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 pdb1c3o.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 C

All-atom RMS fit for the two chains : 0.312
CA-only RMS fit for the two chains : 0.154

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 E

All-atom RMS fit for the two chains : 0.374
CA-only RMS fit for the two chains : 0.196

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 G

All-atom RMS fit for the two chains : 0.392
CA-only RMS fit for the two chains : 0.213

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 G

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 : 0.284
CA-only RMS fit for the two chains : 0.139

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 F

All-atom RMS fit for the two chains : 0.305
CA-only RMS fit for the two chains : 0.143

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 F

Warning: Problem detected upon counting molecules and matrices

The parameter Z as given on the CRYST card represents the molecular multiplicity in the crystallographic cell. Normally, Z equals the number of matrices of the space group multiplied by the number of NCS relations. The value of Z is multiplied by the integrated molecular weight of the molecules in the file to determine the Matthews coefficient. This relation is being validated in this option. Be aware that the validation can get confused if both multiple copies of the molecule are present in the ATOM records and MTRIX records are present in the header of the PDB file.

Space group as read from CRYST card: P 21 21 21
Number of matrices in space group: 4
Highest polymer chain multiplicity in structure: 8
Highest polymer chain multiplicity according to SEQRES: 4
No explicit MTRIX NCS matrices found in the input file
Value of Z as found on the CRYST1 card: 16
Polymer chain multiplicity and SEQRES multiplicity disagree 8 4
Z and NCS seem to support the SEQRES multiplicity (so the matrix counting
problems seem not overly severe)

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.

5774 ADP   (4000-)  A  -
5775 ADP   (4007-)  A  -
5776 ORN   (4011-)  A  -
5778 NET   (4014-)  A  -
5795 ORN   (4033-)  C  -
5797 NET   (4036-)  C  -
5798 ADP   (4023-)  C  -
5800 ADP   (4029-)  C  -
5817 ADP   (4045-)  E  -
5819 ADP   (4051-)  E  -
5820 ORN   (4055-)  E  -
5822 NET   (4058-)  E  -
5840 ADP   (4068-)  G  -
5847 NET   (4081-)  G  -
5848 ORN   (4078-)  G  -
5849 ADP   (4074-)  G  -

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

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'.

 716 PRO   ( 716-)  A      CG
 716 PRO   ( 716-)  A      CD
2153 PRO   ( 716-)  C      CG
2153 PRO   ( 716-)  C      CD
3590 PRO   ( 716-)  E      CG
3590 PRO   ( 716-)  E      CD
5027 PRO   ( 716-)  G      CG
5027 PRO   ( 716-)  G      CD

Warning: What type of B-factor?

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

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

Crystal temperature (K) :100.000

Error: The B-factors of bonded atoms show signs of over-refinement

For each of the bond types in a protein a distribution was derived for the difference between the square roots of the B-factors of the two atoms. All bonds in the current protein were scored against these distributions. The number given below is the RMS Z-score over the structure. For a structure with completely restrained B-factors within residues, this value will be around 0.35, for extremely high resolution structures refined with free isotropic B-factors this number is expected to be near 1.0. Any value over 1.5 is sign of severe over-refinement of B-factors.

RMS Z-score : 4.305 over 35175 bonds
Average difference in B over a bond : 11.34
RMS difference in B over a bond : 15.81

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

Nomenclature related problems

Warning: Tyrosine convention problem

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

  65 TYR   (  65-)  A
 330 TYR   ( 330-)  A
 354 TYR   ( 354-)  A
 438 TYR   ( 438-)  A
 544 TYR   ( 544-)  A
 547 TYR   ( 547-)  A
 594 TYR   ( 594-)  A
 730 TYR   ( 737-)  A
 784 TYR   ( 799-)  A
 823 TYR   ( 838-)  A
 872 TYR   ( 887-)  A
1021 TYR   (1036-)  A
1025 TYR   (1040-)  A
1307 TYR   ( 250-)  B
1434 TYR   ( 377-)  B
1767 TYR   ( 330-)  C
1791 TYR   ( 354-)  C
1875 TYR   ( 438-)  C
1963 TYR   ( 526-)  C
1981 TYR   ( 544-)  C
1984 TYR   ( 547-)  C
2054 TYR   ( 617-)  C
2167 TYR   ( 737-)  C
2221 TYR   ( 799-)  C
2260 TYR   ( 838-)  C
And so on for a total of 61 lines.

Warning: Phenylalanine convention problem

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

 164 PHE   ( 164-)  A
 172 PHE   ( 172-)  A
 188 PHE   ( 188-)  A
 286 PHE   ( 286-)  A
 348 PHE   ( 348-)  A
 409 PHE   ( 409-)  A
 453 PHE   ( 453-)  A
 536 PHE   ( 536-)  A
 837 PHE   ( 852-)  A
 909 PHE   ( 924-)  A
 913 PHE   ( 928-)  A
 954 PHE   ( 969-)  A
1072 PHE   (  15-)  B
1149 PHE   (  92-)  B
1207 PHE   ( 150-)  B
1249 PHE   ( 192-)  B
1371 PHE   ( 314-)  B
1405 PHE   ( 348-)  B
1601 PHE   ( 164-)  C
1625 PHE   ( 188-)  C
1723 PHE   ( 286-)  C
1785 PHE   ( 348-)  C
1846 PHE   ( 409-)  C
1890 PHE   ( 453-)  C
1973 PHE   ( 536-)  C
And so on for a total of 70 lines.

Warning: Aspartic acid convention problem

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

   6 ASP   (   6-)  A
  27 ASP   (  27-)  A
  57 ASP   (  57-)  A
  84 ASP   (  84-)  A
 121 ASP   ( 121-)  A
 124 ASP   ( 124-)  A
 133 ASP   ( 133-)  A
 161 ASP   ( 161-)  A
 207 ASP   ( 207-)  A
 226 ASP   ( 226-)  A
 246 ASP   ( 246-)  A
 338 ASP   ( 338-)  A
 353 ASP   ( 353-)  A
 410 ASP   ( 410-)  A
 416 ASP   ( 416-)  A
 417 ASP   ( 417-)  A
 430 ASP   ( 430-)  A
 441 ASP   ( 441-)  A
 450 ASP   ( 450-)  A
 459 ASP   ( 459-)  A
 499 ASP   ( 499-)  A
 521 ASP   ( 521-)  A
 539 ASP   ( 539-)  A
 558 ASP   ( 558-)  A
 579 ASP   ( 579-)  A
And so on for a total of 254 lines.

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.

  25 GLU   (  25-)  A
  39 GLU   (  39-)  A
  40 GLU   (  40-)  A
  59 GLU   (  59-)  A
  67 GLU   (  67-)  A
  79 GLU   (  79-)  A
  81 GLU   (  81-)  A
 101 GLU   ( 101-)  A
 109 GLU   ( 109-)  A
 110 GLU   ( 110-)  A
 127 GLU   ( 127-)  A
 154 GLU   ( 154-)  A
 190 GLU   ( 190-)  A
 208 GLU   ( 208-)  A
 215 GLU   ( 215-)  A
 219 GLU   ( 219-)  A
 235 GLU   ( 235-)  A
 260 GLU   ( 260-)  A
 274 GLU   ( 274-)  A
 365 GLU   ( 365-)  A
 393 GLU   ( 393-)  A
 419 GLU   ( 419-)  A
 467 GLU   ( 467-)  A
 468 GLU   ( 468-)  A
 473 GLU   ( 473-)  A
And so on for a total of 273 lines.

Error: Chain names not unique

The chain names listed below are given for more than one protein/DNA molecule in the structure ('-' represents a chain without chain identifier).

Chain identifier(s): A, B, C, D, E, F, G, H

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.

  27 ASP   (  27-)  A      CG   OD1   1.34    4.5
 109 GLU   ( 109-)  A      CD   OE1   1.35    5.3
 110 GLU   ( 110-)  A      CD   OE1   1.34    4.6
 121 ASP   ( 121-)  A      CG   OD1   1.33    4.5
 153 GLU   ( 153-)  A      CD   OE2   1.33    4.1
 186 GLU   ( 186-)  A      CD   OE2   1.35    5.1
 217 GLU   ( 217-)  A      CD   OE2   1.33    4.4
 410 ASP   ( 410-)  A      CG   OD1   1.33    4.2
 430 ASP   ( 430-)  A      CG   OD1   1.33    4.0
 512 GLU   ( 512-)  A      CD   OE1   1.33    4.2
 518 ASP   ( 518-)  A      CG   OD2   1.33    4.0
 591 GLU   ( 591-)  A      CD   OE1   1.33    4.2
 604 GLU   ( 604-)  A      CD   OE1   1.33    4.3
 655 GLU   ( 655-)  A      CD   OE1   1.33    4.1
 683 GLU   ( 683-)  A      CD   OE1   1.33    4.2
 699 GLU   ( 699-)  A      CD   OE1   1.33    4.2
 703 GLU   ( 703-)  A      CD   OE1   1.33    4.2
 723 ASP   ( 730-)  A      CG   OD1   1.33    4.4
 726 ASP   ( 733-)  A      CG   OD1   1.33    4.0
 792 ASP   ( 807-)  A      CG   OD1   1.33    4.4
 821 GLU   ( 836-)  A      CD   OE2   1.33    4.1
 938 ASP   ( 953-)  A      CG   OD1   1.33    4.3
 940 GLU   ( 955-)  A      CD   OE1   1.33    4.2
 957 ASP   ( 972-)  A      CG   OD2   1.33    4.1
 994 GLU   (1009-)  A      CD   OE1   1.35    5.2
And so on for a total of 135 lines.

Warning: Possible cell scaling problem

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

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

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

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

Unit Cell deformation matrix

 |  1.001326  0.000184 -0.000027|
 |  0.000184  1.000934 -0.000193|
 | -0.000027 -0.000193  1.000710|
Proposed new scale matrix

 |  0.006548 -0.000001  0.000000|
 | -0.000001  0.006077  0.000001|
 |  0.000000  0.000000  0.003005|
With corresponding cell

    A    = 152.711  B   = 164.546  C    = 332.794
    Alpha=  90.013  Beta=  90.003  Gamma=  89.979

The CRYST1 cell dimensions

    A    = 152.500  B   = 164.400  C    = 332.600
    Alpha=  90.000  Beta=  90.000  Gamma=  90.000

Variance: 187.399
(Under-)estimated Z-score: 10.089

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.

  18 ILE   (  18-)  A      C    CA   CB  102.08   -4.2
  26 PHE   (  26-)  A      C    CA   CB  117.86    4.1
  26 PHE   (  26-)  A      CA   CB   CG  107.76   -6.0
  34 CYS   (  34-)  A      C    CA   CB  100.79   -4.9
  39 GLU   (  39-)  A      C    CA   CB  100.12   -5.3
  40 GLU   (  40-)  A      CG   CD   OE1 108.43   -4.3
 111 PHE   ( 111-)  A      CA   CB   CG  109.08   -4.7
 132 PHE   ( 132-)  A      CA   CB   CG  108.03   -5.8
 172 PHE   ( 172-)  A      CA   CB   CG  106.20   -7.6
 173 THR   ( 173-)  A      N    CA   CB  118.06    4.4
 188 PHE   ( 188-)  A      CA   CB   CG  107.10   -6.7
 200 PRO   ( 200-)  A      N    CA   CB  108.48    5.0
 223 ASP   ( 223-)  A      CB   CG   OD2 109.16   -4.0
 238 ASP   ( 238-)  A      CA   CB   CG  107.74   -4.9
 283 ASN   ( 283-)  A      CA   CB   CG  118.64    6.0
 286 PHE   ( 286-)  A      C    CA   CB  101.95   -4.3
 300 MET   ( 300-)  A      N    CA   CB  117.61    4.2
 300 MET   ( 300-)  A      CG   SD   CE  109.88    4.1
 343 ARG   ( 343-)  A      CG   CD   NE  119.64    5.4
 348 PHE   ( 348-)  A      CA   CB   CG  109.70   -4.1
 360 PRO   ( 360-)  A      N    CA   CB  107.52    4.1
 363 ASN   ( 363-)  A      CA   CB   CG  117.50    4.9
 367 PHE   ( 367-)  A      CA   CB   CG  107.31   -6.5
 396 GLN   ( 396-)  A      CB   CG   CD  105.42   -4.2
 400 ARG   ( 400-)  A      CB   CG   CD  104.70   -4.7
And so on for a total of 339 lines.

Error: Nomenclature error(s)

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

   6 ASP   (   6-)  A
  25 GLU   (  25-)  A
  27 ASP   (  27-)  A
  39 GLU   (  39-)  A
  40 GLU   (  40-)  A
  57 ASP   (  57-)  A
  59 GLU   (  59-)  A
  67 GLU   (  67-)  A
  79 GLU   (  79-)  A
  81 GLU   (  81-)  A
  84 ASP   (  84-)  A
 101 GLU   ( 101-)  A
 109 GLU   ( 109-)  A
 110 GLU   ( 110-)  A
 121 ASP   ( 121-)  A
 124 ASP   ( 124-)  A
 127 GLU   ( 127-)  A
 133 ASP   ( 133-)  A
 154 GLU   ( 154-)  A
 161 ASP   ( 161-)  A
 190 GLU   ( 190-)  A
 207 ASP   ( 207-)  A
 208 GLU   ( 208-)  A
 215 GLU   ( 215-)  A
 219 GLU   ( 219-)  A
And so on for a total of 527 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.

  58 PRO   (  58-)  A      N      7.2    21.06    -2.48
 339 ILE   ( 339-)  A      CA    -7.4    22.09    33.24
 420 ALA   ( 420-)  A      CA    -6.4    26.01    34.09
 984 PRO   ( 999-)  A      N     -9.8   -34.77    -2.48
1241 ALA   ( 184-)  B      CA    -6.3    26.11    34.09
1454 PRO   (  17-)  C      N      6.1    17.44    -2.48
1537 LEU   ( 100-)  C      CA    -6.5    24.30    34.19
1776 ILE   ( 339-)  C      CA   -14.3    11.71    33.24
2421 PRO   ( 999-)  C      N     -6.2   -22.83    -2.48
2876 PRO   (   2-)  E      N     -6.7   -24.61    -2.48
2932 PRO   (  58-)  E      N      7.1    20.78    -2.48
3213 ILE   ( 339-)  E      CA    -9.8    18.38    33.24
3422 GLU   ( 548-)  E      CA    -6.2    23.74    33.96
3858 PRO   ( 999-)  E      N     -8.9   -31.54    -2.48
4177 ALA   ( 246-)  F      CA    -6.4    25.94    34.09
4639 VAL   ( 328-)  G      CA    -6.6    23.71    33.23
4650 ILE   ( 339-)  G      CA    -8.8    19.95    33.24
5177 LYS   ( 881-)  G      CA    -6.9    22.51    33.92
5550 PRO   ( 182-)  H      N      6.9    20.02    -2.48
5601 PRO   ( 233-)  H      N      6.3    18.23    -2.48
5632 PRO   ( 264-)  H      N     -6.1   -22.48    -2.48
The average deviation= 1.508

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.

4650 ILE   ( 339-)  G    8.37
1776 ILE   ( 339-)  C    7.18
3213 ILE   ( 339-)  E    7.00
 339 ILE   ( 339-)  A    6.07
2873 LYS   ( 379-)  D    5.39
5146 VAL   ( 850-)  G    5.34
3486 THR   ( 612-)  E    5.13
4338 ASP   (  27-)  G    5.01
1376 ALA   ( 319-)  B    5.01
4854 MET   ( 543-)  G    4.85
1857 ALA   ( 420-)  C    4.84
1146 ALA   (  89-)  B    4.83
2813 ALA   ( 319-)  D    4.69
1464 ASP   (  27-)  C    4.66
4606 LEU   ( 295-)  G    4.65
4355 VAL   (  44-)  G    4.55
 612 THR   ( 612-)  A    4.54
1980 MET   ( 543-)  C    4.54
3652 ALA   ( 793-)  E    4.47
2088 ALA   ( 651-)  C    4.45
1756 ILE   ( 319-)  C    4.44
 101 GLU   ( 101-)  A    4.40
5089 ALA   ( 793-)  G    4.35
3855 GLU   ( 996-)  E    4.33
4310 LYS   ( 379-)  F    4.33
2042 THR   ( 605-)  C    4.31
  23 ALA   (  23-)  A    4.28
3193 ILE   ( 319-)  E    4.27
1110 VAL   (  53-)  B    4.27
4418 VAL   ( 107-)  G    4.26
 605 THR   ( 605-)  A    4.25
5297 ILE   (1001-)  G    4.21
4630 ILE   ( 319-)  G    4.20
2547 VAL   (  53-)  D    4.20
4731 ALA   ( 420-)  G    4.19
2373 GLU   ( 951-)  C    4.19
3417 MET   ( 543-)  E    4.18
4147 LEU   ( 216-)  F    4.18
4962 ALA   ( 651-)  G    4.17
5625 LYS   ( 257-)  H    4.14
3935 SER   (   4-)  F    4.11
1566 ARG   ( 129-)  C    4.09
5687 ALA   ( 319-)  H    4.03
1352 HIS   ( 295-)  B    4.01
5738 PHE   ( 370-)  H    4.01

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.

3087 TRP   ( 213-)  E    7.39
2304 GLU   ( 882-)  C    5.55
3907 PHE   (1048-)  E    4.59

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.

1525 PRO   (  88-)  C    -3.0
  88 PRO   (  88-)  A    -3.0
2962 PRO   (  88-)  E    -2.9
1689 PRO   ( 252-)  C    -2.9
3981 ARG   (  50-)  F    -2.9
2544 ARG   (  50-)  D    -2.9
4399 PRO   (  88-)  G    -2.8
1996 ARG   ( 559-)  C    -2.7
2763 SER   ( 269-)  D    -2.7
2373 GLU   ( 951-)  C    -2.7
 202 LYS   ( 202-)  A    -2.7
5708 ILE   ( 340-)  H    -2.7
 252 PRO   ( 252-)  A    -2.7
1326 SER   ( 269-)  B    -2.7
1414 SER   ( 357-)  B    -2.6
4842 THR   ( 531-)  G    -2.6
5725 SER   ( 357-)  H    -2.6
3249 THR   ( 375-)  E    -2.6
1812 THR   ( 375-)  C    -2.6
3445 ARG   ( 571-)  E    -2.6
1107 ARG   (  50-)  B    -2.6
1639 LYS   ( 202-)  C    -2.6
4288 SER   ( 357-)  F    -2.6
 375 THR   ( 375-)  A    -2.6
4686 THR   ( 375-)  G    -2.6
And so on for a total of 214 lines.

Warning: Backbone evaluation reveals unusual conformations

The residues listed in the table below have abnormal backbone torsion angles.

Residues with `forbidden' phi-psi combinations are listed, as well as residues with unusual omega angles (deviating by more than 3 sigma from the normal value). Please note that it is normal if about 5 percent of the residues is listed here as having unusual phi-psi combinations.

  23 ALA   (  23-)  A  Poor phi/psi
 164 PHE   ( 164-)  A  PRO omega poor
 172 PHE   ( 172-)  A  Poor phi/psi
 226 ASP   ( 226-)  A  Poor phi/psi
 251 ALA   ( 251-)  A  PRO omega poor
 302 PRO   ( 302-)  A  Poor phi/psi
 303 ARG   ( 303-)  A  Poor phi/psi
 375 THR   ( 375-)  A  Poor phi/psi
 403 GLU   ( 403-)  A  Poor phi/psi
 409 PHE   ( 409-)  A  Poor phi/psi
 457 ASN   ( 457-)  A  Poor phi/psi
 484 LEU   ( 484-)  A  Poor phi/psi
 521 ASP   ( 521-)  A  Poor phi/psi
 530 ASP   ( 530-)  A  Poor phi/psi
 531 THR   ( 531-)  A  Poor phi/psi
 534 ALA   ( 534-)  A  Poor phi/psi
 548 GLU   ( 548-)  A  Poor phi/psi
 558 ASP   ( 558-)  A  Poor phi/psi
 634 LYS   ( 634-)  A  Poor phi/psi
 686 LYS   ( 686-)  A  Poor phi/psi
 710 TYR   ( 710-)  A  PRO omega poor
 743 ASP   ( 758-)  A  Poor phi/psi
 781 LEU   ( 796-)  A  PRO omega poor
 785 THR   ( 800-)  A  Poor phi/psi
 806 GLN   ( 821-)  A  Poor phi/psi
And so on for a total of 169 lines.

Error: chi-1/chi-2 angle correlation Z-score very low

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

chi-1/chi-2 correlation Z-score : -4.225

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.

4215 VAL   ( 284-)  F    0.33
3268 SER   ( 394-)  E    0.36
 312 SER   ( 312-)  A    0.36
1466 SER   (  29-)  C    0.36
2023 SER   ( 586-)  C    0.36
3142 SER   ( 268-)  E    0.37
 268 SER   ( 268-)  A    0.37
4579 SER   ( 268-)  G    0.37
2593 SER   (  99-)  D    0.38
3460 SER   ( 586-)  E    0.38
 394 SER   ( 394-)  A    0.38
4030 SER   (  99-)  F    0.39
1705 SER   ( 268-)  C    0.39

Warning: Unusual backbone conformations

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

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

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

   3 LYS   (   3-)  A      0
   7 ILE   (   7-)  A      0
  17 PRO   (  17-)  A      0
  20 ILE   (  20-)  A      0
  22 GLN   (  22-)  A      0
  23 ALA   (  23-)  A      0
  24 CYS   (  24-)  A      0
  40 GLU   (  40-)  A      0
  49 SER   (  49-)  A      0
  52 ALA   (  52-)  A      0
  60 MET   (  60-)  A      0
  62 ASP   (  62-)  A      0
  69 ILE   (  69-)  A      0
  82 ARG   (  82-)  A      0
  89 THR   (  89-)  A      0
  90 MET   (  90-)  A      0
  93 GLN   (  93-)  A      0
 105 GLN   ( 105-)  A      0
 107 VAL   ( 107-)  A      0
 116 ILE   ( 116-)  A      0
 139 ILE   ( 139-)  A      0
 146 SER   ( 146-)  A      0
 150 HIS   ( 150-)  A      0
 162 VAL   ( 162-)  A      0
 164 PHE   ( 164-)  A      0
And so on for a total of 1991 lines.

Warning: Omega angles too tightly restrained

The omega angles for trans-peptide bonds in a structure are expected to give a gaussian distribution with the average around +178 degrees and a standard deviation around 5.5 degrees. These expected values were obtained from very accurately determined structures. Many protein structures are too tightly restrained. This seems to be the case with the current structure too, as the observed standard deviation is below 4.0 degrees.

Standard deviation of omega values : 1.976

Warning: Backbone oxygen evaluation

The residues listed in the table below have an unusual backbone oxygen position.

For each of the residues in the structure, a search was performed to find 5-residue stretches in the WHAT IF database with superposable C-alpha coordinates, and some restraining on the neighbouring backbone oxygens.

In the following table the RMS distance between the backbone oxygen positions of these matching structures in the database and the position of the backbone oxygen atom in the current residue is given. If this number is larger than 1.5 a significant number of structures in the database show an alternative position for the backbone oxygen. If the number is larger than 2.0 most matching backbone fragments in the database have the peptide plane flipped. A manual check needs to be performed to assess whether the experimental data can support that alternative as well. The number in the last column is the number of database hits (maximum 80) used in the calculation. It is "normal" that some glycine residues show up in this list, but they are still worth checking!

4878 GLY   ( 567-)  G   3.23   26
2004 GLY   ( 567-)  C   3.14   26
 567 GLY   ( 567-)  A   3.10   21
3441 GLY   ( 567-)  E   3.06   22
3583 GLY   ( 709-)  E   2.01   18

Warning: Unusual PRO puckering amplitudes

The proline residues listed in the table below have a puckering amplitude that is outside of normal ranges. Puckering parameters were calculated by the method of Cremer and Pople [REF]. Normal PRO rings have a puckering amplitude Q between 0.20 and 0.45 Angstrom. If Q is lower than 0.20 Angstrom for a PRO residue, this could indicate disorder between the two different normal ring forms (with C-gamma below and above the ring, respectively). If Q is higher than 0.45 Angstrom something could have gone wrong during the refinement. Be aware that this is a warning with a low confidence level. See: Who checks the checkers? Four validation tools applied to eight atomic resolution structures [REF]

   2 PRO   (   2-)  A    0.02 LOW
  17 PRO   (  17-)  A    0.13 LOW
  68 PRO   (  68-)  A    0.11 LOW
  83 PRO   (  83-)  A    0.15 LOW
 165 PRO   ( 165-)  A    0.14 LOW
 170 PRO   ( 170-)  A    0.18 LOW
 200 PRO   ( 200-)  A    0.18 LOW
 290 PRO   ( 290-)  A    0.17 LOW
 350 PRO   ( 350-)  A    0.14 LOW
 360 PRO   ( 360-)  A    0.12 LOW
 411 PRO   ( 411-)  A    0.07 LOW
 418 PRO   ( 418-)  A    0.10 LOW
 524 PRO   ( 524-)  A    0.11 LOW
 555 PRO   ( 555-)  A    0.10 LOW
 647 PRO   ( 647-)  A    0.13 LOW
 660 PRO   ( 660-)  A    0.15 LOW
 666 PRO   ( 666-)  A    0.19 LOW
 690 PRO   ( 690-)  A    0.14 LOW
 711 PRO   ( 711-)  A    0.11 LOW
 716 PRO   ( 716-)  A    0.00 LOW
 782 PRO   ( 797-)  A    0.06 LOW
 836 PRO   ( 851-)  A    0.17 LOW
 845 PRO   ( 860-)  A    0.19 LOW
 870 PRO   ( 885-)  A    0.15 LOW
 871 PRO   ( 886-)  A    0.16 LOW
And so on for a total of 166 lines.

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].

  51 PRO   (  51-)  A   -61.7 half-chair C-beta/C-alpha (-54 degrees)
  58 PRO   (  58-)  A   -14.6 half-chair C-alpha/N (-18 degrees)
  88 PRO   (  88-)  A   -47.5 half-chair C-beta/C-alpha (-54 degrees)
 302 PRO   ( 302-)  A   -25.8 half-chair C-alpha/N (-18 degrees)
 318 PRO   ( 318-)  A   -64.2 envelop C-beta (-72 degrees)
 569 PRO   ( 569-)  A   -52.8 half-chair C-beta/C-alpha (-54 degrees)
 603 PRO   ( 603-)  A   -55.2 half-chair C-beta/C-alpha (-54 degrees)
 635 PRO   ( 635-)  A   -45.5 half-chair C-beta/C-alpha (-54 degrees)
 829 PRO   ( 844-)  A    -6.6 envelop N (0 degrees)
 984 PRO   ( 999-)  A   152.0 envelop C-alpha (144 degrees)
1239 PRO   ( 182-)  B   -40.2 envelop C-alpha (-36 degrees)
1379 PRO   ( 322-)  B  -130.1 half-chair C-delta/C-gamma (-126 degrees)
1415 PRO   ( 358-)  B   -44.1 envelop C-alpha (-36 degrees)
1488 PRO   (  51-)  C   -43.8 envelop C-alpha (-36 degrees)
1525 PRO   (  88-)  C   -39.3 envelop C-alpha (-36 degrees)
1755 PRO   ( 318-)  C   -57.4 half-chair C-beta/C-alpha (-54 degrees)
1782 PRO   ( 345-)  C   -41.7 envelop C-alpha (-36 degrees)
1855 PRO   ( 418-)  C   110.7 envelop C-beta (108 degrees)
2103 PRO   ( 666-)  C   145.3 envelop C-alpha (144 degrees)
2308 PRO   ( 886-)  C   -40.1 envelop C-alpha (-36 degrees)
2540 PRO   (  46-)  D   109.9 envelop C-beta (108 degrees)
2714 PRO   ( 220-)  D   116.6 envelop C-beta (108 degrees)
2840 PRO   ( 346-)  D   -16.3 half-chair C-alpha/N (-18 degrees)
2852 PRO   ( 358-)  D   -60.2 half-chair C-beta/C-alpha (-54 degrees)
2932 PRO   (  58-)  E    -3.1 envelop N (0 degrees)
2962 PRO   (  88-)  E   -47.8 half-chair C-beta/C-alpha (-54 degrees)
3285 PRO   ( 411-)  E   -50.2 half-chair C-beta/C-alpha (-54 degrees)
3540 PRO   ( 666-)  E   115.3 envelop C-beta (108 degrees)
3585 PRO   ( 711-)  E    -4.4 envelop N (0 degrees)
3703 PRO   ( 844-)  E     1.5 envelop N (0 degrees)
3719 PRO   ( 860-)  E   -21.8 half-chair C-alpha/N (-18 degrees)
3858 PRO   ( 999-)  E   169.4 half-chair C-alpha/N (162 degrees)
4113 PRO   ( 182-)  F   -43.0 envelop C-alpha (-36 degrees)
4289 PRO   ( 358-)  F   -41.7 envelop C-alpha (-36 degrees)
4296 PRO   ( 365-)  F   125.0 half-chair C-beta/C-alpha (126 degrees)
4399 PRO   (  88-)  G   -51.1 half-chair C-beta/C-alpha (-54 degrees)
4476 PRO   ( 165-)  G   -56.1 half-chair C-beta/C-alpha (-54 degrees)
4563 PRO   ( 252-)  G   -61.1 half-chair C-beta/C-alpha (-54 degrees)
4613 PRO   ( 302-)  G   -33.4 envelop C-alpha (-36 degrees)
4629 PRO   ( 318-)  G   -42.2 envelop C-alpha (-36 degrees)
4977 PRO   ( 666-)  G   158.7 half-chair C-alpha/N (162 degrees)
5147 PRO   ( 851-)  G   114.3 envelop C-beta (108 degrees)
5201 PRO   ( 905-)  G   -64.3 envelop C-beta (-72 degrees)
5550 PRO   ( 182-)  H   -48.5 half-chair C-beta/C-alpha (-54 degrees)
5601 PRO   ( 233-)  H    -7.2 envelop N (0 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.

2234 GLN   ( 812-)  C      NE2 <-> 5852 HOH   (4684 )  C      O      0.64    2.06  INTRA BF
 977 ASN   ( 992-)  A      ND2 <-> 5271 HIS   ( 975-)  G      NE2    0.52    2.48  INTRA BF
5476 VAL   ( 108-)  H      N   <-> 5857 HOH   (3442 )  H      O      0.48    2.22  INTRA
2875 MET   (   1-)  E      N   <-> 5854 HOH   (4680 )  E      O      0.45    2.25  INTRA BF
2917 ARG   (  43-)  E      NH2 <-> 2955 GLU   (  81-)  E      OE1    0.43    2.27  INTRA BF
2780 MET   ( 286-)  D      CE  <-> 2806 HIS   ( 312-)  D      ND1    0.43    2.67  INTRA
3616 ASP   ( 757-)  E      O   <-> 3692 LYS   ( 833-)  E      NZ     0.43    2.27  INTRA BF
5561 HIS   ( 193-)  H      NE2 <-> 5585 THR   ( 217-)  H      OG1    0.43    2.27  INTRA BF
 194 ARG   ( 194-)  A      NH2 <-> 5850 HOH   (4602 )  A      O      0.42    2.28  INTRA BF
3575 ALA   ( 701-)  E      O   <-> 3579 ALA   ( 705-)  E      N      0.42    2.28  INTRA BF
 715 ARG   ( 715-)  A      NH1 <-> 5850 HOH   (4101 )  A      O      0.41    2.29  INTRA BF
4535 LYS   ( 224-)  G      NZ  <-> 5856 HOH   (2959 )  G      O      0.41    2.29  INTRA BF
5289 LYS   ( 993-)  G      NZ  <-> 5856 HOH   (3612 )  G      O      0.41    2.29  INTRA BF
 636 LYS   ( 636-)  A      NZ  <-> 5850 HOH   (4475 )  A      O      0.41    2.29  INTRA BF
5012 ALA   ( 701-)  G      O   <-> 5016 ALA   ( 705-)  G      N      0.40    2.30  INTRA BF
5084 HIS   ( 788-)  G      ND1 <-> 5086 GLY   ( 790-)  G      N      0.40    2.60  INTRA BL
5570 LYS   ( 202-)  H      NZ  <-> 5723 GLU   ( 355-)  H      OE2    0.40    2.30  INTRA BF
 865 THR   ( 880-)  A      N   <-> 5850 HOH   (4522 )  A      O      0.40    2.30  INTRA BF
 891 LEU   ( 906-)  A      O   <->  897 ARG   ( 912-)  A      NH2    0.40    2.30  INTRA BF
   4 ARG   (   4-)  A      NH1 <-> 5850 HOH   (4110 )  A      O      0.40    2.30  INTRA BF
3217 ARG   ( 343-)  E      NH2 <-> 5854 HOH   (4720 )  E      O      0.40    2.30  INTRA BF
2089 ARG   ( 652-)  C      NH1 <-> 2107 ASP   ( 670-)  C      OD1    0.40    2.30  INTRA BF
1329 HIS   ( 272-)  B      ND1 <-> 1406 SER   ( 349-)  B      OG     0.40    2.30  INTRA
1442 THR   (   5-)  C      N   <-> 5852 HOH   (4129 )  C      O      0.40    2.30  INTRA BF
 636 LYS   ( 636-)  A      NZ  <-> 5850 HOH   (4560 )  A      O      0.40    2.30  INTRA BF
And so on for a total of 1547 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

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.

5294 ARG   ( 998-)  G      -7.69
3857 ARG   ( 998-)  E      -7.35
4654 ARG   ( 343-)  G      -7.34
2420 ARG   ( 998-)  C      -7.31
3217 ARG   ( 343-)  E      -7.16
 343 ARG   ( 343-)  A      -7.16
1780 ARG   ( 343-)  C      -7.11
 983 ARG   ( 998-)  A      -6.84
3057 TYR   ( 183-)  E      -6.53
2344 ARG   ( 922-)  C      -6.50
1620 TYR   ( 183-)  C      -6.49
 907 ARG   ( 922-)  A      -6.48
3854 HIS   ( 995-)  E      -6.32
3781 ARG   ( 922-)  E      -6.25
 174 MET   ( 174-)  A      -6.13
4485 MET   ( 174-)  G      -6.08
 183 TYR   ( 183-)  A      -6.06
3048 MET   ( 174-)  E      -6.03
1611 MET   ( 174-)  C      -5.97
5180 ILE   ( 884-)  G      -5.94
3743 ILE   ( 884-)  E      -5.92
 869 ILE   ( 884-)  A      -5.89
1162 HIS   ( 105-)  B      -5.89
4494 TYR   ( 183-)  G      -5.88
2306 ILE   ( 884-)  C      -5.88
And so on for a total of 67 lines.

Note: Quality value plot

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

Chain identifier: A

Note: Quality value plot

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

Chain identifier: 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

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.

2934 MET   (  60-)  E   -2.94
4334 ALA   (  23-)  G   -2.89
2897 ALA   (  23-)  E   -2.87
4550 ALA   ( 239-)  G   -2.86
1460 ALA   (  23-)  C   -2.85
1676 ALA   ( 239-)  C   -2.84
  60 MET   (  60-)  A   -2.82
 878 VAL   ( 893-)  A   -2.78
3752 VAL   ( 893-)  E   -2.78
1842 GLY   ( 405-)  C   -2.77
  23 ALA   (  23-)  A   -2.75
2315 VAL   ( 893-)  C   -2.74
4716 GLY   ( 405-)  G   -2.74
3279 GLY   ( 405-)  E   -2.73
2935 ALA   (  61-)  E   -2.70
5189 VAL   ( 893-)  G   -2.66
 884 LYS   ( 899-)  A   -2.65
2256 ASN   ( 834-)  C   -2.62
 819 ASN   ( 834-)  A   -2.61
3758 LYS   ( 899-)  E   -2.57
4536 ASN   ( 225-)  G   -2.56
5195 LYS   ( 899-)  G   -2.56
1209 GLY   ( 152-)  B   -2.55
5520 GLY   ( 152-)  H   -2.55

Warning: Abnormal packing Z-score for sequential residues

A stretch of at least four sequential residues with a 2nd generation packing Z-score below -1.75 was found. This could indicate that these residues are part of a strange loop or that the residues in this range are incomplete, but it might also be an indication of misthreading.

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

 575 GLY   ( 575-)  A     -  578 PHE   ( 578-)  A        -1.80
1142 LEU   (  85-)  B     - 1145 ILE   (  88-)  B        -1.56
2012 GLY   ( 575-)  C     - 2015 PHE   ( 578-)  C        -1.86
2314 GLU   ( 892-)  C     - 2317 LEU   ( 895-)  C        -1.91
3449 GLY   ( 575-)  E     - 3452 PHE   ( 578-)  E        -1.85
3751 GLU   ( 892-)  E     - 3754 LEU   ( 895-)  E        -1.90
4016 LEU   (  85-)  F     - 4019 ILE   (  88-)  F        -1.82
4886 GLY   ( 575-)  G     - 4889 PHE   ( 578-)  G        -1.81
5188 GLU   ( 892-)  G     - 5191 LEU   ( 895-)  G        -1.86

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

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.

5850 HOH   (4654 )  A      O    -10.47   42.12  -65.68
5852 HOH   (4217 )  C      O     63.23   36.03   46.56
5852 HOH   (4219 )  C      O     64.93   35.44   53.45
5852 HOH   (4588 )  C      O     70.92   27.24   53.82
5852 HOH   (4613 )  C      O     66.46   47.32   66.78
5852 HOH   (4710 )  C      O     63.57   40.92   49.41
5853 HOH   (1789 )  D      O     55.73   -1.20   76.15
5853 HOH   (1811 )  D      O     47.62   71.82   70.78
5853 HOH   (1812 )  D      O     50.22   66.53   73.19
5855 HOH   (2774 )  F      O      0.29   26.63   81.35

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.

5852 HOH   (4613 )  C      O
5854 HOH   (4609 )  E      O
5854 HOH   (4737 )  E      O
5854 HOH   (4766 )  E      O
5856 HOH   (3302 )  G      O
5856 HOH   (3406 )  G      O
5856 HOH   (3557 )  G      O
5856 HOH   (3599 )  G      O
5857 HOH   (3632 )  H      O
5857 HOH   (3634 )  H      O
Marked this atom as acceptor 5768  CL  (4015-) A     CL
Marked this atom as acceptor 5769  CL  (4016-) A     CL
Marked this atom as acceptor 5770  CL  (4017-) A     CL
Marked this atom as acceptor 5779  CL  (4018-) B     CL
Marked this atom as acceptor 5789  CL  (4037-) C     CL
Marked this atom as acceptor 5790  CL  (4038-) C     CL
Marked this atom as acceptor 5791  CL  (4039-) C     CL
Marked this atom as acceptor 5801  CL  (4040-) D     CL
Marked this atom as acceptor 5812  CL  (4059-) E     CL
Marked this atom as acceptor 5813  CL  (4060-) E     CL
Marked this atom as acceptor 5814  CL  (4061-) E     CL
Marked this atom as acceptor 5824  CL  (4062-) F     CL
Marked this atom as acceptor 5834  CL  (4082-) G     CL
Marked this atom as acceptor 5835  CL  (4083-) G     CL
Marked this atom as acceptor 5836  CL  (4084-) G     CL
Marked this atom as acceptor 5843  CL  (4085-) H     CL
Metal-coordinating Histidine residue 766 fixed to   1
Strange metal coordination for HIS 1073
Metal-coordinating Histidine residue2203 fixed to   1
Strange metal coordination for HIS 2510
Metal-coordinating Histidine residue3640 fixed to   1
Strange metal coordination for HIS 3947
Metal-coordinating Histidine residue5077 fixed to   1
ERROR. No convergence in HB2STD
Old,New value: 5523.662 5523.715
ERROR. No convergence in HB2STD
Old,New value: 5538.377 5538.412
ERROR. No convergence in HB2STD
Old,New value: 5542.651 5542.681
ERROR. No convergence in HB2STD
Old,New value: 5565.612 5565.653

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.

  70 HIS   (  70-)  A
 105 GLN   ( 105-)  A
 243 HIS   ( 243-)  A
 457 ASN   ( 457-)  A
 769 GLN   ( 784-)  A
 773 HIS   ( 788-)  A
 799 GLN   ( 814-)  A
 820 ASN   ( 835-)  A
 987 GLN   (1002-)  A
1108 GLN   (  51-)  B
1186 ASN   ( 129-)  B
1408 GLN   ( 351-)  B
1542 GLN   ( 105-)  C
1680 HIS   ( 243-)  C
1703 ASN   ( 266-)  C
2206 GLN   ( 784-)  C
2210 HIS   ( 788-)  C
2257 ASN   ( 835-)  C
2409 ASN   ( 987-)  C
2422 HIS   (1000-)  C
2457 GLN   (1035-)  C
2545 GLN   (  51-)  D
2553 HIS   (  59-)  D
2599 HIS   ( 105-)  D
2818 ASN   ( 324-)  D
2845 GLN   ( 351-)  D
2944 HIS   (  70-)  E
2979 GLN   ( 105-)  E
3117 HIS   ( 243-)  E
3553 GLN   ( 679-)  E
3643 GLN   ( 784-)  E
3693 ASN   ( 834-)  E
3795 ASN   ( 936-)  E
3846 ASN   ( 987-)  E
3851 ASN   ( 992-)  E
3859 HIS   (1000-)  E
3982 GLN   (  51-)  F
4153 GLN   ( 222-)  F
4282 GLN   ( 351-)  F
4284 HIS   ( 353-)  F
4416 GLN   ( 105-)  G
4768 ASN   ( 457-)  G
5080 GLN   ( 784-)  G
5084 HIS   ( 788-)  G
5283 ASN   ( 987-)  G
5331 GLN   (1035-)  G
5419 GLN   (  51-)  H
5692 ASN   ( 324-)  H
5719 GLN   ( 351-)  H

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.

   3 LYS   (   3-)  A      N
   7 ILE   (   7-)  A      N
  53 THR   (  53-)  A      N
  61 ALA   (  61-)  A      N
  72 GLU   (  72-)  A      N
  89 THR   (  89-)  A      N
 169 ARG   ( 169-)  A      NH1
 173 THR   ( 173-)  A      N
 176 GLY   ( 176-)  A      N
 184 ASN   ( 184-)  A      N
 210 LEU   ( 210-)  A      N
 236 ASN   ( 236-)  A      ND2
 241 GLY   ( 241-)  A      N
 244 THR   ( 244-)  A      N
 245 GLY   ( 245-)  A      N
 344 THR   ( 344-)  A      N
 354 TYR   ( 354-)  A      N
 377 GLN   ( 377-)  A      N
 390 THR   ( 390-)  A      N
 396 GLN   ( 396-)  A      NE2
 482 THR   ( 482-)  A      N
 523 HIS   ( 523-)  A      N
 534 ALA   ( 534-)  A      N
 556 SER   ( 556-)  A      OG
 559 ARG   ( 559-)  A      N
And so on for a total of 262 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.

 207 ASP   ( 207-)  A      OD2
 215 GLU   ( 215-)  A      OE1
 236 ASN   ( 236-)  A      OD1
 262 GLN   ( 262-)  A      OE1
 391 GLN   ( 391-)  A      OE1
 523 HIS   ( 523-)  A      ND1
 746 GLU   ( 761-)  A      OE1
 746 GLU   ( 761-)  A      OE2
 828 ASN   ( 843-)  A      OD1
1119 ASN   (  62-)  B      OD1
1330 GLN   ( 273-)  B      OE1
1673 ASN   ( 236-)  C      OD1
1828 GLN   ( 391-)  C      OE1
1960 HIS   ( 523-)  C      ND1
2175 ASP   ( 753-)  C      OD1
2183 GLU   ( 761-)  C      OE1
2183 GLU   ( 761-)  C      OE2
2767 GLN   ( 273-)  D      OE1
3089 GLU   ( 215-)  E      OE2
3265 GLN   ( 391-)  E      OE1
3397 HIS   ( 523-)  E      ND1
3620 GLU   ( 761-)  E      OE2
3928 HIS   (1069-)  E      ND1
4204 GLN   ( 273-)  F      OE1
4438 GLU   ( 127-)  G      OE2
4547 ASN   ( 236-)  G      OD1
4702 GLN   ( 391-)  G      OE1
4984 GLU   ( 673-)  G      OE2
5049 ASP   ( 753-)  G      OD1
5057 GLU   ( 761-)  G      OE2
5139 ASN   ( 843-)  G      OD1
5641 GLN   ( 273-)  H      OE1

Warning: Unusual ion packing

We implemented the ion valence determination method of Brown and Wu [REF] similar to Nayal and Di Cera [REF]. See also 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 has great potential, but the method has not been validated. Part of our implementation (comparing 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 validation method is untested. See: swift.cmbi.ru.nl/teach/theory/ for a detailed explanation.

The output gives the ion, the valency score for the ion itself, the valency score for the suggested alternative ion, and a series of possible comments *1 indicates that the suggested alternate atom type has been observed in the PDB file at another location in space. *2 indicates that WHAT IF thinks to have found this ion type in the crystallisation conditions as described in the REMARK 280 cards of the PDB file. *S Indicates that this ions is located at a special position (i.e. at a symmetry axis). N4 stands for NH4+.

5761  MN   (4001-)  A   -.-  -.-  Part of ionic cluster
5762  MN   (4002-)  A   -.-  -.-  Part of ionic cluster
5764   K   (4004-)  A   -.-  -.-  Part of ionic cluster
5764   K   (4004-)  A   -.-  -.-  Too few ligands (3)
5765  MN   (4008-)  A   -.-  -.-  Part of ionic cluster
5766   K   (4009-)  A   -.-  -.-  Part of ionic cluster
5766   K   (4009-)  A   -.-  -.-  Too few ligands (3)
5771   K   (4020-)  A   -.-  -.-  Part of ionic cluster
5773   K   (4022-)  A   -.-  -.-  Too few ligands (1)
5782  MN   (4024-)  C   -.-  -.-  Part of ionic cluster
5783  MN   (4025-)  C   -.-  -.-  Part of ionic cluster
5785   K   (4027-)  C   -.-  -.-  Part of ionic cluster
5786  MN   (4030-)  C   -.-  -.-  Part of ionic cluster
5787   K   (4031-)  C   -.-  -.-  Part of ionic cluster
5792   K   (4042-)  C   -.-  -.-  Part of ionic cluster
5792   K   (4042-)  C   -.-  -.-  Too few ligands (3)
5793   K   (4043-)  C   -.-  -.-  Too few ligands (1)
5802   K   (4041-)  D   -.-  -.-  Too few ligands (3)
5804   K   (4066-)  E   -.-  -.-  Too few ligands (2)
5805  MN   (4046-)  E   -.-  -.-  Part of ionic cluster
5806  MN   (4047-)  E   -.-  -.-  Part of ionic cluster
5808   K   (4049-)  E   -.-  -.-  Part of ionic cluster
5809  MN   (4052-)  E   -.-  -.-  Part of ionic cluster
5810   K   (4053-)  E   -.-  -.-  Part of ionic cluster
5815   K   (4064-)  E   -.-  -.-  Part of ionic cluster
5827  MN   (4069-)  G   -.-  -.-  Part of ionic cluster
5828  MN   (4070-)  G   -.-  -.-  Part of ionic cluster
5829   K   (4071-)  G     2.46   0.80 Is perhaps NA
5830   K   (4072-)  G   -.-  -.-  Part of ionic cluster
5831  MN   (4075-)  G   -.-  -.-  Part of ionic cluster
5832   K   (4076-)  G   -.-  -.-  Part of ionic cluster
5832   K   (4076-)  G   -.-  -.-  Too few ligands (2)
5837   K   (4087-)  G   -.-  -.-  Part of ionic cluster
5838   K   (4088-)  G   -.-  -.-  Too few ligands (3)
5839   K   (4089-)  G   -.-  -.-  Too few ligands (3)
5844   K   (4086-)  H   -.-  -.-  Too few ligands (3)

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.

5850 HOH   (4088 )  A      O  1.05  K  4 *1 and *2
5850 HOH   (4126 )  A      O  1.00  K  4 *1 and *2
5850 HOH   (4308 )  A      O  0.87 NA  4
5850 HOH   (4398 )  A      O  1.07  K  4 *1 and *2
5850 HOH   (4411 )  A      O  1.05  K  4 *1 and *2 Ion-B H2O-B
5850 HOH   (4551 )  A      O  1.19  K  4 *1 and *2 Ion-B
5851 HOH   (4065 )  B      O  1.19  K  4 *1 and *2
5851 HOH   (4072 )  B      O  1.07  K  4 *1 and *2
5852 HOH   (4109 )  C      O  1.02  K  5 *1 and *2 NCS 2/2
5852 HOH   (4137 )  C      O  0.96  K  4 *1 and *2 NCS 1/1
5852 HOH   (4462 )  C      O  0.96  K  4 *1 and *2 NCS 2/2
5853 HOH   (1225 )  D      O  0.84  K  4 *1 and *2 NCS 2/2
5853 HOH   (1378 )  D      O  1.04  K  4 *1 and *2 NCS 2/2
5854 HOH   (4416 )  E      O  1.19  K  4 *1 and *2 NCS 2/2
5855 HOH   (2198 )  F      O  1.10  K  4 *1 and *2 NCS 2/2
5855 HOH   (2283 )  F      O  1.09  K  5 *1 and *2 NCS 1/1
5856 HOH   (2943 )  G      O  0.99  K  4 *1 and *2 NCS 3/3
5856 HOH   (2951 )  G      O  0.86 NA  4 H2O-B NCS 4/4
5856 HOH   (3061 )  G      O  0.91 NA  4 NCS 2/2
5856 HOH   (3143 )  G      O  1.01  K  4 *1 and *2 NCS 3/3
5856 HOH   (3244 )  G      O  0.93  K  4 *1 and *2 Ion-B NCS 3/3
5856 HOH   (3325 )  G      O  1.06  K  4 *1 and *2 NCS 3/3
5857 HOH   (3289 )  H      O  0.99  K  4 *1 and *2 NCS 3/3
5857 HOH   (3539 )  H      O  0.86  K  4 *1 and *2 NCS 1/1

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.

  25 GLU   (  25-)  A   H-bonding suggests Gln; but Alt-Rotamer
 334 GLU   ( 334-)  A   H-bonding suggests Gln; but Alt-Rotamer
 410 ASP   ( 410-)  A   H-bonding suggests Asn; but Alt-Rotamer
 518 ASP   ( 518-)  A   H-bonding suggests Asn
 738 ASP   ( 753-)  A   H-bonding suggests Asn
 776 ASP   ( 791-)  A   H-bonding suggests Asn
 792 ASP   ( 807-)  A   H-bonding suggests Asn
1009 GLU   (1024-)  A   H-bonding suggests Gln
1026 ASP   (1041-)  A   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
1098 GLU   (  41-)  B   H-bonding suggests Gln; but Alt-Rotamer
1771 GLU   ( 334-)  C   H-bonding suggests Gln; but Alt-Rotamer
1847 ASP   ( 410-)  C   H-bonding suggests Asn; but Alt-Rotamer
1867 ASP   ( 430-)  C   H-bonding suggests Asn; but Alt-Rotamer
2120 GLU   ( 683-)  C   H-bonding suggests Gln
2175 ASP   ( 753-)  C   H-bonding suggests Asn
2191 ASP   ( 769-)  C   H-bonding suggests Asn; but Alt-Rotamer
2213 ASP   ( 791-)  C   H-bonding suggests Asn
2606 ASP   ( 112-)  D   H-bonding suggests Asn
3208 GLU   ( 334-)  E   H-bonding suggests Gln; but Alt-Rotamer
3284 ASP   ( 410-)  E   H-bonding suggests Asn; but Alt-Rotamer
3628 ASP   ( 769-)  E   H-bonding suggests Asn; but Alt-Rotamer
3650 ASP   ( 791-)  E   H-bonding suggests Asn; but Alt-Rotamer
3666 ASP   ( 807-)  E   H-bonding suggests Asn; but Alt-Rotamer
4043 ASP   ( 112-)  F   H-bonding suggests Asn
4142 ASP   ( 211-)  F   H-bonding suggests Asn
4645 GLU   ( 334-)  G   H-bonding suggests Gln; but Alt-Rotamer
4741 ASP   ( 430-)  G   H-bonding suggests Asn; but Alt-Rotamer
5049 ASP   ( 753-)  G   H-bonding suggests Asn
5065 ASP   ( 769-)  G   H-bonding suggests Asn
5087 ASP   ( 791-)  G   H-bonding suggests Asn
5103 ASP   ( 807-)  G   H-bonding suggests Asn; but Alt-Rotamer
5321 ASP   (1025-)  G   H-bonding suggests Asn
5337 ASP   (1041-)  G   H-bonding suggests Asn; but Alt-Rotamer; Ligand-contact
5452 ASP   (  84-)  H   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 :   0.153
  2nd generation packing quality :  -1.182
  Ramachandran plot appearance   :  -1.621
  chi-1/chi-2 rotamer normality  :  -4.225 (bad)
  Backbone conformation          :   0.293

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.853
  Bond angles                    :   1.234
  Omega angle restraints         :   0.359 (tight)
  Side chain planarity           :   0.897
  Improper dihedral distribution :   1.313
  B-factor distribution          :   4.305 (loose)
  Inside/Outside distribution    :   1.014

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 : 2.10


Structure Z-scores, positive is better than average:

  1st generation packing quality :   0.6
  2nd generation packing quality :  -0.8
  Ramachandran plot appearance   :  -0.7
  chi-1/chi-2 rotamer normality  :  -2.7
  Backbone conformation          :   0.3

RMS Z-scores, should be close to 1.0:
  Bond lengths                   :   0.853
  Bond angles                    :   1.234
  Omega angle restraints         :   0.359 (tight)
  Side chain planarity           :   0.897
  Improper dihedral distribution :   1.313
  B-factor distribution          :   4.305 (loose)
  Inside/Outside distribution    :   1.014
==============

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.