WHAT IF Check report

This file was created 2012-04-04 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 pdb2ybv.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and G

All-atom RMS fit for the two chains : 0.090
CA-only RMS fit for the two chains : 0.050

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 1 21 1
Number of matrices in space group: 2
Highest polymer chain multiplicity in structure: 8
Highest polymer chain multiplicity according to SEQRES: 8
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 8
Z, symmetry, and molecular multiplicity disagree
Could it be that Z must be: 16

Warning: Matthews Coefficient (Vm) 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.

Very high numbers are most often caused by giving the wrong value for Z on the CRYST1 card (or not giving this number at all), but can also result from large fractions missing out of the molecular weight (e.g. a lot of UNK residues, or DNA/RNA missing from virus structures).

Molecular weight of all polymer chains: 479899.500
Volume of the Unit Cell V= 2919947.8
Space group multiplicity: 2
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 6.084
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 2.720 Or should we use the previously suggested Z = 16
which would result in Vm= 3.042
And remember, a matrix counting problem has been reported earlier already

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

Note: Ramachandran plot

Chain identifier: M

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: P

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

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :100.000

Warning: More than 5 percent of buried atoms has low B-factor

For normal protein structures, no more than about 1 percent of the B factors of buried atoms is below 5.0. The fact that this value is much higher in the current structure could be a signal that the B-factors were restraints or constraints to too-low values, misuse of B-factor field in the PDB file, or a TLS/scaling problem. If the average B factor is low too, it is probably a low temperature structure determination.

Percentage of buried atoms with B less than 5 : 25.62

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Note: B-factor plot

Chain identifier: M

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: P

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.

 112 ARG   ( 139-)  A      CZ   NH1   1.21   -6.5
 112 ARG   ( 139-)  A      CZ   NH2   1.21   -6.2
 191 PHE   ( 218-)  A      CG   CD1   1.28   -4.8
 191 PHE   ( 218-)  A      CG   CD2   1.26   -6.1
 191 PHE   ( 218-)  A      CE1  CZ    1.24   -4.6
 191 PHE   ( 218-)  A      CE2  CZ    1.23   -5.1
 390 ARG   ( 421-)  A      CZ   NH2   1.25   -4.0
 666 LYS   ( 161-)  C      CG   CD    1.65    4.3
 677 CYS   ( 172-)  C      CB   SG    1.96    4.6
 723 PHE   ( 218-)  C      CG   CD1   1.29   -4.6
 723 PHE   ( 218-)  C      CG   CD2   1.26   -5.9
 723 PHE   ( 218-)  C      CE1  CZ    1.23   -5.1
 922 ARG   ( 421-)  C      CZ   NH1   1.25   -4.3
1176 ARG   ( 139-)  E      CZ   NH1   1.23   -5.4
1176 ARG   ( 139-)  E      CZ   NH2   1.23   -5.6
1255 PHE   ( 218-)  E      CG   CD2   1.30   -4.2
1255 PHE   ( 218-)  E      CE1  CZ    1.26   -4.2
1380 LEU   ( 343-)  E      CG   CD1   1.67    4.5
1454 ARG   ( 421-)  E      CZ   NH1   1.25   -4.5
1741 CYS   ( 172-)  G      CB   SG    1.95    4.3
1756 ARG   ( 187-)  G      CG   CD    1.64    4.1
1787 PHE   ( 218-)  G      CG   CD2   1.29   -4.3
1986 ARG   ( 421-)  G      CZ   NH1   1.24   -4.9
1986 ARG   ( 421-)  G      CZ   NH2   1.23   -5.5
2273 CYS   ( 172-)  I      CB   SG    1.94    4.0
2518 ARG   ( 421-)  I      CZ   NH1   1.25   -4.3
2518 ARG   ( 421-)  I      CZ   NH2   1.22   -6.1
2805 CYS   ( 172-)  K      CB   SG    1.99    5.5
2846 ARG   ( 213-)  K      C    O     1.31    4.0
2851 PHE   ( 218-)  K      CE2  CZ    1.25   -4.4
2897 ILE   ( 264-)  K      CA   CB    1.61    4.1
3213 THR   (  43-)  M      CB   CG2   1.65    4.0
3383 PHE   ( 218-)  M      CG   CD1   1.30   -4.1
3383 PHE   ( 218-)  M      CG   CD2   1.25   -6.2
3383 PHE   ( 218-)  M      CE1  CZ    1.22   -5.5
3383 PHE   ( 218-)  M      CE2  CZ    1.19   -6.3
3582 ARG   ( 421-)  M      CZ   NH2   1.24   -4.9
3869 CYS   ( 172-)  O      CB   SG    1.96    4.5
1741 CYS   ( 172-)  G      SG  -SG*   2.21    4.3
1761 CYS   ( 192-)  G      SG  -SG*   2.21    4.3

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

 |  0.995710  0.000260  0.000485|
 |  0.000260  0.995703 -0.000066|
 |  0.000485 -0.000066  0.995315|
Proposed new scale matrix

 |  0.008696 -0.000002  0.002985|
 | -0.000002  0.006143  0.000000|
 | -0.000003  0.000000  0.006495|
With corresponding cell

    A    = 114.978  B   = 162.776  C    = 162.744
    Alpha=  90.011  Beta= 108.916  Gamma=  89.971

The CRYST1 cell dimensions

    A    = 115.480  B   = 163.470  C    = 163.540
    Alpha=  90.000  Beta= 108.960  Gamma=  90.000

Variance: 2807.625
(Under-)estimated Z-score: 39.051

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.

 112 ARG   ( 139-)  A      NH1  CZ   NH2 105.60   -7.8
 160 ARG   ( 187-)  A      CG   CD   NE  117.69    4.2
 191 PHE   ( 218-)  A      CD1  CG   CD2 111.82   -4.5
 300 HIS   ( 327-)  A      CG   ND1  CE1 109.70    4.1
 378 HIS   ( 409-)  A      CG   ND1  CE1 109.61    4.0
 390 ARG   ( 421-)  A      NH1  CZ   NH2 111.94   -4.3
 723 PHE   ( 218-)  C      CE1  CZ   CE2 112.30   -4.3
 723 PHE   ( 218-)  C      CD1  CG   CD2 112.25   -4.3
 731 HIS   ( 226-)  C      CG   ND1  CE1 109.80    4.2
 830 HIS   ( 325-)  C      C    CA   CB  102.04   -4.2
1176 ARG   ( 139-)  E      NE   CZ   NH2 127.77    4.1
1176 ARG   ( 139-)  E      NH1  CZ   NH2 105.77   -7.7
1190 HIS   ( 153-)  E      CG   ND1  CE1 109.88    4.3
1224 ARG   ( 187-)  E      CG   CD   NE  117.77    4.3
1331 HIS   ( 294-)  E      CG   ND1  CE1 109.71    4.1
1362 HIS   ( 325-)  E      C    CA   CB  101.90   -4.3
1362 HIS   ( 325-)  E      CG   ND1  CE1 109.61    4.0
1442 HIS   ( 409-)  E      CG   ND1  CE1 109.66    4.1
1454 ARG   ( 421-)  E      NH1  CZ   NH2 111.46   -4.6
1756 ARG   ( 187-)  G      CG   CD   NE  117.84    4.3
1784 ARG   ( 215-)  G      CG   CD   NE  101.06   -5.6
1784 ARG   ( 215-)  G      CD   NE   CZ  139.39    9.8
1784 ARG   ( 215-)  G      NE   CZ   NH1 129.85    5.2
1795 HIS   ( 226-)  G      CG   ND1  CE1 109.61    4.0
1863 HIS   ( 294-)  G      CG   ND1  CE1 110.03    4.4
And so on for a total of 54 lines.

Warning: Chirality deviations detected

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

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

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

1551 PHE   (  61-)  F      CA    -6.9    23.00    33.98
3147 PHE   (  61-)  L      CA    -6.4    23.67    33.98
The average deviation= 1.255

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.

2207 ASP   ( 106-)  I    4.66
3803 ASP   ( 106-)  O    4.65
1358 SER   ( 321-)  E    4.56
 626 VAL   ( 121-)  C    4.34
2739 ASP   ( 106-)  K    4.33
2537 GLU   ( 440-)  I    4.25
3132 SER   (  46-)  L    4.10
3486 SER   ( 321-)  M    4.07

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.

 782 ASN   ( 277-)  C    4.91
 176 ASP   ( 203-)  A    4.61
 708 ASP   ( 203-)  C    4.10

Torsion-related checks

Warning: Torsion angle evaluation shows unusual residues

The residues listed in the table below contain bad or abnormal torsion angles.

These scores give an impression of how `normal' the torsion angles in protein residues are. All torsion angles except omega are used for calculating a `normality' score. Average values and standard deviations were obtained from the residues in the WHAT IF database. These are used to calculate Z-scores. A residue with a Z-score of below -2.0 is poor, and a score of less than -3.0 is worrying. For such residues more than one torsion angle is in a highly unlikely position.

 744 TYR   ( 239-)  C    -2.6
 487 PHE   (  61-)  B    -2.6
3167 PRO   (  81-)  L    -2.5
2340 TYR   ( 239-)  I    -2.5
1583 ILE   (  93-)  F    -2.5
1535 THR   (  45-)  F    -2.5
1019 PHE   (  61-)  D    -2.5
 526 SER   ( 100-)  B    -2.4
2067 THR   (  45-)  H    -2.4
2872 TYR   ( 239-)  K    -2.3
3429 ILE   ( 264-)  M    -2.3
 521 GLN   (  95-)  B    -2.3
2897 ILE   ( 264-)  K    -2.3
3148 ASN   (  62-)  L    -2.3
4134 GLY   ( 441-)  O    -2.3
1022 THR   (  64-)  D    -2.3
2365 ILE   ( 264-)  I    -2.2
1775 ILE   ( 206-)  G    -2.2
1003 THR   (  45-)  D    -2.2
2307 ILE   ( 206-)  I    -2.2
2364 PRO   ( 263-)  I    -2.2
 212 TYR   ( 239-)  A    -2.2
3961 ILE   ( 264-)  O    -2.2
1551 PHE   (  61-)  F    -2.2
1301 ILE   ( 264-)  E    -2.2
And so on for a total of 60 lines.

Warning: Backbone evaluation reveals unusual conformations

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

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

  18 PHE   (  40-)  A  omega poor
  40 SER   (  62-)  A  Poor phi/psi
  46 LEU   (  73-)  A  omega poor
  54 LYS   (  81-)  A  omega poor
  68 ASN   (  95-)  A  Poor phi/psi
  80 LEU   ( 107-)  A  omega poor
  95 GLY   ( 122-)  A  omega poor
  96 ASN   ( 123-)  A  omega poor
 136 ASN   ( 163-)  A  Poor phi/psi
 138 TYR   ( 165-)  A  omega poor
 148 LYS   ( 175-)  A  PRO omega poor
 172 PHE   ( 199-)  A  omega poor
 173 THR   ( 200-)  A  omega poor
 180 ASN   ( 207-)  A  Poor phi/psi
 216 THR   ( 243-)  A  omega poor
 234 GLU   ( 261-)  A  Poor phi/psi
 270 MET   ( 297-)  A  Poor phi/psi
 274 MET   ( 301-)  A  omega poor
 295 GLY   ( 322-)  A  omega poor
 343 SER   ( 370-)  A  Poor phi/psi
 435 ARG   (   9-)  B  omega poor
 437 GLU   (  11-)  B  Poor phi/psi
 439 PHE   (  13-)  B  Poor phi/psi
 473 ASN   (  47-)  B  omega poor
 483 LYS   (  57-)  B  Poor phi/psi
And so on for a total of 234 lines.

Warning: Unusual rotamers

The residues listed in the table below have a rotamer that is not seen very often in the database of solved protein structures. This option determines for every residue the position specific chi-1 rotamer distribution. Thereafter it verified whether the actual residue in the molecule has the most preferred rotamer or not. If the actual rotamer is the preferred one, the score is 1.0. If the actual rotamer is unique, the score is 0.0. If there are two preferred rotamers, with a population distribution of 3:2 and your rotamer sits in the lesser populated rotamer, the score will be 0.667. No value will be given if insufficient hits are found in the database.

It is not necessarily an error if a few residues have rotamer values below 0.3, but careful inspection of all residues with these low values could be worth it.

2220 SER   ( 119-)  I    0.36
1036 SER   (  78-)  D    0.38
2100 SER   (  78-)  H    0.38
3446 SER   ( 281-)  M    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!

   4 THR   (  26-)  A      0
  24 PRO   (  46-)  A      0
  39 SER   (  61-)  A      0
  40 SER   (  62-)  A      0
  41 THR   (  63-)  A      0
  42 GLY   (  64-)  A      0
  43 TRP   (  70-)  A      0
  44 THR   (  71-)  A      0
  47 LEU   (  74-)  A      0
  58 TYR   (  85-)  A      0
  64 PRO   (  91-)  A      0
  67 ASP   (  94-)  A      0
  68 ASN   (  95-)  A      0
  80 LEU   ( 107-)  A      0
  83 GLU   ( 110-)  A      0
  85 SER   ( 112-)  A      0
  94 VAL   ( 121-)  A      0
  96 ASN   ( 123-)  A      0
  97 VAL   ( 124-)  A      0
 100 PHE   ( 127-)  A      0
 104 LYS   ( 131-)  A      0
 109 GLU   ( 136-)  A      0
 110 ASP   ( 137-)  A      0
 121 PHE   ( 148-)  A      0
 124 PRO   ( 151-)  A      0
And so on for a total of 1572 lines.

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

2193 GLY   (  92-)  I   2.00   80
3257 GLY   (  92-)  M   1.93   80
2725 GLY   (  92-)  K   1.91   80
3789 GLY   (  92-)  O   1.90   80
  65 GLY   (  92-)  A   1.82   80
 597 GLY   (  92-)  C   1.78   80
1129 GLY   (  92-)  E   1.75   80
1661 GLY   (  92-)  G   1.64   80
2311 PRO   ( 210-)  I   1.51   10

Warning: Unusual peptide bond conformations

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

 438 THR   (  12-)  B   1.51

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]

  22 PRO   (  44-)  A    0.17 LOW
  27 PRO   (  49-)  A    0.19 LOW
  77 PRO   ( 104-)  A    0.20 LOW
 124 PRO   ( 151-)  A    0.46 HIGH
 125 PRO   ( 152-)  A    0.07 LOW
 218 PRO   ( 245-)  A    0.15 LOW
 554 PRO   (  44-)  C    0.11 LOW
 657 PRO   ( 152-)  C    0.10 LOW
 750 PRO   ( 245-)  C    0.10 LOW
 877 PRO   ( 372-)  C    0.20 LOW
1086 PRO   (  44-)  E    0.19 LOW
1091 PRO   (  49-)  E    0.15 LOW
1141 PRO   ( 104-)  E    0.15 LOW
1189 PRO   ( 152-)  E    0.09 LOW
1618 PRO   (  44-)  G    0.10 LOW
1623 PRO   (  49-)  G    0.17 LOW
1721 PRO   ( 152-)  G    0.14 LOW
2128 PRO   ( 106-)  H    0.17 LOW
2150 PRO   (  44-)  I    0.17 LOW
2155 PRO   (  49-)  I    0.19 LOW
2190 PRO   (  89-)  I    0.46 HIGH
2205 PRO   ( 104-)  I    0.08 LOW
2253 PRO   ( 152-)  I    0.04 LOW
2613 PRO   (  59-)  J    0.16 LOW
2682 PRO   (  44-)  K    0.07 LOW
2687 PRO   (  49-)  K    0.16 LOW
2737 PRO   ( 104-)  K    0.17 LOW
2785 PRO   ( 152-)  K    0.08 LOW
2878 PRO   ( 245-)  K    0.19 LOW
3145 PRO   (  59-)  L    0.20 LOW
3214 PRO   (  44-)  M    0.12 LOW
3219 PRO   (  49-)  M    0.19 LOW
3317 PRO   ( 152-)  M    0.07 LOW
3410 PRO   ( 245-)  M    0.19 LOW
3746 PRO   (  44-)  O    0.15 LOW
3786 PRO   (  89-)  O    0.48 HIGH
3801 PRO   ( 104-)  O    0.05 LOW
3849 PRO   ( 152-)  O    0.13 LOW
3942 PRO   ( 245-)  O    0.11 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].

  24 PRO   (  46-)  A  -153.3 half-chair N/C-delta (-162 degrees)
 464 PRO   (  38-)  B    43.4 envelop C-delta (36 degrees)
 485 PRO   (  59-)  B   104.2 envelop C-beta (108 degrees)
 507 PRO   (  81-)  B   -48.0 half-chair C-beta/C-alpha (-54 degrees)
 556 PRO   (  46-)  C  -151.2 envelop C-delta (-144 degrees)
 559 PRO   (  49-)  C    36.0 envelop C-delta (36 degrees)
 609 PRO   ( 104-)  C    52.4 half-chair C-delta/C-gamma (54 degrees)
 715 PRO   ( 210-)  C   102.5 envelop C-beta (108 degrees)
 996 PRO   (  38-)  D    38.7 envelop C-delta (36 degrees)
1064 PRO   ( 106-)  D  -177.2 envelop N (180 degrees)
1088 PRO   (  46-)  E  -151.7 envelop C-delta (-144 degrees)
1528 PRO   (  38-)  F    33.3 envelop C-delta (36 degrees)
1571 PRO   (  81-)  F   -14.4 half-chair C-alpha/N (-18 degrees)
1620 PRO   (  46-)  G  -150.0 envelop C-delta (-144 degrees)
2027 PRO   (   5-)  H  -125.3 half-chair C-delta/C-gamma (-126 degrees)
2060 PRO   (  38-)  H    38.2 envelop C-delta (36 degrees)
2103 PRO   (  81-)  H   -60.4 half-chair C-beta/C-alpha (-54 degrees)
2152 PRO   (  46-)  I  -154.6 half-chair N/C-delta (-162 degrees)
2592 PRO   (  38-)  J    45.2 half-chair C-delta/C-gamma (54 degrees)
2660 PRO   ( 106-)  J   112.3 envelop C-beta (108 degrees)
2684 PRO   (  46-)  K  -145.8 envelop C-delta (-144 degrees)
3124 PRO   (  38-)  L    46.4 half-chair C-delta/C-gamma (54 degrees)
3167 PRO   (  81-)  L    19.6 half-chair N/C-delta (18 degrees)
3192 PRO   ( 106-)  L   114.3 envelop C-beta (108 degrees)
3216 PRO   (  46-)  M  -148.4 envelop C-delta (-144 degrees)
3316 PRO   ( 151-)  M   101.4 envelop C-beta (108 degrees)
3636 PRO   (  18-)  N   173.7 envelop N (180 degrees)
3656 PRO   (  38-)  N    43.5 envelop C-delta (36 degrees)
3748 PRO   (  46-)  O  -158.2 half-chair N/C-delta (-162 degrees)
3751 PRO   (  49-)  O    29.7 envelop C-delta (36 degrees)
4168 PRO   (  18-)  P    99.7 envelop C-beta (108 degrees)
4188 PRO   (  38-)  P    46.0 half-chair C-delta/C-gamma (54 degrees)

Bump checks

Error: Abnormally short interatomic distances

The pairs of atoms listed in the table below have an unusually short 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.

The last text-item on each line represents the status of the atom pair. The text `INTRA' means that the bump is between atoms that are explicitly listed in the PDB file. `INTER' means it is an inter-symmetry bump. 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). If the last column is 'BF', the sum of the B-factors of the atoms is higher than 80, which makes the appearance of the bump somewhat less severe because the atoms probably are not there anyway. BL, on the other hand, indicates that the bumping atoms both have a low B-factor, and that makes the bumps more worrisome.

It seems likely that at least some of the reported bumps are caused by administrative errors in the chain names. I.e. covalently bound atoms with different non-blank chain-names are reported as bumps. In rare cases this is not an error.

Bumps between atoms for which the sum of their occupancies is lower than one are not reported. If the MODEL number does not exist (as is the case in most X-ray files), a minus sign is printed instead.

 151 LEU   ( 178-)  A      CD1  <->  4280 HOH   (2007 )  I      O    0.47    2.33  INTRA
2811 LEU   ( 178-)  K      CD1  <->  4274 HOH   (2011 )  C      O    0.43    2.37  INTRA
1419 ILE   ( 382-)  E      CG2  <->  1439 PHE   ( 402-)  E      CE1  0.42    2.78  INTRA
3342 LYS   ( 177-)  M      O    <->  3371 ILE   ( 206-)  M      CD1  0.41    2.39  INTRA
1643 LEU   (  74-)  G      O    <->  4245 GLN   (  95-)  P      NE2  0.40    2.30  INTRA BF
3874 LYS   ( 177-)  O      O    <->  3903 ILE   ( 206-)  O      CD1  0.40    2.40  INTRA
 683 LEU   ( 178-)  C      CD1  <->  4282 HOH   (2012 )  K      O    0.39    2.41  INTRA
1951 ILE   ( 382-)  G      CG2  <->  1971 PHE   ( 402-)  G      CE1  0.38    2.82  INTRA
2278 LYS   ( 177-)  I      O    <->  2307 ILE   ( 206-)  I      CD1  0.38    2.42  INTRA
 979 ASP   (  21-)  D      OD2  <->  1032 GLN   (  74-)  D      NE2  0.38    2.32  INTRA
1111 LEU   (  74-)  E      O    <->  3713 GLN   (  95-)  N      NE2  0.38    2.32  INTRA BF
2728 ASN   (  95-)  K      ND2  <->  4282 HOH   (2016 )  K      O    0.36    2.34  INTRA
3901 GLU   ( 204-)  O      OE1  <->  4286 HOH   (2043 )  O      O    0.35    2.05  INTRA
3547 ILE   ( 382-)  M      CG2  <->  3567 PHE   ( 402-)  M      CE1  0.35    2.85  INTRA
3015 ILE   ( 382-)  K      CG2  <->  3035 PHE   ( 402-)  K      CE1  0.35    2.85  INTRA
3881 ASN   ( 184-)  O      ND2  <->  4245 GLN   (  95-)  P      OE1  0.34    2.36  INTRA
1009 ARG   (  51-)  D      CD   <->  1260 ASP   ( 223-)  E      OD2  0.34    2.46  INTRA
 150 LYS   ( 177-)  A      O    <->   179 ILE   ( 206-)  A      CD1  0.34    2.46  INTRA
1854 ARG   ( 285-)  G      NH2  <->  4278 HOH   (2045 )  G      O    0.34    2.36  INTRA BL
2117 GLN   (  95-)  H      NE2  <->  2175 LEU   (  74-)  I      O    0.33    2.37  INTRA BF
3343 LEU   ( 178-)  M      CD1  <->  4276 HOH   (2010 )  E      O    0.33    2.47  INTRA
 887 ILE   ( 382-)  C      CG2  <->   907 PHE   ( 402-)  C      CE2  0.33    2.87  INTRA
1585 GLN   (  95-)  F      NE2  <->  3771 LEU   (  74-)  O      O    0.32    2.38  INTRA BF
2285 ASN   ( 184-)  I      ND2  <->  2649 GLN   (  95-)  J      OE1  0.32    2.38  INTRA
  47 LEU   (  74-)  A      O    <->  2649 GLN   (  95-)  J      NE2  0.31    2.39  INTRA BF
And so on for a total of 438 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

Note: Inside/Outside RMS Z-score plot

Chain identifier: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

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.

4255 LYS   ( 105-)  P      -6.03
3314 GLN   ( 149-)  M      -6.02
1186 GLN   ( 149-)  E      -6.02
2250 GLN   ( 149-)  I      -6.02
3723 LYS   ( 105-)  N      -6.00
3846 GLN   ( 149-)  O      -5.99
1063 LYS   ( 105-)  D      -5.97
2127 LYS   ( 105-)  H      -5.95
 654 GLN   ( 149-)  C      -5.94
2782 GLN   ( 149-)  K      -5.93
1718 GLN   ( 149-)  G      -5.93
 122 GLN   ( 149-)  A      -5.88
2659 LYS   ( 105-)  J      -5.86
1595 LYS   ( 105-)  F      -5.82
2536 ARG   ( 439-)  I      -5.77
4132 ARG   ( 439-)  O      -5.77
3068 ARG   ( 439-)  K      -5.77
 408 ARG   ( 439-)  A      -5.77
2004 ARG   ( 439-)  G      -5.76
1472 ARG   ( 439-)  E      -5.76
3600 ARG   ( 439-)  M      -5.76
 940 ARG   ( 439-)  C      -5.75
3191 LYS   ( 105-)  L      -5.71
 531 LYS   ( 105-)  B      -5.59
 460 GLN   (  34-)  B      -5.53
And so on for a total of 76 lines.

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: G

Note: Quality value plot

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

Chain identifier: H

Note: Quality value plot

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

Chain identifier: I

Note: Quality value plot

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

Chain identifier: J

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: K

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: L

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: M

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: N

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: O

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: P

Warning: Low packing Z-score for some residues

The residues listed in the table below have an unusual packing environment according to the 2nd generation packing check. The score listed in the table is a packing normality Z-score: positive means better than average, negative means worse than average. Only residues scoring less than -2.50 are listed here. These are the unusual residues in the structure, so it will be interesting to take a special look at them.

1674 LEU   ( 105-)  G   -2.69
2738 LEU   ( 105-)  K   -2.65
2206 LEU   ( 105-)  I   -2.65
2740 LEU   ( 107-)  K   -2.64
 147 ILE   ( 174-)  A   -2.59
3272 LEU   ( 107-)  M   -2.58
3270 LEU   ( 105-)  M   -2.58
2275 ILE   ( 174-)  I   -2.57
1211 ILE   ( 174-)  E   -2.56
3339 ILE   ( 174-)  M   -2.55
2807 ILE   ( 174-)  K   -2.55
3871 ILE   ( 174-)  O   -2.55
 679 ILE   ( 174-)  C   -2.55
1743 ILE   ( 174-)  G   -2.54
2208 LEU   ( 107-)  I   -2.52
3804 LEU   ( 107-)  O   -2.52

Note: Second generation quality Z-score plot

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

Chain identifier: A

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

Note: Second generation quality Z-score plot

Chain identifier: M

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: P

Water, ion, and hydrogenbond related checks

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.

4274 HOH   (2048 )  C      O
4274 HOH   (2058 )  C      O
4274 HOH   (2074 )  C      O
4274 HOH   (2083 )  C      O
4276 HOH   (2090 )  E      O
4276 HOH   (2108 )  E      O
4280 HOH   (2012 )  I      O
4280 HOH   (2075 )  I      O
4282 HOH   (2015 )  K      O
4282 HOH   (2055 )  K      O
4286 HOH   (2018 )  O      O
4286 HOH   (2036 )  O      O
Marked this atom as acceptor 4257  CL  (1460-) A     CL
Marked this atom as acceptor 4258  CL  (1461-) A     CL
Marked this atom as acceptor 4259  CL  (1460-) C     CL
Marked this atom as acceptor 4260  CL  (1461-) C     CL
Marked this atom as acceptor 4261  CL  (1460-) E     CL
Marked this atom as acceptor 4262  CL  (1460-) G     CL
Marked this atom as acceptor 4263  CL  (1461-) G     CL
Marked this atom as acceptor 4264  CL  (1460-) I     CL
Marked this atom as acceptor 4265  CL  (1461-) I     CL
Marked this atom as acceptor 4266  CL  (1460-) K     CL
Marked this atom as acceptor 4267  CL  (1461-) K     CL
Marked this atom as acceptor 4268  CL  (1460-) M     CL
Marked this atom as acceptor 4269  CL  (1461-) M     CL
Marked this atom as acceptor 4270  CL  (1460-) O     CL
Marked this atom as acceptor 4271  CL  (1461-) O     CL

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.

 129 GLN   ( 156-)  A
 136 ASN   ( 163-)  A
 180 ASN   ( 207-)  A
 661 GLN   ( 156-)  C
 668 ASN   ( 163-)  C
1193 GLN   ( 156-)  E
1200 ASN   ( 163-)  E
1335 HIS   ( 298-)  E
1725 GLN   ( 156-)  G
1732 ASN   ( 163-)  G
2257 GLN   ( 156-)  I
2264 ASN   ( 163-)  I
2399 HIS   ( 298-)  I
3148 ASN   (  62-)  L
3321 GLN   ( 156-)  M
3463 HIS   ( 298-)  M
3853 GLN   ( 156-)  O
3995 HIS   ( 298-)  O

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.

  45 ASP   (  72-)  A      N
  63 LEU   (  90-)  A      N
  88 ASN   ( 115-)  A      ND2
 140 ARG   ( 167-)  A      N
 140 ARG   ( 167-)  A      NE
 184 PHE   ( 211-)  A      N
 208 ILE   ( 235-)  A      N
 209 LYS   ( 236-)  A      NZ
 212 TYR   ( 239-)  A      OH
 219 THR   ( 246-)  A      N
 258 ARG   ( 285-)  A      NH1
 268 ARG   ( 295-)  A      N
 276 ARG   ( 303-)  A      N
 296 GLY   ( 323-)  A      N
 302 GLY   ( 329-)  A      N
 303 THR   ( 330-)  A      OG1
 346 GLY   ( 373-)  A      N
 358 TRP   ( 385-)  A      N
 374 GLN   ( 401-)  A      NE2
 439 PHE   (  13-)  B      N
 453 GLN   (  27-)  B      NE2
 470 GLU   (  44-)  B      N
 471 THR   (  45-)  B      N
 473 ASN   (  47-)  B      N
 491 ASN   (  65-)  B      N
And so on for a total of 232 lines.

Warning: Buried unsatisfied hydrogen bond acceptors

The buried side-chain hydrogen bond acceptors listed in the table below are not involved in a hydrogen bond in the optimized hydrogen bond network.

Side-chain hydrogen bond acceptors buried inside the protein normally form hydrogen bonds within the protein. If there are any not hydrogen bonded in the optimized hydrogen bond network they will be listed here.

Waters are not listed by this option.

  30 GLU   (  52-)  A      OE2
 241 ASP   ( 268-)  A      OD1
 374 GLN   ( 401-)  A      OE1
 494 ASP   (  68-)  B      OD1
 562 GLU   (  52-)  C      OE2
 712 ASN   ( 207-)  C      OD1
 773 ASP   ( 268-)  C      OD1
 832 HIS   ( 327-)  C      ND1
 906 GLN   ( 401-)  C      OE1
1244 ASN   ( 207-)  E      OD1
1260 ASP   ( 223-)  E      OD2
1305 ASP   ( 268-)  E      OD1
1438 GLN   ( 401-)  E      OE1
1558 ASP   (  68-)  F      OD1
1776 ASN   ( 207-)  G      OD1
1837 ASP   ( 268-)  G      OD1
1970 GLN   ( 401-)  G      OE1
2259 GLU   ( 158-)  I      OE1
2308 ASN   ( 207-)  I      OD1
2369 ASP   ( 268-)  I      OD1
2502 GLN   ( 401-)  I      OE1
2651 GLN   (  97-)  J      OE1
2791 GLU   ( 158-)  K      OE1
2840 ASN   ( 207-)  K      OD1
2901 ASP   ( 268-)  K      OD1
3034 GLN   ( 401-)  K      OE1
3323 GLU   ( 158-)  M      OE1
3372 ASN   ( 207-)  M      OD1
3433 ASP   ( 268-)  M      OD1
3566 GLN   ( 401-)  M      OE1
3686 ASP   (  68-)  N      OD1
3904 ASN   ( 207-)  O      OD1
3965 ASP   ( 268-)  O      OD1
4098 GLN   ( 401-)  O      OE1

Warning: Unusual water packing

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

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

4276 HOH   (2039 )  E      O  1.12  K  4
4280 HOH   (2052 )  I      O  0.88  K  5
4282 HOH   (2045 )  K      O  0.89  K  5
4286 HOH   (2050 )  O      O  0.87  K  5

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.

 133 ASP   ( 160-)  A   H-bonding suggests Asn; but Alt-Rotamer
 241 ASP   ( 268-)  A   H-bonding suggests Asn; but Alt-Rotamer
 259 ASP   ( 286-)  A   H-bonding suggests Asn
 459 ASP   (  33-)  B   H-bonding suggests Asn
 494 ASP   (  68-)  B   H-bonding suggests Asn; but Alt-Rotamer
 773 ASP   ( 268-)  C   H-bonding suggests Asn
 791 ASP   ( 286-)  C   H-bonding suggests Asn
 807 ASP   ( 302-)  C   H-bonding suggests Asn
 991 ASP   (  33-)  D   H-bonding suggests Asn; but Alt-Rotamer
1026 ASP   (  68-)  D   H-bonding suggests Asn; but Alt-Rotamer
1305 ASP   ( 268-)  E   H-bonding suggests Asn
1558 ASP   (  68-)  F   H-bonding suggests Asn; but Alt-Rotamer
1729 ASP   ( 160-)  G   H-bonding suggests Asn; but Alt-Rotamer
1837 ASP   ( 268-)  G   H-bonding suggests Asn; but Alt-Rotamer
1855 ASP   ( 286-)  G   H-bonding suggests Asn
2055 ASP   (  33-)  H   H-bonding suggests Asn; but Alt-Rotamer
2090 ASP   (  68-)  H   H-bonding suggests Asn; but Alt-Rotamer
2369 ASP   ( 268-)  I   H-bonding suggests Asn; but Alt-Rotamer
2587 ASP   (  33-)  J   H-bonding suggests Asn; but Alt-Rotamer
2901 ASP   ( 268-)  K   H-bonding suggests Asn; but Alt-Rotamer
2919 ASP   ( 286-)  K   H-bonding suggests Asn
3154 ASP   (  68-)  L   H-bonding suggests Asn
3433 ASP   ( 268-)  M   H-bonding suggests Asn
3451 ASP   ( 286-)  M   H-bonding suggests Asn
3467 ASP   ( 302-)  M   H-bonding suggests Asn
3686 ASP   (  68-)  N   H-bonding suggests Asn
3965 ASP   ( 268-)  O   H-bonding suggests Asn; but Alt-Rotamer
3983 ASP   ( 286-)  O   H-bonding suggests Asn
4183 ASP   (  33-)  P   H-bonding suggests Asn; but Alt-Rotamer
4218 ASP   (  68-)  P   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.408
  2nd generation packing quality :  -0.099
  Ramachandran plot appearance   :  -1.138
  chi-1/chi-2 rotamer normality  :  -2.397
  Backbone conformation          :  -0.268

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.944
  Bond angles                    :   0.905
  Omega angle restraints         :   1.191
  Side chain planarity           :   0.911
  Improper dihedral distribution :   1.039
  Inside/Outside distribution    :   1.049

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 : 2.30


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :   0.5
  Ramachandran plot appearance   :   0.3
  chi-1/chi-2 rotamer normality  :  -0.9
  Backbone conformation          :  -0.2

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.944
  Bond angles                    :   0.905
  Omega angle restraints         :   1.191
  Side chain planarity           :   0.911
  Improper dihedral distribution :   1.039
  Inside/Outside distribution    :   1.049
==============

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.