected in isoleucine nomenclature.

Note: Leucine nomenclature OK

No errors were detected in leucine nomenclature.

Note: Arginine nomenclature OK

No errors were detected in arginine nomenclature.

Note: Tyrosine torsion conventions OK

No errors were detected in tyrosine torsion angle conventions.

Note: Phenylalanine torsion conventions OK

No errors were detected in phenylalanine torsion angle conventions.

Note: Aspartic acid torsion conventions OK

No errors were detected in aspartic acid torsion angle conventions.

Note: Glutamic acid torsion conventions OK

No errors were detected in glutamic acid torsion angle conventions.

Note: Phosphate group names OK

No errors were detected in phosphate group naming conventions.

Note: Heavy atom naming OK

No errors were detected in the atom names for non-hydrogen atoms. Please be aware that the PDB wants us to deliberately make some nomenclature errors; especially in non-canonical amino acids.

Note: Chain names are OK

All chain names assigned to polymer molecules are unique, and all residue numbers are strictly increasing within each chain.

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.

   1 DCYT  (   2-)  T      C5'  C4'   1.54    4.2
   2 DADE  (   3-)  T      N9   C4    1.42    8.4
   2 DADE  (   3-)  T      C8   N7    1.34    4.8
   4 DCYT  (   5-)  T      C3'  O3'   1.37   -4.8
   4 DCYT  (   5-)  T      O5'  C5'   1.34   -5.9
   4 DCYT  (   5-)  T      N3   C2    1.39    5.1
   4 DCYT  (   5-)  T      C4   N3    1.37    5.4
   5 DTHY  (   6-)  T      C3'  O3'   1.37   -4.5
   5 DTHY  (   6-)  T      P    O5'   1.55   -4.1
   6 DGUA  (   7-)  T      C3'  O3'   1.37   -4.4
   6 DGUA  (   7-)  T      C1'  N9    1.38   -8.3
   6 DGUA  (   7-)  T      N9   C8    1.34   -4.3
   6 DGUA  (   7-)  T      C6   N1    1.36   -4.9
   8 DCYT  (   1-)  P      O5'  C5'   1.35   -5.8
   8 DCYT  (   1-)  P      C5'  C4'   1.48   -4.4
   9 DADE  (   2-)  P      O5'  C5'   1.34   -6.1
   9 DADE  (   2-)  P      C4'  C3'   1.49   -4.1
   9 DADE  (   2-)  P      C6   N1    1.32   -4.1
  10 DGUA  (   3-)  P      C3'  C2'   1.56    4.1
  10 DGUA  (   3-)  P      C5   C6    1.36   -6.0
  10 DGUA  (   3-)  P      C6   N1    1.35   -5.3
  11 DADE  (   4-)  P      N9   C4    1.33   -6.6
  12 DTHY  (   5-)  P      C3'  O3'   1.37   -5.0
  12 DTHY  (   5-)  P      O5'  C5'   1.36   -5.2
  12 DTHY  (   5-)  P      C1'  N1    1.64   11.7
And so on for a total of 52 lines.

Note: Normal bond length variability

Bond lengths were found to deviate normally from the standard bond lengths (values for Protein residues were taken from Engh and Huber [REF], for DNA/RNA from Parkinson et al [REF]).

RMS Z-score for bond lengths: 1.334
RMS-deviation in bond distances: 0.024

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

 |  1.003094  0.000848  0.000578|
 |  0.000848  1.003989  0.000202|
 |  0.000578  0.000202  1.002917|
Proposed new scale matrix

 |  0.005584 -0.000005 -0.000003|
 | -0.000015  0.017254 -0.000003|
 | -0.000012 -0.000004  0.020570|
With corresponding cell

    A    = 179.092  B   =  57.957  C    =  48.615
    Alpha=  89.977  Beta=  89.934  Gamma=  89.903

The CRYST1 cell dimensions

    A    = 178.540  B   =  57.726  C    =  48.473
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 171.927
(Under-)estimated Z-score: 9.664

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.

   1 DCYT  (   2-)  T      C1'  N1   C6  110.04   -9.0
   1 DCYT  (   2-)  T      C1'  N1   C2  129.78   10.0
   2 DADE  (   3-)  T      C5   C4   N3  123.84   -4.2
   2 DADE  (   3-)  T      C2   N3   C4  113.85    6.5
   3 DTHY  (   4-)  T      C1'  N1   C6  103.86  -11.0
   3 DTHY  (   4-)  T      C1'  N1   C2  134.60   10.2
   3 DTHY  (   4-)  T      N3   C2   O2  119.24   -5.1
   4 DCYT  (   5-)  T      P   -C3* -O3* 126.63    5.8
   4 DCYT  (   5-)  T      C1'  N1   C6  105.62  -12.7
   4 DCYT  (   5-)  T      C1'  N1   C2  133.63   13.5
   4 DCYT  (   5-)  T      C5   C4   N3  119.85   -5.1
   5 DTHY  (   6-)  T      O5*  P   -O3*  96.36   -4.0
   5 DTHY  (   6-)  T      P   -C3* -O3* 126.16    5.4
   5 DTHY  (   6-)  T      P    O5'  C5' 114.33   -4.1
   5 DTHY  (   6-)  T      C1'  N1   C6  112.76   -5.1
   5 DTHY  (   6-)  T      C6   N1   C2  124.18    5.8
   6 DGUA  (   7-)  T      C2'  C1'  N9  107.25   -4.3
   8 DCYT  (   1-)  P      C1'  N1   C6  111.94   -7.4
   8 DCYT  (   1-)  P      C1'  N1   C2  127.55    8.0
   9 DADE  (   2-)  P      P   -C3* -O3* 125.47    4.8
   9 DADE  (   2-)  P      C3'  C4'  O4'  98.98   -6.6
   9 DADE  (   2-)  P      C4'  C3'  C2'  96.01   -7.2
   9 DADE  (   2-)  P      C1'  N9   C4  133.85    4.2
  10 DGUA  (   3-)  P      P    O5'  C5' 128.24    4.6
  10 DGUA  (   3-)  P      N9   C8   N7  114.70    7.2
And so on for a total of 120 lines.

Note: Normal bond angle variability

Bond angles were found to deviate normally from the mean 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, and this is indeed observed for very high resolution X-ray structures.

RMS Z-score for bond angles: 1.668
RMS-deviation in bond angles: 2.962

Note: Residue hand error(s)

No atoms are observed that have the wrong handedness. Be aware, though, that WHAT IF might have corrected the handedness of some atoms already. The handedness has not been corrected for any case where the problem is worse than just an administrative discomfort.

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.

  16 LEU   (  11-)  A      CA    -6.6    24.14    34.19
  25 THR   (  20-)  A      CA    -9.1    18.65    33.84
  37 ALA   (  32-)  A      CA   -15.7    14.11    34.09
  45 ARG   (  40-)  A      CA   -10.8    16.16    33.91
  91 GLU   (  86-)  A      CA   -10.5    16.69    33.96
  97 ASP   (  92-)  A      CA   -10.2    13.42    33.73
 128 GLU   ( 123-)  A      CA    -6.8    22.83    33.96
 143 ILE   ( 138-)  A      CB     6.6    40.93    32.31
 157 ARG   ( 152-)  A      CA   -11.8    14.64    33.91
 173 LYS   ( 168-)  A      CA    -9.1    18.89    33.92
 203 PRO   ( 198-)  A      N      6.4    18.46    -2.48
 247 PRO   ( 242-)  A      N      9.5    28.66    -2.48
 251 ASP   ( 246-)  A      CA   -15.2     3.54    33.73
 297 THR   ( 292-)  A      CA   -17.7     4.25    33.84
 312 ALA   ( 307-)  A      CA   -15.3    14.66    34.09
 314 GLU   ( 309-)  A      CA    -6.3    23.68    33.96
 339 SER   ( 334-)  A      CA    -9.0    17.54    34.32
 340 GLU   ( 335-)  A      CA    -6.4    23.53    33.96
The average deviation= 2.181

Warning: High improper dihedral angle deviations

The RMS Z-score for the improper dihedrals in the structure is high. For well refined structures this number is expected to be near 1.0. The fact that it is higher than 2.0 worries us a bit. However, we determined the improper normal distribution from 500 high-resolution X-ray structures, rather than from CSD data, so we cannot be 100 percent certain about these numbers.

Improper dihedral RMS Z-score : 2.252

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.

  37 ALA   (  32-)  A    6.34
 296 PHE   ( 291-)  A    5.55
  45 ARG   (  40-)  A    5.45
 293 GLU   ( 288-)  A    4.42
 230 THR   ( 225-)  A    4.22
 251 ASP   ( 246-)  A    4.21
  33 ASN   (  28-)  A    4.17
 112 GLY   ( 107-)  A    4.15

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 : 1.769

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.

 138 ASN   ( 133-)  A    6.44
 293 GLU   ( 288-)  A    5.69
 221 GLU   ( 216-)  A    5.12
 177 GLU   ( 172-)  A    4.64
 300 GLU   ( 295-)  A    4.54
 268 ASP   ( 263-)  A    4.46
 128 GLU   ( 123-)  A    4.20
 321 GLU   ( 316-)  A    4.10
 319 ASP   ( 314-)  A    4.05

Note: Atoms connected to aromatic rings OK

All of the atoms that are connected to planar aromatic rings in side chains of amino-acid residues are in the plane within expected RMS deviations.

Note: Uncalibrated side chain planarity OK

All of the side chains of DNA/RNA residues (and groups in proteins that contain a proton and are supposed to be planar) are planar within 0.10 Angstrom RMS (or no DNA/RNA was found...). Please be aware that this check cannot be callibrated and that the cutoff of 0.10 Angstrom thus is a wild guess.

Torsion-related checks

Warning: Ramachandran Z-score low

The score expressing how well the backbone conformations of all residues correspond to the known allowed areas in the Ramachandran plot is a bit low.

Ramachandran Z-score : -3.249

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.

  15 THR   (  10-)  A    -3.0
 206 THR   ( 201-)  A    -2.6
 311 VAL   ( 306-)  A    -2.6
  86 LYS   (  81-)  A    -2.5
 260 ILE   ( 255-)  A    -2.5
 253 LYS   ( 248-)  A    -2.5
 298 ILE   ( 293-)  A    -2.5
 207 SER   ( 202-)  A    -2.4
 209 SER   ( 204-)  A    -2.4
 317 PRO   ( 312-)  A    -2.3
 330 TRP   ( 325-)  A    -2.3
 201 THR   ( 196-)  A    -2.3
 314 GLU   ( 309-)  A    -2.3
 212 GLN   ( 207-)  A    -2.3
  38 ILE   (  33-)  A    -2.3
  67 LEU   (  62-)  A    -2.3
 302 THR   ( 297-)  A    -2.2
 106 THR   ( 101-)  A    -2.2
 309 THR   ( 304-)  A    -2.2
 310 GLY   ( 305-)  A    -2.1
 327 TYR   ( 322-)  A    -2.1
 189 GLY   ( 184-)  A    -2.1
 263 ARG   ( 258-)  A    -2.0
 250 ASN   ( 245-)  A    -2.0
 126 THR   ( 121-)  A    -2.0
 247 PRO   ( 242-)  A    -2.0
 308 VAL   ( 303-)  A    -2.0
 231 ASP   ( 226-)  A    -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.

  15 THR   (  10-)  A  Poor phi/psi
  37 ALA   (  32-)  A  Poor phi/psi
  85 GLY   (  80-)  A  Poor phi/psi
  96 ASP   (  91-)  A  Poor phi/psi
 183 CYS   ( 178-)  A  Poor phi/psi
 190 ALA   ( 185-)  A  Poor phi/psi
 207 SER   ( 202-)  A  Poor phi/psi
 211 LYS   ( 206-)  A  Poor phi/psi
 212 GLN   ( 207-)  A  Poor phi/psi
 227 HIS   ( 222-)  A  Poor phi/psi
 238 THR   ( 233-)  A  Poor phi/psi
 249 LYS   ( 244-)  A  Poor phi/psi
 251 ASP   ( 246-)  A  Poor phi/psi
 252 GLU   ( 247-)  A  Poor phi/psi
 279 GLY   ( 274-)  A  omega poor
 294 LYS   ( 289-)  A  Poor phi/psi
 312 ALA   ( 307-)  A  Poor phi/psi
 314 GLU   ( 309-)  A  Poor phi/psi
 chi-1/chi-2 correlation Z-score : -5.168

Error: chi-1/chi-2 angle correlation Z-score very low

The score expressing how well the chi-1/chi-2 angles of all residues correspond to the populated areas in the database is very low.

chi-1/chi-2 correlation Z-score : -5.168

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.

  49 SER   (  44-)  A    0.38
 114 SER   ( 109-)  A    0.39

Warning: Unusual backbone conformations

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

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

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

   3 DTHY  (   4-)  T      0
   4 DCYT  (   5-)  T      0
   5 DTHY  (   6-)  T      0
   6 DGUA  (   7-)  T      0
   7 DTHY  (   8-)  T      0
   8 DCYT  (   1-)  P      0
   9 DADE  (   2-)  P      0
  10 DGUA  (   3-)  P      0
  11 DADE  (   4-)  P      0
  12 DTHY  (   5-)  P      0
  13 DGUA  (   6-)  P      0
  14 GLU   (   9-)  A      0
  15 THR   (  10-)  A      0
  16 LEU   (  11-)  A      0
  36 GLN   (  31-)  A      0
  37 ALA   (  32-)  A      0
  45 ARG   (  40-)  A      0
  54 TYR   (  49-)  A      0
  56 HIS   (  51-)  A      0
  86 LYS   (  81-)  A      0
  96 ASP   (  91-)  A      0
 108 VAL   ( 103-)  A      0
 109 SER   ( 104-)  A      0
 122 GLU   ( 117-)  A      0
 124 ILE   ( 119-)  A      0
And so on for a total of 117 lines.

Note: Backbone conformation Z-score OK

The backbone conformation analysis gives a score that is normal for well refined protein structures.

Backbone conformation Z-score : -0.353

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 : 0.914

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!

 189 GLY   ( 184-)  A   2.21   80

Note: Peptide bond conformations

We could not find any peptide bonds that are likely to actually be a cis bond. This check has not yet fully matured...

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]

  55 PRO   (  50-)  A    0.17 LOW
  68 PRO   (  63-)  A    0.12 LOW
 113 PRO   ( 108-)  A    0.17 LOW
 213 PRO   ( 208-)  A    0.02 LOW
 256 PRO   ( 251-)  A    0.10 LOW
 305 PRO   ( 300-)  A    0.14 LOW
 317 PRO   ( 312-)  A    0.06 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].

 156 PRO   ( 151-)  A   -49.9 half-chair C-beta/C-alpha (-54 degrees)
 203 PRO   ( 198-)  A    33.4 envelop C-delta (36 degrees)
 247 PRO   ( 242-)  A   -64.3 envelop C-beta (-72 degrees)
 266 PRO   ( 261-)  A  -126.5 half-chair C-delta/C-gamma (-126 degrees)
 315 PRO   ( 310-)  A   125.9 half-chair C-beta/C-alpha (126 degrees)
 335 PRO   ( 330-)  A   100.0 envelop C-beta (108 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short interactomic distance; each bump is listed in only one direction.

The contact distances of all atom pairs have been checked. Two atoms are said to `bump' if they are closer than the sum of their Van der Waals radii minus 0.40 Angstrom. For hydrogen bonded pairs a tolerance of 0.55 Angstrom is used. The first number in the table tells you how much shorter that specific contact is than the acceptable limit. The second distance is the distance between the centres of the two atoms. Although we believe that two water atoms at 2.4 A distance are too close, we only report water pairs that are closer than this rather short distance.

The last text-item on each line represents the status of the atom pair. If the final column contains the text 'HB', the bump criterion was relaxed because there could be a hydrogen bond. Similarly relaxed criteria are used for 1-3 and 1-4 interactions (listed as 'B2' and 'B3', respectively). BL indicates that the B-factors of the clashing atoms have a low B-factor thereby making this clash even more worrisome. INTRA and INTER indicate whether the clashes are between atoms in the same asymmetric unit, or atoms in symmetry related asymmetric units, respectively.

   2 DADE  (   3-)  T      N1  <->   12 DTHY  (   5-)  P      N3     0.74    2.26  INTRA BL
   3 DTHY  (   4-)  T      N3  <->   11 DADE  (   4-)  P      N1     0.54    2.46  INTRA BF
  54 TYR   (  49-)  A      CA  <->   55 PRO   (  50-)  A      CD     0.49    2.31  INTRA BL
  36 GLN   (  31-)  A      NE2 <->  117 ARG   ( 112-)  A      NH1    0.49    2.36  INTRA BF
  36 GLN   (  31-)  A      N   <->  346 HOH   ( 641 )  A      O      0.43    2.27  INTRA BF
   1 DCYT  (   2-)  T      N3  <->   13 DGUA  (   6-)  P      N1     0.42    2.58  INTRA BF
   9 DADE  (   2-)  P      N6  <->  345 HOH   ( 598 )  P      O      0.42    2.28  INTRA BF
 255 TYR   ( 250-)  A      N   <->  346 HOH   ( 667 )  A      O      0.41    2.29  INTRA BL
 125 LYS   ( 120-)  A      N   <->  129 ASP   ( 124-)  A      OD2    0.41    2.29  INTRA
 187 ARG   ( 182-)  A      NH2 <->  321 GLU   ( 316-)  A      OE2    0.41    2.29  INTRA BF
 187 ARG   ( 182-)  A      NH1 <->  278 THR   ( 273-)  A      OG1    0.40    2.30  INTRA BF
   1 DCYT  (   2-)  T      O2  <->   13 DGUA  (   6-)  P      N2     0.40    2.30  INTRA BF
  64 ALA   (  59-)  A      O   <->   67 LEU   (  62-)  A      N      0.39    2.31  INTRA BL
  10 DGUA  (   3-)  P      N3  <->  345 HOH   ( 511 )  P      O      0.38    2.32  INTRA
  17 ASN   (  12-)  A      ND2 <->  346 HOH   ( 642 )  A      O      0.36    2.34  INTRA BL
 183 CYS   ( 178-)  A      SG  <->  199 LEU   ( 194-)  A      CD2    0.35    3.05  INTRA BL
 155 ILE   ( 150-)  A      N   <->  193 SER   ( 188-)  A      O      0.35    2.35  INTRA BL
  86 LYS   (  81-)  A      NZ  <->   91 GLU   (  86-)  A      OE1    0.35    2.35  INTRA BF
 157 ARG   ( 152-)  A      NH2 <->  186 PHE   ( 181-)  A      O      0.32    2.38  INTRA BL
  37 ALA   (  32-)  A      O   <->   41 TYR   (  36-)  A      N      0.32    2.38  INTRA BL
 284 ASN   ( 279-)  A      O   <->  288 ARG   ( 283-)  A      N      0.32    2.38  INTRA BF
 187 ARG   ( 182-)  A      NH1 <->  278 THR   ( 273-)  A      CG2    0.30    2.80  INTRA BF
   2 DADE  (   3-)  T      C2  <->   12 DTHY  (   5-)  P      N3     0.30    2.80  INTRA BL
  84 THR   (  79-)  A      O   <->   86 LYS   (  81-)  A      N      0.29    2.41  INTRA BF
   4 DCYT  (   5-)  T      O2  <->   10 DGUA  (   3-)  P      N2     0.29    2.41  INTRA BL
And so on for a total of 198 lines.

Packing, accessibility and threading

Note: Inside/Outside residue distribution normal

The distribution of residue types over the inside and the outside of the protein is normal.

inside/outside RMS Z-score : 0.932

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

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.

 249 LYS   ( 244-)  A      -6.36
 211 LYS   ( 206-)  A      -6.07
  16 LEU   (  11-)  A      -5.82
 301 TYR   ( 296-)  A      -5.71
 250 ASN   ( 245-)  A      -5.68
  95 GLN   (  90-)  A      -5.56
 188 ARG   ( 183-)  A      -5.40
  59 LYS   (  54-)  A      -5.29
 187 ARG   ( 182-)  A      -5.28
 308 VAL   ( 303-)  A      -5.25
 154 ARG   ( 149-)  A      -5.20
  36 GLN   (  31-)  A      -5.15
  33 ASN   (  28-)  A      -5.03
 293 GLU   ( 288-)  A      -5.00

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.

 331 LYS   ( 326-)  A       333 - ARG    328- ( A)         -4.31

Note: Structural average packing environment OK

The structural average packing score is within normal ranges.

Average for range 1 - 340 : -0.884

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: Second generation packing environment OK

None of the individual amino acid residues has a bad packing environment.

Note: No series of residues with abnormal new packing environment

There are no stretches of four or more residues each having a packing Z-score worse than -1.75.

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

Water, ion, and hydrogenbond related checks

Note: Water contacts OK

All water clusters make at least one contact with a non-water atom.

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.

 346 HOH   ( 665 )  A      O     63.40   29.96   72.48

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.

 346 HOH   ( 610 )  A      O
 346 HOH   ( 616 )  A      O
 346 HOH   ( 621 )  A      O
 346 HOH   ( 665 )  A      O

Error: HIS, ASN, GLN side chain flips

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

  17 ASN   (  12-)  A
 141 GLN   ( 136-)  A
 162 GLN   ( 157-)  A
 212 GLN   ( 207-)  A
 284 ASN   ( 279-)  A

Note: Histidine type assignments

For all complete HIS residues in the structure a tentative assignment to HIS-D (protonated on ND1), HIS-E (protonated on NE2), or HIS-H (protonated on both ND1 and NE2, positively charged) is made based on the hydrogen bond network. A second assignment is made based on which of the Engh and Huber [REF] histidine geometries fits best to the structure.

In the table below all normal histidine residues are listed. The assignment based on the geometry of the residue is listed first, together with the RMS Z-score for the fit to the Engh and Huber parameters. For all residues where the H-bond assignment is different, the assignment is listed in the last columns, together with its RMS Z-score to the Engh and Huber parameters.

As always, the RMS Z-scores should be close to 1.0 if the residues were restrained to the Engh and Huber parameters during refinement.

Please note that because the differences between the geometries of the different types are small it is possible that the geometric assignment given here does not correspond to the type used in refinement. This is especially true if the RMS Z-scores are much higher than 1.0.

If the two assignments differ, or the `geometry' RMS Z-score is high, it is advisable to verify the hydrogen bond assignment, check the HIS type used during the refinement and possibly adjust it.

  39 HIS   (  34-)  A     HIS-E   0.88
  56 HIS   (  51-)  A     HIS-H   0.85 HIS-E   0.90
 139 HIS   ( 134-)  A     HIS-E   2.17
 140 HIS   ( 135-)  A     HIS-H   0.72 HIS-D   0.79
 202 HIS   ( 197-)  A     HIS-E   0.42
 217 HIS   ( 212-)  A     HIS-D   0.64 HIS-E   1.09
 227 HIS   ( 222-)  A     HIS-E   0.89
 257 HIS   ( 252-)  A     HIS-E   0.67 HIS-D   0.89
 290 HIS   ( 285-)  A     HIS-E   1.38

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.

  15 THR   (  10-)  A      N
  16 LEU   (  11-)  A      N
  17 ASN   (  12-)  A      N
  44 TYR   (  39-)  A      OH
  46 LYS   (  41-)  A      NZ
  56 HIS   (  51-)  A      N
  60 SER   (  55-)  A      N
  87 LEU   (  82-)  A      N
  90 LEU   (  85-)  A      N
  94 ARG   (  89-)  A      NH1
  94 ARG   (  89-)  A      NH2
 141 GLN   ( 136-)  A      N
 149 GLY   ( 144-)  A      N
 158 GLU   ( 153-)  A      N
 184 GLY   ( 179-)  A      N
 187 ARG   ( 182-)  A      NH1
 208 GLU   ( 203-)  A      N
 212 GLN   ( 207-)  A      N
 214 LYS   ( 209-)  A      N
 219 VAL   ( 214-)  A      N
 249 LYS   ( 244-)  A      N
 250 ASN   ( 245-)  A      N
 253 LYS   ( 248-)  A      N
 257 HIS   ( 252-)  A      N
 300 GLU   ( 295-)  A      N
 301 TYR   ( 296-)  A      N
 310 GLY   ( 305-)  A      N
 311 VAL   ( 306-)  A      N
 312 ALA   ( 307-)  A      N
 318 VAL   ( 313-)  A      N
 320 SER   ( 315-)  A      N
 333 ARG   ( 328-)  A      N
 333 ARG   ( 328-)  A      NE
 339 SER   ( 334-)  A      N

Note: Buried hydrogen bond acceptors OK

All buried polar side-chain hydrogen bond acceptors are involved in a hydrogen bond in the optimized hydrogen bond network.

Note: Crystallisation conditions from REMARK 280

Crystallisation conditions as found in the PDB file header.

CRYSTAL
SOLVENT CONTENT, VS   (%): 59.30
MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.00
CRYSTALLIZATION CONDITIONS: THIS ENTRY DESCRIBES THE STRUCTURE
       THAT RESULTED WHEN A COCRYSTAL OF HUMAN DNA POLYMERASE BETA
       COMPLEXED WITH 6 BASE PAIRS OF DNA (SEE ENTRY 9ICW AND
       REFERENCE 1) HAD BEEN SOAKED IN THE FOLLOWING SOLUTION FOR 7
       DAYS: PEG 3350, 16% MES, 100 MILLIMOLAR, PH 6.5 NACL, 150
       MILLIMOLAR SEE REFERENCE 2 FOR DETAILS CONCERNING EXPERIMENTAL
       PROCEDURES, RESULTS, AND DISCUSSION FOR THIS STRUCTURE.

Note: Overview of ions

When ions are located at special positions, their occupancy should be reduce by a factor that is the same as the multiplicity of that special position. This seems to have been done OK in this PDB file.

Warning: Unusual ion packing

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

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

 343  NA   ( 342-)  A   -.-  -.-  Too few ligands (3)

Note: Water packing OK

All waters seem properly packed, or at least not packed like an ion. This method is experimental. See: swift.cmbi.ru.nl/teach/theory/

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.

 121 ASP   ( 116-)  A   H-bonding suggests Asn
 129 ASP   ( 124-)  A   H-bonding suggests Asn; but Alt-Rotamer
 231 ASP   ( 226-)  A   H-bonding suggests Asn; but Alt-Rotamer
 337 ASP   ( 332-)  A   H-bonding suggests Asn

Note: Content of the PDB file as interpreted by WHAT IF

Content of the PDB file as interpreted by WHAT IF. WHAT IF has read your PDB file, and stored it internally in what is called 'the soup'. The content of this soup is listed here. An extensive explanation of all frequently used WHAT IF output formats can be found at swift.cmbi.ru.nl. Look under output formats. A course on reading this 'Molecules' table is part of the WHAT CHECK web pages.

     1     1 (    2)     7 (    8) T DNA/RNA             pdb9ick.ent
     2     8 (    1)    13 (    6) P DNA/RNA             pdb9ick.ent
     3    14 (    9)   340 (  335) A Protein             pdb9ick.ent
     4   341 (  335)   341 (  335) A E O2 <-   340       pdb9ick.ent
     5   342 (  341)   342 (  341) A  NA                 pdb9ick.ent
     6   343 (  342)   343 (  342) A  NA                 pdb9ick.ent
     7   344 ( HOH )   344 ( HOH ) T water   (   12)     pdb9ick.ent
     8   345 ( HOH )   345 ( HOH ) P water   (   21)     pdb9ick.ent
     9   346 ( HOH )   346 ( HOH ) A water   (  120)     pdb9ick.ent

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 :  -0.960
  2nd generation packing quality :  -1.753
  Ramachandran plot appearance   :  -3.249 (poor)
  chi-1/chi-2 rotamer normality  :  -5.168 (bad)
  Backbone conformation          :  -0.353

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.334
  Bond angles                    :   1.668
  Omega angle restraints         :   0.166 (tight)
  Side chain planarity           :   1.778
  Improper dihedral distribution :   2.252 (loose)
  B-factor distribution          :   1.385
  Inside/Outside distribution    :   0.932

Note: Summary report for depositors of a structure

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

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

Resolution found in PDB file : 2.70


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.1
  2nd generation packing quality :  -0.1
  Ramachandran plot appearance   :  -0.5
  chi-1/chi-2 rotamer normality  :  -2.7
  Backbone conformation          :   0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.334
  Bond angles                    :   1.668
  Omega angle restraints         :   0.166 (tight)
  Side chain planarity           :   1.778
  Improper dihedral distribution :   2.252 (loose)
  B-factor distribution          :   1.385
  Inside/Outside distribution    :   0.932
==============

WHAT IF
    G.Vriend,
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    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,
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    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.