WHAT IF Check report

This file was created 2013-12-09 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 pdb3ril.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    = 109.217  B   =  91.425  C    = 152.659
    Alpha=  90.000  Beta= 110.950  Gamma=  90.000

Dimensions of a reduced cell

    A    =  91.425  B   = 109.217  C    = 152.659
    Alpha= 110.950  Beta=  90.000  Gamma=  90.000

Dimensions of the conventional cell

    A    = 109.217  B   = 285.134  C    =  91.425
    Alpha=  90.000  Beta=  90.000  Gamma=  89.990

Transformation to conventional cell

 |  1.000000  0.000000  0.000000|
 |  1.000000  0.000000  2.000000|
 |  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 C

All-atom RMS fit for the two chains : 0.371
CA-only RMS fit for the two chains : 0.199

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: B and D

All-atom RMS fit for the two chains : 0.400
CA-only RMS fit for the two chains : 0.168

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: B and D

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.

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.

2002 3RK   ( 513-)  A  -
2010 3RK   ( 509-)  B  -
2022 3RK   ( 513-)  C  -
2030 3RK   ( 509-)  D  -

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

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

Warning: B-factors outside the range 0.0 - 100.0

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

 527 PHE   (  31-)  B    High
 809 TYR   ( 313-)  B    High
 840 GLY   ( 344-)  B    High
1309 PHE   ( 316-)  C    High

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.

1877 GLU   ( 388-)  D    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

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: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Nomenclature related problems

Warning: Tyrosine convention problem

The tyrosine residues listed in the table below have their chi-2 not between -90.0 and 90.0

  11 TYR   (  11-)  A
  22 TYR   (  22-)  A
 108 TYR   ( 108-)  A
 116 TYR   ( 116-)  A
 135 TYR   ( 135-)  A
 205 TYR   ( 205-)  A
 212 TYR   ( 212-)  A
 304 TYR   ( 304-)  A
 372 TYR   ( 373-)  A
 411 TYR   ( 412-)  A
 486 TYR   ( 487-)  A
 491 TYR   ( 492-)  A
 507 TYR   (  11-)  B
 518 TYR   (  22-)  B
 604 TYR   ( 108-)  B
 612 TYR   ( 116-)  B
 631 TYR   ( 135-)  B
 701 TYR   ( 205-)  B
 708 TYR   ( 212-)  B
 800 TYR   ( 304-)  B
 869 TYR   ( 373-)  B
 908 TYR   ( 412-)  B
 914 TYR   ( 418-)  B
 983 TYR   ( 487-)  B
 988 TYR   ( 492-)  B
And so on for a total of 52 lines.

Warning: Phenylalanine convention problem

The phenylalanine residues listed in the table below have their chi-2 not between -90.0 and 90.0.

  26 PHE   (  26-)  A
  31 PHE   (  31-)  A
  75 PHE   (  75-)  A
 109 PHE   ( 109-)  A
 128 PHE   ( 128-)  A
 142 PHE   ( 142-)  A
 147 PHE   ( 147-)  A
 330 PHE   ( 331-)  A
 336 PHE   ( 337-)  A
 346 PHE   ( 347-)  A
 410 PHE   ( 411-)  A
 416 PHE   ( 417-)  A
 425 PHE   ( 426-)  A
 478 PHE   ( 479-)  A
 522 PHE   (  26-)  B
 571 PHE   (  75-)  B
 605 PHE   ( 109-)  B
 624 PHE   ( 128-)  B
 638 PHE   ( 142-)  B
 643 PHE   ( 147-)  B
 812 PHE   ( 316-)  B
 827 PHE   ( 331-)  B
 843 PHE   ( 347-)  B
 907 PHE   ( 411-)  B
 913 PHE   ( 417-)  B
And so on for a total of 53 lines.

Warning: Aspartic acid convention problem

The aspartic acid residues listed in the table below have their chi-2 not between -90.0 and 90.0, or their proton on OD1 instead of OD2.

 649 ASP   ( 153-)  B
1435 ASP   ( 443-)  C
1642 ASP   ( 153-)  D
1804 ASP   ( 315-)  D

Warning: Glutamic acid convention problem

The glutamic acid residues listed in the table below have their chi-3 outside the -90.0 to 90.0 range, or their proton on OE1 instead of OE2.

  72 GLU   (  72-)  A
 151 GLU   ( 151-)  A
 348 GLU   ( 349-)  A
 568 GLU   (  72-)  B
 647 GLU   ( 151-)  B
 845 GLU   ( 349-)  B
1144 GLU   ( 151-)  C
1341 GLU   ( 349-)  C
1561 GLU   (  72-)  D
1640 GLU   ( 151-)  D
1815 GLU   ( 326-)  D
1838 GLU   ( 349-)  D

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.

  60 HIS   (  60-)  A      CG   CD2   1.41    5.3
 145 HIS   ( 145-)  A      CG   CD2   1.40    4.0
 223 HIS   ( 223-)  A      CG   CD2   1.41    4.5
 255 HIS   ( 255-)  A      CG   CD2   1.41    4.6
 273 HIS   ( 273-)  A      CG   CD2   1.40    4.2
 274 HIS   ( 274-)  A      CG   CD2   1.40    4.3
 291 TRP   ( 291-)  A      CD2  CE2   1.49    4.8
 312 TRP   ( 312-)  A      CG   CD2   1.51    4.1
 312 TRP   ( 312-)  A      CD2  CE2   1.49    4.8
 373 HIS   ( 374-)  A      CG   CD2   1.41    4.8
 377 TRP   ( 378-)  A      CG   CD2   1.52    4.6
 377 TRP   ( 378-)  A      CD2  CE2   1.51    6.1
 418 HIS   ( 419-)  A      CG   CD2   1.42    5.4
 421 HIS   ( 422-)  A      CG   CD2   1.40    4.1
 450 HIS   ( 451-)  A      CG   CD2   1.42    5.8
 450 HIS   ( 451-)  A      ND1  CE1   1.37    4.2
 489 HIS   ( 490-)  A      CG   CD2   1.42    5.4
 641 HIS   ( 145-)  B      CG   CD2   1.42    5.7
 724 TRP   ( 228-)  B      CD2  CE2   1.48    4.0
 769 HIS   ( 273-)  B      CG   CD2   1.42    6.0
 770 HIS   ( 274-)  B      CG   CD2   1.41    4.9
 787 TRP   ( 291-)  B      CD2  CE2   1.49    5.0
 807 HIS   ( 311-)  B      CG   CD2   1.40    4.0
 874 TRP   ( 378-)  B      CD2  CE2   1.50    5.2
 889 TRP   ( 393-)  B      CD2  CE2   1.49    4.8
And so on for a total of 58 lines.

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

 |  0.998128 -0.000099  0.000961|
 | -0.000099  0.996819 -0.000007|
 |  0.000961 -0.000007  0.995444|
Proposed new scale matrix

 |  0.009170  0.000000  0.003513|
 |  0.000001  0.010973  0.000000|
 | -0.000007  0.000000  0.007046|
With corresponding cell

    A    = 109.014  B   =  91.134  C    = 151.926
    Alpha=  89.999  Beta= 110.908  Gamma=  90.006

The CRYST1 cell dimensions

    A    = 109.217  B   =  91.425  C    = 152.659
    Alpha=  90.000  Beta= 110.950  Gamma=  90.000

Variance: 735.435
(Under-)estimated Z-score: 19.987

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.

  36 THR   (  36-)  A      C    CA   CB  119.15    4.8
  44 ARG   (  44-)  A      CB   CG   CD  100.89   -6.6
 145 HIS   ( 145-)  A      CG   ND1  CE1 109.90    4.3
 162 HIS   ( 162-)  A      CG   ND1  CE1 109.96    4.4
 206 HIS   ( 206-)  A      CG   ND1  CE1 109.97    4.4
 274 HIS   ( 274-)  A      CG   ND1  CE1 109.68    4.1
 290 HIS   ( 290-)  A      CG   ND1  CE1 110.38    4.8
 306 HIS   ( 306-)  A      CG   ND1  CE1 109.65    4.1
 314 LEU   ( 314-)  A     -CA  -C    N   124.49    4.1
 314 LEU   ( 314-)  A     -C    N    CA  134.73    7.2
 349 GLN   ( 350-)  A     -C    N    CA  129.00    4.1
 352 ARG   ( 353-)  A      CB   CG   CD  104.35   -4.9
 405 ILE   ( 406-)  A      C    CA   CB   96.92   -6.9
 421 HIS   ( 422-)  A      CG   ND1  CE1 109.98    4.4
 432 ARG   ( 433-)  A      CG   CD   NE  102.35   -4.8
 479 LEU   ( 480-)  A      CA   CB   CG  135.18    5.4
 494 HIS   ( 495-)  A      CG   ND1  CE1 109.91    4.3
 556 HIS   (  60-)  B      CG   ND1  CE1 109.61    4.0
 702 HIS   ( 206-)  B      CG   ND1  CE1 109.82    4.2
 802 HIS   ( 306-)  B      CG   ND1  CE1 110.05    4.5
 810 LEU   ( 314-)  B      CA   CB   CG  135.02    5.3
 811 ASP   ( 315-)  B     -C    N    CA  129.46    4.3
 861 HIS   ( 365-)  B      CG   ND1  CE1 109.73    4.1
1029 THR   (  36-)  C      C    CA   CB  120.24    5.3
1037 ARG   (  44-)  C      CB   CG   CD  101.03   -6.5
And so on for a total of 56 lines.

Error: Nomenclature error(s)

Checking for a hand-check. WHAT IF has over the course of this session already corrected the handedness of atoms in several residues. These were administrative corrections. These residues are listed here.

  72 GLU   (  72-)  A
 151 GLU   ( 151-)  A
 348 GLU   ( 349-)  A
 568 GLU   (  72-)  B
 647 GLU   ( 151-)  B
 649 ASP   ( 153-)  B
 845 GLU   ( 349-)  B
1144 GLU   ( 151-)  C
1341 GLU   ( 349-)  C
1435 ASP   ( 443-)  C
1561 GLU   (  72-)  D
1640 GLU   ( 151-)  D
1642 ASP   ( 153-)  D
1804 ASP   ( 315-)  D
1815 GLU   ( 326-)  D
1838 GLU   ( 349-)  D

Warning: Chirality deviations detected

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

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

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

Please also see the previous table that lists a series of administrative chirality problems that were corrected automatically upon reading-in the PDB file.

  36 THR   (  36-)  A      CA    -6.9    22.39    33.84
 314 LEU   ( 314-)  A      CA    -9.4    19.77    34.19
 902 ILE   ( 406-)  B      CB     6.7    40.99    32.31
1029 THR   (  36-)  C      CA    -6.4    23.21    33.84
The average deviation= 1.167

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.

1307 LEU   ( 314-)  C    6.36
1560 PRO   (  71-)  D    5.81
 819 THR   ( 323-)  B    4.36
 810 LEU   ( 314-)  B    4.17
 314 LEU   ( 314-)  A    4.01

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.

 559 THR   (  63-)  B    -3.3
 809 TYR   ( 313-)  B    -3.2
1560 PRO   (  71-)  D    -3.1
 481 THR   ( 482-)  A    -2.8
 810 LEU   ( 314-)  B    -2.8
1803 LEU   ( 314-)  D    -2.8
1971 THR   ( 482-)  D    -2.8
1474 THR   ( 482-)  C    -2.7
1959 LEU   ( 470-)  D    -2.7
 966 LEU   ( 470-)  B    -2.6
1311 PRO   ( 319-)  C    -2.6
 978 THR   ( 482-)  B    -2.5
 785 PRO   ( 289-)  B    -2.5
1307 LEU   ( 314-)  C    -2.5
1778 PRO   ( 289-)  D    -2.5
  98 PRO   (  98-)  A    -2.5
1818 ARG   ( 329-)  D    -2.4
 314 LEU   ( 314-)  A    -2.4
1806 LEU   ( 317-)  D    -2.4
1804 ASP   ( 315-)  D    -2.4
1143 PRO   ( 150-)  C    -2.4
1561 GLU   (  72-)  D    -2.3
1519 THR   (  30-)  D    -2.3
 396 PHE   ( 397-)  A    -2.3
1070 LYS   (  77-)  C    -2.3
1472 LEU   ( 480-)  C    -2.3
 612 TYR   ( 116-)  B    -2.2
 405 ILE   ( 406-)  A    -2.2
1639 PRO   ( 150-)  D    -2.2
 479 LEU   ( 480-)  A    -2.2
 646 PRO   ( 150-)  B    -2.2
 811 ASP   ( 315-)  B    -2.2
 249 LEU   ( 249-)  A    -2.2
 840 GLY   ( 344-)  B    -2.1
1842 ARG   ( 353-)  D    -2.1
1868 THR   ( 379-)  D    -2.1
1770 LEU   ( 281-)  D    -2.1
1605 TYR   ( 116-)  D    -2.1
 841 SER   ( 345-)  B    -2.0
 777 LEU   ( 281-)  B    -2.0
1439 VAL   ( 447-)  C    -2.0
 906 THR   ( 410-)  B    -2.0
 246 PHE   ( 246-)  A    -2.0
1337 SER   ( 345-)  C    -2.0
1368 VAL   ( 376-)  C    -2.0
 509 SER   (  13-)  B    -2.0
 465 LYS   ( 466-)  A    -2.0
 902 ILE   ( 406-)  B    -2.0

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.

  14 VAL   (  14-)  A  omega poor
  19 ASN   (  19-)  A  Poor phi/psi
  51 LEU   (  51-)  A  omega poor
  56 ILE   (  56-)  A  omega poor
  75 PHE   (  75-)  A  Poor phi/psi
 108 TYR   ( 108-)  A  omega poor
 114 ILE   ( 114-)  A  omega poor
 124 ALA   ( 124-)  A  Poor phi/psi, omega poor
 133 TYR   ( 133-)  A  Poor phi/psi
 140 ASP   ( 140-)  A  Poor phi/psi
 181 SER   ( 181-)  A  PRO omega poor
 198 LYS   ( 198-)  A  omega poor
 224 LYS   ( 224-)  A  Poor phi/psi
 233 GLU   ( 233-)  A  Poor phi/psi
 251 PHE   ( 251-)  A  omega poor
 261 ALA   ( 261-)  A  omega poor
 281 LEU   ( 281-)  A  Poor phi/psi
 288 LEU   ( 288-)  A  PRO omega poor
 313 TYR   ( 313-)  A  Poor phi/psi, omega poor
 314 LEU   ( 314-)  A  Poor phi/psi
 342 VAL   ( 343-)  A  omega poor
 343 GLY   ( 344-)  A  Poor phi/psi
 348 GLU   ( 349-)  A  omega poor
 349 GLN   ( 350-)  A  Poor phi/psi
 373 HIS   ( 374-)  A  Poor phi/psi
And so on for a total of 163 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.

 726 VAL   ( 230-)  B    0.36
 107 SER   ( 107-)  A    0.37

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!

   6 PRO   (   6-)  A      0
   9 PHE   (   9-)  A      0
  11 TYR   (  11-)  A      0
  12 SER   (  12-)  A      0
  18 CYS   (  18-)  A      0
  22 TYR   (  22-)  A      0
  23 CYS   (  23-)  A      0
  24 ASP   (  24-)  A      0
  34 LEU   (  34-)  A      0
  45 SER   (  45-)  A      0
  48 ARG   (  48-)  A      0
  49 MET   (  49-)  A      0
  53 MET   (  53-)  A      0
  57 GLN   (  57-)  A      0
  59 ASN   (  59-)  A      0
  61 THR   (  61-)  A      0
  65 LEU   (  65-)  A      0
  70 GLN   (  70-)  A      0
  73 GLN   (  73-)  A      0
  75 PHE   (  75-)  A      0
  79 LYS   (  79-)  A      0
  81 PHE   (  81-)  A      0
  85 MET   (  85-)  A      0
  86 THR   (  86-)  A      0
  96 LEU   (  96-)  A      0
And so on for a total of 864 lines.

Warning: Unusual peptide bond conformations

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

1834 SER   ( 345-)  D   2.03

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]

 236 PRO   ( 236-)  A    0.12 LOW
 468 PRO   ( 469-)  A    0.18 LOW
 484 PRO   ( 485-)  A    0.20 LOW
 528 PRO   (  32-)  B    0.17 LOW
 567 PRO   (  71-)  B    0.16 LOW
 924 PRO   ( 428-)  B    0.18 LOW
 965 PRO   ( 469-)  B    0.04 LOW
1021 PRO   (  28-)  C    0.18 LOW
1958 PRO   ( 469-)  D    0.16 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].

  98 PRO   (  98-)  A   106.8 envelop C-beta (108 degrees)
 178 PRO   ( 178-)  A   -64.1 envelop C-beta (-72 degrees)
 182 PRO   ( 182-)  A   104.5 envelop C-beta (108 degrees)
 201 PRO   ( 201-)  A   102.1 envelop C-beta (108 degrees)
 502 PRO   (   6-)  B   -55.3 half-chair C-beta/C-alpha (-54 degrees)
 594 PRO   (  98-)  B   103.9 envelop C-beta (108 degrees)
 674 PRO   ( 178-)  B   -56.3 half-chair C-beta/C-alpha (-54 degrees)
 678 PRO   ( 182-)  B   131.2 half-chair C-beta/C-alpha (126 degrees)
 785 PRO   ( 289-)  B   -29.5 envelop C-alpha (-36 degrees)
 887 PRO   ( 391-)  B   -59.6 half-chair C-beta/C-alpha (-54 degrees)
1091 PRO   (  98-)  C   102.8 envelop C-beta (108 degrees)
1164 PRO   ( 171-)  C   125.5 half-chair C-beta/C-alpha (126 degrees)
1175 PRO   ( 182-)  C   100.9 envelop C-beta (108 degrees)
1194 PRO   ( 201-)  C   106.0 envelop C-beta (108 degrees)
1229 PRO   ( 236-)  C  -116.5 envelop C-gamma (-108 degrees)
1292 PRO   ( 299-)  C    52.2 half-chair C-delta/C-gamma (54 degrees)
1311 PRO   ( 319-)  C    44.7 envelop C-delta (36 degrees)
1407 PRO   ( 415-)  C   109.5 envelop C-beta (108 degrees)
1495 PRO   (   6-)  D   -26.2 half-chair C-alpha/N (-18 degrees)
1560 PRO   (  71-)  D   -56.8 half-chair C-beta/C-alpha (-54 degrees)
1587 PRO   (  98-)  D   100.5 envelop C-beta (108 degrees)
1667 PRO   ( 178-)  D   -57.0 half-chair C-beta/C-alpha (-54 degrees)
1725 PRO   ( 236-)  D  -115.8 envelop C-gamma (-108 degrees)
1808 PRO   ( 319-)  D   102.6 envelop C-beta (108 degrees)
1904 PRO   ( 415-)  D   104.7 envelop C-beta (108 degrees)
1917 PRO   ( 428-)  D   -65.5 envelop C-beta (-72 degrees)
1941 PRO   ( 452-)  D    99.3 envelop C-beta (108 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.

1508 ASN   (  19-)  D      ND2 <-> 1990 NAG   ( 508-)  D      C1     1.13    1.97  INTRA
1802 TYR   ( 313-)  D      CE1 <-> 1831 CYS   ( 342-)  D      SG     0.60    2.80  INTRA BF
1305 TRP   ( 312-)  C      CA  <-> 1306 TYR   ( 313-)  C      O      0.54    2.06  INTRA BF
 808 TRP   ( 312-)  B      O   <->  811 ASP   ( 315-)  B      CB     0.50    2.30  INTRA BF
1801 TRP   ( 312-)  D      O   <-> 1804 ASP   ( 315-)  D      CB     0.45    2.35  INTRA BF
1508 ASN   (  19-)  D      ND2 <-> 1990 NAG   ( 508-)  D      C2     0.40    2.70  INTRA
1644 LYS   ( 155-)  D      NZ  <-> 2034 HOH   ( 747 )  D      O      0.38    2.32  INTRA
1695 HIS   ( 206-)  D      NE2 <-> 1744 HIS   ( 255-)  D      NE2    0.38    2.62  INTRA BL
1801 TRP   ( 312-)  D      O   <-> 1804 ASP   ( 315-)  D      CG     0.38    2.42  INTRA BF
 904 LYS   ( 408-)  B      CB  <->  906 THR   ( 410-)  B      CG2    0.36    2.84  INTRA
 290 HIS   ( 290-)  A      ND1 <-> 1997 SO4   ( 507-)  A      O2     0.32    2.38  INTRA BF
 141 ASP   ( 141-)  A      OD2 <->  146 ASN   ( 146-)  A      N      0.31    2.39  INTRA
1508 ASN   (  19-)  D      CG  <-> 1990 NAG   ( 508-)  D      C1     0.31    2.89  INTRA
 702 HIS   ( 206-)  B      NE2 <->  751 HIS   ( 255-)  B      NE2    0.29    2.71  INTRA BL
1884 ARG   ( 395-)  D      NH1 <-> 2034 HOH   ( 749 )  D      O      0.29    2.41  INTRA
 226 GLN   ( 226-)  A      NE2 <-> 2031 HOH   ( 775 )  A      O      0.29    2.41  INTRA BF
  44 ARG   (  44-)  A      NH1 <-> 1996 SO4   ( 506-)  A      O3     0.26    2.44  INTRA BF
1307 LEU   ( 314-)  C      N   <-> 1308 ASP   ( 315-)  C      N      0.26    2.34  INTRA BF
  44 ARG   (  44-)  A      CD  <-> 1996 SO4   ( 506-)  A      O2     0.25    2.55  INTRA BF
1435 ASP   ( 443-)  C      N   <-> 2033 HOH   ( 802 )  C      O      0.24    2.46  INTRA
1455 ARG   ( 463-)  C      N   <-> 2033 HOH   ( 722 )  C      O      0.23    2.47  INTRA
 432 ARG   ( 433-)  A      NH1 <-> 2031 HOH   ( 725 )  A      O      0.23    2.47  INTRA
1270 ARG   ( 277-)  C      NH2 <-> 2012 SO4   ( 502-)  C      O3     0.23    2.47  INTRA
 169 GLN   ( 169-)  A      NE2 <-> 2031 HOH   ( 799 )  A      O      0.23    2.47  INTRA BF
1332 GLU   ( 340-)  C      OE2 <-> 2022 3RK   ( 513-)  C      CAI    0.22    2.58  INTRA
And so on for a total of 283 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

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.

1520 PHE   (  31-)  D      -7.31
1930 LYS   ( 441-)  D      -6.67
 937 LYS   ( 441-)  B      -6.64
 440 LYS   ( 441-)  A      -6.59
1433 LYS   ( 441-)  C      -6.57
 665 GLN   ( 169-)  B      -6.21
1658 GLN   ( 169-)  D      -6.07
 200 GLN   ( 200-)  A      -6.05
1193 GLN   ( 200-)  C      -6.02
  31 PHE   (  31-)  A      -6.00
 169 GLN   ( 169-)  A      -5.87
1024 PHE   (  31-)  C      -5.81
 696 GLN   ( 200-)  B      -5.74
 992 ARG   ( 496-)  B      -5.73
 527 PHE   (  31-)  B      -5.58
 758 ARG   ( 262-)  B      -5.54
1751 ARG   ( 262-)  D      -5.52
 262 ARG   ( 262-)  A      -5.52
 843 PHE   ( 347-)  B      -5.52
1255 ARG   ( 262-)  C      -5.49
1162 GLN   ( 169-)  C      -5.47
1985 ARG   ( 496-)  D      -5.45
1689 GLN   ( 200-)  D      -5.39
 346 PHE   ( 347-)  A      -5.37
 809 TYR   ( 313-)  B      -5.34
 495 ARG   ( 496-)  A      -5.24
1342 GLN   ( 350-)  C      -5.22
1952 ARG   ( 463-)  D      -5.21
1163 ARG   ( 170-)  C      -5.20
 194 LYS   ( 194-)  A      -5.17
 666 ARG   ( 170-)  B      -5.12
1612 MET   ( 123-)  D      -5.10
1488 ARG   ( 496-)  C      -5.08
  44 ARG   (  44-)  A      -5.04
1533 ARG   (  44-)  D      -5.01

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.

1549 HIS   (  60-)  D      1552 - THR     63- ( D)         -4.43

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

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.

1659 ARG   ( 170-)  D   -2.85
  62 GLY   (  62-)  A   -2.79
1802 TYR   ( 313-)  D   -2.74
1055 GLY   (  62-)  C   -2.71
 809 TYR   ( 313-)  B   -2.61
 126 CYS   ( 126-)  A   -2.54
1163 ARG   ( 170-)  C   -2.53

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

Water, ion, and hydrogenbond related checks

Warning: Water molecules need moving

The water molecules listed in the table below were found to be significantly closer to a symmetry related non-water molecule than to the ones given in the coordinate file. For optimal viewing convenience revised coordinates for these water molecules should be given.

The number in brackets is the identifier of the water molecule in the input file. Suggested coordinates are also given in the table. Please note that alternative conformations for protein residues are not taken into account for this calculation. If you are using WHAT IF / WHAT-CHECK interactively, then the moved waters can be found in PDB format in the file: MOVEDH2O.pdb.

2031 HOH   ( 847 )  A      O      2.54  -70.82   80.04

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.

2031 HOH   ( 734 )  A      O
2031 HOH   ( 751 )  A      O
2031 HOH   ( 763 )  A      O
2031 HOH   ( 800 )  A      O
2031 HOH   ( 862 )  A      O
2031 HOH   ( 883 )  A      O
2032 HOH   ( 610 )  B      O
2032 HOH   ( 795 )  B      O
2032 HOH   ( 863 )  B      O
2033 HOH   ( 890 )  C      O
2033 HOH   ( 901 )  C      O
2033 HOH   ( 902 )  C      O
2034 HOH   ( 702 )  D      O
2034 HOH   ( 835 )  D      O
Bound group on Asn; dont flip   19 ASN  (  19-) A
Bound to: 1987 NAG  ( 512-) A
Bound group on Asn; dont flip  515 ASN  (  19-) B
Bound to: 1988 NAG  ( 508-) B
Bound group on Asn; dont flip 1012 ASN  (  19-) C
Bound to: 1989 NAG  ( 512-) C

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.

 349 GLN   ( 350-)  A
 665 GLN   ( 169-)  B
 846 GLN   ( 350-)  B
 892 ASN   ( 396-)  B
1267 HIS   ( 274-)  C
1320 HIS   ( 328-)  C
1549 HIS   (  60-)  D
1839 GLN   ( 350-)  D
1885 ASN   ( 396-)  D

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.

  57 GLN   (  57-)  A      NE2
 131 ARG   ( 131-)  A      N
 140 ASP   ( 140-)  A      N
 141 ASP   ( 141-)  A      N
 147 PHE   ( 147-)  A      N
 177 SER   ( 177-)  A      OG
 179 TRP   ( 179-)  A      NE1
 184 TRP   ( 184-)  A      N
 197 LEU   ( 197-)  A      N
 227 PHE   ( 227-)  A      N
 246 PHE   ( 246-)  A      N
 286 LEU   ( 286-)  A      N
 312 TRP   ( 312-)  A      NE1
 313 TYR   ( 313-)  A      N
 314 LEU   ( 314-)  A      N
 315 ASP   ( 315-)  A      N
 316 PHE   ( 316-)  A      N
 347 TRP   ( 348-)  A      N
 363 SER   ( 364-)  A      OG
 365 SER   ( 366-)  A      OG
 377 TRP   ( 378-)  A      NE1
 380 TRP   ( 381-)  A      NE1
 381 ASN   ( 382-)  A      ND2
 383 ALA   ( 384-)  A      N
 395 ASN   ( 396-)  A      N
And so on for a total of 100 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.

 311 HIS   ( 311-)  A      ND1
 418 HIS   ( 419-)  A      NE2
 583 ASP   (  87-)  B      OD1
 780 GLN   ( 284-)  B      OE1
1277 GLN   ( 284-)  C      OE1
1362 ASN   ( 370-)  C      OD1
1411 HIS   ( 419-)  C      NE2
1576 ASP   (  87-)  D      OD1
1908 HIS   ( 419-)  D      NE2

Warning: Unusual water packing

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

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

2033 HOH   ( 634 )  C      O  1.03  K  4
2033 HOH   ( 837 )  C      O  1.06  K  4

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.

 137 ASP   ( 137-)  A   H-bonding suggests Asn
 203 ASP   ( 203-)  A   H-bonding suggests Asn
 218 ASP   ( 218-)  A   H-bonding suggests Asn
 233 GLU   ( 233-)  A   H-bonding suggests Gln; but Alt-Rotamer
 379 ASP   ( 380-)  A   H-bonding suggests Asn; but Alt-Rotamer
 633 ASP   ( 137-)  B   H-bonding suggests Asn
 699 ASP   ( 203-)  B   H-bonding suggests Asn
 729 GLU   ( 233-)  B   H-bonding suggests Gln
 822 GLU   ( 326-)  B   H-bonding suggests Gln; but Alt-Rotamer
 876 ASP   ( 380-)  B   H-bonding suggests Asn; but Alt-Rotamer
1130 ASP   ( 137-)  C   H-bonding suggests Asn
1196 ASP   ( 203-)  C   H-bonding suggests Asn
1211 ASP   ( 218-)  C   H-bonding suggests Asn
1226 GLU   ( 233-)  C   H-bonding suggests Gln; but Alt-Rotamer
1308 ASP   ( 315-)  C   H-bonding suggests Asn
1372 ASP   ( 380-)  C   H-bonding suggests Asn; but Alt-Rotamer
1626 ASP   ( 137-)  D   H-bonding suggests Asn
1692 ASP   ( 203-)  D   H-bonding suggests Asn
1707 ASP   ( 218-)  D   H-bonding suggests Asn
1722 GLU   ( 233-)  D   H-bonding suggests Gln; but Alt-Rotamer
1804 ASP   ( 315-)  D   H-bonding suggests Asn
1869 ASP   ( 380-)  D   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 :  -0.375
  2nd generation packing quality :  -1.608
  Ramachandran plot appearance   :  -1.130
  chi-1/chi-2 rotamer normality  :  -2.600
  Backbone conformation          :  -0.578

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.847
  Bond angles                    :   0.897
  Omega angle restraints         :   1.250
  Side chain planarity           :   0.732
  Improper dihedral distribution :   0.965
  B-factor distribution          :   0.581
  Inside/Outside distribution    :   1.029

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 : 2.40


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.5
  2nd generation packing quality :  -0.4
  Ramachandran plot appearance   :   0.5
  chi-1/chi-2 rotamer normality  :  -0.9
  Backbone conformation          :  -0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.847
  Bond angles                    :   0.897
  Omega angle restraints         :   1.250
  Side chain planarity           :   0.732
  Improper dihedral distribution :   0.965
  B-factor distribution          :   0.581
  Inside/Outside distribution    :   1.029
==============

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.