WHAT IF Check report

This file was created 2011-12-13 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 pdb2d69.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 : 0.611
CA-only RMS fit for the two chains : 0.238

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 D

All-atom RMS fit for the two chains : 2.046
CA-only RMS fit for the two chains : 1.792

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 : 0.643
CA-only RMS fit for the two chains : 0.311

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: B and D

All-atom RMS fit for the two chains : 0.967
CA-only RMS fit for the two chains : 0.688

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

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 E

All-atom RMS fit for the two chains : 0.521
CA-only RMS fit for the two chains : 0.255

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 E

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.

1672 SO4   (1001-)  A  -
1673 SO4   (1002-)  A  -
1674 SO4   (1003-)  A  -
1675 SO4   (1004-)  A  -
1676 SO4   (1005-)  A  -
1677 SO4   (2001-)  B  -
1678 SO4   (2002-)  B  -
1679 SO4   (2003-)  B  -
1680 SO4   (2004-)  B  -
1681 SO4   (2005-)  B  -
1682 SO4   (3001-)  D  -
1683 SO4   (3002-)  D  -
1684 SO4   (3003-)  D  -
1685 SO4   (3004-)  D  -
1686 SO4   (4001-)  E  -
1687 SO4   (4002-)  E  -
1688 SO4   (4003-)  E  -
1689 SO4   (4004-)  E  -
1690 SO4   (4005-)  E  -

Administrative problems that can generate validation failures

Warning: Residues with missing backbone atoms.

Residues were detected with missing backbone atoms. This can be a normal result of poor or missing density, but it can also be an error.

In X-ray the coordinates must be located in density. Mobility or disorder sometimes cause this density to be so poor that the positions of the atoms cannot be determined. Crystallographers tend to leave out the atoms in such cases. This is not an error, albeit that we would prefer them to give it their best shot and provide coordinates with an occupancy of zero in cases where only a few atoms are involved. Anyway, several checks depend on the presence of the backbone atoms, so if you find errors in, or directly adjacent to, residues with missing backbone atoms, then please check by hand what is going on.

 424 ALA   ( 424-)  A  -
 842 LYS   ( 425-)  B  -
1261 VAL   ( 419-)  D  -
1671 GLU   ( 418-)  E  -

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: D

Note: Ramachandran plot

Chain identifier: E

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'.

 424 ALA   ( 424-)  A      O
 842 LYS   ( 425-)  B      O
1261 VAL   ( 419-)  D      O
1671 GLU   ( 418-)  E      O

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: 4

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: D

Note: B-factor plot

Chain identifier: E

Nomenclature related problems

Warning: Arginine nomenclature problem

The arginine residues listed in the table below have their N-H-1 and N-H-2 swapped.

 237 ARG   ( 237-)  A
 361 ARG   ( 361-)  A
 654 ARG   ( 237-)  B
 778 ARG   ( 361-)  B
1079 ARG   ( 237-)  D
1203 ARG   ( 361-)  D
1490 ARG   ( 237-)  E
1614 ARG   ( 361-)  E

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
  19 TYR   (  19-)  A
  31 TYR   (  31-)  A
  74 TYR   (  74-)  A
  88 TYR   (  88-)  A
 175 TYR   ( 175-)  A
 207 TYR   ( 207-)  A
 248 TYR   ( 248-)  A
 323 TYR   ( 323-)  A
 428 TYR   (  11-)  B
 436 TYR   (  19-)  B
 448 TYR   (  31-)  B
 491 TYR   (  74-)  B
 505 TYR   (  88-)  B
 546 TYR   ( 129-)  B
 592 TYR   ( 175-)  B
 624 TYR   ( 207-)  B
 665 TYR   ( 248-)  B
 740 TYR   ( 323-)  B
 861 TYR   (  19-)  D
 873 TYR   (  31-)  D
 916 TYR   (  74-)  D
 924 TYR   (  82-)  D
 930 TYR   (  88-)  D
1017 TYR   ( 175-)  D
1090 TYR   ( 248-)  D
1165 TYR   ( 323-)  D
1264 TYR   (  11-)  E
1272 TYR   (  19-)  E
1284 TYR   (  31-)  E
1327 TYR   (  74-)  E
1341 TYR   (  88-)  E
1428 TYR   ( 175-)  E
1460 TYR   ( 207-)  E
1501 TYR   ( 248-)  E
1576 TYR   ( 323-)  E

Warning: Phenylalanine convention problem

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

  14 PHE   (  14-)  A
 110 PHE   ( 110-)  A
 123 PHE   ( 123-)  A
 146 PHE   ( 146-)  A
 191 PHE   ( 191-)  A
 194 PHE   ( 194-)  A
 344 PHE   ( 344-)  A
 363 PHE   ( 363-)  A
 431 PHE   (  14-)  B
 527 PHE   ( 110-)  B
 540 PHE   ( 123-)  B
 563 PHE   ( 146-)  B
 608 PHE   ( 191-)  B
 611 PHE   ( 194-)  B
 761 PHE   ( 344-)  B
 780 PHE   ( 363-)  B
 856 PHE   (  14-)  D
 874 PHE   (  32-)  D
 952 PHE   ( 110-)  D
 965 PHE   ( 123-)  D
 988 PHE   ( 146-)  D
1033 PHE   ( 191-)  D
1036 PHE   ( 194-)  D
1041 PHE   ( 199-)  D
1186 PHE   ( 344-)  D
1205 PHE   ( 363-)  D
1267 PHE   (  14-)  E
1285 PHE   (  32-)  E
1326 PHE   (  73-)  E
1363 PHE   ( 110-)  E
1376 PHE   ( 123-)  E
1399 PHE   ( 146-)  E
1444 PHE   ( 191-)  E
1447 PHE   ( 194-)  E
1597 PHE   ( 344-)  E
1616 PHE   ( 363-)  E

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.

  13 ASP   (  13-)  A
  16 ASP   (  16-)  A
  24 ASP   (  24-)  A
 188 ASP   ( 188-)  A
 211 ASP   ( 211-)  A
 331 ASP   ( 331-)  A
 380 ASP   ( 380-)  A
 430 ASP   (  13-)  B
 433 ASP   (  16-)  B
 441 ASP   (  24-)  B
 605 ASP   ( 188-)  B
 628 ASP   ( 211-)  B
 748 ASP   ( 331-)  B
 797 ASP   ( 380-)  B
 818 ASP   ( 401-)  B
 858 ASP   (  16-)  D
 866 ASP   (  24-)  D
1030 ASP   ( 188-)  D
1053 ASP   ( 211-)  D
1173 ASP   ( 331-)  D
1222 ASP   ( 380-)  D
1266 ASP   (  13-)  E
1269 ASP   (  16-)  E
1277 ASP   (  24-)  E
1441 ASP   ( 188-)  E
1464 ASP   ( 211-)  E
1584 ASP   ( 331-)  E
1633 ASP   ( 380-)  E

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.

  20 GLU   (  20-)  A
  29 GLU   (  29-)  A
  40 GLU   (  40-)  A
  41 GLU   (  41-)  A
  63 GLU   (  63-)  A
 128 GLU   ( 128-)  A
 168 GLU   ( 168-)  A
 176 GLU   ( 176-)  A
 189 GLU   ( 189-)  A
 200 GLU   ( 200-)  A
 201 GLU   ( 201-)  A
 266 GLU   ( 266-)  A
 324 GLU   ( 324-)  A
 411 GLU   ( 411-)  A
 446 GLU   (  29-)  B
 457 GLU   (  40-)  B
 458 GLU   (  41-)  B
 480 GLU   (  63-)  B
 497 GLU   (  80-)  B
 545 GLU   ( 128-)  B
 585 GLU   ( 168-)  B
 593 GLU   ( 176-)  B
 606 GLU   ( 189-)  B
 617 GLU   ( 200-)  B
 618 GLU   ( 201-)  B
And so on for a total of 61 lines.

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.

 954 MET   ( 112-)  D      SD   CE    1.54   -4.3
1146 MET   ( 304-)  D      SD   CE    1.51   -4.8
1484 VAL   ( 231-)  E      CB   CG2   1.39   -4.0
1557 MET   ( 304-)  E      SD   CE    1.54   -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

 |  0.998071  0.000009  0.000343|
 |  0.000009  0.997712  0.000192|
 |  0.000343  0.000192  0.998297|
Proposed new scale matrix

 |  0.005804  0.000000  0.004290|
 |  0.000000  0.006737 -0.000001|
 | -0.000004 -0.000002  0.011488|
With corresponding cell

    A    = 172.259  B   = 148.425  C    = 108.226
    Alpha=  89.976  Beta= 126.453  Gamma=  90.010

The CRYST1 cell dimensions

    A    = 172.591  B   = 148.774  C    = 108.452
    Alpha=  90.000  Beta= 126.490  Gamma=  90.000

Variance: 220.312
(Under-)estimated Z-score: 10.939

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.

 124 HIS   ( 124-)  A      CG   ND1  CE1 110.35    4.7
 157 THR   ( 157-)  A      CG2  CB   OG1 101.22   -4.0
 248 TYR   ( 248-)  A      CA   CB   CG  123.55    5.2
 339 HIS   ( 339-)  A      CG   ND1  CE1 109.82    4.2
 378 HIS   ( 378-)  A      CG   ND1  CE1 109.65    4.1
 665 TYR   ( 248-)  B      CA   CB   CG  121.51    4.2
 678 LEU   ( 261-)  B      CB   CG   CD2 123.39    4.2
 756 HIS   ( 339-)  B      CG   ND1  CE1 110.07    4.5
 882 GLU   (  40-)  D      CA   CB   CG  122.61    4.3
1086 GLU   ( 244-)  D      C    CA   CB  102.29   -4.1
1090 TYR   ( 248-)  D      CA   CB   CG  122.48    4.7
1146 MET   ( 304-)  D      CG   SD   CE   91.79   -4.1
1153 HIS   ( 311-)  D      CG   ND1  CE1 109.71    4.1
1309 THR   (  56-)  E      N    CA   CB  117.57    4.2
1410 THR   ( 157-)  E      N    CA   CB  101.22   -5.5
1484 VAL   ( 231-)  E      N    CA   CB  119.24    5.1
1484 VAL   ( 231-)  E      C    CA   CB  101.13   -4.7
1529 HIS   ( 276-)  E      CG   ND1  CE1 109.79    4.2
1535 HIS   ( 282-)  E      CG   ND1  CE1 109.64    4.0
1597 PHE   ( 344-)  E      C    CA   CB  101.24   -4.7
1631 HIS   ( 378-)  E      CG   ND1  CE1 109.67    4.1

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.

  13 ASP   (  13-)  A
  16 ASP   (  16-)  A
  20 GLU   (  20-)  A
  24 ASP   (  24-)  A
  29 GLU   (  29-)  A
  40 GLU   (  40-)  A
  41 GLU   (  41-)  A
  63 GLU   (  63-)  A
 128 GLU   ( 128-)  A
 168 GLU   ( 168-)  A
 176 GLU   ( 176-)  A
 188 ASP   ( 188-)  A
 189 GLU   ( 189-)  A
 200 GLU   ( 200-)  A
 201 GLU   ( 201-)  A
 211 ASP   ( 211-)  A
 237 ARG   ( 237-)  A
 266 GLU   ( 266-)  A
 324 GLU   ( 324-)  A
 331 ASP   ( 331-)  A
 361 ARG   ( 361-)  A
 380 ASP   ( 380-)  A
 411 GLU   ( 411-)  A
 430 ASP   (  13-)  B
 433 ASP   (  16-)  B
And so on for a total of 97 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.

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

 678 LEU   ( 261-)  B      CG     7.7   -19.38   -33.01
The average deviation= 1.188

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.

 670 ILE   ( 253-)  B    4.87
 372 GLY   ( 372-)  A    4.66
1640 LYS   ( 387-)  E    4.50
1506 ILE   ( 253-)  E    4.31

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.

1529 HIS   ( 276-)  E    4.72
 756 HIS   ( 339-)  B    4.55
 243 ASN   ( 243-)  A    4.08

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.

1309 THR   (  56-)  E    -3.1
1410 THR   ( 157-)  E    -3.0
 898 THR   (  56-)  D    -2.7
1310 THR   (  57-)  E    -2.6
 474 THR   (  57-)  B    -2.5
1160 LYS   ( 318-)  D    -2.5
 847 ARG   (   5-)  D    -2.4
  57 THR   (  57-)  A    -2.4
1313 LYS   (  60-)  E    -2.3
 899 THR   (  57-)  D    -2.3
1602 GLY   ( 349-)  E    -2.2
1191 GLY   ( 349-)  D    -2.2
 372 GLY   ( 372-)  A    -2.2
 349 GLY   ( 349-)  A    -2.2
 477 LYS   (  60-)  B    -2.2
 999 THR   ( 157-)  D    -2.2
1415 LYS   ( 162-)  E    -2.1
1308 TRP   (  55-)  E    -2.1
 319 MET   ( 319-)  A    -2.1
1590 TRP   ( 337-)  E    -2.1
1330 LYS   (  77-)  E    -2.1
 919 LYS   (  77-)  D    -2.1
 766 GLY   ( 349-)  B    -2.1
 723 GLY   ( 306-)  B    -2.0
 306 GLY   ( 306-)  A    -2.0
 427 TRP   (  10-)  B    -2.0
 844 MET   (   2-)  D    -2.0
 735 LYS   ( 318-)  B    -2.0
1065 TYR   ( 223-)  D    -2.0
 162 LYS   ( 162-)  A    -2.0
1004 LYS   ( 162-)  D    -2.0
1251 SER   ( 409-)  D    -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.

  30 TYR   (  30-)  A  omega poor
  51 SER   (  51-)  A  Poor phi/psi
  55 TRP   (  55-)  A  Poor phi/psi
 149 VAL   ( 149-)  A  omega poor
 160 LYS   ( 160-)  A  PRO omega poor
 165 TRP   ( 165-)  A  omega poor
 192 THR   ( 192-)  A  Poor phi/psi
 222 GLU   ( 222-)  A  omega poor
 230 PRO   ( 230-)  A  omega poor
 248 TYR   ( 248-)  A  omega poor
 252 ASP   ( 252-)  A  omega poor
 281 MET   ( 281-)  A  Poor phi/psi
 290 ARG   ( 290-)  A  omega poor
 316 VAL   ( 316-)  A  omega poor
 319 MET   ( 319-)  A  Poor phi/psi
 320 ALA   ( 320-)  A  Poor phi/psi, omega poor
 338 GLU   ( 338-)  A  Poor phi/psi
 367 LEU   ( 367-)  A  omega poor
 372 GLY   ( 372-)  A  Poor phi/psi
 426 GLU   (   9-)  B  omega poor
 427 TRP   (  10-)  B  omega poor
 447 TYR   (  30-)  B  omega poor
 468 SER   (  51-)  B  Poor phi/psi
 472 TRP   (  55-)  B  omega poor
 566 VAL   ( 149-)  B  omega poor
And so on for a total of 92 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.

 890 SER   (  48-)  D    0.36

Warning: Unusual backbone conformations

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

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

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

  15 VAL   (  15-)  A      0
  17 LEU   (  17-)  A      0
  32 PHE   (  32-)  A      0
  35 ASN   (  35-)  A      0
  37 VAL   (  37-)  A      0
  50 SER   (  50-)  A      0
  51 SER   (  51-)  A      0
  52 ILE   (  52-)  A      0
  55 TRP   (  55-)  A      0
  56 THR   (  56-)  A      0
  57 THR   (  57-)  A      0
  58 LEU   (  58-)  A      0
  59 TRP   (  59-)  A      0
  73 PHE   (  73-)  A      0
  75 LEU   (  75-)  A      0
  76 GLU   (  76-)  A      0
  77 LYS   (  77-)  A      0
  78 HIS   (  78-)  A      0
  80 GLU   (  80-)  A      0
  95 GLU   (  95-)  A      0
 106 ALA   ( 106-)  A      0
 108 ASN   ( 108-)  A      0
 112 MET   ( 112-)  A      0
 115 LEU   ( 115-)  A      0
 117 ASN   ( 117-)  A      0
And so on for a total of 574 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]

  21 PRO   (  21-)  A    0.06 LOW
  39 PRO   (  39-)  A    0.18 LOW
  62 PRO   (  62-)  A    0.17 LOW
 153 PRO   ( 153-)  A    0.18 LOW
 382 PRO   ( 382-)  A    0.18 LOW
 570 PRO   ( 153-)  B    0.14 LOW
 612 PRO   ( 195-)  B    0.14 LOW
 759 PRO   ( 342-)  B    0.19 LOW
 799 PRO   ( 382-)  B    0.13 LOW
 904 PRO   (  62-)  D    0.13 LOW
1072 PRO   ( 230-)  D    0.20 LOW
1131 PRO   ( 289-)  D    0.17 LOW
1274 PRO   (  21-)  E    0.10 LOW
1414 PRO   ( 161-)  E    0.02 LOW
1542 PRO   ( 289-)  E    0.19 LOW
1632 PRO   ( 379-)  E    0.17 LOW
1635 PRO   ( 382-)  E    0.11 LOW
1663 PRO   ( 410-)  E    0.20 LOW

Warning: Unusual PRO puckering phases

The proline residues listed in the table below have a puckering phase that is not expected to occur in protein structures. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings approximately show a so-called envelope conformation with the C-gamma atom above the plane of the ring (phi=+72 degrees), or a half-chair conformation with C-gamma below and C-beta above the plane of the ring (phi=-90 degrees). If phi deviates strongly from these values, this is indicative of a very strange conformation for a PRO residue, and definitely requires a manual check of the data. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF].

 230 PRO   ( 230-)  A   104.1 envelop C-beta (108 degrees)
1378 PRO   ( 125-)  E   -65.6 envelop C-beta (-72 degrees)
1448 PRO   ( 195-)  E    99.8 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.

1501 TYR   ( 248-)  E      OH  <-> 1562 GLN   ( 309-)  E      NE2    0.56    2.14  INTRA
1403 LYS   ( 150-)  E      NZ  <-> 1689 SO4   (4004-)  E      O3     0.46    2.24  INTRA BF
 740 TYR   ( 323-)  B      OH  <-> 1692 HOH   (2101 )  B      O      0.40    2.00  INTRA
  66 LYS   (  66-)  A      NZ  <-> 1691 HOH   (1025 )  A      O      0.38    2.32  INTRA BF
1644 ASP   ( 391-)  E      OD2 <-> 1662 SER   ( 409-)  E      OG     0.38    2.02  INTRA
1523 ASP   ( 270-)  E      OD1 <-> 1694 HOH   (4105 )  E      O      0.35    2.05  INTRA
1566 GLY   ( 313-)  E      O   <-> 1694 HOH   (4128 )  E      O      0.33    2.07  INTRA BF
 736 MET   ( 319-)  B      SD  <->  737 ALA   ( 320-)  B      N      0.28    2.92  INTRA BF
1387 LYS   ( 134-)  E      NZ  <-> 1519 GLU   ( 266-)  E      OE2    0.27    2.43  INTRA
 821 GLU   ( 404-)  B      OE2 <->  824 LYS   ( 407-)  B      NZ     0.26    2.44  INTRA
1203 ARG   ( 361-)  D      NH2 <-> 1204 LEU   ( 362-)  D      CD2    0.25    2.85  INTRA
 920 HIS   (  78-)  D      ND1 <-> 1693 HOH   (3018 )  D      O      0.24    2.46  INTRA BF
 327 LYS   ( 327-)  A      NZ  <->  331 ASP   ( 331-)  A      OD1    0.22    2.48  INTRA
 480 GLU   (  63-)  B      O   <-> 1692 HOH   (2084 )  B      O      0.22    2.18  INTRA
1169 LYS   ( 327-)  D      NZ  <-> 1173 ASP   ( 331-)  D      OD1    0.20    2.50  INTRA
1566 GLY   ( 313-)  E      N   <-> 1694 HOH   (4146 )  E      O      0.19    2.51  INTRA
  78 HIS   (  78-)  A      ND1 <-> 1691 HOH   (1027 )  A      O      0.19    2.51  INTRA BF
1220 HIS   ( 378-)  D      NE2 <-> 1253 GLU   ( 411-)  D      O      0.18    2.52  INTRA
 744 LYS   ( 327-)  B      NZ  <->  748 ASP   ( 331-)  B      OD1    0.17    2.53  INTRA
 313 GLY   ( 313-)  A      O   <-> 1691 HOH   (1161 )  A      O      0.16    2.24  INTRA BF
1474 LYS   ( 221-)  E      NZ  <-> 1694 HOH   (4040 )  E      O      0.16    2.54  INTRA
1275 GLY   (  22-)  E      N   <-> 1278 GLU   (  25-)  E      OE2    0.16    2.54  INTRA
  54 THR   (  54-)  A      C   <->   55 TRP   (  55-)  A      CD1    0.16    2.94  INTRA
 387 LYS   ( 387-)  A      NZ  <->  411 GLU   ( 411-)  A      OE1    0.16    2.54  INTRA
 118 LEU   ( 118-)  A      N   <->  291 HIS   ( 291-)  A      CD2    0.16    2.94  INTRA BL
And so on for a total of 127 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: D

Note: Inside/Outside RMS Z-score plot

Chain identifier: E

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.

1670 ARG   ( 417-)  E      -7.01
 704 ARG   ( 287-)  B      -6.89
1129 ARG   ( 287-)  D      -6.87
1161 MET   ( 319-)  D      -6.39
 847 ARG   (   5-)  D      -6.22
  60 LYS   (  60-)  A      -6.16
 902 LYS   (  60-)  D      -6.09
 318 LYS   ( 318-)  A      -6.01
 477 LYS   (  60-)  B      -5.98
 423 LYS   ( 423-)  A      -5.91
 287 ARG   ( 287-)  A      -5.91
1540 ARG   ( 287-)  E      -5.90
1313 LYS   (  60-)  E      -5.90
 862 GLU   (  20-)  D      -5.88
1259 ARG   ( 417-)  D      -5.85
1002 LYS   ( 160-)  D      -5.80
 840 LYS   ( 423-)  B      -5.75
  20 GLU   (  20-)  A      -5.74
 577 LYS   ( 160-)  B      -5.73
 865 ARG   (  23-)  D      -5.71
 494 LYS   (  77-)  B      -5.71
 919 LYS   (  77-)  D      -5.71
1572 MET   ( 319-)  E      -5.70
 437 GLU   (  20-)  B      -5.68
1273 GLU   (  20-)  E      -5.66
And so on for a total of 63 lines.

Warning: Abnormal packing environment for sequential residues

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

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

 595 TRP   ( 178-)  B       597 - GLY    180- ( B)         -4.17
 839 SER   ( 422-)  B       841 - ALA    424- ( B)         -4.85
1020 TRP   ( 178-)  D      1022 - GLY    180- ( D)         -4.17
1431 TRP   ( 178-)  E      1433 - GLY    180- ( E)         -4.22

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: 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

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.

1125 ALA   ( 283-)  D   -2.98
 283 ALA   ( 283-)  A   -2.88
 509 LEU   (  92-)  B   -2.80
  92 LEU   (  92-)  A   -2.79
1345 LEU   (  92-)  E   -2.79
 934 LEU   (  92-)  D   -2.78
  18 ASN   (  18-)  A   -2.60

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: D

Note: Second generation quality Z-score plot

Chain identifier: E

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.

1691 HOH   (1017 )  A      O     77.37  -22.76   62.56
1693 HOH   (3021 )  D      O     63.08   34.67   64.62
1693 HOH   (3123 )  D      O     43.73   -5.35  -22.01
1694 HOH   (4027 )  E      O     60.36   18.05   67.71
1694 HOH   (4141 )  E      O     57.51  -14.98   68.97
1694 HOH   (4161 )  E      O     48.23  -17.34   82.59

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.

1691 HOH   (1100 )  A      O
1691 HOH   (1122 )  A      O
1691 HOH   (1171 )  A      O
1691 HOH   (1186 )  A      O
1691 HOH   (1189 )  A      O
1691 HOH   (1215 )  A      O
1691 HOH   (1216 )  A      O
1691 HOH   (1225 )  A      O
1692 HOH   (2050 )  B      O
1692 HOH   (2082 )  B      O
1692 HOH   (2105 )  B      O
1692 HOH   (2109 )  B      O
1692 HOH   (2115 )  B      O
1692 HOH   (2128 )  B      O
1692 HOH   (2154 )  B      O
1692 HOH   (2159 )  B      O
1692 HOH   (2168 )  B      O
1692 HOH   (2173 )  B      O
1692 HOH   (2178 )  B      O
1693 HOH   (3014 )  D      O
1693 HOH   (3109 )  D      O
1693 HOH   (3111 )  D      O
1693 HOH   (3119 )  D      O
1693 HOH   (3123 )  D      O
1693 HOH   (3168 )  D      O
1693 HOH   (3171 )  D      O
1693 HOH   (3176 )  D      O
1694 HOH   (4047 )  E      O
1694 HOH   (4049 )  E      O
1694 HOH   (4104 )  E      O
1694 HOH   (4158 )  E      O
1694 HOH   (4168 )  E      O
1694 HOH   (4174 )  E      O

Error: HIS, ASN, GLN side chain flips

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

  35 ASN   (  35-)  A
 100 GLN   ( 100-)  A
 190 ASN   ( 190-)  A
 226 ASN   ( 226-)  A
 322 ASN   ( 322-)  A
 452 ASN   (  35-)  B
 517 GLN   ( 100-)  B
 541 HIS   ( 124-)  B
 643 ASN   ( 226-)  B
 708 HIS   ( 291-)  B
 728 HIS   ( 311-)  B
 877 ASN   (  35-)  D
 942 GLN   ( 100-)  D
 966 HIS   ( 124-)  D
 979 GLN   ( 137-)  D
1032 ASN   ( 190-)  D
1068 ASN   ( 226-)  D
1271 ASN   (  18-)  E
1288 ASN   (  35-)  E
1353 GLN   ( 100-)  E
1377 HIS   ( 124-)  E
1479 ASN   ( 226-)  E
1485 ASN   ( 232-)  E
1564 HIS   ( 311-)  E

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.

  55 TRP   (  55-)  A      NE1
  67 ARG   (  67-)  A      N
 118 LEU   ( 118-)  A      N
 150 LYS   ( 150-)  A      N
 151 ASP   ( 151-)  A      N
 152 ARG   ( 152-)  A      N
 152 ARG   ( 152-)  A      NE
 160 LYS   ( 160-)  A      N
 163 MET   ( 163-)  A      N
 165 TRP   ( 165-)  A      N
 196 PHE   ( 196-)  A      N
 197 ASN   ( 197-)  A      ND2
 229 GLY   ( 229-)  A      N
 248 TYR   ( 248-)  A      N
 248 TYR   ( 248-)  A      OH
 279 ARG   ( 279-)  A      NE
 309 GLN   ( 309-)  A      NE2
 315 ALA   ( 315-)  A      N
 316 VAL   ( 316-)  A      N
 318 LYS   ( 318-)  A      N
 319 MET   ( 319-)  A      N
 324 GLU   ( 324-)  A      N
 330 ASN   ( 330-)  A      ND2
 348 SER   ( 348-)  A      N
 352 HIS   ( 352-)  A      N
And so on for a total of 119 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.

 252 ASP   ( 252-)  A      OD1
 252 ASP   ( 252-)  A      OD2
 311 HIS   ( 311-)  A      ND1
 426 GLU   (   9-)  B      OE1
 512 GLU   (  95-)  B      OE2
 669 ASP   ( 252-)  B      OD1
 693 HIS   ( 276-)  B      NE2
1094 ASP   ( 252-)  D      OD1
1118 HIS   ( 276-)  D      NE2
1153 HIS   ( 311-)  D      ND1
1262 GLU   (   9-)  E      OE1
1505 ASP   ( 252-)  E      OD1
1529 HIS   ( 276-)  E      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.

1691 HOH   (1043 )  A      O  1.08  K  4
1691 HOH   (1061 )  A      O  1.06  K  4
1692 HOH   (2098 )  B      O  1.08  K  4
1693 HOH   (3007 )  D      O  0.95  K  4
1693 HOH   (3098 )  D      O  0.86  K  5
1694 HOH   (4100 )  E      O  0.94  K  5

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.

 214 GLU   ( 214-)  A   H-bonding suggests Gln; but Alt-Rotamer
 252 ASP   ( 252-)  A   H-bonding suggests Asn; but Alt-Rotamer
 631 GLU   ( 214-)  B   H-bonding suggests Gln; but Alt-Rotamer
 669 ASP   ( 252-)  B   H-bonding suggests Asn; but Alt-Rotamer
 918 GLU   (  76-)  D   H-bonding suggests Gln
1056 GLU   ( 214-)  D   H-bonding suggests Gln; but Alt-Rotamer
1094 ASP   ( 252-)  D   H-bonding suggests Asn
1236 ASP   ( 394-)  D   H-bonding suggests Asn
1464 ASP   ( 211-)  E   H-bonding suggests Asn
1467 GLU   ( 214-)  E   H-bonding suggests Gln; but Alt-Rotamer
1505 ASP   ( 252-)  E   H-bonding suggests Asn; but Alt-Rotamer
1584 ASP   ( 331-)  E   H-bonding suggests Asn

Final summary

Note: Summary report for users of a structure

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

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


Structure Z-scores, positive is better than average:

  1st generation packing quality :  -0.198
  2nd generation packing quality :  -0.681
  Ramachandran plot appearance   :  -0.843
  chi-1/chi-2 rotamer normality  :  -1.319
  Backbone conformation          :  -0.328

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.782
  Bond angles                    :   0.870
  Omega angle restraints         :   1.214
  Side chain planarity           :   0.998
  Improper dihedral distribution :   1.010
  B-factor distribution          :   0.587
  Inside/Outside distribution    :   1.003

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 : 1.90


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.3
  2nd generation packing quality :  -0.7
  Ramachandran plot appearance   :  -0.6
  chi-1/chi-2 rotamer normality  :  -0.7
  Backbone conformation          :  -0.7

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.782
  Bond angles                    :   0.870
  Omega angle restraints         :   1.214
  Side chain planarity           :   0.998
  Improper dihedral distribution :   1.010
  B-factor distribution          :   0.587
  Inside/Outside distribution    :   1.003
==============

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.