WHAT IF Check report

This file was created 2011-12-18 from WHAT_CHECK output by a conversion script. If you are new to WHAT_CHECK, please study the pdbreport pages. There also exists a legend to the output.

Please note that you are looking at an abridged version of the output (all checks that gave normal results have been removed from this report). You can have a look at the Full report instead.

Verification log for pdb2yjk.ent

Checks that need to be done early-on in validation

Note: Non crystallographic symmetry RMS plot

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

Chain identifiers of the two chains: A and B

All-atom RMS fit for the two chains : 0.526
CA-only RMS fit for the two chains : 0.377

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 : 0.483
CA-only RMS fit for the two chains : 0.295

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 : 0.486
CA-only RMS fit for the two chains : 0.303

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 : 0.480
CA-only RMS fit for the two chains : 0.339

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 : 0.449
CA-only RMS fit for the two chains : 0.339

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: Chain identifier inconsistency

WHAT IF believes that certain residue(s) have the wrong chain identifier. It has corrected these chain identifiers as indicated in the table. In this table the residues (ligands, drugs, lipids, ions, sugars, etc) that got their chain identifier corrected are listed with the new chain identifier that is used throughout this validation report. WHAT IF does not care about the chain identifiers of water molecules.

1821 OFE   (1159-)  A  B
1823 OFE   (1159-)  I  C
1824  FE   (1160-)  A  C
1825 OFE   (1159-)  J  D
1826  FE   (1160-)  G  D
1827 OFE   (1159-)  F  E
1830 OFE   (1159-)  C  H
1831  FE   (1159-)  H  I
1832 OFE   (1159-)  D  J
1833 OFE   (1159-)  L  K
1834 OFE   (1159-)  K  L
1836  FE   (1160-)  F  J

Warning: Ligands for which topology could not be determined

The ligands in the table below are too complicated for the automatic topology determination. WHAT IF uses a local copy of Daan van Aalten's Dundee PRODRG server to automatically generate topology information for ligands. Some molecules are too complicated for this software. If that happens, WHAT IF / WHAT-CHECK continue with a simplified topology that lacks certain information. Ligands with a simplified topology can, for example, not form hydrogen bonds, and that reduces the accuracy of all hydrogen bond related checking facilities.

The reason for topology generation failure is indicated. 'Atom types' indicates that the ligand contains atom types not known to PRODRUG. 'Attached' means that the ligand is covalently attached to a macromolecule. 'Size' indicates that the ligand has either too many atoms, or too many bonds, angles, or torsion angles. 'Fragmented' is written when the ligand is not one fully covalently connected molecule but consists of multiple fragments. 'N/O only' is given when the ligand contains only N and/or O atoms. 'OK' indicates that the automatic topology generation succeeded.

1820 OFE   (1159-)  A  -         Atom types
1821 OFE   (1159-)  A  B         Atom types
1823 OFE   (1159-)  I  C         Atom types
1825 OFE   (1159-)  J  D         Atom types
1827 OFE   (1159-)  F  E         Atom types
1828 OFE   (1159-)  F  -         Atom types
1829 OFE   (1159-)  G  -         Atom types
1830 OFE   (1159-)  C  H         Atom types
1832 OFE   (1159-)  D  J         Atom types
1833 OFE   (1159-)  L  K         Atom types
1834 OFE   (1159-)  K  L         Atom types

Administrative problems that can generate validation failures

Warning: Alternate atom problems encountered

The residues listed in the table below have alternate atoms. One of two problems might have been encountered: 1) The software did not properly deal with the alternate atoms; 2) The alternate atom indicators are too wrong to sort out.

Alternate atom indicators in PDB files are known to often be erroneous. It has been observed that alternate atom indicators are missing, or that there are too many of them. It is common to see that the distance between two atoms that should be covalently bound is far too big, but the distance between the alternate A of one of them and alternate B of the other is proper for a covalent bond. We have discovered many, many ways in which alternate atoms can be abused. The software tries to deal with most cases, but we know for sure that it cannot deal with all cases. If an alternate atom indicator problem is not properly solved, subsequent checks will list errors that are based on wrong coordinate combinations. So, any problem listed in this table should be solved before error messages further down in this report can be trusted.

 534 SER   (  82-)  D  -

Warning: Alternate atom problems quasi solved

The residues listed in the table below have alternate atoms that WHAT IF decided to correct (e.g. take alternate atom B instead of A for one or more of the atoms). Residues for which the use of alternate atoms is non-standard, but WHAT IF left it that way because he liked the non-standard situation better than other solutions, are listed too in this table.

In case any of these residues shows up as poor or bad in checks further down this report, please check the consistency of the alternate atoms in this residue first, correct it yourself if needed, and run the validation again.

 534 SER   (  82-)  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

Note: Ramachandran plot

Chain identifier: E

Note: Ramachandran plot

Chain identifier: F

Note: Ramachandran plot

Chain identifier: G

Note: Ramachandran plot

Chain identifier: H

Note: Ramachandran plot

Chain identifier: I

Note: Ramachandran plot

Chain identifier: J

Note: Ramachandran plot

Chain identifier: K

Note: Ramachandran plot

Chain identifier: L

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

Warning: Missing atoms

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

 302 ASN   (   2-)  C      CG
 302 ASN   (   2-)  C      OD1
 302 ASN   (   2-)  C      ND2
 303 ILE   (   3-)  C      CG1
 303 ILE   (   3-)  C      CG2
 303 ILE   (   3-)  C      CD1
 304 THR   (   4-)  C      OG1
 304 THR   (   4-)  C      CG2
 305 THR   (   5-)  C      OG1
 305 THR   (   5-)  C      CG2
 306 PRO   (   6-)  C      CG
 306 PRO   (   6-)  C      CD
 461 THR   (   9-)  D      OG1
 461 THR   (   9-)  D      CG2
 613 THR   (   9-)  E      OG1
 613 THR   (   9-)  E      CG2
 765 THR   (   9-)  F      OG1
 765 THR   (   9-)  F      CG2
 915 PRO   (   6-)  G      CG
 915 PRO   (   6-)  G      CD
1070 THR   (   9-)  H      OG1
1070 THR   (   9-)  H      CG2
1518 THR   (   9-)  K      OG1
1518 THR   (   9-)  K      CG2

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.

 302 ASN   (   2-)  C    High
 303 ILE   (   3-)  C    High
 304 THR   (   4-)  C    High
 305 THR   (   5-)  C    High
 306 PRO   (   6-)  C    High
 307 ALA   (   7-)  C    High
 308 LEU   (   8-)  C    High
 309 THR   (   9-)  C    High

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: 12

Crystal temperature (K) :100.000

Note: B-factor plot

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

Chain identifier: A

Note: B-factor plot

Chain identifier: B

Note: B-factor plot

Chain identifier: C

Note: B-factor plot

Chain identifier: D

Note: B-factor plot

Chain identifier: E

Note: B-factor plot

Chain identifier: F

Note: B-factor plot

Chain identifier: G

Note: B-factor plot

Chain identifier: H

Note: B-factor plot

Chain identifier: I

Note: B-factor plot

Chain identifier: J

Note: B-factor plot

Chain identifier: K

Note: B-factor plot

Chain identifier: L

Geometric checks

Warning: Unusual bond lengths

The bond lengths listed in the table below were found to deviate more than 4 sigma from standard bond lengths (both standard values and sigmas for amino acid residues have been taken from Engh and Huber [REF], for DNA they were taken from Parkinson et al [REF]). In the table below for each unusual bond the bond length and the number of standard deviations it differs from the normal value is given.

Atom names starting with "-" belong to the previous residue in the chain. If the second atom name is "-SG*", the disulphide bridge has a deviating length.

 103 ASP   ( 112-)  A      CB   CG    1.64    5.1
 152 THR   (   9-)  B      CA   CB    1.63    4.8
 255 ASP   ( 112-)  B      CB   CG    1.67    6.1
 255 ASP   ( 112-)  B      CG   OD1   1.33    4.4
 289 ASP   ( 146-)  B      N    CA    1.55    4.6
 367 ASP   (  67-)  C      CG   OD2   1.33    4.5
 412 ASP   ( 112-)  C      CB   CG    1.65    5.3
 564 ASP   ( 112-)  D      CB   CG    1.67    6.0
 693 GLU   (  89-)  E      CG   CD    1.62    4.3
 716 ASP   ( 112-)  E      CB   CG    1.66    5.7
 868 ASP   ( 112-)  F      CB   CG    1.67    6.2
 868 ASP   ( 112-)  F      CG   OD1   1.34    4.7
1000 THR   (  91-)  G      CB   CG2   1.36   -5.0
1021 ASP   ( 112-)  G      CB   CG    1.66    5.7
1021 ASP   ( 112-)  G      CG   OD1   1.35    5.1
1173 ASP   ( 112-)  H      CB   CG    1.70    7.5
1173 ASP   ( 112-)  H      CG   OD1   1.34    5.0
1173 ASP   ( 112-)  H      CG   OD2   1.33    4.1
1185 ILE   ( 124-)  H      CA   CB    1.61    4.0
1289 ILE   (  80-)  I      CA   CB    1.62    4.6
1321 ASP   ( 112-)  I      CB   CG    1.68    6.4
1424 ASP   (  67-)  J      CB   CG    1.37   -5.9
1469 ASP   ( 112-)  J      CB   CG    1.68    6.4
1469 ASP   ( 112-)  J      CG   OD1   1.33    4.0
1502 VAL   ( 145-)  J      CA   CB    1.62    4.5
1572 GLN   (  63-)  K      CG   CD    1.64    4.8
1621 ASP   ( 112-)  K      CB   CG    1.64    4.8
1649 GLU   ( 140-)  K      CG   CD    1.62    4.0
1752 THR   (  91-)  L      CB   CG2   1.37   -4.5
1773 ASP   ( 112-)  L      CB   CG    1.65    5.3
1773 ASP   ( 112-)  L      CG   OD1   1.33    4.3

Warning: Possible cell scaling problem

Comparison of bond distances with Engh and Huber [REF] standard values for protein residues and Parkinson et al [REF] values for DNA/RNA shows a significant systematic deviation. It could be that the unit cell used in refinement was not accurate enough. The deformation matrix given below gives the deviations found: the three numbers on the diagonal represent the relative corrections needed along the A, B and C cell axis. These values are 1.000 in a normal case, but have significant deviations here (significant at the 99.99 percent confidence level)

There are a number of different possible causes for the discrepancy. First the cell used in refinement can be different from the best cell calculated. Second, the value of the wavelength used for a synchrotron data set can be miscalibrated. Finally, the discrepancy can be caused by a dataset that has not been corrected for significant anisotropic thermal motion.

Please note that the proposed scale matrix has NOT been restrained to obey the space group symmetry. This is done on purpose. The distortions can give you an indication of the accuracy of the determination.

If you intend to use the result of this check to change the cell dimension of your crystal, please read the extensive literature on this topic first. This check depends on the wavelength, the cell dimensions, and on the standard bond lengths and bond angles used by your refinement software.

Unit Cell deformation matrix

 |  0.993676  0.000502  0.000123|
 |  0.000502  0.994106 -0.000443|
 |  0.000123 -0.000443  0.993431|
Proposed new scale matrix

 |  0.011491 -0.000005  0.001215|
 | -0.000006  0.010928  0.000005|
 |  0.000000  0.000004  0.007873|
With corresponding cell

    A    =  87.028  B   =  91.505  C    = 127.729
    Alpha=  90.057  Beta=  96.035  Gamma=  89.942

The CRYST1 cell dimensions

    A    =  87.580  B   =  92.050  C    = 128.580
    Alpha=  90.000  Beta=  96.040  Gamma=  90.000

Variance: 2231.809
(Under-)estimated Z-score: 34.817

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.

  11 GLN   (  20-)  A      C    CA   CB  117.97    4.1
  48 SER   (  57-)  A      C    CA   CB  118.63    4.5
  62 GLU   (  71-)  A      CA   CB   CG  104.81   -4.6
  82 THR   (  91-)  A      N    CA   CB  103.19   -4.3
  82 THR   (  91-)  A      CA   CB   CG2 118.05    4.4
  82 THR   (  91-)  A      CG2  CB   OG1 117.84    4.3
 152 THR   (   9-)  B      C    CA   CB  119.67    5.0
 170 HIS   (  27-)  B      CG   ND1  CE1 109.60    4.0
 214 GLU   (  71-)  B      CA   CB   CG  103.68   -5.2
 234 THR   (  91-)  B      N    CA   CB  102.56   -4.7
 234 THR   (  91-)  B      CG2  CB   OG1 118.72    4.7
 306 PRO   (   6-)  C      N    CA   CB  111.22    7.5
 357 SER   (  57-)  C      C    CA   CB  118.43    4.4
 367 ASP   (  67-)  C      C    CA   CB  101.50   -4.5
 523 GLU   (  71-)  D      CA   CB   CG  105.18   -4.5
 543 THR   (  91-)  D      N    CA   CB  102.80   -4.5
 543 THR   (  91-)  D      CG2  CB   OG1 118.23    4.5
 631 HIS   (  27-)  E      CG   ND1  CE1 109.67    4.1
 648 ARG   (  44-)  E      CG   CD   NE  103.37   -4.2
 759 HIS   ( 155-)  E      CG   ND1  CE1 109.60    4.0
 824 THR   (  68-)  F      CA   CB   OG1 103.57   -4.0
 838 SER   (  82-)  F      CA   CB   OG  102.29   -4.4
 847 THR   (  91-)  F      CG2  CB   OG1 117.54    4.1
 915 PRO   (   6-)  G      N    CA   CB  110.45    6.8
 949 HIS   (  40-)  G      N    CA   CB  102.28   -4.8
And so on for a total of 51 lines.

Warning: Chirality deviations detected

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

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

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

1000 THR   (  91-)  G      CB    -6.4    19.85    34.09
1152 THR   (  91-)  H      CB    -7.3    17.68    34.09
1515 GLU   ( 158-)  J      CA    -7.1    22.26    33.96
The average deviation= 1.330

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.

1517 LEU   (   8-)  K    4.10

Error: Side chain planarity problems

The side chains of the residues listed in the table below contain a planar group that was found to deviate from planarity by more than 4.0 times the expected value. For an amino acid residue that has a side chain with a planar group, the RMS deviation of the atoms to a least squares plane was determined. The number in the table is the number of standard deviations this RMS value deviates from the expected value. Not knowing better yet, we assume that planarity of the groups analyzed should be perfect.

1101 HIS   (  40-)  H    4.26

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.

1670 THR   (   9-)  L    -3.3
 152 THR   (   9-)  B    -3.1
 764 LEU   (   8-)  F    -2.8
1517 LEU   (   8-)  K    -2.7
 917 LEU   (   8-)  G    -2.6
 151 LEU   (   8-)  B    -2.5
 800 ARG   (  44-)  F    -2.5
 234 THR   (  91-)  B    -2.5
1300 THR   (  91-)  I    -2.4
 496 ARG   (  44-)  D    -2.4
 460 LEU   (   8-)  D    -2.4
 953 ARG   (  44-)  G    -2.4
1069 LEU   (   8-)  H    -2.3
  82 THR   (  91-)  A    -2.3
 391 THR   (  91-)  C    -2.3
1705 ARG   (  44-)  L    -2.3
 836 ILE   (  80-)  F    -2.3
1448 THR   (  91-)  J    -2.3
1105 ARG   (  44-)  H    -2.2
 648 ARG   (  44-)  E    -2.2
 847 THR   (  91-)  F    -2.2
1437 ILE   (  80-)  J    -2.2
1253 ARG   (  44-)  I    -2.2
1152 THR   (  91-)  H    -2.1
 380 ILE   (  80-)  C    -2.1
1741 ILE   (  80-)  L    -2.1
 989 ILE   (  80-)  G    -2.1
1401 ARG   (  44-)  J    -2.1
  71 ILE   (  80-)  A    -2.1
 187 ARG   (  44-)  B    -2.1
1553 ARG   (  44-)  K    -2.1
 344 ARG   (  44-)  C    -2.1
  35 ARG   (  44-)  A    -2.1
1600 THR   (  91-)  K    -2.0
 838 SER   (  82-)  F    -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.

  36 GLY   (  45-)  A  omega poor
  81 LYS   (  90-)  A  omega poor
 151 LEU   (   8-)  B  Poor phi/psi, omega poor
 152 THR   (   9-)  B  Poor phi/psi, omega poor
 153 ALA   (  10-)  B  Poor phi/psi, omega poor
 188 GLY   (  45-)  B  omega poor
 233 LYS   (  90-)  B  omega poor
 240 ALA   (  97-)  B  omega poor
 300 ALA   ( 157-)  B  omega poor
 305 THR   (   5-)  C  Poor phi/psi
 306 PRO   (   6-)  C  Poor phi/psi
 307 ALA   (   7-)  C  Poor phi/psi
 309 THR   (   9-)  C  omega poor
 310 ALA   (  10-)  C  omega poor
 341 TRP   (  41-)  C  omega poor
 344 ARG   (  44-)  C  omega poor
 345 GLY   (  45-)  C  omega poor
 382 SER   (  82-)  C  omega poor
 390 LYS   (  90-)  C  omega poor
 429 GLU   ( 129-)  C  omega poor
 457 ALA   ( 157-)  C  omega poor
 460 LEU   (   8-)  D  Poor phi/psi, omega poor
 462 ALA   (  10-)  D  Poor phi/psi, omega poor
 493 TRP   (  41-)  D  omega poor
 497 GLY   (  45-)  D  omega poor
And so on for a total of 68 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.

 994 SER   (  85-)  G    0.35
 537 SER   (  85-)  D    0.35
1320 SER   ( 111-)  I    0.35
 254 SER   ( 111-)  B    0.36
 841 SER   (  85-)  F    0.36
1294 SER   (  85-)  I    0.36
1772 SER   ( 111-)  L    0.36
 277 SER   ( 134-)  B    0.36
 228 SER   (  85-)  B    0.37
 867 SER   ( 111-)  F    0.37
 411 SER   ( 111-)  C    0.37
1620 SER   ( 111-)  K    0.38
  76 SER   (  85-)  A    0.39
1414 SER   (  57-)  J    0.40

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!

  35 ARG   (  44-)  A      0
  37 SER   (  46-)  A      0
  67 LEU   (  76-)  A      0
  73 SER   (  82-)  A      0
  74 ARG   (  83-)  A      0
  81 LYS   (  90-)  A      0
  82 THR   (  91-)  A      0
  85 ALA   (  94-)  A      0
  86 VAL   (  95-)  A      0
  90 PHE   (  99-)  A      0
 121 VAL   ( 130-)  A      0
 122 ASP   ( 131-)  A      0
 148 ALA   ( 157-)  A      0
 149 GLU   ( 158-)  A      0
 150 ALA   (   7-)  B      0
 151 LEU   (   8-)  B      0
 152 THR   (   9-)  B      0
 153 ALA   (  10-)  B      0
 187 ARG   (  44-)  B      0
 189 SER   (  46-)  B      0
 219 LEU   (  76-)  B      0
 225 SER   (  82-)  B      0
 233 LYS   (  90-)  B      0
 234 THR   (  91-)  B      0
 237 ALA   (  94-)  B      0
And so on for a total of 335 lines.

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]

 222 PRO   (  79-)  B    0.18 LOW
 306 PRO   (   6-)  C    0.00 LOW
 531 PRO   (  79-)  D    0.46 HIGH
 852 PRO   (  96-)  F    0.16 LOW
 915 PRO   (   6-)  G    0.00 LOW
 933 PRO   (  24-)  G    0.05 LOW
1085 PRO   (  24-)  H    0.19 LOW
1157 PRO   (  96-)  H    0.16 LOW
1305 PRO   (  96-)  I    0.15 LOW
1588 PRO   (  79-)  K    0.45 HIGH
1757 PRO   (  96-)  L    0.15 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].

 155 PRO   (  12-)  B  -115.7 envelop C-gamma (-108 degrees)
 464 PRO   (  12-)  D   -61.1 half-chair C-beta/C-alpha (-54 degrees)
 616 PRO   (  12-)  E  -121.5 half-chair C-delta/C-gamma (-126 degrees)
 768 PRO   (  12-)  F  -120.1 half-chair C-delta/C-gamma (-126 degrees)
 780 PRO   (  24-)  F   102.0 envelop C-beta (108 degrees)
1073 PRO   (  12-)  H  -129.9 half-chair C-delta/C-gamma (-126 degrees)
1233 PRO   (  24-)  I   138.6 envelop C-alpha (144 degrees)
1288 PRO   (  79-)  I   -65.4 envelop C-beta (-72 degrees)
1369 PRO   (  12-)  J  -115.7 envelop C-gamma (-108 degrees)
1673 PRO   (  12-)  L  -115.2 envelop C-gamma (-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.

  11 GLN   (  20-)  A      NE2 <-> 1837 HOH   (2002 )  A      O      0.94    1.76  INTRA BF
 207 ASP   (  64-)  B      CB  <-> 1838 HOH   (2018 )  B      O      0.79    2.01  INTRA
 823 ASP   (  67-)  F      CB  <-> 1841 HOH   (2013 )  E      O      0.72    2.08  INTRA
1447 LYS   (  90-)  J      CE  <-> 1846 HOH   (2033 )  J      O      0.61    2.19  INTRA BF
 976 ASP   (  67-)  G      CB  <-> 1843 HOH   (2035 )  G      O      0.58    2.22  INTRA
1708 ASN   (  47-)  L      OD1 <-> 1848 HOH   (2012 )  L      O      0.55    1.85  INTRA BF
1447 LYS   (  90-)  J      CE  <-> 1846 HOH   (2032 )  J      O      0.48    2.32  INTRA BF
1058 ARG   ( 149-)  G      NH2 <-> 1843 HOH   (2070 )  G      O      0.46    2.24  INTRA
1520 ASP   (  11-)  K      O   <-> 1847 HOH   (2001 )  K      O      0.45    1.95  INTRA BF
1447 LYS   (  90-)  J      NZ  <-> 1846 HOH   (2033 )  J      O      0.40    2.30  INTRA BF
  58 ASP   (  67-)  A      CB  <-> 1837 HOH   (2024 )  A      O      0.40    2.40  INTRA BF
 885 GLU   ( 129-)  F      N   <-> 1842 HOH   (2049 )  F      O      0.39    2.31  INTRA BF
1708 ASN   (  47-)  L      CG  <-> 1848 HOH   (2012 )  L      O      0.37    2.43  INTRA BF
1074 GLU   (  13-)  H      CG  <-> 1844 HOH   (2004 )  H      O      0.36    2.44  INTRA BF
 937 LYS   (  28-)  G      NZ  <-> 1028 ASP   ( 119-)  G      OD2    0.34    2.36  INTRA
 458 GLU   ( 158-)  C      C   <-> 1838 HOH   (2013 )  B      O      0.32    2.48  INTRA BF
1752 THR   (  91-)  L      CG2 <-> 1848 HOH   (2008 )  L      O      0.32    2.48  INTRA BL
 234 THR   (  91-)  B      CG2 <-> 1838 HOH   (2011 )  B      O      0.31    2.49  INTRA BL
1514 ALA   ( 157-)  J      O   <-> 1515 GLU   ( 158-)  J      CG     0.31    2.39  INTRA BF
1689 LYS   (  28-)  L      NZ  <-> 1780 ASP   ( 119-)  L      OD2    0.31    2.39  INTRA
 337 LYS   (  37-)  C      NZ  <-> 1276 ASP   (  67-)  I      OD2    0.30    2.40  INTRA BF
1726 TYR   (  65-)  L      CE2 <-> 1848 HOH   (2017 )  L      O      0.29    2.51  INTRA BF
 225 SER   (  82-)  B      OG  <-> 1838 HOH   (2023 )  B      O      0.29    2.11  INTRA
1537 LYS   (  28-)  K      NZ  <-> 1628 ASP   ( 119-)  K      OD2    0.29    2.41  INTRA BF
1790 GLU   ( 129-)  L      CB  <-> 1848 HOH   (2044 )  L      O      0.29    2.51  INTRA BF
And so on for a total of 190 lines.

Packing, accessibility and threading

Note: Inside/Outside RMS Z-score plot

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

Chain identifier: A

Note: Inside/Outside RMS Z-score plot

Chain identifier: B

Note: Inside/Outside RMS Z-score plot

Chain identifier: C

Note: Inside/Outside RMS Z-score plot

Chain identifier: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

Note: Inside/Outside RMS Z-score plot

Chain identifier: F

Note: Inside/Outside RMS Z-score plot

Chain identifier: G

Note: Inside/Outside RMS Z-score plot

Chain identifier: H

Note: Inside/Outside RMS Z-score plot

Chain identifier: I

Note: Inside/Outside RMS Z-score plot

Chain identifier: J

Note: Inside/Outside RMS Z-score plot

Chain identifier: K

Note: Inside/Outside RMS Z-score plot

Chain identifier: L

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.

1669 LEU   (   8-)  L      -7.13
 612 LEU   (   8-)  E      -6.86
1069 LEU   (   8-)  H      -6.01
 151 LEU   (   8-)  B      -5.95
 764 LEU   (   8-)  F      -5.70
 308 LEU   (   8-)  C      -5.55
1517 LEU   (   8-)  K      -5.24

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: B

Note: Quality value plot

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

Chain identifier: C

Note: Quality value plot

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

Chain identifier: D

Note: Quality value plot

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

Chain identifier: E

Note: Quality value plot

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

Chain identifier: F

Note: Quality value plot

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

Chain identifier: G

Note: Quality value plot

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

Chain identifier: H

Note: Quality value plot

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

Chain identifier: I

Note: Quality value plot

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

Chain identifier: J

Note: Quality value plot

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

Chain identifier: K

Note: Quality value plot

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

Chain identifier: L

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.

 306 PRO   (   6-)  C   -3.16
1790 GLU   ( 129-)  L   -2.56
1667 GLU   ( 158-)  K   -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

Note: Second generation quality Z-score plot

Chain identifier: E

Note: Second generation quality Z-score plot

Chain identifier: F

Note: Second generation quality Z-score plot

Chain identifier: G

Note: Second generation quality Z-score plot

Chain identifier: H

Note: Second generation quality Z-score plot

Chain identifier: I

Note: Second generation quality Z-score plot

Chain identifier: J

Note: Second generation quality Z-score plot

Chain identifier: K

Note: Second generation quality Z-score plot

Chain identifier: L

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.

1837 HOH   (2059 )  A      O
1838 HOH   (2001 )  B      O
1841 HOH   (2036 )  E      O
1841 HOH   (2045 )  E      O
1843 HOH   (2001 )  G      O
1843 HOH   (2052 )  G      O
1844 HOH   (2047 )  H      O
1845 HOH   (2020 )  I      O
1845 HOH   (2034 )  I      O
1848 HOH   (2010 )  L      O
Metal-coordinating Histidine residue 183 fixed to   1
Metal-coordinating Histidine residue  31 fixed to   1
Metal-coordinating Histidine residue1249 fixed to   1
Metal-coordinating Histidine residue1397 fixed to   1
Metal-coordinating Histidine residue 796 fixed to   1
Metal-coordinating Histidine residue 644 fixed to   1
Metal-coordinating Histidine residue1101 fixed to   1
Metal-coordinating Histidine residue 340 fixed to   1
Metal-coordinating Histidine residue 949 fixed to   1
Metal-coordinating Histidine residue 492 fixed to   1
Metal-coordinating Histidine residue1701 fixed to   1
Metal-coordinating Histidine residue1549 fixed to   1

Error: HIS, ASN, GLN side chain flips

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

 173 GLN   (  30-)  B
 206 GLN   (  63-)  B
 330 GLN   (  30-)  C
 363 GLN   (  63-)  C
 482 GLN   (  30-)  D
 515 GLN   (  63-)  D
 634 GLN   (  30-)  E
 667 GLN   (  63-)  E
 786 GLN   (  30-)  F
 819 GLN   (  63-)  F
1091 GLN   (  30-)  H
1124 GLN   (  63-)  H
1387 GLN   (  30-)  J
1420 GLN   (  63-)  J
1458 GLN   ( 101-)  J
1539 GLN   (  30-)  K
1572 GLN   (  63-)  K

Warning: Buried unsatisfied hydrogen bond donors

The buried hydrogen bond donors listed in the table below have a hydrogen atom that is not involved in a hydrogen bond in the optimized hydrogen bond network.

Hydrogen bond donors that are buried inside the protein normally use all of their hydrogens to form hydrogen bonds within the protein. If there are any non hydrogen bonded buried hydrogen bond donors in the structure they will be listed here. In very good structures the number of listed atoms will tend to zero.

Waters are not listed by this option.

  11 GLN   (  20-)  A      NE2
  38 ASN   (  47-)  A      N
  82 THR   (  91-)  A      OG1
 149 GLU   ( 158-)  A      N
 151 LEU   (   8-)  B      N
 168 VAL   (  25-)  B      N
 190 ASN   (  47-)  B      N
 225 SER   (  82-)  B      OG
 236 THR   (  93-)  B      N
 277 SER   ( 134-)  B      N
 301 GLU   ( 158-)  B      N
 304 THR   (   4-)  C      N
 325 VAL   (  25-)  C      N
 347 ASN   (  47-)  C      N
 429 GLU   ( 129-)  C      N
 458 GLU   ( 158-)  C      N
 499 ASN   (  47-)  D      N
 586 SER   ( 134-)  D      N
 601 ARG   ( 149-)  D      NH1
 610 GLU   ( 158-)  D      N
 618 VAL   (  14-)  E      N
 648 ARG   (  44-)  E      NE
 651 ASN   (  47-)  E      N
 738 SER   ( 134-)  E      N
 746 LYS   ( 142-)  E      NZ
And so on for a total of 59 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.

   4 GLU   (  13-)  A      OE1
  11 GLN   (  20-)  A      OE1
  52 HIS   (  61-)  A      ND1
  96 GLU   ( 105-)  A      OE1
 248 GLU   ( 105-)  B      OE1
 405 GLU   ( 105-)  C      OE1
 557 GLU   ( 105-)  D      OE1
 656 HIS   (  52-)  E      NE2
 709 GLU   ( 105-)  E      OE1
 861 GLU   ( 105-)  F      OE1
1014 GLU   ( 105-)  G      OE1
1166 GLU   ( 105-)  H      OE1
1314 GLU   ( 105-)  I      OE1
1462 GLU   ( 105-)  J      OE1
1614 GLU   ( 105-)  K      OE1
1674 GLU   (  13-)  L      OE1
1766 GLU   ( 105-)  L      OE1

Warning: Unusual water packing

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

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

1838 HOH   (2052 )  B      O  1.13  K  5 Ion-B
1839 HOH   (2032 )  C      O  0.90  K  4
1843 HOH   (2083 )  G      O  0.95  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.

 103 ASP   ( 112-)  A   H-bonding suggests Asn; but Alt-Rotamer
 255 ASP   ( 112-)  B   H-bonding suggests Asn; but Alt-Rotamer
 301 GLU   ( 158-)  B   H-bonding suggests Gln
 412 ASP   ( 112-)  C   H-bonding suggests Asn; but Alt-Rotamer
 429 GLU   ( 129-)  C   H-bonding suggests Gln
 564 ASP   ( 112-)  D   H-bonding suggests Asn; but Alt-Rotamer
 668 ASP   (  64-)  E   H-bonding suggests Asn
 716 ASP   ( 112-)  E   H-bonding suggests Asn; but Alt-Rotamer
 762 GLU   ( 158-)  E   H-bonding suggests Gln
 868 ASP   ( 112-)  F   H-bonding suggests Asn; but Alt-Rotamer
1021 ASP   ( 112-)  G   H-bonding suggests Asn; but Alt-Rotamer
1057 ASP   ( 148-)  G   H-bonding suggests Asn
1173 ASP   ( 112-)  H   H-bonding suggests Asn; but Alt-Rotamer
1175 ASP   ( 114-)  H   H-bonding suggests Asn; but Alt-Rotamer
1321 ASP   ( 112-)  I   H-bonding suggests Asn; but Alt-Rotamer
1334 ASP   ( 125-)  I   H-bonding suggests Asn
1469 ASP   ( 112-)  J   H-bonding suggests Asn; but Alt-Rotamer
1482 ASP   ( 125-)  J   H-bonding suggests Asn
1621 ASP   ( 112-)  K   H-bonding suggests Asn; but Alt-Rotamer
1667 GLU   ( 158-)  K   H-bonding suggests Gln
1725 ASP   (  64-)  L   H-bonding suggests Asn
1773 ASP   ( 112-)  L   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 :   1.095
  2nd generation packing quality :   0.150
  Ramachandran plot appearance   :   0.320
  chi-1/chi-2 rotamer normality  :  -2.072
  Backbone conformation          :   1.279

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.077
  Bond angles                    :   0.945
  Omega angle restraints         :   1.173
  Side chain planarity           :   1.115
  Improper dihedral distribution :   1.131
  B-factor distribution          :   0.560
  Inside/Outside distribution    :   0.986

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 : 2.00


Structure Z-scores, positive is better than average:

  1st generation packing quality :   1.6
  2nd generation packing quality :   0.0
  Ramachandran plot appearance   :   0.8
  chi-1/chi-2 rotamer normality  :  -1.1
  Backbone conformation          :   1.1

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   1.077
  Bond angles                    :   0.945
  Omega angle restraints         :   1.173
  Side chain planarity           :   1.115
  Improper dihedral distribution :   1.131
  B-factor distribution          :   0.560
  Inside/Outside distribution    :   0.986
==============

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.