WHAT IF Check report

This file was created 2011-12-28 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 pdb1fos.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: E and G

All-atom RMS fit for the two chains : 1.988
CA-only RMS fit for the two chains : 1.876

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: E and G

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: F and H

All-atom RMS fit for the two chains : 1.351
CA-only RMS fit for the two chains : 1.016

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: F and H

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: P 21 21 2
Number of matrices in space group: 4
Highest polymer chain multiplicity in structure: 2
Highest polymer chain multiplicity according to SEQRES: 4
Such multiplicity differences are not by definition worrisome as it is very
well possible that this merely indicates that it is difficult to superpose
chains due to crystal induced differences
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 8
Polymer chain multiplicity and SEQRES multiplicity disagree 2 4
Z and NCS seem to support the 3D multiplicity

Error: Matthews Coefficient (Vm) very high

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.

Numbers this high are almost always caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all).

Molecular weight of all polymer chains: 52393.246
Volume of the Unit Cell V= 774699.250
Space group multiplicity: 4
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 7.393
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 3.530 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)
And remember, a matrix counting problem has been reported earlier already

Administrative problems that can generate validation failures

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.

 152 LYS   ( 277-)  F  -   CG
 152 LYS   ( 277-)  F  -   CD
 152 LYS   ( 277-)  F  -   CE
 152 LYS   ( 277-)  F  -   NZ
 155 LYS   ( 280-)  F  -   CG
 155 LYS   ( 280-)  F  -   CD
 155 LYS   ( 280-)  F  -   CE
 155 LYS   ( 280-)  F  -   NZ
 156 ARG   ( 281-)  F  -   CG
 156 ARG   ( 281-)  F  -   CD
 156 ARG   ( 281-)  F  -   NE
 156 ARG   ( 281-)  F  -   CZ
 156 ARG   ( 281-)  F  -   NH1
 156 ARG   ( 281-)  F  -   NH2
 166 GLU   ( 291-)  F  -   CG
 166 GLU   ( 291-)  F  -   CD
 166 GLU   ( 291-)  F  -   OE1
 166 GLU   ( 291-)  F  -   OE2
 169 LYS   ( 294-)  F  -   CG
 169 LYS   ( 294-)  F  -   CD
 169 LYS   ( 294-)  F  -   CE
 169 LYS   ( 294-)  F  -   NZ
 176 SER   ( 301-)  F  -   OG
 203 GLU   ( 145-)  G  -   CG
 203 GLU   ( 145-)  G  -   CD
And so on for a total of 51 lines.

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.

 257 GLU   ( 265-)  H  -   N
 257 GLU   ( 265-)  H  -   CA
 257 GLU   ( 265-)  H  -   C
 257 GLU   ( 265-)  H  -   O
 314 MET   ( 322-)  H  -   O

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: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

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

Warning: 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'.

  86 ARG   ( 144-)  E      CG
  86 ARG   ( 144-)  E      CD
  86 ARG   ( 144-)  E      NE
  86 ARG   ( 144-)  E      CZ
  86 ARG   ( 144-)  E      NH1
  86 ARG   ( 144-)  E      NH2
  99 ARG   ( 157-)  E      CG
  99 ARG   ( 157-)  E      CD
  99 ARG   ( 157-)  E      NE
  99 ARG   ( 157-)  E      CZ
  99 ARG   ( 157-)  E      NH1
  99 ARG   ( 157-)  E      NH2
 141 ARG   ( 266-)  F      CG
 141 ARG   ( 266-)  F      CD
 141 ARG   ( 266-)  F      NE
 141 ARG   ( 266-)  F      CZ
 141 ARG   ( 266-)  F      NH1
 141 ARG   ( 266-)  F      NH2
 145 ARG   ( 270-)  F      CG
 145 ARG   ( 270-)  F      CD
 145 ARG   ( 270-)  F      NE
 145 ARG   ( 270-)  F      CZ
 145 ARG   ( 270-)  F      NH1
 145 ARG   ( 270-)  F      NH2
 187 GLU   ( 312-)  F      CG
And so on for a total of 82 lines.

Warning: B-factors outside the range 0.0 - 100.0

In principle, B-factors can have a very wide range of values, but in practice, B-factors should not be zero while B-factors above 100.0 are a good indicator that the location of that atom is meaningless. Be aware that the cutoff at 100.0 is arbitrary. 'High' indicates that atoms with a B-factor > 100.0 were observed; 'Zero' indicates that atoms with a B-factor of zero were observed.

  18 DADE  (  18-)  A    High
  19 DGUA  (  19-)  A    High
  22 DTHY  (  22-)  B    High
  23 DCYT  (  23-)  B    High
  40 DTHY  (  40-)  B    High
  58 DADE  (  18-)  C    High
  59 DGUA  (  19-)  C    High
  60 DADE  (  20-)  C    High
  62 DTHY  (  22-)  D    High
  63 DCYT  (  23-)  D    High
  65 DCYT  (  25-)  D    High
  82 ARG   ( 140-)  E    High
  83 ARG   ( 141-)  E    High
  85 ARG   ( 143-)  E    High
 113 GLN   ( 171-)  E    High
 147 ARG   ( 272-)  F    High
 195 LYS   ( 320-)  F    High
 283 GLU   ( 291-)  H    High
 294 GLU   ( 302-)  H    High

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:

Temperature cannot be read from the PDB file. This most likely means that the temperature is listed as NULL (meaning unknown) in the PDB file.

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 1.707 over 1598 bonds
Average difference in B over a bond : 5.27
RMS difference in B over a bond : 7.70

Note: B-factor plot

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

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

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.

   4 DGUA  (   4-)  A      C2   N3    1.36    4.6
   6 DADE  (   6-)  A      P    O5'   1.65    5.4
   6 DADE  (   6-)  A      C4'  C3'   1.48   -4.5
   7 DTHY  (   7-)  A      C4'  C3'   1.49   -4.1
  10 DGUA  (  10-)  A      P    O5'   1.63    4.1
  14 DTHY  (  14-)  A      C5   C7    1.53    5.0
  19 DGUA  (  19-)  A      C2   N3    1.36    4.4
  20 DADE  (  20-)  A      C2   N3    1.37    4.1
  21 DTHY  (  21-)  B      N1   C2    1.41    4.7
  22 DTHY  (  22-)  B      N1   C2    1.41    4.3
  24 DTHY  (  24-)  B      N1   C2    1.41    4.8
  24 DTHY  (  24-)  B      C5   C7    1.53    5.3
  27 DTHY  (  27-)  B      N1   C2    1.41    4.0
  27 DTHY  (  27-)  B      C5   C7    1.52    4.6
  29 DTHY  (  29-)  B      C5   C7    1.53    5.0
  31 DADE  (  31-)  B      C5'  C4'   1.47   -4.7
  35 DADE  (  35-)  B      P    O5'   1.64    4.7
  36 DTHY  (  36-)  B      N1   C2    1.41    4.5
  36 DTHY  (  36-)  B      C5   C7    1.52    4.0
  38 DCYT  (  38-)  B      C4'  C3'   1.49   -4.0
  40 DTHY  (  40-)  B      N1   C2    1.42    5.2
  40 DTHY  (  40-)  B      C5   C7    1.53    4.9
  43 DTHY  (   3-)  C      N1   C2    1.41    4.2
  44 DGUA  (   4-)  C      C2   N3    1.36    4.7
  47 DTHY  (   7-)  C      N1   C2    1.41    4.4
  48 DGUA  (   8-)  C      C5'  C4'   1.55    4.5
  48 DGUA  (   8-)  C      C2   N3    1.36    4.1
  48 DGUA  (   8-)  C      C6   N1    1.36   -4.4
  50 DGUA  (  10-)  C      C1'  N9    1.42   -4.2
  54 DTHY  (  14-)  C      N1   C2    1.41    4.2
  57 DGUA  (  17-)  C      C2   N3    1.36    4.4
  62 DTHY  (  22-)  D      N1   C2    1.41    4.5
  64 DTHY  (  24-)  D      N1   C2    1.42    6.1
  64 DTHY  (  24-)  D      C5   C7    1.54    7.0
  67 DTHY  (  27-)  D      N1   C2    1.41    4.1
  67 DTHY  (  27-)  D      C5   C7    1.53    5.3
  68 DADE  (  28-)  D      C4'  C3'   1.48   -4.3
  71 DADE  (  31-)  D      P    O5'   1.64    4.3
  71 DADE  (  31-)  D      C4'  C3'   1.48   -5.0
  73 DTHY  (  33-)  D      N1   C2    1.41    4.5
  73 DTHY  (  33-)  D      C5   C7    1.52    4.7
  80 DTHY  (  40-)  D      N1   C2    1.42    5.2
  80 DTHY  (  40-)  D      C5   C7    1.53    5.6

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

 |  0.998084  0.000331  0.000034|
 |  0.000331  0.997799 -0.000290|
 |  0.000034 -0.000290  1.002341|
Proposed new scale matrix

 |  0.004156 -0.000001  0.000000|
 | -0.000007  0.020583  0.000006|
 |  0.000000  0.000004  0.015117|
With corresponding cell

    A    = 240.618  B   =  48.583  C    =  66.152
    Alpha=  90.033  Beta=  90.002  Gamma=  89.962

The CRYST1 cell dimensions

    A    = 241.100  B   =  48.690  C    =  66.000
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 164.500
(Under-)estimated Z-score: 9.453

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 DADE  (   1-)  A      C5   C6   N1  115.13   -5.1
   1 DADE  (   1-)  A      C6   N1   C2  122.78    7.0
   1 DADE  (   1-)  A      N1   C2   N3  125.16   -8.3
   2 DADE  (   2-)  A      P   -C3* -O3* 125.34    4.7
   2 DADE  (   2-)  A      C4'  C3'  C2' 108.91    5.7
   2 DADE  (   2-)  A      C5   C6   N1  114.93   -5.5
   2 DADE  (   2-)  A      C6   N1   C2  123.26    7.8
   2 DADE  (   2-)  A      N1   C2   N3  125.03   -8.5
   3 DTHY  (   3-)  A      P   -C3* -O3* 125.81    5.1
   3 DTHY  (   3-)  A      C4'  C3'  C2' 107.43    4.2
   3 DTHY  (   3-)  A      N1   C2   N3  118.10    5.8
   3 DTHY  (   3-)  A      C5   C4   N3  118.35    5.3
   3 DTHY  (   3-)  A      C4   N3   C2  122.88   -7.2
   4 DGUA  (   4-)  A      P   -C3* -O3* 124.61    4.1
   4 DGUA  (   4-)  A      C4'  C3'  C2' 107.89    4.7
   4 DGUA  (   4-)  A      N9   C8   N7  114.14    6.1
   4 DGUA  (   4-)  A      C5   C6   N1  114.68    6.4
   5 DGUA  (   5-)  A      C4'  C3'  C2' 108.62    5.4
   5 DGUA  (   5-)  A      N9   C8   N7  114.06    5.9
   5 DGUA  (   5-)  A      C5   C6   N1  114.68    6.4
   6 DADE  (   6-)  A      C4'  C3'  C2' 109.07    5.9
   6 DADE  (   6-)  A      C5   C6   N1  115.19   -5.0
   6 DADE  (   6-)  A      C6   N1   C2  123.18    7.6
   6 DADE  (   6-)  A      N1   C2   N3  124.81   -9.0
   7 DTHY  (   7-)  A      C4'  C3'  C2' 108.64    5.4
And so on for a total of 345 lines.

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.

 234 LYS   ( 176-)  G    5.66
 147 ARG   ( 272-)  F    4.82
 184 MET   ( 309-)  F    4.47
 278 ILE   ( 286-)  H    4.20

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 : 1.760

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 : -3.089

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.

 148 ILE   ( 273-)  F    -2.5
  98 ASN   ( 156-)  E    -2.1

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 : -4.416

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.

  96 SER   ( 154-)  E    0.38
 119 SER   ( 177-)  E    0.38
 212 SER   ( 154-)  G    0.40

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  (   3-)  A      0
   4 DGUA  (   4-)  A      0
   5 DGUA  (   5-)  A      0
   6 DADE  (   6-)  A      0
   7 DTHY  (   7-)  A      0
   8 DGUA  (   8-)  A      0
   9 DADE  (   9-)  A      0
  10 DGUA  (  10-)  A      0
  11 DTHY  (  11-)  A      0
  12 DCYT  (  12-)  A      0
  13 DADE  (  13-)  A      0
  14 DTHY  (  14-)  A      0
  15 DADE  (  15-)  A      0
  16 DGUA  (  16-)  A      0
  17 DGUA  (  17-)  A      0
  18 DADE  (  18-)  A      0
  19 DGUA  (  19-)  A      0
  20 DADE  (  20-)  A      0
  21 DTHY  (  21-)  B      0
  22 DTHY  (  22-)  B      0
  23 DCYT  (  23-)  B      0
  24 DTHY  (  24-)  B      0
  25 DCYT  (  25-)  B      0
  26 DCYT  (  26-)  B      0
  27 DTHY  (  27-)  B      0
And so on for a total of 93 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 : 1.113

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.

  18 DADE  (  18-)  A      N1  <->   24 DTHY  (  24-)  B      N3     0.42    2.58  INTRA BL
  42 DADE  (   2-)  C      N1  <->   80 DTHY  (  40-)  D      N3     0.42    2.58  INTRA BL
  54 DTHY  (  14-)  C      N3  <->   68 DADE  (  28-)  D      N1     0.41    2.59  INTRA BL
  56 DGUA  (  16-)  C      N1  <->   66 DCYT  (  26-)  D      N3     0.40    2.60  INTRA BL
   6 DADE  (   6-)  A      N1  <->   36 DTHY  (  36-)  B      N3     0.39    2.61  INTRA BL
  51 DTHY  (  11-)  C      C4  <->   52 DCYT  (  12-)  C      N4     0.38    2.72  INTRA BL
   2 DADE  (   2-)  A      N1  <->   40 DTHY  (  40-)  B      N3     0.38    2.62  INTRA BL
  47 DTHY  (   7-)  C      N3  <->   75 DADE  (  35-)  D      N1     0.37    2.63  INTRA BL
  10 DGUA  (  10-)  A      N7  <->   97 ARG   ( 155-)  E      NH2    0.37    2.63  INTRA
  46 DADE  (   6-)  C      N1  <->   76 DTHY  (  36-)  D      N3     0.37    2.63  INTRA BL
  55 DADE  (  15-)  C      N1  <->   67 DTHY  (  27-)  D      N3     0.37    2.63  INTRA BL
  44 DGUA  (   4-)  C      N1  <->   78 DCYT  (  38-)  D      N3     0.35    2.65  INTRA BL
  15 DADE  (  15-)  A      N1  <->   27 DTHY  (  27-)  B      N3     0.34    2.66  INTRA BL
  48 DGUA  (   8-)  C      OP2 <->  216 ARG   ( 158-)  G      NH2    0.33    2.37  INTRA BF
  17 DGUA  (  17-)  A      N1  <->   25 DCYT  (  25-)  B      N3     0.30    2.70  INTRA BL
  72 DCYT  (  32-)  D      C5  <->  213 ARG   ( 155-)  G      NH2    0.29    2.81  INTRA BF
  53 DADE  (  13-)  C      N1  <->   69 DTHY  (  29-)  D      N3     0.28    2.72  INTRA BL
   4 DGUA  (   4-)  A      N1  <->   38 DCYT  (  38-)  B      N3     0.28    2.72  INTRA BL
  16 DGUA  (  16-)  A      N1  <->   26 DCYT  (  26-)  B      N3     0.27    2.73  INTRA BL
  19 DGUA  (  19-)  A      N1  <->   23 DCYT  (  23-)  B      N3     0.27    2.73  INTRA BL
   5 DGUA  (   5-)  A      N1  <->   37 DCYT  (  37-)  B      N3     0.26    2.74  INTRA BL
  56 DGUA  (  16-)  C      O6  <->   66 DCYT  (  26-)  D      N4     0.26    2.44  INTRA BL
  49 DADE  (   9-)  C      N1  <->   73 DTHY  (  33-)  D      N3     0.25    2.75  INTRA BL
  48 DGUA  (   8-)  C      P   <->  216 ARG   ( 158-)  G      NH2    0.25    3.05  INTRA BF
 237 LEU   ( 179-)  G      O   <->  240 GLU   ( 182-)  G      N      0.24    2.46  INTRA BL
And so on for a total of 119 lines.

Packing, accessibility and threading

Warning: Inside/Outside residue distribution unusual

The distribution of residue types over the inside and the outside of the protein is unusual. Normal values for the RMS Z-score below are between 0.84 and 1.16. The fact that it is higher in this structure could be caused by transmembrane helices, by the fact that it is part of a multimeric active unit, or by mistraced segments in the density.

inside/outside RMS Z-score : 1.202

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: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: G

Note: Quality value plot

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

Chain identifier: H

Note: 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: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Water, ion, and hydrogenbond related checks

Warning: 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.

  32 DCYT  (  32-)  B      N4
  52 DCYT  (  12-)  C      N4
  72 DCYT  (  32-)  D      N4
  84 ILE   ( 142-)  E      N
 277 ARG   ( 285-)  H      NE
 303 ARG   ( 311-)  H      NE

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.

 175 ASN   ( 300-)  F      OD1
 292 ASN   ( 300-)  H      OD1

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 :   1.327
  2nd generation packing quality :   0.257
  Ramachandran plot appearance   :  -3.089 (poor)
  chi-1/chi-2 rotamer normality  :  -4.416 (bad)
  Backbone conformation          :   4.110

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.168
  Bond angles                    :   1.939
  Omega angle restraints         :   0.202 (tight)
  Side chain planarity           :   0.670
  Improper dihedral distribution :   1.116
  B-factor distribution          :   1.707 (loose)
  Inside/Outside distribution    :   1.202 (unusual)

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 : 3.05


Structure Z-scores, positive is better than average:

  1st generation packing quality :   2.2
  2nd generation packing quality :   1.7
  Ramachandran plot appearance   :  -0.4
  chi-1/chi-2 rotamer normality  :  -2.0
  Backbone conformation          :   4.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.168
  Bond angles                    :   1.939
  Omega angle restraints         :   0.202 (tight)
  Side chain planarity           :   0.670
  Improper dihedral distribution :   1.116
  B-factor distribution          :   1.707 (loose)
  Inside/Outside distribution    :   1.202 (unusual)
==============

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.