WHAT IF Check report

This file was created 2011-12-18 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 pdb1sqv.ent

Checks that need to be done early-on in validation

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: I 41 2 2
Number of matrices in space group: 16
Highest polymer chain multiplicity in structure: 1
Highest polymer chain multiplicity according to SEQRES: 2
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: 16
Polymer chain multiplicity and SEQRES multiplicity disagree 1 2
Z and NCS seem to support the 3D multiplicity
There is strong evidence, though, for multiplicity and Z: 1 16

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: 234464.078
Volume of the Unit Cell V= 13917350.0
Space group multiplicity: 16
No NCS symmetry matrices (MTRIX records) found in PDB file
Matthews coefficient for observed atoms and Z high: Vm= 7.420
Vm by authors and this calculated Vm do not agree very well
Matthews coefficient read from REMARK 280 Vm= 3.600 SEQRES and ATOM multiplicities disagree. Error-reasoning thus is difficult.
(and the absence of MTRIX records doesn't help)
There is strong evidence, though, for multiplicity and Z: 1 16
which would result in the much more normal Vm= 3.710
and which also agrees with the number of NCS matrices (labeled `don't use')
that the user provided in the MTRIX records 1

Warning: Ligands for which a topology was generated automatically

The topology for the ligands in the table below were determined automatically. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. For this PDB file that seems to have gone fine, but be aware that automatic topology generation is a complicated task. So, if you get messages that you fail to understand or that you believe are wrong, and one of these ligands is involved, then check the ligand topology first.

2111 UQ2   ( 384-)  C  -
2112 UHD   ( 383-)  C  -

Non-validating, descriptive output paragraph

Note: Ramachandran plot

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

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

Chain identifier: A

Note: Ramachandran plot

Chain identifier: 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

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: 22

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: 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

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.

1823 ILE   (  34-)  G      CA   CB    1.61    4.2

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

 |  0.996834  0.000060 -0.000105|
 |  0.000060  0.997114 -0.000059|
 | -0.000105 -0.000059  0.997971|
Proposed new scale matrix

 |  0.006528  0.000000  0.000000|
 |  0.000000  0.006526  0.000000|
 |  0.000000  0.000000  0.001700|
With corresponding cell

    A    = 153.194  B   = 153.237  C    = 588.080
    Alpha=  90.004  Beta=  90.004  Gamma=  90.002

The CRYST1 cell dimensions

    A    = 153.681  B   = 153.681  C    = 589.275
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 513.825
(Under-)estimated Z-score: 16.706

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.

 323 HIS   ( 323-)  A      CG   ND1  CE1 109.75    4.2
 495 THR   (  65-)  B      CG2  CB   OG1 100.15   -4.6
 619 VAL   ( 189-)  B      N    CA   CB  117.39    4.1
 670 HIS   ( 240-)  B      CG   ND1  CE1 109.62    4.0
 990 THR   ( 122-)  C      CG2  CB   OG1 100.63   -4.3
1069 HIS   ( 201-)  C      CG   ND1  CE1 109.62    4.0
1213 HIS   ( 345-)  C      N    CA   C   122.53    4.0
1471 ARG   ( 224-)  D      CG   CD   NE  118.04    4.4
1738 VAL   (  59-)  F      N    CA   CB  118.27    4.6
1839 PRO   (  50-)  G      CA   C    O   113.79   -4.1
1840 PRO   (  51-)  G     -CA  -C    N   122.96    4.0
1973 VAL   (  42-)  I      C    CA   CB  120.54    5.5
1974 LEU   (  43-)  I      C    CA   CB  118.86    4.6
2067 VAL   (  18-)  K      C    CA   CB  118.15    4.2

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.

  62 LEU   (  62-)  A      C      6.5    10.41     0.20
 129 LYS   ( 129-)  A      C      6.8    10.32     0.11
 137 GLU   ( 137-)  A      C      7.9    11.39    -0.03
 366 VAL   ( 366-)  A      C      6.7     9.37     0.15
 460 PRO   (  30-)  B      C      6.6    10.81     0.42
 498 LEU   (  68-)  B      C      6.4    10.34     0.20
 530 SER   ( 100-)  B      C     -6.5   -10.30     0.37
 538 THR   ( 108-)  B      C      7.9    12.14     0.30
 548 ILE   ( 118-)  B      CA    -8.6    20.22    33.24
 548 ILE   ( 118-)  B      C      8.5    11.23     0.03
 568 ALA   ( 138-)  B      C      6.6    10.24     0.08
 587 ALA   ( 157-)  B      C      6.4     9.90     0.08
 599 ARG   ( 169-)  B      C      6.1     9.41     0.13
 661 GLY   ( 231-)  B      C     -7.5    -9.82     0.06
 687 LEU   ( 257-)  B      CG     6.7   -21.28   -33.01
 799 LEU   ( 369-)  B      C      6.6    10.64     0.20
 946 ILE   (  78-)  C      C      7.4     9.73     0.03
 947 ILE   (  79-)  C      C      6.5     8.56     0.03
 960 ILE   (  92-)  C      C      6.0     7.90     0.03
1155 LYS   ( 287-)  C      C      6.0     9.20     0.11
1300 GLY   (  53-)  D      C      7.8    10.32     0.06
1333 LYS   (  86-)  D      C      6.6    10.14     0.11
1354 GLY   ( 107-)  D      C     -6.3    -8.24     0.06
1363 ILE   ( 116-)  D      CB    -6.2    24.30    32.31
1545 GLN   (  57-)  E      C      6.2     9.90     0.15
1553 SER   (  65-)  E      CA    -7.3    20.74    34.32
1823 ILE   (  34-)  G      CA    -7.7    21.56    33.24
1934 SER   (   3-)  I      C     -6.5   -10.36     0.37
1942 PHE   (  11-)  I      C     -6.5   -10.29     0.23
1953 VAL   (  22-)  I      C     -7.8   -10.54     0.15
1973 VAL   (  42-)  I      CA   -13.9    13.09    33.23
1974 LEU   (  43-)  I      CA   -11.1    17.21    34.19
2067 VAL   (  18-)  K      CA   -10.1    18.64    33.23
2087 TRP   (  38-)  K      C     -7.8   -11.18     0.23
The average deviation= 2.233

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.

2067 VAL   (  18-)  K    5.58
1213 HIS   ( 345-)  C    5.51
1881 GLU   (  28-)  H    4.86
 192 ALA   ( 192-)  A    4.64
1094 ILE   ( 226-)  C    4.58
1838 ALA   (  49-)  G    4.42
1170 ALA   ( 302-)  C    4.40
1355 ALA   ( 108-)  D    4.11
 195 MET   ( 195-)  A    4.10
1215 TYR   ( 347-)  C    4.08
 548 ILE   ( 118-)  B    4.05
1957 LEU   (  26-)  I    4.05
1553 SER   (  65-)  E    4.03
 404 ALA   ( 404-)  A    4.01

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.

 894 ASN   (  26-)  C    7.93
 600 ASN   ( 170-)  B    7.86
1975 ASP   (  44-)  I    6.30
 534 ASN   ( 104-)  B    6.23
 533 GLU   ( 103-)  B    6.16
 676 GLU   ( 246-)  B    6.07
 588 HIS   ( 158-)  B    5.60
 655 ASN   ( 225-)  B    5.14
 594 HIS   ( 164-)  B    4.96
1413 ASN   ( 166-)  D    4.90
1545 GLN   (  57-)  E    4.72
1811 GLU   (  22-)  G    4.69
 470 ASN   (  40-)  B    4.56
 622 HIS   ( 192-)  B    4.44
1074 ASN   ( 206-)  C    4.41
 573 GLN   ( 143-)  B    4.38
 173 ASN   ( 173-)  A    4.33
1765 ASP   (  86-)  F    4.20
1176 HIS   ( 308-)  C    4.17
 537 TYR   ( 107-)  B    4.16
2092 ASP   (  43-)  K    4.14
 720 ASN   ( 290-)  B    4.11
1064 HIS   ( 196-)  C    4.10

Error: Connections to aromatic rings out of plane

The atoms listed in the table below are connected to a planar aromatic group in the sidechain of a protein residue but were found to deviate from the least squares plane.

For all atoms that are connected to an aromatic side chain in a protein residue the distance of the atom to the least squares plane through the aromatic system was determined. This value was divided by the standard deviation from a distribution of similar values from a database of small molecule structures.

 368 HIS   ( 368-)  A      CB   4.93
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -3.219

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 : -3.219

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.

1132 THR   ( 264-)  C    -3.7
 223 TYR   ( 223-)  A    -3.5
1968 THR   (  37-)  I    -3.4
1386 THR   ( 139-)  D    -3.3
  33 PRO   (  33-)  A    -3.1
1368 HIS   ( 121-)  D    -3.0
1026 THR   ( 158-)  C    -2.9
1409 PRO   ( 162-)  D    -2.9
 450 HIS   (  20-)  B    -2.9
  34 THR   (  34-)  A    -2.9
1816 PRO   (  27-)  G    -2.9
1981 LEU   (  50-)  I    -2.8
1753 ILE   (  74-)  F    -2.8
1003 TRP   ( 135-)  C    -2.8
1090 PRO   ( 222-)  C    -2.8
 825 PRO   ( 395-)  B    -2.8
 107 PRO   ( 107-)  A    -2.8
1797 THR   (   8-)  G    -2.7
 449 PRO   (  19-)  B    -2.7
1939 SER   (   8-)  I    -2.7
2034 ILE   (  46-)  J    -2.7
1305 GLU   (  58-)  D    -2.6
 657 ARG   ( 227-)  B    -2.6
1992 THR   (   4-)  J    -2.6
1991 PRO   (   3-)  J    -2.6
And so on for a total of 172 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.

   2 ALA   (   2-)  A  omega poor
  12 PRO   (  12-)  A  omega poor
  13 GLU   (  13-)  A  omega poor
  20 ASP   (  20-)  A  omega poor
  21 ASN   (  21-)  A  omega poor
  26 ALA   (  26-)  A  omega poor
  29 GLN   (  29-)  A  omega poor
  33 PRO   (  33-)  A  omega poor
  34 THR   (  34-)  A  Poor phi/psi
  35 CYS   (  35-)  A  omega poor
  42 ASP   (  42-)  A  omega poor
  45 SER   (  45-)  A  Poor phi/psi, omega poor
  52 ASN   (  52-)  A  omega poor
  62 LEU   (  62-)  A  omega poor
  65 LYS   (  65-)  A  omega poor
  72 GLY   (  72-)  A  Poor phi/psi
  73 ASN   (  73-)  A  omega poor
  88 ALA   (  88-)  A  omega poor
  93 GLU   (  93-)  A  Poor phi/psi
  96 ALA   (  96-)  A  omega poor
  99 ILE   (  99-)  A  omega poor
 101 ALA   ( 101-)  A  omega poor
 106 LEU   ( 106-)  A  PRO omega poor
 107 PRO   ( 107-)  A  Poor phi/psi
 118 GLN   ( 118-)  A  omega poor
And so on for a total of 394 lines.

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 : -5.752

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.

1376 SER   ( 129-)  D    0.36
1823 ILE   (  34-)  G    0.36
 826 SER   ( 396-)  B    0.37
1427 SER   ( 180-)  D    0.38
 703 SER   ( 273-)  B    0.38

Warning: Unusual backbone conformations

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

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

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

  11 VAL   (  11-)  A      0
  19 LEU   (  19-)  A      0
  21 ASN   (  21-)  A      0
  31 SER   (  31-)  A      0
  32 GLN   (  32-)  A      0
  33 PRO   (  33-)  A      0
  34 THR   (  34-)  A      0
  41 ILE   (  41-)  A      0
  43 ALA   (  43-)  A      0
  45 SER   (  45-)  A      0
  47 TYR   (  47-)  A      0
  52 ASN   (  52-)  A      0
  53 ASN   (  53-)  A      0
  62 LEU   (  62-)  A      0
  65 LYS   (  65-)  A      0
  73 ASN   (  73-)  A      0
  82 MET   (  82-)  A      0
  93 GLU   (  93-)  A      0
  94 HIS   (  94-)  A      0
 102 LEU   ( 102-)  A      0
 119 ASN   ( 119-)  A      0
 121 SER   ( 121-)  A      0
 145 MET   ( 145-)  A      0
 159 GLN   ( 159-)  A      0
 168 GLU   ( 168-)  A      0
And so on for a total of 729 lines.

Warning: Omega angle restraints not strong enough

The omega angles for trans-peptide bonds in a structure is expected to give a gaussian distribution with the average around +178 degrees, and a standard deviation around 5.5. In the current structure the standard deviation of this distribution is above 7.0, which indicates that the omega values have been under-restrained.

Standard deviation of omega values : 12.314

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!

  72 GLY   (  72-)  A   2.01   15
1300 GLY   (  53-)  D   1.96   11
  66 GLY   (  66-)  A   1.88   20
  44 GLY   (  44-)  A   1.75   14
 218 GLY   ( 218-)  A   1.70   41
1076 PRO   ( 208-)  C   1.59   10
1953 VAL   (  22-)  I   1.51   12

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...

1750 ARG   (  71-)  F   1.54
1973 VAL   (  42-)  I   2.42

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]

1809 PRO   (  20-)  G    0.20 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].

  33 PRO   (  33-)  A    18.7 half-chair N/C-delta (18 degrees)
  71 PRO   (  71-)  A    50.0 half-chair C-delta/C-gamma (54 degrees)
 107 PRO   ( 107-)  A  -154.6 half-chair N/C-delta (-162 degrees)
 170 PRO   ( 170-)  A   -54.6 half-chair C-beta/C-alpha (-54 degrees)
 229 PRO   ( 229-)  A    16.1 half-chair N/C-delta (18 degrees)
 249 PRO   ( 249-)  A    10.3 half-chair N/C-delta (18 degrees)
 391 PRO   ( 391-)  A    50.9 half-chair C-delta/C-gamma (54 degrees)
 448 PRO   (  18-)  B   -17.9 half-chair C-alpha/N (-18 degrees)
 449 PRO   (  19-)  B  -157.3 half-chair N/C-delta (-162 degrees)
 451 PRO   (  21-)  B    49.3 half-chair C-delta/C-gamma (54 degrees)
 585 PRO   ( 155-)  B  -147.5 envelop C-delta (-144 degrees)
 609 PRO   ( 179-)  B   146.0 envelop C-alpha (144 degrees)
 644 PRO   ( 214-)  B   108.6 envelop C-beta (108 degrees)
 713 PRO   ( 283-)  B   -57.7 half-chair C-beta/C-alpha (-54 degrees)
 736 PRO   ( 306-)  B  -121.3 half-chair C-delta/C-gamma (-126 degrees)
 785 PRO   ( 355-)  B  -117.8 half-chair C-delta/C-gamma (-126 degrees)
 824 PRO   ( 394-)  B  -128.1 half-chair C-delta/C-gamma (-126 degrees)
 825 PRO   ( 395-)  B  -150.0 envelop C-delta (-144 degrees)
 890 PRO   (  22-)  C    50.0 half-chair C-delta/C-gamma (54 degrees)
1022 PRO   ( 154-)  C   103.8 envelop C-beta (108 degrees)
1115 PRO   ( 247-)  C  -122.3 half-chair C-delta/C-gamma (-126 degrees)
1173 PRO   ( 305-)  C   109.7 envelop C-beta (108 degrees)
1214 PRO   ( 346-)  C   -48.4 half-chair C-beta/C-alpha (-54 degrees)
1258 PRO   (  11-)  D    47.5 half-chair C-delta/C-gamma (54 degrees)
1321 PRO   (  74-)  D    27.6 envelop C-delta (36 degrees)
1331 PRO   (  84-)  D   112.1 envelop C-beta (108 degrees)
1339 PRO   (  92-)  D    41.7 envelop C-delta (36 degrees)
1341 PRO   (  94-)  D   -43.1 envelop C-alpha (-36 degrees)
1343 PRO   (  96-)  D    53.0 half-chair C-delta/C-gamma (54 degrees)
1358 PRO   ( 111-)  D    48.8 half-chair C-delta/C-gamma (54 degrees)
1385 PRO   ( 138-)  D    24.6 half-chair N/C-delta (18 degrees)
1398 PRO   ( 151-)  D    48.7 half-chair C-delta/C-gamma (54 degrees)
1401 PRO   ( 154-)  D    99.2 envelop C-beta (108 degrees)
1409 PRO   ( 162-)  D    30.7 envelop C-delta (36 degrees)
1410 PRO   ( 163-)  D     5.3 envelop N (0 degrees)
1423 PRO   ( 176-)  D  -136.6 envelop C-delta (-144 degrees)
1496 PRO   (   8-)  E  -147.5 envelop C-delta (-144 degrees)
1608 PRO   ( 120-)  E   -24.9 half-chair C-alpha/N (-18 degrees)
1634 PRO   ( 146-)  E    47.8 half-chair C-delta/C-gamma (54 degrees)
1647 PRO   ( 159-)  E   -59.4 half-chair C-beta/C-alpha (-54 degrees)
1663 PRO   ( 175-)  E    51.0 half-chair C-delta/C-gamma (54 degrees)
1671 PRO   ( 183-)  E    26.0 half-chair N/C-delta (18 degrees)
1816 PRO   (  27-)  G    -2.0 envelop N (0 degrees)
1863 PRO   (  74-)  G    24.6 half-chair N/C-delta (18 degrees)
1944 PRO   (  13-)  I  -112.5 envelop C-gamma (-108 degrees)
1966 PRO   (  35-)  I   -17.8 half-chair C-alpha/N (-18 degrees)
1972 PRO   (  41-)  I   -53.0 half-chair C-beta/C-alpha (-54 degrees)
1991 PRO   (   3-)  J    44.7 envelop C-delta (36 degrees)
2057 PRO   (   8-)  K  -135.8 envelop C-delta (-144 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.

 244 ARG   ( 244-)  A      NH2 <-> 2113 HOH   ( 514 )  A      O      0.60    2.10  INTRA
 419 CYS   ( 419-)  A      SG  <->  438 ARG   ( 438-)  A      NH1    0.49    2.81  INTRA
1932 MET   (   1-)  I      SD  <-> 2120 HOH   ( 671 )  I      O      0.40    2.60  INTRA BF
 795 LYS   ( 365-)  B      NZ  <->  833 ASP   ( 403-)  B      OD1    0.40    2.30  INTRA
 244 ARG   ( 244-)  A      NE  <-> 2113 HOH   ( 514 )  A      O      0.37    2.33  INTRA
 675 ARG   ( 245-)  B      NH2 <->  863 THR   ( 433-)  B      O      0.35    2.35  INTRA BL
1084 ASP   ( 216-)  C      OD2 <-> 1480 ARG   ( 233-)  D      NH2    0.30    2.40  INTRA
1982 CYS   (  51-)  I      SG  <-> 1983 ARG   (  52-)  I      N      0.29    2.91  INTRA BF
1287 CYS   (  40-)  D      SG  <-> 1352 ASN   ( 105-)  D      ND2    0.27    3.03  INTRA BL
 154 HIS   ( 154-)  A      NE2 <->  314 TYR   ( 314-)  A      OH     0.26    2.44  INTRA
 131 ARG   ( 131-)  A      NH2 <->  177 LEU   ( 177-)  A      O      0.26    2.44  INTRA BL
1407 MET   ( 160-)  D      SD  <-> 2109 HEM   ( 242-)  D      NA     0.25    3.05  INTRA
 657 ARG   ( 227-)  B      NH2 <->  660 LEU   ( 230-)  B      O      0.25    2.45  INTRA BF
 189 HIS   ( 189-)  A      O   <->  194 ARG   ( 194-)  A      NH1    0.24    2.46  INTRA
 244 ARG   ( 244-)  A      CZ  <-> 2113 HOH   ( 514 )  A      O      0.24    2.56  INTRA
1942 PHE   (  11-)  I      CB  <-> 2114 HOH   ( 623 )  B      O      0.24    2.56  INTRA
 514 LYS   (  84-)  B      O   <->  518 GLY   (  88-)  B      N      0.23    2.47  INTRA BL
 815 GLN   ( 385-)  B      NE2 <->  823 THR   ( 393-)  B      N      0.23    2.62  INTRA BL
1322 ASN   (  75-)  D      O   <-> 1324 ASP   (  77-)  D      N      0.22    2.48  INTRA
1382 CYS   ( 135-)  D      SG  <-> 1383 GLU   ( 136-)  D      N      0.21    2.99  INTRA
1287 CYS   (  40-)  D      SG  <-> 2109 HEM   ( 242-)  D      CAC    0.21    3.19  INTRA
 388 ARG   ( 388-)  A      NH2 <->  394 GLU   ( 394-)  A      OE1    0.21    2.49  INTRA
 245 GLU   ( 245-)  A      OE1 <-> 1800 ARG   (  11-)  G      NE     0.20    2.50  INTRA
1082 ASP   ( 214-)  C      OD1 <-> 1791 ARG   (   2-)  G      NH2    0.20    2.50  INTRA
 388 ARG   ( 388-)  A      NH2 <->  394 GLU   ( 394-)  A      CD     0.18    2.92  INTRA
And so on for a total of 232 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

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.

1023 TYR   ( 155-)  C      -8.14
1391 ARG   ( 144-)  D      -7.66
1987 ARG   (  56-)  I      -7.47
1606 ARG   ( 118-)  E      -7.23
1036 PHE   ( 168-)  C      -7.18
1407 MET   ( 160-)  D      -6.88
 450 HIS   (  20-)  B      -6.79
1485 ARG   ( 238-)  D      -6.50
1356 LEU   ( 109-)  D      -6.46
 662 LEU   ( 232-)  B      -6.42
 851 ARG   ( 421-)  B      -6.40
1368 HIS   ( 121-)  D      -6.39
1983 ARG   (  52-)  I      -6.39
 657 ARG   ( 227-)  B      -6.39
 471 TYR   (  41-)  B      -6.34
 734 HIS   ( 304-)  B      -6.34
1860 ARG   (  71-)  G      -6.32
1861 LYS   (  72-)  G      -6.31
1900 ARG   (  47-)  H      -6.25
1367 ARG   ( 120-)  D      -6.17
 862 HIS   ( 432-)  B      -6.15
 599 ARG   ( 169-)  B      -6.15
  70 ARG   (  70-)  A      -6.14
1383 GLU   ( 136-)  D      -6.04
1924 HIS   (  71-)  H      -6.03
And so on for a total of 71 lines.

Warning: Abnormal packing environment for sequential residues

A stretch of at least three sequential residues with a questionable packing environment was found. This could indicate that these residues are part of a strange loop. It might also be an indication of misthreading in the density. However, it can also indicate that one or more residues in this stretch have other problems such as, for example, missing atoms, very weird angles or bond lengths, etc.

The table below lists the first and last residue in each stretch found, as well as the average residue score of the series.

1135 HIS   ( 267-)  C      1137 - LYS    269- ( C)         -5.25
1249 ASP   (   2-)  D      1253 - HIS      6- ( D)         -4.63
1389 SER   ( 142-)  D      1391 - ARG    144- ( D)         -5.47
1412 TYR   ( 165-)  D      1414 - GLU    167- ( D)         -4.87
1559 MET   (  71-)  E      1561 - LYS     73- ( E)         -4.23
1750 ARG   (  71-)  F      1752 - GLN     73- ( F)         -4.60
1860 ARG   (  71-)  G      1864 - ALA     75- ( G)         -5.21
1900 ARG   (  47-)  H      1902 - GLN     49- ( H)         -5.30

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

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.

1344 ASN   (  97-)  D   -2.77
1006 MET   ( 138-)  C   -2.66
 860 LEU   ( 430-)  B   -2.55

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

The table below lists the first and last residue in each stretch found, as well as the average residue Z-score of the series.

1361 SER   ( 114-)  D     - 1366 ALA   ( 119-)  D        -1.70

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

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.

2113 HOH   ( 510 )  A      O
2113 HOH   ( 562 )  A      O
2113 HOH   ( 572 )  A      O
2114 HOH   ( 580 )  B      O
2114 HOH   ( 584 )  B      O
2114 HOH   ( 600 )  B      O
2114 HOH   ( 606 )  B      O
2114 HOH   ( 616 )  B      O
2114 HOH   ( 624 )  B      O
2114 HOH   ( 634 )  B      O
2114 HOH   ( 635 )  B      O
2114 HOH   ( 639 )  B      O
2114 HOH   ( 677 )  B      O
2115 HOH   ( 688 )  C      O
2115 HOH   ( 689 )  C      O
2115 HOH   ( 709 )  C      O
2116 HOH   ( 715 )  D      O
2118 HOH   ( 748 )  F      O
2118 HOH   ( 754 )  F      O
2118 HOH   ( 756 )  F      O
2118 HOH   ( 765 )  F      O
2119 HOH   ( 769 )  G      O
2119 HOH   ( 775 )  G      O
2121 HOH   ( 787 )  K      O
Metal-coordinating Histidine residue 951 fixed to   1
Metal-coordinating Histidine residue1050 fixed to   1
Metal-coordinating Histidine residue 965 fixed to   1
Metal-coordinating Histidine residue1064 fixed to   1
Metal-coordinating Histidine residue1288 fixed to   1
Metal-coordinating Histidine residue1629 fixed to   1
Metal-coordinating Histidine residue1649 fixed to   1

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.

  18 GLN   (  18-)  A
  69 ASN   (  69-)  A
 119 ASN   ( 119-)  A
 165 GLN   ( 165-)  A
 173 ASN   ( 173-)  A
 341 GLN   ( 341-)  A
 359 ASN   ( 359-)  A
 573 GLN   ( 143-)  B
 604 ASN   ( 174-)  B
 700 ASN   ( 270-)  B
 781 ASN   ( 351-)  B
 792 ASN   ( 362-)  B
 922 HIS   (  54-)  C
 942 ASN   (  74-)  C
1074 ASN   ( 206-)  C
1270 HIS   (  23-)  D
1297 HIS   (  50-)  D
1403 GLN   ( 156-)  D
1701 ASN   (  22-)  F
1962 GLN   (  31-)  I
2061 GLN   (  12-)  K

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.

  23 LEU   (  23-)  A      N
  43 ALA   (  43-)  A      N
  44 GLY   (  44-)  A      N
  46 ARG   (  46-)  A      NE
  47 TYR   (  47-)  A      N
  48 GLU   (  48-)  A      N
  49 SER   (  49-)  A      N
  49 SER   (  49-)  A      OG
  66 GLY   (  66-)  A      N
  75 LEU   (  75-)  A      N
  76 GLU   (  76-)  A      N
  88 ALA   (  88-)  A      N
  97 TYR   (  97-)  A      OH
 102 LEU   ( 102-)  A      N
 103 SER   ( 103-)  A      OG
 159 GLN   ( 159-)  A      NE2
 168 GLU   ( 168-)  A      N
 173 ASN   ( 173-)  A      N
 191 LYS   ( 191-)  A      N
 192 ALA   ( 192-)  A      N
 217 SER   ( 217-)  A      N
 224 ASP   ( 224-)  A      N
 235 ARG   ( 235-)  A      NH1
 250 LEU   ( 250-)  A      N
 252 HIS   ( 252-)  A      ND1
And so on for a total of 249 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.

 240 GLN   ( 240-)  A      OE1
 311 ASN   ( 311-)  A      OD1
 469 GLU   (  39-)  B      OE1
 670 HIS   ( 240-)  B      ND1
 720 ASN   ( 290-)  B      OD1
 743 ASN   ( 313-)  B      OD1
 894 ASN   (  26-)  C      OD1
 900 ASN   (  32-)  C      OD1
 912 GLN   (  44-)  C      OE1
1096 ASP   ( 228-)  C      OD2
1180 GLN   ( 312-)  C      OE1
1199 ASP   ( 331-)  C      OD2
1261 HIS   (  14-)  D      ND1
1414 GLU   ( 167-)  D      OE1
1442 GLU   ( 195-)  D      OE1
1541 ASN   (  53-)  E      OD1
1593 GLU   ( 105-)  E      OE1
1811 GLU   (  22-)  G      OE1
1962 GLN   (  31-)  I      OE1
1984 GLU   (  53-)  I      OE2
2065 ASN   (  16-)  K      OD1

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.

  48 GLU   (  48-)  A   H-bonding suggests Gln; but Alt-Rotamer
 105 ASP   ( 105-)  A   H-bonding suggests Asn
 224 ASP   ( 224-)  A   H-bonding suggests Asn
 258 GLU   ( 258-)  A   H-bonding suggests Gln; but Alt-Rotamer
 673 GLU   ( 243-)  B   H-bonding suggests Gln; but Alt-Rotamer
 680 ASP   ( 250-)  B   H-bonding suggests Asn; but Alt-Rotamer
 811 GLU   ( 381-)  B   H-bonding suggests Gln
1096 ASP   ( 228-)  C   H-bonding suggests Asn; Ligand-contact
1139 GLU   ( 271-)  C   H-bonding suggests Gln
1199 ASP   ( 331-)  C   H-bonding suggests Asn
1326 GLU   (  79-)  D   H-bonding suggests Gln
1414 GLU   ( 167-)  D   H-bonding suggests Gln
1492 ASP   (   4-)  E   H-bonding suggests Asn; but Alt-Rotamer
1568 ASP   (  80-)  E   H-bonding suggests Asn; but Alt-Rotamer
1735 ASP   (  56-)  F   H-bonding suggests Asn; but Alt-Rotamer
1811 GLU   (  22-)  G   H-bonding suggests Gln; but Alt-Rotamer
1894 ASP   (  41-)  H   H-bonding suggests Asn
1895 GLU   (  42-)  H   H-bonding suggests Gln
1913 ASP   (  60-)  H   H-bonding suggests Asn
1975 ASP   (  44-)  I   H-bonding suggests Asn
2092 ASP   (  43-)  K   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -1.571
  2nd generation packing quality :  -2.066
  Ramachandran plot appearance   :  -3.219 (poor)
  chi-1/chi-2 rotamer normality  :  -5.752 (bad)
  Backbone conformation          :  -0.619

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.465 (tight)
  Bond angles                    :   0.875
  Omega angle restraints         :   2.239 (loose)
  Side chain planarity           :   1.740
  Improper dihedral distribution :   1.927 (loose)
  B-factor distribution          :   0.892
  Inside/Outside distribution    :   1.112

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 : 2.85


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.6
  2nd generation packing quality :  -0.4
  Ramachandran plot appearance   :  -0.8
  chi-1/chi-2 rotamer normality  :  -3.3 (poor)
  Backbone conformation          :   0.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.465 (tight)
  Bond angles                    :   0.875
  Omega angle restraints         :   2.239 (loose)
  Side chain planarity           :   1.740
  Improper dihedral distribution :   1.927 (loose)
  B-factor distribution          :   0.892
  Inside/Outside distribution    :   1.112
==============

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.