WHAT IF Check report

This file was created 2011-12-17 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 pdb1rsc.ent

Checks that need to be done early-on in validation

Warning: Unconventional orthorhombic cell

The primitive P 2 2 2 or P 21 21 21 cell specified does not conform to the convention that the axes should be given in order of increasing length.

The CRYST1 cell dimensions

    A    = 224.400  B   = 112.600  C    = 200.300
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Warning: Conventional cell

The conventional cell as mentioned earlier has been derived.

The CRYST1 cell dimensions

    A    = 224.400  B   = 112.600  C    = 200.300
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of a reduced cell

    A    = 112.600  B   = 200.300  C    = 224.400
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    = 112.600  B   = 200.300  C    = 224.400
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Transformation to conventional cell

 |  0.000000  1.000000  0.000000|
 |  0.000000  0.000000  1.000000|
 |  1.000000  0.000000  0.000000|

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.

4617 XBP   ( 476-)  A  -
4618 XBP   ( 476-)  B  -
4619 XBP   ( 476-)  C  -
4620 XBP   ( 476-)  D  -
4621 XBP   ( 476-)  E  -
4622 XBP   ( 476-)  F  -
4623 XBP   ( 476-)  G  -
4624 XBP   ( 476-)  H  -

Administrative problems that can generate validation failures

Warning: Plausible side chain atoms detected with zero occupancy

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

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

   1 SER   (   9-)  A  -   CB
   1 SER   (   9-)  A  -   OG
   2 ALA   (  10-)  A  -   CB
   3 ALA   (  11-)  A  -   CB
  85 GLU   (  93-)  A  -   CB
  85 GLU   (  93-)  A  -   CG
  85 GLU   (  93-)  A  -   CD
  85 GLU   (  93-)  A  -   OE1
  85 GLU   (  93-)  A  -   OE2
  86 GLU   (  94-)  A  -   CB
  86 GLU   (  94-)  A  -   CG
  86 GLU   (  94-)  A  -   CD
  86 GLU   (  94-)  A  -   OE1
  86 GLU   (  94-)  A  -   OE2
 421 GLN   ( 429-)  A  -   CB
 421 GLN   ( 429-)  A  -   CG
 421 GLN   ( 429-)  A  -   CD
 421 GLN   ( 429-)  A  -   OE1
 421 GLN   ( 429-)  A  -   NE2
 423 ARG   ( 431-)  A  -   CB
 423 ARG   ( 431-)  A  -   CG
 423 ARG   ( 431-)  A  -   CD
 423 ARG   ( 431-)  A  -   NE
 423 ARG   ( 431-)  A  -   CZ
 423 ARG   ( 431-)  A  -   NH1
And so on for a total of 784 lines.

Warning: Plausible backbone atoms detected with zero occupancy

Plausible backbone atoms were detected with (near) zero occupancy

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

   1 SER   (   9-)  A  -   N
   1 SER   (   9-)  A  -   CA
   1 SER   (   9-)  A  -   C
   1 SER   (   9-)  A  -   O
   2 ALA   (  10-)  A  -   N
   2 ALA   (  10-)  A  -   CA
   2 ALA   (  10-)  A  -   C
   2 ALA   (  10-)  A  -   O
   3 ALA   (  11-)  A  -   N
   3 ALA   (  11-)  A  -   CA
   3 ALA   (  11-)  A  -   C
   3 ALA   (  11-)  A  -   O
 530 ASP   (  76-)  M  -   N
 530 ASP   (  76-)  M  -   CA
 530 ASP   (  76-)  M  -   C
 530 ASP   (  76-)  M  -   O
 531 CYS   (  77-)  M  -   N
 531 CYS   (  77-)  M  -   CA
 531 CYS   (  77-)  M  -   C
 531 CYS   (  77-)  M  -   O
 532 LYS   (  78-)  M  -   N
 532 LYS   (  78-)  M  -   CA
 532 LYS   (  78-)  M  -   C
 532 LYS   (  78-)  M  -   O
 575 GLY   ( 121-)  M  -   N
And so on for a total of 256 lines.

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: M

Note: Ramachandran plot

Chain identifier: B

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: C

Note: Ramachandran plot

Chain identifier: N

Note: Ramachandran plot

Chain identifier: D

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: O

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: P

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: L

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

Warning: Missing atoms

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

  83 GLN   (  91-)  A      CG
  83 GLN   (  91-)  A      CD
  83 GLN   (  91-)  A      OE1
  83 GLN   (  91-)  A      NE2
 530 ASP   (  76-)  M      CG
 530 ASP   (  76-)  M      OD1
 530 ASP   (  76-)  M      OD2
 532 LYS   (  78-)  M      CG
 532 LYS   (  78-)  M      CD
 532 LYS   (  78-)  M      CE
 532 LYS   (  78-)  M      NZ
 533 SER   (  79-)  M      OG
 659 GLN   (  91-)  B      CG
 659 GLN   (  91-)  B      CD
 659 GLN   (  91-)  B      OE1
 659 GLN   (  91-)  B      NE2
1106 ASP   (  76-)  I      CG
1106 ASP   (  76-)  I      OD1
1106 ASP   (  76-)  I      OD2
1108 LYS   (  78-)  I      CG
1108 LYS   (  78-)  I      CD
1108 LYS   (  78-)  I      CE
1108 LYS   (  78-)  I      NZ
1109 SER   (  79-)  I      OG
1235 GLN   (  91-)  C      CG
And so on for a total of 96 lines.

Warning: What type of B-factor?

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

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

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

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: M

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: N

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: O

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: P

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: L

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.

 119 PHE   ( 127-)  A      CA   CB    1.39   -7.2
 695 PHE   ( 127-)  B      CA   CB    1.39   -7.2
1271 PHE   ( 127-)  C      CA   CB    1.39   -7.2
1847 PHE   ( 127-)  D      CA   CB    1.39   -7.2
2423 PHE   ( 127-)  E      CA   CB    1.39   -7.1
2999 PHE   ( 127-)  F      CA   CB    1.39   -7.2
3575 PHE   ( 127-)  G      CA   CB    1.38   -7.3
4151 PHE   ( 127-)  H      CA   CB    1.39   -7.2

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

 |  0.999988  0.000279  0.000053|
 |  0.000279  0.999985  0.000090|
 |  0.000053  0.000090  0.999124|
Proposed new scale matrix

 |  0.004456 -0.000001  0.000000|
 | -0.000002  0.008881  0.000000|
 |  0.000000  0.000000  0.004997|
With corresponding cell

    A    = 224.414  B   = 112.598  C    = 200.105
    Alpha=  90.002  Beta=  90.002  Gamma=  89.968

The CRYST1 cell dimensions

    A    = 224.400  B   = 112.600  C    = 200.300
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 27.847
(Under-)estimated Z-score: 3.889

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.

 119 PHE   ( 127-)  A      C    CA   CB  118.64    4.5
 195 ASP   ( 203-)  A      CA   CB   CG  116.71    4.1
 317 HIS   ( 325-)  A      CG   ND1  CE1 109.60    4.0
 695 PHE   ( 127-)  B      C    CA   CB  118.67    4.5
 771 ASP   ( 203-)  B      CA   CB   CG  116.68    4.1
 893 HIS   ( 325-)  B      CG   ND1  CE1 109.62    4.0
1271 PHE   ( 127-)  C      C    CA   CB  118.65    4.5
1347 ASP   ( 203-)  C      CA   CB   CG  116.69    4.1
1847 PHE   ( 127-)  D      C    CA   CB  118.64    4.5
1923 ASP   ( 203-)  D      CA   CB   CG  116.74    4.1
2423 PHE   ( 127-)  E      C    CA   CB  118.66    4.5
2999 PHE   ( 127-)  F      C    CA   CB  118.64    4.5
3075 ASP   ( 203-)  F      CA   CB   CG  116.68    4.1
3197 HIS   ( 325-)  F      CG   ND1  CE1 109.62    4.0
3575 PHE   ( 127-)  G      C    CA   CB  118.60    4.5
3601 HIS   ( 153-)  G      CG   ND1  CE1 109.63    4.0
3651 ASP   ( 203-)  G      CA   CB   CG  116.81    4.2
3746 HIS   ( 298-)  G      CG   ND1  CE1 109.61    4.0
3773 HIS   ( 325-)  G      CG   ND1  CE1 109.66    4.1
4151 PHE   ( 127-)  H      C    CA   CB  118.65    4.5
4227 ASP   ( 203-)  H      CA   CB   CG  116.71    4.1

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.

3750 ASP   ( 302-)  G    4.57
3174 ASP   ( 302-)  F    4.54
1446 ASP   ( 302-)  C    4.52
 870 ASP   ( 302-)  B    4.52
 294 ASP   ( 302-)  A    4.52
2022 ASP   ( 302-)  D    4.51
4326 ASP   ( 302-)  H    4.51
2598 ASP   ( 302-)  E    4.48

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.

 785 ARG   ( 217-)  B    4.51
 209 ARG   ( 217-)  A    4.51
1361 ARG   ( 217-)  C    4.50
1937 ARG   ( 217-)  D    4.50
3089 ARG   ( 217-)  F    4.50
2513 ARG   ( 217-)  E    4.50
4241 ARG   ( 217-)  H    4.48
3665 ARG   ( 217-)  G    4.44

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.

2449 HIS   ( 153-)  E      CB   5.33
1873 HIS   ( 153-)  D      CB   5.32
 721 HIS   ( 153-)  B      CB   5.32
3025 HIS   ( 153-)  F      CB   5.32
 145 HIS   ( 153-)  A      CB   5.31
1297 HIS   ( 153-)  C      CB   5.31
4177 HIS   ( 153-)  H      CB   5.31
3601 HIS   ( 153-)  G      CB   5.30
1672 TYR   (  66-)  N      CB   4.64
2248 TYR   (  66-)  J      CB   4.64
 520 TYR   (  66-)  M      CB   4.64
4552 TYR   (  66-)  L      CB   4.64
1096 TYR   (  66-)  I      CB   4.64
3976 TYR   (  66-)  P      CB   4.64
2824 TYR   (  66-)  O      CB   4.64
3400 TYR   (  66-)  K      CB   4.62
Since there is no DNA and no protein with hydrogens, no uncalibrated
planarity check was performed.
 Ramachandran Z-score : -1.187

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.

3743 ARG   ( 295-)  G    -2.7
3167 ARG   ( 295-)  F    -2.7
 287 ARG   ( 295-)  A    -2.7
1439 ARG   ( 295-)  C    -2.7
2591 ARG   ( 295-)  E    -2.7
4319 ARG   ( 295-)  H    -2.7
2015 ARG   ( 295-)  D    -2.7
 863 ARG   ( 295-)  B    -2.7
 732 LYS   ( 164-)  B    -2.5
 156 LYS   ( 164-)  A    -2.5
2460 LYS   ( 164-)  E    -2.5
1884 LYS   ( 164-)  D    -2.5
4188 LYS   ( 164-)  H    -2.5
3612 LYS   ( 164-)  G    -2.5
1308 LYS   ( 164-)  C    -2.5
3036 LYS   ( 164-)  F    -2.5
 647 ARG   (  79-)  B    -2.5
1799 ARG   (  79-)  D    -2.5
3527 ARG   (  79-)  G    -2.5
2375 ARG   (  79-)  E    -2.5
2951 ARG   (  79-)  F    -2.5
  71 ARG   (  79-)  A    -2.5
4103 ARG   (  79-)  H    -2.5
1223 ARG   (  79-)  C    -2.5
2188 GLU   ( 468-)  D    -2.4
And so on for a total of 128 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.

  15 THR   (  23-)  A  omega poor
  54 SER   (  62-)  A  Poor phi/psi
  55 THR   (  63-)  A  Poor phi/psi
  57 THR   (  65-)  A  omega poor
  87 ASN   (  95-)  A  Poor phi/psi
  89 TYR   (  97-)  A  omega poor
 115 ASN   ( 123-)  A  Poor phi/psi
 155 ASN   ( 163-)  A  Poor phi/psi
 167 LYS   ( 175-)  A  PRO omega poor
 191 PHE   ( 199-)  A  omega poor
 199 ASN   ( 207-)  A  Poor phi/psi
 205 ARG   ( 213-)  A  omega poor
 235 THR   ( 243-)  A  omega poor
 289 MET   ( 297-)  A  Poor phi/psi
 293 ILE   ( 301-)  A  omega poor
 317 HIS   ( 325-)  A  omega poor
 323 VAL   ( 331-)  A  Poor phi/psi
 362 SER   ( 370-)  A  Poor phi/psi
 431 ARG   ( 439-)  A  omega poor
 479 GLU   (  13-)  M  Poor phi/psi, omega poor
 481 PHE   (  15-)  M  Poor phi/psi
 520 TYR   (  66-)  M  omega poor
 525 LYS   (  71-)  M  Poor phi/psi
 591 THR   (  23-)  B  omega poor
 630 SER   (  62-)  B  Poor phi/psi
And so on for a total of 184 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.

 220 SER   ( 228-)  A    0.36
 796 SER   ( 228-)  B    0.36
1372 SER   ( 228-)  C    0.36
1948 SER   ( 228-)  D    0.36
2524 SER   ( 228-)  E    0.36
3100 SER   ( 228-)  F    0.36
3676 SER   ( 228-)  G    0.36
4252 SER   ( 228-)  H    0.36

Warning: Unusual backbone conformations

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

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

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

   3 ALA   (  11-)  A      0
   7 ALA   (  15-)  A      0
  15 THR   (  23-)  A      0
  16 TYR   (  24-)  A      0
  17 TYR   (  25-)  A      0
  18 THR   (  26-)  A      0
  38 PRO   (  46-)  A      0
  53 SER   (  61-)  A      0
  54 SER   (  62-)  A      0
  55 THR   (  63-)  A      0
  58 TRP   (  66-)  A      0
  62 TRP   (  70-)  A      0
  66 LEU   (  74-)  A      0
  67 THR   (  75-)  A      0
  69 MET   (  77-)  A      0
  76 CYS   (  84-)  A      0
  77 TYR   (  85-)  A      0
  80 GLU   (  88-)  A      0
  83 GLN   (  91-)  A      0
  86 GLU   (  94-)  A      0
  87 ASN   (  95-)  A      0
  88 SER   (  96-)  A      0
  99 LEU   ( 107-)  A      0
 102 GLU   ( 110-)  A      0
 104 SER   ( 112-)  A      0
And so on for a total of 1614 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!

2701 GLY   ( 405-)  E   1.69   80
3853 GLY   ( 405-)  G   1.69   80
 973 GLY   ( 405-)  B   1.69   80
4429 GLY   ( 405-)  H   1.69   80
 397 GLY   ( 405-)  A   1.69   80
2125 GLY   ( 405-)  D   1.69   80
1549 GLY   ( 405-)  C   1.69   80
3277 GLY   ( 405-)  F   1.69   80
2633 GLY   ( 337-)  E   1.66   15
2057 GLY   ( 337-)  D   1.66   15
3209 GLY   ( 337-)  F   1.66   15
 329 GLY   ( 337-)  A   1.66   15
4361 GLY   ( 337-)  H   1.66   15
1481 GLY   ( 337-)  C   1.66   15
 905 GLY   ( 337-)  B   1.66   15
3785 GLY   ( 337-)  G   1.66   15
 778 PRO   ( 210-)  B   1.53   10
3658 PRO   ( 210-)  G   1.53   10
1930 PRO   ( 210-)  D   1.53   10
3082 PRO   ( 210-)  F   1.53   10
 202 PRO   ( 210-)  A   1.53   10
4234 PRO   ( 210-)  H   1.53   10
2506 PRO   ( 210-)  E   1.53   10
1354 PRO   ( 210-)  C   1.53   10

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].

  36 PRO   (  44-)  A    14.3 half-chair N/C-delta (18 degrees)
 237 PRO   ( 245-)  A  -117.2 half-chair C-delta/C-gamma (-126 degrees)
 445 PRO   ( 453-)  A  -124.0 half-chair C-delta/C-gamma (-126 degrees)
 612 PRO   (  44-)  B    14.5 half-chair N/C-delta (18 degrees)
 813 PRO   ( 245-)  B  -117.3 half-chair C-delta/C-gamma (-126 degrees)
1021 PRO   ( 453-)  B  -123.9 half-chair C-delta/C-gamma (-126 degrees)
1188 PRO   (  44-)  C    14.3 half-chair N/C-delta (18 degrees)
1389 PRO   ( 245-)  C  -117.3 half-chair C-delta/C-gamma (-126 degrees)
1597 PRO   ( 453-)  C  -124.0 half-chair C-delta/C-gamma (-126 degrees)
1764 PRO   (  44-)  D    14.4 half-chair N/C-delta (18 degrees)
1965 PRO   ( 245-)  D  -117.3 half-chair C-delta/C-gamma (-126 degrees)
2173 PRO   ( 453-)  D  -123.9 half-chair C-delta/C-gamma (-126 degrees)
2340 PRO   (  44-)  E    14.3 half-chair N/C-delta (18 degrees)
2541 PRO   ( 245-)  E  -117.2 half-chair C-delta/C-gamma (-126 degrees)
2749 PRO   ( 453-)  E  -124.0 half-chair C-delta/C-gamma (-126 degrees)
2916 PRO   (  44-)  F    14.3 half-chair N/C-delta (18 degrees)
3117 PRO   ( 245-)  F  -117.3 half-chair C-delta/C-gamma (-126 degrees)
3325 PRO   ( 453-)  F  -123.8 half-chair C-delta/C-gamma (-126 degrees)
3492 PRO   (  44-)  G    14.4 half-chair N/C-delta (18 degrees)
3693 PRO   ( 245-)  G  -117.2 half-chair C-delta/C-gamma (-126 degrees)
3901 PRO   ( 453-)  G  -124.0 half-chair C-delta/C-gamma (-126 degrees)
4068 PRO   (  44-)  H    14.2 half-chair N/C-delta (18 degrees)
4269 PRO   ( 245-)  H  -117.2 half-chair C-delta/C-gamma (-126 degrees)
4477 PRO   ( 453-)  H  -124.1 half-chair C-delta/C-gamma (-126 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.

 239 CYS   ( 247-)  A      SG   <->   815 CYS   ( 247-)  B      SG   0.92    2.53  INTRA BL
1391 CYS   ( 247-)  C      SG   <->  1967 CYS   ( 247-)  D      SG   0.88    2.57  INTRA BL
2543 CYS   ( 247-)  E      SG   <->  3119 CYS   ( 247-)  F      SG   0.86    2.59  INTRA BL
3695 CYS   ( 247-)  G      SG   <->  4271 CYS   ( 247-)  H      SG   0.70    2.75  INTRA BL
2546 MET   ( 250-)  E      CE   <->  2563 HIS   ( 267-)  E      NE2  0.66    2.44  INTRA BL
1394 MET   ( 250-)  C      CE   <->  1411 HIS   ( 267-)  C      NE2  0.66    2.44  INTRA BL
 242 MET   ( 250-)  A      CE   <->   259 HIS   ( 267-)  A      NE2  0.66    2.44  INTRA BL
 818 MET   ( 250-)  B      CE   <->   835 HIS   ( 267-)  B      NE2  0.66    2.44  INTRA BL
4274 MET   ( 250-)  H      CE   <->  4291 HIS   ( 267-)  H      NE2  0.66    2.44  INTRA BL
3122 MET   ( 250-)  F      CE   <->  3139 HIS   ( 267-)  F      NE2  0.66    2.44  INTRA BL
1970 MET   ( 250-)  D      CE   <->  1987 HIS   ( 267-)  D      NE2  0.66    2.44  INTRA BL
3698 MET   ( 250-)  G      CE   <->  3715 HIS   ( 267-)  G      NE2  0.66    2.44  INTRA BL
3783 LEU   ( 335-)  G      CD2  <->  4151 PHE   ( 127-)  H      CD1  0.58    2.62  INTRA BF
3701 ARG   ( 253-)  G      NH2  <->  4133 GLU   ( 109-)  H      OE2  0.50    2.20  INTRA BL
3575 PHE   ( 127-)  G      CD1  <->  4359 LEU   ( 335-)  H      CD2  0.47    2.73  INTRA BF
2423 PHE   ( 127-)  E      CD1  <->  3207 LEU   ( 335-)  F      CD2  0.47    2.73  INTRA BF
3751 ARG   ( 303-)  G      NH2  <->  4154 ILE   ( 130-)  H      O    0.44    2.26  INTRA
2530 GLU   ( 234-)  E      OE1  <->  2717 ARG   ( 421-)  E      NH2  0.43    2.27  INTRA BL
1378 GLU   ( 234-)  C      OE1  <->  1565 ARG   ( 421-)  C      NH2  0.43    2.27  INTRA BL
4258 GLU   ( 234-)  H      OE1  <->  4445 ARG   ( 421-)  H      NH2  0.43    2.27  INTRA BL
3106 GLU   ( 234-)  F      OE1  <->  3293 ARG   ( 421-)  F      NH2  0.43    2.27  INTRA BL
1954 GLU   ( 234-)  D      OE1  <->  2141 ARG   ( 421-)  D      NH2  0.43    2.27  INTRA BL
 226 GLU   ( 234-)  A      OE1  <->   413 ARG   ( 421-)  A      NH2  0.43    2.27  INTRA BL
 802 GLU   ( 234-)  B      OE1  <->   989 ARG   ( 421-)  B      NH2  0.43    2.27  INTRA BL
3682 GLU   ( 234-)  G      OE1  <->  3869 ARG   ( 421-)  G      NH2  0.43    2.27  INTRA BL
And so on for a total of 554 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: M

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: N

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: O

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: P

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

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.

4029 ARG   ( 119-)  P      -6.66
2301 ARG   ( 119-)  J      -6.66
1149 ARG   ( 119-)  I      -6.66
2877 ARG   ( 119-)  O      -6.66
4605 ARG   ( 119-)  L      -6.66
1725 ARG   ( 119-)  N      -6.66
 573 ARG   ( 119-)  M      -6.66
3453 ARG   ( 119-)  K      -6.65
4173 GLN   ( 149-)  H      -5.79
1869 GLN   ( 149-)  D      -5.78
2445 GLN   ( 149-)  E      -5.75
1293 GLN   ( 149-)  C      -5.75
3021 GLN   ( 149-)  F      -5.75
 717 GLN   ( 149-)  B      -5.75
 141 GLN   ( 149-)  A      -5.75
3597 GLN   ( 149-)  G      -5.75
1007 ARG   ( 439-)  B      -5.62
3311 ARG   ( 439-)  F      -5.62
4463 ARG   ( 439-)  H      -5.62
1583 ARG   ( 439-)  C      -5.62
 431 ARG   ( 439-)  A      -5.62
2159 ARG   ( 439-)  D      -5.62
2735 ARG   ( 439-)  E      -5.61
3887 ARG   ( 439-)  G      -5.61
3958 GLN   (  36-)  P      -5.59
And so on for a total of 88 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: 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: P

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: L

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.

2387 GLN   (  91-)  E   -2.95
1235 GLN   (  91-)  C   -2.93
  83 GLN   (  91-)  A   -2.81
1443 ALA   ( 299-)  C   -2.78
2019 ALA   ( 299-)  D   -2.78
 867 ALA   ( 299-)  B   -2.76
4323 ALA   ( 299-)  H   -2.76
3747 ALA   ( 299-)  G   -2.75
 291 ALA   ( 299-)  A   -2.74
2595 ALA   ( 299-)  E   -2.74
3171 ALA   ( 299-)  F   -2.73
2977 LEU   ( 105-)  F   -2.66
1825 LEU   ( 105-)  D   -2.65
2401 LEU   ( 105-)  E   -2.64
  97 LEU   ( 105-)  A   -2.64
 155 ASN   ( 163-)  A   -2.59

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: M

Note: Second generation quality Z-score plot

Chain identifier: B

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: C

Note: Second generation quality Z-score plot

Chain identifier: N

Note: Second generation quality Z-score plot

Chain identifier: D

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: O

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: P

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: L

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.

4628 HOH   ( 482 )  C      O

Error: HIS, ASN, GLN side chain flips

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

  78 HIS   (  86-)  A
 148 GLN   ( 156-)  A
 221 GLN   ( 229-)  A
 230 HIS   ( 238-)  A
 233 ASN   ( 241-)  A
 269 ASN   ( 277-)  A
 296 GLN   ( 304-)  A
 319 HIS   ( 327-)  A
 378 HIS   ( 386-)  A
 412 ASN   ( 420-)  A
 535 GLN   (  81-)  M
 560 ASN   ( 106-)  M
 572 HIS   ( 118-)  M
 654 HIS   (  86-)  B
 724 GLN   ( 156-)  B
 797 GLN   ( 229-)  B
 806 HIS   ( 238-)  B
 809 ASN   ( 241-)  B
 845 ASN   ( 277-)  B
 872 GLN   ( 304-)  B
 954 HIS   ( 386-)  B
 988 ASN   ( 420-)  B
1081 HIS   (  39-)  I
1111 GLN   (  81-)  I
1136 ASN   ( 106-)  I
And so on for a total of 92 lines.

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.

   2 ALA   (  10-)  A      N
   4 GLY   (  12-)  A      N
  17 TYR   (  25-)  A      N
  20 ASP   (  28-)  A      N
  57 THR   (  65-)  A      OG1
  59 THR   (  67-)  A      N
  88 SER   (  96-)  A      N
  98 ASP   ( 106-)  A      N
 159 ARG   ( 167-)  A      N
 159 ARG   ( 167-)  A      NE
 167 LYS   ( 175-)  A      N
 167 LYS   ( 175-)  A      NZ
 170 LEU   ( 178-)  A      N
 171 GLY   ( 179-)  A      N
 176 ASN   ( 184-)  A      ND2
 199 ASN   ( 207-)  A      ND2
 203 PHE   ( 211-)  A      N
 204 GLN   ( 212-)  A      NE2
 207 ARG   ( 215-)  A      N
 231 TYR   ( 239-)  A      OH
 238 THR   ( 246-)  A      N
 268 ALA   ( 276-)  A      N
 287 ARG   ( 295-)  A      NE
 295 ARG   ( 303-)  A      NE
 296 GLN   ( 304-)  A      NE2
And so on for a total of 560 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.

 260 ASP   ( 268-)  A      OD2
 284 HIS   ( 292-)  A      NE2
 388 ASP   ( 396-)  A      OD1
 393 GLN   ( 401-)  A      OE1
 424 ASN   ( 432-)  A      OD1
 726 GLU   ( 158-)  B      OE1
 772 GLU   ( 204-)  B      OE1
 802 GLU   ( 234-)  B      OE1
 835 HIS   ( 267-)  B      NE2
 836 ASP   ( 268-)  B      OD2
 862 HIS   ( 294-)  B      NE2
 895 HIS   ( 327-)  B      ND1
 964 ASP   ( 396-)  B      OD1
 988 ASN   ( 420-)  B      OD1
1000 ASN   ( 432-)  B      OD1
1081 HIS   (  39-)  I      NE2
1267 ASN   ( 123-)  C      OD1
1302 GLU   ( 158-)  C      OE1
1348 GLU   ( 204-)  C      OE1
1378 GLU   ( 234-)  C      OE1
1411 HIS   ( 267-)  C      NE2
1412 ASP   ( 268-)  C      OD2
1438 HIS   ( 294-)  C      NE2
1471 HIS   ( 327-)  C      ND1
1540 ASP   ( 396-)  C      OD1
And so on for a total of 79 lines.

Warning: No crystallisation information

No, or very inadequate, crystallisation information was observed upon reading the PDB file header records. This information should be available in the form of a series of REMARK 280 lines. Without this information a few things, such as checking ions in the structure, cannot be performed optimally.

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.

 152 ASP   ( 160-)  A   H-bonding suggests Asn; but Alt-Rotamer
 260 ASP   ( 268-)  A   H-bonding suggests Asn; but Alt-Rotamer
 294 ASP   ( 302-)  A   H-bonding suggests Asn
 452 ASP   ( 460-)  A   H-bonding suggests Asn
 539 ASP   (  85-)  M   H-bonding suggests Asn
 563 GLU   ( 109-)  M   H-bonding suggests Gln
 728 ASP   ( 160-)  B   H-bonding suggests Asn; but Alt-Rotamer
 836 ASP   ( 268-)  B   H-bonding suggests Asn; but Alt-Rotamer
 870 ASP   ( 302-)  B   H-bonding suggests Asn
1028 ASP   ( 460-)  B   H-bonding suggests Asn
1115 ASP   (  85-)  I   H-bonding suggests Asn
1139 GLU   ( 109-)  I   H-bonding suggests Gln
1304 ASP   ( 160-)  C   H-bonding suggests Asn; but Alt-Rotamer
1412 ASP   ( 268-)  C   H-bonding suggests Asn; but Alt-Rotamer
1446 ASP   ( 302-)  C   H-bonding suggests Asn
1604 ASP   ( 460-)  C   H-bonding suggests Asn
1691 ASP   (  85-)  N   H-bonding suggests Asn
1715 GLU   ( 109-)  N   H-bonding suggests Gln
1880 ASP   ( 160-)  D   H-bonding suggests Asn; but Alt-Rotamer
1988 ASP   ( 268-)  D   H-bonding suggests Asn; but Alt-Rotamer
2022 ASP   ( 302-)  D   H-bonding suggests Asn
2180 ASP   ( 460-)  D   H-bonding suggests Asn
2267 ASP   (  85-)  J   H-bonding suggests Asn
2291 GLU   ( 109-)  J   H-bonding suggests Gln
2456 ASP   ( 160-)  E   H-bonding suggests Asn; but Alt-Rotamer
2564 ASP   ( 268-)  E   H-bonding suggests Asn; but Alt-Rotamer
2598 ASP   ( 302-)  E   H-bonding suggests Asn
2756 ASP   ( 460-)  E   H-bonding suggests Asn
2843 ASP   (  85-)  O   H-bonding suggests Asn
2867 GLU   ( 109-)  O   H-bonding suggests Gln
3032 ASP   ( 160-)  F   H-bonding suggests Asn; but Alt-Rotamer
3140 ASP   ( 268-)  F   H-bonding suggests Asn; but Alt-Rotamer
3174 ASP   ( 302-)  F   H-bonding suggests Asn
3332 ASP   ( 460-)  F   H-bonding suggests Asn
3419 ASP   (  85-)  K   H-bonding suggests Asn
3443 GLU   ( 109-)  K   H-bonding suggests Gln
3608 ASP   ( 160-)  G   H-bonding suggests Asn; but Alt-Rotamer
3716 ASP   ( 268-)  G   H-bonding suggests Asn; but Alt-Rotamer
3750 ASP   ( 302-)  G   H-bonding suggests Asn
3908 ASP   ( 460-)  G   H-bonding suggests Asn
3995 ASP   (  85-)  P   H-bonding suggests Asn
4184 ASP   ( 160-)  H   H-bonding suggests Asn; but Alt-Rotamer
4292 ASP   ( 268-)  H   H-bonding suggests Asn; but Alt-Rotamer
4326 ASP   ( 302-)  H   H-bonding suggests Asn
4484 ASP   ( 460-)  H   H-bonding suggests Asn
4571 ASP   (  85-)  L   H-bonding suggests Asn
4595 GLU   ( 109-)  L   H-bonding suggests Gln

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 :  -0.368
  2nd generation packing quality :  -0.204
  Ramachandran plot appearance   :  -1.187
  chi-1/chi-2 rotamer normality  :  -2.233
  Backbone conformation          :  -0.627

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.291 (tight)
  Bond angles                    :   0.520 (tight)
  Omega angle restraints         :   1.139
  Side chain planarity           :   0.917
  Improper dihedral distribution :   1.267
  B-factor distribution          :   1.007
  Inside/Outside distribution    :   1.055

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 :   0.4
  Ramachandran plot appearance   :   0.2
  chi-1/chi-2 rotamer normality  :  -0.7
  Backbone conformation          :  -0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.291 (tight)
  Bond angles                    :   0.520 (tight)
  Omega angle restraints         :   1.139
  Side chain planarity           :   0.917
  Improper dihedral distribution :   1.267
  B-factor distribution          :   1.007
  Inside/Outside distribution    :   1.055
==============

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.