WHAT IF Check report

This file was created 2013-12-10 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 pdb4b3k.ent

Checks that need to be done early-on in validation

Warning: Class of conventional cell differs from CRYST1 cell

The crystal class of the conventional cell is different from the crystal class of the cell given on the CRYST1 card. If the new class is supported by the coordinates this is an indication of a wrong space group assignment.

The CRYST1 cell dimensions

    A    = 106.420  B   = 190.200  C    = 106.170
    Alpha=  90.000  Beta= 118.880  Gamma=  90.000

Dimensions of a reduced cell

    A    = 106.170  B   = 106.420  C    = 190.200
    Alpha=  90.000  Beta=  90.000  Gamma= 118.880

Dimensions of the conventional cell

    A    = 108.090  B   = 183.061  C    = 190.200
    Alpha=  90.000  Beta=  90.000  Gamma=  89.846

Transformation to conventional cell

 |  1.000000  0.000000  1.000000|
 |  1.000000  0.000000 -1.000000|
 |  0.000000  1.000000  0.000000|

Crystal class of the cell: MONOCLINIC

Crystal class of the conventional CELL: ORTHORHOMBIC

Space group name: P 1 21 1

Bravais type of conventional cell is: C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.401
CA-only RMS fit for the two chains : 0.245

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and B

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and C

All-atom RMS fit for the two chains : 0.368
CA-only RMS fit for the two chains : 0.229

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and C

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and D

All-atom RMS fit for the two chains : 0.437
CA-only RMS fit for the two chains : 0.249

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and D

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and E

All-atom RMS fit for the two chains : 0.521
CA-only RMS fit for the two chains : 0.346

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and E

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and F

All-atom RMS fit for the two chains : 0.483
CA-only RMS fit for the two chains : 0.310

Note: Non crystallographic symmetry backbone difference plot

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

Chain identifiers of the two chains: A and F

Warning: Conventional cell is pseudo-cell

The extra symmetry that would be implied by the transition to the previously mentioned conventional cell has not been observed. It must be concluded that the crystal lattice has pseudo-symmetry.

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

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

Warning: Occupancies atoms do not add up to 1.0.

In principle, the occupancy of all alternates of one atom should add up till 1.0. A valid exception is the missing atom (i.e. an atom not seen in the electron density) that is allowed to have a 0.0 occupancy. Sometimes this even happens when there are no alternate atoms given...

Atoms want to move. That is the direct result of the second law of thermodynamics, in a somewhat weird way of thinking. Any way, many atoms seem to have more than one position where they like to sit, and they jump between them. The population difference between those sites (which is related to their energy differences) is seen in the occupancy factors. As also for atoms it is 'to be or not to be', these occupancies should add up to 1.0. Obviously, it is possible that they add up to a number less than 1.0, in cases where there are yet more, but undetected' rotamers/positions in play, but also in those cases a warning is in place as the information shown in the PDB file is less certain than it could have been. The residues listed below contain atoms that have an occupancy greater than zero, but all their alternates do not add up to one.

WARNING. Presently WHAT CHECK only deals with a maximum of two alternate positions. A small number of atoms in the PDB has three alternates. In those cases the warning given here should obviously be neglected! In a next release we will try to fix this.

   5 LYS   (   6-)  A    0.50
 466 LYS   (   6-)  B    0.50
 927 LYS   (   6-)  C    0.50
1388 LYS   (   6-)  D    0.50
1849 LYS   (   6-)  E    0.50
2310 LYS   (   6-)  F    0.50

Warning: What type of B-factor?

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

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


Number of TLS groups mentione in PDB file header: 0

Crystal temperature (K) :120.000

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

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.

  26 HIS   (  27-)  A      CG   CD2   1.41    5.0
  33 TRP   (  34-)  A      CD2  CE2   1.48    4.4
 117 HIS   ( 118-)  A      CG   CD2   1.42    5.8
 118 HIS   ( 119-)  A      CG   CD2   1.40    4.2
 132 TRP   ( 133-)  A      CD2  CE2   1.48    4.2
 162 HIS   ( 163-)  A      CG   CD2   1.41    4.5
 241 HIS   ( 242-)  A      CG   CD2   1.40    4.1
 400 HIS   ( 401-)  A      CG   CD2   1.40    4.4
 470 TRP   (  10-)  B      CD2  CE2   1.48    4.3
 516 HIS   (  56-)  B      CG   CD2   1.41    4.9
 816 HIS   ( 356-)  B      CG   CD2   1.41    4.7
 856 HIS   ( 396-)  B      CG   CD2   1.41    4.7
 874 HIS   ( 414-)  B      CG   CD2   1.40    4.2
 948 HIS   (  27-)  C      CG   CD2   1.41    4.6
 991 HIS   (  70-)  C      CG   CD2   1.41    5.0
1000 TRP   (  79-)  C      CD2  CE2   1.48    4.3
1039 HIS   ( 118-)  C      CG   CD2   1.41    5.0
1081 TRP   ( 160-)  C      CD2  CE2   1.48    4.1
1260 TRP   ( 339-)  C      CD2  CE2   1.48    4.2
1283 TRP   ( 362-)  C      CD2  CE2   1.48    4.2
1337 TRP   ( 416-)  C      CD2  CE2   1.48    4.1
1409 HIS   (  27-)  D      CG   CD2   1.40    4.0
1438 HIS   (  56-)  D      CG   CD2   1.40    4.2
1452 HIS   (  70-)  D      CG   CD2   1.40    4.4
1561 HIS   ( 179-)  D      CG   CD2   1.40    4.2
1738 HIS   ( 356-)  D      CG   CD2   1.41    4.6
1744 TRP   ( 362-)  D      NE1  CE2   1.32   -4.2
1783 HIS   ( 401-)  D      CG   CD2   1.40    4.2
1798 TRP   ( 416-)  D      CD2  CE2   1.49    4.5
1834 TRP   ( 452-)  D      CD2  CE2   1.48    4.2
1913 HIS   (  70-)  E      CG   CD2   1.41    4.7
1976 TRP   ( 133-)  E      CD2  CE2   1.49    4.5
2006 HIS   ( 163-)  E      CG   CD2   1.41    4.7
2085 HIS   ( 242-)  E      CG   CD2   1.40    4.4
2239 HIS   ( 396-)  E      CG   CD2   1.40    4.3
2374 HIS   (  70-)  F      CG   CD2   1.40    4.4
2383 TRP   (  79-)  F      CD2  CE2   1.48    4.1
2437 TRP   ( 133-)  F      CD2  CE2   1.48    4.1
2441 HIS   ( 137-)  F      CG   CD2   1.40    4.1

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

 |  0.997743  0.000008 -0.000183|
 |  0.000008  0.996248  0.000006|
 | -0.000183  0.000006  0.997543|
Proposed new scale matrix

 |  0.009419  0.000000  0.005198|
 |  0.000000  0.005278  0.000000|
 |  0.000002  0.000000  0.010783|
With corresponding cell

    A    = 106.177  B   = 189.473  C    = 105.926
    Alpha=  90.001  Beta= 118.900  Gamma=  90.001

The CRYST1 cell dimensions

    A    = 106.420  B   = 190.200  C    = 106.170
    Alpha=  90.000  Beta= 118.880  Gamma=  90.000

Variance: 782.142
(Under-)estimated Z-score: 20.611

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.

  73 ARG   (  74-)  A      CB   CG   CD  103.17   -5.5
 136 HIS   ( 137-)  A      CG   ND1  CE1 109.70    4.1
 241 HIS   ( 242-)  A      CG   ND1  CE1 109.87    4.3
 395 HIS   ( 396-)  A      CG   ND1  CE1 109.61    4.0
 530 HIS   (  70-)  B      CG   ND1  CE1 109.64    4.0
 639 HIS   ( 179-)  B      CG   ND1  CE1 109.93    4.3
 702 HIS   ( 242-)  B      CG   ND1  CE1 109.92    4.3
 760 HIS   ( 300-)  B      CG   ND1  CE1 109.71    4.1
 816 HIS   ( 356-)  B      CG   ND1  CE1 109.60    4.0
 919 HIS   ( 459-)  B      CG   ND1  CE1 109.62    4.0
 943 ARG   (  22-)  C      CB   CG   CD  104.38   -4.9
 991 HIS   (  70-)  C      CG   ND1  CE1 109.70    4.1
 995 ARG   (  74-)  C      CB   CG   CD  101.82   -6.1
1040 HIS   ( 119-)  C      CG   ND1  CE1 109.60    4.0
1223 LYS   ( 302-)  C      N    CA   C    99.33   -4.2
1500 HIS   ( 118-)  D      CG   ND1  CE1 109.86    4.3
1519 HIS   ( 137-)  D      CG   ND1  CE1 109.87    4.3
1561 HIS   ( 179-)  D      CG   ND1  CE1 109.71    4.1
1624 HIS   ( 242-)  D      CG   ND1  CE1 109.64    4.0
1682 HIS   ( 300-)  D      CG   ND1  CE1 110.01    4.4
2085 HIS   ( 242-)  E      CG   ND1  CE1 109.61    4.0
2283 HIS   ( 440-)  E      CG   ND1  CE1 109.69    4.1
2423 HIS   ( 119-)  F      CG   ND1  CE1 109.77    4.2
2546 HIS   ( 242-)  F      CG   ND1  CE1 109.61    4.0
2562 HIS   ( 258-)  F      CG   ND1  CE1 109.68    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.

2040 ALA   ( 197-)  E    5.68
1534 GLN   ( 152-)  D    4.90
1273 LYS   ( 352-)  C    4.83
1073 GLN   ( 152-)  C    4.74
1414 ASP   (  32-)  D    4.71
1223 LYS   ( 302-)  C    4.63
2017 TYR   ( 174-)  E    4.63
1403 GLY   (  21-)  D    4.47
  56 GLN   (  57-)  A    4.34
2434 TYR   ( 130-)  F    4.23
2254 PHE   ( 411-)  E    4.22
1864 GLY   (  21-)  E    4.09
 354 ASP   ( 355-)  A    4.07
  44 TYR   (  45-)  A    4.01

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 : -3.501

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.

 292 TYR   ( 293-)  A    -3.5
2318 THR   (  14-)  F    -3.5
1675 TYR   ( 293-)  D    -3.4
1857 THR   (  14-)  E    -3.4
 753 TYR   ( 293-)  B    -3.3
1396 THR   (  14-)  D    -3.3
1502 PHE   ( 120-)  D    -3.2
 580 PHE   ( 120-)  B    -3.2
1041 PHE   ( 120-)  C    -3.2
2136 TYR   ( 293-)  E    -3.2
2122 THR   ( 279-)  E    -3.1
 119 PHE   ( 120-)  A    -3.0
2379 THR   (  75-)  F    -3.0
  13 THR   (  14-)  A    -3.0
1963 PHE   ( 120-)  E    -3.0
 935 THR   (  14-)  C    -3.0
2597 TYR   ( 293-)  F    -3.0
 474 THR   (  14-)  B    -2.9
 535 THR   (  75-)  B    -2.9
1214 TYR   ( 293-)  C    -2.9
2530 THR   ( 226-)  F    -2.8
2619 PRO   ( 315-)  F    -2.8
2043 THR   ( 200-)  E    -2.8
1034 PRO   ( 113-)  C    -2.8
 905 ARG   ( 445-)  B    -2.8
And so on for a total of 144 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.

   4 PRO   (   5-)  A  omega poor
   6 GLU   (   7-)  A  Poor phi/psi
  22 PHE   (  23-)  A  omega poor
  23 ALA   (  24-)  A  Poor phi/psi
  44 TYR   (  45-)  A  Poor phi/psi
  50 ALA   (  51-)  A  Poor phi/psi
  67 LEU   (  68-)  A  omega poor
 120 ASP   ( 121-)  A  omega poor
 158 ASP   ( 159-)  A  omega poor
 162 HIS   ( 163-)  A  omega poor
 177 PHE   ( 178-)  A  omega poor
 179 TYR   ( 180-)  A  PRO omega poor
 222 LEU   ( 223-)  A  Poor phi/psi
 259 LYS   ( 260-)  A  omega poor
 292 TYR   ( 293-)  A  Poor phi/psi
 293 LEU   ( 294-)  A  omega poor
 319 GLU   ( 320-)  A  omega poor
 332 MET   ( 333-)  A  omega poor
 339 GLU   ( 340-)  A  omega poor
 355 HIS   ( 356-)  A  Poor phi/psi
 361 TRP   ( 362-)  A  omega poor
 408 ASN   ( 409-)  A  Poor phi/psi
 415 TRP   ( 416-)  A  omega poor
 423 TRP   ( 424-)  A  Poor phi/psi
 426 ALA   ( 427-)  A  Poor phi/psi
And so on for a total of 199 lines.

Warning: chi-1/chi-2 angle correlation Z-score low

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

chi-1/chi-2 correlation Z-score : -3.359

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.

2509 GLN   ( 205-)  F    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!

   5 LYS   (   6-)  A      0
   6 GLU   (   7-)  A      0
   7 PHE   (   8-)  A      0
   8 TRP   (   9-)  A      0
   9 TRP   (  10-)  A      0
  12 ALA   (  13-)  A      0
  18 SER   (  19-)  A      0
  19 GLU   (  20-)  A      0
  21 ARG   (  22-)  A      0
  22 PHE   (  23-)  A      0
  23 ALA   (  24-)  A      0
  26 HIS   (  27-)  A      0
  37 GLU   (  38-)  A      0
  42 TYR   (  43-)  A      0
  43 ASP   (  44-)  A      0
  44 TYR   (  45-)  A      0
  47 PRO   (  48-)  A      0
  50 ALA   (  51-)  A      0
  51 SER   (  52-)  A      0
  52 ASP   (  53-)  A      0
  55 HIS   (  56-)  A      0
  56 GLN   (  57-)  A      0
  67 LEU   (  68-)  A      0
  69 HIS   (  70-)  A      0
  78 TRP   (  79-)  A      0
And so on for a total of 1128 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!

 213 LEU   ( 214-)  A   1.78   10
2057 LEU   ( 214-)  E   1.57   18

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]

 226 PRO   ( 227-)  A    0.19 LOW
 279 PRO   ( 280-)  A    0.14 LOW
 360 PRO   ( 361-)  A    0.04 LOW
 767 PRO   ( 307-)  B    0.17 LOW
1421 PRO   (  39-)  D    0.12 LOW
1609 PRO   ( 227-)  D    0.18 LOW
1689 PRO   ( 307-)  D    0.15 LOW
1743 PRO   ( 361-)  D    0.16 LOW
2611 PRO   ( 307-)  F    0.18 LOW
2629 PRO   ( 325-)  F    0.17 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].

 165 PRO   ( 166-)  A  -113.1 envelop C-gamma (-108 degrees)
 300 PRO   ( 301-)  A   -42.9 envelop C-alpha (-36 degrees)
 310 PRO   ( 311-)  A    42.3 envelop C-delta (36 degrees)
 324 PRO   ( 325-)  A   109.7 envelop C-beta (108 degrees)
 342 PRO   ( 343-)  A  -120.4 half-chair C-delta/C-gamma (-126 degrees)
 445 PRO   ( 446-)  A   105.1 envelop C-beta (108 degrees)
 465 PRO   (   5-)  B   121.0 half-chair C-beta/C-alpha (126 degrees)
 553 PRO   (  93-)  B   105.1 envelop C-beta (108 degrees)
 626 PRO   ( 166-)  B  -125.6 half-chair C-delta/C-gamma (-126 degrees)
 671 PRO   ( 211-)  B   106.0 envelop C-beta (108 degrees)
 761 PRO   ( 301-)  B    20.6 half-chair N/C-delta (18 degrees)
 775 PRO   ( 315-)  B  -119.1 half-chair C-delta/C-gamma (-126 degrees)
 785 PRO   ( 325-)  B   101.4 envelop C-beta (108 degrees)
 821 PRO   ( 361-)  B   108.1 envelop C-beta (108 degrees)
 906 PRO   ( 446-)  B   100.6 envelop C-beta (108 degrees)
 926 PRO   (   5-)  C   109.0 envelop C-beta (108 degrees)
1087 PRO   ( 166-)  C  -115.2 envelop C-gamma (-108 degrees)
1132 PRO   ( 211-)  C  -133.9 half-chair C-delta/C-gamma (-126 degrees)
1232 PRO   ( 311-)  C    48.5 half-chair C-delta/C-gamma (54 degrees)
1236 PRO   ( 315-)  C   120.5 half-chair C-beta/C-alpha (126 degrees)
1240 PRO   ( 319-)  C    42.7 envelop C-delta (36 degrees)
1246 PRO   ( 325-)  C   149.2 envelop C-alpha (144 degrees)
1387 PRO   (   5-)  D   105.3 envelop C-beta (108 degrees)
1548 PRO   ( 166-)  D  -114.2 envelop C-gamma (-108 degrees)
1563 PRO   ( 181-)  D   -42.5 envelop C-alpha (-36 degrees)
1612 PRO   ( 230-)  D    36.2 envelop C-delta (36 degrees)
1662 PRO   ( 280-)  D   102.2 envelop C-beta (108 degrees)
1683 PRO   ( 301-)  D    37.1 envelop C-delta (36 degrees)
1693 PRO   ( 311-)  D    30.0 envelop C-delta (36 degrees)
1697 PRO   ( 315-)  D  -125.0 half-chair C-delta/C-gamma (-126 degrees)
1707 PRO   ( 325-)  D   121.0 half-chair C-beta/C-alpha (126 degrees)
1828 PRO   ( 446-)  D   109.0 envelop C-beta (108 degrees)
1848 PRO   (   5-)  E   106.0 envelop C-beta (108 degrees)
1882 PRO   (  39-)  E  -117.6 half-chair C-delta/C-gamma (-126 degrees)
2054 PRO   ( 211-)  E   101.3 envelop C-beta (108 degrees)
2070 PRO   ( 227-)  E    29.0 envelop C-delta (36 degrees)
2123 PRO   ( 280-)  E   100.9 envelop C-beta (108 degrees)
2150 PRO   ( 307-)  E    45.9 half-chair C-delta/C-gamma (54 degrees)
2154 PRO   ( 311-)  E    27.5 envelop C-delta (36 degrees)
2172 PRO   ( 329-)  E  -164.2 half-chair N/C-delta (-162 degrees)
2186 PRO   ( 343-)  E  -151.4 envelop C-delta (-144 degrees)
2321 PRO   (  17-)  F   106.5 envelop C-beta (108 degrees)
2470 PRO   ( 166-)  F  -119.8 half-chair C-delta/C-gamma (-126 degrees)
2485 PRO   ( 181-)  F   -52.8 half-chair C-beta/C-alpha (-54 degrees)
2566 PRO   ( 262-)  F   100.9 envelop C-beta (108 degrees)
2619 PRO   ( 315-)  F   135.5 envelop C-alpha (144 degrees)
2633 PRO   ( 329-)  F   107.1 envelop C-beta (108 degrees)
2647 PRO   ( 343-)  F  -120.1 half-chair C-delta/C-gamma (-126 degrees)
2665 PRO   ( 361-)  F    49.1 half-chair C-delta/C-gamma (54 degrees)

Bump checks

Error: Abnormally short interatomic distances

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

1948 ALA   ( 105-)  E      O   <-> 1952 ASN   ( 109-)  E      ND2    0.62    2.08  INTRA BF
2224 THR   ( 381-)  E      O   <-> 2288 ARG   ( 445-)  E      NH2    0.58    2.12  INTRA BF
1899 HIS   (  56-)  E      CD2 <-> 2360 HIS   (  56-)  F      CD2    0.58    2.62  INTRA BF
2409 ALA   ( 105-)  F      O   <-> 2413 ASN   ( 109-)  F      ND2    0.55    2.15  INTRA BF
 224 LEU   ( 225-)  A      CD2 <->  352 MET   ( 353-)  A      CE     0.54    2.66  INTRA BL
 791 ARG   ( 331-)  B      NH2 <->  793 MET   ( 333-)  B      SD     0.53    2.77  INTRA BF
1607 LEU   ( 225-)  D      CD2 <-> 1735 MET   ( 353-)  D      CE     0.52    2.68  INTRA BL
1983 ASP   ( 140-)  E      OD1 <-> 2045 LYS   ( 202-)  E      NZ     0.49    2.21  INTRA BF
1635 MET   ( 253-)  D      CE  <-> 1735 MET   ( 353-)  D      CE     0.48    2.72  INTRA BL
  52 ASP   (  53-)  A      OD1 <->   55 HIS   (  56-)  A      CD2    0.47    2.33  INTRA BL
1869 GLN   (  26-)  E      OE1 <-> 1935 ASN   (  92-)  E      ND2    0.46    2.24  INTRA BF
2632 MET   ( 328-)  F      O   <-> 2635 ARG   ( 331-)  F      CD     0.45    2.35  INTRA BF
1249 MET   ( 328-)  C      O   <-> 1252 ARG   ( 331-)  C      CD     0.45    2.35  INTRA BF
 223 ASN   ( 224-)  A      OD1 <->  225 THR   ( 226-)  A      CG2    0.45    2.35  INTRA BF
1606 ASN   ( 224-)  D      OD1 <-> 1608 THR   ( 226-)  D      CG2    0.44    2.36  INTRA
  21 ARG   (  22-)  A      N   <->   48 ASP   (  49-)  A      O      0.42    2.28  INTRA BL
2317 ALA   (  13-)  F      CB  <-> 2378 ARG   (  74-)  F      NH1    0.42    2.68  INTRA
1899 HIS   (  56-)  E      CD2 <-> 2360 HIS   (  56-)  F      NE2    0.41    2.69  INTRA BF
 947 GLN   (  26-)  C      OE1 <-> 1013 ASN   (  92-)  C      ND2    0.40    2.30  INTRA BL
2685 THR   ( 381-)  F      O   <-> 2749 ARG   ( 445-)  F      NH2    0.40    2.30  INTRA BF
1518 LYS   ( 136-)  D      NZ  <-> 1664 GLU   ( 282-)  D      OE1    0.39    2.31  INTRA BF
1252 ARG   ( 331-)  C      NH2 <-> 1254 MET   ( 333-)  C      SD     0.38    2.92  INTRA BF
 614 GLY   ( 154-)  B      O   <->  618 LYS   ( 158-)  B      NZ     0.37    2.33  INTRA
1652 LYS   ( 270-)  D      O   <-> 1655 GLY   ( 273-)  D      N      0.37    2.33  INTRA BF
1220 TYR   ( 299-)  C      OH  <-> 1287 GLU   ( 366-)  C      OE1    0.36    2.04  INTRA BL
And so on for a total of 633 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

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.

1591 ARG   ( 209-)  D      -6.86
1249 MET   ( 328-)  C      -6.57
 669 ARG   ( 209-)  B      -6.52
1709 LEU   ( 327-)  D      -6.51
2170 LEU   ( 327-)  E      -6.49
2171 MET   ( 328-)  E      -6.47
2052 ARG   ( 209-)  E      -6.43
1130 ARG   ( 209-)  C      -6.40
 788 MET   ( 328-)  B      -6.40
 326 LEU   ( 327-)  A      -6.39
2631 LEU   ( 327-)  F      -6.39
 327 MET   ( 328-)  A      -6.37
2763 HIS   ( 459-)  F      -6.36
 787 LEU   ( 327-)  B      -6.33
1659 GLN   ( 277-)  D      -6.33
1380 HIS   ( 459-)  C      -6.30
 458 HIS   ( 459-)  A      -6.29
2632 MET   ( 328-)  F      -6.29
1248 LEU   ( 327-)  C      -6.24
2302 HIS   ( 459-)  E      -6.20
1198 GLN   ( 277-)  C      -6.12
1841 HIS   ( 459-)  D      -6.08
2156 ILE   ( 313-)  E      -6.04
1710 MET   ( 328-)  D      -5.99
2581 GLN   ( 277-)  F      -5.96
And so on for a total of 94 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.

 175 MET   ( 176-)  A       177 - PHE    178- ( A)         -4.27
2480 MET   ( 176-)  F      2482 - PHE    178- ( F)         -4.19

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

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.

1292 ILE   ( 371-)  C   -2.54

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

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.

2767 HOH   (2001 )  A      O

Error: HIS, ASN, GLN side chain flips

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

  56 GLN   (  57-)  A
  77 GLN   (  78-)  A
  99 ASN   ( 100-)  A
 115 ASN   ( 116-)  A
 248 ASN   ( 249-)  A
 257 HIS   ( 258-)  A
 288 ASN   ( 289-)  A
 296 ASN   ( 297-)  A
 358 ASN   ( 359-)  A
 366 ASN   ( 367-)  A
 384 GLN   ( 385-)  A
 458 HIS   ( 459-)  A
 516 HIS   (  56-)  B
 517 GLN   (  57-)  B
 538 GLN   (  78-)  B
 560 ASN   ( 100-)  B
 709 ASN   ( 249-)  B
 718 HIS   ( 258-)  B
 749 ASN   ( 289-)  B
 757 ASN   ( 297-)  B
 819 ASN   ( 359-)  B
 827 ASN   ( 367-)  B
 845 GLN   ( 385-)  B
 977 HIS   (  56-)  C
 978 GLN   (  57-)  C
And so on for a total of 68 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.

  10 GLY   (  11-)  A      N
  11 GLY   (  12-)  A      N
  22 PHE   (  23-)  A      N
  51 SER   (  52-)  A      N
  55 HIS   (  56-)  A      NE2
  73 ARG   (  74-)  A      NE
  73 ARG   (  74-)  A      NH2
  75 SER   (  76-)  A      OG
  78 TRP   (  79-)  A      N
 118 HIS   ( 119-)  A      NE2
 119 PHE   ( 120-)  A      N
 124 ALA   ( 125-)  A      N
 154 ASP   ( 155-)  A      N
 158 ASP   ( 159-)  A      N
 176 GLN   ( 177-)  A      N
 194 ASN   ( 195-)  A      ND2
 212 GLU   ( 213-)  A      N
 220 THR   ( 221-)  A      N
 231 SER   ( 232-)  A      N
 235 ALA   ( 236-)  A      N
 246 TRP   ( 247-)  A      NE1
 251 PHE   ( 252-)  A      N
 264 LEU   ( 265-)  A      N
 275 TRP   ( 276-)  A      N
 292 TYR   ( 293-)  A      N
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.

  52 ASP   (  53-)  A      OD1
  69 HIS   (  70-)  A      ND1
 115 ASN   ( 116-)  A      OD1
 118 HIS   ( 119-)  A      ND1
 333 ASN   ( 334-)  A      OD1
 395 HIS   ( 396-)  A      NE2
 413 HIS   ( 414-)  A      ND1
 435 GLU   ( 436-)  A      OE1
 439 HIS   ( 440-)  A      ND1
 530 HIS   (  70-)  B      NE2
 579 HIS   ( 119-)  B      ND1
 676 ASP   ( 216-)  B      OD1
 794 ASN   ( 334-)  B      OD1
 874 HIS   ( 414-)  B      ND1
 900 HIS   ( 440-)  B      ND1
 982 ASP   (  61-)  C      OD1
1037 ASN   ( 116-)  C      OD1
1040 HIS   ( 119-)  C      ND1
1335 HIS   ( 414-)  C      ND1
1357 GLU   ( 436-)  C      OE1
1361 HIS   ( 440-)  C      ND1
1501 HIS   ( 119-)  D      ND1
1796 HIS   ( 414-)  D      ND1
1892 ASP   (  49-)  E      OD1
1913 HIS   (  70-)  E      ND1
1959 ASN   ( 116-)  E      OD1
1962 HIS   ( 119-)  E      ND1
1964 ASP   ( 121-)  E      OD2
2132 ASN   ( 289-)  E      OD1
2177 ASN   ( 334-)  E      OD1
2239 HIS   ( 396-)  E      NE2
2257 HIS   ( 414-)  E      ND1
2280 ASN   ( 437-)  E      OD1
2374 HIS   (  70-)  F      ND1
2420 ASN   ( 116-)  F      OD1
2423 HIS   ( 119-)  F      ND1
2425 ASP   ( 121-)  F      OD2
2463 ASP   ( 159-)  F      OD2
2638 ASN   ( 334-)  F      OD1
2700 HIS   ( 396-)  F      NE2
2718 HIS   ( 414-)  F      ND1
2744 HIS   ( 440-)  F      ND1

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.

 103 ASP   ( 104-)  A   H-bonding suggests Asn
 120 ASP   ( 121-)  A   H-bonding suggests Asn; but Alt-Rotamer
 133 GLU   ( 134-)  A   H-bonding suggests Gln
 323 ASP   ( 324-)  A   H-bonding suggests Asn; but Alt-Rotamer
 378 ASP   ( 379-)  A   H-bonding suggests Asn; but Alt-Rotamer
 564 ASP   ( 104-)  B   H-bonding suggests Asn
 594 GLU   ( 134-)  B   H-bonding suggests Gln
 619 ASP   ( 159-)  B   H-bonding suggests Asn; but Alt-Rotamer
 784 ASP   ( 324-)  B   H-bonding suggests Asn; but Alt-Rotamer
 839 ASP   ( 379-)  B   H-bonding suggests Asn; but Alt-Rotamer
1025 ASP   ( 104-)  C   H-bonding suggests Asn; but Alt-Rotamer
1042 ASP   ( 121-)  C   H-bonding suggests Asn
1055 GLU   ( 134-)  C   H-bonding suggests Gln
1061 ASP   ( 140-)  C   H-bonding suggests Asn
1080 ASP   ( 159-)  C   H-bonding suggests Asn; but Alt-Rotamer
1166 GLU   ( 245-)  C   H-bonding suggests Gln; but Alt-Rotamer
1209 GLU   ( 288-)  C   H-bonding suggests Gln
1245 ASP   ( 324-)  C   H-bonding suggests Asn
1300 ASP   ( 379-)  C   H-bonding suggests Asn; but Alt-Rotamer
1307 ASP   ( 386-)  C   H-bonding suggests Asn
1486 ASP   ( 104-)  D   H-bonding suggests Asn; but Alt-Rotamer
1503 ASP   ( 121-)  D   H-bonding suggests Asn
1654 ASP   ( 272-)  D   H-bonding suggests Asn
1706 ASP   ( 324-)  D   H-bonding suggests Asn; but Alt-Rotamer
1761 ASP   ( 379-)  D   H-bonding suggests Asn; but Alt-Rotamer
1947 ASP   ( 104-)  E   H-bonding suggests Asn
1977 GLU   ( 134-)  E   H-bonding suggests Gln
2002 ASP   ( 159-)  E   H-bonding suggests Asn
2093 ASP   ( 250-)  E   H-bonding suggests Asn
2167 ASP   ( 324-)  E   H-bonding suggests Asn
2222 ASP   ( 379-)  E   H-bonding suggests Asn; but Alt-Rotamer
2438 GLU   ( 134-)  F   H-bonding suggests Gln
2576 ASP   ( 272-)  F   H-bonding suggests Asn; but Alt-Rotamer
2628 ASP   ( 324-)  F   H-bonding suggests Asn
2683 ASP   ( 379-)  F   H-bonding suggests Asn
2691 ASP   ( 387-)  F   H-bonding suggests Asn; but Alt-Rotamer

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 :  -1.097
  2nd generation packing quality :  -1.398
  Ramachandran plot appearance   :  -3.501 (poor)
  chi-1/chi-2 rotamer normality  :  -3.359 (poor)
  Backbone conformation          :  -1.224

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.743
  Bond angles                    :   0.827
  Omega angle restraints         :   1.247
  Side chain planarity           :   0.571 (tight)
  Improper dihedral distribution :   0.871
  B-factor distribution          :   0.713
  Inside/Outside distribution    :   1.052

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 : 2.60


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.3
  2nd generation packing quality :   0.0
  Ramachandran plot appearance   :  -0.9
  chi-1/chi-2 rotamer normality  :  -1.0
  Backbone conformation          :  -0.5

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.743
  Bond angles                    :   0.827
  Omega angle restraints         :   1.247
  Side chain planarity           :   0.571 (tight)
  Improper dihedral distribution :   0.871
  B-factor distribution          :   0.713
  Inside/Outside distribution    :   1.052
==============

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.